R3WN59 last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:06.983328

The Comprehensive Antibiotic Resistance Database (CARD)
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:06.983328

Other names: CARD, The Comprehensive Antibiotic Resistance Database (CARD)

A bioinformatic database of antimicrobial resistance genes, their products and associated phenotypes.

Webpage:

http://arpcard.mcmaster.ca

Licence:

Name: CARD Copyright and Disclaimer
URL: https://card.mcmaster.ca/about

Publications:

Publications
More detailed information about this field from each metasource.

The comprehensive antibiotic resistance database
PMID: 23650175
metasource: Fairsharing.org
version: FAIRsharing.org: CARD; Comprehensive Antibiotic Resistance Database; DOI: https://doi.org/10.25504/FAIRsharing.9dbmwg; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
PMID: 31665441
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:06.983328

http://dx.doi.org/10.1093/nar/1951
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

The comprehensive antibiotic resistance database PubMed citations: 662.

662 articles citing: The comprehensive antibiotic resistance database

Antibiotic resistance genes are differentially mobilized according to resistance mechanism. PMID:35906888
Characterization and Genomic Analysis of a New Phage Infecting Helicobacter pylori. PMID:35887231
Comparative Genomic Analysis Discloses Differential Distribution of Antibiotic Resistance Determinants between Worldwide Strains of the Emergent ST213 Genotype of Salmonella Typhimurium. PMID:35884180
Genomic Analysis of Ceftazidime/Avibactam-Resistant GES-Producing Sequence Type 235 Pseudomonas aeruginosa Isolates. PMID:35884125
Pathogenomic in silico approach identifies NSP-A and Fe-IIISBP as possible drug targets in Neisseria Meningitidis MC58 and development of pharmacophores as novel therapeutic candidates. PMID:35879631
Genome Analysis of Enterobacter asburiae and Lelliottia spp. Proliferating in Oligotrophic Drinking Water Reservoirs and Lakes. PMID:35862664
A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. PMID:35847383
Genomic and proteomic characterization of two strains of Shigella flexneri 2 isolated from infants' stool samples in Argentina. PMID:35804311
Global genomic and proteomic analysis indicates co-evolution of Neisseria species and with their human host. PMID:35773545
Are Virulence and Antibiotic Resistance Genes Linked? A Comprehensive Analysis of Bacterial Chromosomes and Plasmids. PMID:35740113
Draft Genome Sequences of Nine Stenotrophomonas maltophilia Isolates from a Freshwater Catchment Area in Hong Kong. PMID:35736029
Antimicrobial Resistance Monitoring of Water Environments: A Framework for Standardized Methods and Quality Control. PMID:35732277
Promising Acinetobacter baumannii Vaccine Candidates and Drug Targets in Recent Years. PMID:35720310
A review of the emergence of antibiotic resistance in bioaerosols and its monitoring methods. PMID:35694630
Draft Genome Sequences of Multidrug-Resistant Escherichia coli Strains Isolated from River Water in Malaysia. PMID:35678586
Development of a topical bacteriophage gel targeting Cutibacterium acnes for acne prone skin and results of a phase 1 cosmetic randomized clinical trial. PMID:35677920
Metagenomic assembled plasmids of the human microbiome vary across disease cohorts. PMID:35654877
Antioxidant potential of Pediococcus pentosaceus strains from the sow milk bacterial collection in weaned piglets. PMID:35650642
Longitudinal Evaluation of Gut Bacteriomes and Viromes after Fecal Microbiota Transplantation for Eradication of Carbapenem-Resistant Enterobacteriaceae. PMID:35642928
Preclinical Safety Assessment of Bacillus subtilis BS50 for Probiotic and Food Applications. PMID:35630480
KPC-3-, GES-5-, and VIM-1-Producing Enterobacterales Isolated from Urban Ponds. PMID:35627386
Metagenomics Reveals the Diversity and Taxonomy of Carbohydrate-Active Enzymes and Antibiotic Resistance Genes in Suancai Bacterial Communities. PMID:35627157
Genomic Insights into Omega-3 Polyunsaturated Fatty Acid Producing Shewanella sp. N2AIL from Fish Gut. PMID:35625360
Genetic Resistance Determinants in Clinical Acinetobacter pittii Genomes. PMID:35625320
Antimicrobial Resistance Profile by Metagenomic and Metatranscriptomic Approach in Clinical Practice: Opportunity and Challenge. PMID:35625299
Pangenome analyses of Bacillus pumilus, Bacillus safensis, and Priestia megaterium exploring the plant-associated features of bacilli strains isolated from canola. PMID:35612623
Machine Learning in Antibacterial Drug Design. PMID:35592425
Occurrence of Antimicrobial Resistance in the Environment in Germany, Austria, and Switzerland: A Narrative Review of Existing Evidence. PMID:35456779
In Vitro and In Silico Based Approaches to Identify Potential Novel Bacteriocins from the Athlete Gut Microbiome of an Elite Athlete Cohort. PMID:35456752
Characterization and Genomic Analysis of Bacteriophage vB_KpnM_IME346 Targeting Clinical Klebsiella pneumoniae Strain of the K63 Capsular Type. PMID:35416546
Brachybacterium epidermidis Sp. Nov., a Novel Bacterial Species Isolated from the Back of the Right Hand, in a 67-Year-Old Healthy Woman. PMID:35392139
Cerebral Intraparenchymal Hemorrhage Changes Patients' Gut Bacteria Composition and Function. PMID:35372117
Metagenomics-enabled microbial surveillance. PMID:35365786
Antimicrobial resistance patterns and genetic elements associated with the antibiotic resistance of Helicobacter pylori strains from Shanghai. PMID:35354484
Antimicrobial resistance determinants in silage. PMID:35347213
Review and Comparison of Antimicrobial Resistance Gene Databases. PMID:35326803
Genomic surveillance of Acinetobacter baumannii in the Philippines, 2013-2014. PMID:35251744
Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM. PMID:35241674
Complete Genome Sequence of Clostridium cadaveris IFB3C5, Isolated from a Human Colonic Adenocarcinoma. PMID:35234492
Similarities in Virulence and Extended Spectrum Beta-Lactamase Gene Profiles among Cefotaxime-Resistant Escherichia coli Wastewater and Clinical Isolates. PMID:35203862
A saponin-polybromophenol antibiotic (CU1) from Cassia fistula Bark Against Multi-Drug Resistant Bacteria Targeting RNA polymerase. PMID:35198968
Gut Virome of the World's Highest-Elevation Lizard Species (Phrynocephalus erythrurus and Phrynocephalus theobaldi) Reveals Versatile Commensal Viruses. PMID:35196818
Comparative genomics and evolutionary analysis of Lactococcus garvieae isolated from human endocarditis. PMID:35196218
Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa. PMID:35194028
Complete Genome Sequencing and Comparative Analysis of the Clinically-Derived Apiotrichum mycotoxinivorans Strain GMU1709. PMID:35186802
Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations. PMID:35166655
Accurate and rapid prediction of tuberculosis drug resistance from genome sequence data using traditional machine learning algorithms and CNN. PMID:35165358
Microbial Characteristics and Genomic Analysis of an ST11 Carbapenem-Resistant Klebsiella pneumoniae Strain Carrying bla KPC-2 Conjugative Drug-Resistant Plasmid. PMID:35155355
Multicenter Evaluation of the Acuitas AMR Gene Panel for Detection of an Extended Panel of Antimicrobial Resistance Genes among Bacterial Isolates. PMID:35138924
Diversity of carbapenem-resistant Acinetobacter baumannii and bacteriophage-mediated spread of the Oxa23 carbapenemase. PMID:35104206
ResFinder - an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes. PMID:35072601
Konateibacter massiliensis gen. nov. sp. nov. and Paenibacillus faecalis sp. nov., Two New Species Isolated from the Stool Samples of Infants Suffering from Marasmus. PMID:35059831
Evaluation of Antibiotic Resistance of Salmonella Serotypes and Whole-Genome Sequencing of Multiresistant Strains Isolated from Food Products in Russia. PMID:35052878
Whole genome sequence of bacteremic Clostridium tertium in a World War I soldier, 1914. PMID:34984406
Comparative Genomic Analysis of Streptococcus pneumoniae Strains: Penicillin Non-susceptible Multi-drug-Resistant Serotype 19A Isolates. PMID:34982234
Characterization of a Novel Chromosome-Encoded AmpC β-Lactamase Gene, bla PRC-1, in an Isolate of a Newly Classified Pseudomonas Species, Pseudomonas wenzhouensis A20, From Animal Farm Sewage. PMID:34975778
Probiotic Potential Analysis and Safety Evaluation of Enterococcus durans A8-1 Isolated From a Healthy Chinese Infant. PMID:34970251
First Comparative Analysis of Clostridium septicum Genomes Provides Insights Into the Taxonomy, Species Genetic Diversity, and Virulence Related to Gas Gangrene. PMID:34956133
Mining the Genome of Bacillus velezensis VB7 (CP047587) for MAMP Genes and Non-Ribosomal Peptide Synthetase Gene Clusters Conferring Antiviral and Antifungal Activity. PMID:34946111
Antimicrobial Susceptibility of Lactobacillus delbrueckii subsp. lactis from Milk Products and Other Habitats. PMID:34945696
Pan-Resistome Characterization of Uropathogenic Escherichia coli and Klebsiella pneumoniae Strains Circulating in Uganda and Kenya, Isolated from 2017-2018. PMID:34943759
Amycolatopsis aidingensis sp. nov., a Halotolerant Actinobacterium, Produces New Secondary Metabolites. PMID:34938275
Whole Genome Sequencing of First Janibacter indicus Isolate in China Revealed Three Unique Genomic Islands Compared with Saprophytic Strains. PMID:34934330
Soil Bacteria in Urban Community Gardens Have the Potential to Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer. PMID:34887843
The Facts and Family Secrets of Plasmids That Replicate via the Rolling-Circle Mechanism. PMID:34878299
Quantitative Insights Into β-Lactamase Inhibitor's Contribution in the Treatment of Carbapenemase-Producing Organisms With β-Lactams. PMID:34867880
Identification and Characterization of a Novel Chromosomal Aminoglycoside 2'-N-Acetyltransferase, AAC(2')-If, From an Isolate of a Novel Providencia Species, Providencia wenzhouensis R33. PMID:34867838
Shotgun metagenome sequencing of a Sudanese toombak snuff tobacco: genetic attributes of a high tobacco-specific nitrosamine containing smokeless tobacco product. PMID:34862647
Genomic Analysis of Multidrug-Resistant Mycobacterium tuberculosis Strains From Patients in Kazakhstan. PMID:34858467
Draft Genome Sequence of Bacillus sp. Strain IITD106, Isolated from Oil-Contaminated Soil. PMID:34854725
Antimicrobial Resistance and Genomic Characterization of Six New Sequence Types in Multidrug-Resistant Pseudomonas aeruginosa Clinical Isolates from Pakistan. PMID:34827324
Mobile Antimicrobial Resistance Genes in Probiotics. PMID:34827225
High-quality whole-genome sequence analysis of Lactobacillus paragasseri UBLG-36 reveals oxalate-degrading potential of the strain. PMID:34797858
Deciphering Multidrug-Resistant Acinetobacter baumannii from a Pediatric Cancer Hospital in Egypt. PMID:34787450
Comparing gut resistome composition among patients with acute Campylobacter infections and healthy family members. PMID:34785751
Genetic evaluation of ESBL-producing Escherichia coli urinary isolates in Otago, New Zealand. PMID:34778763
Phage Therapy Related Microbial Succession Associated with Successful Clinical Outcome for a Recurrent Urinary Tract Infection. PMID:34696479
Characterization of a New and Efficient Polyvalent Phage Infecting E. coli O157:H7, Salmonella spp., and Shigella sonnei. PMID:34683426
Complete Genome Sequence of Acinetobacter pittii BHS4, Isolated from Air-Conditioning Condensate in Hong Kong. PMID:34672711
International High-Risk Clones Among Extended-Spectrum β-Lactamase-Producing Escherichia coli in Dhaka, Bangladesh. PMID:34671331
Linear Regression Equations To Predict β-Lactam, Macrolide, Lincosamide, and Fluoroquinolone MICs from Molecular Antimicrobial Resistance Determinants in Streptococcus pneumoniae. PMID:34662197
Metagenomic Analysis Identifies Sex-Related Cecal Microbial Gene Functions and Bacterial Taxa in the Quail. PMID:34660751
Genetic diversity of Salmonella Paratyphi A isolated from enteric fever patients in Bangladesh from 2008 to 2018. PMID:34648506
Molecular Epidemiological Analysis of ST11-K64 Extensively Drug-Resistant Klebsiella pneumoniae Infections Outbreak in Intensive Care and Neurosurgery Units Based on Whole-Genome Sequencing. PMID:34646245
Distribution of bacteriocin genes in the lineages of Lactiplantibacillus plantarum. PMID:34625657
From Strain Characterization to Field Authorization: Highlights on Bacillus velezensis Strain B25 Beneficial Properties for Plants and Its Activities on Phytopathogenic Fungi. PMID:34576819
Quinolone Resistance of Actinobacillus pleuropneumoniae Revealed through Genome and Transcriptome Analyses. PMID:34576206
Genomic Investigation of Methicillin-Resistant Staphylococcus aureus ST113 Strains Isolated from Tertiary Care Hospitals in Pakistan. PMID:34572703
Genome Analysis of Acinetobacter lwoffii Strains Isolated from Permafrost Soils Aged from 15 Thousand to 1.8 Million Years Revealed Their Close Relationships with Present-Day Environmental and Clinical Isolates. PMID:34571748
Characterisation of the rumen resistome in Spanish dairy cattle. PMID:34551823
Genome-wide analysis provides a deeper understanding of the population structure of the Salmonella enterica serotype Paratyphi B complex in Bangladesh. PMID:34550065
Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome. PMID:34546072
Genomic Characterization of a Nalidixic Acid-Resistant Salmonella Enteritidis Strain Causing Persistent Infections in Broiler Chickens. PMID:34540936
Genomic surveillance of Pseudomonas aeruginosa in the Philippines, 2013-2014. PMID:34540307
Identification and Characterization of a Novel Aminoglycoside 3''-Nucleotidyltransferase, ANT(3'')-IId, From Acinetobacter lwoffii. PMID:34531844
Antimicrobial susceptibility patterns of respiratory Gram-negative bacterial isolates from COVID-19 patients in Switzerland. PMID:34493302
Molecular Characterization of Microbiota in Cerebrospinal Fluid From Patients With CSF Shunt Infections Using Whole Genome Amplification Followed by Shotgun Sequencing. PMID:34490140
Inconsistent PCR detection of Shiga toxin-producing Escherichia coli: Insights from whole genome sequence analyses. PMID:34478476
Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights. PMID:34468193
Assessment of Phenotype Relevant Amino Acid Residues in TEM-β-Lactamases by Mathematical Modelling and Experimental Approval. PMID:34442804
Metagenomics-Based Analysis of the Age-Related Cumulative Effect of Antibiotic Resistance Genes in Gut Microbiota. PMID:34439056
Draft Genome Sequence and Annotation of the Synthetic Textile Dye-Decolorizing Strain Bacillus amyloliquefaciens AD20, Isolated from a Dye Waste Pond. PMID:34435869
Isolation of a Virulent Aeromonas salmonicida subsp. masoucida Bacteriophage and Its Application in Phage Therapy in Turbot (Scophthalmus maximus). PMID:34406829
Comparative Evaluation of Assays for Broad Detection of Molecular Resistance Mechanisms in Enterobacterales Isolates. PMID:34406800
The roles of antimicrobial resistance, phage diversity, isolation source and selection in shaping the genomic architecture of Bacillus anthracis. PMID:34402777
Identification of Three Clf-Sdr Subfamily Proteins in Staphylococcus warneri, and Comparative Genomics Analysis of a Locus Encoding CWA Proteins in Staphylococcus Species. PMID:34394031
Draft Genome Sequences of Enterobacter spp., Lelliottia spp., and Serratia spp., Coliform Bacteria from Drinking Water Reservoirs and Lakes. PMID:34382825
Digital Insights Into Nucleotide Metabolism and Antibiotic Treatment Failure. PMID:34355212
Rapid Detection of PBP2a in Staphylococci from Shortly Incubated Subcultures of Positive Blood Cultures by an Immunochromatographic Assay. PMID:34319135
Staphylococcus caledonicus sp. nov. and Staphylococcus canis sp. nov. isolated from healthy domestic dogs. PMID:34296985
Characterization of Proteobacterial Plasmid Integron-Encoded qac Efflux Pump Sequence Diversity and Quaternary Ammonium Compound Antiseptic Selection in Escherichia coli Grown Planktonically and as Biofilms. PMID:34280018
Identification and Characterization of Mycobacterial Species Using Whole-Genome Sequences. PMID:34235665
Accuracy of Broad-Panel PCR-Based Bacterial Identification for Blood Cultures in a Pediatric Oncology Population. PMID:34232100
Antimicrobial Resistance Determinants in Genomes and Plasmids from Acinetobacter baumannii Clinical Isolates. PMID:34206348
Molecular characterization and improved diagnostics of Nocardia strains isolated over the last two decades at a German tertiary care center. PMID:34177407
AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. PMID:34135355
Genomic Sequence Analysis of Methicillin- and Carbapenem-Resistant Bacteria Isolated from Raw Sewage. PMID:34132566
Whole genome sequence analysis of multi drug resistant community associated methicillin resistant Staphylococcus aureus from food fish: detection of clonal lineage ST 28 and its antimicrobial resistance and virulence genes. PMID:34113482
rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data. PMID:34110280
The occurrence of antibiotic resistance genes in the microbiota of yak, beef and dairy cattle characterized by a metagenomic approach. PMID:34103703
Ornithobacterium rhinotracheale: MALDI-TOF MS and Whole Genome Sequencing Confirm That Serotypes K, L and M Deviate from Well-Known Reference Strains and Numerous Field Isolates. PMID:34067063
Composition and Associations of the Infant Gut Fungal Microbiota with Environmental Factors and Childhood Allergic Outcomes. PMID:34060330
ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses. PMID:34055480
Genomic analysis of Neisseria elongata isolate from a patient with infective endocarditis. PMID:34038628
Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils. PMID:34012103
Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria. PMID:34006629
Antimicrobial Resistance Genes in Bacteria Isolated From Japanese Honey, and Their Potential for Conferring Macrolide and Lincosamide Resistance in the American Foulbrood Pathogen Paenibacillus larvae. PMID:33995331
Structural characterization of a Type B chloramphenicol acetyltransferase from the emerging pathogen Elizabethkingia anophelis NUHP1. PMID:33947893
Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time. PMID:33927221
Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts. PMID:33925711
Insights about the epidemiology of Salmonella Typhimurium isolates from different sources in Brazil using comparative genomics. PMID:33910644
Whole genome-based characterisation of antimicrobial resistance and genetic diversity in Campylobacter jejuni and Campylobacter coli from ruminants. PMID:33903652
Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond. PMID:33902740
Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak. PMID:33826490
Genome-Wide Identification and Analysis of Chromosomally Integrated Putative Prophages Associated with Clinical Klebsiella pneumoniae Strains. PMID:33813641
Characterization and Full Genome Sequence of Novel KPP-5 Lytic Phage against Klebsiella pneumoniae Responsible for Recalcitrant Infection. PMID:33800632
Combined effects of composting and antibiotic administration on cattle manure-borne antibiotic resistance genes. PMID:33795006
Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs. PMID:33785729
Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment. PMID:33779498
Complete Genome Analysis of Flavobacterium psychrophilum Strain FPRT1, Isolated from Diseased Rainbow Trout (Oncorhynchus mykiss) in South Korea. PMID:33766901
MetaPrism: A versatile toolkit for joint taxa/gene analysis of metagenomic sequencing data. PMID:33713107
High fecal carriage of blaCTX-M, blaCMY-2, and plasmid-mediated quinolone resistance genes among healthy Korean people in a metagenomic analysis. PMID:33712656
AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata. PMID:33691615
Nitric oxide (NO) elicits aminoglycoside tolerance in Escherichia coli but antibiotic resistance gene carriage and NO sensitivity have not co-evolved. PMID:33682076
Differences in the gut microbiomes of dogs and wolves: roles of antibiotics and starch. PMID:33676490
Draft genome and description of Microvirga mediterraneensis strain Marseille-Q2068T sp. nov., a new bacterium isolated from human healthy skin. PMID:33659063
Evolutionary Dynamics Based on Comparative Genomics of Pathogenic Escherichia coli Lineages Harboring Polyketide Synthase (pks) Island. PMID:33653937
Population Genomic Analysis of Listeria monocytogenes From Food Reveals Substrate-Specific Genome Variation. PMID:33633707
Genome announcement of Steinernema khuongi and its associated symbiont from Florida. PMID:33624756
Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity. PMID:33620305
Draft genome and description of Mixta mediterraneensis strain Marseille-Q2057T sp.nov., a new bacterium isolated from human healthy skin. PMID:33604053
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data. PMID:33597026
A Uniform Computational Approach Improved on Existing Pipelines to Reveal Microbiome Biomarkers of Nonresponse to Immune Checkpoint Inhibitors. PMID:33593881
Metagenomic Sequencing Revealed the Potential Pathogenic Threats of Banknotes. PMID:33585735
Resistome analysis of bloodstream infection bacterial genomes reveals a specific set of proteins involved in antibiotic resistance and drug efflux. PMID:33575606
Metagenomic Approaches to Analyze Antimicrobial Resistance: An Overview. PMID:33537056
Amoxicillin-Clavulanic Acid Resistance in the Genus Bifidobacterium. PMID:33483308
Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance. PMID:33462493
Monitoring Microbial Populations and Antibiotic Resistance Gene Enrichment Associated with Arctic Waste Stabilization Ponds. PMID:33452030
Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients. PMID:33441409
Unearthing Antibiotic Resistance Associated with Disturbance-Induced Permafrost Thaw in Interior Alaska. PMID:33418967
Characterization of four virulent Klebsiella pneumoniae bacteriophages, and evaluation of their potential use in complex phage preparation. PMID:33407669
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes. PMID:33407081
Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen. PMID:33406073
Escherichia ruysiae sp. nov., a novel Gram-stain-negative bacterium, isolated from a faecal sample of an international traveller. PMID:33406029
A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt. PMID:33384459
The Integration of Genome Mining, Comparative Genomics, and Functional Genetics for Biosynthetic Gene Cluster Identification. PMID:33343637
Mini Review: Clinical Routine Microbiology in the Era of Automation and Digital Health. PMID:33330127
A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. PMID:33319778
Draft genome and description of Chryseobacterium manosquense strain Marseille-Q2069T sp. nov., a new bacterium isolated from human healthy skin. PMID:33294197
Whole-Genome Sequence Analysis of an Extensively Drug-Resistant Salmonella enterica Serovar Agona Isolate from an Australian Silver Gull (Chroicocephalus novaehollandiae) Reveals the Acquisition of Multidrug Resistance Plasmids. PMID:33239365
DeepBL: a deep learning-based approach for in silico discovery of beta-lactamases. PMID:33212503
PARMAP: A Pan-Genome-Based Computational Framework for Predicting Antimicrobial Resistance. PMID:33193203
Genome-based characterization of two Colombian clinical Providencia rettgeri isolates co-harboring NDM-1, VIM-2, and other β-lactamases. PMID:33183231
Plant resistome profiling in evolutionary old bog vegetation provides new clues to understand emergence of multi-resistance. PMID:33177608
Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements. PMID:33159058
Antimicrobial Resistance of Coagulase-Positive Staphylococcus Isolates Recovered in a Veterinary University Hospital. PMID:33138100
Amino Acid k-mer Feature Extraction for Quantitative Antimicrobial Resistance (AMR) Prediction by Machine Learning and Model Interpretation for Biological Insights. PMID:33126516
Draft Genome Sequence of Streptomyces mexicanus Strain Q0842, Isolated from Human Skin. PMID:33122417
Whole genome sequence data of Mycobacterium tuberculosis XDR strain, isolated from patient in Kazakhstan. PMID:33102665
Metagenomic characterization of bacterial community and antibiotic resistance genes in representative ready-to-eat food in southern China. PMID:33093543
Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13. PMID:33088176
Colonization of a hand washing sink in a veterinary hospital by an Enterobacter hormaechei strain carrying multiple resistances to high importance antimicrobials. PMID:33087168
MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline. PMID:33087062
Integrated Phenotypic-Genotypic Analysis of Candidate Probiotic Weissella Cibaria Strains Isolated from Dairy Cows in Kuwait. PMID:33085038
Metagenomic analysis of the dust particles collected from the suction tube and the suction funnel of a dermatological laser smoke evacuator system. PMID:33079312
Quantitative characterization of Clostridioides difficile population in the gut microbiome of patients with C. difficile infection and their association with clinical factors. PMID:33077744
Isolation and Characterization of Nitrate-Reducing Bacteria as Potential Probiotics for Oral and Systemic Health. PMID:33042063
Application of whole genome sequencing to query a potential outbreak of Elizabethkingia anophelis in Ontario, Canada. PMID:32974512
Characterization of a Novel Chromosomal Class C β-Lactamase, YOC-1, and Comparative Genomics Analysis of a Multidrug Resistance Plasmid in Yokenella regensburgei W13. PMID:32973731
Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals. PMID:32917913
Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. PMID:32907806
Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C. PMID:32873785
Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial. PMID:32862830
The Development of High-Quality Multispecies Probiotic Formulations: From Bench to Market. PMID:32824147
Complete Genomic Analysis of Enterococcus faecium Heat-Resistant Strain Developed by Two-Step Adaptation Laboratory Evolution Method. PMID:32793575
Temporal encoding of bacterial identity and traits in growth dynamics. PMID:32747578
High relatedness of invasive multi-drug resistant non-typhoidal Salmonella genotypes among patients and asymptomatic carriers in endemic informal settlements in Kenya. PMID:32745137
MYCO WELL D-ONE detection of Ureaplasma spp. and Mycoplasma hominis in sexual health patients in Wales. PMID:32725499
Antibiotic Resistance-Susceptibility Profiles of Enterococcus faecalis and Streptococcus spp. From the Human Vagina, and Genome Analysis of the Genetic Basis of Intrinsic and Acquired Resistances. PMID:32695087
Mobilization of Antibiotic Resistance: Are Current Approaches for Colocalizing Resistomes and Mobilomes Useful? PMID:32695079
Large-scale assessment of antimicrobial resistance marker databases for genetic phenotype prediction: a systematic review. PMID:32658975
Effects of Low-Dose Antibiotics on Gut Immunity and Antibiotic Resistomes in Weaned Piglets. PMID:32655541
The Salmonella enterica Plasmidome as a Reservoir of Antibiotic Resistance. PMID:32650601
Live Biotherapeutic Products, A Road Map for Safety Assessment. PMID:32637416
Determining the Genetic Characteristics of Resistance and Virulence of the "Epidermidis Cluster Group" Through Pan-Genome Analysis. PMID:32596166
AcGI1, a novel genomic island carrying antibiotic resistance integron In687 in multidrug resistant Achromobacter xylosoxidans in a teaching hospital in Thailand. PMID:32592387
Pan drug-resistant Acinetobacter baumannii causing nosocomial infections among burnt children. PMID:32551313
Two Cases of Vancomycin-Resistant Enterococcus faecium Bacteremia With Development of Daptomycin-Resistant Phenotype and its Detection Using Oxford Nanopore Sequencing. PMID:32550237
Genomic and Proteomic Characterization of the Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli Strain CCUG 73778: A Virulent, Nosocomial Outbreak Strain. PMID:32545759
Migratory birds-one major source of environmental antibiotic resistance around Qinghai Lake, China. PMID:32540654
BacEffluxPred: A two-tier system to predict and categorize bacterial efflux mediated antibiotic resistance proteins. PMID:32518231
Draft Genome Sequence of Streptomyces aureoverticillatus HN6, a Strain Antagonistic against Fusarium oxysporum f. sp. cubense Race 4. PMID:32499365
Genomics of Atlantic Forest Mycobacteriaceae strains unravels a mobilome diversity with a novel integrative conjugative element and plasmids harbouring T7SS. PMID:32496186
Rapid Detection of Mobilized Colistin Resistance using a Nucleic Acid Based Lab-on-a-Chip Diagnostic System. PMID:32439986
Metagenomic analysis of an urban resistome before and after wastewater treatment. PMID:32424207
Whole genome sequence analysis of Cupriavidus campinensis S14E4C, a heavy metal resistant bacterium. PMID:32406019
Unravelling the antibiotic and heavy metal resistome of a chronically polluted soil. PMID:32405442
Isolation and characterization of a novel Escherichia coli O157:H7-specific phage as a biocontrol agent. PMID:32399231
Whole genome sequencing and antibiotic diffusion assays, provide new insight on drug resistance in the genus Pedobacter. PMID:32386210
Antibiotic resistomes discovered in the gut microbiomes of Korean swine and cattle. PMID:32369165
Antimicrobial resistance genes in raw milk for human consumption. PMID:32366826
Co-occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site. PMID:32363769
The Biotherapeutic Potential of Lactobacillus reuteri Characterized Using a Target-Specific Selection Process. PMID:32351460
Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial Resistance. PMID:32318038
Genomic investigation of emerging zoonotic pathogen Shewanella xiamenensis. PMID:32269948
Whole Genome Sequencing and Characteristics of mcr-1-Harboring Plasmids of Porcine Escherichia coli Isolates Belonging to the High-Risk Clone O25b:H4-ST131 Clade B. PMID:32265859
The effect of antibiotics on the gut microbiome: a metagenomics analysis of microbial shift and gut antibiotic resistance in antibiotic treated mice. PMID:32228448
Metadata Analysis of mcr-1-Bearing Plasmids Inspired by the Sequencing Evidence for Horizontal Transfer of Antibiotic Resistance Genes Between Polluted River and Wild Birds. PMID:32210943
Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico. PMID:32176604
Microbial and Viral Communities and Their Antibiotic Resistance Genes Throughout a Hospital Wastewater Treatment System. PMID:32140141
Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt. PMID:32139767
Evaluation of Machine Learning Models for Predicting Antimicrobial Resistance of Actinobacillus pleuropneumoniae From Whole Genome Sequences. PMID:32117101
Biofilms: hot spots of horizontal gene transfer (HGT) in aquatic environments, with a focus on a new HGT mechanism. PMID:32109282
Core genome MLST and resistome analysis of Klebsiella pneumoniae using a clinically amenable workflow. PMID:32098688
Abundance of mobile genetic elements in an Acinetobacter lwoffii strain isolated from Transylvanian honey sample. PMID:32076091
Phenotypic and Genotypic Traits of Vancomycin-Resistant Enterococci from Healthy Food-Producing Animals. PMID:32075283
Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe. PMID:32055708
Innovative and rapid antimicrobial susceptibility testing systems. PMID:32055026
Combining Standard Molecular Typing and Whole Genome Sequencing to Investigate Pseudomonas aeruginosa Epidemiology in Intensive Care Units. PMID:32047733
Chitin degradation potential and whole-genome sequence of Streptomyces diastaticus strain CS1801. PMID:32036475
Abundance and diversity of resistomes differ between healthy human oral cavities and gut. PMID:32019923
A Common Practice of Widespread Antimicrobial Use in Horse Production Promotes Multi-Drug Resistance. PMID:31969575
Urbanization and Waterborne Pathogen Emergence in Low-Income Countries: Where and How to Conduct Surveys? PMID:31940838
Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations. PMID:31924621
Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors. PMID:31919110
Composite genome sequence of Bacillus clausii, a probiotic commercially available as Enterogermina®, and insights into its probiotic properties. PMID:31888501
Antimicrobial resistance genetic factor identification from whole-genome sequence data using deep feature selection. PMID:31874612
Use of whole genome sequencing of commensal Escherichia coli in pigs for antimicrobial resistance surveillance, United Kingdom, 2018. PMID:31847943
Omics Potential in Herbicide-Resistant Weed Management. PMID:31847327
Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens. PMID:31844297
Characterization of a Novel Conjugative Plasmid in Edwardsiella piscicida Strain MS-18-199. PMID:31828047
Phenotypic and Molecular Epidemiology of ESBL-, AmpC-, and Carbapenemase-Producing Escherichia coli in Northern and Eastern Europe. PMID:31824436
The human gut resistome: Current concepts & future prospects. PMID:31823916
Mobilome and Resistome Reconstruction from Genomes Belonging to Members of the Bifidobacterium Genus. PMID:31810287
Identifying Microbiota Signature and Functional Rules Associated With Bacterial Subtypes in Human Intestine. PMID:31803234
Effects of the Antimicrobial Peptide LL-37 and Innate Effector Mechanisms in Colistin-Resistant Klebsiella pneumoniae With mgrB Insertions. PMID:31803163
Antimicrobial resistance in chronic liver disease. PMID:31797303
Constructing and Characterizing Bacteriophage Libraries for Phage Therapy of Human Infections. PMID:31781060
First Report and Comparative Genomics Analysis of a blaOXA-244-Harboring Escherichia coli Isolate Recovered in the American Continent. PMID:31766210
Do Organic Substrates Drive Microbial Community Interactions in Arctic Snow? PMID:31749784
High-Risk International Clones of Carbapenem-Nonsusceptible Pseudomonas aeruginosa Endemic to Indonesian Intensive Care Units: Impact of a Multifaceted Infection Control Intervention Analyzed at the Genomic Level. PMID:31719179
Pseudomonas aeruginosa quorum sensing inhibition by clinical isolate Delftia tsuruhatensis 11304: involvement of N-octadecanoylhomoserine lactones. PMID:31712724
High-throughput sequencing data and antibiotic resistance mechanisms of soil microbial communities in non-irrigated and irrigated soils with raw sewage in African cities. PMID:31700955
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. PMID:31667520
Microevolution within ST11 group Clostridioides difficile isolates through mobile genetic elements based on complete genome sequencing. PMID:31666016
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. PMID:31665441
Antimicrobial Resistance in Bacteria: Mechanisms, Evolution, and Persistence. PMID:31659373
Molecular Phenotyping and Genomic Characterization of a Novel Neuroactive Bacterium Strain, Lactobacillus murinus HU-1. PMID:31636567
Insights into the Bacterial Profiles and Resistome Structures Following the Severe 2018 Flood in Kerala, South India. PMID:31635115
Draft Genome Sequences of 43 Enterococcus faecalis and Enterococcus faecium Isolates from a Commercial Beef Processing Plant and Retail Ground Beef. PMID:31624168
Taxonomic and Metabolic Incongruence in the Ancient Genus Streptomyces. PMID:31616394
Plasmid Dissemination and Selection of a Multidrug-Resistant Klebsiella pneumoniae Strain during Transplant-Associated Antibiotic Therapy. PMID:31594809
Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii. PMID:31578249
Comparative genomic analysis and multi-drug resistance differences of Acinetobacter baumannii in Chongqing, China. PMID:31571939
Complete Genome Sequences of Lytic Polysaccharide-Degrading Klebsiella pneumoniae Bacteriophages vB_KpnS_FZ10, vB_KpnP_FZ12, vB_KpnM_FZ14, and vB_KpnS_FZ41. PMID:31558632
An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation. PMID:31537784
Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers. PMID:31513580
Evolution of Outbreak-Causing Carbapenem-Resistant Klebsiella pneumoniae ST258 at a Tertiary Care Hospital over 8 Years. PMID:31481386
Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm. PMID:31466530
Polyamino-Isoprenyl Derivatives as Antibiotic Adjuvants and Motility Inhibitors for Bordetella bronchiseptica Porcine Pulmonary Infection Treatment. PMID:31456758
Clinical and Molecular Characteristics of Klebsiella pneumoniae Isolates Causing Bloodstream Infections in Japan: Occurrence of Hypervirulent Infections in Health Care. PMID:31434721
Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates. PMID:31427293
Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria. PMID:31423298
Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes. PMID:31409850
Development of omics-based protocols for the microbiological characterization of multi-strain formulations marketed as probiotics: the case of VSL#3. PMID:31402586
Complete Genome Sequence of Weissella hellenica 0916-4-2 and Its Comparative Genomic Analysis. PMID:31396169
Identification of Primary Antimicrobial Resistance Drivers in Agricultural Nontyphoidal Salmonella enterica Serovars by Using Machine Learning. PMID:31387929
Identifying subpathway signatures for individualized anticancer drug response by integrating multi-omics data. PMID:31387579
Integrated genomic epidemiology and phenotypic profiling of Clostridium difficile across intra-hospital and community populations in Colombia. PMID:31383872
Population gene introgression and high genome plasticity for the zoonotic pathogen Streptococcus agalactiae. PMID:31350563
Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants. PMID:31337807
Comparative genomic analysis revealed great plasticity and environmental adaptation of the genomes of Enterococcus faecium. PMID:31331270
Gut Colonization Preceding Mucosal Barrier Injury Bloodstream Infection in Pediatric Hematopoietic Stem Cell Transplantation Recipients. PMID:31326608
Molecular variability of Streptococcus uberis isolates from intramammary infections in Canadian dairy farms from the Maritime region. PMID:31308588
Population-based inference of aminoglycoside resistance mechanisms in Escherichia coli. PMID:31307955
A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments. PMID:31307536
Comparative genomics identifies potential virulence factors in Clostridium tertium and C. paraputrificum. PMID:31304854
Antibiotic resistance genes in the Actinobacteria phylum. PMID:31250336
Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes. PMID:31248462
Whole-genome comparative analysis of Campylobacter jejuni strains isolated from patients with diarrhea in northeastern Poland. PMID:31244901
A Next-Generation Sequencing-Based Approach to Identify Genetic Determinants of Antibiotic Resistance in Cambodian Helicobacter pylori Clinical Isolates. PMID:31208076
Emergence of an Australian-like pstS-null vancomycin resistant Enterococcus faecium clone in Scotland. PMID:31194809
Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis. PMID:31189036
Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes. PMID:31170060
Oral Beta-Lactamase Protects the Canine Gut Microbiome from Oral Amoxicillin-Mediated Damage. PMID:31137766
A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network. PMID:31107202
Whole-Genome Sequence of Acinetobacter baumannii HUMV-3743, Isolated from a Human Wound Exudate. PMID:31072890
