Antimicrobial Resistance Profile and ExPEC Virulence Potential in Commensal Escherichia coli of Multiple Sources.

Elisa Massella,Andrea Serraino,Federica Savini,Steven P Djordjevic,Federica Giacometti,Lia Bardasi,Silvia Piva,Cameron J Reid,Paola Massi,Silva Rubini,Laura Fiorentini,Paolo Bonilauri,Cristina Bacci,Giuseppe Merialdi

doi:10.3390/antibiotics10040351

Abstract

We recently described the genetic antimicrobial resistance and virulence profile of a collection of 279 commensal E. coli of food-producing animal (FPA), pet, wildlife and human origin. Phenotypic antimicrobial resistance (AMR) and the role of commensal E. coli as reservoir of extra-intestinal pathogenic Escherichia coli (ExPEC) virulence-associated genes (VAGs) or as potential ExPEC pathogens were evaluated. The most common phenotypic resistance was to tetracycline (76/279, 27.24%), sulfamethoxazole/trimethoprim (73/279, 26.16%), streptomycin and sulfisoxazole (71/279, 25.45% both) among the overall collection. Poultry and rabbit were the sources mostly associated to AMR, with a significant resistance rate (p > 0.01) to quinolones, streptomycin, sulphonamides, tetracycline and, only for poultry, to ampicillin and chloramphenicol. Finally, rabbit was the source mostly associated to colistin resistance. Different pandemic (ST69/69*, ST95, ST131) and emerging (ST10/ST10*, ST23, ST58, ST117, ST405, ST648) ExPEC sequence types (STs) were identified among the collection, especially in poultry source. Both ST groups carried high number of ExPEC VAGs (pandemic ExPEC STs, mean = 8.92; emerging ExPEC STs, mean = 6.43) and showed phenotypic resistance to different antimicrobials (pandemic ExPEC STs, mean = 2.23; emerging ExPEC STs, mean = 2.43), suggesting their role as potential ExPEC pathogens. Variable phenotypic resistance and ExPEC VAG distribution was also observed in uncommon ExPEC lineages, suggesting commensal flora as a potential reservoir of virulence (mean = 3.80) and antimicrobial resistance (mean = 1.69) determinants.

Highlights

Escherichia coli represents a commensal colonizer of human and animal gastrointestinal microbiota [1] and it is the most frequently isolated Gram-negative pathogen impacting human health [2]
In our recent paper [33] we described the population structure, antimicrobial resistance gene (ARG) and virulence-associated genes (VAGs) carriage in a collection of 279 E. coli indicator of animal, food and human origin collected in Italy
Different typical extraintestinal pathogenic Escherichia coli (ExPEC) VAGs and pandemic and emerging ExPEC sequence types (STs) were observed among the overall collection. Considering these previous findings, the current study aims to investigate (i) phenotypic antimicrobial resistance profile of the collection and concordance with genetic AMR profile previously identified, in order to establish the potential AMR risk associated with animals, food and human, (ii) ExPEC virulence potential of commensal E. coli, association with concerning AMR profile and their role of ExPEC VAG reservoir, (iii) phylogroup distribution, considering the revisited phylotyping method proposed by Clermont et al, (2013) [6], for further epidemiological evaluations

Summary

Introduction

Escherichia coli represents a commensal colonizer of human and animal gastrointestinal microbiota [1] and it is the most frequently isolated Gram-negative pathogen impacting human health [2]. ExPEC represents one of the most common causes of bloodstream infections and community/hospital associated urinary tract infections worldwide [7,8]). They are responsible for other extraintestinal diseases, being an important cause of neonatal meningitis [1]. Multiresistant ExPEC strains constitute ongoing healthcare concern and are associated with an increase in infection severity, treatment failure, hospitalisations and mortality, with growing costs for health care [2]. ExPEC mostly belonged to phylogroup B2 and, to a lesser extent, to phylogroup D [9,10]

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