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Background  The tick vector  Rhipicephalus microplus  which transmits  Babesia  spp. and rickettsial pathogens has not been reported in Kenya since 1998. More recently, the pathogenic  Babesia bovis  has been detected in cattle blood DNA. The status of  R. microplus  in Kenya remains unknown. This study employed morphological and molecular tools to characterize  R. microplus  originating from Kenya and assess the genetic relationships between Kenyan and other African  R. microplus  genotypes.    Methods  Ticks were collected in south-eastern Kenya (Kwale County) from cattle and characterized to investigate the existence of  R. microplus . Genetic and phylogenetic relationships between the Kenyan and other annotated  R. microplus  reference sequences was investigated by analysis of the cytochrome  c  oxidase subunit 1 ( cox 1) gene. To further characterize Kenyan ticks, we generated low coverage whole genome sequences of two  R. microplus , one  R. decoloratus  and  R. appendiculatus . A  B. bovis  specific TaqMan probe qPCR assay was used to detect  B. bovis  in gDNA from  R. microplus  ticks.    Results  Occurrence of  R. microplus  was confirmed in Kwale County, Kenya. The Kenyan  R. microplus cox 1 sequences showed very high pairwise identities (> 99%) and clustered very closely with reference African  R. microplus  sequences. We found a low genetic variation and lack of geographical sub-structuring among the African  cox 1 sequences of  R. microplus . Four complete mitochondrial (mt) genomes for two  R. microplus , one  R. decoloratus  and one  R. appendiculatus  were assembled from next generation sequence data. The mitochondrial genome sequences of the two Kenyan  R. microplus  ticks clustered closely with reference genome sequences from Brazil, USA, Cambodia and India forming  R. microplus  Clade A. No  B. bovis  was detected in the Kwale  R. microplus  DNA.    Conclusions  These findings confirm the presence of  R. microplus  in Kenya and suggest that  R. microplus  Clade A is prevalent in cattle in sub-Saharan Africa. These and other recent findings of widespread occurrence of  R. microplus  in Africa provide a strong justification for urgent surveillance to determine and monitor the spread of  R. microplus  and vector competence of  Boophilus  ticks for  B. bovis  in Africa, with the ultimate goal of strategic control.

Molecular evidence confirms occurrence of Rhipicephalus microplus Clade A in Kenya and sub-Saharan Africa