Identifying Potential Determinants of Faecal Contamination on Domestic Floors in Three Settings in Rural Kenya: A Mixed Methods Analysis.

Observational evidence suggests that household floors may be an important domain for the transmission of enteric and parasitic infections. However, little work has been done to investigate how household floors can become contaminated with human and animal faeces. This study uses a mixed methods approach to postulate the proximal and distal determinants of household floor contamination with faeces in groups of rural villages in 3 counties in Kenya (Bungoma, Kwale and Narok). Quantitative data was collected through a household census and analysed descriptively and using mixed effects logistic regression models. Qualitative data was collected through unstructured observations of daily routines and in-depth interviews. These data were analysed thematically with case memos produced for routine activities that were hypothesised to be determinants of floor contamination. Possible proximal determinants of floor contamination included; (1) animal contact with floors; (2) child faeces disposal, and; (3) floor cleaning routines. Distal determinants are suggested to be rooted in the socioeconomic, environmental, and cultural context in which households were located and included; (1) the type and number of animals owned by households; (2) presence/absence of dedicated shelters for housing animals at night, which impacted whether sleeping or cooking areas were exposed to animals; (3) Accessibility of inside spaces to poultry and other roaming animals; (4) ownership of an improved floor; (5) ability of animals to access neighbours compounds; (6) seasonal changes in weather. These results will be of use in identifying the contexts in which faecal contamination of domestic floors may be contributing towards transmission of enteric and parasitic infections and in designing effective interventions to prevent this exposure.

Exploring factors associated with Trichuris trichiura infection in school children in a high-transmission setting in Kenya.

Objectives: Kenya has implemented a national school-based deworming program, which has led to substantial decline in the prevalence of soil-transmitted helminths (STHs), although some pockets of infections remain. To effectively design an STH control program that leads to significant reductions of Trichuris trichiura, there is a need to understand the drivers of persistent infection despite ongoing treatment programs. Methods: This study was conducted between July and September 2019 at the south coast of Kenya, using a two-stage sampling design. First, a school-based cross-sectional survey was conducted in 2265 randomly selected school children from selected schools in areas known to be endemic for T. trichiura. After this, we conducted a nested case-control study wherein all children positive for T. trichiura (142) were matched to 148 negative controls based on age and village. A household survey was then conducted with all household members of cases and controls. In addition, a subsample of 116 children found to be infected with T. trichiura were followed up to assess the efficacy of albendazole at day 21 post-treatment. The predictors of presence of T. trichiura were investigated through multilevel logistic regression, considering clustering of infection. Results: Overall, 34.4% of the children were infected with at least one STH species; T. trichiura was the most common (28.3%), 89.1% of those with T. trichiura had light-intensity infections. The prevalence of T. trichiura was significantly higher in male children and was positively associated with younger age and number of people infected with T. trichiura in a household. The parasitological cure rate and egg reduction rate of T. trichiura were 35% and 51%, respectively. Other STHs identified were hookworm (9.6%) and Ascaris lumbricoides (5.7%). Conclusions: T. trichiura remains a significant public health challenge in the study area with albendazole treatment efficacy against the parasite, remaining lower than the World Health Organization-recommended thresholds. Because of the observed focal transmission of T. trichiura in the current area, control efforts tailored to local conditions and targeting lower implementation units should be used to achieve optimal results on transmission.

Optimal control analysis of a transmission interruption model for the soil-transmitted helminth infections in Kenya.

Kenya is among the countries endemic for soil-transmitted helminthiasis (STH) with over 66 subcounties and over 6 million individuals being at-risk of infection. Currently, the country is implementing mass drug administration (MDA) to all the at-risk groups as the mainstay control strategy. This study aimed to develop and analyze an optimal control (OC) model, from a transmission interruption model, to obtain an optimal control strategy from a mix of three strategies evaluated. The study used the Pontryagin's maximum principle to solve, numerically, the OC model. The analysis results clearly demonstrated that water and sanitation when implemented together with the MDA programme offer the best chances of eliminating these tenacious and damaging parasites. Thus, we advocate for optimal implementation of the combined mix of the two interventions in order to achieve STH elimination in Kenya, and globally, in a short implementation period of less than eight years.

