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

Authors

Fahad Khokhar, University of Cambridge, Cambridge
Derek Pickard, University of Cambridge, Cambridge
Zoe Dyson, University of Cambridge, Cambridge
Junaid Iqbal, Aga Khan UniversityFollow
Agila Pragasam, Christian Medical College, Vellore
Jobin Jacob John, Christian Medical College, Vellore
Balaji Veeraraghavan, Christian Medical College, Vellore
Farah Qamar, Aga Khan UniversityFollow
Gordon Dougan, The Wellcome Trust, London
Hilary MacQueen, The Open University, Milton Keynes

Document Type

Article

Department

Paediatrics and Child Health

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.

Comments

Pagination are not provided by the author/publisher

Publication (Name of Journal)

PloS one

Recommended Citation

Khokhar, F., Pickard, D., Dyson, Z., Iqbal, J., Pragasam, A., John, J. J., Veeraraghavan, B., Qamar, F., Dougan, G., MacQueen, H. (2022). Multiplex PCR assay to detect high risk lineages of Salmonella Typhi and Paratyphi A. PloS one, 17(7).
Available at: https://ecommons.aku.edu/pakistan_fhs_mc_women_childhealth_paediatr/1179

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.