Estimation of global recoverable human and animal fecal biomass

Purchase, consumption, and ownership of chickens and chicken products among households in Maputo, Mozambique: A cross-sectional study

Background

Chickens are an important source of animal protein, nutrition, and income in many low- and middle-income countries (LMICs). They are also a major reservoir of enteropathogens that contribute to the burden of illnesses among children. Food systems present a risk for transmission of enteropathogens from poultry to humans, but there is a lack of population-level data on the pattern of purchase, ownership, and consumption of live chickens and their products in LMICs to better characterize that risk.

Methods

To assess chicken purchase, ownership, and consumption practices, we conducted a population-based survey using a structured questionnaire in Maputo, Mozambique in 2021. Multi-stage cluster sampling was used to obtain a representative sample of households in our study area. To minimize sampling bias and ensure a representative sample, we applied survey weighting using district-level population data and estimated weighted population-level values.

Results

Heads of 570 households in Maputo completed our survey. Approximately half of these households purchased broiler chicken meat (weighted percentage of households: 44.8%) and eggs (46.5%) in the previous week of the survey date, while indigenous chicken meat was less popular (1,950, 1.1%). The most common source of chicken products was corner stores (i.e., small convenience shops on streets), followed by wet markets. Live chickens were raised by 15.6% of households, and chicken feces were observed on the floor or ground at the majority of these households during house visits.

Discussion

Our findings suggest that poultry provides a major source of animal protein in this setting. With the predicted growth of poultry farming in LMICs in the coming decades, ensuring food safety at the primary sources of chicken products (corner stores and wet markets) in urban areas will be critical to mitigate health risks.

Sanitation in urban areas may limit the spread of antimicrobial resistance via flies

Synanthropic filth flies are common where sanitation is poor and fecal wastes are accessible to them. These flies have been proposed as mechanical vectors for the localized transport of fecal microbes including antimicrobial resistant (AMR) organisms and associated antimicrobial resistance genes (ARGs), increasing exposure risks. We evaluated whether an onsite sanitation intervention in Maputo, Mozambique reduced the concentration of enteric bacteria and the frequency of detection of ARGs carried by flies collected in household compounds of low-income neighborhoods. Additionally, we assessed the phenotypic resistance profile of Enterobacteriaceae isolates recovered from flies during the pre-intervention phase. After fly enumeration at study compounds, quantitative polymerase chain reaction was used to quantify an enteric 16S rRNA gene (i.e., specific to a cluster of phylotypes corresponding to 5% of the human fecal microflora), 28 ARGs, and Kirby Bauer Disk Diffusion of Enterobacteriaceae isolates was utilized to assess resistance to eleven clinically relevant antibiotics. The intervention was associated with a 1.5 log10 reduction (95% confidence interval: -0.73, -2.3) in the concentration of the enteric 16S gene and a 31% reduction (adjusted prevalence ratio = 0.69, [0.52, 0.92]) in the mean number of ARGs per fly compared to a control group with poor sanitation. This protective effect was consistent across the six ARG classes that we detected. Enterobacteriaceae isolates-only from the pre-intervention phase-were resistant to a mean of 3.4 antibiotics out of the eleven assessed. Improving onsite sanitation infrastructure in low-income informal settlements may help reduce fly-mediated transmission of enteric bacteria and the ARGs carried by them.

Genomic surveillance for antimicrobial resistance - a One Health perspective

Antimicrobial resistance (AMR) - the ability of microorganisms to adapt and survive under diverse chemical selection pressures - is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted 'One Health' approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.

A review on the effects of discharging conventionally treated livestock waste to the environmental resistome

Globally, animal production has developed rapidly as a consequence of the ongoing population growth, to support food security. This has consequently led to an extensive use of antibiotics to promote growth and prevent diseases in animals. However, most antibiotics are not fully metabolized by these animals, leading to their excretion within urine and faeces, thus making these wastes a major reservoir of antibiotics residues, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment. Farmers normally depend on conventional treatment methods to mitigate the environmental impact of animal waste; however, these methods are not fully efficient to remove the environmental resistome. The present study reviewed the variability of residual antibiotics, ARB, as well as ARGs in the conventionally treated waste and assessed how discharging it could increase resistome in the receiving environments. Wherein, considering the efficiency and environmental safety, an addition of pre-treatments steps with these conventional treatment methods could enhance the removal of antibiotic resistance agents from livestock waste.

Soil carbon sequestration in global working lands as a gateway for negative emission technologies

The ongoing climate crisis merits an urgent need to devise management approaches and new technologies to reduce atmospheric greenhouse gas concentrations (GHG) in the near term. However, each year that GHG concentrations continue to rise, pressure mounts to develop and deploy atmospheric CO2 removal pathways as a complement to, and not replacement for, emissions reductions. Soil carbon sequestration (SCS) practices in working lands provide a low-tech and cost-effective means for removing CO2 from the atmosphere while also delivering co-benefits to people and ecosystems. Our model estimates suggest that, assuming additive effects, the technical potential of combined SCS practices can provide 30%-70% of the carbon removal required by the Paris Climate Agreement if applied to 25%-50% of the available global land area, respectively. Atmospheric CO2 drawdown via SCS has the potential to last decades to centuries, although more research is needed to determine the long-term viability at scale and the durability of the carbon stored. Regardless of these research needs, we argue that SCS can at least serve as a bridging technology, reducing atmospheric CO2 in the short term while energy and transportation systems adapt to a low-C economy. Soil C sequestration in working lands holds promise as a climate change mitigation tool, but the current rate of implementation remains too slow to make significant progress toward global emissions goals by 2050. Outreach and education, methodology development for C offset registries, improved access to materials and supplies, and improved research networks are needed to accelerate the rate of SCS practice implementation. Herein, we present an argument for the immediate adoption of SCS practices in working lands and recommendations for improved implementation.

Quantifying Enteropathogen Contamination along Chicken Value Chains in Maputo, Mozambique: A Multidisciplinary and Mixed-Methods Approach to Identifying High Exposure Settings

BACKGROUND

Small-scale poultry production is widespread and increasing in low- and middle-income countries (LMICs). Exposure to enteropathogens in poultry feces increases the hazard of human infection and related sequela, and the burden of disease due to enteric infection in children < 5 y in particular is substantial. Yet, the containment and management of poultry-associated fecal waste in informal settings in LMICs is largely unregulated.

OBJECTIVES

To improve the understanding of potential exposures to enteropathogens carried by chickens, we used mixed methods to map and quantify microbial hazards along production value chains among broiler, layer, and indigenous chickens in Maputo, Mozambique.

METHODS

To map and describe the value chains, we conducted 77 interviews with key informants working in locations where chickens and related products are sold, raised, and butchered. To quantify microbial hazards, we collected chicken carcasses (n = 75 ) and fecal samples (n = 136 ) from chickens along the value chain and assayed them by qPCR for the chicken-associated bacterial enteropathogens C. jejuni/coli and Salmonella spp.

RESULTS

We identified critical hazard points along the chicken value chains and identified management and food hygiene practices that contribute to potential exposures to chicken-sourced enteropathogens. We detected C. jejuni/coli in 84 (76%) of fecal samples and 52 (84%) of carcass rinses and Salmonella spp. in 13 (11%) of fecal samples and 16 (21%) of carcass rinses. Prevalence and level of contamination increased as chickens progressed along the value chain, from no contamination of broiler chicken feces at the start of the value chain to 100% contamination of carcasses with C. jejuni/coli at informal markets. Few hazard mitigation strategies were found in the informal sector.

DISCUSSION

High prevalence and concentration of C. jejuni/coli and Salmonella spp. contamination along chicken value chains suggests a high potential for exposure to these enteropathogens associated with chicken production and marketing processes in the informal sector in our study setting. We identified critical control points, such as the carcass rinse step and storage of raw chicken meat, that could be intervened in to mitigate risk, but regulation and enforcement pose challenges. This mixed-methods approach can also provide a model to understand animal value chains, sanitary risks, and associated exposures in other settings. https://doi.org/10.1289/EHP11761.

