Carmen Flores-Mendoza

Endemic and (re)emerging infectious diseases pose a major threat to public health and military readiness in Central and South America. The high biodiversity and the differing transmission pathways require the use of highly sensitive methods to track the emergence and spread of these diseases. High-throughput sequencing technologies have become a critical resource for the field of infectious disease monitoring, specifically for tracking pathogen evolution, antimicrobial resistance, and transmission. This review provides an overview of the implementation of genomics-informed infectious disease surveillance conducted by the U.S. Naval Medical Research Unit SOUTH, focusing on operational, infrastructural, and logistical challenges in resource-limited settings and outlining strategies for building sustainable regional capacity. Selected case studies focused on prominent biothreats including dengue, Oropouche, malaria, and antimicrobial resistance demonstrate the significance and applicability of targeted and agnostic sequencing approaches to elucidate transmission pathways, pathogen discovery, and guide public health responses and field-deployable applications.

Infectious diseases transmitted by ectoparasites such as fleas, lice, mites, and ticks constitute a global public health problem. Tick-borne diseases are the most widely studied emerging ectoparasite-borne diseases (EBD) mainly due to their increasing incidence worldwide, including in South America. Furthermore, in Peru and neighboring Andean countries (Bolivia, Colombia, and Ecuador), surveillance reports indicate that Rickettsia species appear to be the most diverse and widely distributed ectoparasite-borne pathogens (EBP) followed by Babesia species, and with fewer species of Anaplasma, Bartonella, Borrelia, Ehrlichia, Coxiella, and Phlebovirus pathogens. Amblyomma, Dermacentor, Rhipicephalus, and Ixodes ticks were reported as the most predominant ectoparasites found infected with a diversity of EBP belonging to Rickettsia, Babesia, Anaplasma, Bartonella, and Ehrlichia species. Overall, people living in rural areas where agriculture and livestock production are their main economic means are at higher risk of EBD.

Dengue is the most widespread vector-borne viral infection globally and a serious public health problem. The 2023–2024 dengue outbreak across Latin America has drastically impacted Peru, including previously unaffected areas such as metropolitan Lima and Amazonian rural communities, presumably due to climate change. Research studies conducted in Iquitos, the largest city in the Peruvian Amazon, showed that ultra-low-volume pyrethroid spray applications against the dengue vector Aedes aegypti were effective when adequate coverage and quality control were carried out. Insecticide-treated curtains were not effective at controlling dengue transmission in Iquitos, whereas the use of passive spatial repellent emanators demonstrated 34% protective efficacy against Aedes-borne virus infection. In modeling studies, targeted indoor residual spray strategies showed promising reductions in dengue transmission, which require empirical evaluation. Trials conducted in Iquitos have shown that larval control alone is not sufficient to control Ae. aegypti, urging that government programs must consider integrated vector management.

Over half the world’s population is at risk for viruses transmitted by Aedes mosquitoes, such as dengue and Zika. The primary vector, Aedes aegypti , thrives in urban environments. Despite decades of effort, cases and geographic range of Aedes -borne viruses (ABVs) continue to expand. Rigorously proven vector control interventions that measure protective efficacy against ABV diseases are limited to Wolbachia in a single trial in Indonesia and do not include any chemical intervention. Spatial repellents, a new option for efficient deployment, are designed to decrease human exposure to ABVs by releasing active ingredients into the air that disrupt mosquito–human contact. A parallel, cluster-randomized controlled trial was conducted in Iquitos, Peru, to quantify the impact of a transfluthrin-based spatial repellent on human ABV infection. From 2,907 households across 26 clusters (13 per arm), 1,578 participants were assessed for seroconversion (primary endpoint) by survival analysis. Incidence of acute disease was calculated among 16,683 participants (secondary endpoint). Adult mosquito collections were conducted to compare Ae. aegypti abundance, blood-fed rate, and parity status through mixed-effect difference-in-difference analyses. The spatial repellent significantly reduced ABV infection by 34.1% (one-sided 95% CI lower limit, 6.9%; one-sided P value = 0.0236, z = 1.98). Aedes aegypti abundance and blood-fed rates were significantly reduced by 28.6 (95% CI 24.1%, ∞); z = −9.11) and 12.4% (95% CI 4.2%, ∞); z = −2.43), respectively. Our trial provides conclusive statistical evidence from an appropriately powered, preplanned cluster-randomized controlled clinical trial of the impact of a chemical intervention, in this case a spatial repellent, to reduce the risk of ABV transmission compared to a placebo.