Multiple sequence analysis to compare polymorphic sites found on our actin sequences, and those retrieved from the GenBank, revealed a total of 33 single nucleotide differences in the open reading frame of the actin gene. Three of these single nucleotide polymorphisms were exclusively found in actin sequences from our study (Additional file 2). The nucleotide sequences obtained of the actin gene for all the 22 isolates were submitted in GenBank under accession numbers: (MF350322–MF350343). The phylogenetic analysis (Fig. 1) showed that actin genotype E clustered with a bootstrap value of 99. Lower bootstrap values were observed for actin genotypes N, G, I and P.Fig. 1Phylogenetic tree for actin gene nuclotide sequences of T. vaginalis. The tree was generated using Maximum Likelihood method. Bootstrap test for 1000 replicates. Sequences from Kilifi isolates (n = 22) have accession numbers with the prefix “MF”, all other sequences were retreived from GenBank and are representative of the five actin genotypes. Scale-bar: 0.001 (1 substitution per 1000 nucleotides)