Prevention of human exposure to livestock faecal waste in the household: a scoping study of interventions conducted in sub-Saharan Africa

BACKGROUND

Poorly managed animal faecal waste can result in detrimental environmental and public health implications. Limiting human exposure to animal waste through Animal inclusive Water Sanitation and Hygiene (A-WASH) strategies is imperative to improve public health in livestock keeping households but has received little attention to date. A small number of A-WASH interventions have previously been identified through a systematic review by another research team, and published in 2017. To inform intervention design with the most up-to-date information, a scoping study was conducted to map the existing evidence for A-WASH in sub-Saharan Africa (SSA) emerging since the previous review.

METHODS

This review followed PRISMA guidelines to identify interventions in SSA published between January 2016 to October 2022. Databases searched included PubMed, PMC Europe, CabDirect and Web of Science. Studies were eligible for inclusion if they were written in English and documented interventions limiting human contact with animal faecal material in the SSA context. Key data extracted included: the intervention itself, its target population, cost, measure of effectiveness, quantification of effect, assessment of success, acceptability and limitations. These data were synthesized into a narrative, structured around the intervention type.

FINDINGS

Eight eligible articles were identified. Interventions to reduce human exposure to animal faecal matter were conducted in combination with 'standard' human-centric WASH practices. Identified interventions included the management of human-animal co-habitation, educational programs and the creation of child-safe spaces. No novel A-WASH interventions were identified in this review, beyond those identified by the review in 2017. Randomised Controlled Trials (RCTs) were used to evaluate six of the eight identified interventions, but as effect was evaluated through various measures, the ability to formally compare efficacy of interventions is lacking.

CONCLUSION

This study indicates that the number of A-WASH studies in SSA is increasing and the use of RCTs suggests a strong desire to create high-quality evidence within this field. There is a need for standardisation of effect measures to enable meta-analyses to be conducted to better understand intervention effectiveness. Evaluation of scalability and sustainability of interventions is still lacking in A - WASH research.

Biochar preparation and evaluation of its effect in composting mechanism: A review

This article provides an overview of biochar application for organic waste co-composting and its biochemical transformation mechanism. As a composting amendment, biochar work in the adsorption of nutrients, the retention of oxygen and water, and the promotion of electron transfer. These functions serve the micro-organisms (physical support of niche) and determine changes in community structure beyond the succession of composing primary microorganisms. Biochar mediates resistance genes, mobile gene elements, and biochemical metabolic activities of organic matter degrading. The participation of biochar enriched the α-diversity of microbial communities at all stages of composting, and ultimately reflects the high γ-diversity. Finally, easy and convincing biochar preparation methods and characteristic need to be explored, in turn, the mechanism of biochar on composting microbes at the microscopic level can be studied in depth.

Sevenfold variation in global feeding capacity depends on diets, land use and nitrogen management

Harvested food carries a fraction of the nitrogen applied through fertilization; the remainder is typically lost into the environment, impairing planetary sustainability. Using a global agriculture model that integrates key drivers of food production and nitrogen cycling, we simulated upper bounds to global feeding capacity-and associated nitrogen pollution-as a function of nitrogen limitation under organic and industrial fertilization regimes. We found that the current agricultural area could feed ~8-20 billion people under unconstrained industrial fertilization and ca. 3-14 billion under organic fertilization. These ranges are inversely correlated with animal proteins in human diets, and are a function of feed-food competition, grassland-to-cropland allocation and-in the case of organic fertilization-nitrogen use efficiency. Improved nitrogen use efficiency is required to bring nitrogen pollution within planetary sustainability limits and is also essential in narrowing down food productivity gaps between organic and industrial fertilization regimes.

Effect of ageing on the physicochemical properties of human faeces in the context of onsite sanitation

Sanitation systems involving onsite storage of faecal matter cause excreta to undergo transformation and primary treatment in-situ. However, little is known about the transformation pathway followed by fresh faeces while contained in situ. The current paper investigated this transformation under ambient conditions during a 16-week in-situ-storage period. Moisture content, drying kinetics, rheological, physicochemical, and thermal properties were analysed to determine the effects of ageing. The faeces experienced dehydration, mainly affecting moisture-dependent characteristics. Moisture content decreased from 79%wt to 26%wt, and water activity of 0.67, which corresponds mainly to the removal of interstitial bound water, reducing mass by 72%. The decreasing moisture content expectantly reduced drying ability, flowability and thermal properties (heat capacity and thermal conductivity). During this period, negligible biodegradation was recorded (volatile solids reduced by 3%), resulting in consistent chemical oxygen demand, particle size, carbon content and calorific values. Ammonium and nitrates decreased, but total nitrogen remained unchanged. Therefore, ageing affects nitrogen chemical forms and not nutrient composition. The findings demonstrate the benefits of source separation and in particular ventilated storage as a passive way to pre-treat and recover resources from faecal material.

Rapid Reverse Purification DNA Extraction Approaches to Identify Microbial Pathogens in Wastewater

Wastewater monitoring became a promising solution in the early detection of outbreaks. Despite the achievements in the identification of pathogens in wastewater using real-time PCR, there is still a lack of reliable rapid nucleic acid extraction protocols. Therefore, in this study, samples were subjected to alkali, proteinase K and/or bead-beating followed by reverse purification magnetic beads-based separation. Wastewater samples spiked with S. aureus, E. coli and C. parvum were used as examples for Gram-positive and -negative bacteria and protozoa, respectively. All results were compared with a spin column technology as a reference method. Proteinase K with bead beating (vortexing with 0.1 mm glass beads for three minutes) was particularly successful for bacterial DNA extraction (three- to five-fold increase). The most useful extraction protocol for protozoa was pre-treatment with proteinase K (eight-fold increase). The selected methods were sensitive as far as detecting one bacterial cell per reaction for S. aureus, ten bacterial cells for E. coli and two oocysts for C. parvum. The extraction reagents are cold chain independent and no centrifuge or other large laboratory equipment is required to perform DNA extraction. A controlled validation trial is needed to test the effectiveness at field levels.

Resourcelized conversion of livestock manure to porous cage microsphere for eliminating emerging contaminants under peroxymonosulfate trigger

Pollution and resource waste caused by the improper disposal of livestock manure, and the threat from the release of emerging contaminants (ECs), are global challenges. Herein, we address the both problems simultaneously by the resourcelized conversion of chicken manure into porous Co@CM cage microspheres (CCM-CMSs) for ECs degradation through the graphitization process and Co-doping modification step. CCM-CMSs exhibit excellent performance for ECs degradation and actual wastewater purification under peroxymonosulfate (PMS) initiation, and show adaptability to complex water environments. The ultra-high activity can maintain after continuous operation over 2160 cycles. The formation of C-O-Co bond bridge structure on the catalyst surface caused an unbalanced electron distribution, which allows PMS to trigger the sustainable electron donation of ECs and electron gain of dissolved oxygen processes, becoming the key to the excellent performance of CCM-CMSs. This process significantly reduces the resource and energy consumption of the catalyst throughout the life cycle of production and application.

Effects of water, sanitation, and hygiene interventions on detection of enteropathogens and host-specific faecal markers in the environment: a systematic review and individual participant data meta-analysis

BACKGROUND

Water, sanitation, and hygiene (WASH) improvements are promoted to reduce diarrhoea in low-income countries. However, trials from the past 5 years have found mixed effects of household-level and community-level WASH interventions on child health. Measuring pathogens and host-specific faecal markers in the environment can help investigate causal pathways between WASH and health by quantifying whether and by how much interventions reduce environmental exposure to enteric pathogens and faecal contamination from human and different animal sources. We aimed to assess the effects of WASH interventions on enteropathogens and microbial source tracking (MST) markers in environmental samples.

METHODS

We did a systematic review and individual participant data meta-analysis, which included searches from Jan 1, 2000, to Jan 5, 2023, from PubMed, Embase, CAB Direct Global Health, Agricultural and Environmental Science Database, Web of Science, and Scopus, of prospective studies with water, sanitation, or hygiene interventions and concurrent control group that measured pathogens or MST markers in environmental samples and measured child anthropometry, diarrhoea, or pathogen-specific infections. We used covariate-adjusted regression models with robust standard errors to estimate study-specific intervention effects and pooled effect estimates across studies using random-effects models.

