Higher livestock abortion burden in arid and semi-arid lands, Kenya, 2019-2020

Tracking livestock abortion patterns over time and across factors such as species and agroecological zones (AEZs) could inform policies to mitigate disease emergence, zoonoses risk, and reproductive losses. We conducted a year-long population-based active surveillance of livestock abortion between 2019 and 2020, in administrative areas covering 52% of Kenya's landmass and home to 50% of Kenya's livestock. Surveillance sites were randomly selected to represent all AEZs in the country. Local animal health practitioners electronically transmitted weekly abortion reports from each ward, the smallest administrative unit, to a central server, using a simple short messaging service (SMS). Data were analyzed descriptively by administrative unit, species, and AEZ to reveal spatiotemporal patterns and relationships with rainfall and temperature. Of 23,766 abortions reported in all livestock species, sheep and goats contributed 77%, with goats alone contributing 53%. Seventy-seven per cent (n = 18,280) of these abortions occurred in arid and semi-arid lands (ASALs) that primarily practice pastoralism production systems. While spatiotemporal clustering of cases was observed in May-July 2019 in the ASALs, there was a substantial seasonal fluctuation across AEZs. Kenya experiences high livestock abortion rates, most of which go unreported. We recommend further research to document the national true burden of abortions. In ASALs, studies linking pathogen, climate, and environmental surveillance are needed to assign livestock abortions to infectious or non-infectious aetiologies and conducting human acute febrile illnesses surveillance to detect any links with the abortions.

Comparative prevalence of diarrheagenic Escherichia coli between children below five years with close contact to food animals in Kisumu County, Kenya

Introduction

diarrheal infections in young children below five years and food animals are caused by diarrheagenic Escherichia coli strains. The study focused on understanding the association between DEC pathotypes in children below five years and food animals to establish the possibility of zoonotic transmission.

Methods

samples from 150 children who presented with diarrhea at the Kisumu County Hospital and 100 stool samples from food animals were collected and processed using culture methods. Molecular identification of the pathotypes was assayed using a primer-specific polymerase chain reaction that targeted the six virulence genes related to the diarrheagenic Escherichia coli pathotypes.

Results

one hundred and fifty-six study subjects (100 children samples and 56 food animals) samples were positive for E. coli polymerase chain reaction detection revealed a prevalence of (23%) among children below five years and a prevalence of (20%) among the food animals. Children samples showed Enteroaggregative Escherichia coli, having high phenotypic frequency of (12%) followed by Enterotoxigenic Escherichia coli, (5.3%) and Enteropathogenic Escherichia (3.3%) the least being mixed infections Enteroaggregative/Enterotoxigenic Escherichia coli and Enteroaggregative/Enteropathogenic Escherichia coli with (1.3%) respectively. The food animals found in children homesteads were detected to harbor pathogenic strains of E. coli. Enteropathogenic Escherichia coli was the most prevalent pathotypes detected in cattle (13%) followed by Enterotoxigenic Escherichia coli detected in goats at (4%) and poultry at (3%).

Conclusion

presence of diarrheagenic Escherichia coli in food animals could serve as reservoirs of transmitting these bacteria to children below five years.

Optimal control and cost-effectiveness analysis for leptospirosis epidemic

This paper aims to apply an optimal control theory for the autonomous model of the leptospirosis epidemic to examine the effect of four time-dependent control measures on the model dynamics with cost-effectiveness. Pontryagin's Maximum Principle was used to derive the optimality system associated with the optimal control problem. Numerical simulations of the optimality system were performed for different control strategies and the results were presented graphically with and without controls. The optimality system was simulated using the Forward-Backward Sweep method in the Matlab programme. The numerical results revealed that the combination of all optimal control measures is the most effective strategy for minimizing the spread and impact of disease in the community. Furthermore, a cost-effectiveness analysis was performed to determine the most cost-effective strategy using the incremental cost-effectiveness ratio approach and we observed that the rodenticide control-only strategy is most effective to combat the spread of disease when available resources are limited.

Mapping brucellosis risk in Kenya and its implications for control strategies in sub-Saharan Africa

