Risk factors for diarrheagenic Escherichia coli infection in children aged 6-24 months in peri-urban community, Nairobi, Kenya

Escherichia coli commonly inhabits the gut of humans and animals as part of their microbiota. Though mostly innocuous, some strains have virulence markers that make them pathogenic. This paper presents results of a cross-sectional epidemiological study examining prevalence of diarrheagenic E. coli (DEC) pathotypes in stool samples of asymptomatic healthy children (n = 540) in Dagoretti South subcounty, Nairobi, Kenya. E. coli was cultured and pathotyped using PCR to target specific virulence markers associated with Shiga-toxin, enteropathogenic, enterotoxigenic, enteroaggregative, entero-invasive and diffusely adherent E. coli. Overall prevalence of DEC pathotypes was 20.9% (113/540) with enteropathogenic E. coli being the most prevalent (34.1%), followed by enteroaggregative E. coli (23.5%) and Shiga-toxin producing E. coli (22.0%) among positive samples. We found evidence of co-infection with multiple pathotypes in 15% of the positive samples. Our models indicated that at the household level, carriage of DEC pathotypes in children was associated with age group [12-18 months] (OR 1.78; 95%CI 1.03-3.07; p = 0.04), eating matoke (mashed bananas) (OR 2.32; 95%CI 1.44-3.73; p = 0.001) and pulses/legumes (OR 1.74; 95%CI 1.01-2.99; p = 0.046) while livestock ownership or contact showed no significant association with DEC carriage (p>0.05). Our findings revealed significant prevalence of pathogenic DEC circulating among presumptive healthy children in the community. Since there has been no previous evidence of an association between any food type and DEC carriage, unhygienic handling, and preparation of matoke and pulses/legumes could be the reason for significant association with DEC carriage. Children 12-18 months old are more prone to DEC infections due to exploration and hand-to-mouth behavior. A detailed understanding is required on what proportion of positive cases developed severe symptomatology as well as fatal outcomes. The co-infection of pathotypes in the rapidly urbanizing environment needs to be investigated for hybrid or hetero-pathotype circulation that have been implicated in previous infection outbreaks.

Prevalence and risk factors associated with the occurrence of Campylobacter sp. in children aged 6-24 months in peri-urban Nairobi, Kenya

Introduction

Campylobacter bacteria is a major cause of foodborne-related bacterial gastroenteritis in humans worldwide. It is known to cause diarrhea in young children which has been shown to directly affect their weight and height as a result of malnutrition. Severe cases of diarrhea can also lead to death. Most of the burden is experienced in resource-limited countries in Africa and Southeast Asia where the disease is linked to poor hygiene and sanitation. The objective of this study was to determine the prevalence of Campylobacter in children aged between 6 and 24 months in Nairobi, Kenya and identify potential risk factors associated with their occurrence.

Methods

A cross-sectional study was carried out between May to December 2021. A total of 585 randomly selected households were visited in two wards (Uthiru/Ruthimitu and Riruta) in Dagoretti South sub-county, Nairobi. A questionnaire regarding how children's food is handled, the major foods consumed, sanitation and hygiene, and animal ownership was conducted among caregivers to identify associated risk factors. Stool samples were collected from 540/585 children and screened for the presence of Campylobacter using culture-based methods and confirmed through PCR.

Results

Of the 540 children's stool samples processed, Campylobacter isolates were detected in 4.8% (26/540). Campylobacter jejuni (C. jejuni) was the most common species in 80.8% of positive samples compared to Campylobacter coli (C. coli) in 26.9% of samples. In six samples, both C. jejuni and C. coli were isolated, while in four samples, it was not possible to speciate the Campylobacter. Drinking cow's milk (OR 4.2, 95% CI 1.4 - 12.6) and the presence of animal feces in the compound (OR 3.4, 95% CI 1.1 - 10.3) were found to be statistically associated with Campylobacter carriage in children.

