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2025
Prevalence of Shiga Toxin-Producing Escherichia coli (STEC) and Risk Characterization Based on Virulence Genes in Retail Raw Ground Meat of Beef, Veal, and Lamb in Canada
Journal of Food Protection
2025
Clostridioides difficile in Honduras: a genomic and phenotypic characterization of the persistent RT027 and emergent RT002 genotypes
Journal of Hospital Infection
2025
Genomic and virulence insights of Western European Aeromonas salmonicida subsp. salmonicida and development of Galleria mellonella infection assay
Journal of Applied Microbiology
2025
Comparative genomics of Mycobacterium avium subsp. hominissuis strains within a group of captive lowland tapirs
PLOS ONE
2025
Comprehensive molecular epidemiology of Acinetobacter baumannii from diverse sources in Nigeria
BMC Microbiology
2025
Pseudomonas aeruginosa investigation in water samples of Campania region, Southern Italy
American Journal of Infection Control
2025
Epidemiology of Staphylococcus aureus food isolates: Comparison of conventional methods with whole genome sequencing typing methods
Food Microbiology
2025
Core genome multilocus sequence typing schemes for epidemiological investigation of Taylorella equigenitalis and Taylorella asinigenitalis
Veterinary Microbiology
2025
Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens
Nature Communications
2025
Genomic characterization of antimicrobial-resistance and virulence factors in Salmonella isolates obtained from pig farms in Antioquia, Colombia
PLOS Neglected Tropical Diseases
2025
Profiling the resistome and virulome of Bacillus strains used for probiotic-based sanitation: a multicenter WGS analysis
BMC Genomics
2025
Molecular characterization of multidrug-resistant E. coli recovered from diarrheagenic children under 5 years from Mukuru Informal Settlement, Nairobi, Kenya, based on whole-genome sequencing analysis
Microbiology Spectrum
2025
Whole-genome sequencing analysis of Staphylococcus aureus isolated from female patients with mastitis in Henan, China
Journal of Global Antimicrobial Resistance
2025
Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection
BMC Genomics
2025
Development and evaluation of a sensitive approach for detection and recovery of third-generation cephalosporin- and carbapenem-resistant Enterobacterales from ready-to-eat frozen stone fruit
Canadian Journal of Microbiology
2025
Whole-genome sequencing of soil- and foodborne Bacillus cereus sensu lato indicates no clear association between their virulence repertoire, genomic diversity and food matrix
International Journal of Food Microbiology
2024
Characterization of MLST-99 Salmonella Typhimurium and the monophasic variant I:4,[5],12:i:- isolated from Canadian Atlantic coast shellfish
Microbiology
2024
Genomic study of European Clostridioides difficile ribotype 002/sequence type 8
Microbial Genomics
2024
ContScout: sensitive detection and removal of contamination from annotated genomes
Nature Communications
2024
Occurrence and diversity of Listeria monocytogenes in Portuguese dairy farms
The Microbe
2024
Escherichia coli in urban marine sediments: interpreting virulence, biofilm formation, halotolerance, and antibiotic resistance to infer contamination or naturalization
FEMS Microbes
2024
Molecular Characterization of Pseudomonas aeruginosa Clinical Isolates Through Whole-Genome Sequencing: A Comprehensive Analysis of Biotypes, Sequence Types, and Antimicrobial and Virulence Genes
Cureus
2024
Molecular Characterization of Escherichia coli Causing Urinary Tract Infections Through Next-Generation Sequencing: A Comprehensive Analysis of Serotypes, Sequence Types, and Antimicrobial and Virulence Genes
Cureus
2024
Genomic insights of Salmonella isolated from dry fermented sausage production chains in Spain and France
Scientific Reports
2024
A retrospective investigation of the population structure and geospatial distribution of Salmonella Paratyphi A in Kathmandu, Nepal
PLOS Neglected Tropical Diseases
2024
SARS-CoV-2 infection predisposes patients to coinfection with Staphylococcus aureus
mBio
2024
Overcoming Microbial Inhibition of S. Sonnei Through the Exploitation of Genomically Predicted Antibiotic Resistance Profiles for the Development of Food Enrichment Media
Journal of Food Protection
2024
NanoMGT: Marker gene typing of low complexity mono-species metagenomic samples using noisy long reads
Biology Methods and Protocols
2024
Genomic diversity of Salmonella Typhimurium and its monophasic variant in pig and pork production in France
Microbiology Spectrum
2024
Molecular Characterization of Klebsiella pneumoniae Clinical Isolates Through Whole-Genome Sequencing: A Comprehensive Analysis of Serotypes, Sequence Types, and Antimicrobial and Virulence Genes
Cureus
2024
Complete genome sequence of a Salmonella enterica strain of serovar Agona associated with an outbreak in France
Microbiology Resource Announcements
2024
Methods in Molecular Biology
2023
Three novel sequencing types from seventeen Staphylococcus aureus genomes isolated from dairy cows milk in the Free State Province of South Africa
Microbiology Resource Announcements
2023
A panel of diverse Klebsiella pneumoniae clinical isolates for research and development
Microbial Genomics
2023
ClinMicroNow
2023
The Good, The Bad, and The Misleading: How to Improve the Quality of ‘Genome Announcements’?
