Characterisation of Early Positive mcr-1 Resistance Gene and Plasmidome in Escherichia coli Pathogenic Strains Associated with Variable Phylogroups under Colistin Selection.

Guerrino Macori,Li Bai,Benjamin Roques,Séamus Fanning,James L Bono,Ankita Naithani,Peadar O’Gaora,Frédérique Woehrlé,Farid El Garch,Scott V Nguyen,Daniel Hurley,Christine Miossec

doi:10.3390/antibiotics10091041

Abstract

An antibiotic susceptibility monitoring programme was conducted from 2004 to 2010, resulting in a collection of 143 Escherichia coli cultured from bovine faecal samples (diarrhoea) and milk-aliquots (mastitis). The isolates were subjected to whole-genome sequencing and were distributed in phylogroups A, B1, B2, C, D, E, and G with no correlation for particular genotypes with pathotypes. In fact, the population structure showed that the strains belonging to the different phylogroups matched broadly to ST complexes; however, the isolates are randomly associated with the diseases, highlighting the necessity to investigate the virulence factors more accurately in order to identify the mechanisms by which they cause disease. The antimicrobial resistance was assessed phenotypically, confirming the genomic prediction on three isolates that were resistant to colistin, although one isolate was positive for the presence of the gene mcr-1 but susceptible to colistin. To further characterise the genomic context, the four strains were sequenced by using a single-molecule long read approach. Genetic analyses indicated that these four isolates harboured complex and diverse plasmids encoding not only antibiotic resistant genes (including mcr-1 and bla) but also virulence genes (siderophore, ColV, T4SS). A detailed description of the plasmids of these four E. coli strains, which are linked to bovine mastitis and diarrhoea, is presented for the first time along with the characterisation of the predicted antibiotic resistance genes. The study highlighted the diversity of incompatibility types encoding complex antibiotic resistance elements such as Tn6330, ISEcp1, Tn6029, and IS5075. The mcr-1 resistance determinant was identified in IncHI2 plasmids pCFS3273-1 and pCFS3292-1, thus providing some of the earliest examples of mcr-1 reported in Europe, and these sequences may be a representative of the early mcr-1 plasmidome characterisation in the EU/EEA.

Highlights

Escherichia coli (E. coli) is generally considered to be commensal in the intestinal tract of mammals
E. coli were isolated from animals presenting with diarrhoea or mastitis symptoms and subjected to whole-genome sequencing
Population Structure, Sequencing and Analysis of Gene Content E. coli were isolated from animals presenting with diarrhoea or mastitis symp3toomf 1s7 and subjected to whole-genome sequencing

Summary

Introduction

Escherichia coli (E. coli) is generally considered to be commensal in the intestinal tract of mammals. As part of a monitoring programme on antimicrobial susceptibility, 147 E. coli strains were isolated from faecal samples of cattle with diarrhoea and from milk-aliquots of cattle with mastitis in both France and Germany [16] This previous study described the presence of resistant phenotypes in the population and considering that it has been suggested that mcr-1 has spread from food animals to humans [17,18] and the importance of comparative studies on mcr-1 carrying isolates on a global level, in this study, the whole-genome sequences of the strains were obtained and the samples positive for the mcr-1 gene were further investigated. This provides an insight into the dynamics of these horizontally acquired resistance genes

Results and Discussion

Genetic Characterisation of Plasmids pCFS3313-1 and pCFS3273-2 Containing

Materials and Methods

Bioinformatics Analysis