Addressing the challenges of establishing quality wastewater or non- sewered sanitation-based surveillance, including laboratory and epidemiological considerations, in Malawi

Learning from clinical laboratories, wastewater or environmental (including non-sewered sanitation) environmental microbiology laboratories can be established in resource-limited settings that focus on pathogen detection and pandemic prevention. Transparent discussions on the laboratory challenges and adaptations required for this can help meet the future requirements of health research and surveillance. This report aims to describe the challenges encountered when setting up a wastewater or environmental laboratory for multipathogen surveillance in Malawi, a resource-limited setting, as well as the lessons learnt. We identified nine unifying themes: what to monitor, human resource capacity, indicators of data quality, equipment availability, supply of consumable goods, ongoing operation and maintenance of the laboratory, application of localised guidelines for laboratory operations, lack of real-time clinical correlation for calibration and localised ethical considerations. Over our 6-month timeline, only Salmonella typhi, Vibrio cholerae and severe acute respiratory syndrome coronavirus 2 analyses were set-up. However, we were unable to set-up measles and tuberculosis analyses owing largely to supply delays. By establishing this system at a public higher education academic laboratory in Malawi, we have ensured that ongoing capacity building and piloting of public health work is conducted in the country, rather than relying on non-governmental organisations or reference laboratory support beyond national borders. This work is not intended to replace clinical testing but rather demonstrates the potential for adapting higher education academic laboratory infrastructure to add wastewater or environmental (including non-sewered sanitation) samples, where appropriate, as additive epidemiological data for better pandemic preparedness

Microbial community function and bacterial pathogen composition in pit latrines in peri-urban Malaw

Despite the widespread global reliance on pit latrines as improved sanitation systems, the decomposition of waste within pit latrines is poorly understood. One area needing elucidation is the characterization and function of microbial communities within pit latrines. To address this gap, we characterized the microbial communities of 55 lined pit latrines at three sampling layers from two communities in peri-urban Malawi. The microbial communities of the fecal sludge samples were analyzed for beta diversity, pathogen presence, and functional profiling. Household surveys were conducted and used to compare microbial community patterns to household characteristics and pit latrine use patterns. Compared to activated sludge, anaerobic digestion in municipal wastewater systems, and human gut microbiomes, pit latrines were found to contain unique microbial communities. While the microbial community composition as a whole did not vary by sampling depth, pathogen composition varied by sampling depth, location, and household water source. The inferred microbial function also varied by depth (e.g., increase in methanogens and decrease in aerobes with depth). The richness of lined pit latrines determined from surface samples from eight latrines was found to be representative for a given area. Samples from middle and lower depths collected using a Gulper pump did not provide more information on richness, a result that informs future sampling designs. These findings are important for improving waste-based epidemiology (WBE) approaches to understand community health and waste degradation characterization of lined pit latrines

Microbial community function and bacterial pathogen composition in pit latrines in peri-urban Malawi

Despite the widespread global reliance on pit latrines as improved sanitation systems, the decomposition of waste within pit latrines is poorly understood. One area needing elucidation is the characterization and function of microbial communities within pit latrines. To address this gap, we characterized the microbial communities of 55 lined pit latrines at three sampling layers from two communities in peri-urban Malawi. The microbial communities of the fecal sludge samples were analyzed for beta diversity, pathogen presence, and functional profiling. Household surveys were conducted and used to compare microbial community patterns to household characteristics and pit latrine use patterns. Compared to activated sludge, anaerobic digestion in municipal wastewater systems, and human gut microbiomes, pit latrines were found to contain unique microbial communities. While the microbial community composition as a whole did not vary by sampling depth, pathogen composition varied by sampling depth, location, and household water source. The inferred microbial function also varied by depth (e.g., increase in methanogens and decrease in aerobes with depth). The richness of lined pit latrines determined from surface samples from eight latrines was found to be representative for a given area. Samples from middle and lower depths collected using a Gulper pump did not provide more information on richness, a result that informs future sampling designs. These findings are important for improving waste-based epidemiology (WBE) approaches to understand community health and waste degradation characterization of lined pit latrines

Addressing the challenges of establishing quality wastewater or non-sewered sanitation-based surveillance, including laboratory and epidemiological considerations, in Malawi

Learning from clinical laboratories, wastewater or environmental (including non-sewered sanitation) environmental microbiology laboratories can be established in resource-limited settings that focus on pathogen detection and pandemic prevention. Transparent discussions on the laboratory challenges and adaptations required for this can help meet the future requirements of health research and surveillance. This report aims to describe the challenges encountered when setting up a wastewater or environmental laboratory for multipathogen surveillance in Malawi, a resource-limited setting, as well as the lessons learnt. We identified nine unifying themes: what to monitor, human resource capacity, indicators of data quality, equipment availability, supply of consumable goods, ongoing operation and maintenance of the laboratory, application of localised guidelines for laboratory operations, lack of real-time clinical correlation for calibration and localised ethical considerations. Over our 6-month timeline, only Salmonella typhi, Vibrio cholerae and severe acute respiratory syndrome coronavirus 2 analyses were set-up. However, we were unable to set-up measles and tuberculosis analyses owing largely to supply delays. By establishing this system at a public higher education academic laboratory in Malawi, we have ensured that ongoing capacity building and piloting of public health work is conducted in the country, rather than relying on non-governmental organisations or reference laboratory support beyond national borders. This work is not intended to replace clinical testing but rather demonstrates the potential for adapting higher education academic laboratory infrastructure to add wastewater or environmental (including non-sewered sanitation) samples, where appropriate, as additive epidemiological data for better pandemic preparedness

Impact of sampling depth on pathogen detection in pit latrines.

Wastewater based epidemiology (WBE) is increasingly used to provide decision makers with actionable data about community health. WBE efforts to date have primarily focused on sewer-transported wastewater in high-income countries, but at least 1.8 billion people in low- and middle-income countries (LMIC) use onsite sanitation systems such as pit latrines and septic tanks. Like wastewater, fecal sludges from such systems offer similar advantages in community pathogen monitoring and other epidemiological applications. To evaluate the distribution of enteric pathogens inside pit latrines-which could inform sampling methods for WBE in LMIC settings unserved by sewers-we collected fecal sludges from the surface, mid-point, and maximum-depth of 33 pit latrines in urban and peri-urban Malawi and analyzed the 99 samples for 20 common enteric pathogens via multiplex quantitative reverse transcription PCR. Using logistic regression adjusted for household population, latrine sharing, the presence of a concrete floor or slab, water source, and anal cleansing materials, we found no significant difference in the odds of detecting the 20 pathogens from the mid-point (adjusted odds ratio, aOR = 1.1; 95% confidence interval = 0.73, 1.6) and surface samples (aOR = 0.80, 95% CI = 0.54, 1.2) compared with those samples taken from the maximum depth. Our results suggest that, for the purposes of routine pathogen monitoring, pit latrine sampling depth does not strongly influence the odds of detecting enteric pathogens by molecular methods. A single sample from the pit latrines' surface, or a composite of surface samples, may be preferred as the most recent material contributed to the pit and may be easiest to collect