Antimicrobial resistance of Escherichia coli isolates from conventional and organic dairy farms; phenotypic and genotypic perspectives : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University

Abstract

The use of antimicrobials has been the main weapon against infectious diseases for over a century. However, the persistent use/abuse of antimicrobials has resulted in resistant strains, and antimicrobial resistance (AMR) is a key health problem for health authorities and governments worldwide. This study aimed to shed light on the impact of antimicrobial usage and AMR development and prevalence by comparing the AMR status of Escherichia coli from the soils of conventional dairy farms to their organic counterparts in the Geraldine area of South Canterbury, New Zealand. Dairy farm soil E. coli (DfSEC) isolates (n=814) were phylogenetically typed and antimicrobial susceptibility tested (AST) against cefoxitin, cefpodoxime, chloramphenicol, ciprofloxacin, gentamicin, meropenem, nalidixic acid, and tetracycline. Twenty of the DfSEC isolates were selected based on their absolute resistance to cefoxitin 30 mg for bioinformatics analysis. The 814 DfSEC isolates were classified into seven main E.coli phylogenetic groups. The phylogeny group B1 was most prevalent at 73.7%. The E group was next at 9.6% while the A was 5.8%, C was 5.3% and the D and B2 groups were 0.5% each. When classified under the newer E. coli phylogeny nomenclature, the cladeI+II and cladeIII+IV+V phylogroups were found to be less than 1%. There was no F phylogeny group member identified in this study and 3.1% of the isolates were placed as unknowns. The AST results indicated 3.7% of the DfSEC isolates were resistant to at least one of the eight selected antimicrobials. Of the selected 20 DfSEC isolates, each carried at least two resistant gene variants. Three isolates from a conventional farm carried up to six resistant gene variants. Each of the 20 isolates may encode nucleotide sequences of either the blaACT-1, blaBIL-1, blaCMY-2, or the blaMIR-1 gene variants for extended-spectrum β-lactamase (ESBL) production and the multi-drug transporter gene mdfA1 for the efflux pump. Two isolates from different farms showed close relatedness (≤ 1 locus difference apart). Statistical analysis indicated that there was no significant difference (P > 0.05) between the effect of the two dairy farming systems on the AMR of the DfSEC isolates but isolates from the conventional dairy farm possessed more resistance gene variants per organism than those from the organic dairy farms. DfSEC isolates commonly associated with humans and their companion animals may be transferred into the dairy farm soil and there is the possibility of farm-to-farm transfer of DfSEC isolates. Virulent mastitis and/or metritis causing E. coli of phylogeny group A may be found in the dairy farm soil. This study archived over 800 dairy farm soil E. coli isolates for future comparative studies and laid a foundation for a future study of the trend of antimicrobial resistance development and their spread in the central region of the South Island of New Zealand.