FINDINGS

Few trials have measured the effect of sanitation interventions on pathogens and MST markers in the environment and they mostly focused on onsite sanitation. We extracted individual participant data on nine environmental assessments from five eligible trials. Environmental sampling included drinking water, hand rinses, soil, and flies. Interventions were consistently associated with reduced pathogen detection in the environment but effect estimates in most individual studies could not be distinguished from chance. Pooled across studies, we found a small reduction in the prevalence of any pathogen in any sample type (pooled prevalence ratio [PR] 0·94 [95% CI 0·90-0·99]). Interventions had no effect on the prevalence of MST markers from humans (pooled PR 1·00 [95% CI 0·88-1·13]) or animals (pooled PR 1·00 [95% CI 0·97-1·03]).

INTERPRETATION

The small effect of these sanitation interventions on pathogen detection and absence of effects on human or animal faecal markers are consistent with the small or null health effects previously reported in these trials. Our findings suggest that the basic sanitation interventions implemented in these studies did not contain human waste and did not adequately reduce exposure to enteropathogens in the environment.

FUNDING

Bill and Melinda Gates Foundation and the UK Foreign and Commonwealth Development Office.

Co-composting of faecal sludge and carbon-rich wastes in the earthworm's synergistic cooperation system: Performance, global warming potential and key microbiome

Composting is an effective alternative for recycling faecal sludge into organic fertilisers. A microflora-earthworm (Eisenia fetida) synergistic cooperation system was constructed to enhance the composting efficiency of faecal sludge. The impact of earthworms and carbon-rich wastes (rice straw (RS) and sawdust (S)) on compost properties, greenhouse gas emissions, and key microbial species of composting were evaluated. The addition of RS or S promoted earthworm growth and reproduction. The earthworm-based system reduced the volatile solid of the final substrate by 13.19-16.24 % and faecal Escherichia coli concentrations by 1.89-3.66 log10 cfu/g dry mass compared with the earthworm-free system. The earthworm-based system increased electrical conductivity by 0.322-1.402 mS/cm and reduced C/N by 56.16-64.73 %. The NH₄⁺:NO₃^- ratio of the final faecal sludge and carbon-rich waste was <0.16. The seed germination index was higher than 80 %. These results indicate that earthworms contribute to faecal sludge maturation. Earthworm addition reduced CO₂ production. The simultaneous addition of earthworms and RS system (FRS2) resulted in the lowest global warming potential (GWP). The microbial diversity increased significantly over time in the RS-only system, whereas it initially increased and later decreased in the FRS2 system. Cluster analysis revealed that earthworms had a more significant impact on the microbial community than the addition of carbon-rich waste. Co-occurrence networks for earthworm-based systems were simple than those for earthworm-free systems, but the major bacterial genera were more complicated. Highly abundant key species (norank_f_Chitinophagaceae and norank_f_Gemmatimonadaceae) are closely related. Microbes may be more cooperative than competitive, facilitating the conversion of carbon and nitrogen in earthworm-based systems. This work has demonstrated that using earthworms is an effective approach for promoting the efficiency of faecal sludge composting and reducing GWP.

Urban Onsite Sanitation Upgrades and Synanthropic Flies in Maputo, Mozambique: Effects on Enteric Pathogen Infection Risks

Synanthropic filth flies transport enteric pathogens from feces to food, which upon consumption poses an infection risk. We evaluated the effect of an onsite sanitation intervention─including fly control measures─in Maputo, Mozambique, on the risk of infection from consuming fly-contaminated food. After enumerating flies at intervention and control sites, we cultured fecal indicator bacteria, quantified gene copies for 22 enteric pathogens via reverse transcription quantitative polymerase chain reaction (RT-qPCR), and developed quantitative microbial risk assessment (QMRA) models to estimate annual risks of infection attributable to fly-contaminated foods. We found that the intervention reduced fly counts at latrine entrances by 69% (aRR = 0.31, [0.13, 0.75]) but not at food preparation areas (aRR = 0.92, [0.33, 2.6]). Half of (23/46) of individual flies were positive for culturable Escherichia coli, and we detected ≥1 pathogen gene from 45% (79/176) of flies, including enteropathogenic E. coli (37/176), adenovirus (25/176), Giardia spp. (13/176), and Trichuris trichiura (12/176). We detected ≥1 pathogen gene from half the flies caught in control (54%, 30/56) and intervention compounds (50%, 17/34) at baseline, which decreased 12 months post-intervention to 43% (23/53) at control compounds and 27% (9/33) for intervention compounds. These data indicate flies as a potentially important mechanical vector for enteric pathogen transmission in this setting. The intervention may have reduced the risk of fly-mediated enteric infection for some pathogens, but infrequent detection resulted in wide confidence intervals; we observed no apparent difference in infection risk between groups in a pooled estimate of all pathogens assessed (aRR = 0.84, [0.61, 1.2]). The infection risks posed by flies suggest that the design of sanitation systems and service delivery should include fly control measures to prevent enteric pathogen transmission.

Persistent Ascaris Transmission Is Possible in Urban Areas Even Where Sanitation Coverage Is High

In low-income, urban, informal communities lacking sewerage and solid waste services, onsite sanitation (sludges, aqueous effluent) and child feces are potential sources of human fecal contamination in living environments. Working in informal communities of urban Maputo, Mozambique, we developed a quantitative, stochastic, mass-balance approach to evaluate plausible scenarios of localized contamination that could explain why the soil-transmitted helminth Ascaris remains endemic despite nearly universal coverage of latrines that sequester most fecal wastes. We used microscopy to enumerate presumptively viable Ascaris ova in feces, fecal sludges, and soils from compounds (i.e., household clusters) and then constructed a steady-state mass-balance model to evaluate possible contamination scenarios capable of explaining observed ova counts in soils. Observed Ascaris counts (mean = -0.01 log10 ova per wet gram of soil, sd = 0.71 log10) could be explained by deposits of 1.9 grams per day (10th percentile 0.04 grams, 90th percentile 84 grams) of child feces on average, rare fecal sludge contamination events that transport 17 kg every three years (10th percentile 1.0 kg, 90th percentile 260 kg), or a daily discharge of 2.7 kg aqueous effluent from an onsite system (10th percentile 0.09 kg, 90th percentile 82 kg). Results suggest that even limited intermittent flows of fecal wastes in this setting can result in a steady-state density of Ascaris ova in soils capable of sustaining transmission, given the high prevalence of Ascaris shedding by children (prevalence = 25%; mean = 3.7 log10 per wet gram, sd = 1.1 log10), the high Ascaris ova counts in fecal sludges (prevalence = 88%; mean = 1.8 log10 per wet gram, sd = 0.95 log10), and the extended persistence and viability of Ascaris ova in soils. Even near-universal coverage of onsite sanitation may allow for sustained transmission of Ascaris under these conditions.

Environmental impacts of mass drug administration programs: exposures, risks, and mitigation of antimicrobial resistance

Mass drug administration (MDA) of antimicrobials has shown promise in the reduction and potential elimination of a variety of neglected tropical diseases (NTDs). However, with antimicrobial resistance (AMR) becoming a global crisis, the risks posed by widespread antimicrobial use need to be evaluated. As the role of the environment in AMR emergence and dissemination has become increasingly recognized, it is likewise crucial to establish the role of MDA in environmental AMR pollution, along with the potential impacts of such pollution. This review presents the current state of knowledge on the antimicrobial compounds, resistant organisms, and antimicrobial resistance genes in MDA trials, routes of these determinants into the environment, and their persistence and ecological impacts, particularly in low and middle-income countries where these trials are most common. From the few studies directly evaluating AMR outcomes in azithromycin MDA trials, it is becoming apparent that MDA efforts can increase carriage and excretion of resistant pathogens in a lasting way. However, research on these outcomes for other antimicrobials used in MDA trials is sorely needed. Furthermore, while paths of AMR determinants from human waste to the environment and their persistence thereafter are supported by the literature, quantitative information on the scope and likelihood of this is largely absent. We recommend some mitigative approaches that would be valuable to consider in future MDA efforts. This review stands to be a valuable resource for researchers and policymakers seeking to evaluate the impacts of MDA.

Effects of local handwashing agents on microbial contamination of the hands in a rural setting in Northwest Ethiopia: a cluster randomised controlled trial

OBJECTIVE

To evaluate the effectiveness of handwashing with water and wood ash in reducing faecal contamination of the hands.