In Sub-Saharan Africa (SSA), effective brucellosis control is limited, in part, by the lack of long-term commitments by governments to control the disease and the absence of reliable national human and livestock population-based data to inform policies. Therefore, we conducted a study to establish the national prevalence and develop a risk map for Brucella spp. in cattle to contribute to plans to eliminate the disease in Kenya by the year 2040. We randomly generated 268 geolocations and distributed them across Kenya, proportionate to the area of each of the five agroecological zones and the associated cattle population. Cattle herds closest to each selected geolocation were identified for sampling. Up to 25 cattle were sampled per geolocation and a semi-structured questionnaire was administered to their owners. We tested 6,593 cattle samples for Brucella immunoglobulin G (IgG) antibodies using an Enzyme-linked immunosorbent assay (ELISA). We assessed potential risk factors and performed spatial analyses and prevalence mapping using approximate Bayesian inference implemented via the integrated nested Laplace approximation (INLA) method. The national Brucella spp. prevalence was 6.8% (95% CI: 6.2-7.4%). Exposure levels varied significantly between agro-ecological zones, with a high of 8.5% in the very arid zone with the lowest agricultural potential relative to a low of 0.0% in the agro-alpine zone with the highest agricultural potential. Additionally, seroprevalence increased with herd size, and the odds of seropositivity were significantly higher for females and adult animals than for males or calves. Similarly, animals with a history of abortion, or with multiple reproductive syndromes had higher seropositivity than those without. At the herd level, the risk of Brucella spp. transmission was higher in larger herds, and herds with a history of reproductive problems such as abortion, giving birth to weak calves, or having swollen testes. Geographic localities with high Brucella seroprevalence occurred in northern, eastern, and southern regions of Kenya all primarily characterized by semi-arid or arid agro-ecological zones dominated by livestock pastoralism interspersed with vast areas with mixed livestock-wildlife systems. The large spatial extent of our survey provides compelling evidence for the widespread geographical distribution of brucellosis risk across Kenya in a manner easily understandable for policymakers. Our findings can provide a basis for risk-stratified pilot studies aiming to investigate the cost-effectiveness and efficacy of singular and combined preventive intervention strategies that seek to inform Kenya's Brucellosis Control Policy.

Spatial distribution of sexual network locations used by long-distance truck drivers along the Northern Corridor highway, Kenya

BACKGROUND

In Kenya, long-distance truck drivers (LDTDs) using the Northern Corridor highway have a high prevalence of HIV and other sexually transmitted infections (STIs) due to their risky sexual networks. However, the spatial distribution of the sexual network locations used by LDTDs is not well understood. Consequently, healthcare stakeholders have found it difficult to provide spatially targeted HIV/STI interventions among LDTDs. Thus, the study sought to establish the spatial distribution of sexual network locations used by LDTDs along the Northern Corridor highway, to inform efficient distribution and use of limited HIV/STI-prevention resources.

METHODS

A cross-sectional study design was used. The study adopted a systematic sampling technique. 296 LDTDs were interviewed using interviewer-administered questionnaires at the Mlolongo weighbridge in Kenya. The LDTDs listed their history of sexual interactions and highway stopovers used during the week preceding data collection. Geospatial modelling techniques, using R statistical software packages for spatial mapping, were employed. Shapefiles were created and overlaid over a map of Kenya using R statistical software to create maps of sexual networks.

RESULTS

Forty-two highway stopovers used by LDTDs were spatially distributed along the highway, from the Kenya coast to the Kenya-Uganda border. In general, LDTDs' sexual network hotspots were restricted to the outskirts of major cities along the Northern Corridor highway (Nairobi, Mombasa and Nakuru) as well as the Kenya-Uganda international border.

CONCLUSIONS

On the Northern Corridor highway, stopovers situated proximal to major urban areas, as well as those at international border points, frequently serve as sexual network hotspots among LDTDs and their sexual partners. Thus, healthcare stakeholders should improve access to HIV/STI-prevention services targeted for LDTDs at the sexual network hotspots identified in this study.

Utilization of digital tools to enhance COVID-19 and tuberculosis testing and linkage to care: A cross-sectional evaluation study among Bodaboda motorbike riders in the Nairobi Metropolis, Kenya

Kenya has registered over 300,000 cases of COVID-19 and is a high-burden tuberculosis country. Tuberculosis diagnosis was significantly disrupted by the pandemic. Access to timely diagnosis, which is key to effective management of tuberculosis and COVID-19, can be expanded and made more efficient through integrated screening. Decentralized testing at community level further increases access, especially for underserved populations, and requires robust systems for data and process management. This study delivered integrated COVID-19 and tuberculosis testing to commercial motorbike (Bodaboda) riders, a population at increased risk of both diseases with limited access to services, in four counties: Nairobi, Kiambu, Machakos and Kajiado. Testing sheds were established where riders congregate, with demand creation carried out by the Bodaboda association. Integrated symptom screening for tuberculosis and COVID-19 was conducted through a digital questionnaire which automatically flagged participants who should be tested for either, or both, diseases. Rapid antigen-detecting tests (Ag-RDTs) for COVID-19 were conducted onsite, while sputum samples were collected and transported to laboratories for tuberculosis diagnosis. End-to-end patient data were captured using digital tools. 5663 participants enrolled in the study, 4946 of whom were tested for COVID-19. Ag-RDT positivity rate was 1% but fluctuated widely across counties in line with broader regional trends. Among a subset tested by PCR, positivity was greater in individuals flagged as high risk by the digital tool (8% compared with 4% overall). Of 355 participants tested for tuberculosis, 7 were positive, with the resulting prevalence rate higher than the national average. Over 40% of riders had elevated blood pressure or abnormal sugar levels. The digital tool successfully captured complete end-to-end data for 95% of all participants. This study revealed high rates of undetected disease among Bodaboda riders and demonstrated that integrated diagnosis can be delivered effectively in communities, with the support of digital tools, to maximize access.

