{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T02:57:07Z","timestamp":1787021827883,"version":"build-2736575974"},"update-to":[{"DOI":"10.1371\/journal.pntd.0012719","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,1,9]],"date-time":"2025-01-09T00:00:00Z","timestamp":1736380800000}}],"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2024,12,5]],"date-time":"2024-12-05T00:00:00Z","timestamp":1733356800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["314892\/2021-4"],"award-info":[{"award-number":["314892\/2021-4"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002322","name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","doi-asserted-by":"publisher","award":["001"],"award-info":[{"award-number":["001"]}],"id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"\n Background<\/jats:title>\n \n Gut-parasite transmission often involves faecal shedding, and detecting parasites in stool samples remains the cornerstone of diagnosis. However, not all samples drawn from infected hosts contain parasites (because of intermittent shedding), and no test can detect the target parasites in 100% of parasite-bearing samples (because of imperfect sensitivity). Disentangling the effects of intermittent shedding and imperfect sensitivity on pathogen detection would help us better understand transmission dynamics, disease epidemiology, and diagnostic-test performance. Using paediatric\n Giardia<\/jats:italic>\n infections as a case-study, here we illustrate a hierarchical-modelling approach to separately estimating the probabilities of host-level infection (\n \n \n \n \n \u03a8<\/mml:mi>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n ); stool-sample\u2013level shedding, given infection (\n \n \n \n \n \u03b8<\/mml:mi>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n ); and test-level detection, given infection and shedding (\n \n \n \n \n p<\/mml:mi>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n ).\n <\/jats:p>\n <\/jats:sec>\n \n Methods\/Findings<\/jats:title>\n \n We collected 1\u20133 stool samples, in consecutive weeks, from 276 children. Samples (413 overall) were independently examined,\n via<\/jats:italic>\n standard sedimentation\/optical microscopy, by a senior parasitologist and a junior, trained student (826 tests overall). Using replicate test results and multilevel hierarchical models, we estimated per-sample\n Giardia<\/jats:italic>\n shedding probability at\n \n \n \n \n \n \n \u03b8<\/mml:mi>\n <\/mml:mrow>\n ^<\/mml:mo>\n <\/mml:mover>\n \u2248<\/mml:mo>\n 0.440<\/mml:mn>\n \u00b1<\/mml:mo>\n 0.116<\/mml:mn>\n \n S<\/mml:mi>\n E<\/mml:mi>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n and observer-specific test sensitivities at\n \n \n \n \n \n \n \n \n p<\/mml:mi>\n <\/mml:mrow>\n ^<\/mml:mo>\n <\/mml:mover>\n <\/mml:mrow>\n \n S<\/mml:mi>\n e<\/mml:mi>\n n<\/mml:mi>\n i<\/mml:mi>\n o<\/mml:mi>\n r<\/mml:mi>\n <\/mml:mrow>\n <\/mml:msub>\n \u2248<\/mml:mo>\n 0.639<\/mml:mn>\n \u00b1<\/mml:mo>\n 0.080<\/mml:mn>\n \n S<\/mml:mi>\n E<\/mml:mi>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n and\n \n \n \n \n \n \n \n \n p<\/mml:mi>\n <\/mml:mrow>\n ^<\/mml:mo>\n <\/mml:mover>\n <\/mml:mrow>\n \n J<\/mml:mi>\n u<\/mml:mi>\n n<\/mml:mi>\n i<\/mml:mi>\n o<\/mml:mi>\n r<\/mml:mi>\n <\/mml:mrow>\n <\/mml:msub>\n \u2248<\/mml:mo>\n 0.460<\/mml:mn>\n \u00b1<\/mml:mo>\n 0.071<\/mml:mn>\n \n S<\/mml:mi>\n E<\/mml:mi>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n . Gender-specific infection-frequency estimates were\n \n \n \n \n \n \n \n \n \u03a8<\/mml:mi>\n <\/mml:mrow>\n ^<\/mml:mo>\n <\/mml:mover>\n <\/mml:mrow>\n \n G<\/mml:mi>\n i<\/mml:mi>\n r<\/mml:mi>\n l<\/mml:mi>\n s<\/mml:mi>\n <\/mml:mrow>\n <\/mml:msub>\n \u2248<\/mml:mo>\n 0.540<\/mml:mn>\n \u00b1<\/mml:mo>\n 