Extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase (AmpC) producing Escherichia coli in dairy calves from the Canterbury region : a dissertation presented in partial fulfilment of the requirements for the degree of Master of Veterinary Studies in Veterinary Public Health at Massey University, Manawatū Campus Palmerston North, New Zealand

Abstract

Antimicrobial resistance (AMR) has become a global public health concern threatening current effective prevention and treatment options. Infections caused by antimicrobial resistance strains are costly, often harder to treat and sometimes fatal. One group of bacteria that contributes to AMR are the extended beta lactamase (ESBL) and AmpC beta lactamase (AmpC) producing E. coli. These are on the critical list of important antibiotic-resistant bacteria of human importance compiled by the World Health Organisation and are a public health concern due to their resistance to an extended range of beta lactams. The main driver for the spread of AMR is the use of antimicrobials in both human and animals. One potential spread is by the feeding of waste milk to calves. Waste milk is the milk that contains antibiotics or other drugs. Waste milk is not recommended as feed for calves due to its association with the development of antibiotic resistance bacteria. Using the culture depended methods and whole genome sequencing, this study aimed to determine the prevalence of ESBL and AmpC producing E. coli isolated from recto-anal mucosal swabs (RAMS) from waste milk fed dairy calves, and to phenotypically and genotypically characterise ESBL and AmpC producing isolates. Recto-anal mucosal swabs samples (n = 40) from waste milk fed dairy calves collected from Canterbury region, New Zealand were screened for antimicrobial resistant E. coli. Fifty-eight percent (23/40) of the calves harboured antibiotic resistant E. coli. 25% (10/40) calves were positive for AmpC producing E. coli and none of the calves were positive for ESBL producing E. coli. The highest prevalence of resistance was observed for tetracycline. PCR and Sanger sequencing revealed that all the AmpC positive E. coli were chromosomal mediated with four mutations in the promoter region of the ampC gene. Whole genome sequencing of eight isolates resistant to both tetracycline and streptomycin revealed additional resistance genes that were not tested phenotypically. Using the Clermont phylogrouping method of E. coli, the AmpC positive, the tetracycline and streptomycin resistant E. coli isolates were distributed among phylogroups B1, C and D. In conclusion, this study revealed the presence of AmpC producing E. coli and other resistance genes in E. coli isolated from waste milk fed calves. Further epidemiological studies are required to determine whether these antibiotic resistant E. coli are associated with waste milk.