Mapping of cholera hotspots in Kenya using epidemiologic and water, sanitation, and hygiene (WASH) indicators as part of Kenya's new 2022-2030 cholera elimination plan

Cholera is an issue of major public health importance. It was first reported in Kenya in 1971, with the country experiencing outbreaks through the years, most recently in 2021. Factors associated with the outbreaks in Kenya include open defecation, population growth with inadequate expansion of safe drinking water and sanitation infrastructure, population movement from neighboring countries, crowded settings such as refugee camps coupled with massive displacement of persons, mass gathering events, and changes in rainfall patterns. The Ministry of Health, together with other ministries and partners, revised the national cholera control plan to a multisectoral cholera elimination plan that is aligned with the Global Roadmap for Ending Cholera. One of the key features in the revised plan is the identification of hotspots. The hotspot identification exercise followed guidance and tools provided by the Global Task Force on Cholera Control (GTFCC). Two epidemiological indicators were used to identify the sub-counties with the highest cholera burden: incidence per population and persistence. Additionally, two indicators were used to identify sub-counties with poor WASH coverage due to low proportions of households accessing improved water sources and improved sanitation facilities. The country reported over 25,000 cholera cases between 2015 and 2019. Of 290 sub-counties, 25 (8.6%) sub-counties were identified as a high epidemiological priority; 78 (26.9%) sub-counties were identified as high WASH priority; and 30 (10.3%) sub-counties were considered high priority based on a combination of epidemiological and WASH indicators. About 10% of the Kenyan population (4.89 million) is living in these 30-combination high-priority sub-counties. The novel method used to identify cholera hotspots in Kenya provides useful information to better target interventions in smaller geographical areas given resource constraints. Kenya plans to deploy oral cholera vaccines in addition to WASH interventions to the populations living in cholera hotspots as it targets cholera elimination by 2030.

Near-Complete SARS-CoV-2 Seroprevalence among Rural and Urban Kenyans despite Significant Vaccine Hesitancy and Refusal

Considering the early inequity in global COVID-19 vaccine distribution, we compared the level of population immunity to SARS-CoV-2 with vaccine uptake and refusal between rural and urban Kenya two years after the pandemic onset. A population-based seroprevalence study was conducted in the city of Nairobi (n = 781) and a rural western county (n = 810) between January and February 2022. The overall SARS-CoV-2 seroprevalence was 90.2% (95% CI, 88.6−91.2%), including 96.7% (95% CI, 95.2−97.9%) among urban and 83.6% (95% CI, 80.6−86.0%) among rural populations. A comparison of immunity profiles showed that >50% of the rural population were strongly immunoreactive compared to <20% of the urban population, suggesting more recent infections or vaccinations in the rural population. More than 45% of the vaccine-eligible (≥18 years old) persons had not taken a single dose of the vaccine (hesitancy), including 47.6% and 46.9% of urban and rural participants, respectively. Vaccine refusal was reported in 19.6% of urban and 15.6% of rural participants, attributed to concern about vaccine safety (>75%), inadequate information (26%), and concern about vaccine effectiveness (9%). Less than 2% of vaccine refusers cited religious or cultural beliefs. These findings indicate that despite vaccine inequity, hesitancy, and refusal, herd immunity had been achieved in Kenya and likely other African countries by early 2022, with natural infections likely contributing to most of this immunity. However, vaccine campaigns should be sustained due to the need for repeat boosters associated with waning of SARS-CoV-2 immunity and emergence of immune-evading virus variants.

Anthrax hotspot mapping in Kenya support establishing a sustainable two-phase elimination program targeting less than 6% of the country landmass

