One-fifth of the global population is infected with soil-transmitted helminths (STH). Mass drug administration (MDA) with deworming medication is widely implemented to control morbidity associated with STH infections. However, surveillance of human infection prevalence by collecting individual stool samples is time-consuming, costly, often stigmatized, and logistically challenging. Current methods of STH detection are poorly sensitive, particularly in low-intensity and low-prevalence populations.
Abstract Identifying bacterial transmission pathways is crucial to inform strategies aimed at curbing the spread of pathogenic and antibiotic-resistant bacteria, especially in rapidly urbanizing low– and middle-income countries. In this study, we assessed bacterial strain-sharing and dissemination of antibiotic resistance across humans, domesticated poultry, canines, household soil, and drinking water in urban informal settlements in Nairobi, Kenya. We collected 321 samples from 50 households and performed Pooling Isolated Colonies-seq (PIC-seq) by sequencing pools of up to five Escherichia coli colonies per sample to capture strain diversity, strain-sharing patterns, and overlap of antibiotic-resistant genes (ARGs). Bacterial strains isolated from the household environment carried clinically relevant ARGs, reinforcing the role of the environment in antibiotic resistance dissemination. Strain-sharing rates and resistome similarities across sample types were strongly correlated within households, suggesting clonal spread of bacteria is a main driver of dissemination of ARGs in the domestic urban environment. Within households, E. coli strain-sharing was rare between humans and animals but more frequent between humans and drinking water. E. coli contamination in stored drinking water was also associated with higher strain-sharing between humans in the same household. Our study demonstrates that contaminated drinking water facilitates human to human strain sharing and water treatment can disrupt transmission.
Abstract One-fifth of the global population is infected with soil-transmitted helminths (STH). Mass drug administration (MDA) with deworming medication is widely implemented to control morbidity associated with STH infections. However, surveillance of human infection prevalence by collecting individual stool samples is time-consuming, costly, often stigmatized, and logistically challenging. Current methods of STH detection are poorly sensitive, particularly in low-intensity and low-prevalence populations. Here, we developed a sensitive and specific molecular method for detecting STH DNA in large volumes of soil by conducting laboratory and proof of concept studies across field sites in Kenya, Benin, and India. We collected human stool (n=669) and soil (n= 478) from 322 households across the three study sites. The overall prevalence of STH in soil was 31% for Ascaris lumbricoides , 3% for T. trichuris , and 24% for any hookworm species. Detection of an STH species in household soil was strongly associated with increased odds of a household member being infected with that species. Soil surveillance for STH has several benefits over stool-based surveillance, including lower cost and higher success rates for sample collection. Considering that delivery of MDA occurs at the community level, environmental surveillance using molecular methods could be a cost-effective alternate strategy for monitoring STH in these populations. Synopsis Limited data exists on the prevalence and reliability of environmental soil-transmitted helminth (STH) DNA as a marker of human infections in endemic populations. We developed a new molecular detection method for STH DNA in large-volume soil samples and field-tested it across three countries.
