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

Tanmoy, A. M. et al. (2022) Paratype: a genotyping tool for Salmonella Paratyphi A reveals its global genomic diversity. Nature Communications, 13, 7912. (doi: 10.1038/s41467-022-35587-6) (PMID:36564386) (PMCID:PMC9782287)

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.

• Item Type: Articles
• Additional Information: The study was partially supported by grants from the Bill and Melinda Gates Foundation (INV-023821) to CHRF and SEAP group of investigators (INV-042340).
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Sajib, Mohammad Saiful Islam
• Authors: Tanmoy, A. M., Hooda, Y., Sajib, M. S.I., da Silva, K. E., Iqbal, J., Qamar, F. N., Luby, S. P., Dougan, G., Dyson, Z. A., Baker, S., Garrett, D. O., Andrews, J. R., Saha, S. K., and Saha, S.
• College/School: College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
• Journal Name: Nature Communications
• Publisher: Nature Research
• ISSN: 2041-1723
• ISSN (Online): 2041-1723
• Copyright Holders: Copyright © 2022 The Authors
• First Published: First published in Nature Communications 13: 7912
• Publisher Policy: Reproduced under a Creative Commons License