{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T16:07:21Z","timestamp":1783008441770,"version":"3.54.5"},"update-to":[{"DOI":"10.1371\/journal.pntd.0012413","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,9,12]],"date-time":"2025-09-12T00:00:00Z","timestamp":1757635200000}}],"reference-count":75,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2025,9,9]],"date-time":"2025-09-09T00:00:00Z","timestamp":1757376000000},"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-008749"],"award-info":[{"award-number":["INV-008749"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["206545\/Z\/17\/Z"],"award-info":[{"award-number":["206545\/Z\/17\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"<jats:sec id=\"sec001\">\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      <jats:italic>\n                        <jats:italic>Salmonella enterica<\/jats:italic>\n                      <\/jats:italic>\n                      encompasses over 2,600 serovars, including several commonly associated with severe infection in humans.\n                      <jats:italic>\n                        <jats:italic>Salmonella<\/jats:italic>\n                      <\/jats:italic>\n                      is a major cause of sepsis in Africa; however, diagnosis requires clinical microbiology facilities. Environmental surveillance has the potential to play a role in\n                      <jats:italic>\n                        <jats:italic>Salmonella<\/jats:italic>\n                      <\/jats:italic>\n                      surveillance.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec002\">\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We undertook water-based environmental surveillance in Blantyre, Malawi, from 2018-2020, taking samples from rivers (87.9%), a sewage plant (8.85%) and other water sources (3.24%), isolating and storing 1,042 non-typhoidal\n                      <jats:italic>Salmonella<\/jats:italic>\n                      (NTS) isolates in this period. Of these, 341 NTS isolates were whole genome sequenced, genome quality was checked, duplicate genomes from any given sample were removed and core genome phylogeny was reconstructed. AMRFinder, PathogenWatch and SISTR were used to further investigate serovar, sequence type and antimicrobial resistance determinants.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec003\">\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      After quality checks, and removal of duplicate genomes, 270 NTS genomes remained for further analysis. Multiple\n                      <jats:italic>\n                        <jats:italic>Salmonella<\/jats:italic>\n                      <\/jats:italic>\n                      serovars associated with human infection were detected, of which\n                      <jats:italic>\n                        <jats:italic>S<\/jats:italic>\n                      <\/jats:italic>\n                      . Typhimurium (55\/270 isolates) was the most common, including 44 of Sequence Type (ST) 313, a serovar commonly associated with severe invasive disease (iNTS). Six lineage 2 ST313 genomes possessed AMR genes predicting multidrug resistance (MDR), while 29 lineage 3 isolates contained no AMR predictive genes. PCR based detection of\n                      <jats:italic>\n                        <jats:italic>staG<\/jats:italic>\n                      <\/jats:italic>\n                      has been proposed as a diagnostic marker of\n                      <jats:italic>\n                        <jats:italic>S<\/jats:italic>\n                      <\/jats:italic>\n                      . Typhi; however, all eight genomes that contained\n                      <jats:italic>\n                        <jats:italic>staG<\/jats:italic>\n                      <\/jats:italic>\n                      identified as\n                      <jats:italic>\n                        <jats:italic>Salmonella enterica<\/jats:italic>\n                      <\/jats:italic>\n                      serovar Orion, raising concerns about the specificity of this marker as a monoplex for environmental surveillance of\n                      <jats:italic>\n                        <jats:italic>S.<\/jats:italic>\n                      <\/jats:italic>\n                      Typhi.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec004\">\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>\n                      The study identified diverse\n                      <jats:italic>\n                        <jats:italic>Salmonella<\/jats:italic>\n                      <\/jats:italic>\n                      serovars in the environment, including those reported to cause invasive disease, emphasizing the complex but potentially valuable contribution of implementing environmental surveillance for\n                      <jats:italic>\n                        <jats:italic>Salmonella<\/jats:italic>\n                      <\/jats:italic>\n                      in high burden areas lacking diagnostic microbiology capacity.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pntd.0012413","type":"journal-article","created":{"date-parts":[[2025,9,9]],"date-time":"2025-09-09T17:40:26Z","timestamp":1757439626000},"page":"e0012413","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Diversity of Salmonella enterica isolates from urban river and sewage water in Blantyre, 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