To explore the sources of and associated risks with drinking water contamination in low-income, densely populated urban areas, we collected human feces, domesticated animal feces, and source and stored drinking water samples in Nairobi, Kenya in 2019; and analyzed them using microbial source tracking (MST) and enteric pathogen TaqMan Array Cards (TACs). We established host-pathogen relationships in this setting, including detecting
Abstract Background. Helminth and protozoan infections affect >1 billion children globally. Improved water, sanitation, handwashing, and nutrition could be more sustainable control strategies for parasite infections than mass drug administration (MDA), while providing other quality of life benefits. Methods and Findings. We enrolled geographic clusters of pregnant women into a cluster-randomized controlled trial that tested six interventions: disinfecting drinking water(W), improved sanitation(S), handwashing with soap(H), combined WSH, improved nutrition(N), and combined WSHN. We assessed intervention effects on parasite infections by measuring Ascaris lumbricoides , Trichuris trichiura , hookworm, and Giardia duodenalis among individual children born to enrolled mothers and their older siblings (ClinicalTrials.gov NCT01704105 ). We collected stool specimens from 9077 total children in 622 clusters, including 2346 children in control, 1117 in water, 1160 in sanitation, 1141 in handwashing, 1064 in WSH, 1072 in nutrition, and 1177 in WSHN. In the control group, 23% of children were infected with Ascaris lumbricoides , 1% with Trichuris trichuria , 2% with hookworm and 39% with Giardia duodenalis . After two years of intervention exposure, Ascaris infection prevalence was 18% lower in the water treatment arm (95% confidence interval (CI) 0%, 33%), 22% lower in the WSH arm (CI 4%, 37%), and 22% lower in the WSHN arm (CI 4%, 36%) compared to control. Individual sanitation, handwashing, and nutrition did not significantly reduce Ascaris infection on their own, and integrating nutrition with WSH did not provide additional benefit. Trichuris and hookworm were rarely detected, resulting in imprecise effect estimates. No intervention reduced Giardia . Reanalysis of stool samples by quantitative polymerase chain reaction (qPCR) confirmed the reductions in Ascaris infections measured by microscopy in the WSH and WSHN groups. Lab technicians and data analysts were blinded to treatment assignment, but participants and sample collectors were not blinded. The trial was funded by the Bill & Melinda Gates Foundation and USAID. Conclusions. Our results suggest integration of improved water quality, sanitation, and handwashing could contribute to sustainable control strategies for Ascaris infections, particularly in similar settings with recent or ongoing deworming programs. Water treatment alone was similarly effective to integrated WSH, providing new evidence that drinking water should be given increased attention as a transmission pathway for Ascaris .
Antimicrobial resistance (AMR) aligns with a One Health framework in that resistant bacteria and antibiotic resistance genes (ARGs) can be transmitted between humans, animals, and the environment. However, there is a critical need to more precisely understand how and to what extent AMR is exchanged between animals and humans. Metagenomic sequencing has low detection for rare targets such as ARGs, while whole genome sequencing of isolates is burdensome and misses exchange between uncultured bacterial species. We developed a novel, targeted sequencing assay using CRISPR-Cas9 to selectively sequence ARGs and their genomic context with long-read sequencing. Using this method, termed Context-Seq, we investigated overlapping AMR elements containing the ARGs
Helminth and protozoan infections affect more than 1 billion children globally. Improving water quality, sanitation, handwashing, and nutrition could be more sustainable control strategies for parasite infections than mass drug administration, while providing other quality of life benefits.We enrolled geographic clusters of pregnant women in rural western Kenya into a cluster-randomized controlled trial (ClinicalTrials.gov NCT01704105) that tested 6 interventions: water treatment, improved sanitation, handwashing with soap, combined water treatment, sanitation, and handwashing (WSH), improved nutrition, and combined WSH and nutrition (WSHN). We assessed intervention effects on parasite infections by measuring Ascaris lumbricoides, Trichuris trichiura, hookworm, and Giardia duodenalis among children born to the enrolled pregnant women (index children) and their older siblings. After 2 years of intervention exposure, we collected stool specimens from 9,077 total children aged 2 to 15 years in 622 clusters, including 2,346 children in an active control group (received household visits but no interventions), 1,117 in the water treatment arm, 1,160 in the sanitation arm, 1,141 in the handwashing arm, 1,064 in the WSH arm, 1,072 in the nutrition arm, and 1,177 in the WSHN arm. In the control group, 23% of children were infected with A. lumbricoides, 1% with T. trichiura, 2% with hookworm, and 39% with G. duodenalis. The analysis included 4,928 index children (median age in years: 2) and 4,149 older siblings (median age in years: 5); study households had an average of 5 people, <10% had electricity access, and >90% had dirt floors. Compared to the control group, Ascaris infection prevalence was lower in the water treatment arm (prevalence ratio [PR]: 0.82 [95% CI 0.67, 1.00], p = 0.056), the WSH arm (PR: 0.78 [95% CI 0.63, 0.96], p = 0.021), and the WSHN arm (PR: 0.78 [95% CI 0.64, 0.96], p = 0.017). We did not observe differences in Ascaris infection prevalence between the control group and the arms with the individual interventions sanitation (PR: 0.89 [95% CI 0.73, 1.08], p = 0.228), handwashing (PR: 0.89 [95% CI 0.73, 1.09], p = 0.277), or nutrition (PR: 86 [95% CI 0.71, 1.05], p = 0.148). Integrating nutrition with WSH did not provide additional benefit. Trichuris and hookworm were rarely detected, resulting in imprecise effect estimates. No intervention reduced Giardia. Reanalysis of stool samples by quantitative polymerase chain reaction confirmed the reductions in Ascaris infections measured by microscopy in the WSH and WSHN groups. Trial limitations included imperfect uptake of targeted intervention behaviors, limited power to detect effects on rare parasite infections, and that it was not feasible to blind participants and sample collectors to treatment status. However, lab technicians and data analysts were blinded to treatment status. The trial was funded by the Bill & Melinda Gates Foundation and the United States Agency for International Development.Integration of improved water quality, sanitation, and handwashing could contribute to sustainable control strategies for Ascaris infections, particularly in similar settings with recent or ongoing deworming programs. Combining nutrition with WSH did not provide further benefits, and water treatment alone was similarly effective to integrated WSH. Our findings provide new evidence that drinking water should be given increased attention as a transmission pathway for Ascaris.ClinicalTrials.gov NCT01704105.
