Insights into the evolution of pathogenicity of Escherichia coli from genomic analysis of intestinal E. coli of Marmota himalayana in Qinghai–Tibet plateau of China

Abstract

Escherichia coli is both of a widespread harmless gut commensal and a versatile pathogen of humans. Domestic animals are a well-known reservoir for pathogenic E. coli. However, studies of E. coli populations from wild animals that have been separated from human activities had been very limited. Here we obtained 580 isolates from intestinal contents of 116 wild Marmot Marmota himalayana from Qinghai–Tibet plateau, China, with five isolates per animal. We selected 125 (hereinafter referred to as strains) from the 580 isolates for genome sequencing, based on unique pulse field gel electrophoresis patterns and at least one isolate per animal. Whole genome sequence analysis revealed that all 125 strains carried at least one and the majority (79.2%) carried multiple virulence genes based on the analysis of 22 selected virulence genes. In particular, the majority of the strains carried virulence genes from different pathovars as potential 'hybrid pathogens'. The alleles of eight virulence genes from the Marmot E. coli were found to have diverged earlier than all known alleles from human and other animal E. coli. Phylogenetic analysis of the 125 Marmot E. coli genomes and 355 genomes selected from 1622 human and other E. coli strains identified two new phylogroups, G and H, both of which diverged earlier than the other phylogroups. Eight of the 12 well-known pathogenic E. coli lineages were found to share a most recent common ancestor with one or more Marmot E. coli strains. Our results suggested that the intestinal E. coli of the Marmots contained a diverse virulence gene pool and is potentially pathogenic to humans. These findings provided a new understanding of the evolutionary origin of pathogenic E. coli.

Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential

“…When the complete genomes of these strains were subsequently analyzed, they were placed between phylogroups F and B2 in the E. coli phylogeny. Similar data were obtained by other groups, one of them proposing a new phylogroup called G to describe these strains (Lu et al ., ; Kallonen et al ., ). In this work, we have described the diversity of this new phylogroup and proposed an easy assay to identify these strains.…”

“…Recently, this method has been adapted in silico to allow E. coli phylotyping using WGS data (Beghain et al, 2018). With the accumulation of WGS data, it is clear that some strains belong to a group intermediate between phylogroups F and B2 (Lu et al, 2016;Kallonen et al, 2017). These strains are closely related to, but distinct from, the phylogroup B2 strains and are assigned to phylogroup F with both in vitro and in silico Clermont methods (Beghain et al, 2018).…”

“…These strains are closely related to, but distinct from, the phylogroup B2 strains and are assigned to phylogroup F with both in vitro and in silico Clermont methods (Beghain et al, 2018). Some authors have proposed that this phylogroup be designated as phylogroup G (Lu et al, 2016).…”

Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling

“…Around 2010-2011, it became clear that group B1 also needed to be reconsidered, and fourteen strains were allocated into group C [52], which was in line with a previous suggestion [48] based on phylogenetic features of four strains. In 2016, two new isolates of intestinal E. coli of Marmota himalayana were characterized [53]. Together with other bacteria with partially assembled genomes, they formed a branch on the phylogenetic tree between groups F and B2 and were assigned to phylogroup G [46].…”

Phenolic profiling and antibacterial potential of Saudi Arabian native date palm (Phoenix dactylifera) cultivars

“…It includes several categories of enterotoxigenic, diffuse adherent, enteropathogenic, enterohemorrhagic, enteroaggregative, enteroinvasive, and extraintestinal pathogenic E. coli. [25,26] In order to provide further detailed information on phenolic compounds and antibacterial activities of Date Palm (Phoenix dactylifera), the current study was devoted to investigate and compare three different highly consumable varieties of date palm (Phoenix dactylifera) cultivars, namely Ajwa, Khalas Alkharj and Al-Qasim for their broad-spectrum antibacterial effect and phenolic compounds. The current study was carried out to revealed the comparative analysis by experimental evidence in order to provide detailed information on phenolic compounds profiling and antibacterial activities of three different local and highly consumable varieties of date palm (Phoenix dactylifera) cultivars, namely Ajwa, Khalas Alkharj, and Al-Qasim.…”