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

Arif M. Tanmoy, Yogesh Hooda, Mohammad S.I. Sajib, Kesia E. da 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, Senjuti Saha*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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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.

Original languageEnglish
Article number7912
JournalNature Communications
Volume13
Issue number1
DOIs
Publication statusPublished - 23 Dec 2022

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© 2022, The Author(s).

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