Impact of a disability-targeted microentrepreneurship programme in Kenya: study protocol for a randomised controlled trial of the InBusiness programme.

BACKGROUND: There is a lack of evidence on the effectiveness of livelihood interventions amongst people with disabilities. In many countries, self-employment or microentrepreneurship is a dominant source of livelihoods for people with disabilities and their caregivers. However, this group may face heightened barriers to successful microentrepreneurship, including discrimination, exclusion from training or inaccessible transport, infrastructure and communication systems. The InBusiness programme is a livelihoods programme targeted to microentrepeneurs with disabilities or their caregivers delivered by a consortium of non-governmental organisations. The programme focuses on improving the skills, practices and opportunities of microentrepreneurs while linking them with procurement opportunities with private and public institutions. This protocol describes a randomised controlled trial of the InBusiness programme in eight counties of Kenya. METHODS: The randomised controlled trial will involve 495 microentrepreneurs who have been verified as eligible for InBusiness by programme implementers. Individuals will be randomised within counties, either being invited to enrol in InBusiness in March 2023 or allocated to a control group. Participants in the control arm will receive information about compliance with business-related laws and available social protection programmes. The trial will assess the impact of InBusiness on household consumption and individual economic empowerment (primary outcomes) as well as food security, well-being, social attitudes, unmet need for disability-related services and microenterprise profits (secondary outcomes). Baseline was conducted in March 2023, and follow-up will be 24 months from baseline (12 months from completion of the programme). Analysis will be through intention to treat. A process evaluation will explore fidelity, mechanisms of impact and the role of context, and complementary qualitative research with participants will be used to triangulate findings across the trial. DISCUSSION: This study will provide evidence on the impact of a large-scale disability-targeted livelihood programme on household and individual financial security and well-being. Currently, there is a lack of evidence on the effectiveness of livelihood programmes amongst people with disabilities, and so this trial can help inform the design and delivery of InBusiness as well as other livelihood programmes targeted to people with disabilities. TRIAL REGISTRATION: ClinicalTrials.gov ISRCTN13693137. Registered on April 24, 2023.

Spatial variation and clustering of anaemia prevalence in school-aged children in Western Kenya.

Anaemia surveillance has overlooked school-aged children (SAC), hence information on this age group is scarce. This study examined the spatial variation of anaemia prevalence among SAC (5-14 years) in western Kenya, a region associated with high malaria infection rates. A total of 8051 SAC were examined from 82 schools across eight counties in Western Kenya in February 2022. Haemoglobin (Hb) concentrations were assessed at the school and village level and anaemia defined as Hb<11.5g/dl for age 5-11yrs and Hb <12.0g/dl for 12-14yrs after adjusting for altitude. Moran's I analysis was used to measure spatial autocorrelation, and local clusters of anaemia were mapped using spatial scan statistics and local indices of spatial association (LISA). The prevalence of anaemia among SAC was 27.8%. The spatial variation of anaemia was non-random, with Global Moran's I 0.2 (p-value < 0.002). Two significant anaemia cluster windows were identified: Cluster 1 (LLR = 38.9, RR = 1.4, prevalence = 32.0%) and cluster 2 (LLR = 23.6, RR = 1.6, prevalence = 45.5%) at schools and cluster 1 (LLR = 41.3, RR = 1.4, prevalence = 33.3%) and cluster 2 (LLR = 24.5, RR = 1.6, prevalence = 36.8%) at villages. Additionally, LISA analysis identified ten school catchments as anaemia hotspots corresponding geographically to SatScan clusters. Anaemia in the SAC is a public health problem in the Western region of Kenya with some localised areas presenting greater risk relative to others. Increasing coverage of interventions, geographically targeting the prevention of anaemia in the SAC, including malaria, is required to alleviate the burden among children attending school in Western Kenya.

Model-based geostatistical design and analysis of prevalence for soil-transmitted helminths in Kenya: Results from ten-years of the Kenya national school-based deworming programme.