DESIGN

A cluster randomised controlled trial was employed with two arms: handwashing with water and wood ash versus handwashing with water alone.

SETTING

Rural households of East Dembiya District, Central Gondar Zone, Amhara National Regional State, Ethiopia.

PARTICIPANTS

440 mothers and caregivers of children younger than 5 years assigned (1:1, 220 in each group) in clusters, with buffer zones between each cluster.

INTERVENTION

Health education on effective handwashing was given to the intervention and control groups. Participants in the intervention group used wood ash of the same quantity (ie, one closed palm).

OUTCOME MEASURES

The primary outcome was microbial contamination of the hands, measured by means of Escherichia coli counts before and after handwashing.

RESULTS

At baseline, 75.9% and 67.7% of the participants in the intervention and control groups, respectively, had dirt on their fingernails, and the hands of all participants in both groups were contaminated with E. coli. The mean E. coli counts recovered at baseline were 3.07 log10 colony forming unit (CFU)/swab in the intervention group and 3.03 log10 CFU/swab in the control group, while at endline it was 1.4 log10 CFU/swab in the intervention group and 3.02 log10 CFU/swab in the control group. The mean E.coli counts was reduced by 1.65 log10 due to the intervention (difference-in-differences: β= -1.65, 95% CI= -1.84 to -1.46).

CONCLUSION

Two-thirds of the swab samples tested positive for E. coli after handwashing with water and wood ash, which indicates wood ash is not very effective in terms of completely removing micro-organisms on the hands. However, wood ash was significantly better than water alone in reducing the concentration of faecal coliform organisms on the hands. Local health authorities should primarily promote handwashing with soap. However, in the absence of soap, use of wood ash over water alone might be appropriate.

TRIAL REGISTRATION NUMBER

PACTR202011855730652.

Microbes and Climate Change: a Research Prospectus for the Future

Climate change is the most serious challenge facing humanity. Microbes produce and consume three major greenhouse gases-carbon dioxide, methane, and nitrous oxide-and some microbes cause human, animal, and plant diseases that can be exacerbated by climate change. Hence, microbial research is needed to help ameliorate the warming trajectory and cascading effects resulting from heat, drought, and severe storms. We present a brief summary of what is known about microbial responses to climate change in three major ecosystems: terrestrial, ocean, and urban. We also offer suggestions for new research directions to reduce microbial greenhouse gases and mitigate the pathogenic impacts of microbes. These include performing more controlled studies on the climate impact on microbial processes, system interdependencies, and responses to human interventions, using microbes and their carbon and nitrogen transformations for useful stable products, improving microbial process data for climate models, and taking the One Health approach to study microbes and climate change.

Fecal indicator bacteria along multiple environmental exposure pathways (water, food, and soil) and intestinal parasites among children in the rural northwest Ethiopia

Background

Children in low-resource settings are exposed to multiple risk factors for enteropathogens. However, the probability of exposures may be different across exposure pathways. Accordingly, this study was conducted to assess environmental exposures of children to intestinal parasites in the east Dembiya district of Ethiopia.

Methods

A cross-sectional study was conducted for 372 households with children aged 24–59 months. The potential for external exposure of children to intestinal parasites was assessed by determining the presence of fecal indicator organism (Escherichia coli (E. coli)) in drinking water at point of use, ready-to-eat foods, and courtyard soil from children’s outdoor play areas. For internal exposure assessment, ova of parasites in stool samples was detected using wet mount and Kato-Katz techniques to estimate exposure to intestinal parasites. The external and internal exposure assessments were also complemented using questionnaire and spot-check observations to assess behaviors that result in high risk of exposure. Individual and community-level predictors of intestinal parasites were identified using a multilevel logistic regression model. Statistically significant variables were identified on the basis of adjusted odds ratio (AOR) with 95% confidence interval (CI) and p-value < 0.05.

Results

Ova of one or more intestinal parasites was detected among 178 (47.8%) (95% CI 42.8, 52.6%) of the children. The most common intestinal parasites were A. lumbricoides (20.7%) and S. mansoni (19.1%). Furthermore, E. coli was detected in 69.1% of drinking water samples at point of use, 67.5% of ready-to-eat food samples, and 83.1% of courtyard soil samples from children’s outdoor play areas. Exposure of children to intestinal parasites among children in the studied region was associated with poor hand hygiene of mothers (AOR 1.98, 95% CI (1.07, 3.66), poor hand hygiene of children (AOR 3.20, 95% CI (1.77, 5.77), mouthing of soil contaminated materials (AOR 2.31, 95% CI (1.26, 4.24), open defecation practices (AOR 2.22, 95% CI (1.20, 4.10), limited access to water (AOR 2.38, 95% CI (1.13, 5.01), water contamination (AOR 2.51, 95% CI (1.31, 4.80), food contamination (AOR 3.21, 95% CI (1.69, 6.09), and soil contamination (AOR 2.56, 95% CI (1.34, 4.90).

Conclusion

An extensive E. coli contamination of water, foods, and courtyard soil was found in the studied region and the potential sources of contamination were open defecation practices, unhygienic disposal of wastes, poor animal husbandry and keeping practices, and poor water and food safety measures at household level. Moreover, fecal contamination of water, foods, and soil linked to exposure of children to intestinal parasites in the studied region. Thus, it is critical to implement individual-level interventions (such as latrine utilization, hand hygiene promotion, food safety, home-based water treatment, and containment of domestic animals), plus community-level interventions (such as protecting water sources from contamination, source-based water treatment, and community-driven sanitation).

Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms

Little is known about the genomic diversity of the microbial communities associated with raw municipal wastewater (sewage), including whether microbial populations specific to sewage exist and how such populations could be used to improve source attribution and apportioning in contaminated waters. Herein, we used the influent of three wastewater treatment plants in Atlanta, Georgia (USA) to perturb laboratory freshwater mesocosms, simulating sewage contamination events, and followed these mesocosms with shotgun metagenomics over a 7-day observational period. We describe 15 abundant non-redundant bacterial metagenome-assembled genomes (MAGs) ubiquitous within all sewage inocula yet absent from the unperturbed freshwater control at our analytical limit of detection. Tracking the dynamics of the populations represented by these MAGs revealed varied decay kinetics, depending on (inferred) phenotypes, e.g., anaerobes decayed faster than aerobes under the well-aerated incubation conditions. Notably, a portion of these populations showed decay patterns similar to those of common markers, Enterococcus and HF183. Despite the apparent decay of these populations, the abundance of β-lactamase encoding genes remained high throughout incubation relative to the control. Lastly, we constructed genomic libraries representing several different fecal sources and outline a bioinformatic approach which leverages these libraries for identifying and apportioning contamination signal among multiple probable sources using shotgun metagenomic data.

Reproduction of Black Soldier Fly (Diptera: Stratiomyidae) Under Different Adult Densities and Light Regimes

The black soldier fly (BSF) Hermetia illucens (L.) (Diptera: Stratiomyidae) has been recognized as a promising insect species for sustainable management of organic waste and by-products. Indoor breeding of BSF with artificial lighting has been proved successful, but efforts are still needed to optimize BSF reproductive output. Increasing adult density seems an option to exploit space, whereas decreasing artificial lighting duration may reduce unnecessary power consumption. This study aimed at investigating the effects of adult density (10, 25, and 50 pairs per 30 × 30 × 30 cm cage; i.e., 370, 926, and 1,852 pairs/m3), light regime (8:16, 12:12, and 16:8 [L:D] h), and their possible interactions, on some BSF life history traits relevant to reproduction. The results show that the overall BSF reproductive output increased with increasing adult density but was not affected by light regimes per se. With the highest BSF adult density tested, an average of more than 20,000 neonate larvae were produced from a cage within 10 d. At this density, increasing photoperiod increased neonate production, but also decreased the number of neonates per watt used for artificial illumination. The temporal oviposition patterns, mean individual female reproductive output, mating success, egg hatching rate, and insect survival rate were not affected by adult density or light regime as simple effects. However, the interaction between adult density and light regime was significant for the first oviposition peak, mean individual female reproductive output, and insect survival rate. The possible mechanisms behind our results are discussed.

