Genomic features and antimicrobial resistance patterns of Shiga toxin‐producing Escherichia coli strains isolated from food in Chile

Abstract

Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen that causes severe illness in humans, often associated with foodborne outbreaks. Antimicrobial resistance among foodborne E. coli has increased over the last decades becoming a public health issue. In this study, the presence and features of STEC were investigated in samples of meat, seafood, vegetables and ready-to-eat street-vended food collected in Chile, using a genomic and microbiological approach. Phenotypic and genotypic antimicrobial resistance profiles were determined, and serotype, phylogroup, sequence type (ST) and phylogenomics were predicted using bioinformatic tools. Three thousand three hundred samples collected in 2019 were screened, of which 18 were positive for STEC strains (0.5%), with stx2a (61.1%) being the predominant stx subtype. The presence of the virulence genes lpfA (100%), iha and ehaA (94.4%), and ehxA, hlyA and saa (83.3%) was confirmed among the STEC strains; the Locus of adhesion and autoaggregation (LAA) was predicted in 14 (77.8%) strains. Strains displayed resistance to colistin (100%), and intermediate resistance to enrofloxacin (11.1%) and chloramphenicol (5.6%). In this regard, mutations in the two-component regulatory system genes pmrA (S29G), pmrB (D283G) and phoP (I44L), and the presence of the qnrB19 gene were confirmed. STEC strains belonged to ST11231 (38.9%), ST297 and ST58 (16.7% each), and ST1635, ST11232, ST446, ST442 and ST54 (5.6% each), and the most frequently detected serotypes were O113:H21 (44.4%), O130:H11 and O116:H21 (16.7% each), and O174:H21 (11.1%). Strains belonging to the international ST58 showed genomic relatedness with worldwide strains from human and non-human sources. Our study reports for the first time the genomic profile of STEC strains isolated from food in Chile, highlighting the presence of international clones and sequence types commonly associated with human infections in different geographical regions, as well as the convergence of virulence and resistance in STEC lineages circulating in this country. | 227 SÁNCHEZ Et al.

Risk Factors for Positivity to Shiga Toxin-Producing Escherichia coli and Salmonella enterica in Backyard Production Systems Animals from Metropolitana Region, Chile: A Threat to Public Health?

“…Recent reports in Chile indicate STEC positivity rates of 17% in cattle and 1% in slaughtered pigs [48]. In addition, reports on meat, seafood, vegetables and ready-toeat street-vended food samples indicate 0.5% positivity (18/3300) [77]. However, the results obtained for STEC in this study are the first reported at BPS level in Chile.…”

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

“…The stx subtype most frequently detected was stx2a (54.6%, n = 71), followed by stx1a (26.9%, n = 35), stx2c (22.3%, n = 29), stx2d (16.2%, n = 21), stx2b and stx2g (1.5%, n = 2), and stx1c (0.8%, n = 1). Among the other virulence genes assessed, the most frequently detected was ehaA (96.2%, n = 125), followed by iha Studies focusing on the AMR of STEC strains isolated from the livestock-beef-human interface in South America are scarce [38,41,[61][62][63]. In this study, genomic analysis revealed a low prevalence of resistance genes.…”

“…Serotypes O157:H7 and O113:H21 have been the most frequently detected in cattle, beef, other foodstuffs, and humans in South American countries [19,55,61,[84][85][86]. In silico analysis confirmed that 96.3% of the O157:H7 strains were isolated in Argentina from beef and human clinical samples, while all O113:H21 strains were isolated in Chile from beef and cattle samples, suggesting selection and predominance of specific serotypes within each country.…”

“…STEC strains of the ST58 have been present in Chile (cattle) and Brazil (humans) [21,61], and have been isolated from cattle in Sweden [90]. Strikingly, as well as the ST223 (alleles adk-6, fumC-4, gyrB-4, icd-18, mdh-24, purA-8, recA-14), the ST58 (alleles adk-6, fumC-4, gyrB-4, icd-16, mdh-24, purA-8, recA-14) is a single-locus variant of the ST155 (alleles adk-6, fumC-4, gyrB-14, icd-16, mdh-24, purA-8, recA-14), which has been designated as the primary founder of the CC155.…”

“…MLST typing revealed the presence of 41 STs among the circulating STEC strains, most of them belonging to ST11 (CC11) (20.8%, n = 27), followed by ST297 (9.2%, n = 12), and ST58 (CC155) (5.4%, n = 7). Figure 1 shows the distribution of the STs of STEC strains circulating in South America, based on analysis of publicly available genomes and data obtained from previous surveillance studies [21,39,[52][53][54][55][56]61]. Of clinical interest, ST677, ST58, ST16, ST342, and ST11 carried multiple resistance genes.…”