Discussion

The carriage of Campylobacter in children in this community indicates a need for further investigation on source attribution to understand transmission dynamics and inform where to target interventions. Awareness creation among caregivers on good personal and food hygiene is needed, including boiling milk before consumption. Implementation of biosecurity measures at the household level is highly recommended to reduce contact between animals and humans.

Improved latrine coverage may reduce porcine cysticercosis: a comparative cross-sectional study, Busia County, Kenya 2021

Introduction

Smallholder pig farming is an important economic activity for many poor, rural communities in developing countries. Porcine cysticercosis is a growing public health risk in countries where pig rearing is popular. A sanitation-based intervention to reduce the prevalence of open defecation was completed in Busia County, Kenya in 2016. We capitalized on this third party intervention to evaluate its impact on porcine cysticercosis prevalence.

Methods

We conducted a comparative cross-sectional survey from August through to September 2021. Household selection was done using multistage sampling. Household questionnaire data on pig production, transmission, risk factors and awareness of porcine cysticercosis were collected from 251 households. Lingual palpation was used to test for cysticerci in 370 pigs while serum was tested for circulating antigen using Ag-ELISA. We compared results of our survey to an effective baseline, which was a near equivalent cross sectional survey conducted in 2012 before the third party sanitary intervention was established. The difference in prevalence was measured using Chi-square tests. Multivariable logistic regression analysis was used to identify risk factors for lingual cysts in pigs.

Results

The prevalence of palpable lingual cysts was estimated to be 3.8% (95% CI 2.3-6.3%) (14/370). This was 6% (95% CI 0.8-13.9%; p-value 0.0178) lower than the prevalence reported in the pre-implementation period of 9.7% (95% CI: 4.5-17.6%). Circulating antigen was detected in 2 samples (0.54%, 95% CI: 0.2-1.9). Latrine coverage was 86% (95% CI: 81-90%), which was 11% (95% CI: 4.8-16.8%; p < 0.001) higher than the pre-implementation period coverage of 75% (95% CI: 71-79%). There was reduced prevalence of lingual cysts in pigs from households that had a latrine (OR = 0.14; 95% CI: 0.05-0.43; p < 0.001) and where pigs were confined or tethered (OR = 0.27; 95% CI: 0.07-1.02; p = 0.053).

Conclusion

There was a reduction in the prevalence of porcine cysticercosis in Busia County over the study period from 2012 to 2021. This was not a trial design so we are unable to directly link the decline to a specific cause, but the data are consistent with previous research indicating that improved sanitation reduces porcine cysticercosis. Programs for controlling porcine cysticercosis should include a focus on sanitation in addition to other integrated One Health approaches.

Characteristics of Staphylococcus aureus Isolated from Patients in Busia County Referral Hospital, Kenya

Staphylococcus aureus is an important pathogen associated with hospital, community, and livestock-acquired infections, with the ability to develop resistance to antibiotics. Nasal carriage by hospital inpatients is a risk for opportunistic infections. Antibiotic susceptibility patterns, virulence genes and genetic population structure of S. aureus nasal isolates, from inpatients at Busia County Referral Hospital (BCRH) were analyzed. A total of 263 inpatients were randomly sampled, from May to July 2015. The majority of inpatients (85.9%) were treated empirically with antimicrobials, including ceftriaxone (65.8%) and metronidazole (49.8%). Thirty S. aureus isolates were cultured from 29 inpatients with a prevalence of 11% (10.3% methicillin-susceptible S. aureus (MSSA), 0.8% methicillin resistant S. aureus (MRSA)). Phenotypic and genotypic resistance was highest to penicillin-G (96.8%), trimethoprim (73.3%), and tetracycline (13.3%) with 20% of isolates classified as multidrug resistant. Virulence genes, Panton-Valentine leukocidin (pvl), toxic shock syndrome toxin-1 (tsst-1), and sasX gene were detected in 16.7%, 23.3% and 3.3% of isolates. Phylogenetic analysis showed 4 predominant clonal complexes CC152, CC8, CC80, and CC508. This study has identified that inpatients of BCRH were carriers of S. aureus harbouring virulence genes and resistance to a range of antibiotics. This may indicate a public health risk to other patients and the community.

