Abstract
Enterotoxigenic Escherichia coli (ETEC) is one of the most common diarrheal pathogens in the low- and middle-income regions of the world, however a systematic examination of the genomic content of isolates from Chile has not yet been undertaken. Whole genome sequencing and comparative analysis of a collection of 125 ETEC isolates from three geographic locations in Chile, allowed the interrogation of phylogenomic groups, sequence types and genes specific to isolates from the different geographic locations. A total of 80.8% (101/125) of the ETEC isolates were identified in E. coli phylogroup A, 15.2% (19/125) in phylogroup B, and 4.0% (5/125) in phylogroup E. The over-representation of genomes in phylogroup A was significantly different from other global ETEC genomic studies. The Chilean ETEC isolates could be further subdivided into sub-clades similar to previously defined global ETEC reference lineages that had conserved multi-locus sequence types and toxin profiles. Comparison of the gene content of the Chilean ETEC identified genes that were unique based on geographic location within Chile, phylogenomic classifications or sequence type. Completion of a limited number of genomes provided insight into the ETEC plasmid content, which is conserved in some phylogenomic groups and not conserved in others. These findings suggest that the Chilean ETEC isolates contain unique virulence factor combinations and genomic content compared to global reference ETEC isolates.
Highlights
We identified genomic content and virulence factor combinations that are common and unique to enterotoxigenic E. coli (ETEC) in Chile compared to a global collection of ETEC
The pathogenic variant of Escherichia coli known as enterotoxigenic E. coli (ETEC) has been implicated in 1 billion cases of diarrhea annually [1], and recent studies, such as the Global Enteric Multicenter Study (GEMS), has further confirmed that ETEC is a significant global pathogen [2]
At least 27 known or putative colonization factors (CFs) have been described in the literature [18, 19] and more CFs have been identified in genomic studies [20], but have yet to be functionally characterized [13, 21]
Summary
The pathogenic variant (pathovar) of Escherichia coli known as enterotoxigenic E. coli (ETEC) has been implicated in 1 billion cases of diarrhea annually [1], and recent studies, such as the Global Enteric Multicenter Study (GEMS), has further confirmed that ETEC is a significant global pathogen [2]. While functional characterization of the contribution of EatA and EtpA ETEC virulence is ongoing, EatA appears to accelerate toxin delivery by degrading MUC2, the major mucin secreted by gastrointestinal goblet cells [25], and EtpA modulates adhesion to blood group antigens [26, 27]. Both EtpA and EatA are immunogenic in humans [28] and have been demonstrated to be protective antigens in animal models [25, 29, 30]
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