Background: Kenya is endemic for soil-transmitted helminths (STH) with over 6 million children in 27 counties currently at-risk. A national school-based deworming programme (NSBDP) was launched in 2012 with a goal to eliminate parasitic worms as a public health problem. This study used model-based geostatistical (MBG) approach to design and analyse the impact of the NSBDP and inform treatment strategy changes. Methods: A cross-sectional study was used to survey 200 schools across 27 counties in Kenya. The study design, school selection and analysis followed the MBG approach which incorporated historical data on treatment, morbidity and environmental covariates to efficiently predict the helminths prevalence in Kenya. Results: Overall, the NSBDP geographic area prevalence for any STH was estimated to sit between 2 % and <10 % with a high predictive probability of >0.999. Species-specific thresholds were between 2 % and <10 % for Ascaris lumbricoides, 0 % to <2 % for hookworm, and 0 % to <2 % for Trichuris trichiura, all with high predictive probability of >0.999. Conclusions: Based on the World Health Organization guidelines, STH treatment requirements can now be confidently refined. Ten counties may consider suspending treatment and implement appropriate surveillance system, while another 10 will require treatment once every two years, and the remaining seven will require treatment once every year.

A positive consequence of the COVID-19 pandemic: how the counterfactual experience of school closures is accelerating a multisectoral response to the treatment of neglected tropical diseases.

Global access to deworming treatment is one of the public health success stories of low-income countries in the twenty-first century. Parasitic worm infections are among the most ubiquitous chronic infections of humans, and early success with mass treatment programmes for these infections was the key catalyst for the neglected tropical disease (NTD) agenda. Since the launch of the 'London Declaration' in 2012, school-based deworming programmes have become the world's largest public health interventions. WHO estimates that by 2020, some 3.3 billion school-based drug treatments had been delivered. The success of this approach was brought to a dramatic halt in April 2020 when schools were closed worldwide in response to the COVID-19 pandemic. These closures immediately excluded 1.5 billion children not only from access to education but also from all school-based health services, including deworming. WHO Pulse surveys in 2021 identified NTD treatment as among the most negatively affected health interventions worldwide, second only to mental health interventions. In reaction, governments created a global Coalition with the twin aims of reopening schools and of rebuilding more resilient school-based health systems. Today, some 86 countries, comprising more than half the world's population, are delivering on this response, and school-based coverage of some key school-based programmes exceeds those from January 2020. This paper explores how science, and a combination of new policy and epidemiological perspectives that began in the 1980s, led to the exceptional growth in school-based NTD programmes after 2012, and are again driving new momentum in response to the COVID-19 pandemic. This article is part of the theme issue 'Challenges and opportunities in the fight against neglected tropical diseases: a decade from the London Declaration on NTDs'.

How important is the spatial movement of people in attempts to eliminate the transmission of human helminth infections by mass drug administration?

Human mobility contributes to the spatial dynamics of many infectious diseases, and understanding these dynamics helps us to determine the most effective ways to intervene and plan surveillance. In this paper, we describe a novel transmission model for the spatial dynamics of hookworm, a parasitic worm which is a common infection across sub-Saharan Africa, East Asia and the Pacific islands. We fit our model, with and without mobility, to data obtained from a sub-county in Kenya, and validate the model's predictions against the decline in prevalence observed over the course of a clustered randomized control trial evaluating methods of administering mass chemotherapy. We find that our model which incorporates human mobility is able to reproduce the observed patterns in decline of prevalence during the TUMIKIA trial, and additionally, that the widespread bounce-back of infection may be possible over many years, depending on the rates of people movement between villages. The results have important implications for the design of mass chemotherapy programmes for the elimination of human helminth transmission. This article is part of the theme issue 'Challenges and opportunities in the fight against neglected tropical diseases: a decade from the London Declaration on NTDs'.

Understanding factors responsible for the slow decline of soil-transmitted helminthiasis following seven rounds of annual mass drug administration (2012-2018) among school children in endemic counties of Kenya: A mixed method study.

