Introduction

Wastewater and environmental surveillance (WES) involves systematic collection, processing, and analysis of wastewater, fecal sludge, or surface waters impacted by human excreta to generate community-level health information on public health threats and inform public health action (Fig. 1). This tends to be viewed more widely in terms of sampling media from wastewater surveillance which generally involves only piped sewer system collection. Beyond outbreak preparedness and response, WES can collect data on pathogens, biomarkers, and antimicrobial resistance genes that could address data gaps and target public health actions related to several of the United Nations’ 17 Sustainable Development Goals (SDGs)1, notably:

  • SDG 3.1–3.3, 3.9, 3.d (good health and well-being)—WES could fill gaps in understanding critical communicable disease health information and presence of hazardous chemicals where community medical access is poor or unreliable.

  • SDG 6 (clean water and sanitation)—WES could be used to monitor enteric diseases to evaluate the health impact of water, sanitation, and hygiene programs.

  • SDG 11.6., 11.7, 11.a, 11.b (sustainable cities and communities)—In urban areas, where population density increases disease transmission risk, information from WES could efficiently guide targeted public health interventions and development of improved sanitation infrastructure and in rural areas to additionally advocate for improved medical access.

  • SDG 13.3 (climate action)—WES can monitor levels of pathogens affected by rising temperatures, changes in rainfall patterns, and increasingly frequent disasters, to drive public health response and adaptation measures.

Fig. 1: The process of wastewater and environmental surveillance in support of community health indicators.
figure 1

The panels present the process for systematic collection, processing, and analysis of wastewater, fecal sludge, or surface waters impacted by human excreta to generate community-level health information on public health threats and inform public health action.

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Outside of funding and lab personnel (which are both in much greater abundance in high-income countries (HICs)), many of the WES challenges faced by low- and middle-income countries (LMICs) are also challenges in HICs, particularly in rural and underserved regions. While 81% of the global population lives in LMICs2, most WES success stories during the COVID-19 pandemic emerged from HICs3. The attention in LMICs has been on polio-specific surveillance, despite high risks of emergence of epidemic- and pandemic prone pathogens such as mpox whereby surveillance is possible but additionally has unique ethical and legal issues in some LMICs4. Additionally, focusing on wastewater surveillance within centralized systems, rather than WES, leaves behind the 58% of the global population not connected to sewers5. Although complex due to variable infrastructure and smaller populations served, non-sewered sanitation systems (NSS)6, which are more common within LMICs, can also be sampled. As WES researchers and practitioners working across three continents, we draw on our experiences in Bangladesh, Ghana, Malawi, South Africa, and the United States, with several of us having worked together and watched the field grow over the past decade. The nature of our WES field experiences spans both sewered and non-sewered sanitation systems, as academics, engineers, and research managers. Working across different national contexts, we came together around the often unmentioned link between WES and the SDGs. Through inter-practitioner dialog and reflection we advocate for the establishment of WES systems to complement other public health surveillance programs (e.g., case-based surveillance, syndromic surveillance) to bridge SDG data gaps in LMICs.

Challenges and considerations for WES in LMICs and non-sewered settings

For WES to be adopted more widely in LMICs, challenges due to knowledge gaps, resource limitations, and context-specific considerations throughout each implementation stage (sample collection in NSS settings, laboratory processing, data analysis and dissemination, and public health action) must be addressed7,8.

Sampling challenges

Selecting NSS or environmental sampling sites can be challenging due to toilet system variation and limited information on the contributing population, unique safety considerations, and possible impact of animal inputs. Given that the efficiency of wastewater surveillance in urban HICs derives often from single samples representing thousands if not millions of people all combined within a single pipe, the application of WES in NSS contexts requires logistical, financial, and ethical (e.g., identifiability of samples/data) considerations for what may be as few as tens or hundreds of people. Automatic composite samples are common for collecting representative wastewater samples in urban HICs but are usually not feasible or even relevant in NSS settings. Instead, passive samplers (i.e., deploying an absorbent material for a specified period of time9;) or grab samples (i.e., collected at a single point in time10) are often used in LMICs. HICs also have low-resource areas11 where passive samplers or grab samples could be appropriate, an opportunity where LMIC and HIC WES communities can work in concert together to address sampling challenges.

