{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T19:21:52Z","timestamp":1790882512507,"version":"4.1.0"},"reference-count":43,"publisher":"American Society for Microbiology","issue":"10","license":[{"start":{"date-parts":[[2024,10,3]],"date-time":"2024-10-03T00:00:00Z","timestamp":1727913600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,10,3]],"date-time":"2024-10-03T00:00:00Z","timestamp":1727913600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000199","name":"U.S. Department of Agriculture","doi-asserted-by":"crossref","award":["2018-67017-27631"],"award-info":[{"award-number":["2018-67017-27631"]}],"id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000199","name":"U.S. Department of Agriculture","doi-asserted-by":"crossref","award":["2018-67017-27631"],"award-info":[{"award-number":["2018-67017-27631"]}],"id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Oregon State University","award":["in-kind supplement from the Oregon State University's Center for Quantitative Life Sciences"],"award-info":[{"award-number":["in-kind supplement from the Oregon State University's Center for Quantitative Life Sciences"]}]},{"name":"Oregon State University","award":["Agricultural Research Foundation"],"award-info":[{"award-number":["Agricultural Research Foundation"]}]},{"name":"Oregon State University","award":["Agricultural Research Foundation"],"award-info":[{"award-number":["Agricultural Research Foundation"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2024,10,3]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Extended-spectrum beta-lactamase (ESBL)-producing\n                      <jats:italic>Escherichia coli<\/jats:italic>\n                      pose a serious threat to human health because of their resistance to the most commonly prescribed antibiotics: penicillins and cephalosporins. In this study, we provide a genomic and metagenomic context for the determinant beta-lactam resistance genes of ESBL-positive\n                      <jats:italic>E. coli<\/jats:italic>\n                      isolated from various wastewater treatment utilities in Oregon, USA. Class A beta-lactamase genes on chromosomes (\n                      <jats:italic>bla<\/jats:italic>\n                      CTX-M,\n                      <jats:italic>bla<\/jats:italic>\n                      TEM) were clustered with antibiotic resistance genes associated with other classes of antibiotics (sulfonamides and aminoglycosides) along with insertional elements. ESBL genes such as\n                      <jats:italic>bla<\/jats:italic>\n                      CTX-M,\n                      <jats:italic>bla<\/jats:italic>\n                      TEM, and\n                      <jats:italic>bla<\/jats:italic>\n                      SHV were also detected on conjugable plasmids of IncF and IncI incompatibility types. One novel IncF plasmid (pSHV2A_ESBLF) was identified, which carried a multidrug resistance genotype (\n                      <jats:italic>bla<\/jats:italic>\n                      SHV-2A,\n                      <jats:italic>aadA22<\/jats:italic>\n                      ,\n                      <jats:italic>aac<\/jats:italic>\n                      3,\n                      <jats:italic>aph<\/jats:italic>\n                      6,\n                      <jats:italic>tet<\/jats:italic>\n                      A, and\n                      <jats:italic>sul<\/jats:italic>\n                      1) in addition to a\n                      <jats:italic>mer<\/jats:italic>\n                      (mercury resistance) operon, colicin, and aerobactin genes. Shotgun metagenomic analysis of the ESBL-producing\n                      <jats:italic>E. coli<\/jats:italic>\n                      -originating wastewater samples showed the presence of class A beta-lactamases; however, the ESBL genes identified in the\n                      <jats:italic>E. coli<\/jats:italic>\n                      genomes were below the detection limits. Other ESBL-associated genes (i.e.,\n                      <jats:italic>bla<\/jats:italic>\n                      OXA.11,\n                      <jats:italic>bla<\/jats:italic>\n                      FOX.7, and\n                      <jats:italic>bla<\/jats:italic>\n                      GES.17) were identified in the wastewater samples, and their occurrences were correlated with the core microbial genera (e.g.,\n                      <jats:italic>Paraprevotella<\/jats:italic>\n                      ). In the\n                      <jats:italic>E. coli<\/jats:italic>\n                      genomes and wastewater samples, tetracycline, aminoglycoside, and beta-lactam resistance determinants frequently co-occurred. The combination of whole-genome and metagenomic analysis provides a holistic description of ESBL-producing organisms and genes in wastewater systems.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        Using a hybrid sequencing and assembly strategy (short- and long-read sequencing), we identified the distribution of ARGs and virulence factors harbored on plasmids and chromosomes. We further characterized plasmids\u2019 incompatibility types and the co-occurrences of ARGs and virulence factors on plasmids and chromosomes. We investigated the transferability of plasmid-mediated beta-lactams via conjugation. Finally, using shotgun metagenomic analysis of the ESBL-producing\n                        <jats:italic>Escherichia coli<\/jats:italic>\n                        -originated wastewater samples, we described the microbial community, the resistome composition, and the potential associations with plasmid-mediated beta-lactam genes and other ARGs.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.00717-24","type":"journal-article","created":{"date-parts":[[2024,8,21]],"date-time":"2024-08-21T21:02:05Z","timestamp":1724274125000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":9,"title":["Resolved genomes of wastewater ESBL-producing\n                    <i>Escherichia coli<\/i>\n                    and metagenomic analysis of source wastewater samples"],"prefix":"10.1128","volume":"12","author":[{"given":"Clinton","family":"Cheney","sequence":"first","affiliation":[{"name":"School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0967-1946","authenticated-orcid":true,"given":"Jared D.","family":"Johnson","sequence":"additional","affiliation":[{"name":"Department of Food Science and Technology, Oregon State University, Corvallis, Oregon, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John P.","family":"Ste. 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