Developing a one health approach by using a multi-dimensional matrix

The One Health concept that human, animal, plant, environmental, and ecosystem health are linked provides a framework for examining and addressing complex health challenges. This framework can be represented as a multi-dimensional matrix that can be used as a tool to identify upstream drivers of disease potential in a concise, systematic, and comprehensive way. The matrix can involve up to four dimensions depending on users' needs. This paper describes and illustrates how the matrix tool might be used to facilitate systems thinking, enabling the development of effective and equitable public policies. The multidimensional One Health matrix tool will be used to examine, as an example, global human and animal fecal wastes. The fecal wastes are analyzed at the microbial and population levels over a timeframe of years. Political, social, and economic factors are part of the matrix and will be examined as well. The One Health matrix tool illustrates how foodborne illnesses, food insecurity, antimicrobial resistance, and climate change are inter-related. Understanding these inter-relationships is essential to develop the public policies needed to achieve many of the United Nations' Sustainable Development Goals.

The role of Environmental Health in preventing antimicrobial resistance in low- and middle-income countries

Antimicrobial resistance (AMR) is increasingly becoming a threat to global public health, not least in low- and middle-income countries (LMICs) where it is contributing to longer treatment for illnesses, use of higher generation drugs, more expenditure on antimicrobials, and increased deaths attributed to what should be treatable diseases. Some of the known causes of AMR include misuse and overuse of antimicrobials in both humans and animals, unnecessary use of antimicrobials in animals as growth promoters, and lack of awareness among the public on how to protect antimicrobials. As a result, resistant organisms are circulating in the wider environment, and there is a need to consider the One Health approach to minimise the continuing development of AMR. Environmental Health, specifically water, sanitation and hygiene (WASH), waste management, and food hygiene and safety, are key components of One Health needed to prevent the spread of antimicrobial-resistant microorganisms particularly in LMICs and reduce the AMR threat to global public health. The key Environmental Health practices in the prevention of AMR include: (1) adequate WASH through access and consumption of safe water; suitable containment, treatment and disposal of human excreta and other wastewater including from health facilities; good personal hygiene practices such as washing hands with soap at critical times to prevent the spread of resistant microorganisms, and contraction of illnesses which may require antimicrobial treatment; (2) proper disposal of solid waste, including the disposal of unused and expired antimicrobials to prevent their unnecessary exposure to microorganisms in the environment; and (3) ensuring proper food hygiene and safety practices, such as sale and consumption of animal products in which adequate antimicrobial withdrawal periods have been observed, and growing vegetables on unpolluted soil. Environmental Health is therefore crucial in the prevention of infectious diseases that would require antimicrobials, reducing the spread of resistant organisms, and exposure to antimicrobial residues in LMICs. Working with other professionals in One Health, Environmental Health Practitioners have a key role in reducing the spread of AMR including health education and promotion, surveillance, enforcement of legislation, and research.

Toward Zero Hunger Through Coupled Ecological Sanitation-Agriculture Systems

Ecological sanitation (EcoSan) systems capture and sanitize human excreta and generate organic nutrient resources that can support more sustainable nutrient management in agricultural ecosystems. An emerging EcoSan system that is implemented in Haiti and several other contexts globally couples container-based household toilets with aerobic, thermophilic composting. This closed loop sanitation system generates organic nutrient resources that can be used as part of an ecological approach to soil nutrient management and thus has the potential to contribute to Sustainable Development Goals 2 (zero hunger), 6 (clean water and sanitation for all), and 13 (climate change solutions). However, the role of organic nutrient resources derived from human excreta in food production is poorly studied. We conducted a greenhouse experiment comparing the impact of feces-derived compost on crop production, soil nutrient cycling, and nutrient losses with two amendments produced from wastewater treatment (pelletized biosolids and biofertilizer), urea, and an unfertilized control. Excreta-derived amendments increased crop yields 2.5 times more than urea, but had differing carry-over effects. After a one-time application of compost, crop production remained elevated throughout all six crop cycles. In contrast, the carry-over of crop response lasted two and four crop cycles for biosolids and biofertilizer, respectively, and was absent for urea. Soil carbon concentration in the compost amended soils increased linearly through time from 2.0 to 2.5%, an effect not seen with other treatments. Soil nitrous oxide emissions factors ranged from 0.3% (compost) to 4.6% (biosolids), while nitrogen leaching losses were lowest for biosolids and highest for urea. These results indicate that excreta-derived compost provides plant available nutrients, while improving soil health through the addition of soil organic carbon. It also improved biogeochemical functions, indicating the potential of excreta-derived compost to close nutrient loops if implemented at larger scales. If captured and safely treated through EcoSan, human feces produced in Haiti can meet up to 13, 22, and 11% of major crop needs of nitrogen, phosphorus, and potassium, respectively.

Impacts of an Urban Sanitation Intervention on Fecal Indicators and the Prevalence of Human Fecal Contamination in Mozambique

Fecal source tracking (FST) may be useful to assess pathways of fecal contamination in domestic environments and to estimate the impacts of water, sanitation, and hygiene (WASH) interventions in low-income settings. We measured two nonspecific and two human-associated fecal indicators in water, soil, and surfaces before and after a shared latrine intervention from low-income households in Maputo, Mozambique, participating in the Maputo Sanitation (MapSan) trial. Up to a quarter of households were impacted by human fecal contamination, but trends were unaffected by improvements to shared sanitation facilities. The intervention reduced Escherichia coli gene concentrations in soil but did not impact culturable E. coli or the prevalence of human FST markers in a difference-in-differences analysis. Using a novel Bayesian hierarchical modeling approach to account for human marker diagnostic sensitivity and specificity, we revealed a high amount of uncertainty associated with human FST measurements and intervention effect estimates. The field of microbial source tracking would benefit from adding measures of diagnostic accuracy to better interpret findings, particularly when FST analyses convey insufficient information for robust inference. With improved measures, FST could help identify dominant pathways of human and animal fecal contamination in communities and guide the implementation of effective interventions to safeguard health.

Assessment of Single- vs. Two-Stage Process for the Anaerobic Digestion of Liquid Cow Manure and Cheese Whey

The growing interest in processes that involve biomass conversion to renewable energy, such as anaerobic digestion, has stimulated research in this field in order to assess the optimum conditions for biogas production from abundant feedstocks, like agro-industrial wastes. Anaerobic digestion is an attractive process for the decomposition of organic wastes via a complex microbial consortium and subsequent conversion of metabolic intermediates to hydrogen and methane. The present study focused on the exploitation of liquid cow manure (LCM) and cheese whey (CW) as noneasily and easily biodegradable sources, respectively, using continuous stirred-tank reactors for biogas production, and a comparison was presented between single- and two-stage anaerobic digestion systems. No significant differences were found concerning LCM treatment, in a two-stage system compared to a single one, concluding that LCM can be treated by implementing a single-stage process, as a recalcitrant substrate, with the greatest methane production rate of 0.67 L CH4/(LR·d) at an HRT of 16 d. On the other hand, using the easily biodegradable CW as a monosubstrate, the two-stage process was considered a better treatment system compared to a single one. During the single-stage process, operational problems were observed due to the limited buffering capacity of CW. However, the two-stage anaerobic digestion of CW produced a stable methane production rate of 0.68 L CH4/(LR·d) or 13.7 L CH4/Lfeed, while the total COD was removed by 76%.

Impact of an Urban Sanitation Intervention on Enteric Pathogen Detection in Soils

Environmental fecal contamination is common in many low-income cities, contributing to a high burden of enteric infections and associated negative sequelae. To evaluate the impact of a shared onsite sanitation intervention in Maputo, Mozambique on enteric pathogens in the domestic environment, we collected 179 soil samples at shared latrine entrances from intervention (n = 49) and control (n = 51) compounds during baseline (preintervention) and after 24 months (postintervention) as part of the Maputo Sanitation Trial. We tested soils for the presence of nucleic acids associated with 18 enteric pathogens using a multiplex reverse transcription qPCR platform. We detected at least one pathogen-associated gene target in 91% (163/179) of soils and a median of 3 (IQR = 1, 5) pathogens. Using a difference-in-difference analysis and adjusting for compound population, visibly wet soil, sun exposure, wealth, temperature, animal presence, and visible feces, we estimate the intervention reduced the probability of detecting ≥1 pathogen gene by 15% (adjusted prevalence ratio, aPR = 0.85; 95% CI: 0.70, 1.0) and the total number of pathogens by 35% (aPR = 0.65; 0.44, 0.95) in soil 24 months following the intervention. These results suggest that the intervention reduced the presence of some fecal contamination in the domestic environment, but pathogen detection remained prevalent 24 months following the introduction of new latrines.