BACKGROUND: Soil-transmitted helminthiasis (STH) continue to be a significant health problem in Sub-Saharan Africa especially among school children. In Kenya, treatment of over five million children has been conducted annually in 28 endemic counties since the year 2012. However, the latest monitoring and evaluation (M&E) results indicated a slow decline of prevalence and intensity of STH in some counties after the seven rounds of annual mass drug administration (MDA). The current study sought to determine the factors associated with the slow decline in prevalence and intensity of STH among school children participating in the school deworming programme. METHODOLOGY: Mixed methods cross-sectional study was conducted in three endemic counties of Kenya. For quantitative technique, simple random sampling was used to select 1,874 school children from six purposively selected primary schools. The school children were interviewed, and a single stool collected and analysed using Kato-Katz technique. While for qualitative methods, 15 focus group discussions (FGDs) were conducted with purposively selected parents/guardians of school children. Data was collected through voice records using FGD and analyzed using NVIVO. FINDINGS: Prevalence of any STH infection was 30.8% (95%CI: 28.7-32.9), with the highest prevalence observed in Vihiga County (40.7%; 95%CI: 37.4-44.4). Multivariable analysis revealed that geographical location (OR = 3.78, (95%CI: 1.81-7.88) p<0.001), and not washing hands after defecation (OR = 1.91, (95%CI: 1.13-3.20) p = 0.015) were significantly associated with any STH infection. For qualitative analysis, majority of the parents/guardians of SAC felt that poor water sanitation and hygiene practices (WASH) both in school and household level could be a cause of continued STH infection. Also failing to include the rest of the community members in the MDAs were mentioned as possible contributors to observed slow decline of STH. CONCLUSIONS: There was moderate STH prevalence and mean intensity despite the seven rounds of repeated annual MDA. The study recommends a revamped awareness creation on WASH and community wide treatment.

An adaptive phase II/III safety and efficacy randomized controlled trial of single day or three-day fixed-dose albendazole-ivermectin co-formulation versus albendazole for the treatment of Trichuris trichiura and other STH infections. ALIVE trial protocol.

Background: Soil-transmitted helminths (STH) are targeted for control through mass drug-administration campaigns to prevent morbidity affecting at-risk groups in endemic regions. Although broadly successful, the use of albendazole and mebendazole achieved variable progress, with deficiencies against Trichuris trichiura and a predictable low efficacy against Strongyloides stercoralis. Novel drug combinations offer a potential solution, providing they can be delivered safely and maintain efficacy against all STH species. Here we present the protocol of a clinical trial to evaluate a fixed-dose combination (FDC) tablet containing albendazole and ivermectin that will be compared against albendazole against STH . Methods: An adaptive phase II/III randomized controlled trial will be undertaken in STH endemic sites in Ethiopia, Kenya and Mozambique to evaluate an oral FDC of 400 mg albendazole and either 9- or 18 mg ivermectin. FDC will be administered as a single dose or single doses over three-consecutive days and assessed against a single dose of 400 mg albendazole. In the phase II trial, 126 T. trichiura-infected children weighting 15 to 45 kg will be treated in a dose-escalation manner to determine safety objectives. In the phase III trial, 1097 participants aged 5 to 18 years old infected with T. trichiura, hookworm and S. stercoralis will be recruited to determine safety and efficacy. The trial will be open-label with blinded outcome assessors. Cure rate measured 21-days after-treatment in duplicate Kato-Katz is the primary efficacy outcome. Secondary objectives include efficacy evaluation by quantitative polymerase chain reaction (PCR) as an outcome measurement, description of pharmacokinetic parameters, palatability and acceptability evaluations, and monitoring of anthelmintic resistance. Conclusions: This trial with registrational goals seeks to evaluate an innovative fixed-dose combination of albendazole and ivermectin co-formulated tablets, with the goal of providing an anthelmintic regimen with improved efficacy and spectrum of coverage against STH. ClinicalTrials.gov registration: NCT05124691 (18/11/2021).

Prevalence, types, patterns and risk factors associated with drugs and substances of use and abuse: A cross-sectional study of selected counties in Kenya.