Whole-genome sequencing and characterization of an antibiotic resistant Neisseria meningitidis B isolate from a military unit in Vietnam. PMID:31060558
Draft Genome Sequence of a bla NDM-1- and bla PME-1-Harboring Pseudomonas aeruginosa Clinical Isolate from Pakistan. PMID:31023810
Use of online tools for antimicrobial resistance prediction by whole-genome sequencing in methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). PMID:31005733
Evolution of a major bovine mastitic genotype (rpoB sequence type 10-2) of Staphylococcus aureus in cows. PMID:30982119
Independent Microevolution Mediated by Mobile Genetic Elements of Individual Clostridium difficile Isolates from Clade 4 Revealed by Whole-Genome Sequencing. PMID:30944881
Identification and reconstruction of novel antibiotic resistance genes from metagenomes. PMID:30935407
Human gut resistome can be country-specific. PMID:30923648
Predicting Antibiotic Resistance in Gram-Negative Bacilli from Resistance Genes. PMID:30917985
Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species. PMID:30905286
The antibiotic resistance and pathogenicity of a multidrug-resistant Elizabethkingia anophelis isolate. PMID:30891912
Extended Spectrum Beta-Lactamase-Producing Gram-Negative Bacteria Recovered From an Amazonian Lake Near the City of Belém, Brazil. PMID:30873145
PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome. PMID:30871454
Detection of critical antibiotic resistance genes through routine microbiome surveillance. PMID:30870464
Emergence of New Delhi Metallo-β-Lactamase (NDM-5) in Klebsiella quasipneumoniae from Neonates in a Nigerian Hospital. PMID:30867330
Comparative genomic analysis of 127 Escherichia coli strains isolated from domestic animals with diarrhea in China. PMID:30866824
Salmonella Typhi From Blood Cultures in the Democratic Republic of the Congo: A 10-Year Surveillance. PMID:30845337
Taxonomic Distribution of FosB in Human-Microbiota and Activity Comparison of Fosfomycin Resistance. PMID:30814984
Identification of the OXA-48 Carbapenemase Family by Use of Tryptic Peptides and Liquid Chromatography-Tandem Mass Spectrometry. PMID:30814261
Reversal of carbapenem-resistance in Shewanella algae by CRISPR/Cas9 genome editing. PMID:30809393
Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes. PMID:30808697
Oral Metallo-Beta-Lactamase Protects the Gut Microbiome From Carbapenem-Mediated Damage and Reduces Propagation of Antibiotic Resistance in Pigs. PMID:30804903
Draft Genome Sequences of Four Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates, Including Two Colistin-Resistant Strains, from Cairo, Egypt. PMID:30801061
Draft genome sequence of Enterococcus faecium SP15, a potential probiotic strain isolated from spring water. PMID:30795795
Complete genome sequence data of multidrug-resistant Aeromonas veronii strain MS-18-37. PMID:30788401
Genome plasticity favours double chromosomal Tn4401b-blaKPC-2 transposon insertion in the Pseudomonas aeruginosa ST235 clone. PMID:30786858
Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles. PMID:30784601
An Integrative Database of β-Lactamase Enzymes: Sequences, Structures, Functions, and Phylogenetic Trees. PMID:30783007
Draft Genome Sequence of Enterococcus plantarum Strain TRW2, Isolated from Lettuce. PMID:30746515
Lytic KFS-SE2 phage as a novel bio-receptor for Salmonella Enteritidis detection. PMID:30706346
Enterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa Mill.). PMID:30696492
Complete Genome Sequence Analysis and Characterization of Selected Iron Regulation Genes of Pasteurella Multocida Serotype A Strain PMTB2.1. PMID:30691021
Evaluation of apramycin against spectinomycin-resistant and -susceptible strains of Neisseria gonorrhoeae. PMID:30689929
Dose-dependent impact of oxytetracycline on the veal calf microbiome and resistome. PMID:30660184
Using the wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens. PMID:30631644
Development of New Tools to Detect Colistin-Resistance among Enterobacteriaceae Strains. PMID:30631384
Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut. PMID:30630933
Genomic and Virulence Characterization of Intrauterine Pathogenic Escherichia coli With Multi-Drug Resistance Isolated From Cow Uteri With Metritis. PMID:30619205
Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis. PMID:30567558
Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota. PMID:30559406
Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens. PMID:30555448
Clinical, immunological and bacteriological characteristics of H7N9 patients nosocomially co-infected by Acinetobacter Baumannii: a case control study. PMID:30551738
Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data. PMID:30550564
Genomic Alterations of Staphylococcus aureus ATCC 25923 after Prolonged Passage in the Laboratory. PMID:30533771
Diverse Distribution of Resistomes in the Human and Environmental Microbiomes. PMID:30532649
Diverse Vectors and Mechanisms Spread New Delhi Metallo-β-Lactamases among Carbapenem-Resistant Enterobacteriaceae in the Greater Boston Area. PMID:30530605
Effects of Probiotic Supplementation on the Gut Microbiota and Antibiotic Resistome Development in Preterm Infants. PMID:30505830
Whole Genome Sequencing detects Inter-Facility Transmission of Carbapenem-resistant Klebsiella pneumoniae. PMID:30503842
Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci. PMID:30475919
Pilot Safety Evaluation of a Novel Strain of Bacteroides ovatus. PMID:30459813
The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei. PMID:30427852
Temporal Variability of Escherichia coli Diversity in the Gastrointestinal Tracts of Tanzanian Children with and without Exposure to Antibiotics. PMID:30404930
Complete genome sequence of Bacillus velezensis ZY-1-1 reveals the genetic basis for its hemicellulosic/cellulosic substrate-inducible xylanase and cellulase activities. PMID:30402367
Whole-Genome Sequencing of Russian Neisseria Gonorrhoeae Isolates Related to ST 1407 Genogroup. PMID:30397529
Genome-Based Prediction of Bacterial Antibiotic Resistance. PMID:30381421
Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles. PMID:30373468
Genus-Wide Assessment of Antibiotic Resistance in Lactobacillus spp. PMID:30366997
Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes. PMID:30340417
Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost. PMID:30326830
Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements. PMID:30250208
Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes. PMID:30250051
Enterobacter cloacae Complex Sequence Type 171 Isolates Expressing KPC-4 Carbapenemase Recovered from Canine Patients in Ohio. PMID:30249699
Antibiotic multidrug resistance in the cystic fibrosis airway microbiome is associated with decreased diversity. PMID:30238064
Whole-genome sequence data and analysis of a Staphylococcus aureus strain SJTUF_J27 isolated from seaweed. PMID:30225298
Spfy: an integrated graph database for real-time prediction of bacterial phenotypes and downstream comparative analyses. PMID:30212910
Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation. PMID:30210232
Comparative genomics reveals diverse capsular polysaccharide synthesis gene clusters in emerging Raoultella planticola. PMID:30204830
Evaluating the Safety of Potential Probiotic Enterococcus durans KLDS6.0930 Using Whole Genome Sequencing and Oral Toxicity Study. PMID:30186262
Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains. PMID:30180794
Comprehensive antibiotic-linked mutation assessment by resistance mutation sequencing (RM-seq). PMID:30165908
Large-scale comparative analysis of microbial pan-genomes using PanOCT. PMID:30165579
Integrative metagenomic and biochemical studies on rifamycin ADP-ribosyltransferases discovered in the sediment microbiome. PMID:30108275
Whole Genome Sequencing of Klebsiella pneumoniae Strain Unravels a New Model for the Development of Extensive Drug Resistance in Enterobacteriaceae. PMID:30069258
Past and Present Perspectives on β-Lactamases. PMID:30061284
Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14. PMID:30060533
Gut Bacterial Microbiota and its Resistome Rapidly Recover to Basal State Levels after Short-term Amoxicillin-Clavulanic Acid Treatment in Healthy Adults. PMID:30046129
Emergence of Resistance to Colistin During the Treatment of Bloodstream Infection Caused by Klebsiella pneumoniae Carbapenemase-Producing Klebsiella pneumoniae. PMID:30014001
Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life. PMID:30001517
Comparative genomic analysis of Enterococcus faecalis: insights into their environmental adaptations. PMID:29996769
Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community. PMID:29976643
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes. PMID:29963641
Complete genome sequence of Bacillus sp. HBCD-sjtu, an efficient HBCD-degrading bacterium. PMID:29963351
Comparative genomics of Campylobacter concisus: Analysis of clinical strains reveals genome diversity and pathogenic potential. PMID:29946138
Dispersal-competition tradeoff in microbiomes in the quest for land colonization. PMID:29930350
Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract. PMID:29925834
High genomic diversity of multi-drug resistant wastewater Escherichia coli. PMID:29895899
Multidrug resistant pathogens respond differently to the presence of co-pathogen, commensal, probiotic and host cells. PMID:29872152
Genome Sequencing and Comparative Analysis of Stenotrophomonas acidaminiphila Reveal Evolutionary Insights Into Sulfamethoxazole Resistance. PMID:29867899
Isolation, Functional Characterization and Transmissibility of p3PS10, a Multidrug Resistance Plasmid of the Fish Pathogen Piscirickettsia salmonis. PMID:29867834
The Genomic Basis of Intrinsic and Acquired Antibiotic Resistance in the Genus Serratia. PMID:29867787
Complete Genome Sequence of the Virulent Aeromonas salmonicida subsp. masoucida Strain RFAS1. PMID:29853510
Genome analyses of blaNDM-4 carrying ST 315 Escherichia coli isolate from sewage water of one of the Indian hospitals. PMID:29849769
Comparative genomic analysis of Myroides odoratimimus isolates. PMID:29797432
Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern British Columbia. PMID:29765365
Genome Analysis of Multidrug-Resistant Shewanella algae Isolated From Human Soft Tissue Sample. PMID:29755354
Complete Genome Sequence of Multiple-Antibiotic-Resistant Streptococcus parauberis Strain SPOF3K, Isolated from Diseased Olive Flounder (Paralichthys olivaceus). PMID:29700142
Draft Genome Sequence of Multidrug-Resistant Escherichia coli NIVEDI-P44, Isolated from a Chicken Fecal Sample in Northeast India. PMID:29700135
Antibiotic Treatment Leads to Fecal Escherichia coli and Coliphage Expansion in Severely Malnourished Diarrhea Patients. PMID:29675461
Plasmids carrying DHA-1 β-lactamases. PMID:29663096
Listeria monocytogenes Sequence Types 121 and 14 Repeatedly Isolated Within One Year of Sampling in a Rabbit Meat Processing Plant: Persistence and Ecophysiology. PMID:29662481
KRDS: a web server for evaluating drug resistance mutations in kinases by molecular docking. PMID:29633047
Genomic epidemiology of multidrug-resistant Gram-negative organisms. PMID:29604079
Comparative Genomics of Environmental and Clinical Burkholderia cenocepacia Strains Closely Related to the Highly Transmissible Epidemic ET12 Lineage. PMID:29559964
Design of a Broad-Range Bacteriophage Cocktail That Reduces Pseudomonas aeruginosa Biofilms and Treats Acute Infections in Two Animal Models. PMID:29555626
Genomic differences between nasal Staphylococcus aureus from hog slaughterhouse workers and their communities. PMID:29509797
Current Bioinformatics resources in combating infectious diseases. PMID:29497257
Comparative transcriptomics of multidrug-resistant Acinetobacter baumannii in response to antibiotic treatments. PMID:29476162
Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins. PMID:29463654
Biochemical mechanisms determine the functional compatibility of heterologous genes. PMID:29410400
Detection of antimicrobial resistance genes associated with the International Space Station environmental surfaces. PMID:29339831
In-depth resistome analysis by targeted metagenomics. PMID:29335005
Genomics of Corynebacterium striatum, an emerging multidrug-resistant pathogen of immunocompromised patients. PMID:29326010
Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae. PMID:29323230
Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio. PMID:29319806
High Prevalence of CTX-M-15-Type ESBL-Producing E. coli from Migratory Avian Species in Pakistan. PMID:29312186
Strong Genomic and Phenotypic Heterogeneity in the Aeromonas sobria Species Complex. PMID:29276504
Antimicrobial peptide capsids of de novo design. PMID:29273729
MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data. PMID:29258574
The Emerging Fish Pathogen Flavobacterium spartansii Isolated from Chinook Salmon: Comparative Genome Analysis and Molecular Manipulation. PMID:29250046
Discovery of the fourth mobile sulfonamide resistance gene. PMID:29246178
Arsenic exposure and intestinal microbiota in children from Sirajdikhan, Bangladesh. PMID:29211769
In vivo selection of a multidrug-resistant Aeromonas salmonicida during medicinal leech therapy. PMID:29204282
Genome sequencing and analysis of the first spontaneous Nanosilver resistant bacterium Proteus mirabilis strain SCDR1. PMID:29204271
Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics. PMID:29186015
Complete Genome Sequence of Enterococcus thailandicus Strain a523 Isolated from Urban Raw Sewage. PMID:29167245
Comparative Genomics Reveals Specific Genetic Architectures in Nicotine Metabolism of Pseudomonas sp. JY-Q. PMID:29163390
Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starch-degrader Ruminococcus bromii. PMID:29159997
Genomic Analysis of Third Generation Cephalosporin Resistant Escherichia coli from Dairy Cow Manure. PMID:29149094
Alternative Growth Promoters Modulate Broiler Gut Microbiome and Enhance Body Weight Gain. PMID:29123512
Whole-Genome Sequencing of Lactobacillus Species from Two Commercial Probiotic Products. PMID:29122883
Complete Genome Sequence of Vibrio campbellii LMB 29 Isolated from Red Drum with Four Native Megaplasmids. PMID:29109705
PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens. PMID:29091202
Adaptation in toxic environments: comparative genomics of loci carrying antibiotic resistance genes derived from acid mine drainage waters. PMID:29090447
Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages. PMID:29066550
New opportunities for managing acute and chronic lung infections. PMID:29062070
Prohibition of antibiotic growth promoters has affected the genomic profiles of Lactobacillus salivarius inhabiting the swine intestine. PMID:29059217
Draft Genome Sequence of a Salmonella enterica Serovar Typhi Strain Resistant to Fourth-Generation Cephalosporin and Fluoroquinolone Antibiotics. PMID:29051234
Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing. PMID:29041965
Household triclosan and triclocarban effects on the infant and maternal microbiome. PMID:29030459
Antimicrobial Resistance Gene Acquisition and Depletion Following Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection. PMID:29020222
Draft Genome Sequence of the Type Strain Aeromonas salmonicida subsp. salmonicida ATCC 33658. PMID:28982999
Metagenomic Sequencing of Bronchoalveolar Lavage Samples from Feedlot Cattle Mortalities Associated with Bovine Respiratory Disease. PMID:28982998
PATRIC as a unique resource for studying antimicrobial resistance. PMID:28968762
Safety Assessment of Lactobacillus helveticus KLDS1.8701 Based on Whole Genome Sequencing and Oral Toxicity Studies. PMID:28946645
Global proteomic profiling of Yersinia ruckeri strains. PMID:28931430
Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes. PMID:28915922
Draft Genome Sequence of Epilithonimonas sp. FP211-J200, Isolated from an Outbreak Episode on a Rainbow Trout (Oncorhynchus mykiss) Farm. PMID:28912308
Impact of "Raised without Antibiotics" Beef Cattle Production Practices on Occurrences of Antimicrobial Resistance. PMID:28887421
Complete Genome Sequences of Four Extensively Drug-Resistant Pseudomonas aeruginosa Strains, Isolated from Adults with Ventilator-Associated Pneumonia at a Tertiary Referral Hospital in Mexico City. PMID:28883139
Genomic Characteristics of Bifidobacterium thermacidophilum Pig Isolates and Wild Boar Isolates Reveal the Unique Presence of a Putative Mobile Genetic Element with tetW for Pig Farm Isolates. PMID:28861055
Genomic, Physiologic, and Symbiotic Characterization of Serratia marcescens Strains Isolated from the Mosquito Anopheles stephensi. PMID:28861046
Complete Genome Sequences of Two Pseudomonas aeruginosa Strains Isolated from Children with Bacteremia. PMID:28860262
Genomic insights of Pannonibacter phragmitetus strain 31801 isolated from a patient with a liver abscess. PMID:28857514
Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. PMID:28855266
Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients. PMID:28827811
Comparative Genomics of Escherichia coli Isolated from Skin and Soft Tissue and Other Extraintestinal Infections. PMID:28811343
Genomic insights into the pathogenicity and environmental adaptability of Enterococcus hirae R17 isolated from pork offered for retail sale. PMID:28799224
Whole genome of Klebsiella aerogenes PX01 isolated from San Jacinto River sediment west of Baytown, Texas reveals the presence of multiple antibiotic resistance determinants and mobile genetic elements. PMID:28794987
A population genomics approach to exploiting the accessory 'resistome' of Escherichia coli. PMID:28785420
Draft Genome Sequences of the Multiresistant Escherichia coli C20 Strain, Isolated from Domestic Chicken Gut Microbiota. PMID:28774986
Characterization and diversity of phages infecting Aeromonas salmonicida subsp. salmonicida. PMID:28765570
Beta-lactamase database (BLDB) - structure and function. PMID:28719998
Aquarium Viromes: Viromes of Human-Managed Aquatic Systems. PMID:28713358
Genomic characterization of a large plasmid containing a bla NDM-1 gene carried on Salmonella enterica serovar Indiana C629 isolate from China. PMID:28687066
Expanding landscapes of the diversified mcr-1-bearing plasmid reservoirs. PMID:28683827
Characterization of the emerging zoonotic pathogen Arcobacter thereius by whole genome sequencing and comparative genomics. PMID:28671965
Viromes As Genetic Reservoir for the Microbial Communities in Aquatic Environments: A Focus on Antimicrobial-Resistance Genes. PMID:28663745
New Genome Sequence of an Echinaceapurpurea Endophyte, Arthrobacter sp. Strain EpSL27, Able To Inhibit Human-Opportunistic Pathogens. PMID:28642378
A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis. PMID:28626454
A Primer on Infectious Disease Bacterial Genomics. PMID:28590251
Dissemination of antibiotic resistance genes from antibiotic producers to pathogens. PMID:28589945
Whole-Genome Sequence Analysis of Antimicrobial Resistance Genes in Streptococcus uberis and Streptococcus dysgalactiae Isolates from Canadian Dairy Herds. PMID:28589129
Genomics of antibiotic-resistance prediction in Pseudomonas aeruginosa. PMID:28574575
Differences in Microbiota Membership along the Gastrointestinal Tract of Piglets and Their Differential Alterations Following an Early-Life Antibiotic Intervention. PMID:28536561
Draft Genome Sequence of Pseudomonas sp. Strain Ep R1 Isolated from Echinacea purpurea Roots and Effective in the Growth Inhibition of Human Opportunistic Pathogens Belonging to the Burkholderia cepacia Complex. PMID:28522712
Identification of beta-Lactamases and beta-Lactam-Related Proteins in Human Pathogenic Bacteria using a Computational Search Approach. PMID:28508147
The Threat of Antimicrobial Resistance on the Human Microbiome. PMID:28492988
