Assessment of the pathogen genomics landscape highlights disparities and challenges for effective AMR Surveillance and outbreak response in the East African community.

The East African Community (EAC) grapples with many challenges in tackling infectious disease threats and antimicrobial resistance (AMR), underscoring the importance of regional and robust pathogen genomics capacities. However, a significant disparity exists among EAC Partner States in harnessing bacterial pathogen sequencing and data analysis capabilities for effective AMR surveillance and outbreak response. This study assesses the current landscape and challenges associated with pathogen next-generation sequencing (NGS) within EAC, explicitly focusing on World Health Organization (WHO) AMR-priority pathogens. The assessment adopts a comprehensive approach, integrating a questionnaire-based survey amongst National Public Health Laboratories (NPHLs) with an analysis of publicly available metadata on bacterial pathogens isolated in the EAC countries. In addition to the heavy reliance on third-party organizations for bacterial NGS, the findings reveal a significant disparity among EAC member States in leveraging bacterial pathogen sequencing and data analysis. Approximately 97% (n = 4,462) of publicly available high-quality bacterial genome assemblies of samples collected in the EAC were processed and analyzed by external organizations, mainly in Europe and North America. Tanzania led in-country sequencing efforts, followed by Kenya and Uganda. The other EAC countries had no publicly available samples or had all their samples sequenced and analyzed outside the region. Insufficient local NGS sequencing facilities, limited bioinformatics expertise, lack of adequate computing resources, and inadequate data-sharing mechanisms are among the most pressing challenges that hinder the EAC's NPHLs from effectively leveraging pathogen genomics data. These insights emphasized the need to strengthen microbial pathogen sequencing and data analysis capabilities within the EAC to empower these laboratories to conduct pathogen sequencing and data analysis independently. Substantial investments in equipment, technology, and capacity-building initiatives are crucial for supporting regional preparedness against infectious disease outbreaks and mitigating the impact of AMR burden. In addition, collaborative efforts should be developed to narrow the gap, remedy regional imbalances, and harmonize NGS data standards. Supporting regional collaboration, strengthening in-country genomics capabilities, and investing in long-term training programs will ultimately improve pathogen data generation and foster a robust NGS-driven AMR surveillance and outbreak response in the EAC, thereby supporting global health initiatives.

Risks of snakebite and challenges to seeking and providing treatment for agro-pastoral communities in Tanzania.

BACKGROUND: Continuous occurrence of snakebite incidences and the vulnerability of some communities remain a critical problem in sub-Saharan Africa. Despite causing permanent disability to almost half a million people annually and numerous deaths, snakebite and associated complications are still largely neglected. This study aimed at elucidating risk factors associated with snakebite cases, treatment availability and case management practices for vulnerable agro-pastoralist communities in Northern Tanzania. METHODS: Data was collected in the Monduli (Arusha region) and the Simanjiro (Manyara region) districts in Tanzania. Interviews with 101 snakebite victims or their guardians and 13 health professionals from 3 health centers in the districts were conducted. Additionally, case records of patients admitted between 2007 and 2019 to the Meserani Snakebite Clinic were obtained. RESULTS: This study showed that appropriate treatment for snakebite including anti-venom, is difficult to access and that snakebite incidences were significantly linked to factors such as gender, age, socio-economic activity, season of the year, and whether being at home or out in the fields. Anti-venom and trained health professionals were only available at the Meserani Snake Park Clinic. Men were bitten most often (χ2 = 62.08, df = 4, p-value < 0.0001). Overall, adults between the ages of 18 and 60 years (χ2 = 62.08, df = 4, p-value < 0.0001) received most bites, usually while outdoors herding cattle in the dry season. A significant majority of victims looked for traditional treatment first (52.7%, χ2 = 29.541, df = 2, p-value = 0.0001). The results of this study present crucial information on what is needed to improve the accessibility to appropriate treatment after a snakebite among agro-pastoral communities. CONCLUSION: The situation regarding morbidity and mortality due to the inaccessibility of common treatment for snakebite in northern Tanzania is challenging. Reliance on traditional medicine exacerbates the situation. There is dire need to involve affected communities, researchers, the government, clinicians and the public in general, to work together and take part in the global snakebite initiative. Communities and health professionals recognise the underlying challenges and have valuable suggestions on how to improve the situation.