Using data collected from previous (n = 86) and prospective (n = 132) anthrax outbreaks, we enhanced prior ecological niche models (ENM) and added kernel density estimation (KDE) approaches to identify anthrax hotspots in Kenya. Local indicators of spatial autocorrelation (LISA) identified clusters of administrative wards with a relatively high or low anthrax reporting rate to determine areas of greatest outbreak intensity. Subsequently, we modeled the impact of vaccinating livestock in the identified hotspots as a national control measure. Anthrax suitable areas included high agriculture zones concentrated in the western, southwestern and central highland regions, consisting of 1043 of 1450 administrative wards, covering 18.5% country landmass, and hosting 30% of the approximately 13 million cattle population in the country. Of these, 79 wards covering 5.5% landmass and hosting 9% of the cattle population fell in identified anthrax hotspots. The rest of the 407 administrative wards covering 81.5% of the country landmass, were classified as low anthrax risk areas and consisted of the expansive low agricultural arid and semi-arid regions of the country that hosted 70% of the cattle population, reared under the nomadic pastoralism. Modelling targeted annual vaccination of 90% cattle population in hotspot administrative wards reduced > 23,000 human exposures. These findings support an economically viable first phase of anthrax control program in low-income countries where the disease is endemic, that is focused on enhanced animal and human surveillance in burden hotspots, followed by rapid response to outbreaks anchored on public education, detection and treatment of infected humans, and ring vaccination of livestock. Subsequently, the global anthrax elimination program focused on sustained vaccination and surveillance in livestock in the remaining few hotspots for a prolonged period (> 10 years) may be implemented.

Six-Months Retention on Treatment and Attrition Risk Factors among People Living with HIV in Kibera Informal Settlement, Nairobi, Kenya

Early retention of patients on HIV treatment is vital in preventing new infections, reducing transmissions, preventing AIDS related deaths and achieving viral suppression. This study sought to determine the effectiveness of non-cash intervention (reminding HIV positive patients at every clinic visit that they stand to receive free T-shirts of their favorite football team or free Kiondos based on preference if they made it to the sixth month visit without missing a treatment appointment) and psychosocial support on retention during the first six months of HIV treatment. This unblinded randomized control trial was conducted at three health centers within the Kibera informal settlement in Nairobi, Kenya. Participants were randomly assigned to the intervention and control groups at a ratio of 1:1. Eligible participants were patients who newly tested HIV positive and enrolled for treatment at the study sites, were 18 years and older and were willing and able to provide informed consent to participate in the study. The primary outcome of interest was retention on treatment at six months. The overall retention on treatment at six months was 93%. Retention at six months among the intervention and control groups was 94% and 91%, respectively (aRR: 1.03; 95% CI: 0.98-1.09; p-value = 0.24). Attrition from treatment was significantly associated with being divorced, being single/never married, time to clinic, participant weight and being on other first line ART regimens other than TDF/3TC/DTG and TDF/3TC/EFV. Mortality and lost to follow-up rates were 1.6 and 13.5 per 100 person-years, respectively. The combination of non-cash incentives and psychosocial support did not improve retention during the first six months of HIV treatment. To reduce further attrition in the early stages of HIV treatment, innovative strategies are needed to reach divorced and not married/single patients earlier and support them to remain on treatment. Efforts should also be made to further decentralize ART treatment to reduce costs and time associated with travelling to and from hospitals.

Outbreak of Middle East Respiratory Syndrome Coronavirus in Camels and Probable Spillover Infection to Humans in Kenya

The majority of Kenya’s > 3 million camels have antibodies against Middle East respiratory syndrome coronavirus (MERS-CoV), although human infection in Africa is rare. We enrolled 243 camels aged 0−24 months from 33 homesteads in Northern Kenya and followed them between April 2018 to March 2020. We collected and tested camel nasal swabs for MERS-CoV RNA by RT-PCR followed by virus isolation and whole genome sequencing of positive samples. We also documented illnesses (respiratory or other) among the camels. Human camel handlers were also swabbed, screened for respiratory signs, and samples were tested for MERS-CoV by RT-PCR. We recorded 68 illnesses among 58 camels, of which 76.5% (52/68) were respiratory signs and the majority of illnesses (73.5% or 50/68) were recorded in 2019. Overall, 124/4692 (2.6%) camel swabs collected from 83 (34.2%) calves in 15 (45.5%) homesteads between April−September 2019 screened positive, while 22 calves (26.5%) recorded reinfections (second positive swab following ≥ 2 consecutive negative tests). Sequencing revealed a distinct Clade C2 virus that lacked the signature ORF4b deletions of other Clade C viruses. Three previously reported human PCR positive cases clustered with the camel infections in time and place, strongly suggesting sporadic transmission to humans during intense camel outbreaks in Northern Kenya.

Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemic

Background

Using classical and genomic epidemiology, we tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression.

Methods

SARS-CoV-2 surveillance and testing data were obtained from the Kenya Ministry of Health, collected daily from 306 health facilities. COVID-19-associated fatality data were also obtained from these health facilities and communities. Whole SARS-CoV-2 genome sequencing were carried out on 1241 specimens.

Results

Over the pandemic duration (March 2020 - January 2022) Kenya experienced five waves characterized by attack rates (AR) of between 65.4 and 137.6 per 100,000 persons, and intra-wave case fatality ratios (CFR) averaging 3.5%, two-fold higher than the national average COVID-19 associated CFR. The first two waves that occurred before emergence of global variants of concerns (VoC) had lower AR (65.4 and 118.2 per 100,000). Waves 3, 4, and 5 that occurred during the second year were each dominated by multiple introductions each, of Alpha (74.9% genomes), Delta (98.7%), and Omicron (87.8%) VoCs, respectively. During this phase, government-imposed restrictions failed to alleviate pandemic progression, resulting in higher attack rates spread across the country.

