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Porcine commensal Escherichia coli: A reservoir for class 1 integrons associated with IS26

By Cameron J. Reid, Ethan R. Wyrsch, Piklu Roy Chowdhury, Tiziana Zingali, Michael Liu, Aaron E. Darling, Toni A. Chapman, Steven P. Djordjevic

Posted 03 Jul 2017
bioRxiv DOI: 10.1101/158808 (published DOI: 10.1099/mgen.0.000143)

Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial resistance and virulence-associated genes (VAGs) and the zoonotic potential of commensal Escherichia coli from swine is largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilisation of antimicrobial resistance genes between food animals and the environment. Here, we report whole genome sequence analysis of 141 E. coli from the faeces of healthy pigs. Most strains belonged to phylogroups A and B1 and carried i) a class 1 integron; ii) VAGs linked with extraintestinal infection in humans; iii) antimicrobial resistance genes blaTEM, aphA1, cmlA, strAB, tet(A)A, dfrA12, dfrA5, sul1, sul2, sul3; iv) IS26; and v) heavy metal resistance genes (merA, cusA, terA). Carriage of the sulphonamide resistance gene sul3 was notable in this study. The 141 strains belonged to 42 multilocus sequence types, but clonal complex 10 featured prominently. Structurally diverse class 1 integrons that were frequently associated with IS26 carried unique genetic features that were also identified in extraintestinal pathogenic E. coli (ExPEC) from humans. This study provides the first detailed genomic analysis and point of reference for commensal E. coli of porcine origin, facilitating tracking of specific lineages and the mobile resistance genes they carry.

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