{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T21:46:14Z","timestamp":1768945574051,"version":"3.49.0"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2026,1,19]],"date-time":"2026-01-19T00:00:00Z","timestamp":1768780800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"name":"Children\u2019s Hospital Foundation Preclinical and Clinical Early Career Research Grant","award":["ECR0122020"],"award-info":[{"award-number":["ECR0122020"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Salmonella enterica serovar Typhi results in &amp;gt;160\u200a000 deaths annually. In endemic regions, infections disproportionately affect infants and children. Current diagnostics rely on culture-based approaches that lack sensitivity and require infrastructure and skills that are not always possible in developing regions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Objectives<\/jats:title>\n                    <jats:p>We developed a suite of rapid, sensitive and specific molecular diagnostic tools to detect S. Typhi, and markers of extensive antimicrobial resistance (AMR), with the capacity to be used in low- and middle-income countries (LMIC).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Singleplex and multiplex PCR assays, recombinase polymerase amplification with lateral flow detection (RPA-LF) assays and loop-mediated isothermal amplification (LAMP) assays were developed, targeting markers consistent with Salmonella Typhi and makers of extensive AMR (blaCTX-M-15 and qnrS1). Assays were tested across four banks of samples (n\u200a=\u200a115 total) to assess sensitivity, specificity and limit of detection.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Singleplex and multiplex PCR assays demonstrated excellent sensitivity (100%) and specificity (96%\u2013100%) for detection of XDR S. Typhi and extensive AMR, particularly the H58 clade deletion and STY4669 genes of S. Typhi. Similarly, sensitivity and specificity were also observed for RPA-LF assays (100% sensitivity, 96%\u2013100% specificity) and LAMP assays (100% sensitivity, 87.5%\u2013100% specificity) for all targets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>These tools are timely, providing a range of options for targeted detection of XDR S. Typhi in the laboratory or nearer to the point of care. These assays have the potential to improve resistance-guided therapy for S. Typhi, which is important given the increasing prevalence of XDR S. Typhi in endemic regions of Pakistan, and increasing case reports globally.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/jac\/dkaf481","type":"journal-article","created":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T12:55:28Z","timestamp":1766062528000},"source":"Crossref","is-referenced-by-count":0,"title":["Rapid molecular diagnostics for detection of extensively drug-resistant\n                    <i>Salmonella<\/i>\n                    Typhi"],"prefix":"10.1093","volume":"81","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3199-6432","authenticated-orcid":false,"given":"Emma L","family":"Sweeney","sequence":"first","affiliation":[{"name":"The University of Queensland Centre for Clinical Research, The University of Queensland , Brisbane ,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacob A","family":"Tickner","sequence":"additional","affiliation":[{"name":"The University of Queensland Centre for Clinical Research, The University of Queensland , Brisbane ,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicole G","family":"Ertl","sequence":"additional","affiliation":[{"name":"The University of Queensland Centre for Clinical Research, The University of Queensland , Brisbane ,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michelle J","family":"Bauer","sequence":"additional","affiliation":[{"name":"The University of Queensland Centre for Clinical Research, The University of Queensland , Brisbane ,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-7448-7235","authenticated-orcid":false,"given":"Budi","family":"Permana","sequence":"additional","affiliation":[{"name":"Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brian","family":"Forde","sequence":"additional","affiliation":[{"name":"The University of Queensland Centre for Clinical Research, The University of Queensland , Brisbane ,","place":["Australia"]},{"name":"Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saba","family":"Riaz","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Molecular Genetics, University of the Punjab , Lahore ,","place":["Pakistan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David M","family":"Whiley","sequence":"additional","affiliation":[{"name":"The University of Queensland Centre for Clinical Research, The University of Queensland , Brisbane ,","place":["Australia"]},{"name":"Molecular Diagnostics Unit, Pathology Queensland Central Laboratory , Brisbane ,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8974-6789","authenticated-orcid":false,"given":"Adam D","family":"Irwin","sequence":"additional","affiliation":[{"name":"The University of Queensland Centre for Clinical Research, The University of Queensland , Brisbane ,","place":["Australia"]},{"name":"Infection Management and Prevention Service, Queensland Children\u2019s Hospital , Brisbane, Queensland, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2026,1,20]]},"reference":[{"key":"2026012003230532800_dkaf481-B1","doi-asserted-by":"publisher","DOI":"10.1177\/2324709616652642","article-title":"Salmonella Typhi-induced septic shock and acute respiratory distress syndrome in a previously healthy teenage patient treated with high-dose dexamethasone","volume":"4","author":"Ugas","year":"2016","journal-title":"J Investig Med High Impact Case Rep"},{"key":"2026012003230532800_dkaf481-B2","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1017\/S0950268807009338","article-title":"Part I. 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