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Our study aims to longitudinally assemble the genomic characteristics of CREC isolates from fecal samples from an index patient with recurrent CREC-related urinary tract infections and his family and swabs from his home environment 12 times between 2019 and 2021 to investigate the distribution of antibiotic resistance genes. CREC identified using the VITEK 2 were subjected to nanopore whole-genome sequencing (WGS). The WGS of 27 CREC isolates discovered in 137 specimens (1 urine, 123 feces, and 13 environmental) revealed the predominance of ST101 and ST131. Among these sequence types, blaCTX-M (44.4%, n = 12) was the predominant ESBL gene family, with blaCTX-M-14 (n = 6) being the most common. The remaining 15 (55.6%) isolates harbored blaCMY-2 genes and were clonally diverse. All E. coli isolated from the index patient\u2019s initial urine and fecal samples belonged to O25b:H4-B2-ST131 and carried blaCTX-M-14. The results of sequence analysis indicate plasmid-mediated household transmission of blaCMY-2 or blaCTX-M-55. A strong genomic similarity was discovered between fecal ESBL-producing E. coli and uropathogenic strains. Furthermore, blaCMY-2 genes were widely distributed among the CREC isolated from family members and their home environment.<\/jats:p>","DOI":"10.3390\/antibiotics11091152","type":"journal-article","created":{"date-parts":[[2022,8,25]],"date-time":"2022-08-25T21:28:12Z","timestamp":1661462892000},"page":"1152","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Distribution and Genomic Characterization of Third-Generation Cephalosporin-Resistant Escherichia coli Isolated from a Single Family and Home Environment: A 2-Year Longitudinal Study"],"prefix":"10.3390","volume":"11","author":[{"given":"Yin-Chih","family":"Feng","sequence":"first","affiliation":[{"name":"Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung 813414, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ci-Hong","family":"Liou","sequence":"additional","affiliation":[{"name":"National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Hsinchu 35053, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wailap Victor","family":"Ng","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng-Jui","family":"Chen","sequence":"additional","affiliation":[{"name":"National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Hsinchu 35053, Taiwan"},{"name":"Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chih-Hsin","family":"Hung","sequence":"additional","affiliation":[{"name":"Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung 84001, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Po-Yen","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung 813414, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4360-7932","authenticated-orcid":false,"given":"Yu-Chieh","family":"Liao","sequence":"additional","affiliation":[{"name":"Institute of Population Health Sciences, National Health Research Institutes, Miaoli 35053, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2638-7883","authenticated-orcid":false,"given":"Han-Chieh","family":"Wu","sequence":"additional","affiliation":[{"name":"National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Hsinchu 35053, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ming-Fang","family":"Cheng","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung 813414, Taiwan"},{"name":"School of Nursing, Fooyin University, Kaohsiung 83102, Taiwan"},{"name":"School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,8,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"14372","DOI":"10.1038\/srep14372","article-title":"Pathogenic Escherichia coli producing Extended Spectrum \u03b2-Lactamases isolated from surface water and wastewater","volume":"5","author":"Franz","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Cui, L., Zhao, X., Li, R., Han, Y., Hao, G., Wang, G., and Sun, S. (2022). Companion Animals as Potential Reservoirs of Antibiotic Resistant Diarrheagenic Escherichia coli in Shandong, China. Antibiotics, 11.","DOI":"10.3390\/antibiotics11060828"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Imre, K., Ban-Cucerzan, A., Herman, V., Sallam, K.I., Cristina, R.T., Abd-Elghany, S.M., Morar, D., Popa, S.A., Imre, M., and Morar, A. (2022). Occurrence, Pathogenic Potential and Antimicrobial Resistance of Escherichia coli Isolated from Raw Milk Cheese Commercialized in Banat Region, Romania. Antibiotics, 