{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T17:02:57Z","timestamp":1775926977283,"version":"3.50.1"},"reference-count":45,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T00:00:00Z","timestamp":1762128000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Accurate assignment of whole-genome sequences to clusters in foodborne outbreak investigations remains challenging. Variability in bioinformatics tools and quality metrics significantly impacts clustering outcomes. This study assessed inter-laboratory variance in cluster identification by providing four datasets of 50 raw Illumina paired-end sequences covering Shiga toxin-producing\n                    <jats:italic>Escherichia coli, Listeria monocytogenes, Salmonella enterica<\/jats:italic>\n                    , and\n                    <jats:italic>Campylobacter jejuni<\/jats:italic>\n                    . Following general rules of a specified guideline, participants applied in-house protocols for read quality assessment, 7-gene MLST, cgMLST, and SNP calling, then assigned samples to predefined focus clusters based on allele distance (AD) and mutations. Results revealed that differences in the interpretation of raw sequence and genome assembly quality influenced sample inclusion and finally cluster composition. Here, intra-species contamination was the most significant factor driving variability in decisions on whether to include or exclude samples. With one exception, 7-gene Multilocus-Sequence Typing (MLST) yielded consistent sequence types using different bioinformatics tools. The largest influence on cgMLST-defined clusters was the inclusion or exclusion of samples. Regarding bioinformatics, cgMLST was mainly reproducible. For\n                    <jats:italic>S. enterica<\/jats:italic>\n                    , discrepancies due to different software (Ridom SeqSphere+ vs. ChewieSnake) were larger than discrepancies due to different schemas. For other species, different schemas introduced larger discrepancies than different software. Most notably,\n                    <jats:italic>C. jejuni<\/jats:italic>\n                    cluster assignment was strongly affected by cgMLST schemas differing by a factor of two in the number of loci. SNP calling using Snippy produced concordant results across participants, except for\n                    <jats:italic>C. jejuni<\/jats:italic>\n                    when recombination filtering was used. This study highlights the impact caused by different interpretations of quality values when assessing clusters. Low-resolution cgMLST schemas were unsuitable for\n                    <jats:italic>Campylobacter jejuni<\/jats:italic>\n                    , and clustering near cut-off values was sensitive to bioinformatics tool selection. Standardized protocols are essential for reliable inter-laboratory comparison in foodborne pathogen surveillance.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2025.1629731","type":"journal-article","created":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T15:16:42Z","timestamp":1762183002000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["An inter-laboratory study characterizes the impact of bioinformatic approaches on genome-based cluster detection for foodborne bacterial pathogens"],"prefix":"10.3389","volume":"16","author":[{"given":"Leonie F.","family":"Forth","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Burkhard","family":"Malorny","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Markus","family":"B\u00f6nn","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erik","family":"Brinks","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gr\u00e9goire","family":"Denay","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlus","family":"Deneke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hosny","family":"El-Adawy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jennie","family":"Fischer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jannika","family":"Fuchs","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ekkehard","family":"Hiller","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nancy","family":"Bretschneider","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sylvia","family":"Kleta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefanie","family":"L\u00fcth","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tilman","family":"Schultze","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henning","family":"Petersen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michaela","family":"Projahn","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Sch\u00e4fers","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kerstin","family":"Stingl","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas J.","family":"Stroehlein","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laura","family":"Uelze","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kathrin","family":"Szabo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne","family":"W\u00f6hlke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00f6rg","family":"Linde","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2025,11,3]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"e1002776","DOI":"10.1371\/journal.ppat.1002776","article-title":"Multilocus sequence typing as a replacement for serotyping in Salmonella enterica","volume":"8","author":"Achtman","year":"2012","journal-title":"PLoS Pathog."