Conclusions

The emergence of Alpha, Delta, and Omicron variants was a turning point that resulted in widespread and higher SARS-CoV-2 infections across the country.

High seroprevalence of SARS-CoV-2 but low infection fatality ratio eight months after introduction in Nairobi, Kenya

BACKGROUND

The lower than expected COVID-19 morbidity and mortality in Africa has been attributed to multiple factors, including weak surveillance. This study estimated the burden of SARS-CoV-2 infections eight months into the epidemic in Nairobi, Kenya.

METHODS

A population-based, cross-sectional survey was conducted using multi-stage random sampling to select households within Nairobi in November 2020. Sera from consenting household members were tested for antibodies to SARS-CoV-2. Seroprevalence was estimated after adjusting for population structure and test performance. Infection fatality ratios (IFRs) were calculated by comparing study estimates with reported cases and deaths.

RESULTS

Among 1,164 individuals, the adjusted seroprevalence was 34.7% (95% CI 31.8-37.6). Half of the enrolled households had at least one positive participant. Seropositivity increased in more densely populated areas (spearman's r=0.63; p=0.009). Individuals aged 20-59 years had at least two-fold higher seropositivity than those aged 0-9 years. The IFR was 40 per 100,000 infections, with individuals ≥60 years old having higher IFRs.

CONCLUSION

Over one-third of Nairobi residents had been exposed to SARS-CoV-2 by November 2020, indicating extensive transmission. However, the IFR was >10-fold lower than that reported in Europe and the USA, supporting the perceived lower morbidity and mortality in sub-Saharan Africa.

Mapping of Podoconiosis Cases and Risk Factors in Kenya: A Nationwide Cross-sectional Study

Podoconiosis is a type of tropical lymphedema that is clinically distinguished from lymphatic filariasis (LF) because it is ascending and commonly bilateral but asymmetric. The disease is a result of a genetically determined inflammatory reaction to long-term exposure to mineral particles in irritant red clay soils derived mainly from volcanic soils. We conducted the first nationwide mapping of the prevalence and risk factors of podoconiosis in Kenya. We performed a population-based cross-sectional survey to determine the national prevalence of podoconiosis and included 6,228 individuals from 48 villages in 24 sub-counties across 15 counties. Participants answered a questionnaire about the history of symptoms compatible with podoconiosis, received a point-of-care antigen test, and underwent a physical examination if they had lymphedema. A confirmed case of podoconiosis was defined as a case in a resident of the study village who had lower limb bilateral and asymmetric lymphedema lasting more than 1 year, negative test results for Wuchereria bancrofti antigen, and other causes of lymphedema ruled out. Of all the individuals surveyed, 89 had lymphedema; of those, 16 of 6228 (0.3%; 95% confidence interval [CI], 0.1-0.5) were confirmed to have podoconiosis. A high prevalence of podoconiosis was found in western (Siaya, 3.1%; Busia, 0.9%) and central (Meru, 1.1%) regions, and a low prevalence was observed in northern (Marsabit, 0.2%), eastern (Makueni, 0.2%), and coastal (Tana River, 0.1%) regions. The identified risk factors were age 56 years or older (adjusted odds ratio [aOR], 5.66; 95% CI, 2.32-13.83; P < 0.001) and rarely wearing shoes (aOR, 18.92; 95% CI, 4.55-78.71; P < 0.001). These results indicated that the podoconiosis prevalence is low and localized in Kenya; therefore, elimination is achievable if appropriate disease prevention, management, and behavioral strategies are promoted.

Lessons Learned From a Large Cross-Border Field Simulation Exercise to Strengthen Emergency Preparedness in East Africa, 2019

Field simulation exercises (FSXs) require substantial time, resources, and organizational experience to plan and implement and are less commonly undertaken than drills or tabletop exercises. Despite this, FSXs provide an opportunity to test the full scope of operational capacities, including coordination across sectors. From June 11 to 14, 2019, the East African Community Secretariat conducted a cross-border FSX at the Namanga One Stop Border Post between the Republic of Kenya and the United Republic of Tanzania. The World Health Organization Department of Health Security Preparedness was the technical lead responsible for developing and coordinating the exercise. The purpose of the FSX was to assess and further enhance multisectoral outbreak preparedness and response in the East Africa Region, using a One Health approach. Participants included staff from the transport, police and customs, public health, animal health, and food inspection sectors. This was the first FSX of this scale, magnitude, and complexity to be conducted in East Africa for the purpose of strengthening emergency preparedness capacities. The FSX provided an opportunity for individual learning and national capacity strengthening in emergency management and response coordination. In this article, we describe lessons learned and propose recommendations relevant to FSX design, management, and organization to inform future field exercises.

