{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T01:28:05Z","timestamp":1792027685231,"version":"4.4.0"},"reference-count":56,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2022,2,15]],"date-time":"2022-02-15T00:00:00Z","timestamp":1644883200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Stool culture is the gold standard method to diagnose enteric bacterial infections; however, many clinical laboratories are transitioning to syndromic multiplex PCR panels. PCR is rapid, accurate, and affordable, yet does not yield subtyping information critical for foodborne disease surveillance. A metagenomics-based stool testing approach could simultaneously provide diagnostic and public health information. Here, we evaluated shotgun metagenomics to assess the detection of common enteric bacterial pathogens in stool. We sequenced 304 stool specimens from 285 patients alongside routine diagnostic testing for Salmonella spp., Campylobacter spp., Shigella spp., and shiga-toxin producing Escherichia coli. Five analytical approaches were assessed for pathogen detection: microbiome profiling, Kraken2, MetaPhlAn, SRST2, and KAT-SECT. Among analysis tools and databases compared, KAT-SECT analysis provided the best sensitivity and specificity for all pathogens tested compared to culture (91.2% and 96.2%, respectively). Where metagenomics detected a pathogen in culture-negative specimens, standard PCR was positive 85% of the time. The cost of metagenomics is approaching the current combined cost of PCR, reflex culture, and whole genome sequencing for pathogen detection and subtyping. As cost, speed, and analytics for single-approach metagenomics improve, it may be more routinely applied in clinical and public health laboratories.<\/jats:p>","DOI":"10.3390\/microorganisms10020441","type":"journal-article","created":{"date-parts":[[2022,2,15]],"date-time":"2022-02-15T22:44:47Z","timestamp":1644965087000},"page":"441","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Clinical Metagenomics Is Increasingly Accurate and Affordable to Detect Enteric Bacterial Pathogens in Stool"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8075-9727","authenticated-orcid":false,"given":"Christy-Lynn","family":"Peterson","sequence":"first","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Alexander","sequence":"additional","affiliation":[{"name":"Cadham Provincial Laboratory, Winnipeg, MB R3E 3J7, Canada"},{"name":"Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julie Chih-Yu","family":"Chen","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada"},{"name":"Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heather","family":"Adam","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada"},{"name":"Shared Health, Winnipeg, MB R3A 1R9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Walker","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Ali","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"Forbes","sequence":"additional","affiliation":[{"name":"Roy Romanow Provincial Laboratory, Regina, SK S4S 0A4, Canada"},{"name":"Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK S7N 0W8, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eduardo","family":"Taboada","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada"},{"name":"Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dillon O. R.","family":"Barker","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morag","family":"Graham","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada"},{"name":"Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalie","family":"Knox","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada"},{"name":"Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1706-7936","authenticated-orcid":false,"given":"Aleisha R.","family":"Reimer","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,2,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1097\/01.inf.0000195623.57945.87","article-title":"Diarrhea in American Infants and Young Children in the Community Setting: Incidence, Clinical Presentation and Microbiology","volume":"25","author":"Vernacchio","year":"2006","journal-title":"Pediatr. 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