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

Elisa Massella,Kay Anantanawat,Silvia Piva,Federica Giacometti,Cameron J Reid,Steven P Djordjevic,Andrea Serraino,Max L Cummins,Tiziana Zingali

doi:10.3390/antibiotics9110782

Elisa Massella, Kay Anantanawat + Show 7 more

Open Access

https://doi.org/10.3390/antibiotics9110782

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Abstract

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.

Highlights

Antimicrobial resistance has been recognized as one of the world’s most pressing public health problems, with implications for human and veterinary medicine, wildlife and environmental ecosystems.In recent decades we have witnessed a dramatic spread and diffusion of multidrug resistant (MDR)pathogens
Horizontal gene transfer (HGT) of antimicrobial resistance genes (ARGs) is mediated by mobile genetic elements (MGEs) and facilitated by the interconnection between bacteria, their hosts and the environment [3]
The European Union has defined antimicrobial resistance (AMR) as a special health issue to be monitored by epidemiological surveillance systems [9]

Summary

Introduction

Antimicrobial resistance has been recognized as one of the world’s most pressing public health problems, with implications for human and veterinary medicine, wildlife and environmental ecosystems.In recent decades we have witnessed a dramatic spread and diffusion of multidrug resistant (MDR)pathogens. Animals (livestock, companion animals, wildlife), the community, hospital and industrial settings (including food-production) have been investigated as possible sources of AMR [4,5,6]. The interaction between these environments is complex and understanding vectors of AMR transfer is a central tenet in mitigation efforts to limit its impact. Data describing spatial and temporal trends of AMR carriage are essential for epidemiological evaluation and preventive measure implementation In this context, the European Union has defined AMR as a special health issue to be monitored by epidemiological surveillance systems [9]

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