Quantitative Microbial Risk Assessment of Pediatric Infections Attributable to Ingestion of Fecally Contaminated Domestic Soils in Low-Income Urban Maputo, Mozambique

Rigorous studies of water, sanitation, and hygiene interventions in low- and middle-income countries (LMICs) suggest that children are exposed to enteric pathogens via multiple interacting pathways, including soil ingestion. In 30 compounds (household clusters) in low-income urban Maputo, Mozambique, we cultured Escherichia coli and quantified gene targets from soils (E. coli: ybbW, Shigella/enteroinvasive E. coli (EIEC): ipaH, Giardia duodenalis: β-giardin) using droplet digital PCR at three compound locations (latrine entrance, solid waste area, dishwashing area). We found that 88% of samples were positive for culturable E. coli (mean = 3.2 log10 CFUs per gram of dry soil), 100% for molecular E. coli (mean = 5.9 log10 gene copies per gram of dry soil), 44% for ipaH (mean = 2.5 log10), and 41% for β-giardin (mean = 2.1 log10). Performing stochastic quantitative microbial risk assessment using soil ingestion parameters from an LMIC setting for children 12-23 months old, we estimated that the median annual infection risk by G. duodenalis was 7100-fold (71% annual infection risk) and by Shigella/EIEC was 4000-fold (40% annual infection risk) greater than the EPA's standard for drinking water. Compounds in Maputo, and similar settings, require contact and source control strategies to reduce the ingestion of contaminated soil and achieve acceptable levels of risk.

Wood Pastures: A Transitional Habitat between Forests and Pastures for Dung Beetle Assemblages

Wood pastures are home to a variety of species, including the dung beetle. Dung beetles are an important functional group in decomposition. Specifically, in terms of livestock manure, they not only contribute to nutrient cycling but are key players in supporting human and animal health. Dung beetles, however, are declining in population, and urgent recommendations are needed to reverse this trend. Recommendations need to be based on solid evidence and specific habitats. Herein, we aimed to investigate the role of an intermediate habitat type between forests and pastures. Wood pastures are key areas for dung beetle conservation. For this reason, we compared dung beetle assemblages among forests, wood pastures, and grasslands. We complemented this with studies on the effects of dung type and season at three Hungarian locations. Pitfall traps baited with cattle, sheep, or horse dung were used in forests, wood pastures, and pasture habitats in spring, summer, and autumn. Dung beetle assemblages of wood pastures showed transient characteristics between forests and pastures regarding their abundance, species richness, Shannon diversity, assemblage composition, and indicator species. We identified a strong effect of season and a weak of dung type. Assemblage composition proved to be the most sensitive measure of differences among habitats. The conservation of dung beetles, and the decomposition services they provide, need continuous livestock grazing to provide fresh dung, as well as the maintenance of wood pastures where dung beetle assemblages typical of forests and pastures can both survive.

Validation of microbial source tracking markers for the attribution of fecal contamination in indoor-household environments of the Peruvian Amazon

The performance of eight microbial source tracking (MST) markers was evaluated in a low-resource, tropical community located in Iquitos, Peru. Fecal samples from humans, dogs, cats, rats, goats, buffalos, guinea-pigs, chickens, ducks, pigeons, and parrots were collected (n = 117). All samples were tested with human (BacHum, HF183-Taqman), dog (BactCan), pig (Pig-2-Bac), and avian (LA35, Av4143, ND5, cytB) markers using quantitative PCR (qPCR). Internal validity metrics were calculated using all animal fecal samples, as well as animal fecal samples contextually relevant for the Peruvian Amazon. Overall, Pig-2-Bac performed best, with 100% sensitivity and 88.5% specificity to detect the correct fecal source. Human-associated markers showed a sensitivity of 80.0% and 76.7%, and specificity of 66.2% and 67.6%. When limiting the analysis to contextually relevant animal fecal samples for the Peruvian Amazon, Av143 surpassed cytB with 95.7% sensitivity and 81.8% specificity. BactCan demonstrated 100% sensitivity and 47.4% specificity. The gene copy number detected by BacHum and HF183-Taqman were positively correlated (Pearson's correlation coefficient: 0.785), as well as avian markers cytB with Av4143 (Pearson's correlation coefficient: 0.508) and nd5 (Pearson's correlation coefficient: 0.949). These findings suggest that markers such as Av4143, Pig2Bac, cytb and BacHum have acceptable performance to be impactful in source attribution studies for zoonotic enteric disease transmission in this and similar low-resource communities.

Systems Science Approaches for Global Environmental Health Research: Enhancing Intervention Design and Implementation for Household Air Pollution (HAP) and Water, Sanitation, and Hygiene (WASH) Programs

BACKGROUND

Two of the most important causes of global disease fall in the realm of environmental health: household air pollution (HAP) and poor water, sanitation, and hygiene (WASH) conditions. Interventions, such as clean cookstoves, household water treatment, and improved sanitation facilities, have great potential to yield reductions in disease burden. However, in recent trials and implementation efforts, interventions to improve HAP and WASH conditions have shown few of the desired health gains, raising fundamental questions about current approaches.

OBJECTIVES

We describe how the failure to consider the complex systems that characterize diverse real-world conditions may doom promising new approaches prematurely. We provide examples of the application of systems approaches, including system dynamics, network analysis, and agent-based modeling, to the global environmental health priorities of HAP and WASH research and programs. Finally, we offer suggestions on how to approach systems science.

METHODS

Systems science applied to environmental health can address major challenges by a) enhancing understanding of existing system structures and behaviors that accelerate or impede aims; b) developing understanding and agreement on a problem among stakeholders; and c) guiding intervention and policy formulation. When employed in participatory processes that engage study populations, policy makers, and implementers, systems science helps ensure that research is responsive to local priorities and reflect real-world conditions. Systems approaches also help interpret unexpected outcomes by revealing emergent properties of the system due to interactions among variables, yielding complex behaviors and sometimes counterintuitive results.

DISCUSSION

Systems science offers powerful and underused tools to accelerate our ability to identify barriers and facilitators to success in environmental health interventions. This approach is especially useful in the context of implementation research because it explicitly accounts for the interaction of processes occurring at multiple scales, across social and environmental dimensions, with a particular emphasis on linkages and feedback among these processes. https://doi.org/10.1289/EHP7010.

COVID-19: urgent actions, critical reflections and future relevance of 'WaSH': lessons for the current and future pandemics

The COVID-19 pandemic placed hygiene at the centre of disease prevention. Yet, access to the levels of water supply that support good hand hygiene and institutional cleaning, our understanding of hygiene behaviours, and access to soap are deficient in low-, middle- and high-income countries. This paper reviews the role of water, sanitation and hygiene (WaSH) in disease emergence, previous outbreaks, combatting COVID-19 and in preparing for future pandemics. We consider settings where these factors are particularly important and identify key preventive contributions to disease control and gaps in the evidence base. Urgent substantial action is required to remedy deficiencies in WaSH, particularly the provision of reliable, continuous piped water on-premises for all households and settings. Hygiene promotion programmes, underpinned by behavioural science, must be adapted to high-risk populations (such as the elderly and marginalised) and settings (such as healthcare facilities, transport hubs and workplaces). WaSH must be better integrated into preparation plans and with other sectors in prevention efforts. More finance and better use of financing instruments would extend and improve WaSH services. The lessons outlined justify no-regrets investment by government in response to and recovery from the current pandemic; to improve day-to-day lives and as preparedness for future pandemics.

