Whole-Genome Phylogenetic Analysis Reveals a Wide Diversity of Non-O157 STEC Isolated From Ground Beef and Cattle Feces.

Sebastián Gutiérrez,Jianghong Meng,Angélica Reyes-Jara,Xun Yang,Leonela Díaz,Narjol González-Escalona,Magaly Toro

doi:10.3389/fmicb.2020.622663

Abstract

Shiga toxin-producing Escherichia coli (STEC) causes foodborne outbreaks that can lead to complications such as hemolytic uremic syndrome. Their main reservoir is cattle, and ground beef has been frequently associated with disease and outbreaks. In this study, we attempted to understand the genetic relationship among STEC isolated in Chile from different sources, their relationship to STEC from the rest of the world, and to identify molecular markers of Chilean STEC. We sequenced 62 STEC isolated in Chile using MiSeq Illumina. In silico typing was determined using tools of the Center Genomic Epidemiology, Denmark University (CGE/DTU). Genomes of our local STEC collection were compared with 113 STEC isolated worldwide through a core genome MLST (cgMLST) approach, and we also searched for distinct genes to be used as molecular markers of Chilean isolates. Genomes in our local collection were grouped based on serogroup and sequence type, and clusters were formed within local STEC. In the worldwide STEC analysis, Chilean STEC did not cluster with genomes of the rest of the world suggesting that they are not phylogenetically related to previously described STEC. The pangenome of our STEC collection was 11,650 genes, but we did not identify distinct molecular markers of local STEC. Our results showed that there may be local emerging STEC with unique features, nevertheless, no molecular markers were detected. Therefore, there might be elements such as a syntenic organization that might explain differential clustering detected between local and worldwide STEC.

Highlights

Shiga toxin-producing Escherichia coli (STEC) is a significant pathogen; it can cause serious diseases in humans, as sporadic cases and as outbreaks of foodborne disease (FAO/WHO, 2018)
This study demonstrated the diversity among O157 STEC and found 37 different PFGE profiles among 39 isolates
To select candidate genes, we compared both lists: core genes of our local STEC collection versus those present only in the template but not in E. coli K-12. In this way we identified genes that were present in all STEC in our collection but not in E. coli K-12

Summary

Introduction

Shiga toxin-producing Escherichia coli (STEC) is a significant pathogen; it can cause serious diseases in humans, as sporadic cases and as outbreaks of foodborne disease (FAO/WHO, 2018). The main STEC virulence factors are Shiga toxins, which are encoded. Shiga toxins are required for STEC pathogenicity and play a key role in complications such as hemorrhagic colitis and hemolytic uremic syndrome (HUS) (FAO/WHO, 2018). It is estimated that STEC causes over 2,800,000 cases/year worldwide and 3,890 cases of HUS. STEC is considered an emergent pathogen in Chile; the main transmission route is through contaminated foods affecting mainly children between 6 months and 4 years, and mortality rates reach 3% (Vidal et al, 2010; ISP, 2017; Cavagnaro, 2019). The serotypes most frequently causing disease in 2010–2016 were O157:H7 (55.7%), O26:H11 (28.5%), and O26:H- (6.4%) (ISP, 2017)

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