ArticleBMC genomics2022
In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- cgDist: Nucleotide-level distance calculation from cgMLST allelic profiles.NAR genomics and bioinformatics · 2026Article
- Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation ofJournal of clinical microbiology · 2025Article
- Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens.Nature communications · 2025Article
- Unraveling the impact of genome assembly on bacterial typing: a one health perspective.BMC genomics · 2024Article
- High density genomic surveillance and risk profiling of clinical Listeria monocytogenes subtypes in Germany.Genome medicine · 2024Article
- Development and implementation of a core genome multilocus sequence typing scheme forMicrobial genomics · 2024Article
- Why doesJournal of veterinary research · 2023Article
- Introduction and benchmarking of pyMLST: open-source software for assessing bacterial clonality using core genome MLST.Microbial genomics · 2023Article
- Harmonization of supervised machine learning practices for efficient source attribution of Listeria monocytogenes based on genomic data.BMC genomics · 2023Article
- Sanitary installations and wastewater plumbing as reservoir for the long-term circulation and transmission of carbapenemase producing Citrobacter freundii clones in a hospital setting.Antimicrobial resistance and infection control · 2023Article
- A comprehensive investigation of protein expression profiles inFrontiers in microbiology · 2023Article
- Core Genome Multilocus Sequence Typing Scheme for Improved Characterization and Epidemiological Surveillance of Pathogenic Brucella.Journal of clinical microbiology · 2022Article
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12 authors.
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Abstract
backgroundWhole genome sequencing analyzed by core genome multi-locus sequence typing (cgMLST) is widely used in surveillance of the pathogenic bacteria Listeria monocytogenes. Given the heterogeneity of available bioinformatics tools to define cgMLST alleles, our aim was to identify parameters influencing the precision of cgMLST profiles.
methodsWe used three L. monocytogenes reference genomes from different phylogenetic lineages and assessed the impact of in vitro (i.e. tested genomes, successive platings, replicates of DNA extraction and sequencing) and in silico parameters (i.e. targeted depth of coverage, depth of coverage, breadth of coverage, assembly metrics, cgMLST workflows, cgMLST completeness) on cgMLST precision made of 1748 core loci. Six cgMLST workflows were tested, comprising assembly-based (BIGSdb, INNUENDO, GENPAT, SeqSphere and BioNumerics) and assembly-free (i.e. kmer-based MentaLiST) allele callers. Principal component analyses and generalized linear models were used to identify the most impactful parameters on cgMLST precision.
resultsThe isolate's genetic background, cgMLST workflows, cgMLST completeness, as well as depth and breadth of coverage were the parameters that impacted most on cgMLST precision (i.e. identical alleles against reference circular genomes). All workflows performed well at ≥40X of depth of coverage, with high loci detection (> 99.54% for all, except for BioNumerics with 97.78%) and showed consistent cluster definitions using the reference cut-off of ≤7 allele differences.
conclusionsThis highlights that bioinformatics workflows dedicated to cgMLST allele calling are largely robust when paired-end reads are of high quality and when the sequencing depth is ≥40X.
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