Multiplex PCR assay to detect high risk lineages of Salmonella Typhi and Paratyphi A

Fahad Khokhar, Derek Pickard, Zoe Dyson, Junaid Iqbal, Agila Pragasam, Jobin Jacob John, Balaji Veeraraghavan, Farah Qamar, Gordon Dougan, Hilary MacQueen, Sushila Rigas, Mark Holmes, Ankur Mutreja

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)


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.

Original languageEnglish
Article numbere0267805
JournalPLoS ONE
Issue number7 July
Publication statusPublished - Jul 2022


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