Multi-Drug Resistant Staphylococcus aureus Carriage in Abattoir Workers in Busia, Kenya

Abattoir workers have been identified as high-risk for livestock-associated Staphylococcus aureus carriage. This study investigated S. aureus carriage in abattoir workers in Western Kenya. Nasal swabs were collected once from participants between February-November 2012. S. aureus was isolated using bacterial culture and antibiotic susceptibility testing performed using the VITEK 2 instrument and disc diffusion methods. Isolates underwent whole genome sequencing and Multi Locus Sequence Types were derived from these data. S. aureus (n = 126) was isolated from 118/737 (16.0%) participants. Carriage was higher in HIV-positive (24/89, 27.0%) than HIV−negative participants (94/648, 14.5%; p = 0.003). There were 23 sequence types (STs) identified, and half of the isolates were ST152 (34.1%) or ST8 (15.1%). Many isolates carried the Panton-Valentine leucocidin toxin gene (42.9%). Only three isolates were methicillin resistant S. aureus (MRSA) (3/126, 2.4%) and the prevalence of MRSA carriage was 0.4% (3/737). All MRSA were ST88. Isolates from HIV-positive participants (37.0%) were more frequently resistant to sulfamethoxazole/trimethoprim compared to isolates from HIV-negative participants (6.1%; p < 0.001). Similarly, trimethoprim resistance genes were more frequently detected in isolates from HIV-positive (81.5%) compared to HIV-negative participants (60.6%; p = 0.044). S. aureus in abattoir workers were representative of major sequence types in Africa, with a high proportion being toxigenic isolates. HIV-positive individuals were more frequently colonized by antimicrobial resistant S. aureus which may be explained by prophylactic antimicrobial use.

The Epidemiology of Bovine Viral Diarrhea Virus in Low- and Middle-Income Countries: A Systematic Review and Meta-Analysis

Introduction

Bovine viral diarrhea virus (BVDV) causes reproductive inefficiencies and negatively impacts the economy of low- and middle-income countries (LMICs). It is characterized by a combination of syndromes that result in poor production performance and calf morbidity and mortality. BVDV control is possible by introduction of biosecurity measures, test-and-cull, and vaccination programs as accomplished in high-income countries. Knowledge of BVDV epidemiology is limited in many LMICs, which hinders implementation of effective control programs. We carried out a systematic review and meta-analysis to estimate the burden of BVDV, identify risk factors related to its occurrence, and health and economic impacts on production systems.

Materials and Methods

Relevant BVD articles were collated from library databases; 690 abstracts and full texts were found in an initial search followed by filtering of 59 manuscripts. We accounted for quality and risk of bias in the meta-analysis. Prevalence, exposure, and current infection at regional, production, and farming system levels were estimated using logistic random-effects meta-regression models. Finally, we calculated the proportion of studies that addressed risk factors and health and economic impacts across different production systems to inform future preventative strategies in LMICs.

Results

Seroprevalence was high and varied between regions. Mean weighted prevalence was 39.5% (95% CI 25-56.1), 45.2% (95% CI 35.9-54.8), 49.9% (95% CI 25.5-74.3), and 21.6% (95% CI 0.5-56) for sub-Saharan Africa, South America, Middle East, and Asia, respectively. Seroprevalence varied across farming systems, with smallholder farming showing the highest values. Herdsize was the most frequently reported risk factor, and the percentage of articles that reported herdsize as a risk factor were 20.6%, 33.3%, and 38.4% for dairy, beef and mixed systems respectively. Abortion (13.7% of articles) was the main reported health impact in dairy systems. Some articles reported milk drop (4.6% of articles), but no article investigated the economic cost of BVDV in farming systems.

Conclusion

Animal-level seroprevalence varied across all regions. Most of the studies focused on BVDV seroprevalence. There were some articles that investigated risk factors and health impacts, and there were even less that investigated economic impacts. Future studies should focus on identifying risk factors and quantifying health and economic impacts across systems. Understanding these aspects is crucial to develop management strategies to apply across diverse production systems in LMICs.