Molecular Plant-Microbe Interactions®
2023
Enteric fever cluster identification in South Africa using genomic surveillance of Salmonella enterica serovar Typhi
Microbial Genomics
2023
Whole genome sequencing of increased number of azithromycin-resistant Shigella flexneri 1b isolates in Ontario
Scientific Reports
2023
Hybrid Genome Assemblies of 245 Avian and Broiler Barn Environment-Associated Escherichia coli Strains Isolated from Saskatchewan Broiler Farms
Microbiology Resource Announcements
2023
Cont-ID: detection of sample cross-contamination in viral metagenomic data
BMC Biology
2023
Harmonization of supervised machine learning practices for efficient source attribution of Listeria monocytogenes based on genomic data
BMC Genomics
2023
Whole-Genome Sequencing-Based Screening of MRSA in Patients and Healthcare Workers in Public Hospitals in Benin
Microorganisms
2023
Whole-Genome Sequence of Salmonella enterica Serovar Bispebjerg from Turkey Reveals Its Pathogenic Potential
Microbiology Resource Announcements
2023
Genomic Characterization of Salmonella enterica serovar Weltevreden Associated with Human Diarrhea
Microbiology Spectrum
2023
Identification of plasmids in avian-associated Escherichia coli using nanopore and illumina sequencing
BMC Genomics
2023
The Role of Mobile Genetic Elements in Virulence Factor Carriage from Symptomatic and Asymptomatic Cases of Escherichia coli Bacteriuria
Microbiology Spectrum
2023
Tell me if you prefer bovine or poultry sectors and I’ll tell you who you are: Characterization of Salmonella enterica subsp. enterica serovar Mbandaka in France
Frontiers in Microbiology
2023
Capsular Polysaccharide Is Essential for the Virulence of the Antimicrobial-Resistant Pathogen Enterobacter hormaechei
mBio
2023
Antimicrobial overproduction sustains intestinal inflammation by inhibiting Enterococcus colonization
Cell Host & Microbe
2023
Transmission dynamics variability of lineage 2 Mycobacterium tuberculosis strains in Kobe, Japan, determined using population-based whole-genome sequencing analysis
Infection, Genetics and Evolution
2022
Whole genome sequencing of cyanobacterium Nostoc sp. CCCryo 231-06 using microfluidic single cell technology
iScience
2022
A European-wide dataset to uncover adaptive traits of Listeria monocytogenes to diverse ecological niches
Scientific Data
2022
Occurrence and Diversity of <i>Listeria monocytogenes</i> Isolated from Two Pig Manure Treatment Plants in France
Microbes and Environments
2022
Background Filtering of Clinical Metagenomic Sequencing with a Library Concentration-Normalized Model
Microbiology Spectrum
2022
Brucella ceti and Brucella pinnipedialis genome characterization unveils genetic features that highlight their zoonotic potential
MicrobiologyOpen
2022
In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes
BMC Genomics
2022
Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps
Molecular Biology Reports
2022
Guidelines for reporting Whole Genome Sequencing‐based typing data through the EFSA One Health WGS System
EFSA Supporting Publications
2022
Contamination detection in genomic data: more is not enough
Genome Biology
2022
Core Genome Multilocus Sequence Typing Scheme for Improved Characterization and Epidemiological Surveillance of Pathogenic Brucella
Journal of Clinical Microbiology
2022
Beyond Nuclear Ribosomal DNA Sequences: Evolution, Taxonomy, and Closest Known Saprobic Relatives of Powdery Mildew Fungi (Erysiphaceae) Inferred From Their First Comprehensive Genome-Scale Phylogenetic Analyses
Frontiers in Microbiology
2022
Non-random genetic alterations in the cyanobacterium Nostoc sp. exposed to space conditions
Scientific Reports
2022
Microbiome-Independent Effects of Antibiotics in a Murine Model of Nosocomial Infections
mBio
2022
Genomic Study on Blood Culture Isolates From Patients With Staphylococcus Infection-associated Glomerulonephritis
Kidney International Reports
2022
CleanSeq: A Pipeline for Contamination Detection, Cleanup, and Mutation Verifications from Microbial Genome Sequencing Data
Applied Sciences
2022
Genomic elements located in the accessory repertoire drive the adaptation to biocides in Listeria monocytogenes strains from different ecological niches