Bifidobacterium Bacteremia: Clinical Characteristics and a Genomic Approach To Assess Pathogenicity. PMID:28490487
The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery. PMID:28472505
Accumulation and expression of multiple antibiotic resistance genes in Arcobacter cryaerophilus that thrives in sewage. PMID:28462059
Reduction in fecal microbiota diversity and short-chain fatty acid producers in Methicillin-resistant Staphylococcus aureus infected individuals as revealed by PacBio single molecule, real-time sequencing technology. PMID:28455781
Toward a Metagenomic Understanding on the Bacterial Composition and Resistome in Hong Kong Banknotes. PMID:28450856
Genome Sequence of Staphylococcus saprophyticus DPC5671, a Strain Isolated from Cheddar Cheese. PMID:28428298
Antibiotic Resistance Markers in Burkholderia pseudomallei Strain Bp1651 Identified by Genome Sequence Analysis. PMID:28396541
Next-generation approaches to understand and combat the antibiotic resistome. PMID:28392565
A Pan-Genomic Approach to Understand the Basis of Host Adaptation in Achromobacter. PMID:28383665
First Complete Genome Sequence of Corynebacterium riegelii. PMID:28360160
Epidemiological and Molecular Characterization of an Invasive Group A Streptococcus emm32.2 Outbreak. PMID:28356413
Complete Genome Sequence of the Plasmid-Bearing Lactobacillus fermentum Strain SNUV175, a Probiotic for Women's Health Isolated from the Vagina of a Healthy South Korean Woman. PMID:28336593
ResistoMap-online visualization of human gut microbiota antibiotic resistome. PMID:28334267
Cross-resistance to lincosamides, streptogramins A and pleuromutilins in Streptococcus agalactiae isolates from the USA. PMID:28333320
Genomic confirmation of vancomycin-resistant Enterococcus transmission from deceased donor to liver transplant recipient. PMID:28301471
GEAR: A database of Genomic Elements Associated with drug Resistance. PMID:28294141
Complete Genome Sequence of Lactobacillus jensenii Strain SNUV360, a Probiotic for Treatment of Bacterial Vaginosis Isolated from the Vagina of a Healthy Korean Woman. PMID:28280032
Within-host whole genome analysis of an antibiotic resistant Pseudomonas aeruginosa strain sub-type in cystic fibrosis. PMID:28273168
Comparative genomics of Enterococcus spp. isolated from bovine feces. PMID:28270110
Virulence factor activity relationships (VFARs): a bioinformatics perspective. PMID:28261716
Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology. PMID:28232822
Whole-Genome Sequence of a Colombian Acinetobacter baumannii Strain, a Coproducer of OXA-72 and OXA-255-Like Carbapenemases. PMID:28209815
Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details. PMID:28187782
Draft genome sequences of eight bacteria isolated from the indoor environment: Staphylococcus capitis strain H36, S. capitis strain H65, S. cohnii strain H62, S. hominis strain H69, Microbacterium sp. strain H83, Mycobacterium iranicum strain H39, Plantibacter sp. strain H53, and Pseudomonas oryzihabitans strain H72. PMID:28163826
A Clostridium difficile Lineage Endemic to Costa Rican Hospitals Is Multidrug Resistant by Acquisition of Chromosomal Mutations and Novel Mobile Genetic Elements. PMID:28137804
FARME DB: a functional antibiotic resistance element database. PMID:28077567
Rapid resistome mapping using nanopore sequencing. PMID:28062856
Whole-Genome Sequences and Classification of Streptococcus agalactiae Strains Isolated from Laboratory-Reared Long-Evans Rats (Rattus norvegicus). PMID:28057750
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. PMID:28053165
RelA Mutant Enterococcus faecium with Multiantibiotic Tolerance Arising in an Immunocompromised Host. PMID:28049149
Single-Molecule Sequencing (PacBio) of the Staphylococcus capitis NRCS-A Clone Reveals the Basis of Multidrug Resistance and Adaptation to the Neonatal Intensive Care Unit Environment. PMID:28018320
Novel thermostable antibiotic resistance enzymes from the Atlantis II Deep Red Sea brine pool. PMID:28004885
Antimicrobial usage and resistance in beef production. PMID:27999667
Comparative genomics analyses revealed two virulent Listeria monocytogenes strains isolated from ready-to-eat food. PMID:27999619
Draft Genome Sequence of Cloacibacterium normanense NRS-1 Isolated from Municipal Wastewater. PMID:27979947
Evaluation of Machine Learning and Rules-Based Approaches for Predicting Antimicrobial Resistance Profiles in Gram-negative Bacilli from Whole Genome Sequence Data. PMID:27965630
Genome sequencing and annotation of Aeromonas veronii strain Ae52, a multidrug-resistant isolate from septicaemic gold fish (Carassius auratus) in Sri Lanka. PMID:27942459
A diverse intrinsic antibiotic resistome from a cave bacterium. PMID:27929110
Carbapenemase-Producing Enterobacteriaceae Recovered from the Environment of a Swine Farrow-to-Finish Operation in the United States. PMID:27919894
Metagenomic profiling of historic Colorado Front Range flood impact on distribution of riverine antibiotic resistance genes. PMID:27917931
Sponge Microbiota Are a Reservoir of Functional Antibiotic Resistance Genes. PMID:27909433
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. PMID:27899627
MEGARes: an antimicrobial resistance database for high throughput sequencing. PMID:27899569
Prevalence of Antibiotic Resistance Genes among Human Gut-Derived Bifidobacteria. PMID:27864179
A Decade-Long Commitment to Antimicrobial Resistance Surveillance in Portugal. PMID:27843438
Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment. PMID:27822528
The mosaic architecture of Aeromonas salmonicida subsp. salmonicida pAsa4 plasmid and its consequences on antibiotic resistance. PMID:27812409
Finished Genome Sequence of the Highly Multidrug-Resistant Human Urine Isolate Citrobacter freundii Strain SL151. PMID:27811104
Genomic analysis of the multi-drug-resistant clinical isolate Myroides odoratimimus PR63039. PMID:27796642
Characterization and Comparative Overview of Complete Sequences of the First Plasmids of Pandoraea across Clinical and Non-clinical Strains. PMID:27790203
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. PMID:27789705
Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes. PMID:27768825
Evaluating the mobility potential of antibiotic resistance genes in environmental resistomes without metagenomics. PMID:27767072
Translational metagenomics and the human resistome: confronting the menace of the new millennium. PMID:27766372
Endless Resistance. Endless Antibiotics? PMID:27746889
Genomic Comparison of Campylobacter spp. and Their Potential for Zoonotic Transmission between Birds, Primates, and Livestock. PMID:27736787
Deciphering the Resistome of the Widespread Pseudomonas aeruginosa Sequence Type 175 International High-Risk Clone through Whole-Genome Sequencing. PMID:27736752
Functional Metagenomics as a Tool for Identification of New Antibiotic Resistance Genes from Natural Environments. PMID:27709246
Draft Genome Sequence of the Environmentally Isolated Acinetobacter pittii Strain IPK_TSA6.1. PMID:27688336
Genome Sequence of a Novel Multiple-Antibiotic-Resistant Member of the Erysipelotrichaceae Family Isolated from a Swine Manure Storage Pit. PMID:27660777
Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction. PMID:27648812
MetaStorm: A Public Resource for Customizable Metagenomics Annotation. PMID:27632579
The Bacterial Mobile Resistome Transfer Network Connecting the Animal and Human Microbiomes. PMID:27613679
Molecular Epidemiology and Genome Dynamics of New Delhi Metallo-β-Lactamase-Producing Extraintestinal Pathogenic Escherichia coli Strains from India. PMID:27600040
Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome. PMID:27599587
Genome-based insights into the resistome and mobilome of multidrug-resistant Aeromonas sp. ARM81 isolated from wastewater. PMID:27590015
Complete Genome Sequence of Mycobacterium avium, Isolated from Commercial Domestic Pekin Ducks (Anas platyrhynchos domestica), Determined Using PacBio Single-Molecule Real-Time Technology. PMID:27587804
Assess drug-resistance phenotypes, not just genotypes. PMID:27573119
Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. PMID:27572443
Diversity of the Tetracycline Mobilome within a Chinese Pig Manure Sample. PMID:27565618
Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing. PMID:27559074
Draft Genome Sequences of Nine Clinical Isolates of Vancomycin-Resistant Enterococci. PMID:27540059
Salmonella Enteritidis Isolate Harboring Multiple Efflux Pumps and Pathogenicity Factors, Shows Absence of O Antigen Polymerase Gene. PMID:27536269
Draft Genome Sequence of an Enterococcus thailandicus Strain Isolated from Bovine Feces. PMID:27445365
Separate F-Type Plasmids Have Shaped the Evolution of the H30 Subclone of Escherichia coli Sequence Type 131. PMID:27390780
Whole-Genome Sequence of Multidrug-Resistant Pseudomonas aeruginosa Strain BAMCPA07-48, Isolated from a Combat Injury Wound. PMID:27389262
Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses. PMID:27326545
Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. PMID:27306663
SSTAR, a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor. PMID:27303709
Antimicrobial Resistance Prediction in PATRIC and RAST. PMID:27297683
Complete Genome Sequence of Mycobacterium chelonae Type Strain CCUG 47445, a Rapidly Growing Species of Nontuberculous Mycobacteria. PMID:27284158
Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants. PMID:27258951
Commentary: Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. PMID:27242778
Draft Genome Sequence of Flavobacterium sp. Strain TAB 87, Able To Inhibit the Growth of Cystic Fibrosis Bacterial Pathogens Belonging to the Burkholderia cepacia Complex. PMID:27198032
Interconnected microbiomes and resistomes in low-income human habitats. PMID:27172044
Self-resistance in Streptomyces, with Special Reference to β-Lactam Antibiotics. PMID:27171072
Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study. PMID:27166072
Graph mining for next generation sequencing: leveraging the assembly graph for biological insights. PMID:27154001
MOCAT2: a metagenomic assembly, annotation and profiling framework. PMID:27153620
Genome Sequence of Riemerella anatipestifer Strain RCAD0122, a Multidrug-Resistant Isolate from Ducks. PMID:27151800
In vivo gene expression in a Staphylococcus aureus prosthetic joint infection characterized by RNA sequencing and metabolomics: a pilot study. PMID:27150914
Prediction of Putative Resistance Islands in a Carbapenem-Resistant Acinetobacter baumannii Global Clone 2 Clinical Isolate. PMID:27139604
Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems. PMID:27095377
Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology. PMID:27092134
SuperPhy: predictive genomics for the bacterial pathogen Escherichia coli. PMID:27067409
Complete Genome Sequence of Streptococcus mitis Strain SVGS_061 Isolated from a Neutropenic Patient with Viridans Group Streptococcal Shock Syndrome. PMID:27056234
Validation of a High-Throughput Screening Assay for Identification of Adjunctive and Directly Acting Antimicrobials Targeting Carbapenem-Resistant Enterobacteriaceae. PMID:27045615
Fecal Microbial Transplants Reduce Antibiotic-resistant Genes in Patients With Recurrent Clostridium difficile Infection. PMID:27025836
Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T. PMID:27013051
Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database. PMID:27008877
Complete Genome Sequence of Bacillus methylotrophicus Strain B25, a Potential Plant Growth-Promoting Rhizobacterium. PMID:26966215
Intraspecies Transfer of the Chromosomal Acinetobacter baumannii blaNDM-1 Carbapenemase Gene. PMID:26953198
Resistome diversity in cattle and the environment decreases during beef production. PMID:26952213
Draft Genome Sequence of an Invasive Streptococcus agalactiae Isolate Lacking Pigmentation. PMID:26950320
The Challenge and Potential of Metagenomics in the Clinic. PMID:26870044
Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens. PMID:26850162
Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation. PMID:26834722
Characterization of VCC-1, a Novel Ambler Class A Carbapenemase from Vibrio cholerae Isolated from Imported Retail Shrimp Sold in Canada. PMID:26824956
Consolidating and Exploring Antibiotic Resistance Gene Data Resources. PMID:26818666
Complete Genome Sequence of Serratia marcescens SmUNAM836, a Nonpigmented Multidrug-Resistant Strain Isolated from a Mexican Patient with Obstructive Pulmonary Disease. PMID:26798087
Dam and Dcm methylations prevent gene transfer into Clostridium pasteurianum NRRL B-598: development of methods for electrotransformation, conjugation, and sonoporation. PMID:26793273
Genomic and Functional Characterization of qnr-Encoding Plasmids from Municipal Wastewater Biosolid Klebsiella pneumoniae Isolates. PMID:26696974
Complete Genome Sequencing of Stenotrophomonas acidaminiphila ZAC14D2_NAIMI4_2, a Multidrug-Resistant Strain Isolated from Sediments of a Polluted River in Mexico, Uncovers New Antibiotic Resistance Genes and a Novel Class-II Lasso Peptide Biosynthesis Gene Cluster. PMID:26659678
Molecular Characterization by Using Next-Generation Sequencing of Plasmids Containing blaNDM-7 in Enterobacteriaceae from Calgary, Canada. PMID:26643346
The role of biofilms as environmental reservoirs of antibiotic resistance. PMID:26583011
Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. PMID:26578582
The molecular characterisation of Escherichia coli K1 isolated from neonatal nasogastric feeding tubes. PMID:26497222
The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. PMID:26489866
Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. PMID:26483767
Stepwise evolution of pandrug-resistance in Klebsiella pneumoniae. PMID:26478520
Genome Sequence of a Multidrug-Resistant Strain of Stenotrophomonas maltophilia with Carbapenem Resistance, Isolated from King Abdullah Medical City, Makkah, Saudi Arabia. PMID:26472828
Draft Genome Sequence of a Diarrheagenic Morganella morganii Isolate. PMID:26450735
Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities. PMID:26441948
Clonal Dissemination of Enterobacter cloacae Harboring blaKPC-3 in the Upper Midwestern United States. PMID:26438492
Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients. PMID:26401445
Draft Genome Sequence of Turicella otitidis TD1, Isolated from a Patient with Bacteremia. PMID:26383669
Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics. PMID:26369961
The initial state of the human gut microbiome determines its reshaping by antibiotics. PMID:26359913
Draft Genome Sequence of Mycobacterium heckeshornense Strain RLE. PMID:26316632
Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes. PMID:26309137
Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes. PMID:26296728
Metagenomic Analysis of Antibiotic Resistance Genes in Dairy Cow Feces following Therapeutic Administration of Third Generation Cephalosporin. PMID:26258869
Complete Genome Sequence of Acinetobacter baumannii CIP 70.10, a Susceptible Reference Strain for Comparative Genome Analyses. PMID:26227605
Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System. PMID:26220969
Draft Genome Sequence of Mycobacterium heraklionense Strain Davo. PMID:26205863
Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data. PMID:26197475
Genomic and Functional Portrait of a Highly Virulent, CTX-M-15-Producing H30-Rx Subclone of Escherichia coli Sequence Type 131. PMID:26195517
A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii. PMID:26195261
Draft Genome Sequence of Mycobacterium elephantis Strain Lipa. PMID:26112791
Draft Genome Sequence of Mycobacterium arupense Strain GUC1. PMID:26067970
Draft Genome Sequence of Mycobacterium obuense Strain UC1, Isolated from Patient Sputum. PMID:26067960
Toward a new focus in antibiotic and drug discovery from the Streptomyces arsenal. PMID:26029195
Complete Genome Sequence and Transcriptomic Analysis of the Novel Pathogen Elizabethkingia anophelis in Response to Oxidative Stress. PMID:26019164
DBDiaSNP: An Open-Source Knowledgebase of Genetic Polymorphisms and Resistance Genes Related to Diarrheal Pathogens. PMID:25978092
Who qualifies to be a bioinformatician? PMID:25964799
The human gut resistome. PMID:25918444
IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. PMID:25916842
Comparative genomic analysis of a multiple antimicrobial resistant enterotoxigenic E. coli O157 lineage from Australian pigs. PMID:25888127
Fighting microbial drug resistance: a primer on the role of evolutionary biology in public health. PMID:25861380
Complete Genome Sequence of a Carbapenem-Resistant Extraintestinal Pathogenic Escherichia coli Strain Belonging to the Sequence Type 131 H30R Subclade. PMID:25858844
Influence of a non-hospital medical care facility on antimicrobial resistance in wastewater. PMID:25821977
Tackling antibiotic resistance: the environmental framework. PMID:25817583
Population structure of Neisseria gonorrhoeae based on whole genome data and its relationship with antibiotic resistance. PMID:25780762
RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. PMID:25666585
Identification and characterization of a serious multidrug resistant Stenotrophomonas maltophilia strain in China. PMID:25654114
CBMAR: a comprehensive β-lactamase molecular annotation resource. PMID:25475113
Characterization of Antimicrobial Resistance Dissemination across Plasmid Communities Classified by Network Analysis. PMID:25437804
Genomic epidemiology of Klebsiella pneumoniae in Italy and novel insights into the origin and global evolution of its resistance to carbapenem antibiotics. PMID:25367909
Evaluation of a hybrid approach using UBLAST and BLASTX for metagenomic sequences annotation of specific functional genes. PMID:25347677
PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands. PMID:25336619
Whole genome and transcriptome analyses of environmental antibiotic sensitive and multi-resistant Pseudomonas aeruginosa isolates exposed to waste water and tap water. PMID:25186059
Abundances of tetracycline, sulphonamide and beta-lactam antibiotic resistance genes in conventional wastewater treatment plants (WWTPs) with different waste load. PMID:25084517
Draft Whole-Genome Sequence of OXA-48-Producing Multidrug-Resistant Klebsiella pneumoniae KP_ST11_OXA-48. PMID:25081259
Simulate_PCR for amplicon prediction and annotation from multiplex, degenerate primers and probes. PMID:25005023
Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. PMID:25003965
Genome-wide analysis captures the determinants of the antibiotic cross-resistance interaction network. PMID:25000950
Bacterial phylogeny structures soil resistomes across habitats. PMID:24847883
Microbiology: Barriers to the spread of resistance. PMID:24847882
Exploring N-acylhydrazone derivatives against clinical resistant bacterial strains. PMID:24807624
Comparative genomic analysis of malaria mosquito vector-associated novel pathogen Elizabethkingia anophelis. PMID:24803570
Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing. PMID:24501024
Draft Genome Sequence of a Multidrug-Resistant New Delhi Metallo-β-Lactamase-1 (NDM-1)-Producing Escherichia coli Isolate Obtained in Singapore. PMID:24356827
BacMet: antibacterial biocide and metal resistance genes database. PMID:24304895
The innate growth bistability and fitness landscapes of antibiotic-resistant bacteria. PMID:24288338
ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. PMID:24145532
Draft Whole-Genome Sequence of VIM-1-Producing Multidrug-Resistant Enterobacter cloacae EC_38VIM1. PMID:24009122
Draft Genome Sequence of Strain SA_ST125_MupR of Methicillin-Resistant Staphylococcus aureus ST125, a Major Clone in Spain. PMID:23929481
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database PubMed citations: 543.

