{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,16]],"date-time":"2025-12-16T12:32:27Z","timestamp":1765888347930,"version":"build-2065373602"},"reference-count":82,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2020,6,4]],"date-time":"2020-06-04T00:00:00Z","timestamp":1591228800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["LP150100912"],"award-info":[{"award-number":["LP150100912"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Intensive pig production systems often rely on the use of antimicrobials and heavy metal feed additives to maintain animal health and welfare. To gain insight into the carriage of antimicrobial resistance genes (ARGs) in the faecal flora of commercially reared healthy swine, we characterised the genome sequences of 117 porcine commensal E. coli that carried the class 1 integrase gene (intI1+). Isolates were sourced from 42 healthy sows and 126 of their offspring from a commercial breeding operation in Australia in 2017. intI1+ E. coli was detected in 28\/42 (67%) sows and 90\/126 (71%) piglets. Phylogroup A, particularly clonal complex 10, and phylogroup B1 featured prominently in the study collection. ST10, ST20, ST48 and ST361 were the dominant sequence types. Notably, 113\/117 isolates (96%) carried three or more ARGs. Genes encoding resistance to \u03b2-lactams, aminoglycosides, trimethoprim, sulphonamides, tetracyclines and heavy metals were dominant. ARGs encoding resistance to last-line agents, such as carbapenems and third generation cephalosporins, were not detected. IS26, an insertion sequence noted for its ability to capture and mobilise ARGs, was present in 108\/117 (92%) intI1+ isolates, and it played a role in determining class 1 integron structure. Our data shows that healthy Australian pig faeces are an important reservoir of multidrug resistant E. coli that carry genes encoding resistance to multiple first-generation antibiotics and virulence-associated genes.<\/jats:p>","DOI":"10.3390\/microorganisms8060843","type":"journal-article","created":{"date-parts":[[2020,6,5]],"date-time":"2020-06-05T03:32:21Z","timestamp":1591327941000},"page":"843","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["Whole Genome Sequencing Analysis of Porcine Faecal Commensal Escherichia coli Carrying Class 1 Integrons from Sows and Their Offspring"],"prefix":"10.3390","volume":"8","author":[{"given":"Tiziana","family":"Zingali","sequence":"first","affiliation":[{"name":"The ithree institute, University of Technology Sydney, Sydney NSW 2007, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cameron J.","family":"Reid","sequence":"additional","affiliation":[{"name":"The ithree institute, University of Technology Sydney, Sydney NSW 2007, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4571-1629","authenticated-orcid":false,"given":"Toni A.","family":"Chapman","sequence":"additional","affiliation":[{"name":"NSW Department of Primary Industries, Elizabeth MacArthur Agricultural Institute, Menangle NSW 2568, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniela","family":"Gaio","sequence":"additional","affiliation":[{"name":"The ithree institute, University of Technology Sydney, Sydney NSW 2007, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Liu","sequence":"additional","affiliation":[{"name":"The ithree institute, University of Technology Sydney, Sydney NSW 2007, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aaron E.","family":"Darling","sequence":"additional","affiliation":[{"name":"The ithree institute, University of Technology Sydney, Sydney NSW 2007, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9301-5372","authenticated-orcid":false,"given":"Steven P.","family":"Djordjevic","sequence":"additional","affiliation":[{"name":"The ithree institute, University of Technology Sydney, Sydney NSW 2007, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,6,4]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1111\/j.1574-6976.2011.00273.x","article-title":"Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens","volume":"35","author":"Stokes","year":"2011","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1234","DOI":"10.2527\/2004.8241234x","article-title":"Effect of dietary copper source (cupric citrate and cupric sulfate) and concentration on growth performance and fecal copper excretion in weanling pigs","volume":"82","author":"Armstrong","year":"2004","journal-title":"J. Anim. Sci."