Identifying risk factors for and genetic diversity of Campylobacter in Australia

Abstract

Background: Campylobacter infections are the most commonly notified cause of bacterial gastroenteritis in Australia, with foodborne gastroenteritis estimated to cost the Australian economy $1.2 billion annually. Morbidity associated with campylobacteriosis includes common symptoms of gastroenteritis, and potential chronic sequelae including irritable bowel syndrome, reactive arthritis, and Guillain-Barre syndrome.Past case-control studies from Australia were combined in meta-analyses to increase the power of results in identifying locally-relevant risk factors. Investigations into human campylobacteriosis rely on questionnaire data, with cases often interviewed after a noteworthy delay. There is a level of uncertainty around these studies’ results, which was assessed in a validation study.Data used for most of this thesis were collected for an NHMRC-funded case-control study that includes Queensland, New South Wales, Victoria, and the Australian Capital Territory. As these data may be used to inform public health policy for the whole nation, the generalisability of study results was assessed by collecting further isolates from cases in regions not covered by the NHMRC-funded study.Aims: This PhD thesis aims to: a) develop and validate questionnaires used in gastroenteritis investigations; b) identify the main sources of and risk factors for Campylobacter infection in Australia; and c) characterise Campylobacter strains from different geographical locations across Australia at the same point in time.Methods: A systematic review and meta-analysis of case-control studies investigating risk factors for campylobacteriosis in Australia and New Zealand were conducted to identify risk factors for disease. A new questionnaire was designed to investigate risk factors in greater detail, which I piloted on cases and controls. I conducted a validation study on select food-related questions, undertook data cleaning and conducted an analysis of an NHMRC-funded case-control study including multivariable logistic regression modelling. Campylobacter isolates from excluded regions were collected in an overlapping time frame to determine the case-control studies’ generalisability. I assessed whole genome sequences from this national snapshot of isolates for genetic diversity and performed cluster analyses.Results: The systematic review and meta-analysis (Chapter 3) identified four statistically significant risk factors: eating undercooked poultry (OR=3.88, 95%CI 2.75-5.47), poultry cooked outside the home (OR=2.13, 95%CI 1.66-2.72), having pet chickens (OR=3.29, 95%CI 2.12-5.10), and overseas travel (OR=5.55, 95%CI 3.20-9.63). The validation study (Chapter 4) included a 14-day delay to interview to mimic that of a public health investigation. I found that most questions targeting high-risk foods had at least a moderate level of agreement (κ=0.410-0.600). Case-control study results (Chapter 5) identified several locally-relevant risk and protective factors of foodborne, zoonotic, and demographic origin. Risk factors include the regular use of proton pump inhibitors in the four weeks prior to illness (aOR=2.92, 95%CI 1.93-4.43), eating undercooked chicken (aOR=66.72, 95%CI 8.26-539.14), and having a pet dog aged less than six months (aOR=6.35, 95%CI 3.37-11.97). Protective factors include the use of antibiotics in the four weeks prior to illness/interview (aOR=0.35, 95%CI 0.20-0.62), and eating lamb (aOR=0.60, 95%CI 0.44-0.81). The national snapshot study (Chapter 6) indicated a high level of diversity among Australian human Campylobacter isolates, and a higher proportion of C. coli than expected (16% compared to 5-10%). Additionally, when a single nucleotide polymorphism (SNP) threshold of 5 SNPs was used for cluster analysis, 34% (56/164) of isolates were found to belong to one of 19 clusters. Clusters were not temporally or geographically confined, aside from some in Western Australia.Conclusions: This thesis shows that the epidemiology of campylobacteriosis in Australia is comparable to that found in international studies, with some differences identified. The findings of major risk factors being consumption of undercooked chicken highlights the difficulty of controlling Campylobacter spp., as interventions to date have targeted the poultry industry as a priority. Zoonotic transmission was found to be especially important in young children aged less than five years in the meta-analysis, with consumption of poultry a less important risk in this age group. Good hand hygiene should be emphasised for those with puppies aged less than six months, and supervised child-animal interactions particularly encouraged for young children. The increased risk of campylobacteriosis associated with proton pump inhibitors is consistent with findings from other studies, including those investigating other bacterial causes of gastroenteritis. Alternative medications should be prescribed or risks for gastroenteritis conveyed to users of these medications if possible.Validated questions were found to be reasonably accurate. These questions have been made available for use in gastroenteritis investigations and are suitable for use when investigating foodborne infectious organisms other than Campylobacter.Campylobacter coli was isolated more often than expected. Further investigations should be conducted to determine if there are differences in the epidemiology between C. jejuni and C. coli in Australia. The large proportion of Campylobacter isolates included in clusters should be examined to determine if this is due to sequencing methods used or the result of point-source or continuous outbreaks.