543 articles citing: CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

Investigation of memory-enhancing effects of Streptococcus thermophilus EG007 in mice and elucidating molecular and metagenomic characteristics using nanopore sequencing. PMID:35918353
Combined comparative genomics and clinical modeling reveals plasmid-encoded genes are independently associated with Klebsiella infection. PMID:35915063
Antibiotic resistance genes are differentially mobilized according to resistance mechanism. PMID:35906888
Whole-genome sequence analysis of high-level penicillin-resistant strains and antimicrobial susceptibility of Neisseria gonorrhoeae clinical isolates from Thailand. PMID:35905043
Draft-genome analysis provides insights into the virulence properties and genome plasticity of Vibrio fluvialis organisms isolated from shrimp farms and Turag river in Bangladesh. PMID:35895240
Two Newly Isolated Enterobacter-Specific Bacteriophages: Biological Properties and Stability Studies. PMID:35891499
Genome Analysis of ESBL-Producing Escherichia coli Isolated from Pigs. PMID:35890020
Metagenomic Characterization of Resistance Genes in Deception Island and Their Association with Mobile Genetic Elements. PMID:35889151
Antibiotic Resistance Properties among Pseudomonas spp. Associated with Salmon Processing Environments. PMID:35889139
Combatting Planktonic and Biofilm Populations of Carbapenem-Resistant Acinetobacter baumannii with Polymyxin-Based Combinations. PMID:35884213
Comparative Genomic Analysis Discloses Differential Distribution of Antibiotic Resistance Determinants between Worldwide Strains of the Emergent ST213 Genotype of Salmonella Typhimurium. PMID:35884180
Aminoglycoside-Modifying Enzymes Are Sufficient to Make Pseudomonas aeruginosa Clinically Resistant to Key Antibiotics. PMID:35884138
Novel Pseudomonas sp. SCA7 Promotes Plant Growth in Two Plant Families and Induces Systemic Resistance in Arabidopsis thaliana. PMID:35875540
Comparative Genomic Analysis of the Human Pathogen Wohlfahrtiimonas Chitiniclastica Provides Insight Into the Identification of Antimicrobial Resistance Genotypes and Potential Virulence Traits. PMID:35873140
Genome characteristics of clinical Salmonella enterica population from a state public health laboratory, New Hampshire, USA, 2017-2020. PMID:35870884
Genomic Insights Into the Interspecific Diversity and Evolution of Mobiluncus, a Pathogen Associated With Bacterial Vaginosis. PMID:35865929
Genomic Insights of Enterococcus faecium UC7251, a Multi-Drug Resistant Strain From Ready-to-Eat Food, Highlight the Risk of Antimicrobial Resistance in the Food Chain. PMID:35814695
Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon. PMID:35814690
Features and Colonization Strategies of Enterococcus faecalis in the Gut of Bombyx mori. PMID:35814682
Using Targeted Liquid Chromatography-Tandem Mass Spectrometry to Rapidly Detect β-Lactam, Aminoglycoside, and Fluoroquinolone Resistance Mechanisms in Blood Cultures Growing E. coli or K. pneumoniae. PMID:35814653
Genomic and proteomic characterization of two strains of Shigella flexneri 2 isolated from infants' stool samples in Argentina. PMID:35804311
PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes. PMID:35787295
In vivo Trial of Bifidobacterium longum Revealed the Complex Network Correlations Between Gut Microbiota and Health Promotional Effects. PMID:35783421
Environmental and Anthropogenic Factors Shape the Snow Microbiome and Antibiotic Resistome. PMID:35783390
Genomic Characterization of Mutli-Drug Resistant Pseudomonas aeruginosa Clinical Isolates: Evaluation and Determination of Ceftolozane/Tazobactam Activity and Resistance Mechanisms. PMID:35782142
Epidemiology, Antimicrobial Resistance, and Virulence Determinants of Group B Streptococcus in an Australian Setting. PMID:35774462
Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy. PMID:35773283
Genome Sequence Analysis and Characterization of Shiga Toxin 2 Production by Escherichia coli O157:H7 Strains Associated With a Laboratory Infection. PMID:35770066
Complete Genome Sequence of a Listeria monocytogenes Strain from a Sample of Kale Salad. PMID:35762752
A genome and gene catalog of glacier microbiomes. PMID:35760913
Novel thermophilic polyhydroxyalkanoates producing strain Aneurinibacillus thermoaerophilus CCM 8960. PMID:35759037
Identification of a Stable Chromosomal Tandem Multicopy of blaVIM-63, a New blaVIM-2 Carbapenemase. PMID:35758752
Genomic analysis of a novel active prophage of Hafnia paralvei. PMID:35752683
Targeted Large-Scale Genome Mining and Candidate Prioritization for Natural Product Discovery. PMID:35736201
SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning. PMID:35725628
Characterization of metal(loid)s and antibiotic resistance in bacteria of human gut microbiota from chronic kidney disease subjects. PMID:35715831
An Epistatic Network Describes oppA and glgB as Relevant Genes for Mycobacterium tuberculosis. PMID:35712352
A 16th century Escherichia coli draft genome associated with an opportunistic bile infection. PMID:35710940
Genomic Analysis of Carbapenem-Resistant Comamonas in Water Matrices: Implications for Public Health and Wastewater Treatments. PMID:35708324
Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing. PMID:35705638
Mining therapeutic targets from the antibiotic-resistant Campylobacter coli and virtual screening of natural product inhibitors against its riboflavin synthase. PMID:35699868
Health-Promoting Nature of Lactococcus lactis IBB109 and Lactococcus lactis IBB417 Strains Exhibiting Proliferation Inhibition and Stimulation of Interleukin-18 Expression in Colorectal Cancer Cells. PMID:35694291
Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes. PMID:35688988
Antibiotic resistance: bioinformatics-based understanding as a functional strategy for drug design. PMID:35685616
Phenotypic and Genetic Characterization of Klebsiella pneumoniae Isolates from Wild Animals in Central Italy. PMID:35681810
Host gut resistome in Gulf War chronic multisymptom illness correlates with persistent inflammation. PMID:35672382
Complete genome sequence of the Pogostemon cablin bacterial wilt pathogen Ralstonia solanacearum strain SY1. PMID:35670995
Metagenomic Analysis Reveals Changes in Bacterial Communities and Antibiotic Resistance Genes in an Eye Specialty Hospital and a General Hospital Before and After Wastewater Treatment. PMID:35663906
Identification of Promoter Region Markers Associated With Altered Expression of Resistance-Nodulation-Division Antibiotic Efflux Pumps in Acinetobacter baumannii. PMID:35663863
Liverpool Epidemic Strain Isolates of Pseudomonas aeruginosa Display High Levels of Antimicrobial Resistance during Both Planktonic and Biofilm Growth. PMID:35658710
Complete Genome Sequences of Three Listeria monocytogenes Strains from Microgreens Obtained with MinION and MiSeq Sequencing. PMID:35658702
Soil Collected in the Great Smoky Mountains National Park Yielded a Novel Listeria sensu stricto Species, L. swaminathanii. PMID:35658601
Complete Genome Sequence of a Listeria monocytogenes Strain Isolated from Sprouts and Carrying an Antimicrobial Resistance Gene. PMID:35658560
Complete Genome Sequence of a Listeria monocytogenes Strain with Antimicrobial Resistance Genes Isolated from Lettuce in Canada. PMID:35658536
Flexible protein database based on amino acid k-mers. PMID:35650262
Performance Characteristics of Next-Generation Sequencing for the Detection of Antimicrobial Resistance Determinants in Escherichia coli Genomes and Metagenomes. PMID:35642524
Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen. PMID:35641522
5NosoAE: a web server for nosocomial bacterial antibiogram investigation and epidemiology survey. PMID:35639518
Identification and Comparative Genomic Analysis of Type VI Secretion Systems and Effectors in Klebsiella pneumoniae. PMID:35633723
Bacterial Community and Genomic Analysis of Carbapenem-Resistant Acinetobacter baumannii Isolates from the Environment of a Health Care Facility in the Western Region of Saudi Arabia. PMID:35631436
Antimicrobial Resistance and Virulence Characteristics of Klebsiella pneumoniae Isolates in Kenya by Whole-Genome Sequencing. PMID:35631066
The Notable Achievements and the Prospects of Bacterial Pathogen Genomics. PMID:35630482
Preclinical Safety Assessment of Bacillus subtilis BS50 for Probiotic and Food Applications. PMID:35630480
Genomic Analysis of Endophytic Bacillus-Related Strains Isolated from the Medicinal Plant Origanum vulgare L. Revealed the Presence of Metabolic Pathways Involved in the Biosynthesis of Bioactive Compounds. PMID:35630363
Imported Pet Reptiles and Their "Blind Passengers"-In-Depth Characterization of 80 Acinetobacter Species Isolates. PMID:35630338
Biomarker Characterization and Prediction of Virulence and Antibiotic Resistance from Helicobacter pylori Next Generation Sequencing Data. PMID:35625618
Whole-Genome Characterisation of ESBL-Producing E. coli Isolated from Drinking Water and Dog Faeces from Rural Andean Households in Peru. PMID:35625336
Identification of Therapeutic Targets in an Emerging Gastrointestinal Pathogen Campylobacter ureolyticus and Possible Intervention through Natural Products. PMID:35625323
Antimicrobial Resistance and Comparative Genomic Analysis of Elizabethkingia anophelis subsp. endophytica Isolated from Raw Milk. PMID:35625292
Whole-Genome Sequencing of a Colistin-Resistant Acinetobacter baumannii Strain Isolated at a Tertiary Health Facility in Pretoria, South Africa. PMID:35625238
Comparative Analyses of Scylla olivacea Gut Microbiota Composition and Function Suggest the Capacity for Polyunsaturated Fatty Acid Biosynthesis. PMID:35618944
Transcriptomics and metagenomics of common cutworm (Spodoptera litura) and fall armyworm (Spodoptera frugiperda) demonstrate differences in detoxification and development. PMID:35596140
Machine Learning in Antibacterial Drug Design. PMID:35592425
Genome mining reveals polysaccharide-degrading potential and new antimicrobial gene clusters of novel intestinal bacterium Paenibacillus jilinensis sp. nov. PMID:35590262
Genomic, morphological, and biochemical analyses of a multi-metal resistant but multi-drug susceptible strain of Bordetella petrii from hospital soil. PMID:35589928
Streptomyces sp. AC04842: Genomic Insights and Functional Expression of Its Latex Clearing Protein Genes (lcp1 and lcp2) When Cultivated With Natural and Vulcanized Rubber as the Sole Carbon Source. PMID:35586859
A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients. PMID:35585088
AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data. PMID:35583675
Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria. PMID:35580059
Genomic Features of High-Level Gentamicin-Resistant Enterococcus faecalis Strain LREF-1 from India. PMID:35575556
Natural selenium stress influences the changes of antibiotic resistome in seleniferous forest soils. PMID:35570296
Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies. PMID:35568730
Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation. PMID:35546409
Text mining for identification of biological entities related to antibiotic resistant organisms. PMID:35539017
Evolutionary Genome Mining for the Discovery and Engineering of Natural Product Biosynthesis. PMID:35524049
Comparative Genomics Revealed Fluoroquinolone Resistance Determinants and OmpF Deletion in Carbapenem-Resistant Escherichia coli. PMID:35516434
Data on complete genome sequence and annotation of two multidrug resistant atypical enteropathogenic Escherichia coli O177 serotype isolated from cattle faeces. PMID:35510268
First Identification of a Multidrug-Resistant Pseudomonas putida Co-Carrying Five β-Lactam Resistance Genes Recovered from a Urinary Tract Infection in China. PMID:35510158
Biochemical and molecular characterization of three serologically different Vibrio harveyi strains isolated from farmed Dicentrarchus labrax from the Adriatic Sea. PMID:35508554
Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women. PMID:35505248
Identification of Antibiotic Resistance Proteins via MiCId's Augmented Workflow. A Mass Spectrometry-Based Proteomics Approach. PMID:35500907
Metagenomics Insights Into the Microbial Diversity and Microbiome Network Analysis on the Heterogeneity of Influent to Effluent Water. PMID:35495647
Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes. PMID:35487919
Evolution of the murine gut resistome following broad-spectrum antibiotic treatment. PMID:35484157
Comparative Analysis of Short- and Long-Read Sequencing of Vancomycin-Resistant Enterococci for Application to Molecular Epidemiology. PMID:35463637
Characterisation of Waterborne Psychrophilic Massilia Isolates with Violacein Production and Description of Massilia antarctica sp. nov. PMID:35456753
A New Variant of the aadE-sat4-aphA-3 Gene Cluster Found in a Conjugative Plasmid from a MDR Campylobacter jejuni Isolate. PMID:35453217
Epidemiology of Klebsiella michiganensis Carrying Multidrug-Resistant IncHI5 Plasmids in the Southeast Coastal Area of China. PMID:35444429
Carbendazim shapes microbiome and enhances resistome in the earthworm gut. PMID:35436900
The Dynamics of the Antimicrobial Resistance Mobilome of Salmonella enterica and Related Enteric Bacteria. PMID:35432284
Pan-Genome Analysis of Laribacter hongkongensis: Virulence Gene Profiles, Carbohydrate-Active Enzyme Prediction, and Antimicrobial Resistance Characterization. PMID:35432229
Comprehensive Analysis of the Nocardia cyriacigeorgica Complex Reveals Five Species-Level Clades with Different Evolutionary and Pathogenicity Characteristics. PMID:35430877
Enhancing predictions of antimicrobial resistance of pathogens by expanding the potential resistance gene repertoire using a pan-genome-based feature selection approach. PMID:35428201
Drinking water chlorination has minor effects on the intestinal flora and resistomes of Bangladeshi children. PMID:35422497
The Atypical Antipsychotic Quetiapine Promotes Multiple Antibiotic Resistance in Escherichia coli. PMID:35416690
Emergence of a Multidrug-Resistant Escherichia coli Co-Carrying a New mcr-1.33 Variant and bla NDM-5 Genes Recovered from a Urinary Tract Infection. PMID:35411158
An engineered live biotherapeutic for the prevention of antibiotic-induced dysbiosis. PMID:35411114
A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens. PMID:35402883
Evaluating approved and alternative treatments against an oxytetracycline-resistant bacterium responsible for European foulbrood disease in honey bees. PMID:35393467
Responses of the Soil Bacterial Community, Resistome, and Mobilome to a Decade of Annual Exposure to Macrolide Antibiotics. PMID:35384705
Draft Genome Sequences of Two Acinetobacter soli Clinical Isolates from a Tertiary Hospital in Terengganu, Malaysia. PMID:35377171
A Systematic Immuno-Informatic Approach to Design a Multiepitope-Based Vaccine Against Emerging Multiple Drug Resistant Serratia marcescens. PMID:35371033
Genetic Diversity, Distribution, and Genomic Characterization of Antibiotic Resistance and Virulence of Clinical Pseudomonas aeruginosa Strains in Kenya. PMID:35369511
Detection and characterization of mutations in genes related to isoniazid resistance in Mycobacterium tuberculosis clinical isolates from Iran. PMID:35366177
Prolonged Outbreak of Carbapenem and Colistin-Resistant Klebsiella pneumoniae at a Large Tertiary Hospital in Brazil. PMID:35356529
Whole-Genome and Transcriptome Sequencing-Based Characterization of Bacillus Cereus NR1 From Subtropical Marine Mangrove and Its Potential Role in Sulfur Metabolism. PMID:35356521
Clustering biological sequences with dynamic sequence similarity threshold. PMID:35354426
Genome sequence of Corynebacterium amycolatum ICIS 99 isolated from human vagina reveals safety and beneficial properties. PMID:35352202
Exploring the genome of Lactobacillaceae spp. Sy-1 isolated from Heterotrigona itama honey. PMID:35345581
Complete Genome Sequence of Kluyvera sp. CRP, a Cellulolytic Strain Isolated from Red Panda Feces (Ailurus fulgens). PMID:35343763
PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies. PMID:35338232
Molecular Characterization of Salmonella Detected along the Broiler Production Chain in Trinidad and Tobago. PMID:35336145
Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming. PMID:35333870
Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome. PMID:35332832
Sequencing Depth Has a Stronger Effect than DNA Extraction on Soil Bacterial Richness Discovery. PMID:35327556
Review and Comparison of Antimicrobial Resistance Gene Databases. PMID:35326803
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes. PMID:35323968
Draft Genome Sequence of a Uropathogenic Escherichia coli Sequence Type 44 Strain Carrying Multiple Antimicrobial Resistance Genes. PMID:35323043
Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates. PMID:35303917
Genomic and antigenic diversity of colonizing Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi. PMID:35302438
Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring (DARTE-QM): a method for detection of antimicrobial resistance in environmental samples. PMID:35301418
Draft genome sequence data of a clinical Enterococcus faecalis isolate SHH039 from a patient with cholecystitis from a tertiary care hospital in Sabah, Malaysia. PMID:35295870
Liquid Chromatography-Tandem Mass Spectrometry Analysis Demonstrates a Decrease in Porins and Increase in CMY-2 β-Lactamases in Escherichia coli Exposed to Increasing Concentrations of Meropenem. PMID:35295306
Classification of 27 Corynebacterium kroppenstedtii-Like Isolates Associated with Mastitis in China and Descriptions of C. parakroppenstedtii sp. nov. and C. pseudokroppenstedtii sp. nov. PMID:35289670
A Metagenomic Approach for Characterizing Antibiotic Resistance Genes in Specific Bacterial Populations: Demonstration with Escherichia coli in Cattle Manure. PMID:35285243
Rural Raccoons (Procyon lotor) Not Likely to Be a Major Driver of Antimicrobial Resistant Human Salmonella Cases in Southern Ontario, Canada: A One Health Epidemiological Assessment Using Whole-Genome Sequence Data. PMID:35280127
Genetic Diversity of Antimicrobial Resistance and Key Virulence Features in Two Extensively Drug-Resistant Acinetobacter baumannii Isolates. PMID:35270562
Limosilactobacillus fermentum ING8, a Potential Multifunctional Non-Starter Strain with Relevant Technological Properties and Antimicrobial Activity. PMID:35267336
A Glyphosate-Based Herbicide Cross-Selects for Antibiotic Resistance Genes in Bacterioplankton Communities. PMID:35266795
Computer Program for Detection and Analyzing the Porin-Mediated Antibiotic Resistance of Bacteria. PMID:35265355
Complete Genome Sequence of Morganella morganii CTX51T, Isolated from a Human Cecal Adenocarcinoma. PMID:35254123
Impact of a Regulation Restricting Critical Antimicrobial Usage on Prevalence of Antimicrobial Resistance in Escherichia coli Isolates From Fecal and Manure Pit Samples on Dairy Farms in Québec, Canada. PMID:35252426
Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance. PMID:35246246
Microbiota dynamics in a randomized trial of gut decontamination during allogeneic hematopoietic cell transplantation. PMID:35239511
Draft genome of Serratia sp. R1 gives an insight into the antibiotic resistant genes against multiple antibiotics. PMID:35237932
The Dissemination of NDM-1 in Acinetobacter baumannii Strains. PMID:35218435
Whole Genome Analysis of 335 New Bacterial Species from Human Microbiota Reveals a Huge Reservoir of Transferable Antibiotic Resistance Determinants. PMID:35216256
Genomic Investigation of Two Acinetobacter baumannii Outbreaks in a Veterinary Intensive Care Unit in The Netherlands. PMID:35215067
Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing. PMID:35212354
Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr. PMID:35208747
Comparison of Reference-Based Assembly and De Novo Assembly for Bacterial Plasmid Reconstruction and AMR Gene Localization in Salmonella enterica Serovar Schwarzengrund Isolates. PMID:35208682
In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health. PMID:35208669
Comparative Genomics of Clostridium baratii Reveals Strain-Level Diversity in Toxin Abundance. PMID:35208668
Of Cockroaches and Symbionts: Recent Advances in the Characterization of the Relationship between Blattella germanica and Its Dual Symbiotic System. PMID:35207577
Assessment of In-Vitro Synergy of Fosfomycin with Meropenem, Amikacin and Tigecycline in Whole Genome Sequenced Extended and Pan Drug Resistant Klebsiella Pneumoniae: Exploring A Colistin Sparing Protocol. PMID:35203756
Francisella sp., a Close Relative of Francisella orientalis, Causing Septicemia with Cholestatic Hepatitis in a Patient with Anti-Interferon-γ (IFN-γ) Autoantibodies. PMID:35202220
Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing. PMID:35196800
Evidence for common ancestry and microevolution of passerine-adapted Salmonella enterica serovar Typhimurium in the UK and USA. PMID:35195512
Heat-Killed Lacticaseibacillus paracasei GMNL-653 Exerts Antiosteoporotic Effects by Restoring the Gut Microbiota Dysbiosis in Ovariectomized Mice. PMID:35187034
Hi-C Metagenomics in the ICU: Exploring Clinically Relevant Features of Gut Microbiome in Chronically Critically Ill Patients. PMID:35185811
Draft Genome Sequencing of Three Glutaraldehyde-Tolerant Bacteria from Produced Water from Hydraulic Fracturing. PMID:35175117
Complete Genome Sequence of Micrococcus luteus Strain CW.Ay, Isolated from Indoor Air in a Hong Kong School. PMID:35175116
The Resistance Mechanism Governs Physiological Adaptation of Escherichia coli to Growth With Sublethal Concentrations of Carbapenem. PMID:35173695
Optimizing Nanopore Sequencing for Rapid Detection of Microbial Species and Antimicrobial Resistance in Patients at Risk of Surgical Site Infections. PMID:35171692
Comparative genome analyses of five Vibrio penaeicida strains provide insights into their virulence-related factors. PMID:35171089
Characterization of a Conjugative Multidrug Resistance IncP-2 Megaplasmid, pPAG5, from a Clinical Pseudomonas aeruginosa Isolate. PMID:35171033
A Bacterial Genome and Culture Collection of Gut Microbial in Weanling Piglet. PMID:35171009
Accurate and rapid prediction of tuberculosis drug resistance from genome sequence data using traditional machine learning algorithms and CNN. PMID:35165358
Application and Challenge of 3rd Generation Sequencing for Clinical Bacterial Studies. PMID:35163319
Pilot Study on Poultry Meat from Antibiotic Free and Conventional Farms: Can Metagenomics Detect Any Difference? PMID:35159402
Neiella holothuriorum sp. nov., isolated from the gut of a sea cucumber Apostichopus japonicus. PMID:35149918
The gut microbiome and antibiotic resistome of chronic diarrhea rhesus macaques (Macaca mulatta) and its similarity to the human gut microbiome. PMID:35139923
