{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T14:02:18Z","timestamp":1790258538177,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.ppat.1010650","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,5,10]],"date-time":"2023-05-10T00:00:00Z","timestamp":1683676800000}}],"reference-count":43,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2023,4,28]],"date-time":"2023-04-28T00:00:00Z","timestamp":1682640000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["INV-009497 OPP1159351"],"award-info":[{"award-number":["INV-009497 OPP1159351"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    Paratyphoid fever caused by\n                    <jats:italic>S<\/jats:italic>\n                    . Paratyphi A is endemic in parts of South Asia and Southeast Asia. The proportion of enteric fever cases caused by\n                    <jats:italic>S<\/jats:italic>\n                    . 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\n                    <jats:italic>S<\/jats:italic>\n                    . Paratyphi A isolates collected as part of the Indian enteric fever surveillance study \u201cSurveillance of Enteric Fever in India (SEFI).\u201d In the study period (2017\u20132020),\n                    <jats:italic>S<\/jats:italic>\n                    . 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\n                    <jats:italic>S<\/jats:italic>\n                    . Paratyphi A collection into seven lineages (A-G), and the present study isolates were distributed in lineages A, C and F. Our analysis highlights that the genome degradation events and gene acquisitions or losses are key molecular events in the evolution of new\n                    <jats:italic>S<\/jats:italic>\n                    . Paratyphi A lineages\/sub-lineages. A total of 10 hypothetically disrupted coding sequences (HDCS) or pseudogenes-forming mutations possibly associated with the emergence of lineages were identified. The pan-genome analysis identified the insertion of P2\/PSP3 phage and acquisition of IncX1 plasmid during the selection in 2.3.2\/2.3.3 and 1.2.2 genotypes, respectively. We have identified six characteristic missense mutations associated with lipopolysaccharide (LPS) biosynthesis genes of\n                    <jats:italic>S<\/jats:italic>\n                    . Paratyphi A, however, these mutations confer only a low structural impact and possibly have minimal impact on vaccine effectiveness. Since\n                    <jats:italic>S<\/jats:italic>\n                    . Paratyphi A is human-restricted, high levels of genetic drift are not expected unless these bacteria transmit to naive hosts. However, public-health investigation and monitoring by means of genomic surveillance would be constantly needed to avoid\n                    <jats:italic>S<\/jats:italic>\n                    . Paratyphi A serovar becoming a public health threat similar to the\n                    <jats:italic>S<\/jats:italic>\n                    . Typhi of today.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1010650","type":"journal-article","created":{"date-parts":[[2023,4,28]],"date-time":"2023-04-28T13:33:54Z","timestamp":1682688834000},"page":"e1010650","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. 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