ArticleMicrobial genomics2023
Introduction and benchmarking of pyMLST: open-source software for assessing bacterial clonality using core genome MLST.
Article in Microbial genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
- Comparative genomic characterization and antimicrobial resistance of bacteremia-causingMicrobiology spectrum · 2026Article
- Epidemiological and Molecular Surveillance of Multiresistant Citrobacter freundii Complex in a Tertiary Care Hospital: A Retrospective Cohort Study.The Journal of infectious diseases · 2026Article
- chewBBACA 3: lowering the barrier for scalable and detailed whole- and core-genome multilocus sequence typing.Genome medicine · 2026Article
- Genomic characterization of multidrug-resistant Klebsiella pneumoniae from an outbreak in Northeastern Brazil: mechanisms of virulence and resistance.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Clonal spread of Mycobacterium monacense strains among patients with extrapulmonary mycobacteriosis.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Emergence of ST3390: A Novel Apigmented MRSA Clone From the CC5 Lineage.The Journal of infectious diseases · 2026Article
- Foodborne antibiotics enrich human gut microbiota with pathogens producing extended-spectrum β-lactamases and carbapenemases.The ISME journal · 2026Article
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- Antimicrobial susceptibility and virulence traits ofFrontiers in microbiology · 2026Article
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- Genomic characterization ofApplied and environmental microbiology · 2025Article
- PqsE has a conserved sequence, yet a variable impact inJournal of bacteriology · 2025Article
- MiST: rapid, accurate and flexible (core-genome) multi-locus sequence typing (MLST) allele calling from draft genomes.BMC genomics · 2025Article
- High-resolution genomic and molecular characterization of vancomycin-resistant enterococci from hospitalized patients in a tertiary care center in Riyadh, Saudi Arabia.Scientific reports · 2025Article
- Comprehensive genomic analysis of antibiotic resistance plasmids in animal-associatedMicrobiology spectrum · 2025Article
- An open-source nanopore-only sequencing workflow for analysis of clonal outbreaks delivers short-read level accuracy.Journal of clinical microbiology · 2025Article
- Genomic and Phenotypic Characterization of Mupirocin-resistantOpen forum infectious diseases · 2025Article
- Plasmid diversity ofMicrobiology spectrum · 2025Article
- Prevalence and characteristics of tigecycline- and carbapenem-resistantAntimicrobial agents and chemotherapy · 2025Article
- Genomic epidemiology of third-generation cephalosporin-resistantOne health (Amsterdam, Netherlands) · 2025Article
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5 authors.
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Abstract
Core genome multilocus sequence typing (cgMLST) has gained in popularity for bacterial typing since whole-genome sequencing (WGS) has become affordable. We introduce here pyMLST, a new complete, stand-alone, free and open source pipeline for cgMLST analysis. pyMLST can create or import a core genome database. For each gene, the first allele is aligned against the bacterial genome of interest using BLAT. Incomplete genes are aligned using MAFT. All data are stored in a SQLite database. pyMLST accepts assembly genomes or raw data (with the option pyMLST-KMA) as input. To evaluate our new tool, we selected three genome collections of major bacterial pathogens (
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