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Objectives. To estimate the population lacking at least basic water and sanitation access in the urban United States. Methods. We compared national estimates of water and sanitation access from the World Health Organization/United Nations Children’s Fund Joint Monitoring Program with estimates from the US Department of Housing and Urban Development on homelessness and the American Community Survey on household water and sanitation facilities. Results. We estimated that at least 930 000 persons in US cities lacked sustained access to at least basic sanitation and 610 000 to at least basic water access, as defined by the United Nations. Conclusions. After accounting for those experiencing homelessness and substandard housing, our estimate of people lacking at least basic water equaled current estimates (n = 610 000)—without considering water quality—and greatly exceeded estimates of sanitation access (n = 28 000). Public Health Implications. Methods to estimate water and sanitation access in the United States should include people experiencing homelessness and other low-income groups, and specific policies are needed to reduce disparities in urban sanitation. We recommend similar estimation efforts for other high-income countries currently reported as having near universal sanitation access.

DNA analysis of ancient, desiccated feces – termed paleofeces – can unlock insights into the lives of ancient peoples, including through examination of the gut microbiome and identification of specific pathogens and parasites. We collected desiccated feces from the Cave of the Dead Children (La Cueva de Los Muertos Chiquitos) in the Rio Zape Valley in Mexico dated to 725–920 CE, for targeted pathogen analysis. First, we extracted DNA with methods previously optimized for paleofeces. Then, we applied highly sensitive modern molecular tools (i.e., PCR pre-amplification followed by multi-parallel qPCR) to assess the presence of 30 enteric pathogens and gut microbes. We detected ≥1 pathogen or gut microbe associated gene in each of the ten samples and a mean of 3.9 targets per sample. The targets detected included Blastocystis spp. (n = 7), atypical enteropathogenic E. coli (n = 7), Enterobius vermicularis (n = 6), Entamoeba spp. (n = 5), enterotoxigenic E. coli (n = 5), Shigella spp./enteroinvasive E. coli (n = 3), Giardia spp. (n = 2), and E. coli O157:H7 (n = 1). The protozoan pathogens we detected (i.e., Giardia spp. and Entamoeba spp.) have been previously detected in paleofeces via enzyme-linked immunoassay (ELISA), but not via PCR. This work represents the first detection of Blastocystis spp. atypical enteropathogenic E. coli, enterotoxigenic E. coli , Shigella spp./enteroinvasive E. coli , and E. coli O157:H7 in paleofeces. These results suggest that enteric infection may have been common among the Loma San Gabriel people, who lived in the Rio Zape Valley in Mexico during this period.

We conducted a cross-sectional study to determine the prevalence of soil-transmitted helminthiases (STH) in areas of rural Alabama, USA, that have sanitation deficits. We enrolled 777 children; 704 submitted stool specimens and 227 a dried blood spot sample. We microscopically examined stool specimens from all 704 children by using Mini-FLOTAC for helminth eggs. We tested a subset by using molecular techniques: real-time PCR analysis for 5 STH species, TaqMan Array Cards for enteric helminths, and digital PCR for Necator americanus hookworm. We analyzed dried blood spots for Strongyloides stercoralis and Toxocara spp. roundworms by using serologic testing. Despite 12% of our cohort reporting living in homes that directly discharge untreated domestic wastewater, stool testing for STH was negative; however, 5% of dried blood spots were positive for Toxocara spp. roundworms. Survey data suggests substantial numbers of children in this region may be exposed to raw sewage, which is itself a major public health concern.