Molecular characterization of porcine reproductive and respiratory syndrome virus (PRRSv) identified from slaughtered pigs in northern Uganda

Background

A cross sectional study was conducted to detect and characterize species of porcine reproductive and respiratory syndrome virus (PRRSv) identified from slaughtered pigs in Lira district, northern Uganda. The study was conducted from March to September 2019 in three selected slaughter slabs. Pigs brought for slaughter were randomly sampled. At necropsy, lungs were extracted from the thoracic cavity and examined for pneumonic lesions. Seventy-three (73) pigs with gross lung lesions were sampled, from which one hundred and one (101) tissue samples were taken. A real-time reverse transcriptase PCR (RT-qPCR) was used to characterize PRRSv species.

Results

A total of 20 samples tested positive for PRRSv. The respective prevalence of PRRSv type 1 and type 2 were 24.65% (n = 18) and 2.73% (n = 2) respectively. Of the pigs sampled (n = 73), only two pigs, 2.73% (n = 2) tested positive to both species. The likelihood of PRRSv detection decreased with pig age, but increased with gross pneumonic pathology.

Conclusions

This study demonstrated dual circulation of both species in northern Uganda. The association between PRRSv and lung pathology suggests that it may be an important cause of lung disease in pigs in Uganda and hence loss of production. This calls for further investigations on potential economic impacts of PRRSv on pig productivity. These findings contribute to discussions about the need of surveillance and possible vaccination strategies against PRRSv in Uganda.

A locus conferring tolerance to Theileria infection in African cattle

East Coast fever, a tick-borne cattle disease caused by the Theileria parva parasite, is among the biggest natural killers of cattle in East Africa, leading to over 1 million deaths annually. Here we report on the genetic analysis of a cohort of Bos indicus (Boran) cattle demonstrating heritable tolerance to infection with T. parva (h² = 0.65, s.e. 0.57). Through a linkage analysis we identify a 6 Mb genomic region on bovine chromosome 15 that is significantly associated with survival outcome following T. parva exposure. Testing this locus in an independent cohort of animals replicates this association with survival following T. parva infection. A stop gained variant in a paralogue of the FAF1 gene in this region was found to be highly associated with survival across both related and unrelated animals, with only one of the 20 homozygote carriers (T/T) of this change succumbing to the disease in contrast to 44 out of 97 animals homozygote for the reference allele (C/C). Consequently, we present a genetic locus linked to tolerance of one of Africa’s most important cattle diseases, raising the promise of marker-assisted selection for cattle that are less susceptible to infection by T. parva.

More than a million cattle die of East Coast fever in Africa each year, the impact of which disproportionately falls onto low-income, smallholder farmers. The lack of a widely accessible vaccine, heavy reliance on chemicals to control the tick vector and inadequate drug treatments means that new approaches for controlling the disease are urgently required. Through a genetic study of an extended pedigree of Boran cattle that are more than three times less likely to succumb to the disease than matched controls, we identify a region on chromosome 15 of the cattle genome associated with a high level of tolerance to the disease. We show that a nonsense variant in a predicted paralogue of FAS-associated factor 1 (FAF1) in this region is also associated with survival in an independent cohort, and is linked to rates of cell expansion during infection. This genetic variant can therefore support marker-assisted selection, allowing farmers to breed tolerant cattle and offers a route to introduce this beneficial DNA to non-native breeds, enabling reduced disease incidence and increased productivity, which would be of benefit to millions of rural smallholder farmers across Africa.

