{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T20:06:57Z","timestamp":1791230817720,"version":"4.1.0"},"reference-count":70,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T00:00:00Z","timestamp":1786492800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T00:00:00Z","timestamp":1786492800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100001411","name":"Indian Council of Medical Research","doi-asserted-by":"publisher","award":["DDR\/IIRP23\/2500"],"award-info":[{"award-number":["DDR\/IIRP23\/2500"]}],"id":[{"id":"10.13039\/501100001411","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mBio"],"published-print":{"date-parts":[[2026,8,12]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                      is a globally distributed zoonotic pathogen with widespread environmental persistence; however, genomic characterization of environmental isolates from underrepresented regions remains limited. Current global data sets are predominantly populated with genomes from high-income countries, restricting our ability to resolve evolutionary trajectories, ecological adaptations, and emerging antimicrobial resistance (AMR). We performed a comparative genomic analysis of 1,399 high-quality\n                      <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                      genomes, integrating 54 newly sequenced isolates from India (representing surface water and soil samples) with global data sets. Phenotypic analysis showed that 55.6% of the Indian isolates were multidrug-resistant, and 72.2% displayed strong biofilm-forming capacity. Integration of global genomes revealed extensive phylogenetic interspersion, reflecting widely distributed lineages shaped by shared ancestry or environmentally mixed\n                      <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                      populations. The pangenome comprised 20,915 genes, with a 3,394 core, and a large accessory genome (&gt;16,001 cloud genes). Serogroups B and C2-C3 dominated globally and carried the broadest AMR repertoires. While efflux-associated and regulatory resistance genes were conserved across subspecies, acquired determinants such as aminoglycoside-modifying enzymes,\n                      <jats:italic toggle=\"yes\">tet(A\/B)<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">sul<\/jats:italic>\n                      genes, and rare extended-spectrum \u03b2-lactamases (ESBLs) varied by serogroup. Detection of\n                      <jats:italic toggle=\"yes\">mcr-1<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">mcr-5<\/jats:italic>\n                      , and\n                      <jats:italic toggle=\"yes\">mcr-9<\/jats:italic>\n                      highlights early circulation of colistin resistance in environmental reservoirs. Core virulence loci (SPI-1\/SPI-2) remained uniformly conserved, whereas accessory modules, including\n                      <jats:italic toggle=\"yes\">spv<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">pef<\/jats:italic>\n                      operons, siderophore systems (\n                      <jats:italic toggle=\"yes\">iro<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">iuc\/iut<\/jats:italic>\n                      ), and stress-response genes, showed serogroup-specific enrichment. Plasmidome analysis revealed marked diversity, dominated by IncF and colicinogenic plasmids, with serogroup-specific patterns, suggesting niche adaptation and horizontal gene transfer. Overall, environmental\n                      <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                      constitute a globally connected and genetically dynamic reservoir where conserved virulence backbones coexist with rapidly evolving resistance and plasmid repertoires. These findings position environmental surveillance as a cornerstone of One Health preparedness for tackling high-risk, pathogenic lineages of\n                      <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                      .\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                        inhabiting environmental niches, such as water and soil, remain underexplored despite their potential role in pathogen gene pool evolution and infection burden. Using a global data set that includes newly sequenced genomes of isolates from India, we show that environmental populations are active evolutionary reservoirs that maintain a conserved virulence core while rapidly exchanging antimicrobial resistance genes via horizontal gene transfer. The detection of early-stage colistin resistance and multidrug-resistant lineages in global ecosystems identify these environments as potential early-warning systems for emerging clinical threats. Our findings demonstrate that Indian environmental strains of\n                        <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                        are deeply interconnected with global lineages, underscoring the need for global surveillance. Collectively, genomic epidemiology as described herein reinforces a One Health framework and highlights environmental surveillance as a critical requirement in the context of high-risk pathogens such as\n                        <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                        .\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/mbio.01142-26","type":"journal-article","created":{"date-parts":[[2026,6,22]],"date-time":"2026-06-22T13:01:11Z","timestamp":1782133271000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":1,"title":["Global genomic surveillance of\n                    <i>Salmonella<\/i>\n                    in the environment: assessing virulence and antimicrobial resistance at 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