A novel droplet digital PCR human mtDNA assay for fecal source tracking

Human mitochondrial DNA provides a promising target for fecal source tracking because it is unique and intrinsic to humans. We developed a TaqMan chemistry assay, hCYTB484, targeting the cytochrome b gene of the human mitochondrial genome on a droplet digital PCR (ddPCR) platform and compared the performance of hCYTB484 with the HF183/BacR287 assay, a widely used assay targeting human-associated Bacteroides. For both assays, we defined the analytical limit of detection and analytical lower limit of quantification using frequency of detection and imprecision goals, respectively. We then established these analytical limits using empirical ddPCR data, presenting a novel approach to determining the analytical lower limit of quantification. We evaluated assay sensitivity using individual human feces from US, Bangladesh, and Mozambique and evaluated assay specificity using cow, pig, chicken, and goat samples collected from the US. To compare assay performance across a range of thresholds, we utilized receiver operating characteristic curves. The hCYTB484 marker was detected and quantifiable in 100% of the human feces from the 3 geographical distant regions whereas the HF183/BacR287 marker was detectable and quantifiable in 51% and 31% (respectively) of human feces samples. The hCYTB484 marker also was more specific (97%), having fewer detections in pig, chicken, and goat samples than the HF183/BacR287 marker (80%). The higher performance of the hCYTB484 marker in individual feces from geographically distant regions is desirable in the detection of fecal pollution from sources to which fewer individuals contribute, such as the non-sewered forms of sanitation (e.g. pit latrines and septic tanks) that serve most of Earth's population and carry the highest risk of exposure to fecal-oral pathogens.

From hogs to HABs: impacts of industrial farming in the US on nitrogen and phosphorus and greenhouse gas pollution

Nutrient pollution and greenhouse gas emissions related to crop agriculture and confined animal feeding operations (CAFOs) in the US have changed substantially in recent years, in amounts and forms. This review is intended to provide a broad view of how nutrient inputs-from fertilizer and CAFOs-as well as atmospheric NH3 and greenhouse gas emissions, are changing regionally within the US and how these changes compare with nutrient inputs from human wastewater. Use of commercial nitrogen (N) fertilizer in the US, which now exceeds 12,000,000 metric tonnes (MT) continues to increase, at a rate of 60,000 MT per year, while that of phosphorus (P) has remained nearly constant over the past decade at around 1,800,000 MT. The number of CAFOs in the US has increased nearly 10% since 2012, driven largely by a near 13% increase in hog production. The annualized inventory of cattle, dairy cows, hogs, broiler chickens and turkeys is approximately 8.7 billion, but CAFOs are highly regionally concentrated by animal sector. Country-wide, N applied by fertilizer is about threefold greater than manure N inputs, but for P these inputs are more comparable. Total manure inputs now exceed 4,000,000 MT as N and 1,400,000 MT as P. For both N and P, inputs and proportions vary widely by US region. The waste from hog and dairy operations is mainly held in open lagoons that contribute to NH3 and greenhouse gas (as CH4 and N2O) emissions. Emissions of NH3 from animal waste in 2019 were estimated at > 4,500,000 MT. Emissions of CH4 from manure management increased 66% from 1990 to 2017 (that from dairy increased 134%, cattle 9.6%, hogs 29% and poultry 3%), while those of N2O increased 34% over the same time period (dairy 15%, cattle 46%, hogs 58%, and poultry 14%). Waste from CAFOs contribute substantially to nutrient pollution when spread on fields, often at higher N and P application rates than those of commercial fertilizer. Managing the runoff associated with fertilizer use has improved with best management practices, but reducing the growing waste from CAFO operations is essential if eutrophication and its effects on fresh and marine waters-namely hypoxia and harmful algal blooms (HABs)-are to be reduced.

Human faeces-associated extended-spectrum β-lactamase-producing Escherichia coli discharge into sanitation systems in 2015 and 2030: a global and regional analysis

BACKGROUND

Improving management of and treatment within sanitation waste streams could slow the development and transmission of antimicrobial-resistant organisms, but the magnitude of impact has not been quantified. Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are a major cause of antimicrobial-resistant infections and are frequently detected in faecal waste streams, making them model indicators of the distribution of antimicrobial-resistant organisms that are transmitted through the faecal-oral route. We aimed to estimate the mass of faeces containing ESBL-producing E coli entering different levels of the sanitation ladder globally and by WHO region to determine the global scale at which sanitation infrastructure serves as a vehicle for dissemination of antimicrobial-resistant organisms.

METHODS

In this global and regional analysis, we used publicly available sanitation coverage data from the WHO/UNICEF Joint Monitoring Programme and most recent available scientific literature on human faecal production (2018) and carriage of ESBL-producing E coli by healthy individuals (2016) to estimate the quantity of faeces that has been discharged that contains ESBL-producing E coli for 2015 and projected for 2030. We estimated the mass of faeces containing ESBL-producing E coli by WHO region and at different levels of the Sustainable Development Goal sanitation ladder-ie, into at-least basic (ie, safely managed or basic) systems, limited systems, and unimproved systems, and via open defecation. We modelled three scenarios in which the proportion of ESBL-producing E coli among all E coli that was excreted by carriers varied on the basis of the scientific literature: 100% (scenario A), 10% (scenario B), or 1% (scenario C).

FINDINGS

Under scenario B, we estimated that approximately 19 billion kg of faeces carrying ESBL-producing E coli was excreted in 2015 globally. Approximately 65·8% (1·2-120 billion kg depending on modelled scenario) of this faecal biomass was managed in at-least basic sanitation systems, 8·4% (160 million-16 billion kg) in limited sanitation systems, 14·4% (270 million-27 billion kg) in unimproved sanitation systems, and 11·4% (220 million-22 billion kg) was openly defecated. The regions with the highest proportion of openly defecated faeces containing ESBL-producing E coli were the South-East Asia (29·4%) and African (21·8%) regions. The South-East Asia, Western Pacific, and African regions produced 524 billion kg (63%) of the total global human faecal biomass, but 16·9 billion kg (90%) of faeces containing ESBL-producing E coli under scenario B. By 2030, estimates under scenario B will have approximately doubled to 37·6 billion kg of faeces carrying ESBL-producing E coli under the most conservative projections.

INTERPRETATION

At-least basic sanitation does not guarantee effective removal or inactivation of antimicrobial-resistant organisms from faecal biomass. However, our findings indicate the need for mitigating transport of antimicrobial-resistant organisms via sanitation systems that are not safely managed, including open defecation, which might result in direct environmental discharge and subsequent risk of transmission back to humans.

FUNDING

None.

Effect of Sanitation Improvements on Pathogens and Microbial Source Tracking Markers in the Rural Bangladeshi Household Environment

Diarrheal illnesses from enteric pathogens are a leading cause of death in children under five in low- and middle-income countries (LMICs). Sanitation is one way to reduce the spread of enteric pathogens in the environment; however, few studies have investigated the effectiveness of sanitation in rural LMICs in reducing pathogens in the environment. In this study, we measured the impact of a sanitation intervention (dual-pit latrines, sani-scoops, child potties delivered as part of a randomized control trial, WASH Benefits) in rural Bangladeshi household compounds by assessing prevalence ratios, differences, and changes in the concentration of pathogen genes and host-specific fecal markers. We found no difference in the prevalence of pathogenic Escherichia coli, norovirus, or Giardia genes in the domestic environment in the sanitation and control arms. The prevalence of the human fecal marker was lower on child hands and the concentration of animal fecal marker was lower on mother hands in the sanitation arm in adjusted models, but these associations were not significant after correcting for multiple comparisons. In the subset of households with ≥10 individuals per compound, the prevalence of enterotoxigenic E. coli genes on child hands was lower in the sanitation arm. Incomplete removal of child and animal feces or the compound (versus community-wide) scale of intervention could explain the limited impacts of improved sanitation.

