A year after the implementation of WGS for food safety purposes in the United States, outbreaks were reported faster, and more cases were linked to an outbreak than before ( Jagadeesan et al., 2019). This technique provides high discriminating power among isolates ( Nadon et al., 2017 Rantsiou et al., 2018 Simon et al., 2018 Jenkins et al., 2019). Many countries currently study foodborne pathogens and investigate outbreaks by analysis of the Whole Genome Sequencing (WGS) of the isolates. Many of these studies have used techniques such as MLST, traditional serotyping, and PFGE to study STEC isolates ( Feng et al., 2014 Cadona et al., 2016 Ferdous et al., 2016 Jajarmi et al., 2017 Nakamura et al., 2018). Reports indicate a wide variety of serotypes and sequence types of STEC isolated in Iran, Japan, Argentina, Brazil, among others, from diverse sources. STEC O157 has been the most studied serogroup, but other serotypes isolated from human clinical cases, animals, foods, and the environment have been also characterized.

coli isolated from different sources have been characterized worldwide. Chilean law dictates that STEC is a pathogen under mandatory laboratory surveillance, so every clinical laboratory must send their isolates to the National Public Health laboratory (ISP) for confirmation.

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). In Latin America, STEC is endemic and represents 2% of cases of acute diarrhea and up to 30% of bloody diarrhea, and Chile, Uruguay, and Argentina are the most affected countries in the area ( Torres et al., 2018). It is estimated that STEC causes over 2,800,000 cases/year worldwide and 3,890 cases of HUS. 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). The main STEC virulence factors are Shiga toxins, which are encoded by genes stx 1 and stx 2 and their subtypes. Cattle are the main STEC reservoir, and beef has been frequently associated with human disease, but STEC has been also isolated from other sources ( Álvarez-Suárez et al., 2016 Sanches et al., 2017 Rios et al., 2019). Shiga toxin-producing Escherichia coli (STEC) is a significant pathogen it can cause serious diseases in humans, not only as sporadic cases but also as outbreaks of foodborne disease ( FAO/WHO, 2018). Therefore, there might be elements such as a syntenic organization that might explain differential clustering detected between local and worldwide STEC. Our results showed that there may be local emerging STEC with unique features, nevertheless, no molecular markers were detected. The pangenome of our STEC collection was 11,650 genes, but we did not identify distinct molecular markers of 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. Genomes in our local collection were grouped based on serogroup and sequence type, and clusters were formed within local STEC. 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. In silico typing was determined using tools of the Center Genomic Epidemiology, Denmark University (CGE/DTU). We sequenced 62 STEC isolated in Chile using MiSeq Illumina. 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. Their main reservoir is cattle, and ground beef has been frequently associated with disease and outbreaks.

Shiga toxin-producing Escherichia coli (STEC) causes foodborne outbreaks that can lead to complications such as hemolytic uremic syndrome. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD, United States

3Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, College Park, MD, United States.

2Department of Nutrition and Food Science, University of Maryland, College Park, College Park, MD, United States.1Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Macul, Santiago, Chile.Sebastián Gutiérrez 1, Leonela Díaz 1, Angélica Reyes-Jara 1, Xun Yang 2, Jianghong Meng 2,3, Narjol González-Escalona 4 and Magaly Toro 1*

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