BACKGROUND: The increasing trend of drugs and substances abuse (DSA) by different age groups and gender in parts of Kenya is not only a socio-economic problem but a public health concern. There is a need to determine prevalence, types and patterns of DSA by age and gender in order to develop all-inclusive and long-term strategies to prevent and manage the DSA within different communities. In this study we determined the prevalence of DSA, types and patterns of drugs and substances being abused and risk factors associated with this abuse. METHODS: A descriptive cross-sectional mixed methods study was conducted in four counties; Isiolo, Kajiado, Murang'a and Nyamira, all purposively selected from the 47 counties of Kenya based on the review reports of the Kenya Medical Research Institute's County Cluster Coordinators which indicated that DSA was a priority health concern in the selected counties. From each county, two sub-locations each from two locations in one sub-county were purposively selected. In each sub-location, 225 households were systematically selected. Hence, a total of 3,600 participants were systematically sampled for quantitative data collection using an interviewer-based questionnaire to gather information on magnitude and causes of DSA. Additionally, in each county, qualitative data through in-depth interviews (IDIs) with 16 opinion leaders, 16 healthcare personnel, 16 previous DSAs, at least 5 county personnel, 32 current DSAs; and through 16 focus group discussions (FGDs) were concurrently collected to elicit more information on types, patterns and causes of DSA. The observed overall prevalence of DSA was calculated using binomial logistic regression model and factors associated with DSA analyzed using multilevel logistic regression model. Qualitative data was analyzed using QSR NVIVO version 10, thematically by types, patterns and causes of DSA by age and gender. RESULTS: Prevalence of DSA was 86.0% (95%CI: 84.9-87.2) with the highest prevalence being observed in Nyamira County, 89.8% (95%CI: 87.9-91.7). Age-wise, the highest prevalence was observed in persons aged between 45 to 53 years, 89.4% (95%CI: 86.9-92.0), followed by those aged 36 to 44 years, 88.0% (95%CI: 85.4-90.6). Majority of those who abuse drugs and substances were males; 94.5% (95%CI: 93.6-95.4). The most abused drugs or substances were packaged/legal alcohol at 25.2% (745), cigarettes 20.3% (600), local brew (chang'aa) 16.3% (482), and khat (miraa) 10.5% (311). Risk factors analysis revealed that DSA was significantly higher among males (adjusted odds ratio (aOR) = 7.02 (95%CI: 5.21-9.45), p<0.001), government employees (aOR = 2.27 (95%CI: 1.05-4.91), p = 0.036) and unmarried (aOR = 1.71 (95%CI: 1.06-2.77), p = 0.028). CONCLUSIONS: These study findings are useful in informing development of specific control programmes which will address age, gender and county needs of DSA in Kenya in order to comprehensively respond to this public health problem. This study was conducted in line with the Kenya National Authority for the Campaign against Alcohol and Drug Abuse (NACADA) mandate to promote use of research on drugs and substances abuse.

Correction: Prevalence, intensity and associated risk factors of soil-transmitted helminth and schistosome infections in Kenya: Impact assessment after five rounds of mass drug administration in Kenya.

[This corrects the article DOI: 10.1371/journal.pntd.0008604.].

Sensitivity Analysis of a Transmission Interruption Model for the Soil-Transmitted Helminth Infections in Kenya.

As the world rallies toward the endgame of soil-transmitted helminths (STH) elimination by the year 2030, there is a need for efficient and robust mathematical models that would enable STH programme managers to target the scarce resources and interventions, increase treatment coverage among specific sub-groups of the population, and develop reliable surveillance systems that meet sensitivity and specificity requirements for the endgame of STH elimination. However, the considerable complexities often associated with STH-transmission models underpin the need for specifying a large number of parameters and inputs, which are often available with considerable degree of uncertainty. Additionally, the model may behave counter-intuitive especially when there are non-linearities in multiple input-output relationships. In this study, we performed a global sensitivity analysis (GSA), based on a variance decomposition method: extended Fourier Amplitude Sensitivity Test (eFAST), to a recently developed STH-transmission model in Kenya (an STH endemic country) to; (1) robustly compute sensitivity index (SI) for each parameter, (2) rank the parameters in order of their importance (from most to least influential), and (3) quantify the influence of each parameter, singly and cumulatively, on the model output. The sensitivity analysis (SA) results demonstrated that the model outcome (STH worm burden elimination in the human host) was significantly sensitive to some key parameter groupings: combined effect of improved water source and sanitation (ϕ), rounds of treatment offered (τ), efficacy of the drug used during treatment (h), proportion of the adult population treated (ga : akin to community-wide treatment), mortality rate of the mature worms in the human host (µ), and the strength of the -dependence of worm egg production (γ). For STH control programmes to effectively reach the endgame (STH elimination in the entire community), these key parameter groupings need to be targeted since together they contribute to a strategic public health intervention.

