Genomic Insights into Drug Resistance and Virulence Platforms, CRISPR-Cas Systems and Phylogeny of Commensal E. coli from Wildlife.

Carla Andrea Alonso,María De Toro,Carmen Torres,Fernando De La Cruz

doi:10.3390/microorganisms9050999

Abstract

Commensal bacteria act as important reservoirs of virulence and resistance genes. However, existing data are generally only focused on the analysis of human or human-related bacterial populations. There is a lack of genomic studies regarding commensal bacteria from hosts less exposed to antibiotics and other selective forces due to human activities, such as wildlife. In the present study, the genomes of thirty-eight E. coli strains from the gut of various wild animals were sequenced. The analysis of their accessory genome yielded a better understanding of the role of the mobilome on inter-bacterial dissemination of mosaic virulence and resistance plasmids. The study of the presence and composition of the CRISPR/Cas systems in E. coli from wild animals showed some viral and plasmid sequences among the spacers, as well as the relationship between CRISPR/Cas and E. coli phylogeny. Further, we constructed a single nucleotide polymorphisms-based core tree with E. coli strains from different sources (humans, livestock, food and extraintestinal environments). Bacteria from humans or highly human-influenced settings exhibit similar genetic patterns in CRISPR-Cas systems, plasmids or virulence/resistance genes-carrying modules. These observations, together with the absence of significant genetic changes in their core genome, suggest an ongoing flow of both mobile elements and E. coli lineages between human and natural ecosystems.

Highlights

Intestine segments with fecal content were collected from wild boars legally hunted in their own habitat during the regular hunting season (October to February 2014–2015) approved by the Consejería de Agricultura of Castilla-La Mancha [8]; no approval was needed from an ethical committee since the sacrifice of animals was not performed for research purposes, following the Spanish Policy for Animal Protection RD53/2013 and the European Union
Our analysis of the 38 genomes of E. coli isolated from wild animals focused on their
Different biological roles have been proposed, various functional assays demonstrated that CRISPR/Cas acts as an adaptive and heritable immunity system able to target and neutralize exogenous DNA through a pathway similar to RNA interference (RNAi) in eukaryotes [21]

Summary

Introduction

Escherichia coli is a well-known commensal of the gut of humans and a wide-range of other animals, but it can reproduce and persist for long periods of time in extraintestinal natural environments. Beside these habitats, some strains of E. coli have the potential to cause severe intestinal and extraintestinal illness, such as meningitis, septicemia, pneumonia or urinary tract infections. Some strains of E. coli have the potential to cause severe intestinal and extraintestinal illness, such as meningitis, septicemia, pneumonia or urinary tract infections This diversity in terms of niche distribution and host–pathogen interactions is due to the high plasticity of the E. coli genome, which allows the bacteria to adapt to the varying selective pressures exerted by the different environments. Plus the easy and fast growth characteristics of E. coli, makes this species an excellent model to study the evolution and epidemiology of antimicrobial resistance or bacterial virulence [1]

Methods

Results

Conclusion