0.137<\/mml:mn>\n \n S<\/mml:mi>\n E<\/mml:mi>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n and\n \n \n \n \n \n \n \n \n \u03a8<\/mml:mi>\n <\/mml:mrow>\n ^<\/mml:mo>\n <\/mml:mover>\n <\/mml:mrow>\n \n B<\/mml:mi>\n o<\/mml:mi>\n y<\/mml:mi>\n s<\/mml:mi>\n <\/mml:mrow>\n <\/mml:msub>\n \u2248<\/mml:mo>\n 0.337<\/mml:mn>\n \u00b1<\/mml:mo>\n 0.098<\/mml:mn>\n \n S<\/mml:mi>\n E<\/mml:mi>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n . Had we used a (hypothetical)\n P<\/jats:underline>\n erfect\n T<\/jats:underline>\n est with 100% narrow-sense sensitivity (\n \n \n \n \n \n \n p<\/mml:mi>\n <\/mml:mrow>\n \n \n P<\/mml:mi>\n T<\/mml:mi>\n <\/mml:mrow>\n _<\/mml:mo>\n <\/mml:munder>\n <\/mml:msub>\n \u2261<\/mml:mo>\n 1.0<\/mml:mn>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n ), the average probability of detecting\n Giardia<\/jats:italic>\n in a sample drawn from an infected child (\n \n \n \n \n \u03a8<\/mml:mi>\n \u2261<\/mml:mo>\n 1.0<\/mml:mn>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n ) would have been\n \n \n \n \n \n \n Pr<\/mml:mi>\n <\/mml:mrow>\n \n (<\/mml:mo>\n \n d<\/mml:mi>\n <\/mml:mrow>\n |<\/mml:mo>\n \n i<\/mml:mi>\n ,<\/mml:mo>\n \n \n P<\/mml:mi>\n T<\/mml:mi>\n <\/mml:mrow>\n _<\/mml:mo>\n <\/mml:munder>\n <\/mml:mrow>\n )<\/mml:mo>\n <\/mml:mrow>\n <\/mml:mrow>\n =<\/mml:mo>\n \u03a8<\/mml:mi>\n \u00d7<\/mml:mo>\n \u03b8<\/mml:mi>\n \u00d7<\/mml:mo>\n \n \n p<\/mml:mi>\n <\/mml:mrow>\n \n \n P<\/mml:mi>\n T<\/mml:mi>\n <\/mml:mrow>\n _<\/mml:mo>\n <\/mml:munder>\n <\/mml:msub>\n \u2248<\/mml:mo>\n 1.0<\/mml:mn>\n \u00d7<\/mml:mo>\n 0.44<\/mml:mn>\n \u00d7<\/mml:mo>\n 1.0<\/mml:mn>\n \u2248<\/mml:mo>\n 0.44<\/mml:mn>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n . Because no test can be >100% sensitive,\n \n \n \n \n \n \n Pr<\/mml:mi>\n <\/mml:mrow>\n \n (<\/mml:mo>\n \n d<\/mml:mi>\n <\/mml:mrow>\n |<\/mml:mo>\n \n i<\/mml:mi>\n <\/mml:mrow>\n )<\/mml:mo>\n <\/mml:mrow>\n <\/mml:mrow>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n (which measures\n clinical<\/jats:italic>\n sensitivity) can only be brought above ~ 0.44 by tinkering with the availability of\n Giardia<\/jats:italic>\n in stool samples (i.e.,\n \n \n \n \n \u03b8<\/mml:mi>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n ); for example, drawing-and-pooling 3 replicate samples would yield\n \n \n \n \n \n \n \n \n \u03b8<\/mml:mi>\n <\/mml:mrow>\n ^<\/mml:mo>\n <\/mml:mover>\n <\/mml:mrow>\n \n 3<\/mml:mn>\n s<\/mml:mi>\n <\/mml:mrow>\n <\/mml:msub>\n \u2248<\/mml:mo>\n 1<\/mml:mn>\n \u2212<\/mml:mo>\n (<\/mml:mo>\n \n \n 1<\/mml:mn>\n \u2212<\/mml:mo>\n 0.44<\/mml:mn>\n )<\/mml:mo>\n <\/mml:mrow>\n \n 3<\/mml:mn>\n <\/mml:mrow>\n <\/mml:msup>\n \u2248<\/mml:mo>\n 0.82<\/mml:mn>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n .\n <\/jats:p>\n <\/jats:sec>\n \n Conclusions<\/jats:title>\n By allowing separate estimation (and modelling) of pathogen-shedding probabilities, the approach we illustrate provides a means to study pathogen transmission cycles and dynamics in unprecedented detail. Separate estimation (and modelling) of true test sensitivity, moreover, may cast new light on the performance of diagnostic tests and procedures, whether novel or routine-practice.<\/jats:p>\n <\/jats:sec>","DOI":"10.1371\/journal.pntd.0012719","type":"journal-article","created":{"date-parts":[[2024,12,5]],"date-time":"2024-12-05T14:25:23Z","timestamp":1733408723000},"page":"e0012719","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":5,"title":["Disentangling the effects of intermittent faecal shedding and imperfect test sensitivity on the microscopy-based detection of gut parasites in stool samples"],"prefix":"10.1371","volume":"18","author":[{"given":"Lana C. 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