Targeted Amplicon Deep Sequencing for Monitoring Antimalarial Resistance Markers in Western Kenya.

Molecular surveillance of Plasmodium falciparum parasites is important to track emerging and new mutations and trends in established mutations and should serve as an early warning system for antimalarial resistance. Dried blood spots were obtained from a Plasmodium falciparum malaria survey in school children conducted across eight counties in western Kenya in 2019. Real-time PCR identified 500 P. falciparum-positive samples that were amplified at five drug resistance loci for targeted amplicon deep sequencing (TADS). The absence of important kelch 13 mutations was similar to previous findings in Kenya pre-2019, and low-frequency mutations were observed in codons 569 and 578. The chloroquine resistance transporter gene codons 76 and 145 were wild type, indicating that the parasites were chloroquine and piperaquine sensitive, respectively. The multidrug resistance gene 1 haplotypes based on codons 86, 184, and 199 were predominantly present in mixed infections with haplotypes NYT and NFT, driven by the absence of chloroquine pressure and the use of lumefantrine, respectively. The sulfadoxine-pyrimethamine resistance profile was a "superresistant" combination of triple mutations in both Pfdhfr (51I 59R 108N) and Pfdhps (436H 437G 540E), rendering sulfadoxine-pyrimethamine ineffective. TADS highlighted the low-frequency variants, allowing the early identification of new mutations, Pfmdr1 codon 199S and Pfdhfr codon 85I and emerging 164L mutations. The added value of TADS is its accuracy in identifying mixed-genotype infections and for high-throughput monitoring of antimalarial resistance markers.

Schistosomiasis, soil transmitted helminthiasis, and malaria co-infections among women of reproductive age in rural communities of Kwale County, coastal Kenya.

BACKGROUND: Schistosoma haematobium, soil transmitted helminthes (STH), and malaria lead to a double burden in pregnancy that eventually leads to poor immunity, increased susceptibility to other infections, and poor pregnancy outcomes. Many studies have been carried out on pre-school and school aged children but very little has been done among the at risk adult population including women of reproductive age (WRA). Our current study sought to establish the risk factors and burden of co-infection with S. haematobium, STH, and Plasmodium sp. among WRA in Kwale County, Coastal Kenya. METHODS: A total of 534 WRA between the ages of 15-50 were enrolled in this cross-sectional study from four villages; Bilashaka and Mwaluphamba in Matuga sub-County, and Mwachinga and Dumbule in Kinango sub-County. Socio-demographic information was collected using a pre-tested standardized questionnaire. Parasitological examination was done using urine filtration method for Schistosoma haematobium, Kato Katz for STH (Ascaris lumbricoides, Hookworm, Trichuris trichiura), and standard slide microscopy for Plasmodium sp. Statistical analyses were carried out using STATA version 15.1. RESULTS: The overall prevalence of S. haematobium was 3.8% (95% CI: 2.6-5.4) while that for malaria was 4.9% (95% CI: 2.0-11.7). The prevalence of STH was 5.6% (95% CI: 2.8-11.3) with overall prevalence of 5.3% (95% CI: 2.5-10.9) for hookworm and 0.6% (95% CI: 0.2-1.9) for T. trichiura. The occurrence of co-infection was low and was recorded between S. haematobium and P. falciparum (0.6%), followed by S. haematobium and STH (0.4%). Among pregnant women, 2.6% had co-infection with S. haematobium and P. falciparum. Only 1.3% had co-infection with S. haematobium and hookworm or T. trichiura. Among non-pregnant women, co-infection with S. haematobium and P. falciparum was 0.2%. Similarly, co-infection with S. haematobium and hookworm or T. trichiura was 0.2%. Bed net ownership and usage among pregnant women was 87.8 and 96.6%, respectively. 66.3% of the women reported using improved water sources for drinking while 78.1% reported using improved sanitation facilities. CONCLUSION: The use of improved WASH activities might have contributed to the low prevalence of STHs and S. haematobium infections. Further, bed net ownership and usage might have resulted in the low prevalence of Plasmodium sp. infections observed.

