{"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":1790258538342,"version":"4.1.0"},"reference-count":60,"publisher":"Microbiology Society","issue":"11","license":[{"start":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T00:00:00Z","timestamp":1762819200000},"content-version":"unspecified","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":"crossref","award":["INV-030857"],"award-info":[{"award-number":["INV-030857"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"crossref","award":["215515\/Z\/19\/Z"],"award-info":[{"award-number":["215515\/Z\/19\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,11]]},"abstract":"<jats:p>\n                    <jats:italic>Salmonella enterica<\/jats:italic>\n                    serovar Paratyphi A is a significant but under-characterised cause of enteric fever in South Asia. In Pakistan, where the typhoid conjugate vaccine has been introduced to combat\n                    <jats:italic>S<\/jats:italic>\n                    . Typhi,\n                    <jats:italic>S<\/jats:italic>\n                    . Paratyphi A remains a prominent cause of bacteraemia, raising concerns about shifts in disease burden and antimicrobial resistance (AMR). Here, we provide a comprehensive genomic and phylogenetic analysis of 354\u2009\n                    <jats:italic>S<\/jats:italic>\n                    . Paratyphi A isolates collected from three provinces in Pakistan between 2017 and early 2022. Whole-genome sequencing revealed the dominance of genotypes 2.3.3 and 2.4.5, indicating a largely stable population structure over time, and the presence of widespread fluoroquinolone-associated\n                    <jats:italic>gyrA<\/jats:italic>\n                    mutations. Although multidrug resistance was not detected, we identified one isolate harbouring an\n                    <jats:italic>acrB<\/jats:italic>\n                    -R717Q mutation associated with azithromycin resistance. Plasmid and replicon analysis revealed low prevalence of extrachromosomal elements, including cryptic plasmids with unknown function. Phylogenetic placement of these isolates in a global context demonstrated close relatedness to contemporary South Asian organisms. Our findings establish a genomic baseline for\n                    <jats:italic>S<\/jats:italic>\n                    . Paratyphi A in Pakistan, essential for future surveillance, AMR monitoring, and evaluating the potential impact of forthcoming paratyphoid vaccines.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001561","type":"journal-article","created":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T17:17:11Z","timestamp":1762881431000},"source":"Crossref","is-referenced-by-count":2,"title":["A contemporary genomic snapshot of Salmonella Paratyphi A in Pakistan"],"prefix":"10.1099","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2638-0713","authenticated-orcid":false,"given":"Elli","family":"Mylona","sequence":"first","affiliation":[{"name":"Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK"},{"name":"Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, 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