Characterisation of multidrug-resistant, avian pathogenic-like Escherichia coli O78 from dairy-bred calves with atypical colisepticaemia.

The objective of this work was to identify and characterise the causative agent(s) of an atypical septicaemic syndrome in 3- to 6-month-old calves. Nine cattle from three Scottish dairy farms were subject to post-mortem in 2020 and 2021, and tissue samples were screened via routine bacteriology. Escherichia coli was isolated from all sampled tissues and a representative isolate from each calf was taken forward for whole-genome sequencing for strain typing, identification of putative virulence factors and antimicrobial resistance genes, and assessment of phylogenetic relationships with other sequenced strains. The nine E. coli isolates were highly-related, being separated by a maximum of 5 single nucleotide polymorphisms. The isolates were serotyped in silico as O78, H9 and were multilocus sequence typed as ST23. Further analysis revealed 13 virulence genes, with the most frequent being associated with serum survival, cytotoxic protein and haemolysin production, and iron transport. These strains encode a novel fimH variant - designated fimH-1571 - which has a mutation potentially linked to increased adherence and invasion. Phylogeny and virulence gene profile indicate an avian pathogenic-like E. coli within a poultry lineage, however there were no poultry units in the vicinity of these farms. Ampicillin, amoxicillin, streptomycin and tetracycline resistance was predicted from their genome sequences, which agreed with phenotypic antimicrobial susceptibility testing. In conclusion, while not demonstrated here, these data are consistent with a transmission event between cattle units (or a common source) and suggest the possible emergence of virulent avian pathogenic-like E. coli in cattle for which future surveillance is merited.