Epidemiology of Porcine Cysticercosis in Eastern and Southern Africa: Systematic Review and Meta-Analysis

Taenia solium cysticercosis is the most common cause of acquired epilepsy in pig-raising and pork-consuming parts of Africa, Latin America, and Asia. This review aimed to systematically compile and synthesize data on the epidemiology of porcine cysticercosis in the Eastern and Southern Africa (ESA) region. Comprehensive searching strategies were employed to retrieve the studies published or reported between January 1,1997 and March 1, 2021, from Pub Med, Hinari, and Google Scholar databases and search platforms. The identified studies that met the inclusion criteria were then appraised for methodological quality. Finally, 44 studies obtained from nine countries were selected and included in this review. Relevant data were extracted using standardized templates for qualitative synthesis and meta-analysis. The overall pooled prevalence estimate of porcine cysticercosis in the ESA region was 17% (95% CI: 14-20%). The prevalence level between and within countries showed high variability. The pooled estimate showed high heterogeneity among the reports (the inverse variance index value (I2) of 98.99%, p < 0.05). The meta-analysis sub-grouped by the type of diagnostic test showed the pooled prevalence estimate of 27% (95% CI: 9-50) by carcass dissection; 23% (95% CI: 14-33) by Antibody-based immunodiagnostic techniques; 23% (95% CI: 18-29) by antigen detecting (Ag)-ELISA, 12% (95% CI: 7-18) by meat inspection, and 9% (95% CI: 7-11) by lingual examination. The meta-analysis sub-grouped by region showed a relatively higher pooled prevalence estimate for the Southern region 22% (95% CI: 15-30) compared to 13% (95% CI: 11-15) in the Eastern region. The highest country-based pooled prevalence was obtained from South Africa (33%, 95% CI: 20-48) and Zambia (22%, 95% CI: 16-29), whereas the lowest pooled prevalence was identified in Madagascar (5%, 95% CI: 4-5) and Rwanda (7%, 95% CI: 6-8). The lack of latrine, traditional pig husbandry practices, unprotected water sources, and increase in age were identified as significant risk factors for the occurrence of porcine cysticercosis in the pooled studies. The findings of this review will provide context-specific input to prioritize the possible intervention programs for T. solium control in the ESA region. More sensitive and specific test-based prevalence estimates, detailed risk factor investigations, and financial losses analysis are needed to establish feasible control strategies.

Systematic Review Registration

http://www.crd.york.ac.uk/PROSPERO/, identifier: CRD42021238931.

Inherited Tolerance in Cattle to the Apicomplexan Protozoan Theileria parva is Associated with Decreased Proliferation of Parasite-Infected Lymphocytes

Theileria parva is the causative agent of East Coast fever and Corridor disease, which are fatal, economically important diseases of cattle in eastern, central and southern Africa. Improved methods of control of the diseases are urgently required. The parasite transforms host lymphocytes, resulting in a rapid, clonal expansion of infected cells. Resistance to the disease has long been reported in cattle from T. parva-endemic areas. We reveal here that first- and second-generation descendants of a single Bos indicus bull survived severe challenge with T. parva, (overall survival rate 57.3% compared to 8.7% for unrelated animals) in a series of five field studies. Tolerant cattle displayed a delayed and less severe parasitosis and febrile response than unrelated animals. The in vitro proliferation of cells from surviving cattle was much reduced compared to those from animals that succumbed to infection. Additionally, some pro-inflammatory cytokines such as IL1β, IL6, TNFα or TGFβ which are usually strongly expressed in susceptible animals and are known to regulate cell growth or motility, remain low in tolerant animals. This correlates with the reduced proliferation and less severe clinical reactions observed in tolerant cattle. The results show for the first time that the inherited tolerance to T. parva is associated with decreased proliferation of infected lymphocytes. The results are discussed in terms of whether the reduced proliferation is the result of a perturbation of the transformation mechanism induced in infected cells or is due to an innate immune response present in the tolerant cattle.

Clinical Evaluation of Corridor Disease in Bos indicus (Boran) Cattle Naturally Infected With Buffalo-Derived Theileria parva

