Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination

Abstract

BackgroundEscherichia coli strains are commonly found in the gut microflora of warm-blooded animals. These strains can be assigned to one of the four main phylogenetic groups, A, B1, B2 and D, which can be divided into seven subgroups (A0, A1, B1, B22, B23, D1 and D2), according to the combination of the three genetic markers chuA, yjaA and DNA fragment TspE4.C2. Distinct studies have demonstrated that these phylo-groups differ in the presence of virulence factors, ecological niches and life-history. Therefore, the aim of this work was to analyze the distribution of these E. coli phylo-groups in 94 human strains, 13 chicken strains, 50 cow strains, 16 goat strains, 39 pig strains and 29 sheep strains and to verify the potential of this analysis to investigate the source of fecal contamination.ResultsThe results indicated that the distribution of phylogenetic groups, subgroups and genetic markers is non-random in the hosts analyzed. Strains from group B1 were present in all hosts analyzed but were more prevalent in cow, goat and sheep samples. Subgroup B23 was only found in human samples. The diversity and the similarity indexes have indicated a similarity between the E. coli population structure of human and pig samples and among cow, goat and sheep samples. Correspondence analysis using contingence tables of subgroups, groups and genetic markers frequencies allowed the visualization of the differences among animal samples and the identification of the animal source of an external validation set. The classifier tools Binary logistic regression and Partial least square -- discriminant analysis, using the genetic markers profile of the strains, differentiated the herbivorous from the omnivorous strains, with an average error rate of 17%.ConclusionsThis is the first work, as far as we are aware, that identifies the major source of fecal contamination of a pool of strains instead of a unique strain. We concluded that the analysis of the E. coli population structure can be useful as a supplementary bacterial source tracking tool.

Type II toxin–antitoxin systems are unevenly distributed among Escherichia coli phylogroups

“…However, the rationale behind this observation is challenging, as our knowledge of the role of TAs in bacteria, especially chromosomal TAs, is controversial (Tsilibaris et al, 2007;Van Melderen, 2010;Wang & Wood, 2011;Yamaguchi & Inouye, 2011). Nevertheless, another feature may distinguish the B2 group from the other E. coli phylogroups, besides its ancestral position (Chaudhuri & Henderson, 2012), unique virulence properties (Johnson et al, 2001), distinct metabolic networks (Vieira et al, 2011), highest genetic diversity (Tenaillon et al, 2010), specialized host adaptation (Carlos et al, 2010) and potential subspecies status (Tenaillon et al, 2010). Therefore, we analysed our data in this context.…”

“…Regarding lifestyle and host preferences of E. coli, groups A and B1 are considered to be 'generalists', colonizing a broad host range (Gordon & Cowling, 2003;Carlos et al, 2010). Moreover, the latter predominate among E. coli strains with the ability to survive in the environment (Walk et al, 2007).…”

“…enterohaemorrhagic, enteroinvasive and enterotoxigenic E. coli pathovars, belong to groups A, B1 or D (Chaudhuri & Henderson, 2012). Furthermore, the E. coli phylogroups also differ with regard to growth rate (Gordon & Cowling, 2003;Walk et al, 2007;Carlos et al, 2010), genome size (Bergthorsson & Ochman, 1998), metabolic networks (Vieira et al, 2011) and antibiotic resistance profiles (Bukh et al, 2009). Therefore, we assumed the existence of a potential link between TAs and E. coli phylogeny, as these genetic elements are ubiquitous in E. coli genomes, and appear to be implicated in the cell physiology at various levels.…”

The type 1 pili regulator gene fimX and pathogenicity island PAI-X as molecular markers of uropathogenic Escherichia coli

“…Phylogenetic group analysis was performed as previously described ( Consistent with previous results (Carlos et al, 2010), commensal E. coli of non-human origin contained a larger percentage of group B1 strains (46.2 %) than those of human origin (11.8 %; P50.004) while, not surprisingly, faecal isolates of human origin contained a larger percentage of group B2 strains (26.5 %; P50.03 compared with faecal isolates of non-human origin) (Fig. 2a).…”

Temporal variations in patterns ofEscherichia colistrain diversity and antimicrobial resistance in the migrant Egyptian vulture

“…E. coli showed a much greater geographical effect in non-domesticated, resident wild species relative to isolates in humans suggesting that differential movement patterns influence E. coli strains that predominate in a species [3]. Similarly, in wild species, E. coli exhibit very strong geographic effects, which is likely due to a combination of host taxonomy, diet and climate [2,13,14,15]. Phylogeny of E. coli of wild birds varied concomitant to exposure to humans and human-associated vertebrates such as domestic fowl underscoring the influence of anthropogenic components [5,10].…”