Mobile microscopy and telemedicine platform assisted by deep learning for the quantification of Trichuris trichiura infection.

Soil-transmitted helminths (STH) are the most prevalent pathogens among the group of neglected tropical diseases (NTDs). The Kato-Katz technique is the diagnosis method recommended by the World Health Organization (WHO) although it often presents a decreased sensitivity in low transmission settings and it is labour intensive. Visual reading of Kato-Katz preparations requires the samples to be analyzed in a short period of time since its preparation. Digitizing the samples could provide a solution which allows to store the samples in a digital database and perform remote analysis. Artificial intelligence (AI) methods based on digitized samples can support diagnosis by performing an objective and automatic quantification of disease infection. In this work, we propose an end-to-end pipeline for microscopy image digitization and automatic analysis of digitized images of STH. Our solution includes (a) a digitization system based on a mobile app that digitizes microscope samples using a 3D printed microscope adapter, (b) a telemedicine platform for remote analysis and labelling, and (c) novel deep learning algorithms for automatic assessment and quantification of parasitological infections by STH. The deep learning algorithm has been trained and tested on 51 slides of stool samples containing 949 Trichuris spp. eggs from 6 different subjects. The algorithm evaluation was performed using a cross-validation strategy, obtaining a mean precision of 98.44% and a mean recall of 80.94%. The results also proved the potential of generalization capability of the method at identifying different types of helminth eggs. Additionally, the AI-assisted quantification of STH based on digitized samples has been compared to the one performed using conventional microscopy, showing a good agreement between measurements. In conclusion, this work has presented a comprehensive pipeline using smartphone-assisted microscopy. It is integrated with a telemedicine platform for automatic image analysis and quantification of STH infection using AI models.

Prevalence and Correlation Analysis of Soil-Transmitted Helminths Infections and Treatment Coverage for Preschool and School Aged Children in Kenya: Secondary Analysis of the National School Based Deworming Program Data.

Background: Soil-transmitted helminths (STH) are among the most common parasitic infections globally, disproportionately affecting children. Treatment of STH in Kenya is often targeted at preschool (PSAC) and school aged (SAC) children delivered through annual mass drug administration (MDA) in primary schools. Understanding group-specific prevalence and dynamics between treatment and coverage is critical for continued treatment success. This study aims to provide detailed information on group-specific infection prevalence and relative reductions (RR), and their relationships with treatment coverage over time. Additionally, it aims to quantify the correlation between the observed school level infection prevalence and treatment coverage. Methods: Secondary analysis of existing data collected between 2012 and 2018 by the monitoring and evaluation (M&E) program of the National School-Based Deworming (NSBD) program was used. The M&E program conducted surveys utilizing cross-sectional study design, at four survey time points, in a nationally-representative sample of schoolchildren across counties in Kenya. In each participating school, the program randomly sampled 108 children per school, of both groups. Infection prevalence was estimated using binomial regression, RR in prevalence using multivariable mixed effects model, statistical correlations using structural equation modeling, and change-point-analysis using the binary segmentation algorithm. Results: Overall, STH prevalence for PSAC was 33.7, 20.2, 19.0, and 17.9% during Year 1 (Y1), Year 3 (Y3), Year 5 (Y5), and Year 6 (Y6) surveys, respectively with an overall RR of 46.9% (p = 0.001) from Y1 to Y6. Similarly, overall STH prevalence for SAC was 33.6, 18.4, 14.7, and 12.5% during Y1, Y3, Y5, and Y6 surveys, respectively with an overall RR of 62.6% (p < 0.001). An overall (all time points) significant but very weak negative correlation was found between treatment coverage and undifferentiated STH prevalence (r = -0.144, p = 0.002) among PSAC but not in SAC. Further, we observed inter-county heterogeneity variation in infection prevalence, RR, as well as correlations. Conclusion: The analysis showed that after six rounds of MDA, prevalence of STH has significantly declined among both groups of children, however not to a point where it is not a public health problem (below 1%). The analysis, additionally established an overall significant but weak negative correlation between treatment coverage and prevalence, indicating that the current treatment coverage might not be sufficient to drive the overall STH prevalence to below 1%. These findings will allow STH control programs in Kenya to make decisions that will accelerate the attainment of STH elimination as a public health problem.

