Sequence analysis of bacterial tick-borne pathogens in cattle from two provinces of South Africa using 16S rRNA PacBio approach

Ticks are obligate ectoparasites recognised worldwide as major vectors of several disease-causing pathogens and are good indicators of disease distribution and epidemiology. The objective of the study was to give an insight to current tick distribution and pathogens they transmit that may pose threat to cattle in the sampled study sites. About 150 cattle were randomly selected from three study sites, one in Kwa-Zulu Natal (Bergville) and two (Harrismith and Phuthaditjhaba) in Free State Provinces. Blood samples were collected from the coccygeal vein of individual animals into 10-ml sterile EDTA vacutainer tubes. DNA was extracted from about 200 microl of blood using QIAamp DNA Mini Kit. Ticks were collected from the predilection sites (ears, dewlap, tail switch, back, groin, udder, around anus, lower abdomen) from the cattle. Ticks were belonging to 8 species: Hyalomma rufipes, H. truncatum, Rhipicephalus afranicus, R. appendiculatus, R. decoloratus, R. evertsi evertsi, R. microplus and R. simus. In order of abundance, the most common species was R. evertsi evertsi (78.7%), followed by R. appendiculatus (11.6%), R. afranicus (2.6%), R. simus (2.6%), R. decoloratus (1.9%), H. rufipes (1.2%), H. truncatum (0.7%) and R. microplus (0.01%). Up to 13 phyla and 23 classes were identified in the metagenome of the three study sites. At phylum level, the composition of bovine blood microbiomes was numerically dominated by Proteobacteria with a relative abundance of 67.2% (Bergville), 73.8% (Harrismith) and 84.8% (Phuthaditjhaba), followed by Firmicutes at 9.6% (Phuthaditjhaba), 18.9% (Bergville) and 19.6% (Harrismith). With pairwise analysis, the alpha-diversity varied significantly between microbial communities in three study sites based on Chao 1 index estimator (P = 0.0064 and P = 0,00025, respectively). This study expands the knowledge on tick fauna and microbial communities in the three study sites.