Variation in E. coli concentrations in open drains across neighborhoods in Accra, Ghana: The influence of onsite sanitation coverage and interconnectedness of urban environments

Alongside efforts to improve safe management of feces along the entire sanitation chain, including after the toilet, global sanitation efforts are focusing on universal access 'basic' services: onsite facilities that safely contain excreta away from human contact. Although fecal sludge management is improving in urban areas, open drains remain a common fate for feces in these often densely-populated neighborhoods in low-income countries. To-date, it is unclear to what extent complete coverage of onsite sanitation reduces fecal contamination in the urban environment and how fecal contamination varies within urban drains across neighborhoods by sanitation status within a city. We assessed how neighborhood levels of environmental fecal contamination (via spatially-representative sampling of open drains for E. coli) varied across four neighborhoods with varying income, type and coverage of household sanitation facilities, and population density in Accra, Ghana. Neighborhoods with very high sanitation coverage (≥89%) still had high (>4 log10 CFU/100 mL) E. coli concentrations in drains. Between-neighborhood variation in E. coli levels among the high coverage neighborhoods was significant: drain concentrations in neighborhoods with 93% and 89% coverage (4.7 (95% CI: 4.5, 4.9) & 4.9 (95% CI: 4.5, 5.3) log10 CFU/100 mL, respectively) were higher than in the neighborhood with 97% coverage (4.1 log10 CFU/100 mL, 95% CI: 3.8, 4.4 log10 CFU/100 mL). Compared with the highest coverage neighborhood, the neighborhood with lowest coverage (48%) also had higher E. coli concentrations (5.6 log10 CFU/100 mL, 95% CI: 5.3, 5.9 log10 CFU/100 mL). Although fecal contamination in open drains appeared lower in neighborhoods with higher onsite sanitation coverage (and vice versa), other factors (e.g. fecal sludge management, animals, population density) may affect drain concentrations. These results underscore that neighborhood-level onsite sanitation improvements alone may not sufficiently reduce fecal hazards to public health from open drains. These findings supporting the need for integrated, city-level fecal sludge management alongside multifaceted interventions to reduce fecal contamination levels and human exposure.

Complexities in understanding antimicrobial resistance across domesticated animal, human, and environmental systems

Antimicrobial resistance (AMR) is a significant threat to both human and animal health. The spread of AMR bacteria and genes across systems can occur through a myriad of pathways, both related and unrelated to agriculture, including via wastewater, soils, manure applications, direct exchange between humans and animals, and food exposure. Tracing origins and drivers of AMR bacteria and genes is challenging due to the array of contexts and the complexity of interactions overlapping health practice, microbiology, genetics, applied science and engineering, as well as social and human factors. Critically assessing the diverse and sometimes contradictory AMR literature is a valuable step in identifying tractable mitigation options to stem AMR spread. In this article we review research on the nonfoodborne spread of AMR, with a focus on domesticated animals and the environment and possible exposures to humans. Attention is especially placed on delineating possible sources and causes of AMR bacterial phenotypes, including underpinning the genetics important to human and animal health.

Improving phosphorus sustainability of sugarcane production in Brazil

Phosphorus (P) use in global food and bioenergy production needs to become more efficient and sustainable to reduce environmental impacts and conserve a finite and critical resource (Carpenter & Bennett, Environmental Research Letters, 2011, 6, 014009; Springmann et al., Nature, 2018, 562, 519). Sugarcane is one crop with a large P footprint because production is centered on P-fixing soils with low P availability (Roy et al., Nature Plants, 2016, 2, 16043; Withers et al., Scientific Reports, 2018, 8, 2537). As global demand for processed sugar and bioethanol continues to increase, we advocate that improving P efficiency could become a key sustainability goal for the sugarcane industry. Here, we applied the 5R global P stewardship framework (Withers et al., Ambio, 2015, 44, 193) to identify more sustainable options to manage P in Brazilian sugarcane production. We show that current inputs of P fertilizer to the current crop area could be reduced by over 305 Gg, or 63%, over the next three decades by reducing unnecessary P fertilizer use, better utilization of recyclable bioresources and redesigning recommendation systems. Adoption of these 5R options would save the sugarcane industry in Brazil 528 US$ million and help safeguard global food and energy security.

Gut carriage of antimicrobial resistance genes among young children in urban Maputo, Mozambique: Associations with enteric pathogen carriage and environmental risk factors

Because poor sanitation is hypothesized as a major direct and indirect pathway of exposure to antimicrobial resistance genes (ARGs), we sought to determine a) the prevalence of and b) environmental risk factors for gut carriage of key ARGs in a pediatric cohort at high risk of enteric infections due to poor water, sanitation, and hygiene (WASH) conditions. We investigated ARGs in stool from young children in crowded, low-income settlements of Maputo, Mozambique, and explored potential associations with concurrent enteric pathogen carriage, diarrhea, and environmental risk factors, including WASH. We collected stool from 120 children <14 months old and tested specimens via quantal, multiplex molecular assays for common bacterial, viral, and protozoan enteric pathogens and 84 ARGs encoding potential resistance to 7 antibiotic classes. We estimated associations between ARG detection (number and diversity detected) and concurrently-measured enteric pathogen carriage, recently-reported diarrhea, and risk factors in the child’s living environment. The most commonly-detected ARGs encoded resistance to macrolides, lincosamides, and streptogramins (100% of children); tetracyclines (98%); β-lactams (94%), aminoglycosides (84%); fluoroquinolones (48%); and vancomycin (38%). Neither concurrent diarrhea nor measured environmental (including WASH) conditions were associated with ARG detection in adjusted models. Enteric pathogen carriage and ARG detection were associated: on average, 18% more ARGs were detected in stool from children carrying bacterial pathogens than those without (adjusted risk ratio (RR): 1.18, 95% confidence interval (CI): 1.02, 1.37), with 16% fewer ARGs detected in children carrying parasitic pathogens (protozoans, adjusted RR: 0.84, 95% CI: 0.71, 0.99). We observed gut ARGs conferring potential resistance to a range of antibiotics in this at-risk cohort that had high rates of enteric infection, even among children <14 months-old. Gut ARGs did not appear closely correlated with WASH, though environmental conditions were generally poor. ARG carriage may be associated with concurrent carriage of bacterial enteric pathogens, suggesting indirect linkages to WASH that merit further investigation.

A localized sanitation status index as a proxy for fecal contamination in urban Maputo, Mozambique

Sanitary surveys are used in low- and middle-income countries to assess water, sanitation, and hygiene conditions, but have rarely been compared with direct measures of environmental fecal contamination. We conducted a cross-sectional assessment of sanitary conditions and E. coli counts in soils and on surfaces of compounds (household clusters) in low-income neighborhoods of Maputo, Mozambique. We adapted the World Bank's Urban Sanitation Status Index to implement a sanitary survey tool specifically for compounds: a Localized Sanitation Status Index (LSSI) ranging from zero (poor sanitary conditions) to one (better sanitary conditions) calculated from 20 variables that characterized local sanitary conditions. We measured the variation in the LSSI with E. coli counts in soil (nine locations/compound) and surface swabs (seven locations/compound) in 80 compounds to assess reliability. Multivariable regression indicated that a ten-percentage point increase in LSSI was associated with 0.05 (95% CI: 0.00, 0.11) log10 fewer E. coli/dry gram in courtyard soil. Overall, the LSSI may be associated with fecal contamination in compound soil; however, the differences detected may not be meaningful in terms of public health hazards.

Enhanced insights from human and animal host-associated molecular marker genes in a freshwater lake receiving wet weather overflows

This study investigated the magnitude of wet weather overflow (WWO)-driven sewage pollution in an urban lake (Lake Parramatta) located in Sydney, New South Wales, Australia. Water samples were collected during a dry weather period and after two storm events, and tested for a range of novel and established sewage- [Bacteroides HF183, crAssphage CPQ_056 and pepper mild mottle virus (PMMoV)] and animal feces-associated (Bacteroides BacCan-UCD, cowM2 and Helicobacter spp. associated GFD) microbial source tracking marker genes along with the enumeration of culturable fecal indicator bacteria (FIB), namely Escherichia coli (E. coli) and Enterococcus spp. The magnitude of general and source-specific fecal pollution was low in water samples collected during dry weather compared to storm events. The levels of HF183, crAssphage and PMMoV in water samples collected during storm events were as high as 6.39, 6.33 and 5.27 log₁₀ GC/L of water, respectively. Moderate to strong positive correlations were observed among the quantitative occurrence of sewage-associated marker genes. The concentrations of HF183 and PMMoV in most storm water samples exceeded the risk benchmark threshold values established in the literature for primary contact recreators. None of the samples tested was positive for the cowM2 (cow) marker gene, while BacCan-UCD (dog) and GFD (avian) animal-associated markers were sporadically detected in water samples collected from both dry weather and storm events. Based on the results, the ongoing advice that swimming should be avoided for several days after storm events appears appropriate. Further research to determine the decay rates of sewage-associated marker genes in relation to each other and enteric viruses would help refine current advice. Microbial source tracking approaches employed in this study provided insights into sources of contamination over currently used FIB.