Introduction The microscopy-based Kato-Katz and urine filtration techniques have traditionally faced challenges in the detection of schistosomiasis in areas with low infection levels. A modified singleplex Schistosoma genus-specific quantitative real-time polymerase chain reaction (qPCR) assay was therefore evaluated as a sensitive and confirmatory schistosomiasis diagnostic test. Methodology The qPCR assay utilized primers and probe targeting internal transcribed spacer– 2 (ITS2) sequence of S . mansoni , S . haematobium and S . intercalatum . A plasmid (pDMD801, 100pg/ul) was used as an internal amplification control and its qPCR assays were run in parallel to the Schistosoma assays. This assay utilized samples collected from 774 participants and microscopically examined for three consecutive days. A total of 699 day-one samples (urine and stools) from two schistosomiasis endemic sites were analyzed. Similarly, 75 persons from a non-endemic control site provided both urine and stool samples that were also analyzed. Results Using microscopy, the proportion of positives in the two endemic regions altogether was 289/699 (41.3%). Using qPCR, 50.4% of the samples (352/699) were found to be positive for schistosome infection. The percentage of positive samples was slightly higher at 57.8% (203/351) in the S . mansoni endemic site compared with the S . haematobium site at 42.8% (149/348). Majority of the microscopy results were light infections at 26.8% (n = 94) and 26.1% (n = 91) while qPCR majority of the infections were high at 41.6% (n = 146) and 31.3% (n = 109) for the S . mansoni and S . haematobium sites, respectively. There were no positives detected by either microscopy or qPCR in the non-endemic site. Using Bayesian Latent Class Model, which does not use any technique as a gold standard, qPCR showed higher sensitivity (86.4% (PCI: 82.1–90.3)) compared to microscopy (75.6% (PCI: 71.1–80.0)). Conclusions This study documents a single day-one sample modified Schistosoma qPCR assay as a powerful improved molecular assay for the detection of schistosomiasis infection that utilize either stool or urine samples. The assay is therefore recommended for monitoring in areas with low infection levels to enable accurate determination of the disease’s control endpoint.
The current standard diagnostic tests for Schistosoma mansoni are the Kato-Katz and circulating cathodic antigen (CCA) techniques. However, these techniques have been documented to have several limitations that have a direct impact on schistosomiasis control programmes. Therefore, there is a need for more sensitive and specific tests for diagnosing schistosomiasis. This study compared the performance of quantitative polymerase chain reaction (qPCR), Kato-Katz, and point-of-care circulating cathodic antigen (POC-CCA) techniques in the diagnosis of S. mansoni infection in the Mwea irrigation scheme, Kirinyaga County in Central Kenya. We carried out a cross-sectional study on 357 individuals residing in four villages in the Mwea irrigation scheme. The participants provided urine and stool samples which were screened for S. mansoni infections using the three techniques. The prevalence of S. mansoni by each technique was calculated and 95% confidence intervals estimated using binomial regression model. Sensitivity and specificity were determined using 2 × 2 contingency tables and compared using the McNemar's chi-square test. Positive and negative predictive values were also determined using the weighted generalized score chi-square test for paired data. The study showed that the prevalence of S. mansoni was 32.8%, 62.5% and 72.8% using Kato-Katz, POC-CCA and qPCR techniques, respectively. Further, when using Kato-Katz as a gold standard, POC-CCA sensitivity was 78.6% and specificity was 45.4%, while qPCR sensitivity was 97.4% and specificity was 39.2%. When using qPCR as the gold standard, Kato-Katz sensitivity was 43.8% and specificity was 96.9%, while POC-CCA sensitivity was 78.1% and specificity was 79.4%. Finally, when using the averaged results from the three techniques as the gold standard, the sensitivity was 41.6%, 79.4% and 92.5% for Kato-Katz, POC-CCA and qPCR, respectively, with a specificity of 100% for all techniques. Kato-Katz technique showed low sensitivity compared to the POC-CCA and qPCR despite it being the most commonly preferred method of choice to diagnose S. mansoni infections. qPCR showed superior sensitivity followed by POC-CCA, hence it can be used as an alternative or to confirm the results obtained by the Kato-Katz technique.