Modeling the Potential Future Distribution of Anthrax Outbreaks under Multiple Climate Change Scenarios for Kenya

The climate is changing, and such changes are projected to cause global increase in the prevalence and geographic ranges of infectious diseases such as anthrax. There is limited knowledge in the tropics with regards to expected impacts of climate change on anthrax outbreaks. We determined the future distribution of anthrax in Kenya with representative concentration pathways (RCP) 4.5 and 8.5 for year 2055. Ecological niche modelling (ENM) of boosted regression trees (BRT) was applied in predicting the potential geographic distribution of anthrax for current and future climatic conditions. The models were fitted with presence-only anthrax occurrences (n = 178) from historical archives (2011-2017), sporadic outbreak surveys (2017-2018), and active surveillance (2019-2020). The selected environmental variables in order of importance included rainfall of wettest month, mean precipitation (February, October, December, July), annual temperature range, temperature seasonality, length of longest dry season, potential evapotranspiration and slope. We found a general anthrax risk areal expansion i.e., current, 36,131 km2, RCP 4.5, 40,012 km2, and RCP 8.5, 39,835 km2. The distribution exhibited a northward shift from current to future. This prediction of the potential anthrax distribution under changing climates can inform anticipatory measures to mitigate future anthrax risk.

Modeling the spatial distribution of anthrax in southern Kenya

BACKGROUND

Anthrax is an important zoonotic disease in Kenya associated with high animal and public health burden and widespread socio-economic impacts. The disease occurs in sporadic outbreaks that involve livestock, wildlife, and humans, but knowledge on factors that affect the geographic distribution of these outbreaks is limited, challenging public health intervention planning.

METHODS

Anthrax surveillance data reported in southern Kenya from 2011 to 2017 were modeled using a boosted regression trees (BRT) framework. An ensemble of 100 BRT experiments was developed using a variable set of 18 environmental covariates and 69 unique anthrax locations. Model performance was evaluated using AUC (area under the curve) ROC (receiver operating characteristics) curves.

RESULTS

Cattle density, rainfall of wettest month, soil clay content, soil pH, soil organic carbon, length of longest dry season, vegetation index, temperature seasonality, in order, were identified as key variables for predicting environmental suitability for anthrax in the region. BRTs performed well with a mean AUC of 0.8. Areas highly suitable for anthrax were predicted predominantly in the southwestern region around the shared Kenya-Tanzania border and a belt through the regions and highlands in central Kenya. These suitable regions extend westwards to cover large areas in western highlands and the western regions around Lake Victoria and bordering Uganda. The entire eastern and lower-eastern regions towards the coastal region were predicted to have lower suitability for anthrax.

CONCLUSION

These modeling efforts identified areas of anthrax suitability across southern Kenya, including high and medium agricultural potential regions and wildlife parks, important for tourism and foreign exchange. These predictions are useful for policy makers in designing targeted surveillance and/or control interventions in Kenya. We thank the staff of Directorate of Veterinary Services under the Ministry of Agriculture, Livestock and Fisheries, for collecting and providing the anthrax historical occurrence data.

Frequency of sexual interactions and associated factors among long-distance truck drivers operating along the Northern Corridor Highway, Kenya

Introduction

harsh working conditions among long-distance truck drivers (LDTDs) expose them to risky sexual interactions while on transit. As a result, the risky sexual interactions among the LDTDs place them at a high risk of contracting human immunodeficiency virus (HIV) and sexually transmitted infections (STIs). This study sought to assess the sexual interactions and associated factors among the LDTDs in Kenya.

Methods

two hundred ninety-six (296) LDTDs were interviewed using interviewer-administered questionnaires. A systematic sampling technique was adopted. The number of sexual acts reported by the respondents was used to generate an ordered outcome variable (frequency of sexual interactions), in the order of; no sexual acts (zero), one to three sexual acts (1), and four to six sexual acts (2). Association between the predictor variables and the outcome variable was analysed using ordered logistic regression analysis in R statistical software.

Results

the mean age of the study participants was 38.4 years, with the youngest being 24 years and the oldest 57 years. Slightly above half of the participants (52.4%) reported no sexual interactions, while the rest (47.6%) had sexual interactions with either casual or regular sexual partners on the week preceding the survey. Age, the number of weeks spent on a transit journey, and drug use were independently associated with the frequency of sexual interactions among LDTDs involved in the study.

Conclusion

the frequencies of sexual interactions are likely to be higher among the younger LDTDs, those who spent more than one week on transit, and those who use alcohol and khat, hence a high exposure risk to HIV/STIs among them.

