Intergenic sequence comparison of Escherichia coli isolates reveals lifestyle adaptations but not host specificity

Hierarchical clustering of genetic diversity associated to different levels of mutation and recombination in Escherichia coli: a study based on Mexican isolates

Escherichia coli occur as either free-living microorganisms, or within the colons of mammals and birds as pathogenic or commensal bacteria. Although the Mexican population of intestinal E. coli maintains high levels of genetic diversity, the exact mechanisms by which this occurs remain unknown. We therefore investigated the role of homologous recombination and point mutation in the genetic diversification and population structure of Mexican strains of E. coli. This was explored using a multi locus sequence typing (MLST) approach in a non-outbreak related, host-wide sample of 128 isolates. Overall, genetic diversification in this sample appears to be driven primarily by homologous recombination, and to a lesser extent, by point mutation. Since genetic diversity is hierarchically organized according to the MLST genealogy, we observed that there is not a homogeneous recombination rate, but that different rates emerge at different clustering levels such as phylogenetic group, lineage and clonal complex (CC). Moreover, we detected clear signature of substructure among the A+B1 phylogenetic group, where the majority of isolates were differentiated into four discrete lineages. Substructure pattern is revealed by the presence of several CCs associated to a particular life style and host as well as to different genetic diversification mechanisms. We propose these findings as an alternative explanation for the maintenance of the clear phylogenetic signal of this species despite the prevalence of homologous recombination. Finally, we corroborate using both phylogenetic and genetic population approaches as an effective mean to establish epidemiological surveillance tailored to the ecological specificities of each geographic region.

Phylogenetic distribution of traits associated with plant colonization in Escherichia coli

Plants are increasingly considered as secondary reservoirs for commensal and pathogenic Escherichia coli strains, but the ecological and functional factors involved in this association are not clear. To address this question, we undertook a comparative approach combining phenotypic and phylogenetic analyses of E. coli isolates from crops and mammalian hosts. Phenotypic profiling revealed significant differences according to the source of isolation. Notably, isolates from plants displayed higher biofilm and extracellular matrix production and higher frequency of utilization of sucrose and the aromatic compound p-hydroxyphenylacetic acid. However, when compared with mammalian-associated strains, they reached lower growth yields on many C-sources commonly used by E. coli. Strikingly, we observed a strong association between phenotypes and E. coli phylogenetic groups. Strains belonging to phylogroup B1 were more likely to harbour traits indicative of a higher ability to colonize plants, whereas phylogroup A and B2 isolates displayed phenotypes linked to an animal-associated lifestyle. This work provides clear indications that E. coli phylogroups are specifically affected by niche-specific selective pressures, and provides an explanation on why E. coli population structures vary in natural environments, implying that different lineages in E. coli have substantially different transmission ecology.

Fimbriation and curliation in Escherichia coli O157:H7: a paradigm of intestinal and environmental colonization

Shiga toxin-producing Escherichia coli (STEC) serotypes, particularly E. coli O157:H7, possess a variety of fimbrial and afimbrial adhesins which have emerged as important contributors to intestinal colonization. E. coli O157:H7 possesses two chromosomal operons encoding long polar fimbriae (Lpf), which have been found to influence adherence in vitro and colonization in vivo. In a recent Infection and Immunity paper, we further explored the role of Lpf in E. coli O157:H7 intestinal colonization by using the infant rabbit model of STEC infection. We found that an E. coli O157:H7 Lpf-deficient mutant was outcompeted in the rabbit intestine by its parental strain, which may suggest that Lpf contributes to colonization. In contrast, the Lpf-deficient mutant showed an increased adherence to cultured intestinal epithelial cells, and we discovered that this strain overexpressed curli fibers. In this addendum article, we provide a continued perspective on the predicted roles of Lpf and curli, both in vivo and in vitro.