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Background  Hard ticks act as arthropod vectors in the transmission of human and animal pathogens and are widely distributed in northern China. The aim of this study is to screen the important tick-borne pathogens (TBPs) carried by hard ticks in Inner Mongolia using metagenomic next-generation sequencing (mNGS) and to estimate the risk of human infection imposed by tick bites.    Methods  The adult  Dermacentor nuttalli  ( n  = 203) and  Ixodes persulcatus  ( n  = 36) ticks feeding on cattle were collected. The pooled DNA samples prepared from these ticks were sequenced as the templates for mNGS to survey the presence of TBPs at the genus level. Individual tick DNA samples were detected by genus--specific or group-specific nested polymerase chain reaction (PCR) of these TBPs and combined with DNA sequencing assay to confirm the results of mNGS.    Results   R. raoultii  (45.32%, 92/203),  Candidatus R. tarasevichiae  (5.42%, 11/203),  Anaplasma  sp. Mongolia (26.60%, 54/203),  Coxiella- like endosymbiont (CLE) (53.69%, 109/203), and  Babesia venatorum  (7.88%, 16/203) were detected in  D. nuttalli , while  R. raoultii  (30.56%, 11/36),  Anaplasma  sp. Mongolia (27.80%, 10/36), and CLE (27.80%, 10/36) were detected in  I. persulcatus . The double- and triple-pathogen/endosymbiont co-infections were detected in 40.39% of  D. nuttalli  and 13.89% of  I. persulcatus , respectively. The dual co-infection with  R. raoultii  and CLE (14.29%, 29/203) and triple co-infection with  R. raoultii ,  Anaplasma  sp. Mongolia, and CLE (13.79%, 28/203) were most frequent in  D. nuttalli .    Conclusions  This study provides insight into the microbial diversity of  D. nuttalli  and  I. persulcatus  in Inner Mongolia, China, reporting for the first time that  Candidatus R. tarasevichiae  had been found in  D. nuttalli  in China, and for the first time in the world that  Anaplasma  sp. Mongolia has been detected in  I. persulcatus . This study proves that various vertically transmitted pathogens co-inhabit  D. nuttalli  and  I. persulcatus , and indicates that cattle in Inner Mongolia are exposed to several TBPs.    Graphic AbstractSupplementary Information  The online version contains supplementary material available at 10.1186/s13071-021-04740-3.

parasites and vectors

Identification of tick-borne pathogens by metagenomic next-generation sequencing in Dermacentor nuttalli and Ixodes persulcatus in Inner Mongolia, China