Why is There Low Morbidity and Mortality of COVID-19 in Africa?

Three months since the detection of the first COVID-19 case in Africa, almost all countries of the continent continued to report lower morbidity and mortality than the global trend, including Europe and North America. We reviewed the merits of various hypotheses advanced to explain this phenomenon, including low seeding rate, effective mitigation measures, population that is more youthful, favorable weather, and possible prior exposure to a cross-reactive virus. Having a youthful population and favorable weather appears compelling, particularly their combined effect; however, progression of the pandemic in the region and globally may dispel these in the coming months.

Recurrent Anthrax Outbreaks in Humans, Livestock, and Wildlife in the Same Locality, Kenya, 2014-2017

Epidemiologic data indicate a global distribution of anthrax outbreaks associated with certain ecosystems that promote survival and viability of Bacillus anthracis spores. Here, we characterized three anthrax outbreaks involving humans, livestock, and wildlife that occurred in the same locality in Kenya between 2014 and 2017. Clinical and epidemiologic data on the outbreaks were collected using active case finding and review of human, livestock, and wildlife health records. Information on temporal and spatial distribution of prior outbreaks in the area was collected using participatory epidemiology. The 2014-2017 outbreaks in Nakuru West subcounty affected 15 of 71 people who had contact with infected cattle (attack rate = 21.1%), including seven with gastrointestinal, six with cutaneous, and two with oropharyngeal forms of the disease. Two (13.3%) gastrointestinal human anthrax cases died. No human cases were associated with infected wildlife. Of the 54 cattle owned in 11 households affected, 20 died (attack rate = 37%). The 2015 outbreak resulted in death of 10.5% of the affected herbivorous wildlife at Lake Nakuru National Park, including 745 of 4,500 African buffaloes (species-specific mortality rate = 17%) and three of 18 endangered white rhinos (species-specific mortality rate = 16%). The species mortality rate ranged from 1% to 5% for the other affected wildlife species. Participatory epidemiology identified prior outbreaks between 1973 and 2011 in the same area. The frequency and severity of outbreaks in this area suggests that it is an anthrax hotspot ideal for investigating risk factors associated with long-term survival of anthrax spores and outbreak occurrence.

Depression, injecting drug use, and risky sexual behavior syndemic among women who inject drugs in Kenya: a cross-sectional survey

BACKGROUND

Injecting drug use (IDU) is a key driver of the HIV epidemic particularly when individuals experience psychosocial conditions and risky sexual behavior in a syndemic manner. This study sets out to assess evidence of a syndemic pattern of psychosocial conditions (IDU, depression, intimate partner violence (IPV)) on one the hand and risky sexual behavior on the other while accounting for the socio-economic disadvantage among women who inject drugs (WWID) in low-income urban settings in Kenya.

METHODS

Using a cross-sectional study design, this study recruited 306 WWIDs from two sites in Nairobi between January 2017 and July 2017. Multiple methodologies including descriptive analyses of co-occurrences of psychosocial conditions at the individual level, standard logistic regression analyses to examine relationships and interactions within and between psychosocial conditions and risky sexual behavior, and classification trees algorithm for predictive modeling via machine learning were employed.

RESULTS

The prevalence of the psychosocial conditions was as follows: IDU, 88%; depression, 77.1%; and IPV, 84%. The prevalence of risky sexual behavior was 69.3%. IDU and depression were related to each other (P < 0.05) and each of them with risky sexual behavior (P < 0.05). The highest 2-way and 3-way co-occurrence of conditions were reported in IDU and depression (72%) and in IDU, depression, and risky sexual behavior (62%), respectively, indicating clustering of the conditions at the individual level. Further, each additional psychosocial condition (IDU and depression) was associated with sixfold odds (P = 0.000) of having risky sexual behavior suggesting a dose-response relationship. Logistic regression analyses incorporating multiplicative interactive effects returned three significant variables (P < 0.05): IDU*depression interaction effect, "Age when delivered the first child," and "Income." Classification tree modeling represented a 5-level interaction analysis with IDU and depression predicted to have the highest influence on risky sexual behavior.

CONCLUSION

Findings provide possible evidence of a syndemic pattern involving IDU, depression, and risky sexual behavior suggesting the need for an integrated approach to the implementation of harm reduction interventions among WWID in low-income urban settings in Kenya. This work highlights the need for further studies to authenticate the findings and to characterize pathways in the syndemic development in WWID.

Soil iron and aluminium concentrations and feet hygiene as possible predictors of Podoconiosis occurrence in Kenya

Background

Podoconiosis (mossy foot) is a neglected non-filarial elephantiasis considered to be caused by predisposition to cumulative contact of uncovered feet to irritative red clay soil of volcanic origins in the tropical regions. Data from structured observational studies on occurrence of Podoconiosis and related factors are not available in Kenya.

