Genomic characterisation of an endometrial pathogenic Escherichia coli strain reveals the acquisition of genetic elements associated with extra-intestinal pathogenicity

Abstract

BackgroundStrains of Escherichia coli cause a wide variety of intestinal and extra-intestinal diseases in both humans and animals, and are also often found in healthy individuals or the environment. Broadly, a strong phylogenetic relationship exists that distinguishes most E. coli causing intestinal disease from those that cause extra-intestinal disease, however, isolates within a recently described subclass of Extra-Intestinal Pathogenic E. coli (ExPEC), termed endometrial pathogenic E. coli, tend to be phylogenetically distant from the vast majority of characterised ExPECs, and more closely related to human intestinal pathogens. In this work, we investigate the genetic basis for ExPEC infection in the prototypic endometrial pathogenic E. coli strain MS499.ResultsBy investigating the genome of MS499 in comparison with a range of other E. coli sequences, we have discovered that this bacterium has acquired substantial lengths of DNA which encode factors more usually associated with ExPECs and less frequently found in the phylogroup relatives of MS499. Many of these acquired factors, including several iron acquisition systems and a virulence plasmid similar to that found in several ExPECs such as APEC O1 and the neonatal meningitis E. coli S88, play characterised roles in a variety of typical ExPEC infections and appear to have been acquired recently by the evolutionary lineage leading to MS499.ConclusionsTaking advantage of the phylogenetic relationship we describe between MS499 and several other closely related E. coli isolates from across the globe, we propose a step-wise evolution of a novel clade of sequence type 453 ExPECs within phylogroup B1, involving the recruitment of ExPEC virulence factors into the genome of an ancestrally non-extraintestinal E. coli, which has repurposed this lineage with the capacity to cause extraintestinal disease. These data reveal the genetic components which may be involved in this phenotype switching, and argue that horizontal gene exchange may be a key factor in the emergence of novel lineages of ExPECs.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1075) contains supplementary material, which is available to authorized users.

Genomic content typifying a prevalent clade of bovine mastitis-associated Escherichia coli

“…To build an initial phylogenetic tree to confirm the placement of the 66 MPEC genomes into phylogroup A, we extracted the nucleotide sequences of 159 core genes from all of the E. coli genome sequences, aligned these genes by Muscle, concatenated them, and built a maximum likelihood tree under the GTR model using RaxML, as outlined previously 45 . Due to the size of this tree, bootstrapping was not carried out, although we have previously performed bootstrapping using these concatenated sequences on a subset of genomes which shows high support for the principal branches 45 .…”

“…The sequences for these 520 genes were concatenated for each strain. The Gblocks program was used to eliminate poorly aligned regions 47 , and the resulting 366312 bp alignment used to build a maximum likelihood tree based on the GTR substitution model using RaxML with 100 bootstrap replicates 45 .…”

Coexistence of CTX-M-2, CTX-M-55, CMY-2, FosA3, and QnrB19 in Extraintestinal Pathogenic Escherichia coli from Poultry in Brazil

“…Regarding ST457, this lineage has been related to the coproduction of KPC-3 and CTX-M-55 in clinical E. coli isolates from Italy (17). Moreover, ExPEC ST453 (CC86) has been reported from human and animal infections worldwide, including in Brazil (18,19). In summary, this study reports for the first time FosA3-and CTX-M-55-producing E. coli strains in Brazil, where these important resistance determinants coexist with pAmpC and PMQR genes.…”

A Highly Conserved Bacterial D-Serine Uptake System Links Host Metabolism and Virulence

“…The nucleotide sequences for 159 E . coli core-genes were elaborated as described by previously [ 21 , 74 ]. At each iteration, the core gene set (initialised as the nucleotide sequence for genes present in strain MG1655) was aligned to the next E .…”