Comparative genomic study of 147 Escherichia coli of bovine origin recovered from animals presenting with diarrhoea and mastitis

Escherichia coli (E. coli) is a bacterium of importance to the agri-food industry, particularly the beef and dairy sectors, as it causes two common bovine diseases: diarrhoea and mastitis. These infectious agents not only exert an impact on animal welfare, but also on productivity of bovine-derived foodstuffs. Therefore, to prevent economic losses and increase animal wellness as well as improving food safety and reducing public health risks, it is important to characterise E. coli strains responsible for these infections.Here, we study the genetic diversity of E. coli isolated from animals presenting with mastitis and diarrhoeal infections. From 2004 to 2010, 147 E. coli were cultured from faecal samples (diarrhoea) and milk-aliquots (mastitis) taken from cattle located in both France and Germany. These isolates were subjected to whole genome sequencing. Genotypes consisting of O-serotype and H- antigens, along with MLST; antimicrobial resistance determinants and virulence genes were extracted from these genomic data for each isolate. Some 47 phenotypically multidrug resistant isolates were identified and found to represent broad genetic diversity with no strong correlation of resistances among strains. The predominant O-serotype was O17 (31 isolates). Sequence Type (ST) 10 was dominant followed by ST58 and ST88. The majority of isolates (73 %) belonged to phylogroups B2 or D.Four isolates were selected for further characterisation based on their colistin resistance phenotype and closed genomes were generated using Single Molecule Real-Time (SMRT) sequencing. Genetic analyses indicated that these isolates harboured complex and diverse plasmids encoding not only antibiotic resistant genes (including mcr-1, and bla) but also virulence genes (siderophore, ColV, T4SS). This study provides detailed genomic insights describing a 147-isolate collection of E. coli linked to bovine mastitis and diarrhoea.