},{"key":"B2","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1016\/j.copbio.2017.11.002","article-title":"Genomics of foodborne pathogens for microbial food safety","volume":"49","author":"Allard","year":"2018","journal-title":"Curr. Opin. Biotechnol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1016\/j.tim.2018.08.004","article-title":"From theory to practice: translating Whole-Genome Sequencing (WGS) into the clinic","volume":"26","author":"Balloux","year":"2018","journal-title":"Trends Microbiol."},{"key":"B4","article-title":"Untersuchung von Lebensmittel - Gesamtgenomsequenzierung zur Typisierung und Charakterisierung von Salmonella enterica, Listeria monocytogenes, thermotolerante Campylobacter spp. und Shigatoxin-bildenden sowie kommensalen Escherichia coli, die aus Lebensmitteln isoliert wurden","year":"2023"},{"key":"B5","unstructured":"Vorgehensweise und Empfehlungen f\u00fcr die Clusteranalyse von Gesamtgenomsequenzdaten aus Salmonella enterica, Listeria monocytogenes, Campylobacter jejuni\/C. coli und Shigatoxin-bildenden sowie kommensalen Escherichia coli\n          \n          2024"},{"key":"B6","doi-asserted-by":"publisher","first-page":"2086","DOI":"10.1128\/JCM.00080-17","article-title":"Core genome multilocus sequence typing scheme for stable, comparative analyses of Campylobacter jejuni and C. coli human disease isolates","volume":"55","author":"Cody","year":"2017","journal-title":"J. Clin. Microbiol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1099\/mgen.0.000612","article-title":"Centre-specific bacterial pathogen typing affects infection-control decision making","volume":"7","author":"Coolen","year":"2021","journal-title":"Microb. Genom."},{"key":"B8","doi-asserted-by":"publisher","first-page":"644","DOI":"10.3390\/genes12050644","article-title":"Species-specific quality control, assembly and contamination detection in microbial isolate sequences with AQUAMIS","volume":"12","author":"Deneke","year":"","journal-title":"Genes"},{"key":"B9","doi-asserted-by":"publisher","first-page":"649517","DOI":"10.3389\/fmicb.2021.649517","article-title":"Decentralized investigation of bacterial outbreaks based on hashed cgMLST","volume":"12","author":"Deneke","year":"","journal-title":"Front. 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Infect."},{"key":"B12","doi-asserted-by":"publisher","first-page":"e05898","DOI":"10.2903\/j.efsa.2019.5898","article-title":"Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms","volume":"17","author":"EFSA Panel on Biological Hazards","year":"2019","journal-title":"EFSA J."},{"key":"B13","doi-asserted-by":"publisher","first-page":"1092179","DOI":"10.3389\/fvets.2023.1092179","article-title":"Genomic insight into Campylobacter jejuni isolated from commercial turkey flocks in Germany using whole-genome sequencing analysis","volume":"10","author":"El-Adawy","year":"2023","journal-title":"Front. Vet. Sci."},{"key":"B14","unstructured":"Applications of Whole Genome Sequencing in Food Safety Management.\n          \n          2016"},{"key":"B15","doi-asserted-by":"publisher","first-page":"1253362","DOI":"10.3389\/fmicb.2023.1253362","article-title":"Impact of wet-lab protocols on quality of whole-genome short-read sequences from foodborne microbial pathogens","volume":"14","author":"Forth","year":"2023","journal-title":"Front. Microbiol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"00941","DOI":"10.1099\/mgen.0.000941","article-title":"Whole-genome-based characterization of Campylobacter jejuni from human patients with gastroenteritis collected over an 18 year period reveals increasing prevalence of antimicrobial resistance","volume":"9","author":"Ghielmetti","year":"2023","journal-title":"Microb. Genom."},{"key":"B17","volume-title":"ISO 23418:2022, Microbiology of the Food Chain \u2014 Whole Genome Sequencing for Typing and Genomic Characterization of Bacteria \u2014 General Requirements and Guidance","year":"2022"},{"key":"B18","doi-asserted-by":"publisher","first-page":"560","DOI":"10.1186\/1471-2164-9-560","article-title":"Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains","volume":"9","author":"Jaureguy","year":"2008","journal-title":"BMC Genom."},{"key":"B19","doi-asserted-by":"crossref","unstructured":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications\n          \n          124\n          \n            \n              Jolley\n              K. A.