TY - JOUR
T1 - Paratype
T2 - a genotyping tool for Salmonella Paratyphi A reveals its global genomic diversity
AU - Tanmoy, Arif M.
AU - Hooda, Yogesh
AU - Sajib, Mohammad S.I.
AU - da Silva, Kesia E.
AU - Iqbal, Junaid
AU - Qamar, Farah N.
AU - Luby, Stephen P.
AU - Dougan, Gordon
AU - Dyson, Zoe A.
AU - Baker, Stephen
AU - Garrett, Denise O.
AU - Andrews, Jason R.
AU - Saha, Samir K.
AU - Saha, Senjuti
N1 - Funding Information:
We are thankful to Mr. Hafizur Rahman, Mr. Dipu Chandra Das, Ms. Nusrat Alam, Ms Sharmistha Goswami, Md Mobarok Hossain, Ms. Tasnim Jabin and Mr. Nikkon Sarker of the Child Health Research Foundation for their assistance with the wet-lab procedures. We are also thankful to the entire SEAP team for their unwavering support and coordination between the teams. We are grateful to Dr. Nicol Janecko, Dr. Bilal Djeghout and Professor John Wain of the Quadrum Institute, Norwich, UK, for generously providing us with the MinION devices for conducting long read sequencing of 33 Salmonella Paratyphi A genomes. 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).
Funding Information:
We are thankful to Mr. Hafizur Rahman, Mr. Dipu Chandra Das, Ms. Nusrat Alam, Ms Sharmistha Goswami, Md Mobarok Hossain, Ms. Tasnim Jabin and Mr. Nikkon Sarker of the Child Health Research Foundation for their assistance with the wet-lab procedures. We are also thankful to the entire SEAP team for their unwavering support and coordination between the teams. We are grateful to Dr. Nicol Janecko, Dr. Bilal Djeghout and Professor John Wain of the Quadrum Institute, Norwich, UK, for generously providing us with the MinION devices for conducting long read sequencing of 33 Salmonella Paratyphi A genomes. 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).
Publisher Copyright:
© 2022, The Author(s).
PY - 2022/12
Y1 - 2022/12
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85144635527&partnerID=8YFLogxK
U2 - 10.1038/s41467-022-35587-6
DO - 10.1038/s41467-022-35587-6
M3 - Article
C2 - 36564386
AN - SCOPUS:85144635527
SN - 2041-1723
VL - 13
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 7912
ER -