Corridor disease (CD) is a fatal condition of cattle caused by buffalo-derived Theileria parva. Unlike the related condition, East Coast fever, which results from infection with cattle-derived T. parva, CD has not been extensively studied. We describe in detail the clinical and laboratory findings in cattle naturally infected with buffalo-derived T. parva. Forty-six cattle were exposed to buffalo-derived T. parva under field conditions at the Ol Pejeta Conservancy, Kenya, between 2013 and 2018. The first signs of disease observed in all animals were nasal discharge (mean day of onset was 9 days post-exposure), enlarged lymph nodes (10 days post-exposure), and pyrexia (13.7 days post-exposure). Coughing and labored breathing were observed in more than 50% of animals (14 days post-exposure). Less commonly observed signs, corneal edema (22%) and diarrhea (11%), were observed later in the disease progression (19 days post-exposure). All infections were considered clinically severe, and 42 animals succumbed to infection. The mean time to death across all studies was 18.4 days. The mean time from onset of clinical signs to death was 9 days and from pyrexia to death was 4.8 days, indicating a relatively short duration of clinical illness. There were significant relationships between days to death and the days to first temperature (chi2 = 4.00, p = 0.046), and days to peak temperature (chi2 = 25.81, p = 0.001), animals with earlier onset pyrexia died sooner. These clinical indicators may be useful for assessing the severity of disease in the future. All infections were confirmed by the presence of macroschizonts in lymph node biopsies (mean time to parasitosis was 11 days). Piroplasms were detected in the blood of two animals (4%) and 20 (43%) animals seroconverted. In this study, we demonstrate the successful approach to an experimental field study for CD in cattle. We also describe the clinical progression of CD in naturally infected cattle, including the onset and severity of clinical signs and pathology. Laboratory diagnoses based on examination of blood samples are unreliable, and alternatives may not be available to cattle keepers. The rapid development of CD requires recognition of the clinical signs, which may be useful for early diagnosis of the disease and effective intervention for affected animals.

Molecular epidemiology of Brucella species in mixed livestock-human ecosystems in Kenya

Brucellosis, caused by several species of the genus Brucella, is a zoonotic disease that affects humans and animal species worldwide. Information on the Brucella species circulating in different hosts in Kenya is largely unknown, thus limiting the adoption of targeted control strategies. This study was conducted in multi-host livestock populations in Kenya to detect the circulating Brucella species and assess evidence of host-pathogen associations. Serum samples were collected from 228 cattle, 162 goats, 158 sheep, 49 camels, and 257 humans from Narok and Marsabit counties in Kenya. Information on age, location and history of abortion or retained placenta were obtained for sampled livestock. Data on age, gender and location of residence were also collected for human participants. All samples were tested using genus level real-time PCR assays with primers specific for IS711 and bcsp31 targets for the detection of Brucella. All genus positive samples (positive for both targets) were further tested with a speciation assay for AlkB and BMEI1162 targets, specific for B. abortus and B. melitensis, respectively. Samples with adequate quantities aggregating to 577 were also tested with the Rose Bengal Test (RBT). A total of 199 (33.3%) livestock and 99 (38.5%) human samples tested positive for genus Brucella. Animal Brucella PCR positive status was positively predicted by RBT positive results (OR = 8.3, 95% CI 4.0-17.1). Humans aged 21-40 years had higher odds (OR = 2.8, 95% CI 1.2-6.6) of being Brucella PCR positive compared to the other age categories. The data on detection of different Brucella species indicates that B. abortus was detected more often in cattle (OR = 2.3, 95% CI 1.1-4.6) and camels (OR = 2.9, 95% CI 1.3-6.3), while B. melitensis was detected more in sheep (OR = 3.6, 95% CI 2.0-6.7) and goats (OR = 1.7, 95% CI 1.0-3.1). Both B. abortus and B. melitensis DNA were detected in humans and in multiple livestock host species, suggesting cross-transmission of these species among the different hosts. The detection of these two zoonotic Brucella species in humans further underpins the importance of One Health prevention strategies that target multiple host species, especially in the multi-host livestock populations.