Automated extraction of genes associated with antibiotic resistance from the biomedical literature. PMID:35134132
Isolation, characterization and comparative genomics of potentially probiotic Lactiplantibacillus plantarum strains from Indian foods. PMID:35121802
Complete genome sequence of the kiwifruit bacterial canker pathogen Pseudomonas savastanoi strain MHT1. PMID:35120460
Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways. PMID:35113778
Salmonella enterica Serovar Typhimurium Isolates from Wild Birds in the United States Represent Distinct Lineages Defined by Bird Type. PMID:35108089
Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults. PMID:35102136
Probiotic Properties of Bifidobacterium longum KABP042 and Pediococcus pentosaceus KABP041 Show Potential to Counteract Functional Gastrointestinal Disorders in an Observational Pilot Trial in Infants. PMID:35095783
Ontology-aware neural network: a general framework for pattern mining from microbiome data. PMID:35091743
Genomic and functional characterization of bacteriocinogenic lactic acid bacteria isolated from Boza, a traditional cereal-based beverage. PMID:35087086
Phage Annotation Guide: Guidelines for Assembly and High-Quality Annotation. PMID:35083439
F Plasmid Lineages in Escherichia coli ST95: Implications for Host Range, Antibiotic Resistance, and Zoonoses. PMID:35076267
The promiscuous and highly mobile resistome of Acinetobacter baumannii. PMID:35075990
Peritoneal Effluent Cell-Free DNA Sequencing in Peritoneal Dialysis Patients With and Without Peritonitis. PMID:35072047
Mobile Genetic Elements Drive Antimicrobial Resistance Gene Spread in Pasteurellaceae Species. PMID:35069478
Phages in the Gut Ecosystem. PMID:35059329
The Genomic Characterization of KPC-Producing Klebsiella pneumoniae from the ICU of a Teaching Hospital in Shanghai, China. PMID:35046672
Transcriptomics Reveals How Minocycline-Colistin Synergy Overcomes Antibiotic Resistance in Multidrug-Resistant Klebsiella pneumoniae. PMID:35041511
Metagenomic community composition and resistome analysis in a full-scale cold climate wastewater treatment plant. PMID:35033203
Isolation, characterization, molecular analysis and application of bacteriophage DW-EC to control Enterotoxigenic Escherichia coli on various foods. PMID:35017610
Antimicrobial Resistance of Acetobacter and Komagataeibacter Species Originating from Vinegars. PMID:35010733
Changpingibacter yushuensis gen. nov., sp. nov., isolated from fluvial sediment in Qinghai Tibet Plateau of China. PMID:34994958
Genomic analysis of Elizabethkingia species from aquatic environments: Evidence for potential clinical transmission. PMID:34988536
Saline lakes on the Qinghai-Tibet Plateau harbor unique viral assemblages mediating microbial environmental adaption. PMID:34988389
Genomic Analyses of Pediococcus pentosaceus ST65ACC, a Bacteriocinogenic Strain Isolated from Artisanal Raw-Milk Cheese. PMID:34984631
Species-Level Analysis of the Human Gut Microbiome Shows Antibiotic Resistance Genes Associated With Colorectal Cancer. PMID:34975790
A catalogue of 1,167 genomes from the human gut archaeome. PMID:34969981
Spontaneous Phage Resistance in Avian Pathogenic Escherichia coli. PMID:34966369
Detection of antimicrobial resistance genes in urban air. PMID:34964297
Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents. PMID:34960611
The First Bacterial Endocarditis Due to Achromobacter xylosoxidans in a Dog. PMID:34959535
Genomic Characteristics of Stx2e-Producing Escherichia coli Strains Derived from Humans, Animals, and Meats. PMID:34959506
Molecular Characteristics of Streptococcus pyogenes Isolated From Chinese Children With Different Diseases. PMID:34956108
Classification of In Vitro Phage-Host Population Growth Dynamics. PMID:34946072
The Antimicrobial Susceptibility of Porphyromonas gingivalis: Genetic Repertoire, Global Phenotype, and Review of the Literature. PMID:34943650
Isolation and genomic analysis of temperate phage 5W targeting multidrug-resistant Acinetobacter baumannii. PMID:34939149
Genome-Based Characterization of a Plasmid-Associated Micrococcin P1 Biosynthetic Gene Cluster and Virulence Factors in Mammaliicoccus sciuri IMDO-S72. PMID:34936836
A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001-15: introduction and spread of ESBLs facilitated by clonal groups CG15 and CG307. PMID:34935048
Genomic characterization of bacteriophage BI-EHEC infecting strains of Enterohemorrhagic Escherichia coli. PMID:34930434
Prevalence and antimicrobial resistance profiling of Staphylococcus aureus isolated from traditional cheese in Yunnan, China. PMID:34926114
Genome analysis provides insight into hyper-virulence of Streptococcus suis LSM178, a human strain with a novel sequence type 1005. PMID:34907269
A Novel Multidrug Resistant, Non-Tn4401 Genetic Element-Bearing, Strain of Klebsiella pneumoniae Isolated From an Urban Lake With Drinking and Recreational Water Reuse. PMID:34899623
Success of ceftazidime-avibactam and aztreonam in combination for a refractory biliary infection with recurrent bacteraemia due to blaIMP-4 carbapenemase-producing Enterobacter hormaechei subsp. oharae. PMID:34888479
Genome-Wide Mutation Scoring for Machine-Learning-Based Antimicrobial Resistance Prediction. PMID:34884852
Draft Genome Sequences of Two Strains of Enterococcus lactis Showing High Potential as Cattle Probiotic Supplements. PMID:34881976
Genome Sequence of the Reuterin-Producing Strain Limosilactobacillus reuteri INIA P572. PMID:34881975
Genomic Characterization of Extensively Drug-Resistant NDM-Producing Acinetobacter baumannii Clinical Isolates With the Emergence of Novel bla ADC-257. PMID:34880837
Transcriptome Analysis of Pseudomonas aeruginosa Biofilm Infection in an Ex Vivo Pig Model of the Cystic Fibrosis Lung. PMID:34878811
Sabulicella rubraurantiaca gen. nov., sp. nov., a new member of the family Acetobacteraceae, isolated from desert soil. PMID:34870748
Systematic Evaluation of Whole-Genome Sequencing Based Prediction of Antimicrobial Resistance in Campylobacter jejuni and C. coli. PMID:34867917
Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains. PMID:34867904
Quantitative Insights Into β-Lactamase Inhibitor's Contribution in the Treatment of Carbapenemase-Producing Organisms With β-Lactams. PMID:34867880
Lactiplantibacillus plantarum LRCC5314 includes a gene for serotonin biosynthesis via the tryptophan metabolic pathway. PMID:34865198
Aerobiology from an Inactive Pyrite Mine: the Genome Sequence of the Airborne Pseudomonas sp. Strain L5B5. PMID:34854724
Draft Genome Sequences of Cefepime-Resistant and -Susceptible Escherichia coli Strains and Imipenem-Resistant and -Susceptible Pseudomonas aeruginosa Strains. PMID:34854701
Train-the-Trainer as an Effective Approach to Building Global Networks of Experts in Genomic Surveillance of Antimicrobial Resistance (AMR). PMID:34850831
PLSDB: advancing a comprehensive database of bacterial plasmids. PMID:34850116
Gene sharing among plasmids and chromosomes reveals barriers for antibiotic resistance gene transfer. PMID:34839702
Functional Characterisation of Bile Metagenome: Study of Metagenomic Dark Matter. PMID:34835325
Characterization and Genome Study of Novel Lytic Bacteriophages against Prevailing Saprophytic Bacterial Microflora of Minimally Processed Plant-Based Food Products. PMID:34830335
Enterococcus faecium Regulates Honey Bee Developmental Genes. PMID:34829986
Genomic and Phylogenetic Analysis of Lactiplantibacillus plantarum L125, and Evaluation of Its Anti-Proliferative and Cytotoxic Activity in Cancer Cells. PMID:34829947
Natural Bred ε2-Phages Have an Improved Host Range and Virulence against Uropathogenic Escherichia coli over Their Ancestor Phages. PMID:34827275
Isolation and characterization of tick-borne Roseomonas haemaphysalidis sp. nov. and rodent-borne Roseomonas marmotae sp. nov. PMID:34826100
In silico Methods for Identification of Potential Therapeutic Targets. PMID:34826045
Data on the genome of Bacillus subtilis A1- Midalam from beach soil. PMID:34820494
Comparative pangenomic analyses and biotechnological potential of cocoa-related Acetobacter senegalensis strains. PMID:34817761
Weaning Age and Its Effect on the Development of the Swine Gut Microbiome and Resistome. PMID:34812652
Chlorhexidine gluconate usage is associated with antiseptic tolerance in staphylococci from the neonatal intensive care unit. PMID:34806010
Phylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China. PMID:34803966
Serotypes, Virulence-Associated Factors, and Antimicrobial Resistance of Streptococcus suis Isolates Recovered From Sick and Healthy Pigs Determined by Whole-Genome Sequencing. PMID:34796225
A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile. PMID:34793295
Antimicrobial Resistance in Enterococcus Spp. Isolated from a Beef Processing Plant and Retail Ground Beef. PMID:34787441
Plasmid-Mediated Ciprofloxacin Resistance Imparts a Selective Advantage on Escherichia coli ST131. PMID:34780264
A Strategy for the Rapid Development of a Safe Vibrio cholerae Candidate Vaccine Strain. PMID:34769085
Genetic diversity and transmission patterns of Burkholderia pseudomallei on Hainan island, China, revealed by a population genomics analysis. PMID:34762026
Gene Amplification Uncovers Large Previously Unrecognized Cryptic Antibiotic Resistance Potential in E. coli. PMID:34756069
Antibiotic resistance in the environment. PMID:34737424
fIDBAC: A Platform for Fast Bacterial Genome Identification and Typing. PMID:34733246
Burkholderiaceae and Multidrug Resistance Genes Are Key Players in Resistome Development in a Germfree Soil Model. PMID:34726494
Genomic Epidemiology and Characterization of Methicillin-Resistant Staphylococcus aureus from Bloodstream Infections in China. PMID:34726482
Within patient genetic diversity of blaKPC harboring Klebsiella pneumoniae in a Colombian hospital and identification of a new NTEKPC platform. PMID:34725422
Lactitol Supplementation Modulates Intestinal Microbiome in Liver Cirrhotic Patients. PMID:34722597
Nutrient Scarcity in a New Defined Medium Reveals Metabolic Resistance to Antibiotics in the Fish Pathogen Piscirickettsia salmonis. PMID:34707589
Phages from Genus Bruynoghevirus and Phage Therapy: Pseudomonas Phage Delta Case. PMID:34696396
RamAp Is an Efflux Pump Regulator Carried by an IncHI2 Plasmid. PMID:34694885
Concurrent Resistance to Carbapenem and Colistin Among Enterobacteriaceae Recovered From Human and Animal Sources in Nigeria Is Associated With Multiple Genetic Mechanisms. PMID:34690985
Novel methods of microbiome analysis in the food industry. PMID:34686940
Rubber Degrading Strains: Microtetraspora and Dactylosporangium. PMID:34685283
Genomic Analysis of Limosilactobacillus fermentum ATCC 23271, a Potential Probiotic Strain with Anti-Candida Activity. PMID:34682216
Comparative Genomic Analysis of Bifidobacterium bifidum Strains Isolated from Different Niches. PMID:34680899
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. PMID:34676613
Whole-Genome Assessment of Clinical Acinetobacter baumannii Isolates Uncovers Potentially Novel Factors Influencing Carbapenem Resistance. PMID:34659144
Complete Genome Sequence of Weissella confusa LM1 and Comparative Genomic Analysis. PMID:34650545
Draft Genome Sequence of NDM-Encoding Klebsiella pneumoniae Isolated from Feral Swine. PMID:34647798
Complete Genome Sequence of SMBL-WEM22, a Halotolerant Strain of Kosakonia cowanii Isolated from Hong Kong Seawater. PMID:34647797
Identification and Antibiotic Profiling of Wohlfahrtiimonas chitiniclastica, an Underestimated Human Pathogen. PMID:34630346
Isolation of AmpC- and extended spectrum β-lactamase-producing Enterobacterales from fresh vegetables in the United States. PMID:34629764
Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth-gut axis. PMID:34620880
Insight Into Whole Genome of Aeromonas veronii Isolated From Freshwater Fish by Resistome Analysis Reveal Extensively Antibiotic Resistant Traits. PMID:34603262
Genotypic and Phenotypic Characterization of Antimicrobial Resistance Profiles in Non-typhoidal Salmonella enterica Strains Isolated From Cambodian Informal Markets. PMID:34603240
Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola. PMID:34598677
Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter. PMID:34593021
Isolation and characterization of a lytic bacteriophage against Pseudomonas aeruginosa. PMID:34588479
Ciprofloxacin induced antibiotic resistance in Salmonella Typhimurium mutants and genome analysis. PMID:34585273
Non-Penicillin-Susceptible Streptococcus suis Isolated from Humans. PMID:34578210
Comparative Genomics and Specific Functional Characteristics Analysis of Lactobacillus acidophilus. PMID:34576887
Isolation and Characterization of Outer Membrane Vesicles of Pectobacterium brasiliense 1692. PMID:34576813
Comparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota. PMID:34576801
Whole Genome Sequencing of Methicillin-Resistant Staphylococcus epidermidis Clinical Isolates Reveals Variable Composite SCCmec ACME among Different STs in a Tertiary Care Hospital in Oman. PMID:34576720
The First Report of mcr-1-Carrying Escherichia coli Originating from Animals in Serbia. PMID:34572647
Colistin and Carbapenem-Resistant Acinetobacter baumannii Aci46 in Thailand: Genome Analysis and Antibiotic Resistance Profiling. PMID:34572636
Antibiotic Resistance Genes and Associated Phenotypes in Escherichia coli and Enterococcus from Cattle at Different Production Stages on a Dairy Farm in Central California. PMID:34572624
Analysis of Phenol Biodegradation in Antibiotic and Heavy Metal Resistant Acinetobacter lwoffii NL1. PMID:34566929
Multidrug-Resistant Lineage of Enterotoxigenic Escherichia coli ST182 With Serotype O169:H41 in Airline Waste. PMID:34557175
Comparative analysis of prophages carried by human and animal-associated Staphylococcus aureus strains spreading across the European regions. PMID:34556764
Complete Genome Sequence of Escherichia Phage 590B, Active against an Extensively Drug-Resistant Uropathogenic Escherichia coli Isolate. PMID:34554004
Draft Genome Sequence of Streptomyces sp. Strain PAM3C, a Prospective Probiotic Agent Isolated from the Gut of the Bay Scallop, Argopecten purpuratus (Lamarck, 1819). PMID:34554003
Draft Genome Sequences of Four Novel Strains of Microbes Isolated from Lepidocephalichthys guntea. PMID:34553989
Heat-killed Mycolicibacterium aurum Aogashima: An environmental nonpathogenic actinobacteria under development as a safe novel food ingredient. PMID:34531996
Genomic characterization of nine Clostridioides difficile strains isolated from Korean patients with Clostridioides difficile infection. PMID:34530913
Genome Mining of Three Plant Growth-Promoting Bacillus Species from Maize Rhizosphere. PMID:34529229
A review: antimicrobial resistance data mining models and prediction methods study for pathogenic bacteria. PMID:34522024
TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis. PMID:34517763
Flavobacterium erciyesense sp. nov., a putative non-pathogenic fish symbiont. PMID:34515811
Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions. PMID:34507539
Virulent Drexlervirial Bacteriophage MSK, Morphological and Genome Resemblance With Rtp Bacteriophage Inhibits the Multidrug-Resistant Bacteria. PMID:34504479
Draft Genome Sequence of the Multidrug-Resistant Strain Pseudomonas aeruginosa PA291, Isolated from Cystic Fibrosis Sputum. PMID:34498926
Antimicrobial susceptibility patterns of respiratory Gram-negative bacterial isolates from COVID-19 patients in Switzerland. PMID:34493302
Physiology of the Nitrite-Oxidizing Bacterium Candidatus Nitrotoga sp. CP45 Enriched From a Colorado River. PMID:34484146
Duo: A Signature Based Method to Batch-Analyze Functional Similarities of Proteins. PMID:34475860
An Ohio State Scenic River Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent. PMID:34468194
Functional meta-omics provide critical insights into long- and short-read assemblies. PMID:34453168
KARGA: Multi-platform Toolkit for k-mer-based Antibiotic Resistance Gene Analysis of High-throughput Sequencing Data. PMID:34447942
Concordance Between Antibiotic Resistance Genes and Susceptibility in Symptomatic Urinary Tract Infections. PMID:34447256
Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes. PMID:34446072
The Pheno- and Genotypic Characterization of Porcine Escherichia coli Isolates. PMID:34442755
Genetic Diversity of Leuconostoc mesenteroides Isolates from Traditional Montenegrin Brine Cheese. PMID:34442691
Metagenomics-Based Analysis of the Age-Related Cumulative Effect of Antibiotic Resistance Genes in Gut Microbiota. PMID:34439056
Whole-Genome Sequencing for Molecular Characterization of Carbapenem-Resistant Enterobacteriaceae Causing Lower Urinary Tract Infection among Pediatric Patients. PMID:34439022
Draft Genome Sequence and Annotation of the Synthetic Textile Dye-Decolorizing Strain Bacillus amyloliquefaciens AD20, Isolated from a Dye Waste Pond. PMID:34435869
Recovery of small plasmid sequences via Oxford Nanopore sequencing. PMID:34431763
Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK. PMID:34427554
Machine Learning Prediction of Resistance to Subinhibitory Antimicrobial Concentrations from Escherichia coli Genomes. PMID:34427505
Streptomyces tardus sp. nov.: A Slow-Growing Actinobacterium Producing Candicidin, Isolated From Sediments of the Trondheim Fjord. PMID:34421874
Genomic Analysis of Antibiotic-Resistant Staphylococcus epidermidis Isolates From Clinical Sources in the Kwazulu-Natal Province, South Africa. PMID:34421833
Genomic islands targeting dusA in Vibrio species are distantly related to Salmonella Genomic Island 1 and mobilizable by IncC conjugative plasmids. PMID:34415925
Paenarthrobacter sp. GOM3 Is a Novel Marine Species With Monoaromatic Degradation Relevance. PMID:34413843
Complete Genome Sequence of Acinetobacter junii Strain INC8271, Isolated from a Patient with Metastatic Cancer and Bacteremia. PMID:34410161
Comparative Evaluation of Assays for Broad Detection of Molecular Resistance Mechanisms in Enterobacterales Isolates. PMID:34406800
Genetic characterization of livestock-associated methicillin-resistant Staphylococcus aureus isolated in Greece. PMID:34387854
Antimicrobial Resistance Profiling and Phylogenetic Analysis of Neisseria gonorrhoeae Clinical Isolates From Kenya in a Resource-Limited Setting. PMID:34385981
Protein Integrated Network Analysis to Reveal Potential Drug Targets Against Extended Drug-Resistant Mycobacterium tuberculosis XDR1219. PMID:34382159
A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes. PMID:34379107
Classification of a Violacein-Producing Psychrophilic Group of Isolates Associated with Freshwater in Antarctica and Description of Rugamonas violacea sp. nov. PMID:34378950
ARG-SHINE: improve antibiotic resistance class prediction by integrating sequence homology, functional information and deep convolutional neural network. PMID:34377977
Emergence of Erythromycin Resistance Methyltransferases in Campylobacter coli Strains in France. PMID:34370579
Insights from Bacteroides Species in Children with Type 1 Diabetes. PMID:34361871
Characterisation of Colistin -Resistant Enterobacterales and Acinetobacter Strains Carrying mcr Genes from Asian Aquaculture Products. PMID:34356760
Emergence and Clonal Spread of CTX-M-65-Producing Escherichia coli From Retail Meat in Portugal. PMID:34354678
Draft Genome Sequences of Two Multidrug-Resistant Sequence Type 405 Escherichia coli Isolates without Clinical Infection. PMID:34351225
Evidence of an epidemic spread of KPC-producing Enterobacterales in Czech hospitals. PMID:34344951
Genome-Scale Metabolic Models and Machine Learning Reveal Genetic Determinants of Antibiotic Resistance in Escherichia coli and Unravel the Underlying Metabolic Adaptation Mechanisms. PMID:34342537
COPLA, a taxonomic classifier of plasmids. PMID:34332528
Mechanisms of antibiotic resistance of Clostridioides difficile. PMID:34297842
Comparative Whole Genome Sequence Analysis and Biological Features of Clostridioides difficile Sequence Type 2‡. PMID:34290677
Linking plasmid-based beta-lactamases to their bacterial hosts using single-cell fusion PCR. PMID:34282723
Comprehensive Molecular Dissection of Dermatophilus congolensis Genome and First Observation of tet(Z) Tetracycline Resistance. PMID:34281179
Hospital transmission of borderline oxacillin-resistant Staphylococcus aureus evaluated by whole-genome sequencing. PMID:34269673
Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly. PMID:34261503
COVIDomic: A multi-modal cloud-based platform for identification of risk factors associated with COVID-19 severity. PMID:34260589
Let-7b-5p in vesicles secreted by human airway cells reduces biofilm formation and increases antibiotic sensitivity of P. aeruginosa. PMID:34260396
Metagenome-Wide Analysis of Rural and Urban Surface Waters and Sediments in Bangladesh Identifies Human Waste as a Driver of Antibiotic Resistance. PMID:34254820
Essential gene acquisition destabilizes plasmid inheritance. PMID:34252089
Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy. PMID:34248876
Genomic-based characterization of Enterococcus spp.: an emerging pathogen isolated from human gut. PMID:34232463
Achromobacter spp. genetic adaptation in cystic fibrosis. PMID:34232117
Accuracy of Broad-Panel PCR-Based Bacterial Identification for Blood Cultures in a Pediatric Oncology Population. PMID:34232100
Pathogenic Vibrio Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes. PMID:34227831
Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner. PMID:34226711
Comprehensive pan-genome analysis of Lactiplantibacillus plantarum complete genomes. PMID:34216519
The infant gut resistome is associated with E. coli and early-life exposures. PMID:34215179
Metagenomics analysis revealed the distinctive ruminal microbiome and resistive profiles in dairy buffaloes. PMID:34210366
Diversity and Adaptations of Escherichia coli Strains: Exploring the Intestinal Community in Crohn's Disease Patients and Healthy Individuals. PMID:34203637
Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures. PMID:34203511
Testudines as Sentinels for Monitoring the Dissemination of Antibiotic Resistance in Marine Environments: An Integrative Review. PMID:34202175
Complete Genome Sequence of Pasteurella multocida HuN001, a Capsular Type A Strain from a Human. PMID:34197193
Mosaic Ends Tagmentation (METa) Assembly for Highly Efficient Construction of Functional Metagenomic Libraries. PMID:34184912
Unexpected Discovery of Hypermutator Phenotype Sounds the Alarm for Quality Control Strains. PMID:34180992
The Virulence of S. marcescens Strains Isolated From Contaminated Blood Products Is Divergent in the C. elegans Infection Model. PMID:34178032
Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus. PMID:34172889
Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review. PMID:34170311
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. PMID:34168315
Effect of metronidazole on vaginal microbiota associated with asymptomatic bacterial vaginosis. PMID:34151180
Antibiotic resistance: Time of synthesis in a post-genomic age. PMID:34141134
Predicting Antimicrobial Resistance Using Partial Genome Alignments. PMID:34128695
Exploring antimicrobial resistance to beta-lactams, aminoglycosides and fluoroquinolones in E. coli and K. pneumoniae using proteogenomics. PMID:34127720
Population-level faecal metagenomic profiling as a tool to predict antimicrobial resistance in Enterobacterales isolates causing invasive infections: An exploratory study across Cambodia, Kenya, and the UK. PMID:34124634
Whole genome sequence analysis of multi drug resistant community associated methicillin resistant Staphylococcus aureus from food fish: detection of clonal lineage ST 28 and its antimicrobial resistance and virulence genes. PMID:34113482
Whole-Genome Sequencing and Machine Learning Analysis of Staphylococcus aureus from Multiple Heterogeneous Sources in China Reveals Common Genetic Traits of Antimicrobial Resistance. PMID:34100643
A deep-sea bacterium related to coastal marine pathogens. PMID:34097814
Insight into phenotypic and genotypic differences between vaginal Lactobacillus crispatus BC5 and Lactobacillus gasseri BC12 to unravel nutritional and stress factors influencing their metabolic activity. PMID:34096840
The repertoire of ABC proteins in Clostridioides difficile. PMID:34094001
Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers. PMID:34092249
A Quantitative Metagenomic Sequencing Approach for High-Throughput Gene Quantification and Demonstration with Antibiotic Resistance Genes. PMID:34085862
Draft Genome Sequence of Pandrug-Resistant Pseudomonas aeruginosa SPA03, Isolated from a Patient with Benign Prostatic Hyperplasia. PMID:34080904
Isolation and Genomic Analysis of the Phage vB_PaeP_fHoPae04 Infecting Pseudomonas aeruginosa. PMID:34080897
Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria. PMID:34076490
Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals. PMID:34072783
Pan-Resistome Insights into the Multidrug Resistance of Acinetobacter baumannii. PMID:34069870
A Peek into the Plasmidome of Global Sewage. PMID:34061588
Comprehensive Scanning of Prophages in Lactobacillus: Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems. PMID:34060909
The effects of combined environmental factors on the intestinal flora of mice based on ground simulation experiments. PMID:34059794
Draft Genome Sequences of 40 Dermatophilus congolensis Isolates from Bovine Dermatophilosis Cases in St. Kitts and Nevis. PMID:34042483
A Machine Learning Bioinformatics Method to Predict Biological Activity from Biosynthetic Gene Clusters. PMID:34042443
Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda. PMID:34032566
Analysis of Genome Sequences of Coagulase-Negative Staphylococci Isolates from South Africa and Nigeria Highlighted Environmentally Driven Heterogeneity. PMID:34025805
Regional Spread of blaNDM-1-Containing Klebsiella pneumoniae ST147 in Post-Acute Care Facilities. PMID:33999991
Listeria cossartiae sp. nov., Listeria farberi sp. nov., Listeria immobilis sp. nov., Listeria portnoyi sp. nov. and Listeria rustica sp. nov., isolated from agricultural water and natural environments. PMID:33999788
Comparative metagenomic analysis of the vaginal microbiome in healthy women. PMID:33997357
Complete genome sequence of Salmonella enterica strain K_SA184, multidrug resistance bacterium isolated from lamb (Ovis aries). PMID:33987597
Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19. PMID:33986253
Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei. PMID:33976138
Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts. PMID:33925711
Distribution of β-Lactamase Genes in Clinical Isolates from California Central Valley Hospital Deviates from the United States Nationwide Trends. PMID:33925352
The Bacterial Genomic Context of Highly Trimethoprim-Resistant DfrB Dihydrofolate Reductases Highlights an Emerging Threat to Public Health. PMID:33924456
Presence of Broad-Spectrum Beta-Lactamase-Producing Enterobacteriaceae in Zoo Mammals. PMID:33919869
ε2-Phages Are Naturally Bred and Have a Vastly Improved Host Range in Staphylococcus aureus over Wild Type Phages. PMID:33918287
Clinically Relevant Concentrations of Polymyxin B and Meropenem Synergistically Kill Multidrug-Resistant Pseudomonas aeruginosa and Minimize Biofilm Formation. PMID:33918040
Rapid and Accurate Detection of Aminoglycoside-Modifying Enzymes and 16S rRNA Methyltransferases by Targeted Liquid Chromatography-Tandem Mass Spectrometry. PMID:33910961
Comparative genomics and physiological investigation supported safety, cold adaptation, efficient hydrolytic and plant growth-promoting potential of psychrotrophic Glutamicibacter arilaitensis LJH19, isolated from night-soil compost. PMID:33910515
Enabling One Health solutions through genomics. PMID:33906989
The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania. PMID:33902716
Phenotypic and Genomic Variability of Serial Peri-Lung Transplantation Pseudomonas aeruginosa Isolates From Cystic Fibrosis Patients. PMID:33897629
Signal Versus Noise: How to Analyze the Microbiome and Make Progress on Antimicrobial Resistance. PMID:33880565
Impact of Antibiotic Resistance Genes in Gut Microbiome of Patients With Cirrhosis. PMID:33857456
Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil. PMID:33854845
Draft Genome of Proteus mirabilis Serogroup O18 Elaborating Phosphocholine-Decorated O Antigen. PMID:33842384
Genomic characterization of four Escherichia coli strains isolated from oral lichen planus biopsies. PMID:33828821
Case Report: A New Mycobacterium ulcerans Genotype Causing Buruli Ulcer in Côte d'Ivoire. PMID:33819173
Nanopore sequencing and its application to the study of microbial communities. PMID:33815688
Genomic Background and Phylogeny of cfiA-Positive Bacteroides fragilis Strains Resistant to Meropenem-EDTA. PMID:33809460
Potential Target Site for Inhibitors in MLSB Antibiotic Resistance. PMID:33807634
GABA-Producing Lactococcus lactis Strains Isolated from Camel's Milk as Starters for the Production of GABA-Enriched Cheese. PMID:33802798
Epidemic HI2 Plasmids Mobilising the Carbapenemase Gene blaIMP-4 in Australian Clinical Samples Identified in Multiple Sublineages of Escherichia coli ST216 Colonising Silver Gulls. PMID:33801844
Taxonomic Identification of Different Species of the Genus Aeromonas by Whole-Genome Sequencing and Use of Their Species-Specific β-Lactamases as Phylogenetic Markers. PMID:33800590
ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data. PMID:33796850
Identification of Microbiome Etiology Associated With Drug Resistance in Pleural Empyema. PMID:33796482
Genomic Insights Into Last-Line Antimicrobial Resistance in Multidrug-Resistant Staphylococcus and Vancomycin-Resistant Enterococcus. PMID:33796088
Prevalence and Genetic Diversity of Listeria monocytogenes Isolated From Retail Pork in Wuhan, China. PMID:33767677
Draft Genome Sequence of a Polymyxin-Resistant Klebsiella pneumoniae Clinical Strain Carrying mcr-8.1 and bla NDM-5. PMID:33766905
Whole-genome analysis of probiotic product isolates reveals the presence of genes related to antimicrobial resistance, virulence factors, and toxic metabolites, posing potential health risks. PMID:33761872
The Emergence of Invasive Streptococcus pneumoniae Serotype 24F in Lebanon: Complete Genome Sequencing Reveals High Virulence and Antimicrobial Resistance Characteristics. PMID:33746930
Market Chickens as a Source of Antibiotic-Resistant Escherichia coli in a Peri-Urban Community in Lima, Peru. PMID:33737922
Genomic Insights Into the Pathogenicity of a Novel Biofilm-Forming Enterococcus sp. Bacteria (Enterococcus lacertideformus) Identified in Reptiles. PMID:33737921
Phenotypic and Genomic Profiling of Staphylococcus argenteus in Canada and the United States and Recommendations for Clinical Result Reporting. PMID:33731414
Tracking the Origin of Austrian Human Brucellosis Cases Using Whole Genome Sequencing. PMID:33718408
Description and genomic insights into a multidrug resistant novel bacterium Savagea serpentis sp. nov., isolated from the scats of a vine snake (Ahaetulla nasuta). PMID:33715106
Helicobacter pylori Antimicrobial Resistance and Gene Variants in High- and Low-Gastric-Cancer-Risk Populations. PMID:33692136
Biodegradation of lignin monomers and bioconversion of ferulic acid to vanillic acid by Paraburkholderia aromaticivorans AR20-38 isolated from Alpine forest soil. PMID:33687503
Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column. PMID:33673397
Gentamicin Adsorption onto Soil Particles Prevents Overall Short-Term Effects on the Soil Microbiome and Resistome. PMID:33672037
Janthinobacterium tructae sp. nov., Isolated from Kidney of Rainbow Trout (Oncorhynchus mykiss). PMID:33669546
Hypo- and Hyper-Virulent Listeria monocytogenes Clones Persisting in Two Different Food Processing Plants of Central Italy. PMID:33668440
Impact of Probiotic B. infantis EVC001 Feeding in Premature Infants on the Gut Microbiome, Nosocomially Acquired Antibiotic Resistance, and Enteric Inflammation. PMID:33665175
Genome-Wide Association Studies for the Detection of Genetic Variants Associated With Daptomycin and Ceftaroline Resistance in Staphylococcus aureus. PMID:33658988
Exploring Antibiotic Resistance Diversity in Leuconostoc spp. by a Genome-Based Approach: Focus on the lsaA Gene. PMID:33652718
Genomic analysis revealed a novel genotype of methicillin-susceptible Staphylococcus aureus isolated from a fatal sepsis case in dengue patient. PMID:33649330
Genetic Plurality of OXA/NDM-Encoding Features Characterized From Enterobacterales Recovered From Czech Hospitals. PMID:33633720
Draft Genome Sequence of Invasive Salmonella enterica Serovar Cannstatt Harboring mcr-1.1, Isolated from a Fatal Sepsis Case. PMID:33632863
Genomic islands mediate environmental adaptation and the spread of antibiotic resistance in multiresistant Enterococci - evidence from genomic sequences. PMID:33602143
Comparative genomics reveals broad genetic diversity, extensive recombination and nascent ecological adaptation in Micrococcus luteus. PMID:33602135
Genomic Investigation of Virulence Potential in Shiga Toxin Escherichia coli (STEC) Strains From a Semi-Hard Raw Milk Cheese. PMID:33597935
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data. PMID:33597026
Genomic Characterization of Multidrug-Resistant Escherichia coli BH100 Sub-strains. PMID:33584554
Antimicrobial resistance and interspecies gene transfer in Campylobacter coli and Campylobacter jejuni isolated from food animals, poultry processing, and retail meat in North Carolina, 2018-2019. PMID:33571292
Ruminal resistome of dairy cattle is individualized and the resistotypes are associated with milking traits. PMID:33568223
Epidemiological analysis of pneumococcal strains isolated at Yangon Children's Hospital in Myanmar via whole-genome sequencing-based methods. PMID:33565958
ApmA Is a Unique Aminoglycoside Antibiotic Acetyltransferase That Inactivates Apramycin. PMID:33563840
Genotypic and Phenotypic Characterization of Staphylococcus aureus Isolates from the Respiratory Tract in Mechanically-Ventilated Patients. PMID:33562023
Genetic Diversity, Biochemical Properties, and Detection Methods of Minor Carbapenemases in Enterobacterales. PMID:33553210
Exploring Prediction of Antimicrobial Resistance Based on Protein Solvent Accessibility Variation. PMID:33552147
Metagenomics of antimicrobial and heavy metal resistance in the cecal microbiome of fattening pigs raised without antibiotics. PMID:33547058
Sequence characterisation and novel insights into bovine mastitis-associated Streptococcus uberis in dairy herds. PMID:33542314
Draft Genome Sequences of 27 Northern Maine Clinical Isolates. PMID:33541879
Metagenomic Quantification of Genes with Internal Standards. PMID:33531401
Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary. PMID:33520430
Distribution of Beta-Lactamase Producing Gram-Negative Bacterial Isolates in Isabela River of Santo Domingo, Dominican Republic. PMID:33519720
Resistance determinants and their genetic context in enterobacteria from a longitudinal study of pigs reared under various husbandry conditions. PMID:33514521
Comparative Genomics of Leuconostoc carnosum. PMID:33505375
Whole-Genome Sequencing of Clinically Isolated Carbapenem-Resistant Enterobacterales Harboring mcr Genes in Thailand, 2016-2019. PMID:33505364
Complete Genome Sequencing of Acinetobacter baumannii AC1633 and Acinetobacter nosocomialis AC1530 Unveils a Large Multidrug-Resistant Plasmid Encoding the NDM-1 and OXA-58 Carbapenemases. PMID:33504662
Genomic Characterization of Clinical Extensively Drug-Resistant Acinetobacter pittii Isolates. PMID:33503968
Peeling the Layers Away: The Genomic Characterization of Bacillus pumilus 64-1, an Isolate With Antimicrobial Activity From the Marine Sponge Plakina cyanorosea (Porifera, Homoscleromorpha). PMID:33488540
GC-MS analysis of the methanolic extracts of Smilax china and Salix alba and their antioxidant activity. PMID:33488162
Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States. PMID:33479326
Peritoneal Dialysis-Associated Peritonitis Caused by Mycobacterium abscessus in Children-A Case Report. PMID:33447640
Draft Genome Sequence of Multidrug-Resistant Pseudomonas protegens Strain 11HC2, Isolated from Marine Plastic Collected from the West Coast of Norway. PMID:33446595
Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water. PMID:33444384
Whole genome sequencing of coagulase positive staphylococci from a dog-and-owner screening survey. PMID:33428679
Genomic Characterization of VIM and MCR Co-Producers: The First Two Clinical Cases, in Italy. PMID:33418979
Unearthing Antibiotic Resistance Associated with Disturbance-Induced Permafrost Thaw in Interior Alaska. PMID:33418967
Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance. PMID:33416461
Extended-Spectrum β-Lactamases in Human Isolates of Multidrug-Resistant Non-typhoidal Salmonella enterica. PMID:33414769
Closed Genome and Plasmid Sequences of Legionella pneumophila AW-13-4, Isolated from a Hot Water Loop System of a Large Occupational Building. PMID:33414354
Whole Genome Sequence-Based Prediction of Resistance Determinants in High-Level Multidrug-Resistant Campylobacter jejuni Isolates in Lithuania. PMID:33383765
Plasmid Identification and Plasmid-Mediated Antimicrobial Gene Detection in Norwegian Isolates. PMID:33375502
Genomic Insight into Pediococcus acidilactici HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang. PMID:33375492
An Acinetobacter non-baumannii Population Study: Antimicrobial Resistance Genes (ARGs). PMID:33375352
Cell membrane components of Brucella melitensis play important roles in the resistance of low-level rifampicin. PMID:33373362
Dissemination of Extended-Spectrum-β-Lactamase-Producing Enterobacter cloacae Complex from a Hospital to the Nearby Environment in Guadeloupe (French West Indies): ST114 Lineage Coding for a Successful IncHI2/ST1 Plasmid. PMID:33361294
A Novel Family of Acinetobacter Mega-Plasmids Are Disseminating Multi-Drug Resistance Across the Globe While Acquiring Location-Specific Accessory Genes. PMID:33343549
Phylogenomic analysis of Clostridioides difficile ribotype 106 strains reveals novel genetic islands and emergent phenotypes. PMID:33335199
Plant Species-Dependent Increased Abundance and Diversity of IncP-1 Plasmids in the Rhizosphere: New Insights Into Their Role and Ecology. PMID:33329469
Raw Cow Milk Bacterial Consortium as Bioindicator of Circulating Anti-Microbial Resistance (AMR). PMID:33322611
Distribution of Important Probiotic Genes and Identification of the Biogenic Amines Produced by Lactobacillus acidophilus PNW3. PMID:33321968
Genomic Analysis of Aeromonas veronii C198, a Novel Mcr-3.41-Harboring Isolate from a Patient with Septicemia in Thailand. PMID:33317051
Genome sequences of antibiotic-resistant Streptococcus suis strains isolated from human patients and diseased and asymptomatic pigs in Thailand. PMID:33316429
HARP: a database of structural impacts of systematic missense mutations in drug targets of Mycobacterium leprae. PMID:33304465
Wound infection caused by Photobacterium damselae in a 32-year-old woman: case report and review of the literature. PMID:33299740
Antimicrobial Resistance and Genomic Characterization of OXA-48- and CTX-M-15-Co-Producing Hypervirulent Klebsiella pneumoniae ST23 Recovered from Nosocomial Outbreak. PMID:33287207
Comparative Genome Analysis Reveals the Molecular Basis of Niche Adaptation of Staphylococcus epidermidis Strains. PMID:33240320
Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance. PMID:33240317
Metagenomic Characterization of the Microbiome and Resistome of Retail Ground Beef Products. PMID:33240224
Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections. PMID:33206038
Transcriptome-based design of antisense inhibitors potentiates carbapenem efficacy in CRE Escherichia coli. PMID:33199638
The Effect of Iodine-Containing Nano-Micelles, FS-1, on Antibiotic Resistance, Gene Expression and Epigenetic Modifications in the Genome of Multidrug Resistant MRSA Strain Staphylococcus aureus ATCC BAA-39. PMID:33193215
Restoring carbapenem efficacy: a novel carbapenem companion targeting metallo-β-lactamases in carbapenem-resistant Enterobacterales. PMID:33152764
Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum. PMID:33150080
Genomic and Physiological Properties of a Facultative Methane-Oxidizing Bacterial Strain of Methylocystis sp. from a Wetland. PMID:33147874
Systematic Investigation of Resistance Evolution to Common Antibiotics Reveals Conserved Collateral Responses across Common Human Pathogens. PMID:33106260
Predicting antimicrobial resistance using conserved genes. PMID:33075053
Genome Sequences of Four Shigella boydii Strains Representative of the Major S. boydii Clades. PMID:33033129
Genomic Virulence Features of Two Novel Species Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., Isolated from Patients with Chronic Pulmonary Diseases. PMID:33019781
Exploration of the Neisseria Resistome Reveals Resistance Mechanisms in Commensals That May Be Acquired by N. gonorrhoeae through Horizontal Gene Transfer. PMID:33007823
Complete Genome Sequences of Four Extensively Drug-Resistant Acinetobacter baumannii Isolates from Thailand. PMID:33004459
Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands. PMID:33001022
Latilactobacillus curvatus: A Candidate Probiotic with Excellent Fermentation Properties and Health Benefits. PMID:32993033
Antibiotic Resistance: Moving From Individual Health Norms to Social Norms in One Health and Global Health. PMID:32983000
Outer Membrane Disruption Overcomes Intrinsic, Acquired, and Spontaneous Antibiotic Resistance. PMID:32963002
Gene Duplications in the Genomes of Staphylococci and Enterococci. PMID:32850954
Tracking Antimicrobial Resistance Determinants in Diarrheal Pathogens: A Cross-Institutional Pilot Study. PMID:32824772
Pan-genome analysis of Paenibacillus polymyxa strains reveals the mechanism of plant growth promotion and biocontrol. PMID:32816227
Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination. PMID:32796589
Marine Plastics from Norwegian West Coast Carry Potentially Virulent Fish Pathogens and Opportunistic Human Pathogens Harboring New Variants of Antibiotic Resistance Genes. PMID:32784594
Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon. PMID:32776937
Antimicrobial resistance in enteric bacteria: current state and next-generation solutions. PMID:32772817
Description of Komagataeibacter melaceti sp. nov. and Komagataeibacter melomenusus sp. nov. Isolated from Apple Cider Vinegar. PMID:32756518
Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes. PMID:32753501
Fecal Pollution Drives Antibiotic Resistance and Class 1 Integron Abundance in Aquatic Environments of the Bolivian Andes Impacted by Mining and Wastewater. PMID:32722600
Identification of Antimicrobial Resistance-Associated Genes through Whole Genome Sequencing of Mycoplasma bovis Isolates with Different Antimicrobial Resistances. PMID:32707642
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. PMID:32706331
Integrated genome-based probiotic relevance and safety evaluation of Lactobacillus reuteri PNW1. PMID:32687505
Metagenomic Profiling of Ocular Surface Microbiome Changes in Meibomian Gland Dysfunction. PMID:32673387
Experimental approaches to tracking mobile genetic elements in microbial communities. PMID:32672812
Reservoirs of antimicrobial resistance genes in retail raw milk. PMID:32591006
Draft Genome Sequence of Bifidobacterium pseudocatenulatum Bif4, Isolated from Healthy Infant Feces. PMID:32586871
Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients. PMID:32553019
Whole-Genome Sequence of Geobacillus thermoleovorans ARTRW1, Isolated from Armutlu Geothermal Spring, Turkey. PMID:32527772
Whole-genome sequence analysis of environmental Escherichia coli from the faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands. PMID:32519939
Metagenomics as a Tool To Monitor Reclaimed-Water Quality. PMID:32503906
Exploring potential of vaginal Lactobacillus isolates from South African women for enhancing treatment for bacterial vaginosis. PMID:32497109
Survey of drug resistance associated gene mutations in Mycobacterium tuberculosis, ESKAPE and other bacterial species. PMID:32488120
Emerging Threat of Antimicrobial Resistance in β-Hemolytic Streptococci. PMID:32477287
Nanopore sequencing reveals genomic map of CTX-M-type extended-spectrum β-lactamases carried by Escherichia coli strains isolated from blue mussels (Mytilus edulis) in Norway. PMID:32450819
Genomic profiling of antimicrobial resistance genes in clinical isolates of Salmonella Typhi from patients infected with Typhoid fever in India. PMID:32427945
Whole-Genome Draft Assemblies of Difficult-to-Classify Escherichia coli O157 and Non-O157 Isolates from Feces of Canadian Feedlot Cattle. PMID:32273360
PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data. PMID:32108861
Broad-Spectrum Cephalosporin-Resistant Klebsiella spp. Isolated from Diseased Horses in Austria. PMID:32093201
Draft whole-genome sequence of Brevibacterium casei strain isolated from a bloodstream infection. PMID:32067212
Complete Genome Sequences of Four Isolates of Vancomycin-Resistant Enterococcus faecium with the vanA Gene and Two Daptomycin Resistance Mutations, Obtained from Two Inpatients with Prolonged Bacteremia. PMID:32029568
The 27th annual Nucleic Acids Research database issue and molecular biology database collection. PMID:31906604
http://dx.doi.org/10.1093/nar/1951

