Paratype: a genotyping tool for Salmonella Paratyphi A reveals its global genomic diversity

Arif M. Tanmoy, Yogesh Hooda, Mohammad S. I. Sajib, Kesia E. Silva, Junaid Iqbal, Farah N. Qamar, Stephen P. Luby, Gordon Dougan, Zoe A. Dyson, Stephen Baker, Denise O. Garrett, Jason R. Andrews, Samir K. Saha and Senjuti Saha ()
Additional contact information
Arif M. Tanmoy: Child Health Research Foundation
Yogesh Hooda: Child Health Research Foundation
Mohammad S. I. Sajib: Child Health Research Foundation
Kesia E. Silva: Stanford University School of Medicine
Junaid Iqbal: Aga Khan University
Farah N. Qamar: Aga Khan University
Stephen P. Luby: Stanford University School of Medicine
Gordon Dougan: Wellcome Trust Sanger Institute, Hinxton
Zoe A. Dyson: Wellcome Trust Sanger Institute, Hinxton
Stephen Baker: University of Cambridge
Denise O. Garrett: Applied Epidemiology Team, Sabin Vaccine Institute
Jason R. Andrews: Stanford University School of Medicine
Samir K. Saha: Child Health Research Foundation
Senjuti Saha: Child Health Research Foundation

Nature Communications, 2022, vol. 13, issue 1, 1-10

Abstract: Abstract Salmonella Paratyphi A, the primary etiology of paratyphoid, is estimated to cause 3.4 million infections annually, worldwide. With rising antimicrobial resistance and no licensed vaccines, genomic surveillance is key to track and monitor transmission, but there is currently no reliable genotyping framework for this pathogen. Here, we sequence 817 isolates from South Asia and add 562 publicly available genomes to build a global database representing 37 countries, covering 1917–2019. We develop a single nucleotide polymorphism-based genotyping scheme, Paratype, that segregates Salmonella Paratyphi A population into three primary and nine secondary clades, and 18 genotypes. Each genotype is assigned a unique allele definition located on an essential gene. Using Paratype, we identify spatiotemporal genomic variation and antimicrobial resistance markers. We release Paratype as an open-access tool that can use raw read files from both Illumina and Nanopore platforms, and thus can assist surveillance studies tracking Salmonella Paratyphi A across the globe.

Date: 2022
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DOI: 10.1038/s41467-022-35587-6

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