Spatial Distribution of Trypanosomes in Cattle From Western Kenya

African Animal Trypanosomiasis (AAT) is a tsetse-transmitted protozoan disease endemic in “the tsetse belt” of Africa. Past studies investigating the epidemiology of the disease rarely focused on spatial distribution when reporting the prevalence. The challenge of understanding the spatial epidemiology of the disease is further confounded by low-sensitive parasitological techniques used in field investigations. This study aimed to identify trypanosome species in cattle and their spatial distribution in western Kenya. Low-sensitive microscopic analysis and highly-sensitive polymerase chain reaction (PCR) techniques were also compared to better understand the epidemiology of Trypanosoma infections by use of the geographical information system (GIS). Blood samples from 888 cattle, collected between August 2010 and July 2012, were examined for Trypanosoma parasites by light microscopy and PCR. The spatial distribution of Trypanosoma positive cases by species were mapped and overlaid on the map for tsetse distribution. The estimated prevalence was 4.17% by PCR compared to 2.48% by microscopy. Trypanosomes were detected in tsetse free areas. Trypanosoma vivax and Trypanosoma b. brucei were identified, but not the zoonotic Trypanosoma b. rhodesiense. This study demonstrated the importance of geospatial data analysis to understand the epidemiology of the parasite, to inform future research and formulate control strategies.

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Seropositive Camel Handlers in Kenya

Middle East respiratory syndrome (MERS) is a respiratory disease caused by a zoonotic coronavirus (MERS-CoV). Camel handlers, including slaughterhouse workers and herders, are at risk of acquiring MERS-CoV infections. However, there is limited evidence of infections among camel handlers in Africa. The purpose of this study was to determine the presence of antibodies to MERS-CoV in high-risk groups in Kenya. Sera collected from 93 camel handlers, 58 slaughterhouse workers and 35 camel herders, were screened for MERS-CoV antibodies using ELISA and PRNT. We found four seropositive slaughterhouse workers by PRNT. Risk factors amongst the slaughterhouse workers included being the slaughterman (the person who cuts the throat of the camel) and drinking camel blood. Further research is required to understand the epidemiology of MERS-CoV in Africa in relation to occupational risk, with a need for additional studies on the transmission of MERS-CoV from dromedary camels to humans, seroprevalence and associated risk factors.

Household socio-economic position and individual infectious disease risk in rural Kenya

The importance of household socio-economic position (SEP) in shaping individual infectious disease risk is increasingly recognised, particularly in low income settings. However, few studies have measured the extent to which this association is consistent for the range of pathogens that are typically endemic among the rural poor in the tropics. This cross-sectional study assessed the relationship between SEP and human infection within a single community in western Kenya using a set of pathogens with diverse transmission routes. The relationships between household SEP and individual infection with Plasmodium falciparum, hookworm (Ancylostoma duodenale and/or Necator americanus), Entamoeba histolytica/dispar, Mycobacterium tuberculosis, and HIV, and co-infections between hookworm, P. falciparum and E. histolytica/dispar, were assessed using multivariable logistic and multinomial regression. Individuals in households with the lowest SEP were at greatest risk of infection with P. falciparum, hookworm and E. histolytica/dispar, as well as co-infection with each pathogen. Infection with M. tuberculosis, by contrast, was most likely in individuals living in households with the highest SEP. There was no evidence of a relationship between individual HIV infection and household SEP. We demonstrate the existence of a household socio-economic gradient within a rural farming community in Kenya which impacts upon individual infectious disease risk. Structural adjustments that seek to reduce poverty, and therefore the socio-economic inequalities that exist in this community, would be expected to substantially reduce overall infectious disease burden. However, policy makers and researchers should be aware that heterogeneous relationships can exist between household SEP and infection risk for different pathogens in low income settings.

Infection and treatment method (ITM) vaccine against East Coast fever: reducing the number of doses per straw for use in smallholder dairy herds by thawing, diluting and refreezing already packaged vaccine

Background

The Infection and Treatment Method (ITM) of vaccination is the only immunization procedure currently available to protect cattle against East Coast fever (ECF), a tick-transmitted disease responsible for losses of several hundreds of millions of dollars per year in sub-Saharan Africa. The vaccine comprises a homogenized preparation of infected ticks packaged in straws and stored in liquid nitrogen. The current manufacturing protocol results in straws containing 30–40 doses (ILRI 0804), which is impractical for immunizing small herds as found in dairy and smallholder farming systems. The ILRI 0804 SD stabilate was prepared as a 1:5 dilution of the parent stabilate, with the aim of producing vaccine stabilate straws containing between four to eight doses and thus suitable for smallholder farming systems. Infectivity of the diluted stabilate was assessed and the protective efficacy of the diluted stabilate was determined by performing experimental and field immunizations.

