Multiplex PCR Assay to Detect High Risk Lineages of Salmonella Typhi and Paratyphi A
Multiplex PCR Assay to Detect High Risk Lineages of Salmonella Typhi and Paratyphi A
Abstract 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 S. 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 S. Paratyphi A as well as the H58 and XDR lineages of S. Typhi on a collection of bacterial strains. Our assay was 100% specific for the identification of lineage specific S. Typhi and S. Paratyphi A, when tested with a mix of non-Typhi Salmonella and non-Salmonella 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 Salmonella Typhi. Data StatementAll supporting data, code and protocols have been provided within the article or through supplementary data files.
Pickard Derek DJ、Iqbal Junaid、Veeraraghavan Balaji、Qamar Farah N、Dougan Gordon、Dyson Zoe A、John Jobin Jacob、Khokhar Fahad A、Rigas Sushila H、Mutreja Ankur、Holmes Mark A、Pragasam Agila K、MacQueen Hilary
Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of CambridgeDepartment of Paediatrics and Child Health, Aga Khan UniversityDepartment of Clinical Microbiology, Christian Medical CollegeDepartment of Paediatrics and Child Health, Aga Khan UniversityCambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge||The Wellcome TrustCambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge||London School of Hygiene & Tropical Medicine||Department of Infectious Diseases, Central Clinical School, Monash University||Wellcome Sanger Institute, Wellcome Genome CampusDepartment of Clinical Microbiology, Christian Medical CollegeCambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of CambridgeSchool of Life, Health & Chemical Sciences, The Open UniversityCambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge||Department of Clinical Microbiology, Christian Medical CollegeDepartment of Veterinary Medicine, University of CambridgeDepartment of Clinical Microbiology, Christian Medical CollegeSchool of Life, Health & Chemical Sciences, The Open University
医学研究方法微生物学预防医学
Salmonellatyphoid feverTyphiH58XDRDiagnosticsPCR
Pickard Derek DJ,Iqbal Junaid,Veeraraghavan Balaji,Qamar Farah N,Dougan Gordon,Dyson Zoe A,John Jobin Jacob,Khokhar Fahad A,Rigas Sushila H,Mutreja Ankur,Holmes Mark A,Pragasam Agila K,MacQueen Hilary.Multiplex PCR Assay to Detect High Risk Lineages of Salmonella Typhi and Paratyphi A[EB/OL].(2025-03-28)[2025-04-27].https://www.medrxiv.org/content/10.1101/2021.09.14.21263553.点此复制
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