Abstract
AbstractSalmonella 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.
Funder
Bill and Melinda Gates Foundation
Publisher
Springer Science and Business Media LLC
Subject
General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry,Multidisciplinary
Reference41 articles.
1. Stanaway, J. D. et al. The global burden of typhoid and paratyphoid fevers: a systematic analysis for the Global Burden of Disease Study 2017. Lancet Infect. Dis. 19, 369–381 (2019).
2. Crump, J. A. & Mintz, E. D. Global trends in typhoid and paratyphoid fever. Clin. Infect. Dis. 50, 241–246 (2010).
3. Lu, X. et al. Regional transmission of Salmonella Paratyphi A, China, 1998–2012. Emerg. Infect. Dis. 23, 833–836 (2017).
4. Furuse, Y. Analysis of research intensity on infectious disease by disease burden reveals which infectious diseases are neglected by researchers. Proc. Natl. Acad. Sci. USA 116, 478–483 (2019).
5. Zhou, Z. et al. Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever. Proc. Natl Acad. Sci. USA 111, 12199–12204 (2014).
Cited by
7 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献