11.","DOI":"10.3390\/antibiotics11060721"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1111\/j.1574-6976.2009.00198.x","article-title":"Broad-spectrum \u03b2-lactamases among Enterobacteriaceae of animal origin: Molecular aspects, mobility and impact on public health","volume":"34","author":"Smet","year":"2010","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2981","DOI":"10.1128\/AAC.00971-12","article-title":"Distribution of extended-spectrum \u03b2-lactamases, AmpC \u03b2-lactamases, and carbapenemases among Enterobacteriaceae isolates causing intra-abdominal infections in the Asia-Pacific region: Results of the study for Monitoring Antimicrobial Resistance Trends (SMART)","volume":"57","author":"Sheng","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1093\/jac\/dkaa399","article-title":"The global prevalence and trend of human intestinal carriage of ESBL-producing Escherichia coli in the community","volume":"76","author":"Bezabih","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1097\/INF.0000000000000623","article-title":"Emergence of extended spectrum-beta-lactamase-producing Escherichia coli O25b-ST131: A major community-acquired uropathogen in infants","volume":"34","author":"Cheng","year":"2015","journal-title":"Pediatr. Infect. Dis. J."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Huang, I.F., Lee, W.Y., Wang, J.L., Hung, C.H., Hu, H.H., Hung, W.Y., Hung, Y.J., Chen, W.C., Shen, Y.T., and Cheng, M.F. (2018). Fecal carriage of multidrug-resistant Escherichia coli by community children in southern Taiwan. BMC Gastroenterol., 18.","DOI":"10.1186\/s12876-018-0807-x"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/j.jmii.2017.08.005","article-title":"Extended-spectrum beta-lactamase-producing Escherichia coli bacteremia: Comparison of pediatric and adult populations","volume":"51","author":"Tsai","year":"2018","journal-title":"J. Microbiol. Immunol. Infect."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Chen, W.C., Hung, C.H., Chen, Y.S., Cheng, J.S., Lee, S.S., Tseng, F.C., Cheng, M.F., and Wang, J.L. (2021). Bloodstream Infections Caused by Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Patients with Liver Cirrhosis. Pathogens, 10.","DOI":"10.3390\/pathogens10010037"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.1007\/s00467-016-3338-0","article-title":"Urinary tract infection in infants caused by extended-spectrum beta-lactamase-producing Escherichia coli: Comparison between urban and rural hospitals","volume":"31","author":"Cheng","year":"2016","journal-title":"Pediatr. Nephrol."},{"key":"ref_12","first-page":"173","article-title":"Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer","volume":"7","author":"Penders","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"610656","DOI":"10.3389\/fmicb.2021.610656","article-title":"Antibiotics and Antibiotic Resistance Genes in Animal Manure\u2014Consequences of Its Application in Agriculture","volume":"12","author":"Zalewska","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Reuland, E.A., Halaby, T., Hays, J.P., de Jongh, D.M., Snetselaar, H.D., van Keulen, M., Elders, P.J., Savelkoul, P.H., Vandenbroucke-Grauls, C.M., and Al Naiemi, N. (2015). Plasmid-mediated AmpC: Prevalence in community-acquired isolates in Amsterdam, the Netherlands, and risk factors for carriage. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0113033"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"5154217","DOI":"10.1155\/2020\/5154217","article-title":"Carriage of Extended-Spectrum-\u03b2-Lactamase- and AmpC-\u03b2-Lactamase-Producing Enterobacteriaceae (ESBL-PE) in Healthy Community and Outpatient Department (OPD) Patients in Nepal","volume":"2020","author":"Mandal","year":"2020","journal-title":"Can. J. Infect. Dis. Med. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"13588","DOI":"10.1038\/s41598-020-70491-3","article-title":"Assembly methods for nanopore-based metagenomic sequencing: A comparative study","volume":"10","author":"Pascual","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1186\/s13059-021-02282-6","article-title":"Homopolish: A method for the removal of systematic errors in nanopore sequencing by homologous polishing","volume":"22","author":"Huang","year":"2021","journal-title":"Genome Biol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1128\/JCM.06094-11","article-title":"Multilocus sequence typing of total-genome-sequenced bacteria","volume":"50","author":"Larsen","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2410","DOI":"10.1128\/JCM.00008-15","article-title":"Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data","volume":"53","author":"Joensen","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.2147\/IDR.S201086","article-title":"Prevalence and risk factors for colonization by extended-spectrum beta-lactamase-producing or ST 131 Escherichia coli among asymptomatic adults in community settings in Southern Taiwan","volume":"12","author":"Wu","year":"2019","journal-title":"Infect. Drug Resist."