{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T13:43:19Z","timestamp":1792590199322,"version":"4.5.0"},"reference-count":75,"publisher":"American Society for Microbiology","issue":"10","license":[{"start":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T00:00:00Z","timestamp":1792540800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T00:00:00Z","timestamp":1792540800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"Medical Research Future Fund (MRFF), Australian Government","award":["MRFCRI000195"],"award-info":[{"award-number":["MRFCRI000195"]}]},{"name":"Medical Research Future Fund (MRFF), Australian Government","award":["MRFCRI000195"],"award-info":[{"award-number":["MRFCRI000195"]}]},{"name":"Melbourne Water","award":["LV0554-60245"],"award-info":[{"award-number":["LV0554-60245"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2026,10,21]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      The use of treated wastewater is increasingly important for sustainable water management under a changing climate, yet conventional monitoring based on\n                      <jats:italic toggle=\"yes\">Escherichia coli<\/jats:italic>\n                      enumeration provides limited insight into strain diversity and associated public health hazards. Here, we applied longitudinal whole-genome sequencing (WGS) to 180\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      isolates collected across the treatment continuum of a recycled water facility, from influent to final effluent. Genomic analysis revealed extensive strain-level heterogeneity, comprising 88 sequence types across eight phylogroups, with greater diversity in influent than in treated effluent. Phylogenetic comparisons with contextual Australian genomes indicated clustering with strains associated with companion animals, wild birds, humans, and livestock, suggesting multiple potential source reservoirs rather than a single dominant origin, although source contributions were not definitive. Despite a &gt;90% reduction in total\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      loads, isolates recovered from upstream and downstream stages exhibited broadly comparable virulence factor and antimicrobial resistance gene (ARG) profiles, suggesting that, within the cultured isolate collection, reductions in abundance exceeded shifts in genomic composition. To assess operational relevance, we prototyped a genomics-informed hazard framework integrating virulence determinants, ARGs, plasmid-associated mobility, and reuse-specific exposure context. Using this framework, 92.8% of isolates were classified as low hazard, and 7.2% as moderate hazard, with no isolates meeting criteria for high or critical hazard classifications. These findings demonstrate that genomic profiling of indicator organisms can reveal population structure and hazard heterogeneity not captured by conventional enumeration alone, and can provide a practical basis for incorporating genomic information into hazard-informed monitoring of recycled water systems.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Routine recycled water monitoring relies largely on culture-based\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      counts, which indicate regulatory compliance but provide limited insight into strain diversity, persistence, and genomic characteristics relevant to public health. Using longitudinal whole-genome sequencing, we show that genetically distinct\n                      <jats:italic toggle=\"yes\">E. coli l<\/jats:italic>\n                      ineages, including isolates carrying combinations of virulence and antimicrobial resistance determinants, can persist through advanced treatment despite substantial reductions in overall\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      loads. While most isolates were classified as low genomic hazard and no high- or critical-hazard isolates were detected, these findings demonstrate that conventional enumeration alone cannot distinguish between genetically diverse lineages with differing hazard potential in highly treated systems. By integrating genomic data into a hazard classification framework, this study demonstrates an applied approach to contextualize\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      detections and distinguish low-risk background populations from isolates with elevated genomic hazard profiles. This work supports the use of genomic profiling of indicator organisms to improve surveillance, inform treatment performance assessment, and enable more risk-based management of recycled water systems.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/aem.01342-26","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T13:00:10Z","timestamp":1789477210000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Whole-genome surveillance supports hazard profiling of\n                    <i>Escherichia coli<\/i>\n                    lineages in recycled water treatment systems"],"prefix":"10.1128","volume":"92","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2775-9079","authenticated-orcid":true,"given":"Dewa A. P. Rasmika","family":"Dewi","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bfwt286","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Public Health and Preventive Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University","place":["Melbourne, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harshanie","family":"Abeywardena","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01r7sqp31","id-type":"ROR","asserted-by":"publisher"}],"name":"Melbourne Water Corporation","place":["Melbourne, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dieter","family":"Bulach","sequence":"additional","affiliation":[{"name":"Melbourne Veterinary School, Faculty of Science, University of Melbourne","place":["Parkville, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chi-Wen","family":"Tseng","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bfwt286","id-type":"ROR","asserted-by":"publisher"}],"name":"One Water Laboratory, Department of Civil and Environmental Engineering, Monash University","place":["Clayton, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lamiya","family":"Bata","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bfwt286","id-type":"ROR","asserted-by":"publisher"}],"name":"One Water Laboratory, Department of Civil and Environmental Engineering, Monash University","place":["Clayton, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fiona","family":"Lynch","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bfwt286","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Public Health and Preventive Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University","place":["Melbourne, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melita","family":"Stevens","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01r7sqp31","id-type":"ROR","asserted-by":"publisher"}],"name":"Melbourne Water Corporation","place":["Melbourne, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas D.","family":"Crosbie","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01r7sqp31","id-type":"ROR","asserted-by":"publisher"}],"name":"Melbourne Water Corporation","place":["Melbourne, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebekah","family":"Henry","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bfwt286","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Public Health and Preventive Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University","place":["Melbourne, Australia"]},{"id":[{"id":"https:\/\/ror.org\/02bfwt286","id-type":"ROR","asserted-by":"publisher"}],"name":"One Water Laboratory, Department of Civil and Environmental Engineering, Monash University","place":["Clayton, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.3390\/membranes13060612"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2021.151676"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1093\/femsre\/fuac008"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0245910"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.4014\/jmb.2211.11027"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.811755"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.01423-22"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2014.00317"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.envint.2019.105449"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.est.6b05100"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2022.158698"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-62455-w"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1155\/2020\/2534130"},{"key":"e_1_3_4_15_2","unstructured":"Health-Victoria. 2024. 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