An assessment of deer as hosts of livestock-associated pathogens in Northern Ireland and an exploration of meat juice serology as a future surveillance tool

Abstract

Wildlife can act as sentinel species to monitor for the emergence and adaption of pathogenic diseases and related public and veterinary health and welfare threats, such as antimicrobial and anthelmintic resistance. As ruminants, deer are closely related to the domesticated livestock species raised in Northern Ireland, making them susceptible to many of the same multi-species pathogens (chapter 1). Campylobacter and Salmonella were absent in deer faecal samples in this study (chapter 2) and E.coli was isolated in 52.4% of samples. Antimicrobial resistant phenotypes, determined by MIC, were seen in 9.0% of E.coli isolates (n= 111), with sulfamethoxazole resistance the most commonly detected (n= 9 ), followed by tetracycline resistance (n= 2), chloramphenicol resistance (n= 1) and ampicillin resistance (n= 1). No statistically significant differences were seen in resistance phenotype by season or sampling method, nor species or wild/farmed-status of the deer (p> 0.05). Good agreement was found between MIC phenotype and the AMR genes detected in the sequences by genotype-phenotype predicting software, ResFinder, on a small subset of E. coli isolates (chapter 3). Infectious Bovine Rhinotracheitis (IBR) antibodies were absent in all deer sera (n=116) and pestivirus antibodies were detected at low levels, 2.6% (n=116), in deer from County Fermanagh, all of which were sika deer. Although Pestivirus antibodies were detected, virus neutralization to determine the species of Pestivirus to which antibodies were raised was inconclusive (chapter 4). Meat juice serology on cattle and deer tissue exudate; ‘meat juice’, and corresponding sera identified pre-thaw freeze temperature as an important factor in the volume of sample retrieved, with samples stored at -20°C yielding more meat juice than those thawed from -80°C (p<0.05). Meat juice correlated well to serum from cattle on commercial ELISA assays for BVD and IBR tested to manufacturer’s recommended protocols (r=0.64, p<0.05 and rho=0.57, p<0.05, respectively). As it is accepted that meat juice contains fewer antibodies than serum, meat juice samples were also tested at modified dilution, which resulted in poor correlation with serum (r=0.18, p=0.28). Modified dilution of deer meat juice tested against sera on BVD p80 ELISA showed modest agreement (r=0.49, p<0.05). Deer meat juice samples did not correlate well to sera at either recommended or modified, lower dilution for IBR (r=0.13, p=0.24 and r=0.08, p=0.54, respectively). Thus, meat juice serology may be considered a suitable future surveillance tool for BVD and IBR in cattle and BVD in deer (chapter 5). No Single Nucleotide Polymorphisms (SNPs) were found in deer-associated gastrointestinal helminths, Spiculopteragia asymmetrica and Ostertagia leptospicularis, at benzimidazole (BZ) resistance conferring codons of the beta-tubulin gene; sites 167, 198 or 200. However, species-specific PCR yielded potentially problematic false positive hits using several primers available for the detection of livestock associated GINs; H. contortus, Teladorsagia circimcincta, Trichostrongylus axei, Trichostrongylus colubriformis, Trichostrongylus vitrinus, and Ostertagia ostertagi (chapter 6). Overall, this work highlights the value of surveillance in wild deer populations for livestock-associated pathogens, the development and validation of robust laboratory methods for detection of infections in this wildlife species to strengthen the surveillance systems and the importance of coordinated, collaborative research to enhance our knowledge base and inform livestock biosecurity policy decisions.