Breed effects on the virulence gene profiles and genetic diversity at FUT1, MUC4, MUC13 and MUC20 candidate genes for controlling diarrhoea-causing Escherichia coli.

Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.Escherichia (E) coli infections result in diarrhoea and oedema in growing pigs. Enterotoxigenic (ETEC), shigatoxin producing (STEC) and enteroaggregative (EAEC) E. coli have been identified as the principal causes of colibacillosis in most pig production systems. These E. coli use fimbrial and non-fimbrial adhesins to adhere to the intestines and cause infection. Absence or presence of the receptors on the intestinal walls determines the resistance or susceptibility of the host to the E. coli. In other populations, candidate genes linked to the receptors have been found to be associated with resistance/susceptibility to infection and are used in marker-assisted selection programs. This study investigated the presence and prevalence of ETEC, STEC and EAEC and the associated virulence genes in 263 E. coli isolates sampled from Landrace, Large White, Duroc and Indigenous piglets from the Animal Production Institute of the Agricultural Research Council (ARC) in Irene and Middledrift farm in Eastern Cape Province. The study also investigated polymorphisms at six candidate genes associated with two E. coli receptors in the same pig populations. Over 39 % of the isolates tested positive for the E. coli virulent genes investigated. None of the samples had fimbrial adhesins. The mode of attachment of the investigated E. coli was through non-fimbrial adhesins which were found in 49.06% of the isolates. The 106 E. coli isolates were categorized into 25 pathotypes carrying definable and unique combinations of E. coli virulence factors. The resistant allele for Alfa (1) fucosyltransferase 1 (FUT1) M307, a candidate gene for FI8R, was present in less than 1 % of the population. Various mutations of mucin genes MUC4 g.8227, MUC20 c1600 and g.191 were found in the population. Their respective alleles for controlling F4ab/ac E. coli adhesion in pigs were predominant in both breeds. Three loci (FUT1, MUC20 g.191 and MUC20 c.1600) deviated from Hardy Weinberg equilibrium (HWE) in the Indigenous and the Large White breeds. Heterozygotes deficiency and high levels of within breed diversity was observed in these two breeds at the mentioned loci. Overall, the study observed a wide range of toxin and colonisation factors (CFs) giving rise to diverse pathotypes in South African pigs. The absence of fimbrial adhesins suggests a different colibacillosis control program from that previously used. The presence of the resistant alleles in most of the loci investigated was low, however their presence suggest it is possible to use them to generate a resistant population using marker assisted selection. This study serves as a foundation for future pig colibacillosis control and immunity studies in the South African pig herds