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Jacela, J.Y., DeRouchey, J.M., Tokach, M.D., Goodband, R.D., Nelssen, J.L., Renter, D.G., and Dritz, S.S. (2010). Feed additives for swine: Fact sheets \u2013 high dietary levels of copper and zinc for young pigs, and phytase. J. Swine Health Prod.","DOI":"10.4148\/2378-5977.7068"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/2049-1891-4-35","article-title":"Alternatives to antibiotics as growth promoters for use in swine production: A review","volume":"4","author":"Thacker","year":"2013","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1917","DOI":"10.2527\/2002.8071917x","article-title":"Effect of feeding organic and inorganic sources of additional zinc on growth performance and zinc balance in nursery pigs","volume":"80","author":"Case","year":"2002","journal-title":"J. Anim. Sci."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"5649","DOI":"10.1073\/pnas.1503141112","article-title":"Global trends in antimicrobial use in food animals","volume":"112","author":"Brower","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_7","unstructured":"National Research Council (2012). National Research Council Nutrient requirements of Swine: Eleventh Revised Edition, National Academies Press."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1111\/jam.12840","article-title":"Genetic relatedness of commensal Escherichia coli from nursery pigs in intensive pig production in Denmark and molecular characterization of genetically different strains","volume":"119","author":"Larsen","year":"2015","journal-title":"J. Appl. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1111\/j.1574-6941.2008.00526.x","article-title":"Piggery manure used for soil fertilization is a reservoir for transferable antibiotic resistance plasmids","volume":"66","author":"Binh","year":"2008","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1111\/j.1574-6941.2007.00393.x","article-title":"Short-term effects of amoxicillin on bacterial communities in manured soil","volume":"62","author":"Binh","year":"2007","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1016\/j.scitotenv.2014.11.010","article-title":"Long-term application of fresh and composted manure increase tetracycline resistance in the arable soil of eastern China","volume":"506\u2013507","author":"Peng","year":"2015","journal-title":"Sci. Total Environ."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"fix185","DOI":"10.1093\/femsec\/fix185","article-title":"Antimicrobial resistance and the environment: Assessment of advances, gaps and recommendations for agriculture, aquaculture and pharmaceutical manufacturing","volume":"94","author":"Topp","year":"2018","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.mib.2017.03.002","article-title":"Class 1 integrons as invasive species","volume":"38","author":"Gillings","year":"2017","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1704","DOI":"10.1128\/AEM.03172-12","article-title":"Increased abundance and transferability of resistance genes after field application of manure from sulfadiazine-treated pigs","volume":"79","author":"Jechalke","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1128\/MMBR.00056-13","article-title":"Integrons: Past, present, and future","volume":"78","author":"Gillings","year":"2014","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1111\/j.1574-6976.2011.00277.x","article-title":"Analysis of antibiotic resistance regions in Gram-negative bacteria","volume":"35","author":"Partridge","year":"2011","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1007\/s40726-018-0076-x","article-title":"DNA as a pollutant: The clinical class 1 integron","volume":"4","author":"Gillings","year":"2018","journal-title":"Curr. Pollut. Rep."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"16270","DOI":"10.1038\/nmicrobiol.2016.270","article-title":"Continental-scale pollution of estuaries with antibiotic resistance genes","volume":"2","author":"Zhu","year":"2017","journal-title":"Nat. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"3435","DOI":"10.1073\/pnas.1222743110","article-title":"Diverse and abundant antibiotic resistance genes in Chinese swine farms","volume":"110","author":"Zhu","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1111\/1348-0421.12289","article-title":"Characterization of IS26-composite transposons and multidrug resistance in conjugative plasmids from Enterobacter cloacae","volume":"59","author":"Chen","year":"2015","journal-title":"Microbiol. Immunol."