Genome Based Phylogeny and Comparative Genomic Analysis of Intra-Mammary Pathogenic Escherichia coli

Abstract

Escherichia coli is an important cause of bovine mastitis and can cause both severe inflammation with a short-term transient infection, as well as less severe, but more chronic inflammation and infection persistence. E. coli is a highly diverse organism that has been classified into a number of different pathotypes or pathovars, and mammary pathogenic E. coli (MPEC) has been proposed as a new such pathotype. The purpose of this study was to use genome sequence data derived from both transient and persistent MPEC isolates (two isolates of each phenotype) to construct a genome-based phylogeny that places MPEC in its phylogenetic context with other E. coli pathovars. A subsidiary goal was to conduct comparative genomic analyses of these MPEC isolates with other E. coli pathovars to provide a preliminary perspective on loci that might be correlated with the MPEC phenotype. Both concatenated and consensus tree phylogenies did not support MPEC monophyly or the monophyly of either transient or persistent phenotypes. Three of the MPEC isolates (ECA-727, ECC-Z, and ECA-O157) originated from within the predominately commensal clade of E. coli, referred to as phylogroup A. The fourth MPEC isolate, of the persistent phenotype (ECC-1470), was sister group to an isolate of ETEC, falling within the E. coli B1 clade. This suggests that the MPEC phenotype has arisen on numerous independent occasions and that this has often, although not invariably, occurred from commensal ancestry. Examination of the genes present in the MPEC strains relative to the commensal strains identified a consistent presence of the type VI secretion system (T6SS) in the MPEC strains, with only occasional representation in commensal strains, suggesting that T6SS may be associated with MPEC pathogenesis and/or as an inter-bacterial competitive attribute and therefore could represent a useful target to explore for the development of MPEC specific inhibitors.

An update on environmental mastitis: Challenging perceptions

“…Richards et al. () noted that the type VI secretion system (T6SS) was present in all four MPEC isolates, compared with a prevalence of 38.6% in non‐mammary isolates of E. coli ( n = 56) and Shigella ( n = 9), and suggested that further research should be conducted into the role of T6SS. This was not supported by comparative genomic analysis of E. coli by Kempf et al.…”

“…(Wenz et al, 2001). Subclinical and mild clinical manifestations of Klebsiella mastitis also occur quite commonly (Oliveira, Hulland, & Ruegg, 2013;Figure 2 Genomic analysis of mammary pathogenic E. coli (MPEC) suggests that the MPEC phenotype may have arisen from the wider E. coli population on multiple occasions (Richards et al, 2015). Isolates from both transient and persistent E. coli infections are genetically heterogeneous, and there is no consistent genotype or virulence profile associated with either manifestation, making the existence of an MPEC genotype a matter of debate (Dogan et al, 2012;Richards et al, 2015).…”

“…Subclinical and mild clinical manifestations of Klebsiella mastitis also occur quite commonly (Oliveira, Hulland, & Ruegg, 2013;Figure 2 Genomic analysis of mammary pathogenic E. coli (MPEC) suggests that the MPEC phenotype may have arisen from the wider E. coli population on multiple occasions (Richards et al, 2015). Isolates from both transient and persistent E. coli infections are genetically heterogeneous, and there is no consistent genotype or virulence profile associated with either manifestation, making the existence of an MPEC genotype a matter of debate (Dogan et al, 2012;Richards et al, 2015). Richards et al (2015) noted that the type VI secretion system (T6SS) was present in all four MPEC isolates, compared with a prevalence of 38.6% in non-mammary isolates of E. coli (n = 56) and Shigella (n = 9), and suggested that further research should be conducted into the role of T6SS.…”

“…Isolates from both transient and persistent E. coli infections are genetically heterogeneous, and there is no consistent genotype or virulence profile associated with either manifestation, making the existence of an MPEC genotype a matter of debate (Dogan et al, 2012;Richards et al, 2015). Richards et al (2015) noted that the type VI secretion system (T6SS) was present in all four MPEC isolates, compared with a prevalence of 38.6% in non-mammary isolates of E. coli (n = 56) and Shigella (n = 9), and suggested that further research should be conducted into the role of T6SS. This was not supported by comparative genomic analysis of E. coli by Kempf et al (2016), who agreed with Dogan's conclusion regarding the absence of specific virulence genes.…”

No evidence for a bovine mastitisEscherichia colipathotype

“…The flexible genome consists largely of mobile genetic elements (MGEs), including plasmids, genomic islands (GI), and phages, which facilitate horizontal gene transfer (HGT) and are the driving forces for microbial diversity, evolution, and adaptation potential [21].Despite the proposal of a mammary pathogenic E. coli (MPEC) pathotype [3] and extensive research, no common genetic traits or VFs have been identified for E. coli mastitis isolates, so far [11,[22][23][24]. Recently, several publications analyzed E. coli genomes from intramammary infections, thereby expanding the method spectrum by comparative genomics approaches [25][26][27][28]. All of these studies identified various MPEC genome regions and genes with different 5 of 54 60 65 70 75 80 specificity criteria and significance, many of which are not considered to be classical VFs (or even encode for unknown hypothetical functions), but also genes coding for a type VI secretion system (T6SS), LPS biosynthesis, biofilm association, metabolic functions, and the ferric iron(III)-dicitrate (Fec) uptake system.…”