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

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.

Genomic characteristics, virulence and antimicrobial resistance in avian pathogenic Escherichia coli MTR_BAU02 strain isolated from layer farms in Bangladesh

“…Phylogenetic analysis using complete genomes (WGS) provides a greater resolution that helps to determine the evolutionary relatedness among isolates. This type of analysis allows automated and more robust epidemiological surveillance [41, 42]. In this study, phylogenetic analysis of the 34 E. coli genomes was performed to comparing the evolutionary relatedness of the strains.…”

“…There are reports that resistant E. coli strains might enhance antimicrobial resistance (AMR) in other organisms (pathogenic and non-pathogenic) within gastrointestinal tract of the chicken [3,16], and help in transmitting and disseminating multidrug resistant (MDR) strains, and antimicrobial resistance (AMR) genes between animal and human pathogens [3]. Many of the earlier studies have explored the association between pathogenic traits of APEC, and their virulence factors associated genes (VFGs) repertoire [40][41][42][43]; however, potential pathogenic traits associated with APEC strains warrant the attention into the potential role of VGFs, MDR properties, and their cross-talk with specific host.…”

Research progress on detection techniques for point-of-care testing of foodborne pathogens

“…There was a significant difference in the microbial community structure among the sample types ( p < 0.1). Gutierrez et al (2021) sequenced 62 cases of Shiga toxin-producing E . coli (STEC) isolated from Chile using MiSeq Illumina.…”

“…There was a significant difference in the microbial community structure among the sample types (p < 0.1). Gutierrez et al (2021) sequenced 62 cases of Shiga toxinproducing E. coli (STEC) isolated from Chile using MiSeq Illumina. The results indicated that there may be local emerging STEC with unique features, nevertheless, no molecular markers were detected.…”

Molecular characterization and phylogeny of Shiga toxin-producing Escherichia coli derived from cattle farm

“…WGS data have the potential to provide powerful, high-level phylogenetic analysis and to show insight into the evolutionary background of the outbreak strains by using quantifiable genetic differences (Baltasar et al, 2014 ; Mikhail et al, 2018 ). For example, the comparison of 62 STEC local isolates from Chile with STEC isolated from the rest of the world by core genome multilocus sequence typing (cgMLST) typing method showed Chile STEC did not cluster with genomes of the rest of the world, suggesting local STEC isolates and STEC isolated from worldwide were not phylogenetical (Smith et al, 2014 ; Gutierrez et al, 2021 ) and indicating STEC phylogeny was affected by the origin of geographical isolation.…”