{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T01:05:32Z","timestamp":1785546332792,"version":"3.56.0"},"reference-count":53,"publisher":"American Society for Microbiology","issue":"10","license":[{"start":{"date-parts":[[2011,5,15]],"date-time":"2011-05-15T00:00:00Z","timestamp":1305417600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2011,5,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            We hypothesized that bacterial populations growing in the absence of antibiotics will accumulate more resistance gene mutations than bacterial populations growing in the presence of antibiotics. If this is so, the prevalence of dysfunctional resistance genes (resistance pseudogenes) could provide a measure of the level of antibiotic exposure present in a given environment. As a proof-of-concept test, we assayed field strains of\n            <jats:named-content content-type=\"genus-species\">Escherichia coli<\/jats:named-content>\n            for their resistance genotypes using a resistance gene microarray and further characterized isolates that had resistance phenotype-genotype discrepancies. We found a small but significant association between the prevalence of isolates with resistance pseudogenes and the lower antibiotic use environment of a beef cow-calf operation versus a higher antibiotic use dairy calf ranch (Fisher's exact test,\n            <jats:italic>P<\/jats:italic>\n            = 0.044). Other significant findings include a very strong association between the dairy calf ranch isolates and phenotypes unexplained by well-known resistance genes (Fisher's exact test,\n            <jats:italic>P<\/jats:italic>\n            &lt; 0.0001). Two novel resistance genes were discovered in\n            <jats:named-content content-type=\"genus-species\">E. coli<\/jats:named-content>\n            isolates from the dairy calf ranch, one associated with resistance to aminoglycosides and one associated with resistance to trimethoprim. In addition, isolates resistant to expanded-spectrum cephalosporins but negative for\n            <jats:italic>bla<\/jats:italic>\n            <jats:sub>CMY-2<\/jats:sub>\n            had mutations in the promoter regions of the chromosomal\n            <jats:named-content content-type=\"genus-species\">E. coli<\/jats:named-content>\n            <jats:italic>ampC<\/jats:italic>\n            gene consistent with reported overexpression of native AmpC beta-lactamase. Similar mutations in hospital\n            <jats:named-content content-type=\"genus-species\">E. coli<\/jats:named-content>\n            isolates have been reported worldwide. Prevalence or rates of\n            <jats:named-content content-type=\"genus-species\">E. coli<\/jats:named-content>\n            <jats:italic>ampC<\/jats:italic>\n            promoter mutations may be used as a marker for high expanded-spectrum cephalosporin use environments.\n          <\/jats:p>","DOI":"10.1128\/aem.02588-10","type":"journal-article","created":{"date-parts":[[2011,3,19]],"date-time":"2011-03-19T04:30:19Z","timestamp":1300509019000},"page":"3293-3299","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":68,"title":["Genotypic-Phenotypic Discrepancies between Antibiotic Resistance Characteristics of Escherichia coli Isolates from Calves in Management Settings with High and Low Antibiotic Use"],"prefix":"10.1128","volume":"77","author":[{"given":"Margaret A.","family":"Davis","sequence":"first","affiliation":[{"name":"Veterinary Microbiology and Pathology Department, Washington State University, Pullman, Washington 99164-7040"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas E.","family":"Besser","sequence":"additional","affiliation":[{"name":"Veterinary Microbiology and Pathology Department, Washington State University, Pullman, Washington 99164-7040"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa H.","family":"Orfe","sequence":"additional","affiliation":[{"name":"Veterinary Microbiology and Pathology Department, Washington State University, Pullman, Washington 99164-7040"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine N. K.","family":"Baker","sequence":"additional","affiliation":[{"name":"Veterinary Microbiology and Pathology Department, Washington State University, Pullman, Washington 99164-7040"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amelia S.","family":"Lanier","sequence":"additional","affiliation":[{"name":"Veterinary Microbiology and Pathology Department, Washington State University, Pullman, Washington 99164-7040"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shira L.","family":"Broschat","sequence":"additional","affiliation":[{"name":"Veterinary Microbiology and Pathology Department, Washington State University, Pullman, Washington 99164-7040"},{"name":"School of Electrical Engineering and Computer Science, Washington State University, Pullman, Washington 99164-7040"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"New","sequence":"additional","affiliation":[{"name":"Veterinary Microbiology and Pathology Department, Washington State University, Pullman, Washington 99164-7040"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Douglas R.","family":"Call","sequence":"additional","affiliation":[{"name":"Veterinary Microbiology and Pathology Department, Washington State University, Pullman, Washington 