Genomic Epidemiology of Shiga Toxin-Producing Escherichia coli Isolated from the Livestock-Food-Human Interface in South America.

Nicolás Galarce,Lisette Lapierre,Raúl Alegría-Morán,Danny Fuentes-Castillo,Víctor Martínez,Beatriz Escobar,Nilton Lincopan,Víctor Neira,Elder Sano,Javiera Cornejo,Fernando Sánchez,Timothy Johnson

doi:10.3390/ani11071845

Abstract

Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens responsible for causing food-borne diseases in humans. While South America has the highest incidence of human STEC infections, information about the genomic characteristics of the circulating strains is scarce. The aim of this study was to analyze genomic data of STEC strains isolated in South America from cattle, beef, and humans; predicting the antibiotic resistome, serotypes, sequence types (STs), clonal complexes (CCs) and phylogenomic backgrounds. A total of 130 whole genome sequences of STEC strains were analyzed, where 39.2% were isolated from cattle, 36.9% from beef, and 23.8% from humans. The ST11 was the most predicted (20.8%) and included O-:H7 (10.8%) and O157:H7 (10%) serotypes. The successful expansion of non-O157 clones such as ST16/CC29-O111:H8 and ST21/CC29-O26:H11 is highlighted, suggesting multilateral trade and travel. Virulome analyses showed that the predominant stx subtype was stx2a (54.6%); most strains carried ehaA (96.2%), iha (91.5%) and lpfA (77.7%) genes. We present genomic data that can be used to support the surveillance of STEC strains circulating at the livestock-food-human interface in South America, in order to control the spread of critical clones "from farm to table".

Highlights

Shiga toxin-producing Escherichia coli (STEC) is a zoonotic diarrheagenic pathotype ofE. coli with the common characteristic of producing cytotoxins of the Shiga toxin family (Stx) [1]
The aim of this study was to analyze genomic data of STEC strains isolated from cattle in Chile, and to perform a comparative genomic analysis of STEC strains circulating at the cattle-beef-human interface in South America, extracting clinically and epidemiologically relevant information, including virulome, antimicrobial resistance genes, sequence types, clonal complexes, and phylogenomics, in order to provide relevant epidemiological data to surveillance programs at national and international level, under a One Health approach
We report the genomic characteristics of STEC strains circulating in the livestock-beefhuman interface in South America, highlighting the successful expansion of O157:H7 (ST11)

Summary

Introduction

Shiga toxin-producing Escherichia coli (STEC) is a zoonotic diarrheagenic pathotype of. E. coli with the common characteristic of producing cytotoxins of the Shiga toxin family (Stx) [1]. Their participation in different diarrheal processes in animals is recognized, their frequency is low; they are considered as reservoirs and disseminators of STEC. Gut colonization favors transmission to other animals, the environment, and humans [2]. Cattle, which lack cellular receptors for Stx [3], are asymptomatic carriers of STEC strains and are recognized as the main source for human STEC infections. Some animals known as “super-shedders” can excrete more than

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