Molecular characterisation of selected enteric pathogens and antimicrobial resistance of Salmonella in rangeland goats in Western Australia

The Australian goat meat industry is largely supported by the sale of captured feral goats derived from rangeland production systems. Diarrhoea and ill-thrift following capture is a major issue for the industry, yet relatively little is known about the role of infectious disease and the public health significance of gastrointestinal infections. The aim of this thesis was to characterise faecal carriage of selected enteric pathogens by rangeland goats using molecular tools, and to determine potential impacts for goat productivity and public health. A longitudinal study conducted using qPCR and sequencing to screen faecal samples revealed that faecal carriage (prevalence) and shedding intensity of enteric pathogens were generally highest on arrival at the goat depot (feedlot), immediately after capture and transport. Three Cryptosporidium species (C. xiaoi, C. ubiquitum and C. parvum), Giardia duodenalis Assemblage E, three Eimeria species (E. ahsata, E. crandallis and E. arloingi), E. bovis-like Entamoeba sp., Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Haemonchus contortus and Trichostrongylus spp. were identified in faecal samples from the rangeland goats using molecular tools. Of these, C. ubiquitum subtype XIIa, C. parvum subtypes IIaA17G2R1 and IIaA17G4R1, G. duodenalis Assemblage E, S. enterica serovar Typhimurium and C. jejuni are considered zoonotic or emerging zoonotic pathogens. These studies provided the first description of caprine Eimeria cytochrome c oxidase subunit I (COI) and Entamoeba bovis-like actin sequences, and successfully produced a longer (1,229 bp) 18S rRNA sequence of E. arloingi. Of the pathogens identified in faecal samples, only Cryptosporidium was associated with an increased risk of scouring (diarrhoea) and reduced growth in the following one-month period. Giardia faecal carriage and higher Eimeria oocyst counts were associated with looser faecal consistency, but not to the point where scouring risk was increased. A subsequent investigation of rangeland goats consigned from four locations identified high rates (23-30%) Salmonella faecal carriage, with three serovars identified (S. Typhimurium, S. Chester and S. Saintpaul) at slaughter, indicating the potential for downstream carcass contamination and food safety concerns. A high percentage of Salmonella isolates (84.0%) remained entirely susceptible to all antimicrobials tested, which is encouraging, with low rates (4/106) of multi-drug resistance (resistant to three of more classes of antimicrobials) and no resistance to critically important antimicrobials (fluoroquinolones and third generation cephalosporins) was observed. The findings of the present study have important implications for management and animal welfare of captured rangeland goats starting from capture yards and feedlots through to slaughter to reduce public health risks