Tags:

Tags
More detailed information about this field from each metasource.

antimicrobial
metasource: Fairsharing.org
version: FAIRsharing.org: CARD; Comprehensive Antibiotic Resistance Database; DOI: https://doi.org/10.25504/FAIRsharing.9dbmwg; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

dna sequence data
metasource: Fairsharing.org
version: FAIRsharing.org: CARD; Comprehensive Antibiotic Resistance Database; DOI: https://doi.org/10.25504/FAIRsharing.9dbmwg; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: re3data.org
version: re3data.org: Comprehensive Antibiotic Resistance Database; editing status 2022-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3WN59 last accessed: 2022-11-04

phenotype
metasource: Fairsharing.org
version: FAIRsharing.org: CARD; Comprehensive Antibiotic Resistance Database; DOI: https://doi.org/10.25504/FAIRsharing.9dbmwg; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

polypeptide_region
metasource: Fairsharing.org
version: FAIRsharing.org: CARD; Comprehensive Antibiotic Resistance Database; DOI: https://doi.org/10.25504/FAIRsharing.9dbmwg; Last edited: Jan. 3, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

other molecular biology databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

drugs and drug design
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

amr
metasource: re3data.org
version: re3data.org: Comprehensive Antibiotic Resistance Database; editing status 2022-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3WN59 last accessed: 2022-11-04

aro
metasource: re3data.org
version: re3data.org: Comprehensive Antibiotic Resistance Database; editing status 2022-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3WN59 last accessed: 2022-11-04

rgi
metasource: re3data.org
version: re3data.org: Comprehensive Antibiotic Resistance Database; editing status 2022-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3WN59 last accessed: 2022-11-04

antibiotic resistance ontology
metasource: re3data.org
version: re3data.org: Comprehensive Antibiotic Resistance Database; editing status 2022-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3WN59 last accessed: 2022-11-04

antimicrobial resistance
metasource: re3data.org
version: re3data.org: Comprehensive Antibiotic Resistance Database; editing status 2022-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3WN59 last accessed: 2022-11-04

gene
metasource: re3data.org
version: re3data.org: Comprehensive Antibiotic Resistance Database; editing status 2022-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3WN59 last accessed: 2022-11-04

ontology
metasource: re3data.org
version: re3data.org: Comprehensive Antibiotic Resistance Database; editing status 2022-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3WN59 last accessed: 2022-11-04

resistance gene identifier
metasource: re3data.org
version: re3data.org: Comprehensive Antibiotic Resistance Database; editing status 2022-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3WN59 last accessed: 2022-11-04

ontology and terminology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:06.983328

metagenomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:06.983328

whole genome sequencing
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:06.983328

public health and epidemiology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:06.983328

dna polymorphism
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:06.983328

antimicrobial dna sequences phenotype polypeptide region molecular biology drug amr aro rgi antibiotic resistance ontology antimicrobial resistance gene ontology resistance gene identifier ontology and terminology metagenomics whole genome sequencing public health and epidemiology dna polymorphism

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ARDB

FARME DB

BacMet

MEGaRes

HIV Drug Resistance Database

Shared Platform for Antibiotic Research and Knowledge

SEAR: Search Engine for Antimicrobial Resistance

ARS

resistomedb

Plant Resistance Gene Database

GEAR-base

Arctic Report Card

MEGARes 2.0

Antimicrobial prescribing surveillance data during the COVID-19 pandemic

Mosquito Insecticide Resistance Ontology

Infectious Diseases and Antimicrobial Resistance

resistancebank.org

Stanford HIV Drug Resistance Database

MvirDB

StreptomeDB