Metagenomic Investigation of Ticks From Kenyan Wildlife Reveals Diverse Microbial Pathogens and New Country Pathogen Records

Abstract

Focusing on the utility of ticks as xenosurveillance sentinels to expose circulating pathogens in Kenyan drylands, host-feeding ticks collected from wild ungulates [buffaloes, elephants, giraffes, hartebeest, impala, rhinoceros (black and white), zebras (Grévy’s and plains)], carnivores (leopards, lions, spotted hyenas, wild dogs), as well as regular domestic and Boran cattle were screened for pathogens using metagenomics. A total of 75 host-feeding ticks [Rhipicephalus (97.3%) and Amblyomma (2.7%)] collected from 15 vertebrate taxa were sequenced in 46 pools. Fifty-six pathogenic bacterial species were detected in 35 pools analyzed for pathogens and relative abundances of major phyla. The most frequently observed species was Escherichia coli (62.8%), followed by Proteus mirabilis (48.5%) and Coxiella burnetii (45.7%). Francisella tularemia and Jingmen tick virus (JMTV) were detected in 14.2 and 13% of the pools, respectively, in ticks collected from wild animals and cattle. This is one of the first reports of JMTV in Kenya, and phylogenetic reconstruction revealed significant divergence from previously known isolates and related viruses. Eight fungal species with human pathogenicity were detected in 5 pools (10.8%). The vector-borne filarial pathogens (Brugia malayi, Dirofilaria immitis, Loa loa), protozoa (Plasmodium spp., Trypanosoma cruzi), and environmental and water-/food-borne pathogens (Entamoeba histolytica, Encephalitozoon intestinalis, Naegleria fowleri, Schistosoma spp., Toxoplasma gondii, and Trichinella spiralis) were detected. Documented viruses included human mastadenovirus C, Epstein-Barr virus and bovine herpesvirus 5, Trinbago virus, and Guarapuava tymovirus-like virus 1. Our findings confirmed that host-feeding ticks are an efficient sentinel for xenosurveillance and demonstrate clear potential for wildlife-livestock-human pathogen transfer in the Kenyan landscape.

Detection of pathogenic bacteria in ticks from Isiolo and Kwale counties of Kenya using metagenomics

“…On the lower end, one failed to detect it (48) and another reported a prevalence of 5.5% (49). On the higher end, a study reported a prevalence of 45.7% (50) which is comparable to the current detected level of 37.88%. This shows that more research is required to ascertain what other factors may be affecting the prevalence of C. burnetii in ticks.…”

“…On the lower end, one failed to detect it (48) and another reported a prevalence of 5.5% (49). On the higher end, a study reported a prevalence of 45.7% (50) which is comparable to the current detected level of 37.88%. This…”

Ticks; a reservoir for virus emergence at the human-livestock interface in Uganda

“…We have named these as Engoha virus isolates 1-3. We also detected Trinbago virus, another member of the Flaviviridae in six Rhipicephalus tick pools from Nakaseke and Lyantonde districts, four of which were used for phylogenetic analysis (P158, P171, P172, P176; Fig 4d ), a virus first detected in Trinidad and Tobago in R. sanguineus, R. microplus, and A. ovale ticks in 2019 and more recently detected in Kenya (14). Viruses in this clade are assigned to the Pestiviruslike group and species differ by 15% in the polyprotein amino acid sequence.…”

Canine Distemper Virus in Autochtonous and Imported Dogs, Southern Italy (2014–2021)

“…Interestingly, out of the 65 CDV-positive dogs, only in 20 animals was CDV the only pathogen identified, with CPV2 and CCoV being frequently detetced in co-infection. Co-infections are frequently found in dogs [ 65 , 66 ] and the extent of this phenomenon has been revealed by the adoption of syndromic diagnostics (i.e., multi-screening of samples against a recognized panel of pathogens) [ 67 ] and, more recently, by metagenomic investigations in domestic and wildlife animals [ 68 , 69 ]. We cannot rule out that concomitant changes in the epidemiology of viruses with immune-suppressive activity may also occur in the local canine population, amplifying the magnitude of the CDV epidemic.…”