Malaria infection and severe disease risks in Africa.

The relationship between community prevalence of Plasmodium falciparum and the burden of severe, life-threatening disease remains poorly defined. To examine the three most common severe malaria phenotypes from catchment populations across East Africa, we assembled a dataset of 6506 hospital admissions for malaria in children aged 3 months to 9 years from 2006 to 2020. Admissions were paired with data from community parasite infection surveys. A Bayesian procedure was used to calibrate uncertainties in exposure (parasite prevalence) and outcomes (severe malaria phenotypes). Each 25% increase in prevalence conferred a doubling of severe malaria admission rates. Severe malaria remains a burden predominantly among young children (3 to 59 months) across a wide range of community prevalence typical of East Africa. This study offers a quantitative framework for linking malaria parasite prevalence and severe disease outcomes in children.

Modeling the Interruption of the Transmission of Soil-Transmitted Helminths Infections in Kenya: Modeling Deworming, Water, and Sanitation Impacts.

Kenya, just like other countries with endemic soil-transmitted helminths (STH), has conducted regular mass drug administration (MDA) program for the last 5 years among school aged children as a way to reduce STH infections burden in the country. However, the point of interruption of transmission of these infections still remains unclear. In this study, we developed and analyzed an age structured mathematical model to predict the elimination period (i.e., time taken to interrupt STH transmission) of these infections in Kenya. The study utilized a deterministic age structured model of the STH population dynamics under a regular treatment program. The model was applied to three main age groups: pre-school age children (2-4 years), school age children (5-14 years), and adult populations (≥15 years) and compared the impact of two interventions on worm burden and elimination period. The model-simulated results were compared with the 5 year field data from the Kenyan deworming program for all the three types of STH (Ascaris lumbricoides, Trichuris trichiura, and hookworm). The model demonstrated that the reduction of worm burden and elimination period depended heavily on four parameter groups; drug efficacy, number of treatment rounds, MDA and water, sanitation and hygiene (WASH) coverage. The analysis showed that for STH infections to be eliminated using MDA alone in a short time period, 3-monthly MDA plan is desired. However, complementation of MDA with WASH at an optimal (95%) coverage level was most effective. These results are important to the Kenyan STH control program as it will guide the recently launched Breaking Transmission Strategy.

Model-Based Geostatistical Methods Enable Efficient Design and Analysis of Prevalence Surveys for Soil-Transmitted Helminth Infection and Other Neglected Tropical Diseases.

Maps of the geographical variation in prevalence play an important role in large-scale programs for the control of neglected tropical diseases. Precontrol mapping is needed to establish the appropriate control intervention in each area of the country in question. Mapping is also needed postintervention to measure the success of control efforts. In the absence of comprehensive disease registries, mapping efforts can be informed by 2 kinds of data: empirical estimates of local prevalence obtained by testing individuals from a sample of communities within the geographical region of interest, and digital images of environmental factors that are predictive of local prevalence. In this article, we focus on the design and analysis of impact surveys, that is, prevalence surveys that are conducted postintervention with the aim of informing decisions on what further intervention, if any, is needed to achieve elimination of the disease as a public health problem. We show that geospatial statistical methods enable prevalence surveys to be designed and analyzed as efficiently as possible so as to make best use of hard-won field data. We use 3 case studies based on data from soil-transmitted helminth impact surveys in Kenya, Sierra Leone, and Zimbabwe to compare the predictive performance of model-based geostatistics with methods described in current World Health Organization (WHO) guidelines. In all 3 cases, we find that model-based geostatistics substantially outperforms the current WHO guidelines, delivering improved precision for reduced field-sampling effort. We argue from experience that similar improvements will hold for prevalence mapping of other neglected tropical diseases.