Monophasic Salmonella Typhimurium in Australian pigs

© 2017 Dr. Thomas Richard David WeaverSalmonella enterica enterica 1,4,[5],12:i:- colonization in Australian pig herds was investigated. The research considered: the distribution of S. 1,4,[5],12:i:- in the Australian pig industry; dynamics of colonization in herds; diversity in the Australian porcine population; comparison of study strains with related domestic serovars and strains reported internationally; antimicrobial resistance characteristics and determinants; and implications for optimal typing and surveillance. In total, 773 faecal samples were collected from Australian pig herds in cross-sectional (16 herds) and longitudinal (five herds) observational epidemiological studies. Samples were cultured and where Salmonella was confirmed multiple colonies were collected, 2326 isolates in total. Representative isolates were characterized by serotyping, phage typing, antimicrobial susceptibility testing and multiple-locus variable-number tandem-repeat analysis (MLVA). In addition, the genomes of a sample of the study collection isolates were sequenced. The results indicated that S. 1,4,[5],12:i:- has spread rapidly through the Australian pig industry. Persistent S. 1,4,[5],12:i:- shedding and considerable escalation among weaners was observed in the sampled herds. High levels of shedding were also observed among finisher pigs, indicating a possible pathway into the human food chain. Low S. 1,4,[5],12:i:- phenotypic and MLVA profile diversity was observed, suggesting the Australian porcine S. 1,4,[5],12:i:- population is closely related. Comparative genomic studies demonstrated that the S. 1,4,[5],12:i:- had undergone clonal expansion, consistent with the population having emerged from a single event. The characteristics of the study S. 1,4,[5],12:i:- strains closely resembled those of the European clone strains, supporting the hypothesis that S. 1,4,[5],12:i:- was recently introduced to Australia from overseas. In spite of the close relatedness of the study strains, phylogenetic analyses readily differentiated S. 1,4,[5],12:i:- strains on the basis of source. Little resistance to critical antimicrobials for the treatment of human salmonellosis was observed. Salmonella resistance types varied considerably between herds and were serovar associated within herds. The majority of S. 1,4,[5],12:i:- were multidrug resistant, whereas the majority of non-S. 1,4,[5],12:i:- serovars were pansusceptible. The variation in resistance types between contemporary serovars within herds indicated that antimicrobial use on farm was not driving selection for Salmonella resistance types. However, selection pressure for resistance types appeared to vary between herds. In some herds resistance diminished over time due and gene loss was identified. In other herds, there were indications of horizontal resistance gene acquisition among some of the more resistant strains. The most common resistance genes identified among the study S. 1,4,[5],12:i:- isolates also matched reports from overseas. Phage typing proved to be of limited value in differentiating Australian porcine S. 1,4,[5],12:i:- strains but MLVA showed promise for surveillance and broader epidemiological purposes. However, these studies further illustrated the value of comparative genomics for surveillance, source attribution and broader epidemiological purposes. This research has generated original insights into the epidemiology of S. 1,4,[5],12:i:- in pig herds. The findings have implications for pig industry and public health risk mitigation and risk management