A food chain approach to control of Shiga toxin-producing Escherichia coli in New Zealand : 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

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This thesis describes the prevalence and molecular epidemiology of Shiga toxin-producing Escherichia coli (STEC) in New Zealand using microbiological, genomic, molecular, and statistical methods. STEC are a zoonotic pathogen that can cause bloody diarrhoea and acute kidney failure. Cattle are a well-recognized STEC reservoir, and previous research has identified living near cattle and contact with their faeces as an increased risk for human infection. Seven STEC serogroups (O157, O26, O45, O103, O111, O121, O145), known as the ‘Top 7’ STEC, have been identified as an increased risk to human health, with the New Zealand meat industry undertaking testing to ensure that veal beef exports to some international markets are free of these ‘Top 7’ serogroups. A random stratified cross-sectional study of ‘Top 7’ STEC prevalence of young dairy calves (n=1,508) on New Zealand dairy farms (n=102) found that approximately 20% of calves and 75% of farms were positive for one or more of the ‘Top 7’ STEC. ‘Top 7’ STEC prevalence was positively associated with increased number of calves in a calf pen, and prevalence significantly varied by region. This study utilized a new culture-independent diagnostic test, NeoSEEK (PCR/MALDI-TOF method), and used statistical and microbiological techniques to evaluate the sensitivity and specificity of the method for this and further studies. A longitudinal study evaluating prevalence and transmission of ‘Top 7’ STEC in animals and the dairy farm environment found evidence of calf-to-calf, dam-to-calf, and environment-to-calf transmission. Whole genome sequencing analysis and prevalence data revealed cross-contamination of young veal calf hides occurs during transport and lairage to processing plants. Analysis of New Zealand serogroup O26 bacterial isolates (n=152), in comparison to publicly available genome sequence data (n=252) from other countries (n=14), suggested introduction of STEC and non-STEC O26 into New Zealand during few periods in the 20th and early 21st century. Populations of New Zealand serogroup O26 E. coli are monophyletic, possibly due to minimal live cattle importations into the country. Further research in this area should focus on effective interventions at the farm and meat processing level to decrease the risk of veal beef contamination, while protecting public health.
Part of Chapter 3 has been published as: Browne, A.S., Midwinter, A.C., Withers, H., Cookson, A.L., Biggs, P.J., Marshall J.C., Benschop, J., Hathaway, S., Haack, N., Akhter, R., & French, N.P. (2018). Molecular epidemiology of Shiga toxin-producing Escherichia coli (STEC) on New Zealand dairy farms: Application of a culture-independent assay and whole-genome sequencing. Applied and Environmental Microbiology, 84(14). DOI: 10.1128/AEM.00481-18
Verocytotoxins, Escherichia coli infections in animals -- New Zealand -- Epidemiology, Calves -- Intestines -- Diseases -- New Zealand -- Epidemiology, Bacterial diseases -- Transmission -- New Zealand, Meat -- Contamination