Food Microbiology
2022
A retrospective and regional approach assessing the genomic diversity ofSalmonellaDublin
NAR Genomics and Bioinformatics
2022
Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review
Briefings in Functional Genomics
2021
Systematic Evaluation of Whole-Genome Sequencing Based Prediction of Antimicrobial Resistance in Campylobacter jejuni and C. coli
Frontiers in Microbiology
2021
Incidence and genetic variability of Listeria monocytogenes isolated from vegetables in Poland
International Journal of Food Microbiology
2021
read_haps: using read haplotypes to detect same species contamination in DNA sequences
Bioinformatics
2021
Genetic diversity of Listeria monocytogenes isolated from ready-to-eat food products in retail in Poland
International Journal of Food Microbiology
2021
Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS
Genes
2021
Antibiotic Susceptibility Profiles of Pediococcus pentosaceus from Various Origins and Their Implications for the Safety Assessment of Strains with Food-Technology Applications
Journal of Food Protection
2021
A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch
Genome Medicine
2021
Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel
Microbial Genomics
2021
Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics using Brucella as a model pathogen
Microbial Genomics
2021
Comprehensive Foodomics
2021
Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines
Clinical Infectious Diseases
2021
The Spatiotemporal Dynamics and Microevolution Events That Favored the Success of the Highly Clonal Multidrug-Resistant Monophasic Salmonella Typhimurium Circulating in Europe
Frontiers in Microbiology
2021
Genomic Markers for Quaternary Ammonium Compound Resistance as a Persistence Indicator for Listeria monocytogenes Contamination in Food Manufacturing Environments
Journal of Food Protection
2021
Contamination in Reference Sequence Databases: Time for Divide-and-Rule Tactics
Frontiers in Microbiology
2021
Antimicrobial Susceptibility of Lactobacillus delbrueckii subsp. lactis from Milk Products and Other Habitats
Foods
2021
Detection of carbapenem-resistance genes in bacteria isolated from wastewater in Ontario
FACETS
2021
Overcoming Data Bottlenecks in Genomic Pathogen Surveillance
Clinical Infectious Diseases
2021
Whole-Genome Sequence Datasets: A Powerful Resource for the Food Microbiology Laboratory Toolbox
Frontiers in Sustainable Food Systems
2021
Microbiological Survey of Wheat Flour Sold at Retail in Canada, 2018 to 2019
Journal of Food Protection
2021
Effects of environmental conditions (temperature, pH, and glucose) on biofilm formation of Salmonella enterica serotype Kentucky and virulence gene expression
Poultry Science
2021
Resistance Determinants and Their Genetic Context in Enterobacteria from a Longitudinal Study of Pigs Reared under Various Husbandry Conditions
Applied and Environmental Microbiology
2021
A panel of diverse Pseudomonas aeruginosa clinical isolates for research and development
JAC-Antimicrobial Resistance
2021
High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates: A Multicentric Retrospective Indian Study
Clinical Infectious Diseases
2020
Persistent Asymptomatic Human Infections by Salmonella enterica Serovar Newport in China
mSphere
2020
Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial Resistance
Frontiers in Microbiology
2020
First Report on the Finding of Listeria mnocytogenes ST121 Strain in a Dolphin Brain
Pathogens
2020
Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap
BMJ Global Health
2020
A Diverse Panel of Clinical Acinetobacter baumannii for Research and Development
Antimicrobial Agents and Chemotherapy
2020
Concordance of SNP- and allele-based typing workflows in the context of a large-scale international Salmonella Enteritidis outbreak investigation
Microbial Genomics
2020
Contaminations in (meta)genome data: An open issue for the scientific community
IUBMB Life
2019
Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination
Genome Biology
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