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Dolejska, M., Papagiannitsis, C.C., Medvecky, M., Davidova-Gerzova, L., and Valcek, A. (2018). Characterization of the Complete Nucleotide Sequences of IMP-4-Encoding Plasmids, Belonging to Diverse Inc Families, Recovered from Enterobacteriaceae Isolates of Wildlife Origin. Antimicrob. Agents Chemother., 62.","DOI":"10.1128\/AAC.02434-17"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Mangat, C.S., Bekal, S., Irwin, R.J., and Mulvey, M.R. (2017). A Novel Hybrid Plasmid Carrying Multiple Antimicrobial Resistance and Virulence Genes in Salmonella enterica Serovar Dublin. Antimicrob. Agents Chemother., 61.","DOI":"10.1128\/AAC.02601-16"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1016\/j.jmii.2017.03.003","article-title":"The plasmid-mediated fosfomycin resistance determinants and synergy of fosfomycin and meropenem in carbapenem-resistant Klebsiella pneumoniae isolates in Taiwan","volume":"50","author":"Tseng","year":"2017","journal-title":"J. Microbiol. Immunol. Infect."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Venturini, C., Hassan, K.A., Roy Chowdhury, P., Paulsen, I.T., Walker, M.J., and Djordjevic, S.P. (2013). Sequences of two related multiple antibiotic resistance virulence plasmids sharing a unique IS26-related molecular signature isolated from different Escherichia coli pathotypes from different hosts. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0078862"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Reid, C.J., Wyrsch, E.R., Roy Chowdhury, P., Zingali, T., Liu, M., Darling, A.E., Chapman, T.A., and Djordjevic, S.P. (2017). Porcine commensal Escherichia coli: A reservoir for class 1 integrons associated with IS26. Microb. Genom., 3.","DOI":"10.1099\/mgen.0.000143"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.plasmid.2015.04.005","article-title":"Tn6026 and Tn6029 are found in complex resistance regions mobilised by diverse plasmids and chromosomal islands in multiple antibiotic resistant Enterobacteriaceae","volume":"80","author":"Reid","year":"2015","journal-title":"Plasmid"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"4971","DOI":"10.1128\/AAC.00025-11","article-title":"Recombination in IS26 and Tn2 in the evolution of multiresistance regions carrying blaCTX-M-15 on conjugative IncF plasmids from Escherichia coli","volume":"55","author":"Partridge","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Liu, B.-T., Song, F.-J., Zou, M., Hao, Z.-H., and Shan, H. (2017). Emergence of Colistin Resistance Gene mcr-1 in Cronobacter sakazakii Producing NDM-9 and in Escherichia coli from the Same Animal. Antimicrob. Agents Chemother., 61.","DOI":"10.1128\/AAC.01444-16"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/s41426-018-0057-6","article-title":"Potential transferability of mcr-3 via IS26-mediated homologous recombination in Escherichia coli","volume":"7","author":"Wang","year":"2018","journal-title":"Emerg. Microbes Infect."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1089\/mdr.2010.0042","article-title":"Transposons related to Tn1696 in IncHI2 plasmids in multiply antibiotic resistant Salmonella enterica serovar Typhimurium from Australian animals","volume":"16","author":"Cain","year":"2010","journal-title":"Microb. Drug Resist."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1016\/j.copbio.2008.05.006","article-title":"Antibiotics and antibiotic resistance in water environments","volume":"19","author":"Baquero","year":"2008","journal-title":"Curr. Opin. Biotechnol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2893","DOI":"10.1016\/j.envpol.2009.05.051","article-title":"Environmental pollution by antibiotics and by antibiotic resistance determinants","volume":"157","author":"Martinez","year":"2009","journal-title":"Environ. Pollut."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.prevetmed.2017.11.007","article-title":"Persistence of antimicrobial resistance genes from sows to finisher pigs","volume":"149","author":"Halasa","year":"2018","journal-title":"Prev. Vet. Med."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1089\/mdr.2014.0037","article-title":"Presence of antimicrobial resistance and antimicrobial use in sows are risk factors for antimicrobial resistance in their offspring","volume":"21","author":"Callens","year":"2015","journal-title":"Microb. Drug Resist."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1089\/fpd.2005.2.212","article-title":"Effects of antibiotic use in sows on resistance of E. coli and Salmonella enterica Typhimurium in their offspring","volume":"2","author":"Mathew","year":"2005","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2650","DOI":"10.1093\/jac\/dku180","article-title":"Characterization of extended-spectrum \u03b2-lactamase (ESBL)-producing Escherichia coli obtained from Danish pigs, pig farmers and their families from farms with high or no consumption of third- or fourth-generation cephalosporins","volume":"69","author":"Hammerum","year":"2014","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1046\/j.1472-765X.1998.00445.x","article-title":"PCR differentiation of Escherichia coli from other Gram-negative bacteria using primers derived from the nucleotide sequences flanking the gene encoding the universal stress protein","volume":"27","author":"Chen","year":"1998","journal-title":"Lett. Appl. Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1089\/mdr.1995.1.195","article-title":"Molecular epidemiology of integron-associated antibiotic resistance genes in clinical isolates of Enterobacteriaceae","volume":"1","author":"Sallen","year":"1995","journal-title":"Microb. Drug Resist."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1022","DOI":"10.1128\/AAC.45.4.1022-1029.2001","article-title":"Rapid screening technique for class 1 integrons in Enterobacteriaceae and nonfermenting gram-negative bacteria and its use in molecular epidemiology","volume":"45","author":"Maguire","year":"2001","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1038\/ismej.2014.226","article-title":"Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution","volume":"9","author":"Gillings","year":"2015","journal-title":"ISME J."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1093\/bioinformatics\/btu661","article-title":"A5-miseq: An updated pipeline to assemble microbial genomes from Illumina MiSeq data","volume":"31","author":"Coil","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"4555","DOI":"10.1128\/AEM.66.10.4555-4558.2000","article-title":"Rapid and simple determination of theEscherichia coli phylogenetic group","volume":"66","author":"Clermont","year":"2000","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_43","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_44","doi-asserted-by":"crossref","first-page":"2253","DOI":"10.1128\/jcm.25.12.2253-2257.1987","article-title":"Expression of type 1 fimbriae may be required for persistence of Escherichia coli in the catheterized urinary tract","volume":"25","author":"Mobley","year":"1987","journal-title":"J. Clin. Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1126\/science.276.5312.607","article-title":"Prevention of mucosal Escherichia coli infection by FimH-adhesin-based systemic vaccination","volume":"276","author":"Langermann","year":"1997","journal-title":"Science"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1023\/A:1022854902700","article-title":"Resistance to serum complement, iss, and virulence of avian Escherichia coli","volume":"27","author":"Nolan","year":"2003","journal-title":"Vet. Res. Commun."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"7839","DOI":"10.1073\/pnas.87.20.7839","article-title":"A genetic locus of enteropathogenic Escherichia coli necessary for the production of attaching and effacing lesions on tissue culture cells","volume":"87","author":"Jerse","year":"1990","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1111\/j.1574-6968.1998.tb13301.x","article-title":"Molecular and ultrastructural characterisation of EspA from different enteropathogenicEscherichia coli serotypes","volume":"169","author":"Neves","year":"1998","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1016\/j.ijmm.2005.07.005","article-title":"Molecular epidemiology of extraintestinal pathogenic (uropathogenic) Escherichia coli","volume":"295","author":"Johnson","year":"2005","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Micenkov\u00e1, L., \u0160taudov\u00e1, B., Bos\u00e1k, J., Mikalov\u00e1, L., Littnerov\u00e1, S., Vrba, M., \u0160ev\u010d\u00edkov\u00e1, A., Woznicov\u00e1, V., and \u0160majs, D. (2014). Bacteriocin-encoding genes and ExPEC virulence determinants are associated in human fecal Escherichia coli strains. BMC Microbiol., 14.","DOI":"10.1186\/1471-2180-14-109"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.3389\/fmicb.2018.01207","article-title":"Antimicrobial Susceptibility of Escherichia coli and Salmonella spp. Isolates From Healthy Pigs in Australia: Results of a Pilot National Survey","volume":"9","author":"Kidsley","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"3300","DOI":"10.1017\/S0950268816001412","article-title":"Multilocus sequence typing and CTX-M characterization of ESBL-producing E. coli: A prospective single-centre study in Lower Saxony, Germany","volume":"144","author":"Gerhold","year":"2016","journal-title":"Epidemiol. Infect."