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Background  Globally, bacterial vector-borne disease (VBD) exerts a large toll on dogs in terms of morbidity and mortality but nowhere is this more pronounced than in the tropics. Tropical environments permit a burgeoning diversity and abundance of ectoparasites some of which can transmit an extensive range of infectious agents, including bacteria, amongst others. Although some of these vector-borne bacteria are responsible for both animal and human diseases in the tropics, there is a scarcity of epidemiological investigation into these pathogens’ prevalence. The situation is further exacerbated by frequent canine co-infection, complicating symptomatology that regular diagnostic techniques may miss or be unable to fully characterise. Such limitations draw attention to the need to develop screening tools capable of detecting a wide range of pathogens from a host simultaneously.    Results  Here, we detail the employment of a next-generation sequencing (NGS) metabarcoding methodology to screen for the spectrum of bacterial VBD that are infecting semi-domesticated dogs across temple communities in Bangkok, Thailand. Our NGS detection protocol was able to find high levels of  Ehrlichia canis ,  Mycoplasma haemocanis  and  Anaplasma platys  infection rates as well as less common pathogens, such as “ Candidatus  Mycoplasma haematoparvum”,  Mycoplasma turicensis  and  Bartonella  spp. We also compared our high-throughput approach to conventional endpoint PCR methods, demonstrating an improved detection ability for some bacterial infections, such as  A. platys  but a reduced ability to detect  Rickettsia .    Conclusions  Our methodology demonstrated great strength at detecting coinfections of vector-borne bacteria and rare pathogens that are seldom screened for in canines in the tropics, highlighting its advantages over traditional diagnostics to better characterise bacterial pathogens in environments where there is a dearth of research.    Electronic supplementary material  The online version of this article (10.1186/s13071-019-3651-0) contains supplementary material, which is available to authorized users.

Assessment of a metabarcoding approach for the characterisation of vector-borne bacteria in canines from Bangkok, Thailand