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

Fernando Sánchez, Verónica Fuenzalida, Romina Ramos, Beatriz Escobar, Víctor Neira, Consuelo Borie, Lisette Lapierre, Paulina López, Lucas Venegas, Phillip Dettleff, Timothy Johnson, Danny Fuentes-Castillo, Nilton Lincopan, Nicolás Galarce

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Pages (from-to)226-238
Number of pages13
JournalZoonoses and Public Health
Volume68
Issue number3
DOIs
StateAccepted/In press - 2021

Bibliographical note

Funding Information:
We would like to thank Dr. David Montero, from the Enteropathogens Laboratory of the Instituto de Ciencias Biomédicas of the Universidad de Chile, for his kind contribution in the search of LAA PAI, and Drs. Belén Agüero and Valentina Valdés for DNA processing. Nilton Lincopan is a research fellow of CNPq (Grant 312249/2017‐9). Given the nature of the samples obtained, no ethics approvals were required.

Funding Information:
This work was supported by the Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) Grant/Award Number: 11170363.

Funding Information:
This work was supported by the Fondo Nacional de Desarrollo Cient?fico y Tecnol?gico (FONDECYT) Grant/Award Number: 11170363. We would like to thank Dr. David Montero, from the Enteropathogens Laboratory of the Instituto de Ciencias Biom?dicas of the Universidad de Chile, for his kind contribution in the search of LAA PAI, and Drs. Bel?n Ag?ero and Valentina Vald?s for DNA processing. Nilton Lincopan is a research fellow of CNPq (Grant 312249/2017-9). Given the nature of the samples obtained, no ethics approvals were required.

Publisher Copyright:
© 2021 Wiley-VCH GmbH

Keywords

  • Escherichia coli
  • Shiga toxin
  • antimicrobial resistance
  • foodborne diseases
  • whole-genome sequencing

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