In developing countries like India considerable economic losses occurs in large and small holding livestock productivity farming system due to TBDs . Prevalence studies are of immense importance for disease mapping and investigating the epidemiological triad. The agro-climatic conditions of the Jammu region are highly favourable for growth and multiplication of ticks which act as natural vectors of theileriosis, babesiosis and anaplasmosis. In the present study, high prevalence of Babesia bigemina (14.02%, 39/278), A. marginale (23.74%, 66/278) and low prevalence of Theileria annulata (1.079%, 3/278) can be attributed to Rhipicephalus (Boophilus) microplus being the only tick which infests the bovines of Jammu region . A thorough review of literature reveals varying incidence of babesiosis ranging from 0.76 to 18.50% in India [13, 14, 15]. Anaplasma is also associated with a long term/life long carrier state  and so the probability of detecting positive animals, particularly in areas of endemic instability, is increased, primarily with use of molecular tools [6, 17]. The animals found positive for theileriosis had a history of importation from the neighbouring state, Punjab, having high prevalence of H. anatolicum  and T. annulata . Owing to meagre presence of vector tick (H. anatolicum), considerably low prevalence of theileriosis was found in union territory of Jammu and Kashmir . Livestock owners import high yielding animals from bordering states of Punjab and Haryana without proper quarantine and thus carrier cattle get transported to non endemic areas, increasing the likelihood of transboundary outbreaks. PCR assay has been employed for sensitive detection of haemoparasites in many diagnostic laboratories and is considered as an alternative to microscopy  particularly in latent infections. In our study as well, PCR was able to identify more than twice the number of cases as detected by microscopy.
There were no uncharacteristic clinical signs in the animals found positive for haemoprotozoan and rickettsial infection. High temperature, pale mucous membranes and decrease in milk production were however prominent signs. The endogenous pyrogens released in the blood due to cellular lysis lead to fever and consequently, inappetence . Anemia occurs due to erythrophagocytosis, lysis of RBCs due to parasite multiplication and subsequent removal by reticuloendothelial system. [21, 22] Consequently, the vital blood parameters which include level of haemoglobin, PCV, MCHC, MCV, TLC and TEC get deranged and further aggravated by the continuous loss of blood sucked out by the ticks. The impact of haemoprotozoan and rickettsial infection on the milk production is a major economical set back. Our results reflect the deviations in the blood parameters following the same cascade and are in agreement with [15, 17, 24].
The study suggests that outbreaks are likely to occur in the rainy and post rainy season due to interplay of epidemiological factors. During rainy season the epizootiological determinants such as ambient temperature and atmospheric humidity and microclimate of grazing lands are favourable for growth and development of ticks. This is unlikely to differ in other parts of country as well, based on earlier reports viz 29.31%  and 58.55% . The vector population was observed as a major differential factor in the prevalence of TBDs in organised and unorganized farms (p = 0.007), latter showing increased prevalence. These farms are Kuchha houses (non cemented) or made of bricks only, having cracks and crevices, with improper drainage and poor ventilation, favouring survival and breeding of vector ticks. Moreover, the owners of unorganized farms are comparatively uneducated, so lack of awareness regarding use of acaricidals and sustainable managemental practices against ticks was observed at the time of sample collection. The other determinants recorded for disease occurrence are age and breed of animal. Inverse age resistance shields the young population from clinical outbreak of diseases . The highest prevalence (37.50%) was observed in animals > 3 years of age which is supported by studies from [26, 28]. Also, the adult cattle are predisposed to various stresses due to cycling heat, production, vaccination and reproduction which may augment the pathogenesis of diseases. Cross bred animals revealed higher prevalence of infection (33.62%) than indigenous breeds (15.38%), in agreement with earlier reports [26, 29]. Some workers have attributed susceptibility to the difference in the immune response to produce pro-inflammatory cytokine, which is higher in exotic animals or native breeds harbouring genetic loci for greater tolerance [30, 31].
Intracellular haemoprotozoons are under constant pressure from the immune system of their hosts, leading to emergence of genetic variants . The genetic polymorphism of Babesia spp. has been reported earlier using sequence information of 18S rRNA gene [1, 33, 34]. In the phylogenetic tree, the isolates of the present study formed a separate sub clade but clustered with an isolate from Iraq. However, these distinguished itself from South African and American isolates, simulating reports from Kerala , wherein the isolates appeared in two different clades. In another study from India , close genetic relatedness was observed between B. bigemina isolates from North Eastern India with Argentina and Kenya rather than with China. Sequence information of A. marginale isolates from the present study revealed a marked divergence from A. capra, A. central and A. ovis, although, small length of nucleotide sequence couldn’t reveal any marked genetic heterogeneity from isolates of A. marginale across the world. In a study from south India, minimal heterogeneity was revealed within 16S rRNA and msp4 genes among the field isolates from Kerala .
The key mechanism responsible for genetic diversity among Theileria spp., is recombination during sexual reproduction . The Tams1 gene has been shown to be a promising candidate for carrying antigenic diversity studies in T. annulata parasites [36, 37], however some studies have suggested no geographic specificity and other showing region specificity based on the gene polymorphism [36, 37, 38]. In the present study, T. annulata showed 99% nucleotide homology with Indian isolates and clustered together with an Indian isolate in the phylogenetic clade. Parasite diversity reports from India suggests that the Indian isolates were distributed into two groups along with other countries like Spain, Italy, Tunisia, Iran, Bahrain, Turkey and Iraq [39, 40]. The genetic diversity among the parasite strains can be one of the reasons for vaccination failures and inability to constraint the disease.