Molecular epidemiology of Salmonella in the broiler industry of Sri Lanka : thesis presented in 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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Massey University
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The increasing occurrence of non-typhoidal Salmonella in poultry is an emerging threat for public health in Sri Lanka, and salmonellosis has incurred massive economic loss for the poultry industry in the country. Thus, the thesis presented encompasses a comprehensive study to understand prevalence and possible risk factors for Salmonella carriage in broiler farms as well as whole-genome sequence-based population structure, phylogenetic relationships and antimicrobial resistance in Salmonella in Sri Lankan poultry. The studies described in this thesis include a cross-sectional survey (i.e., sampling and questionnaire-based study) conducted from July to December 2017 in broiler farms (115) from poultry-dense areas and associated hatcheries (15) as well as an outbreak study (from 2010 to 2018), based on isolates and metadata from poultry salmonellosis outbreaks. After initial identification and PCR confirmation of a total of 164 Salmonella isolates, whole-genome sequencing was performed and antimicrobial resistance profiles of the isolates were determined. Results revealed a Salmonella prevalence of 32.2%, CI 95% [23.6-40.7] in broiler farms and 66.7%, CI 95% [42.8-90.5] in the associated hatcheries. Litter management, rest period between flocks, feed storage, district and farmers’ knowledge of sick birds were identified as risk factors for Salmonella carriage in the broiler farms, through multivariate logistic regression modelling. Eighteen different multi-locus sequence types of Salmonella were identified, including nine which were reported for the first time in Sri Lankan poultry. The most common serovars were S. Kentucky ST314 (26.8%, CI 95% [20.0-33.6]) and S. Enteritidis ST11 (19.5%, CI 95% [13.4-25.6]). A high percentage of quinolone resistance manifesting as resistance to nalidixic acid (41.5%, CI 95% [33.9-49.1]) and intermediate resistance to ciprofloxacin (45.1%, CI 95% [37.5-52.7]) and enrofloxacin (35.4%, CI 95% [28.0-42.7]) was found. The findings of this thesis, especially in the absence of previous comprehensive studies, will enable the design of control strategies to strengthen the national Salmonella control programme in Sri Lanka.
Broilers (Chickens), Diseases, Epidemiology, Salmonella infections in poultry, Molecular epidemiology, Sri Lanka