Co-infection by intestinal helminths and Plasmodium spp. may be common in endemic communities. In 2003, Uganda instituted a national deworming program, with anti-helminth medication provided twice annually to children 6 months to 5 years of age, but few follow-up studies have been conducted. Several studies have identified a relationship between helminth infection, Plasmodium spp. infection and malaria severity. However, the relationship is not well defined, and results are inconclusive. We analyzed 177 stool samples from a cohort of children with severe malaria enrolled in two hospitals in Uganda from 2014–2017. All children were 6 months to 48 months of age and had a clinical presentation of and laboratory confirmation for severe malaria. We also analyzed 25 stool samples from community children who were negative for malaria via rapid diagnostic test and were enrolled from the same household or neighborhood and matched by age, sex, and time of enrollment. We investigated if intestinal helminth infection modified risk of severe malaria. We extracted nucleic acids from stool and tested them for six helminth species ( Anyclostoma duodenal e , Ascaris lumbricoides , Necator americanus , Strongyloides stercolaris , Trichuris trichiura , Shistosoma mansoni ) using highly sensitive quantitative PCR. We found a low prevalence of infection by ≥1 intestinal helminth species in children with severe malaria (5.1%, n = 9/177) and community control children (4.0%, n = 1/25). Helminth infection did not increase or decrease the risk of severe malaria in this cohort (aRR = 1.0, 95% Confidence Interval = 0.82, 1.3, p = 0.78). In these areas of Uganda, the national deworming campaign has been highly successful, as stool-based helminth infection was rare even when using sensitive methods of detection and helminths were not associated with severe malaria in this study.

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 log 10 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.

Achieving universal safely managed sanitation (SMS) is an ambitious long-term goal in resource-limited rural areas. The non-governmental organization, iDE, introduced the alternating dual-pit latrine (ADP), which treats fecal sludge (FS) on-site using storage and lime to increase SMS in rural Cambodia. However, SMS via ADPs requires adherence to recommended practices (e.g., how and when to switch between pits). We surveyed 765 rural households with ADPs across five of 25 Cambodian provinces to understand how real-world household sanitation practices and knowledge affect and are related to adherence to recommended practices at scale. We calculated summary statistics of household survey responses and used regression models of composite indices to describe how households’ practices and attitudes related to ADPs affect adherence to recommended ADP practices. By 24 months after training, three in five households did not recall how long treatment must proceed until emptying can be performed safely. No household waited the recommended two years to empty their pits. While households appreciated the advantages of owning an ADP (e.g., reduced costs and required land area compared to single-pit latrines over time), no household followed recommended treatment practices. This lack of adherence could have health and environmental implications for households using ADPs. Household practices also varied by province, flood proneness, and education level, adding complexity to how to improve adherence; for example, having at least one household member that completed formal education surprisingly reduced compliance with recommended ADP practices. Household behaviors impact the use and maintenance of on-site sanitation systems in rural areas, with proper adherence is necessary to achieve sustained SMS. Increased access to affordable and safe emptying service providers could enable households to manage the pits of their ADPs and dispose of FS in-situ according to treatment duration, while also ensuring that household practices in operating on-site sanitation systems are integrated into the design, installation, and SMS monitoring of such systems.

We collected stool from school-age children from 352 households living in the Black Belt region of Alabama, USA, where sanitation infrastructure is lacking. We used quantitative reverse transcription PCR to measure key pathogens in stool that may be associated with water and sanitation, as an indicator of exposure. We detected genes associated with >1 targets in 26% of specimens, most frequently Clostridioides difficile (6.6%), atypical enteropathogenic Escherichia coli (6.1%), and enteroaggregative E. coli (3.9%). We used generalized estimating equations to assess reported risk factors for detecting >1 pathogen in stool. We found no association between lack of sanitation and pathogen detection (adjusted risk ratio 0.95 [95% CI 0.55–1.7]) compared with specimens from children served by sewerage. However, we did observe an increased risk for pathogen detection among children living in homes with well water (adjusted risk ratio 1.7 [95% CI 1.1–2.5]) over those reporting water utility service.

We conducted a controlled before-and-after trial to evaluate the impact of an onsite urban sanitation intervention on the prevalence of enteric infection, soil transmitted helminth re-infection, and diarrhea among children in Maputo, Mozambique. A non-governmental organization replaced existing poor-quality latrines with pour-flush toilets with septic tanks serving household clusters. We enrolled children aged 1–48 months at baseline and measured outcomes before and 12 and 24 months after the intervention, with concurrent measurement among children in a comparable control arm. Despite nearly exclusive use, we found no evidence that intervention affected the prevalence of any measured outcome after 12 or 24 months of exposure. Among children born into study sites after intervention, we observed a reduced prevalence of Trichuris and Shigella infection relative to the same age group at baseline (<2 years old). Protection from birth may be important to reduce exposure to and infection with enteric pathogens in this setting.

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

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.