As an example, researchers in South Africa found that it was challenging to establish a WES sampling strategy for NSS where sample variation can be high, as toilet systems vary from communal or shared facilities to household, wet (flushing water) to dry (no flushing water), and temporary (e.g. chemical toilets) to permanent. Specifically, Urine Diversion Dry Toilets proved to be impractical12. To overcome sampling challenges in South Africa, run-off and stream samples with passive sampling devices near urban, informal, non-sewered settlements provided a SARS-CoV-2 RNA signal indicating the presence of the pathogen in the community12. Additionally, there are unique safety considerations for sample collectors noted in Malawi, such as needing to clean workwear by hand after sample collection. A similar key challenge for researchers in Bangladesh was filling gaps in information about the sanitation systems to develop sampling designs where there is a combination of sewerage, non-sewered sanitation, and discharge of feces directly to open drains and canals. Researchers in that case went through an extensive process that included: (1) engaging key partners from government and development organizations to understand sanitation and drainage infrastructures/networks, the population density of the sampling areas, community maps, and watersheds; (2) scoping visits and transect walks to “ground truth” information obtained from meetings and to identify potential sampling points; and (3) evaluating the logistical feasibility of sampling from potential sampling points. Further, in Ghana, sampling sites with public latrines were identified through engagement with national, regional, and local authorities13. Partner engagements also led to schools, hospitals, market centers, and streams used for clothes washing each being selected as representative WES sampling sites, based on understanding where most of the population convenes daily13.

Limited laboratory capacity

Laboratory capacity for WES is often limited in LMICs. In HICs, WES is usually based on molecular methods, which may not be practical in LMICs due to the significant human capacity and technology required. Instead, some LMIC sites have found culture-based methods to be more feasible. Due to the focus on molecular work for WES in HICs, many downstream steps for culture methods, including interpretation and public health action, are less developed. Culture-based methods also generally limit surveillance to a smaller subset of pathogens due to the specificity of the methods as opposed to molecular methods where multiple target integration is easier. Further, though laboratory analysis methods for fecal sludge samples may be similar to highly standardized and validated methods used for testing wastewater treatment plant biosolids for pathogens, this helpful similarity between HICs and LMICs laboratory capacity is not often recognized.

Requirements of refrigerators, freezers, laboratory benches, and centrifuges often cause basic procurement, operating, and maintenance challenges8. There are also often supply chain challenges related to personal protective equipment, sampling supplies, controls/standards, cartridges, filters, primers/probes, extraction kits, and other consumables. Importing laboratory supplies can be costly if local or regional retailers and supply manufacturers are limited or non-existent. As an example, in Malawi, the average SARS-CoV-2 wastewater processing cost per sample ranged from $25−$74 (Blantyre)14. Potential solutions to overcome equipment and supply obstacles requires manufacturing in LMICs along the entire supply chain, another area of potential partnership with HICs.

In some instances, there are no laboratories in the LMIC available to process WES samples, meaning countries may be required to ship samples to surrounding countries or within the same country for testing, which increases costs and time associated with analysis and reporting. There can also be administrative barriers to shipping samples, e.g. in terms of preparing and knowing required accompanying documentation such as Material Transfer Agreements. In two municipalities in Northern Ghana with a lack of a laboratory facilities to process and analyze environmental samples13,15, samples were stored in a refrigerator for a week after collection, before being transported in cold chain for over 500 km (9–10 h in a bus) to a central lab in the capital Accra. Similarly, in the Rohingya Refugee Camp in Cox’s Bazar, Bangladesh, WES samples were transported by bus for 12−14 h, maintaining cold chain, to the capital city of Dhaka for processing. From our experience, LMIC WES delays in sample processing are common. WES is most interpretable and actionable when assessing trends over time, so any laboratory disruption (e.g., delayed transport, staff turnover, supply chain challenges, skipped samples) may impact data interpretability. Efforts should be made to increase basic environmental laboratory capacity, including training laboratory staff, developing and implementing laboratory-specific standard operating procedures and quality management systems, and procuring equipment, to strengthen institutional knowledge, retention, technical capacity, supply chains and defined spaces for processing WES samples. Novel onsite rapid testing technologies could provide testing capability for certain targets16,17 in settings with insufficient laboratory capacity. These rapid, automated testing technologies should be seen as secondary to building environmental microbiology laboratory capacity though, as onsite rapid testing technologies are generally less sensitive than traditional laboratory techniques. Furthermore, these rapid testing technologies do not increase environmental laboratory capacity, which is one of the main factors that contributes to the sustainability of WES programs across several SDGs.

