In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes
Abstract Background Whole 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 param...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-03-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-022-08437-4 |
| _version_ | 1818774379848269824 |
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| author | Federica Palma Iolanda Mangone Anna Janowicz Alexandra Moura Alexandra Chiaverini Marina Torresi Giuliano Garofolo Alexis Criscuolo Sylvain Brisse Adriano Di Pasquale Cesare Cammà Nicolas Radomski |
| author_facet | Federica Palma Iolanda Mangone Anna Janowicz Alexandra Moura Alexandra Chiaverini Marina Torresi Giuliano Garofolo Alexis Criscuolo Sylvain Brisse Adriano Di Pasquale Cesare Cammà Nicolas Radomski |
| author_sort | Federica Palma |
| collection | DOAJ |
| description | Abstract Background Whole 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. Methods We 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. Results The 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. Conclusions This 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. |
| first_indexed | 2024-12-18T10:40:13Z |
| format | Article |
| id | doaj.art-517b19c87103476982e268e47d85dc95 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-18T10:40:13Z |
| publishDate | 2022-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-517b19c87103476982e268e47d85dc952022-12-21T21:10:40ZengBMCBMC Genomics1471-21642022-03-0123112410.1186/s12864-022-08437-4In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenesFederica Palma0Iolanda Mangone1Anna Janowicz2Alexandra Moura3Alexandra Chiaverini4Marina Torresi5Giuliano Garofolo6Alexis Criscuolo7Sylvain Brisse8Adriano Di Pasquale9Cesare Cammà10Nicolas Radomski11Institut Pasteur, Université de Paris, Biological Resources Center of Institut PasteurIstituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT)Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), Bacteriology UnitInstitut Pasteur, National Reference Center and WHO Collaborating Center ListeriaIstituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), National Reference Labororatory (LNR) for Listeria monocytogenesIstituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), National Reference Labororatory (LNR) for Listeria monocytogenesIstituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), Bacteriology UnitInstitut Pasteur, Université de Paris, Bioinformatics and Biostatistics HubInstitut Pasteur, Université de Paris, Biological Resources Center of Institut PasteurIstituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT)Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT)Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT)Abstract Background Whole 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. Methods We 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. Results The 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. Conclusions This 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.https://doi.org/10.1186/s12864-022-08437-4cgMLSTComparability of workflowsListeria monocytogenesPrincipal component analysisGeneralized linear model |
| spellingShingle | Federica Palma Iolanda Mangone Anna Janowicz Alexandra Moura Alexandra Chiaverini Marina Torresi Giuliano Garofolo Alexis Criscuolo Sylvain Brisse Adriano Di Pasquale Cesare Cammà Nicolas Radomski In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes BMC Genomics cgMLST Comparability of workflows Listeria monocytogenes Principal component analysis Generalized linear model |
| title | In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes |
| title_full | In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes |
| title_fullStr | In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes |
| title_full_unstemmed | In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes |
| title_short | In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes |
| title_sort | in vitro and in silico parameters for precise cgmlst typing of listeria monocytogenes |
| topic | cgMLST Comparability of workflows Listeria monocytogenes Principal component analysis Generalized linear model |
| url | https://doi.org/10.1186/s12864-022-08437-4 |
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