Study finds high levels of enteric pathogens in children from Alabama’s rural areas, highlights sanitation issues

In a recent study published in the United States (U.S.) Centers for Disease Control and Prevention’s (CDC Emerging Infectious Diseases Journal, a team of scientists conducted a cross-sectional analysis of stool samples from children in Alabama’s Black Belt region to determine the enteric pathogen prevalence and the risk factors associated with exposure to such pathogens.

Study: Risk Factors for Enteric Pathogen Exposure among Children in Black Belt Region of Alabama, USA. Image Credit: Kateryna Kon / Shutterstock


Alabama’s Black Belt region has been so named due to the rich, clayey black soil found in the region. Outside of areas such as towns and cities that have conventional sewage systems, the residents of rural areas in the region do not have adequate sanitation facilities. Furthermore, the soil’s high clay content reduces surface infiltration, causing domestic wastewater to be discharged close to the surface. The counties that fall within the region are also some of Alabama’s poorest areas, and the unaffordability of septic system alternatives has resulted in ineffective or non-existent wastewater disposal systems.

Improperly managed human feces can be transported back to humans through various fecal-oral pathways, such as contaminated drinking water, flies, hands, fomites, and soil. Downstream contamination of drinking water sources and food can cause enteric pathogen infections, resulting in diarrheal diseases and, eventually, environmental enteric dysfunction, cognitive impairments, immune system problems, and growth deficits.

About the study

In the present study, the scientists conducted a cross-sectional analysis of fecal samples collected from close to 500 children in the Black Belt region and used molecular methods to determine the enteric pathogen prevalence in the samples. They also aimed to identify the enteric pathogen-associated risk factors to understand the health burden due to poor sanitization facilities in rural areas and to assess the infrastructural changes needed to address this public health problem.

The study was part of a more extensive study carried out in rural Alabama to survey helminths and was conducted using community-based participatory research principles that aim to work with stakeholders in the community. Children between the ages of two and 18 were included in the study, and all the children in each household were encouraged to participate. Stool collection kits were provided to all the children, and samples were collected for three bowel movements.

The participants were also required to complete a questionnaire to provide information about demographic characteristics, household sanitation infrastructure, and potential exposure to enteric pathogens. All participants were monetarily compensated for their participation in the study.

The stool samples were initially visually inspected to rule out contamination of non-human origin, such as dirt, animal hair, or anything of atypical morphology. Total nucleic acids were then extracted from the samples, and digital polymerase chain reaction (dPCR) was used to further screen for human mitochondrial deoxyribonucleic acid (DNA). The samples were screened for the presence of 30 enteric pathogens, including Acanthamoeba species, Cyclospora cayetanensi, Clostridioides difficile, Escherichia coli, Giardia species, Entamoeba species, Shigella species, Helicobacter pylori, Salmonella species, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and many more.

The data was analyzed using Poisson regression to calculate the adjusted and unadjusted risk ratios and to determine whether the independent variables such as the sanitation infrastructure in a household, existence of a water connection, reports of raw sewage in and around the home, and demographic factors and recent travel history of the child predict the detection of nucleic acids from one or more enteric pathogens in the stool samples.


The results indicated the presence of numerous enteric pathogens in the stool samples collected from children residing in the Black Belt region of Alabama. Furthermore, the discharge of fecal waste directly into the environment around the households through straight pipes was not linked to a higher risk of enteric pathogen detection in the stool samples compared to the conventional sewage disposal mechanisms.

However, the study found that well water consumption was linked to a higher probability of detecting enteric pathogens in the stool samples, indicating groundwater contamination due to a lack of proper sanitation facilities. The soil’s high clay content causes repeated shrinking and swelling due to desiccation and moistening, which can lead to fecal waste getting transported from improperly functioning septic tanks or discharges from straight pipes into the groundwater.

The collective public health impacts of improper sanitation highlight the need for new models of delivering and managing sanitation infrastructure to households in the Black Belt region.


Overall, the findings suggested that while sanitation facilities involving straight pipes that discharged fecal waste into the environment were not directly linked to an increase in enteric pathogen detection in stool samples, the fecal contamination of groundwater in the Black Belt region of Alabama was potentially associated with an increase in the risk of enteric pathogen detection. Households that used well water as opposed to a water utility service were at a higher risk of contracting enteric pathogens.

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