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Ding, Y., Tang, X., Lu, P., Wu, B., Xu, Z., Liu, W., Zhang, R., Bei, W., Chen, H., and Tan, C. (2012). Clonal analysis and virulent traits of pathogenic extraintestinal Escherichia coli isolates from swine in China. BMC Vet. Res., 8.","DOI":"10.1186\/1746-6148-8-140"},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Reid, C.J., DeMaere, M.Z., and Djordjevic, S.P. (2018). Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogeny. Microb. Genom., 5.","DOI":"10.1099\/mgen.0.000225"},{"key":"ref_55","first-page":"62","article-title":"Some husbandry factors influencing weaning stresses in piglets","volume":"60","author":"Spencer","year":"1989","journal-title":"J. S. Afr. Vet. Assoc."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1688","DOI":"10.3389\/fmicb.2017.01688","article-title":"The Maturing Development of Gut Microbiota in Commercial Piglets during the Weaning Transition","volume":"8","author":"Chen","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Herrero-Fresno, A., Ahmed, S., Hansen, M.H., Denwood, M., Zachariasen, C., and Olsen, J.E. (2017). Genotype variation and genetic relationship among Escherichia coli from nursery pigs located in different pens in the same farm. BMC Microbiol., 17.","DOI":"10.1186\/s12866-016-0912-3"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Ahmed, S., Olsen, J.E., and Herrero-Fresno, A. (2017). The genetic diversity of commensal Escherichia coli strains isolated from non-antimicrobial treated pigs varies according to age group. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0178623"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1017\/S175173111200119X","article-title":"Effects of feeding finisher pigs with chicory or lupine feed for one week or two weeks before slaughter with respect to levels of Bifidobacteria and Campylobacter","volume":"7","author":"Jensen","year":"2013","journal-title":"Animal"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1152\/physrev.00045.2009","article-title":"Gut microbiota in health and disease","volume":"90","author":"Sekirov","year":"2010","journal-title":"Physiol. Rev."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Dawes, F.E., Kuzevski, A., Bettelheim, K.A., Hornitzky, M.A., Djordjevic, S.P., and Walker, M.J. (2010). Distribution of class 1 integrons with IS26-mediated deletions in their 3\u2032-conserved segments in Escherichia coli of human and animal origin. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0012754"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1016\/j.ijantimicag.2018.06.017","article-title":"Genomic analysis of multidrug-resistant Escherichia coli ST58 causing urosepsis","volume":"52","author":"McKinnon","year":"2018","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.1128\/AAC.47.3.1169-1172.2003","article-title":"A new sulfonamide resistance gene (sul3) in Escherichia coli is widespread in the pig population of Switzerland","volume":"47","author":"Perreten","year":"2003","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Billman-Jacobe, H., Liu, Y., Haites, R., Weaver, T., Robinson, L., Marenda, M., and Dyall-Smith, M. (2018). pSTM6-275, a Conjugative IncHI2 Plasmid of Salmonella enterica That Confers Antibiotic and Heavy-Metal Resistance under Changing Physiological Conditions. Antimicrob. Agents Chemother., 62.","DOI":"10.1128\/AAC.02357-17"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.plasmid.2016.02.002","article-title":"pCERC3 from a commensal ST95 Escherichia coli: A ColV virulence-multiresistance plasmid carrying a sul3-associated class 1 integron","volume":"84\u201385","author":"Moran","year":"2016","journal-title":"Plasmid"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1099\/jmm.0.034140-0","article-title":"Antimicrobial resistance and distribution of sul genes and integron-associated intI genes among uropathogenic Escherichia coli in Queensland, Australia","volume":"60","author":"Long","year":"2011","journal-title":"J. Med. Microbiol."},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Cummins, M.L., Reid, C.J., Roy Chowdhury, P., Bushell, R.N., Esbert, N., Tivendale, K.A., Noormohammadi, A.H., Islam, S., Marenda, M.S., and Browning, G.F. (2019). Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene. Microb. Genom., 5.","DOI":"10.1099\/mgen.0.000250"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"86","DOI":"10.3389\/fmicb.2013.00086","article-title":"Mobile elements, zoonotic pathogens and commensal bacteria: Conduits for the delivery of resistance genes into humans, production animals and soil microbiota","volume":"4","author":"Djordjevic","year":"2013","journal-title":"Front. Microbiol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"25312","DOI":"10.1038\/srep25312","article-title":"Co-spread of metal and antibiotic resistance within ST3-IncHI2 plasmids from E. coli isolates of food-producing animals","volume":"6","author":"Fang","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Reid, C.J., McKinnon, J., and Djordjevic, S.P. (2019). Clonal ST131-H22 Escherichia coli strains from a healthy pig and a human urinary tract infection carry highly similar resistance and virulence plasmids. Microb. Genom., 5.","DOI":"10.1099\/mgen.0.000295"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1186\/s13567-018-0562-6","article-title":"Phytochemicals as antibiotic alternatives to promote growth and enhance host health","volume":"49","author":"Lillehoj","year":"2018","journal-title":"Vet. Res."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1086\/315217","article-title":"Extended virulence genotypes of Escherichia coli strains from patients with urosepsis in relation to phylogeny and host compromise","volume":"181","author":"Johnson","year":"2000","journal-title":"J. Infect. Dis."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"574","DOI":"10.3389\/fmicb.2016.00574","article-title":"Characterization of Shiga Toxin Subtypes and Virulence Genes in Porcine Shiga Toxin-Producing Escherichia coli","volume":"7","author":"Baranzoni","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"3098","DOI":"10.3389\/fmicb.2019.03098","article-title":"Escherichia coli ST302: Genomic Analysis of Virulence Potential and Antimicrobial Resistance Mediated by Mobile Genetic Elements","volume":"10","author":"Jarocki","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"18","DOI":"10.3389\/fsufs.2019.00018","article-title":"Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia","volume":"3","author":"Wyrsch","year":"2019","journal-title":"Front. Sustain. Food Syst."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Wyrsch, E., Roy Chowdhury, P., Abraham, S., Santos, J., Darling, A.E., Charles, I.G., Chapman, T.A., and Djordjevic, S.P. (2015). Comparative genomic analysis of a multiple antimicrobial resistant enterotoxigenic E. coli O157 lineage from Australian pigs. BMC Genomics, 16.","DOI":"10.1186\/s12864-015-1382-y"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.tvjl.2018.12.015","article-title":"Multidrug resistance and multivirulence plasmids in enterotoxigenic and hybrid Shiga toxin-producing\/enterotoxigenic Escherichia coli isolated from diarrheic pigs in Switzerland","volume":"244","author":"Brilhante","year":"2019","journal-title":"Vet. J."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1016\/j.meegid.2016.09.008","article-title":"The role of IS26 in evolution of a derivative of the virulence plasmid of Salmonella enterica serovar Enteritidis which confers multiple drug resistance","volume":"45","author":"Rodicio","year":"2016","journal-title":"Infect. Genet. Evol."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/j.vetmic.2010.04.004","article-title":"Antimicrobial resistance and virulence gene profiles in multi-drug resistant enterotoxigenic Escherichia coli isolated from pigs with post-weaning diarrhoea","volume":"145","author":"Smith","year":"2010","journal-title":"Vet. Microbiol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/j.jgar.2015.08.002","article-title":"First detection of extended-spectrum cephalosporin- and fluoroquinolone-resistant Escherichia coli in Australian food-producing animals","volume":"3","author":"Abraham","year":"2015","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"2750","DOI":"10.1093\/jac\/dkx238","article-title":"IS26-mediated formation of a virulence and resistance plasmid in Salmonella Enteritidis","volume":"72","author":"Wong","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_82","unstructured":"(2019, August 03). Australian Pork Limited Submission to Foreign Policy White Paper\u2014Australian Pork Limited. Available online: https:\/\/australianpork.com.au\/wp-content\/uploads\/2013\/11\/170228_-APL-Submission-to-Foreign-Policy-White-Paper.pdf."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/8\/6\/843\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T09:35:42Z","timestamp":1760175342000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/8\/6\/843"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,6,4]]},"references-count":82,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2020,6]]}},"alternative-id":["microorganisms8060843"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms8060843","relation":{},"ISSN":["2076-2607"],"issn-type":[{"type":"electronic","value":"2076-2607"}],"subject":[],"published":{"date-parts":[[2020,6,4]]}}}