The highest burden of endemic, neglected, and emerging zoonotic diseases occur in low and middle-income countries (LMICs) (Worsley-Tonks et al., 2022). However, limited resources, surveillance infrastructure and access to advanced molecular techniques in these regions can severely impact the rapid detection and characterization necessary to mitigate and respond to outbreak events. Metagenomics approaches continue to become less expensive, and now represent a potentially cost-effective approach to conduct biosurveillance and monitor molecular epidemiology (Ko et al., 2022). Compared to PCR, which only detects pathogen based on specific primers, metagenomic agnostic sequencing allows for the identification of known and unknown microbes (viruses, bacteria and protozoans) from a single sample (Govender et al., 2021). Forward-facing portable sequencing platforms such as the MinION can provide expansive knowledge of circulating pathogens from a wide array of field-collected samples, including arthropod vectors, soil and water samples and a variety of swabs and bloods from vertebrates, both in the field and in basic laboratory conditions (Gardy and Loman, 2018; Achee et al.). Using metagenomics approaches, detection of known, emergent, and emerging zoonotic pathogens of human and veterinary importance can be made available to decision-makers, researchers, and policymakers in near real-time, to inform effective containment or mitigation efforts to minimize public health impacts.The nine publications presented here in this Research Topic capture a wide range of settings that metagenomics can be applied to through a One Health lens, including outbreak response, clinical management, biosurveillance, and disease monitoring within the human animal interface. Publication summaries can be found in Table 1.
