Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach

Abstract

BackgroundWorldwide, the number of emerging and re-emerging infectious diseases is increasing, highlighting the importance of global disease pathogen surveillance. Traditional population-based methods may fail to capture important events, particularly in settings with limited access to health care, such as urban informal settlements. In such environments, a mixture of surface water runoff and human feces containing pathogenic microorganisms could be used as a surveillance surrogate.MethodWe conducted a temporal metagenomic analysis of urban sewage from Kibera, an urban informal settlement in Nairobi, Kenya, to detect and quantify bacterial and associated antimicrobial resistance (AMR) determinants, viral and parasitic pathogens. Data were examined in conjunction with data from ongoing clinical infectious disease surveillance.ResultsA large variation of read abundances related to bacteria, viruses, and parasites of medical importance, as well as bacterial associated antimicrobial resistance genes over time were detected. Significant increased abundances were observed for a number of bacterial pathogens coinciding with higher abundances of AMR genes. Vibrio cholerae as well as rotavirus A, among other virus peaked in several weeks during the study period whereas Cryptosporidium spp. and Giardia spp, varied more over time.ConclusionThe metagenomic surveillance approach for monitoring circulating pathogens in sewage was able to detect putative pathogen and resistance loads in an urban informal settlement. Thus, valuable if generated in real time to serve as a comprehensive infectious disease agent surveillance system with the potential to guide disease prevention and treatment. The approach may lead to a paradigm shift in conducting real-time global genomics-based surveillance in settings with limited access to health care.

Wastewater Surveillance of Antimicrobial Resistance in Human Populations: A Systematic Review

“…Longitudinal studies demonstrating a human-wastewater AMR correlation typically included longer sampling intervals (six months versus two months for negative/inconclusive studies) and timeframes. For the highest resolution sampling campaigns 26,40 which used two week sampling intervals across different timeframes, one study observed an association between ampicillin-resistant wastewater and contemporaneous clinical isolates over 12 months, whereas the other found changes in metagenomic read abundances were not matched by changes in contemporaneous clinical surveillance over three months. Directly comparing these studies is difficult due to different methodologies, but the findings would support the fact that studies sampling over a timeframe of ≥6 months are more likely to capture associations with human population-level AMR (Fig.3B).…”

“…Only 2/6 indirect studies reported significant relationships compared to 4/9 direct studies. Smaller catchments also limit sample sizes potentially obscuring signals from detection which may have contributed to unclear/negative outcomes 40 . When comparing direct studies, similar sampling methods and test approaches are seen, but amongst studies identifying wastewater-human AMR correlations, more…”

“…The remaining 3/7 sequencing-based studies reported no relationship 33 between wastewater and human AMR or inconclusive results 33,40 . One inconclusive study conducted a metagenomics-based longitudinal surveillance study 40 comparing resistomes generated from drainage ditch wastewater and contemporaneous local surveillance data consisting of household morbidity and healthcare usage, including diarrhoea/fever cases and clinical faecal culture. Significant increases/decreases in resistome read abundance were not associated with increases in reported diarrhoea or clinical faecal isolates.…”

The Pathogen Genomics in Public HeAlth Surveillance Evaluation (PG-PHASE) Framework: An Implementation Science Approach to Evaluating Pathogen Whole Genome Sequencing in Public Health

“…The United States and the United Kingdom have both implemented national WGS services [1,2], and in 2016, 26 European countries reported the use of WGS in routine public health practice [3]. The reduction in cost and advancement of portable sequencing technologies has continued to increase accessibility for low-resource settings and low-and middle-income countries [4][5][6].…”

Could Water and Sanitation Shortfalls Exacerbate SARS-CoV-2 Transmission Risks?

“…On the positive side, fecal shedding of SARS-CoV-2 can be exploited for community surveillance of wastewater or human waste using similar methods that would be required for risk evaluation. 22 , 40 Enteric pathogen, polio, and antimicrobial resistance environmental surveillance could be leveraged, where these have been initiated, 10 , 41 , 42 but sites with no access to sewerage, typically not used for surveillance, must also be included. In high-risk settings, waste and wastewater-based epidemiology could help balance sampling biases inherent in case- and contact-tracing–based human testing for COVID-19 and consequently predict prevalence.…”