{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T05:56:32Z","timestamp":1776837392031,"version":"3.51.2"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1009389","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,3,7]],"date-time":"2022-03-07T00:00:00Z","timestamp":1646611200000}}],"reference-count":100,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2022,2,17]],"date-time":"2022-02-17T00:00:00Z","timestamp":1645056000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Wellcome Trust and the Royal Society","award":["104169\/Z\/14\/A"],"award-info":[{"award-number":["104169\/Z\/14\/A"]}]},{"DOI":"10.13039\/100004330","name":"GlaxoSmithKline","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004330","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"UK Medical Research Council","doi-asserted-by":"crossref","award":["MR\/R015600\/1"],"award-info":[{"award-number":["MR\/R015600\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000265","name":"UK Medical Research Council","doi-asserted-by":"crossref","award":["MR\/T016434\/1"],"award-info":[{"award-number":["MR\/T016434\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    The disease burden attributable to opportunistic pathogens depends on their prevalence in asymptomatic colonisation and the rate at which they progress to cause symptomatic disease. Increases in infections caused by commensals can result from the emergence of \u201chyperinvasive\u201d strains. Such pathogens can be identified through quantifying progression rates using matched samples of typed microbes from disease cases and healthy carriers. This study describes Bayesian models for analysing such datasets, implemented in an RStan package (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/nickjcroucher\/progressionEstimation\" xlink:type=\"simple\">https:\/\/github.com\/nickjcroucher\/progressionEstimation<\/jats:ext-link>\n                    ). The models converged on stable fits that accurately reproduced observations from meta-analyses of\n                    <jats:italic>Streptococcus pneumoniae<\/jats:italic>\n                    datasets. The estimates of invasiveness, the progression rate from carriage to invasive disease, in cases per carrier per year correlated strongly with the dimensionless values from meta-analysis of odds ratios when sample sizes were large. At smaller sample sizes, the Bayesian models produced more informative estimates. This identified historically rare but high-risk\n                    <jats:italic>S<\/jats:italic>\n                    .\n                    <jats:italic>pneumoniae<\/jats:italic>\n                    serotypes that could be problematic following vaccine-associated disruption of the bacterial population. The package allows for hypothesis testing through model comparisons with Bayes factors. Application to datasets in which strain and serotype information were available for\n                    <jats:italic>S<\/jats:italic>\n                    .\n                    <jats:italic>pneumoniae<\/jats:italic>\n                    found significant evidence for within-strain and within-serotype variation in invasiveness. The heterogeneous geographical distribution of these genotypes is therefore likely to contribute to differences in the impact of vaccination in between locations. Hence genomic surveillance of opportunistic pathogens is crucial for quantifying the effectiveness of public health interventions, and enabling ongoing meta-analyses that can identify new, highly invasive variants.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1009389","type":"journal-article","created":{"date-parts":[[2022,2,17]],"date-time":"2022-02-17T13:47:56Z","timestamp":1645105676000},"page":"e1009389","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":26,"title":["Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8068-1293","authenticated-orcid":true,"given":"Alessandra","family":"L\u00f8chen","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2555-7636","authenticated-orcid":true,"given":"James E.","family":"Truscott","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6303-8768","authenticated-orcid":true,"given":"Nicholas J.","family":"Croucher","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,2,17]]},"reference":[{"key":"pcbi.1009389.ref001","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1016\/j.tim.2012.04.005","article-title":"Evolution of virulence in opportunistic pathogens: generalism, plasticity, and control","volume":"20","author":"SP Brown","year":"2012","journal-title":"Trends Microbiol"},{"key":"pcbi.1009389.ref002","doi-asserted-by":"crossref","first-page":"1853","DOI":"10.1093\/cid\/cix673","article-title":"Pan-serotype reduction in progression of Streptococcus pneumoniae to otitis media after rollout of pneumococcal conjugate vaccines","volume":"65","author":"JA Lewnard","year":"2017","journal-title":"Clin Infect 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