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1111\/1469-0691.12646","article-title":"Pandemic lineages of extraintestinal pathogenic Escherichia coli","volume":"20","author":"Riley","year":"2014","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1111\/j.1469-0691.2012.03850.x","article-title":"Extended-spectrum \u03b2-lactamase-producing and AmpC-producing Escherichia coli from livestock and companion animals, and their putative impact on public health: A global perspective","volume":"18","author":"Ewers","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1128\/AAC.01993-13","article-title":"Extended-spectrum-\u03b2-lactamase-producing Escherichia coli as intestinal colonizers in the German community","volume":"58","author":"Valenza","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1093\/jac\/dkp484","article-title":"Prevalence and molecular characterization of clinical isolates of Escherichia coli expressing an AmpC phenotype","volume":"65","author":"Nielsen","year":"2010","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/jac\/dkw398","article-title":"Distribution of ESBLs, AmpC \u03b2-lactamases and carbapenemases among Enterobacteriaceae isolates causing intra-abdominal and urinary tract infections in the Asia-Pacific region during 2008\u201314: Results from the Study for Monitoring Antimicrobial Resistance Tr","volume":"72","author":"Jean","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1353","DOI":"10.1128\/AAC.48.4.1353-1356.2004","article-title":"Dissemination of bla CMY-2 among Escherichia coli Isolates from Food Animals, Retail Ground Meats, and Humans in Southern Taiwan","volume":"48","author":"Yan","year":"2004","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1016\/j.ijantimicag.2015.10.007","article-title":"Molecular characterisation of acquired and overproduced chromosomal blaAmpC in Escherichia coli clinical isolates","volume":"47","author":"Alonso","year":"2016","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"van Hoek, A.H., Schouls, L., van Santen, M.G., Florijn, A., de Greeff, S.C., and van Duijkeren, E. (2015). Molecular characteristics of extended-spectrum cephalosporin-resistant Enterobacteriaceae from humans in the community. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0129085"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Karaiskos, I., and Giamarellou, H. (2020). Carbapenem-Sparing Strategies for ESBL Producers: When and How. Antibiotics, 9.","DOI":"10.3390\/antibiotics9020061"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1016\/j.jgar.2020.03.011","article-title":"High prevalence of bla(CMY) AmpC beta-lactamase in ESBL co-producing Escherichia coli and Klebsiella spp. clinical isolates in the northeast of Iran","volume":"22","author":"Rizi","year":"2020","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_31","first-page":"50","article-title":"Plasmid-mediated AmpC beta-lactamase-producing Escherichia coli causing urinary tract infection in the Auckland community likely to be resistant to commonly prescribed antimicrobials","volume":"128","author":"Drinkovic","year":"2015","journal-title":"N. Z. Med. J."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"S164","DOI":"10.1086\/500663","article-title":"Extended-Spectrum \u03b2-Lactamases and Clinical Outcomes: Current Data","volume":"42","author":"Ramphal","year":"2006","journal-title":"Clin. Infect. Dis."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1179\/joc.2009.21.6.621","article-title":"Emergence of carbapenem-resistant Escherichia coli in Taiwan: Resistance due to combined CMY-2 production and porin deficiency","volume":"21","author":"Chia","year":"2009","journal-title":"J. Chemother."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"748525","DOI":"10.3389\/fmicb.2021.748525","article-title":"Risk Factors and Prevalence of mcr-1-Positive Escherichia coli in Fecal Carriages Among Community Children in Southern Taiwan","volume":"12","author":"Wu","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1128\/JCM.00945-08","article-title":"Impact of diversity of colonizing strains on strategies for sampling Escherichia coli from fecal specimens","volume":"46","author":"Lautenbach","year":"2008","journal-title":"J. Clin. