Fig. 1

Mixed genotypes of O. tsutsugamushi identified from both eschar and blood samples of the patient. A A crater-shaped eschar (5 × 5 mm) was discovered on the left waist of the patient. B Five of the seven conserved genes showing mixed genotypes of O. tsutsugamushi in the patient’s eschar and blood samples. C, D The results of direct sequencing of PCR amplicon and colony verification of the gpsA and mdh genes. The logo presents the nested PCR fragments of gpsA and mdh genes collected in the pubMLST database. Mixed sites are indicated by filled arrows. These mixed sites are either synonymous (light blue letters) or missense (red letters). Two novel SNP sites in the mdh gene are also indicated by the unfilled line. These sites are all verified by sequencing of 30–40 clones for each gene and each sample