Abstract Animal feces can contain zoonotic enteropathogens capable of causing human diarrheal disease. Limited knowledge exists on domestic animal management in low-income urban settlements. We leveraged survey data and environmental samples collected from 120 urban Kenyan households to understand poultry husbandry practices and assess if household poultry ownership was associated with Escherichia coli contamination in stored water and soil. Fifty-five percent (n = 66) of households were in poultry-owning compounds, and 59.1% (n = 39) of these households reported poultry entering the household quarters. Among these 39 households, 53.9% (n = 21) kept poultry in the sleeping quarters of under-5 children. Household poultry ownership (49.2%, n = 59) was associated with increased E. coli concentrations in soil but not with E. coli prevalence in stored water. Poultry husbandry in urban settings may promote zoonotic disease transmission, and household soil may be an important transmission pathway for poultry-associated fecal contamination.
'/%3e%3c/defs%3e%3cpath fill='%23fff' d='M-120-80h240V80h-240z'/%3e%3cpath d='M-120-80h240v48h-240z'/%3e%3cpath fill='%23060' d='M-120 32h240v48h-240z'/%3e%3cg id='b'%3e%3cuse xlink:href='%23a' stroke='%23000'/%3e%3cuse xlink:href='%23a' fill='%23fff'/%3e%3c/g%3e%3cuse xlink:href='%23b' transform='scale(-1 1)'/%3e%3cpath fill='%23b00' d='M-120-24v48h101c3 8 13 24 19 24s16-16 19-24h101v-48H19C16-32 6-48 0-48s-16 16-19 24z'/%3e%3cpath id='c' d='M19 24c3-8 5-16 5-24s-2-16-5-24c-3 8-5 16-5 24s2 16 5 24'/%3e%3cuse xlink:href='%23c' transform='scale(-1 1)'/%3e%3cg fill='%23fff'%3e%3cellipse rx='4' ry='6'/%3e%3cpath id='d' d='M1 5.85s4 8 4 21-4 21-4 21z'/%3e%3cuse xlink:href='%23d' transform='scale(-1)'/%3e%3cuse xlink:href='%23d' transform='scale(-1 1)'/%3e%3cuse xlink:href='%23d' transform='scale(1 -1)'/%3e%3c/g%3e%3c/svg%3e)
'%3e%3ccircle r='20' fill='%23008'/%3e%3ccircle r='17.5' fill='%23fff'/%3e%3ccircle r='3.5' fill='%23008'/%3e%3cg id='d'%3e%3cg id='c'%3e%3cg id='b'%3e%3cg id='a' fill='%23008'%3e%3ccircle r='.875' transform='rotate(7.5 -8.75 133.5)'/%3e%3cpath d='M0 17.5.6 7 0 2l-.6 5L0 17.5z'/%3e%3c/g%3e%3cuse xlink:href='%23a' transform='rotate(15)'/%3e%3c/g%3e%3cuse xlink:href='%23b' transform='rotate(30)'/%3e%3c/g%3e%3cuse xlink:href='%23c' transform='rotate(60)'/%3e%3c/g%3e%3cuse xlink:href='%23d' transform='rotate(120)'/%3e%3cuse xlink:href='%23d' transform='rotate(-120)'/%3e%3c/g%3e%3c/svg%3e)