{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,5]],"date-time":"2026-11-05T18:44:31Z","timestamp":1793904271864,"version":"4.8.0"},"reference-count":22,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2022,7,22]],"date-time":"2022-07-22T00:00:00Z","timestamp":1658448000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>\n                    Enteric fever infections remain a significant public health issue, with up to 20 million infections per year. Increasing rates of antibiotic resistant strains have rendered many first-line antibiotics potentially ineffective. Genotype 4.3.1 (H58) is the main circulating lineage of\n                    <jats:italic>S<\/jats:italic>\n                    . Typhi in many South Asian countries and is associated with high levels of antibiotic resistance. The emergence and spread of extensively drug resistant (XDR) typhoid strains has increased the need for a rapid molecular test to identify and track these high-risk lineages for surveillance and vaccine prioritisation. Current methods require samples to be cultured for several days, followed by DNA extraction and sequencing to determine the specific lineage. We designed and evaluated the performance of a new multiplex PCR assay, targeting\n                    <jats:italic>S<\/jats:italic>\n                    . Paratyphi A as well as the H58 and XDR lineages of\n                    <jats:italic>S<\/jats:italic>\n                    . Typhi on a collection of bacterial strains. Our assay was 100% specific for the identification of lineage specific\n                    <jats:italic>S<\/jats:italic>\n                    . Typhi and\n                    <jats:italic>S<\/jats:italic>\n                    . Paratyphi A, when tested with a mix of non-Typhi\n                    <jats:italic>Salmonella<\/jats:italic>\n                    and non-\n                    <jats:italic>Salmonella<\/jats:italic>\n                    strains. With additional testing on clinical and environmental samples, this assay will allow rapid lineage level detection of typhoid of clinical significance, at a significantly lower cost to whole-genome sequencing. To our knowledge, this is the first report of a SNP-based multiplex PCR assay for the detection of lineage specific serovars of\n                    <jats:italic>Salmonella<\/jats:italic>\n                    Typhi.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0267805","type":"journal-article","created":{"date-parts":[[2022,7,22]],"date-time":"2022-07-22T13:27:37Z","timestamp":1658496457000},"page":"e0267805","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":17,"title":["Multiplex PCR assay to detect high risk lineages of Salmonella Typhi and Paratyphi A"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5959-0680","authenticated-orcid":true,"given":"Fahad","family":"Khokhar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Derek","family":"Pickard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zoe","family":"Dyson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junaid","family":"Iqbal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agila","family":"Pragasam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jobin Jacob","family":"John","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Balaji","family":"Veeraraghavan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Farah","family":"Qamar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gordon","family":"Dougan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hilary","family":"MacQueen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sushila","family":"Rigas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Holmes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ankur","family":"Mutreja","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,7,22]]},"reference":[{"key":"pone.0267805.ref001","unstructured":"Typhoid fever: World Health Organisation; [cited 2020 November]. http:\/\/www.emro.who.int\/health-topics\/typhoid-fever\/."},{"issue":"1","key":"pone.0267805.ref002","article-title":"The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa","volume":"9","author":"SE Park","year":"2018","journal-title":"Nature Communications"},{"issue":"1","key":"pone.0267805.ref003","doi-asserted-by":"crossref","first-page":"e00105","DOI":"10.1128\/mBio.00105-18","article-title":"Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins","volume":"9","author":"EJ Klemm","year":"2018","journal-title":"mBio"},{"issue":"11","key":"pone.0267805.ref004","doi-asserted-by":"crossref","first-page":"e0007868","DOI":"10.1371\/journal.pntd.0007868","article-title":"Molecular mechanism of azithromycin resistance among typhoidal Salmonella strains in Bangladesh identified through passive pediatric surveillance","volume":"13","author":"Y Hooda","year":"2019","journal-title":"PLOS Neglected Tropical Diseases"},{"issue":"4","key":"pone.0267805.ref005","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00215-20","article-title":"A Race against Time: Reduced Azithromycin Susceptibility in Salmonella enterica Serovar Typhi in Pakistan","volume":"5","author":"J Iqbal","year":"2020","journal-title":"mSphere"},{"issue":"6","key":"pone.0267805.ref006","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1586\/eri.11.47","article-title":"The utility of diagnostic tests for enteric fever in endemic locations","volume":"9","author":"CM Parry","year":"2011","journal-title":"Expert Review of Anti-infective Therapy"},{"issue":"06","key":"pone.0267805.ref007","doi-asserted-by":"crossref","DOI":"10.3855\/jidc.155","article-title":"The laboratory diagnosis of enteric fever","volume":"2","author":"S Hosoglu","year":"2008","journal-title":"The Journal of Infection in Developing Countries"},{"issue":"2","key":"pone.0267805.ref008","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/j.ijmm.2005.01.003","article-title":"Quantitative detection of serovar Typhi from blood of suspected typhoid fever patients by real-time PCR","volume":"295","author":"M. 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