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"5005","DOI":"10.1128\/AEM.01423-13","article-title":"Real-time PCR for quantitative analysis of human commensal Escherichia coli populations reveals a high frequency of subdominant phylogroups","volume":"79","author":"Smati","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_37","unstructured":"Weinstein, M.P., Kim, T.J., Lewis, J.S., Limbago, B., Bobenchik, A.M., Mathers, A.J., Campeau, S., Mazzulli, T., Cullen, S.K., and Satlin, M. (2020). Performance Standards for Antimicrobial Testing; CLSI Supplement M100, Clinical and Laboratory Standards Institute. [30th ed.]."},{"key":"ref_38","unstructured":"(2021, October 01). FDA-Recognized Antimicrobial Susceptibility Test Interpretive Criteria: Tigecycline, Available online: https:\/\/www.fda.gov\/drugs\/development-resources\/tigecycline-injection-products."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"dlaa101","DOI":"10.1093\/jacamr\/dlaa101","article-title":"Evaluation of Vitek\u00ae2 performance for colistin susceptibility testing for Gram-negative isolates","volume":"2","author":"Khurana","year":"2020","journal-title":"JAC-Antimicrob. Resist."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","article-title":"Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: An international expert proposal for interim standard definitions for acquired resistance","volume":"18","author":"Magiorakos","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1038\/nprot.2007.94","article-title":"Pulsed-field gel electrophoresis","volume":"2","author":"Herschleb","year":"2007","journal-title":"Nat. Protocols"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.3389\/fmicb.2019.02068","article-title":"Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run With Barcoding","volume":"10","author":"Liao","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"e01269-20","DOI":"10.1128\/JCM.01269-20","article-title":"In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data","volume":"58","author":"Johnson","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"766","DOI":"10.3389\/fmicb.2016.00766","article-title":"Implementation of Whole Genome Sequencing (WGS) for Identification and Characterization of Shiga Toxin-Producing Escherichia coli (STEC) in the United States","volume":"7","author":"Lindsey","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"ofv083","DOI":"10.1093\/ofid\/ofv083","article-title":"Host Characteristics and Bacterial Traits Predict Experimental Virulence for Escherichia coli Bloodstream Isolates From Patients With Urosepsis","volume":"2","author":"Johnson","year":"2015","journal-title":"Open Forum Infect. Dis."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"4115","DOI":"10.1128\/IAI.00752-12","article-title":"Escherichia coli isolates that carry vat, fyuA, chuA, and yfcV efficiently colonize the urinary tract","volume":"80","author":"Spurbeck","year":"2012","journal-title":"Infect. Immun."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"3987","DOI":"10.1128\/JCM.00816-08","article-title":"Identification of minimal predictors of avian pathogenic Escherichia coli virulence for use as a rapid diagnostic tool","volume":"46","author":"Johnson","year":"2008","journal-title":"J. Clin. Microbiol."},{"key":"ref_48","unstructured":"(2022, March 08). Center for Genomic Epidemiology. Available online: http:\/\/www.genomicepidemiology.org\/services\/."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1111\/1758-2229.12019","article-title":"The Clermont Escherichia coli phylo-typing method revisited: Improvement of specificity and detection of new phylo-groups","volume":"5","author":"Clermont","year":"2013","journal-title":"Environ. Microbiol. Rep."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1128\/JCM.03617-13","article-title":"Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli","volume":"52","author":"Joensen","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_53","first-page":"D801","article-title":"TYGS and LPSN: A database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes","volume":"50","author":"Carbasse","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Alikhan, N.-F., Petty, N.K., Ben Zakour, N.L., and Beatson, S.A. (2011). BLAST Ring Image Generator (BRIG): Simple prokaryote genome comparisons. 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