99164-7040"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1742-7843.2005.pto960401.x"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.17.3389"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1093\/ajcp\/45.4_ts.493"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00800-08"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.2460\/javma.236.12.1338"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.patbio.2009.07.035"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dki370"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009233"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.47.6.1238-1242.1984"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/0378-1119(94)00721-4"},{"key":"e_1_3_3_12_2","unstructured":"Clinical and Laboratory Standards Institute. \n2008. Performance standards for antimicrobial disk and dilution susceptibility tests for bacteria isolated from animals: approved standard 3rd ed. CLSI document M31-A3. Clinical and Laboratory Standards Institute Wayne PA."},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkm284"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.2010.03298.x"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1086\/502306"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01325-07"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01743-09"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2010.03.017"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(00)04519-0"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.rvsc.2009.05.021"},{"key":"e_1_3_3_21_2","unstructured":"FleissJ. L. 1981. Statistical methods for rates and proportions 2nd ed. John Wiley & Sons New York NY."},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1086\/379668"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkn257"},{"key":"e_1_3_3_24_2","unstructured":"HartlD. L.\nClarkA. G.. 1997. Principles of population genetics 3rd ed. Sinauer Associates Inc. Sunderland MA."},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.49.6.2561-2564.2005"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.01174-09"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkp484"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.145.3.1365-1373.1981"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.2001.tb10962.x"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01534-07"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02584-05"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.72.1.443-448.2006"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.70.2.752-757.2004"},{"key":"e_1_3_3_34_2","unstructured":"LewinB. 1997. Genes. Oxford University Press New York NY."},{"key":"e_1_3_3_35_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.44.5.1630-1634.2006"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkm538"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.70.10.5764-5768.2004"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01353-08"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetmic.2008.08.018"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.43.4.957"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.diagmicrobio.2010.02.008"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.2009.01635.x"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.72.1.516-521.2006"},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00284-001-0100-y"},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/46.5.848"},{"key":"e_1_3_3_46_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-294X.1996.tb00299.x"},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msm092"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.43.11.5705-5714.2005"},{"key":"e_1_3_3_49_2","unstructured":"U.S. Department of Agriculture. \n2010. Beef 2007-08 part IV: reference of beef cow-calf management practices in the United States 2007-08 no. 532.0210. USDA APHIS VS Centers for Epidemiology and Animal Health Fort Collins CO."},{"key":"e_1_3_3_50_2","unstructured":"U.S. Department of Agriculture. \n2008. Dairy 2007 part II: changes in the U.S. dairy cattle industry 1991-2007 no. N481.0308. USDA APHIS VS Centers for Epidemiology and Animal Health Fort Collins CO."},{"key":"e_1_3_3_51_2","doi-asserted-by":"publisher","DOI":"10.1086\/502487"},{"key":"e_1_3_3_52_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0007646"},{"key":"e_1_3_3_53_2","doi-asserted-by":"publisher","DOI":"10.1098\/rsbl.2006.0478"},{"key":"e_1_3_3_54_2","doi-asserted-by":"publisher","DOI":"10.1089\/10665270050081478"}],"container-title":["Applied and Environmental Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/AEM.02588-10","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/AEM.02588-10","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,2,23]],"date-time":"2022-02-23T20:19:39Z","timestamp":1645647579000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/AEM.02588-10"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,5,15]]},"references-count":53,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2011,5,15]]}},"alternative-id":["10.1128\/AEM.02588-10"],"URL":"https:\/\/doi.org\/10.1128\/aem.02588-10","relation":{},"ISSN":["0099-2240","1098-5336"],"issn-type":[{"value":"0099-2240","type":"print"},{"value":"1098-5336","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,5,15]]},"assertion":[{"value":"2010-11-03","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2011-03-07","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2011-05-11","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}