2026-10-12T08:57:55Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33958944 2026-09-21T18:00:16Z category_4 category_8 category_12 category_13 category_14 category_21 category_734 category_811 category_64 category_106 category_132 category_134 category_135 portal_5 item_type_3 month_year_09_2026

<p>BLAST results of the unbinned sequences.</p> Katie O’Brien (5505920) Ajay Elamaran (25085040) Mehmet Dayi (5215748) Georgia Keeling (25085043) William D. Nevin (17854751) Yuchen Liu (112600) Mark Viney (781677) Kieran Reynolds (17318449) Charmaine Bishop (25085046) Banchob Sripa (32216) Menebere Woubshete (17781279) Pamela Sachs Nique (25085049) Rhiannon Wright (17456902) Jane Younger (3456935) Vicky L. Hunt (3266973) Biochemistry Microbiology Cell Biology Genetics Molecular Biology Biotechnology Biological Sciences not elsewhere classified Mathematical Sciences not elsewhere classified Cancer Science Policy Infectious Diseases Virology Computational Biology pose significant challenges standard laboratory doses standard laboratory dose necessitating reliable methods human faecal samples necator americanus </ mitochondrial sequence mapping known infection intensity validated shotgun metagenomics false positives remain div >< p strongyloides ratti </ marker gene detection read shotgun metagenomics read sequencing methods read outperformed long low intensity infection reliably detect sths faecal samples mitochondrial mapping infection intensity shotgun metagenomics false positives ratti </ sth infection sequencing technology laboratory system laboratory model analytical methods read vs ascaris </ public health protein matching pervasive issue least one findings indicate endemic areas dna levels accurately detected <div><p>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 <i>Strongyloides ratti</i> 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. <i>S. ratti</i> 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 <i>S. ratti</i> 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 <i>Necator americanus</i> and 92% of <i>Ascaris</i> 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.</p></div> 2026-09-21T18:01:54Z Dataset Dataset 10.1371/journal.pntd.0014130.s017 https://figshare.com/articles/dataset/_p_BLAST_results_of_the_unbinned_sequences_p_/33958944 CC BY 4.0