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

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

doi:10.3389/fmicb.2020.622663

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

Front Microbiol. 2021 Jan 18:11:622663. doi: 10.3389/fmicb.2020.622663. eCollection 2020.

Authors

Sebastián Gutiérrez¹, Leonela Díaz¹, Angélica Reyes-Jara¹, Xun Yang², Jianghong Meng^{2

3}, Narjol González-Escalona⁴, Magaly Toro¹

Affiliations

¹ Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Macul, Santiago, Chile.
² Department of Nutrition and Food Science, University of Maryland, College Park, College Park, MD, United States.
³ Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, College Park, MD, United States.
⁴ U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD, United States.

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.

Keywords: STEC; WGS; diversity; genomics; non-O157 E. coli.