\n            \n            \n              Bray\n              J. E.\n            \n            \n              Maiden\n              M. C. J.\n            \n          \n          10.12688\/wellcomeopenres.14826.1\n          30345391\n          Wellcome Open Res.\n          3\n          2018","DOI":"10.12688\/wellcomeopenres.14826.1"},{"key":"B20","doi-asserted-by":"publisher","first-page":"e107014","DOI":"10.1371\/journal.pone.0107014","article-title":"GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers","volume":"9","author":"J\u00fcnemann","year":"2014","journal-title":"PLoS ONE"},{"key":"B21","doi-asserted-by":"publisher","first-page":"e104984","DOI":"10.1371\/journal.pone.0104984","article-title":"Solving the problem of comparing whole bacterial genomes across different sequencing platforms","volume":"9","author":"Kaas","year":"2014","journal-title":"PLoS ONE"},{"key":"B22","doi-asserted-by":"publisher","first-page":"e6995","DOI":"10.7717\/peerj.6995","article-title":"ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data","volume":"7","author":"Low","year":"2019","journal-title":"PeerJ"},{"key":"B23","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1099\/mgen.0.000491","article-title":"Translatability of WGS typing results can simplify data exchange for surveillance and control of Listeria monocytogenes","volume":"7","author":"L\u00fcth","year":"2021","journal-title":"Microb. 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Microbiol."},{"key":"B29","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1186\/s13059-019-1914-x","article-title":"Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination","volume":"20","author":"Pightling","year":"2019","journal-title":"Genome Biol."},{"key":"B30","unstructured":"R: A Language and Environment for Statistical Computing.\n          \n          2022"},{"key":"B31","doi-asserted-by":"publisher","first-page":"e1000146","DOI":"10.1371\/journal.ppat.1000146","article-title":"A new perspective on Listeria monocytogenes evolution","volume":"4","author":"Ragon","year":"2008","journal-title":"PLoS Pathog."},{"key":"B32","unstructured":"Rossi\n              M.\n            \n            \n              Santos Da Silva\n              M.\n            \n            \n              Ribeiro-Gon\u00e7alves\n              B. F.\n            \n            \n              Silva\n              D. N.\n            \n            \n              Machado\n              M. P.\n            \n            \n              Oleastro\n              M.\n            \n          \n          INNUENDO Whole Genome and Core Genome MLST Schemas and Datasets for Campylobacter jejuni"},{"key":"B33","unstructured":"Rossi\n              M.\n            \n            \n              Santos Da Silva\n              M.\n            \n            \n              Ribeiro-Gon\u00e7alves\n              B. F.\n            \n            \n              Silva\n              D. N.\n            \n            \n              Machado\n              M. P.\n            \n            \n              Oleastro\n              M.\n            \n          \n          INNUENDO Whole Genome and Core Genome MLST Schemas and Datasets for Escherichia coli"},{"key":"B34","doi-asserted-by":"publisher","first-page":"2869","DOI":"10.1128\/JCM.01193-15","article-title":"Defining and evaluating a core genome multilocus sequence typing scheme for Whole-Genome Sequence-based typing of Listeria monocytogenes","volume":"53","author":"Ruppitsch","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"B35","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1016\/j.cmi.2017.12.016","article-title":"Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches","volume":"24","author":"Sch\u00fcrch","year":"2018","journal-title":"Clin. Microbiol. 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Microbiol."},{"key":"B43","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"B44","doi-asserted-by":"publisher","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"Wood","year":"2014","journal-title":"Genome Biol."},{"key":"B45","doi-asserted-by":"publisher","first-page":"138","DOI":"10.1101\/gr.251678.119","article-title":"The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity","volume":"30","author":"Zhou","year":"2020","journal-title":"Genome Res."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1629731\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T15:16:45Z","timestamp":1762183005000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1629731\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,3]]},"references-count":45,"alternative-id":["10.3389\/fmicb.2025.1629731"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2025.1629731","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,3]]},"article-number":"1629731"}}