biostudies-literatureJacob JJBill and Melinda Gates FoundationWellcome Truste1010650https://www.ebi.ac.uk/biostudies/studies/S-EPMC10171690biostudies-literatureUnknown19(4)Paratyphoid fever caused by S. Paratyphi A is endemic in parts of South Asia and Southeast Asia. The proportion of enteric fever cases caused by S. Paratyphi A has substantially increased, yet only limited data is available on the population structure and genetic diversity of this serovar. We examined the phylogenetic distribution and evolutionary trajectory of S. Paratyphi A isolates collected as part of the Indian enteric fever surveillance study "Surveillance of Enteric Fever in India (SEFI)." In the study period (2017-2020), S. Paratyphi A comprised 17.6% (441/2503) of total enteric fever cases in India, with the isolates highly susceptible to all the major antibiotics used for treatment except fluoroquinolones. Phylogenetic analysis clustered the global S. Paratyphi A collection into PLoS pathogensGenomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages.PMC10171690INV-009497 OPP1159351Alexander APJinka DRNagaraj SJohn JBavdekar ARay PAnandan SPriya Teekaraman MJacob JJPragasam AKThomas MKang GSrivastava SKVeeraraghavan BGupta MEbenezer SESaigal KKoshy RMDe AVasudevan KDutta SSingh AKapil AMutreja APriya Thirumoorthy TShastri JDougan GBai SPVelmurugan AChandola TRfalseGenomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages.Paratyphoid fever caused by S. Paratyphi A is endemic in parts of South Asia and Southeast Asia. The proportion of enteric fever cases caused by S. Paratyphi A has substantially increased, yet only limited data is available on the population structure and genetic diversity of this serovar. We examined the phylogenetic distribution and evolutionary trajectory of S. Paratyphi A isolates collected as part of the Indian enteric fever surveillance study "Surveillance of Enteric Fever in India (SEFI)." In the study period (2017-2020), S. Paratyphi A comprised 17.6% (441/2503) of total enteric fever cases in India, with the isolates highly susceptible to all the major antibiotics used for treatment except fluoroquinolones. Phylogenetic analysis clustered the global S. Paratyphi A collection into 2023-01-01T00:00:00Z2023 Apr2026-07-15T01:26:59.301Z2025-02-19T02:22:42.757ZS-EPMC101716903711580410.1371/journal.ppat.1010650