Methodology/Principal findings

To establish the occurrence and aspects associated with Podoconiosis, a cross-sectional survey was implemented in an area located within 30 km from the foot of volcanic Mount Longonot in the Great Rift Valley in Kenya. Five villages and 385 households were selected using multistage and systematic random sampling procedures respectively during the survey. Podoconiosis was determined by triangulating (1) the clinical diagnosis, (2) molecular assaying of sputum samples to rule out Wuchereria bancrofti microfilaria and (3) determining the concentration of six elements and properties in the soil known to be associated with Podoconiosis. A structured questionnaire was used to identify possible risk factors. Univariable and multivariable Poisson regression analyses were carried out to determine factors associated with Podoconiosis. Thirteen participants were clinically positive for Podoconiosis giving an overall prevalence of 3.4%. The prevalence ranged between 0% and 18.8% across the five villages. Molecular assay for W. bancrofti test turned negative in the 13 samples. The following factors were positively associated with the Podoconiosis prevalence (P<0.1) in the univariable analyses: (i) age, (ii) gender, (iii) education level, (iv) frequency of washing legs, (v) frequency of wearing shoes, (vi) soil pH, and (vii) village. Unexpectedly, the concentration of soil minerals previously thought to be associated with Podoconiosis was found to be negatively associated with the Podoconiosis prevalence (P<0.1). In the multivariable analyses, only frequency of wearing shoes and village turned out significant (P≤0.05). By modeling the different soil mineral concentrations and pH while adjusting for the variable frequency of wearing shoes, only iron concentration was significant and in the negative dimension (P≤0.05). However, controlling for Iron, Aluminum concentrations turned significant.

Conclusion/Significance

This study has pointed to a hitherto unreported occurrence of Podoconiosis cases and has contributed to the baseline knowledge on the occurrence of Podoconiosis in Kenya. Consistent with many studies, wearing shoes remain an important risk factor for the occurrence of the disease. However, our findings are inconsistent with some of the hitherto postulations that associate Podoconiosis prevalence with certain minerals in the soil in other regions in Africa. These findings provide new beginnings for the cross-disciplinary research of Podoconiosis in environmental health, socio-ecology and ecological niche and geo-spatial modeling and prediction.

Podoconiosis is a neglected disease in the tropical regions of the world considered to be caused by prolonged contact of uncovered feet to irritant particles found in red clay soil from volcanic origins. The disease presents like filarial elephantiasis. Data from observational studies from Kenya are not available. We conducted a cross-sectional household survey to establish the prevalence and aspects related with Podoconiosis at the foot of Mount Longonot in the Great Rift Valley in Kenya. Podoconiosis was determined by combining results of clinical diagnosis, ruling out filarial elephantiasis in clinically positive Podoconiosis patients using molecular techniques and determining the concentration of elements and properties in the soil known to be associated with Podoconiosis. A structured questionnaire was used to identify possible risk factors. Out of 385 study participants, thirteen were clinically positive for Podoconiosis giving an overall prevalence of 3.4%. Molecular tests for filarial elephantiasis turned negative in the 13 participants. Factors that were associated with Podoconiosis prevalence were age, gender, education level, and frequency of washing legs, frequency of wearing shoes, soil pH and village. The concentration of soil minerals previously thought to be associated with Podoconiosis was found to be negatively associated with the Podoconiosis prevalence. However, the final analyses found frequency of wearing shoes, iron and aluminium as possible predictors of Podoconiosis occurrence in the study area. This is the first structured observational study to report occurrence of Podoconiosis in Kenya. Although some of our findings are inconsistent with some previous reports about the association of Podoconiosis and certain minerals in the soil, this study offers new beginnings for the cross-disciplinary research of Podoconiosis in fields known to influence occurrence of the disease including environmental health, socio-ecology and medical geographical approaches and predictions.

Effects of climate change on the occurrence and distribution of livestock diseases

The planet's mean air and ocean temperatures have been rising over the last century because of increasing greenhouse gas (GHG) emissions. These changes have substantial effects on the epidemiology of infectious diseases. We describe direct and indirect processes linking climate change and infectious diseases in livestock with reference to specific case studies. Some of the studies are used to show a positive association between temperature and expansion of the geographical ranges of arthropod vectors (e.g. Culicoides imicola, which transmits bluetongue virus) while others are used to illustrate an opposite trend (e.g. tsetse flies that transmit a range of trypanosome parasites in sub-Saharan Africa). We further describe a positive association between extreme events: droughts and El Niño/southern oscillation (ENSO) weather patterns and Rift Valley fever outbreaks in East Africa and some adaptation practices used to mitigate the impacts of climate change that may increase risk of exposure to infectious pathogens. We conclude by outlining mitigation and adaptation measures that can be used specifically in the livestock sector to minimize the impacts of climate change-associated livestock diseases.