Browsing by Author "Collis, Rose"
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- ItemMetabolic characteristics and genomic epidemiology of Escherichia coli serogroup O145 : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Microbiology at Massey University, Palmerston North, New Zealand(Massey University, 2018) Collis, RoseShiga toxin-producing Escherichia coli (STEC) are a global public health concern, and can cause severe human disease. Ruminants are asymptomatic reservoirs of STEC, shedding this pathogen via their faeces. There is ‘zero tolerance’ for the Top 7 STEC serogroups (O26, O45, O103, O111, O121, O145 and O157) in ground beef products exported to the USA. STEC may contaminate carcasses during processing and therefore are a major regulatory concern for New Zealand’s meat industry. A previous study investigating the prevalence of STEC in young calves (n=1508) throughout New Zealand identified STEC O145 as the most prevalent serogroup (43%) at the dairy farm level compared to the other Top 7 serogroups. This high prevalence underlines STEC O145 as a public health concern and an issue for the meat industry. Current culture-based methods for STEC detection are not fully discriminatory due to the lack of consistent differential characteristics between STEC and non-pathogenic E. coli. This study aims to (i) investigate metabolic characteristics of E. coli O145 to facilitate the differential culture of this serogroup and (ii) understand the genomic epidemiology of E. coli O145 using whole genome sequencing (WGS). E. coli O145 strains examined in this study were genetically and metabolically diverse, according to carbon utilisation. The metabolic and genomic analyses were unable to differentiate between stx-positive and stx-negative O145 strains and there was no association with isolation source. However, clustering of O145 strains was observed according to multi-locus sequence type and at the level of eae subtype, a gene encoding the protein intimin which is involved in bacterial attachment to intestinal epithelial cells. Carbon substrates such as D-serine and D-malic acid were identified as candidate metabolites to differentiate defined O145 sequence types and may assist with identification in conjunction with currently available molecular methods. This research has demonstrated the genetic heterogeneity of serogroup O145 and has made significant progress in the identification of metabolites that may prove beneficial in the development of a differential media for certain subsets of serogroup O145. Such a medium would prove a valuable tool for maintaining and monitoring public health and providing food quality and safety assurances that New Zealand meat for export is free of this pathogen.
- ItemMetagenomic analysis and culture-based methods to examine the prevalence and distribution of antimicrobial resistance on two New Zealand dairy farms : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Palmerston North, New Zealand(Massey University, 2022) Collis, RoseAntimicrobial resistance (AMR) is a global threat to human and animal health, with the misuse and overuse of antimicrobials being suggested as the main driver of resistance. In a global context, New Zealand (NZ) is a relatively low user of antimicrobials in animal production. However, antimicrobial usage on NZ dairy farms and its potential for driving the spread of AMR within the dairy farm environment is under-researched. This research addresses the hypothesis that antimicrobial use on NZ dairy farms influences the prevalence of AMR in dairy farm environments, taking into consideration seasonality and contrasting farm management practices. The aims of this study, focused on two NZ dairy farm environments over an 15 month period, were to (i) determine the prevalence and distribution of AmpC- and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli, utilising culture-based methods, and (ii) to determine the abundance and diversity of antimicrobial resistance genes (ARGs), utilising a metagenomic approach, and lastly (iii), to assess the impact of systemic antimicrobial treatment on the bovine faecal microbiome. Overall, the research presented in this thesis has shown a low sample level prevalence of ESBL-producing E. coli from two NZ dairy farms (faeces 0%, 1.7%; farm dairy effluent (FDE) 0%, 6.7% from Dairy 1 and Dairy 4, respectively) but AmpC-producing E. coli were more frequently isolated across both farms (faeces 3.3%, 8.3%; FDE 38.4%, 6.7% from Dairy 1 and Dairy 4, respectively). AmpC- and ESBL-producing E. coli were isolated in spring and summer, during months with varying levels of antimicrobial use. Analysis at the individual animal level showed a decrease in bacterial diversity and richness during systemic antimicrobial treatment and in many cases the microbiome diversity recovered post-treatment when the cow re-entered the milking herd. Compared to overseas data in a similar context, NZ dairy farm environments had a low abundance of ARGs, with the highest abundance detected in soil (0.20 - 0.63 copies of ARG per 16S rRNA gene). However, many of the ARGs identified in soil are not frequently found in human pathogens or acquired genes. FDE had a lower ARG abundance but the ARGs were more diverse (0.03 - 0.37 copies of ARG per 16S rRNA gene). There was no association between the normalised ARG abundance and antimicrobial use or collection date, however the low ARG abundance in the farm samples may have made any associations difficult to detect. AMR is a burden for human, animal and environmental health and requires a holistic "One Health" approach to address. The outcomes from this research improve our understanding of the current levels of AMR on two NZ dairy farms and identifies areas for future research. Prevention is better than a cure and urgent action is required to slow the development and dissemination of AMR and to improve antimicrobial stewardship in humans and animals.