Objective To understand the microbial community and antibiotic resistance genes (ARGs) in Rhipicephalus microplus in Guizhou Province, China. Methods From April to May in 2022 and 2023, R. microplus was collected from cattle surface in Daozhen, Ziyun, Xiuwen counties, and Panzhou City of Guizhou Province using the method of examining ticks on animal body surface. The collected tick specimens were grouped by region, and 15 female ticks were randomly selected from each region and divided into 3 tubes for metagenomic sequencing. The sequencing data were subjected to quality control, splicing, and assembly, followed by comparison against the structured antibiotic resistance gene database and the non-redundant protein library of the National Center for Biotechnology Information to obtain the annotation information of species and ARGs from each specimen. Then visual analysis was performed using R 3.6.3 and GraPhlAn 1.1.3, including taxonomical composition, ARG composition, and group similarities. Results A total of 550 blood-sucking R. microplus were collected, including 404 females, 85 males, and 61 nymphs. The dominant phylum of bacteria in R. microplus was Proteobacteria, with an average relative abundance of 60.01%, followed by Firmicutes (36.76%). The dominant genus was Klebsiella (38.58%), followed by Staphylococcus (22.00%). The dominant species was K. pneumoniae (38.58%), followed by Sta. aureus (22.00%). In addition, tick-borne pathogens such as Anaplasma phagocytophilum, Rickettsia fournieri, R. conorii, R. japonica, Borrelia garinii, and Coxiella burnetii were also detected, accounting for 3.08%, 3.04%, 0.76%, 0.70%, 0.01%, and 0.01%, respectively. The analysis of group similarities showed that the difference between groups was greater than that within groups (R=0.586, P=0.002). ARG annotation identified 3 316 genes related to resistance against β-lactams (54.22%), aminoglycosides (20.18%), chloramphenicols (13.61%), and multidrugs (11.99%). The types and abundance of ARGs were different in different regions. Conclusions The microflora in R. microplus in Guizhou Province is diverse, and there are many types of pathogens in R. microplus. Moreover, R. microplus carries a large number of ARGs. Therefore, it is necessary to strengthen the study of tick microflora and resistance genes, so as to guide the rational use of drugs and prevent the occurrence of tick-borne diseases.
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