Data reporting and integration

Online dashboards can efficiently communicate WES data with citizens in HICs18; but recently many HICs are also facing difficulties in integrating WES into their routine monitoring campaigns, especially after COVID-19 was no longer a severe issue. With rapid-response pathogens (such as mpox and measles in new outbreak areas) emerging quickly, there often is neither time nor resources to quickly develop data reporting and integration strategies. In many LMIC settings these challenges are further complicated by limited or unreliable internet access, making online dashboards difficult to access. Ethical considerations around dashboards sharing data from vulnerable populations is an area where high-poverty and rural communities in both HICs and LMICs can learn from one another. For example, small communities and tribal communities in the United States are not included on the National Wastewater Surveillance System dashboard19 as sharing their data may cause harm or stigma. In Ghana, there is an existing online platform for clinical surveillance data reporting but there is no complementary structure for WES. Similarly, in Malawi, there are several WhatsApp groups sharing clinical surveillance data, but there are no complementary structures for sharing WES data. WES project planning should also cover arrangements for feeding back results to communities, not just professionals. Written communications or reports shared with public health leadership, policymakers, and other interested parties on a regular basis may be more sustainable than an internet hosted public dashboard with regards to data reporting and integration for WES considerations in LMICs. Also, animal fecal inputs, whether from livestock or wildlife, may enter environmental samples such as surface waters and create additional challenges for interpreting data, particularly for zoonotic diseases (e.g., cryptosporidiosis, giardiasis, and highly pathogenic avian influenza). The impact of animal inputs of these diseases could be especially high in areas of LMICs where humans and animals live in closer proximity.

Community participation and partner engagement

Non-sewered and environmental surveillance samples are likely to be collected from institutions, communal facilities, and surface water sources in or near communities, making sample collection activities more visibly prominent as compared to sampling from sewered settings (e.g., manholes and wastewater treatment plants). Structured partner engagement, emphasizing transparency and building trust with community members, is necessary to ensure:

  • The community is supportive and understands the purpose of the work;

  • Sampling sites are representative of all population groups and distributed equitably;

  • There are clear expectations on data ownership;

  • Findings are effectively translated for culturally-appropriate public health action; and

  • The WES program is sustainable over the long term.

For non-sewered and environmental surveillance data to be useful, it is important, but quite difficult, to determine who is contributing to samples to validate epidemiological data. A comprehensive partner engagement strategy developed during the startup phase should be followed, revisited, and revised as needed, to ensure the right parties are involved in the right way at the right time20. Partners must be meaningfully engaged by structured community meetings and other means, throughout all phases of the process. Decisions must be informed by community/partner needs and opinions, ensuring informed public health decisions and actions that maximize benefits for the community of interest. A recent example of this approach was implemented in Accra, Ghana, during the COVID-19 pandemic and subsequently replicated in Nanumba North Municipality and Mion Districts in Northern Ghana13,15. In both, a stakeholder analysis and an engagement plan were developed and implemented from the outset for real-time public health actions that benefited the communities of interest, complementing clinical surveillance. In Malawi, field sampling teams conversant with the language and culture found that building trust and gaining consent were necessary during each sample collection day and not just at the start of the project8.

Also crucial is engaging key local and national government entities throughout the WES process. For example, WES programs that originate within public health agencies or ministries of health need the cooperation of wastewater utilities, pit latrine emptiers, and other city sanitation authorities who may manage access to sampling points. Water and sanitation authorities may also be interested and able to act on results that fall within their purview and align with SDG 6. Likewise, it would be impossible for sanitation authorities to establish WES programs without engaging the public health sector, including government entities.

Ethics

Numerous ethical dimensions warrant consideration during program design and implementation to ensure WES for public health promotes the common good in LMICs21,22,23. Data from WES programs that capture relatively small populations (a few hundred to a few thousand people)—expected to be common in NSS systems—should be stored securely and given careful consideration before locations are shared to minimize the chance for group stigmatization or other identifiability concerns. WES programs must be based on effective methods that can be expected to produce reliable results, based on the available evidence, to generate data that merit the expenditure of limited public health resources. The rationale behind any WES program needs to be well-articulated and the plans for data ownership, sharing, and use—including any potential future uses of archived samples—needs to be clearly specified across all partners. Issues surrounding biobanking and sample storage also need to be addressed prior to establishing WES systems, clearly identifying who is empowered to make decisions on future uses of the samples. Ultimately, ethical WES implementation requires balancing data utility with community protection and trust.

