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Article

Snapshot Study of Whole Genome Sequences of Escherichia coli from Healthy Companion Animals, Livestock, Wildlife, Humans and Food in Italy

1
Department of Veterinary Medical Sciences, University of Bologna, 40126 Bologna, Italy
2
The ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
*
Author to whom correspondence should be addressed.
Antibiotics 2020, 9(11), 782; https://doi.org/10.3390/antibiotics9110782
Received: 15 September 2020 / Revised: 4 November 2020 / Accepted: 5 November 2020 / Published: 6 November 2020
(This article belongs to the Special Issue Spread of Multidrug-Resistant Microorganisms )
Animals, humans and food are all interconnected sources of antimicrobial resistance (AMR), allowing extensive and rapid exchange of AMR bacteria and genes. Whole genome sequencing (WGS) was used to characterize 279 Escherichia coli isolates obtained from animals (livestock, companion animals, wildlife), food and humans in Italy. E. coli predominantly belonged to commensal phylogroups B1 (46.6%) and A (29%) using the original Clermont criteria. One hundred and thirty-six sequence types (STs) were observed, including different pandemic (ST69, ST95, ST131) and emerging (ST10, ST23, ST58, ST117, ST405, ST648) extraintestinal pathogenic Escherichia coli (ExPEC) lineages. Eight antimicrobial resistance genes (ARGs) and five chromosomal mutations conferring resistance to highest priority critically important antimicrobials (HP-CIAs) were identified (qnrS1, qnrB19, mcr-1, blaCTX-M1,15,55, blaCMY-2, gyrA/parC/parE, ampC and pmrB). Twenty-two class 1 integron arrangements in 34 strains were characterized and 11 ARGs were designated as intI1 related gene cassettes (aadA1, aadA2, aadA5, aad23, ant2_Ia, dfrA1, dfrA7, dfrA14, dfrA12, dfrA17, cmlA1). Notably, most intI1 positive strains belonged to rabbit (38%) and poultry (24%) sources. Three rabbit samples carried the mcr-1 colistin resistance gene in association with IS6 family insertion elements. Poultry meat harbored some of the most prominent ExPEC STs, including ST131, ST69, ST10, ST23, and ST117. Wildlife showed a high average number of virulence-associated genes (VAGs) (mean = 10), mostly associated with an ExPEC pathotype and some predominant ExPEC lineages (ST23, ST117, ST648) were identified. View Full-Text
Keywords: commensal Escherichia coli; antimicrobial resistance; whole genome sequencing; genomic epidemiology commensal Escherichia coli; antimicrobial resistance; whole genome sequencing; genomic epidemiology
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MDPI and ACS Style

Massella, E.; Reid, C.J.; Cummins, M.L.; Anantanawat, K.; Zingali, T.; Serraino, A.; Piva, S.; Giacometti, F.; Djordjevic, S.P. Snapshot Study of Whole Genome Sequences of Escherichia coli from Healthy Companion Animals, Livestock, Wildlife, Humans and Food in Italy. Antibiotics 2020, 9, 782. https://doi.org/10.3390/antibiotics9110782

AMA Style

Massella E, Reid CJ, Cummins ML, Anantanawat K, Zingali T, Serraino A, Piva S, Giacometti F, Djordjevic SP. Snapshot Study of Whole Genome Sequences of Escherichia coli from Healthy Companion Animals, Livestock, Wildlife, Humans and Food in Italy. Antibiotics. 2020; 9(11):782. https://doi.org/10.3390/antibiotics9110782

Chicago/Turabian Style

Massella, Elisa, Cameron J. Reid, Max L. Cummins, Kay Anantanawat, Tiziana Zingali, Andrea Serraino, Silvia Piva, Federica Giacometti, and Steven P. Djordjevic. 2020. "Snapshot Study of Whole Genome Sequences of Escherichia coli from Healthy Companion Animals, Livestock, Wildlife, Humans and Food in Italy" Antibiotics 9, no. 11: 782. https://doi.org/10.3390/antibiotics9110782

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