{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T18:51:03Z","timestamp":1791399063988,"version":"4.3.3"},"update-to":[{"DOI":"10.1371\/journal.pntd.0014130","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T00:00:00Z","timestamp":1791331200000}}],"reference-count":102,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000270","name":"Natural Environment Research Council","doi-asserted-by":"publisher","award":["NE\/S007504\/1"],"award-info":[{"award-number":["NE\/S007504\/1"]}],"id":[{"id":"10.13039\/501100000270","id-type":"DOI","asserted-by":"publisher"}]},{"name":"MRC","award":["MR\/N0137941\/1"],"award-info":[{"award-number":["MR\/N0137941\/1"]}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["211227\/Z\/18\/Z"],"award-info":[{"award-number":["211227\/Z\/18\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008668","name":"NERC Environmental Bioinformatics Centre","doi-asserted-by":"publisher","award":["NEOF1396"],"award-info":[{"award-number":["NEOF1396"]}],"id":[{"id":"10.13039\/100008668","id-type":"DOI","asserted-by":"publisher"}]},{"name":"China Scholarship Council and by the University of Liverpool","award":["na"],"award-info":[{"award-number":["na"]}],"id":[{"id":"https:\/\/ror.org\/04atp4p48","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"<jats:p>\n                    Soil-transmitted helminths (STHs) pose significant challenges to public health in endemic areas, necessitating reliable methods for their detection. Shotgun metagenomics enables simultaneous detection of STHs and microbes in a sample without prior knowledge of what is present. However, validation of shotgun metagenomics with known infection intensity or across different sequencing platforms has not been carried out for eukaryote parasites including STHs, and false positives remain a pervasive issue. We validated shotgun metagenomics as a method of STH detection in faecal samples. Using the\n                    <jats:italic>Strongyloides ratti<\/jats:italic>\n                    laboratory model of a STH infection we investigated how analytical methods (nucleotide-nucleotide matching, nucleotide-protein matching, marker gene detection, mitochondrial mapping), infection intensity (low and standard laboratory doses) and sequencing technology (short-read vs. long-read) affects sensitivity and specificity of detection.\n                    <jats:italic>S. ratti<\/jats:italic>\n                    was accurately detected at a standard laboratory dose, but low intensity infection were more difficult to detect. Only mitochondrial sequence mapping was 100% accurate at identifying\n                    <jats:italic>S. ratti<\/jats:italic>\n                    with no false positives. Overall, short-read outperformed long-read sequencing methods. We applied the same analytical methods to human faecal samples with confirmed infections for at least one of four STHs. Mitochondrial sequence mapping was also the most effective method for detecting STHs in human faecal samples, detecting 100% of\n                    <jats:italic>Necator americanus<\/jats:italic>\n                    and 92% of\n                    <jats:italic>Ascaris<\/jats:italic>\n                    spp. infections, but could not reliably detect STHs where DNA levels are expected to be low or variable. In conclusion, mitochondrial mapping was the most effective method of detection for sensitivity and specificity in both the laboratory system and human faecal samples. Our findings indicate that shotgun metagenomics should be approached cautiously using validated methods, particularly when infection intensity or DNA levels are expected to be low.\n                  <\/jats:p>","DOI":"10.1371\/journal.pntd.0014130","type":"journal-article","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T17:59:43Z","timestamp":1790013583000},"page":"e0014130","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Hunting for Helminths: short- and long-read shotgun metagenomics for helminth detection in faecal samples"],"prefix":"10.1371","volume":"20","author":[{"given":"Katie","family":"O\u2019Brien","sequence":"first","affiliation":[{"name":"University of Bath","place":["Bath, United Kingdom"],"department":["Life Sciences 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