Public health action

Appropriate use cases for WES implementation (e.g., disease elimination or monitoring of seasonal trends) have not been unequivocally established for many health targets for HICs or LMICs. At a minimum, longitudinal and continuous WES in static locations provides public health authorities with data regarding the presence of pathogens or biomarkers and trends in magnitude within community under surveillance. These data, together with other available public health surveillance data, allow authorities to make informed intervention decisions. For example, knowledge of antimicrobial resistance profiles in health facility effluent may provide important data on which to base therapeutic decisions in the absence of available clinical or facility level (such as surface swab testing). In resource-limited settings, where funding a WES program might mean not funding another valuable program, a key research question is how to determine if WES data outweighs the cost or value of the alternative public health data or program. This is another area where researchers from HICs can collaborate with those in LMICs to answer such questions.

Policy and funding for sustainable programs

As with policy development for any public health area, research at every level of the WES data-to-policy pipeline is required to establish an evidence base for chosen interventions and their application towards the SDGs. There are several LMIC-specific applied research questions to be answered to address these policy challenges across systematic reviews, modeling and cost effectiveness studies, guidelines, health technology assessments, and non-binding recommendations. Figure 2 provides examples of some of the most critical research questions that need to be answered. The LMIC WES research community needs to adequately respond to these specific research questions that can lead to WES policy, with the goal of finding the optimal balance of data sources to support public health decision-making in various contexts. Critically, horizontal multi-pathogen WES systems that complement other public health surveillance programs must be established and evaluated for cost and impact alongside existing surveillance systems.

Fig. 2: Wastewater and environmental surveillance data-to-policy pipeline.
figure 2

Example research questions for low- and middle-income country researchers working in support of the Sustainable Development Goals (SDGs) are presented.

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Quantifying WES benefits and the cost-effectiveness of surveillance is a challenge24, and additional data are often needed when designing downstream public health interventions. Health economists have taken an “expected value of information” approach25,26 in comparing surveillance data from different modalities and weighing these against hypothetical counterfactuals of not having data in order to discern optimal surveillance approaches. One of the most sustainable and long-term impacts of WES programs might lie in archived or biobanked samples, a resource constraint in LMICs in terms of available freezers with reliable power sources and ongoing personnel time to ensure chain-of-custody. Potential WES funders need to appreciate these methodological considerations when they outline funding agendas so that appropriate evidence is gathered to support recommendations or practice regarding integrating WES with other public health surveillance systems or even using WES as a standalone tool. On the laboratory side, for example, the Global Polio Eradication Initiative (GPEI) laboratory platforms alongside clinical genomic capacity building efforts provide building blocks for WES programs: GPEI could provide processing spaces for environmental samples prior to those samples entering more clinically-focused molecular/genomic workflow spaces. However, this integration would require policy- and coordination-focused efforts to expand GPEI platforms to other pathogen targets alongside laboratory efforts to ensure quality practices are maintained and GPEI or clinical workflows are not compromised. To enable ethical implementation of WES, the principles of ethical public health surveillance23 need be extended to WES systems, such that WES is ethically and otherwise embedded as an extension of—and not in conflict with—the existing public health surveillance infrastructure. Currently, WES is often housed within pathogen-specific programs now, due to how policy is written. In order to make costs and benefits balance, WES policy and funding schemes need to be integrated across both public health decision-making and sanitation infrastructure themes.

A call to action

We have presented an argument for advancing complementary wastewater and environmental surveillance in LMICs, recognizing its importance for global public health outbreak prevention and response. We also highlight its potential to deliver additional benefits, such as bridging SDG data gaps, and issue a call to action with specific applied research questions that must be addressed to achieve this. Critical applied research questions can be answered via systematic reviews, modeling or cost effectiveness studies, guidelines, health technology assessments, and non-binding recommendations. Because LMICs and HICs share many of the same challenges, this is an area ripe for collaboration27,28. Method development, context-specific considerations, and target or program priorities may be shared between countries. This collaboration can be supported through Communities of Practice at both the global and regional levels. Global CoPs can bring together HIC and LMIC colleagues to address shared challenges, while regional CoPs allow peer countries to exchange experiences that strengthen WES programs, accelerate new advances, and improve response efforts29. WES can play a critical role in addressing data gaps needed to measure progress toward SDGs, particularly with respect to goals 3, 6, 11, and 13. LMIC study sites should play a greater role in establishing the science of when and how WES programs can be useful for addressing the SDGs, especially as health funding appears increasingly limited, for coordinated research along the data-to-policy pipeline.