Results

Two groups of six cattle were inoculated with 1 ml of the diluted stabilate at 1:20 (equivalent to the recommended field dose for ILRI 0804, assuming no loss of sporozoite viability during thawing and refreezing) and 1:14 (assuming 30–35% loss of sporozoite viability). Schizonts were detected in all 12 animals, showing viability of sporozoites. Ten animals from the infectivity study and two control animals not previously exposed to T. parva were challenged with the parental ILRI 0804 stabilate. The results show that the two control animals displayed severe ECF reactions and were treated 14 days after challenge. Of the previously infected animals, only one underwent a severe reaction following challenge, a result in accord with the challenge experiments performed previously with the parent stabilate [Ticks Tick-Borne Dis 7:306-314, 2016]. The animal that displayed a severe reaction had no detectable schizonts and did not seroconvert following the initial inoculation with ILRI 0804 SD. In addition, 62 animals immunized under field conditions showed a mean seroconversion rate of 82%.

Conclusion

The results presented in this article demonstrate that it is possible to prepare straws suitable for use in smallholder herds by thawing, diluting and refreezing already packaged vaccine.

General contextual effects on neglected tropical disease risk in rural Kenya

The neglected tropical diseases (NTDs) are characterized by their tendency to cluster within groups of people, typically the poorest and most marginalized. Despite this, measures of clustering, such as within-group correlation or between-group heterogeneity, are rarely reported from community-based studies of NTD risk. We describe a general contextual analysis that uses multi-level models to partition and quantify variation in individual NTD risk at multiple grouping levels in rural Kenya. The importance of general contextual effects (GCE) in structuring variation in individual infection with Schistosoma mansoni, the soil-transmitted helminths, Taenia species, and Entamoeba histolytica/dispar was examined at the household-, sublocation- and constituency-levels using variance partition/intra-class correlation co-efficients and median odds ratios. These were compared with GCE for HIV, Plasmodium falciparum and Mycobacterium tuberculosis. The role of place of residence in shaping infection risk was further assessed using the spatial scan statistic. Individuals from the same household showed correlation in infection for all pathogens, and this was consistently highest for the gastrointestinal helminths. The lowest levels of household clustering were observed for E. histolytica/dispar, P. falciparum and M. tuberculosis. Substantial heterogeneity in individual infection risk was observed between sublocations for S. mansoni and Taenia solium cysticercosis and between constituencies for infection with S. mansoni, Trichuris trichiura and Ascaris lumbricoides. Large overlapping spatial clusters were detected for S. mansoni, T. trichiura, A. lumbricoides, and Taenia spp., which overlapped a large cluster of elevated HIV risk. Important place-based heterogeneities in infection risk exist in this community, and these GCEs are greater for the NTDs and HIV than for TB and malaria. Our findings suggest that broad-scale contextual drivers shape infectious disease risk in this population, but these effects operate at different grouping-levels for different pathogens. A general contextual analysis can provide a foundation for understanding the complex ecology of NTDs and contribute to the targeting of interventions.

Serological and spatial analysis of alphavirus and flavivirus prevalence and risk factors in a rural community in western Kenya

Alphaviruses, such as chikungunya virus, and flaviviruses, such as dengue virus, are (re)-emerging arboviruses that are endemic in tropical environments. In Africa, arbovirus infections are often undiagnosed and unreported, with febrile illnesses often assumed to be malaria. This cross-sectional study aimed to characterize the seroprevalence of alphaviruses and flaviviruses among children (ages 5-14, n = 250) and adults (ages 15 ≥ 75, n = 250) in western Kenya. Risk factors for seropositivity were explored using Lasso regression. Overall, 67% of participants showed alphavirus seropositivity (CI95 63%-70%), and 1.6% of participants showed flavivirus seropositivity (CI95 0.7%-3%). Children aged 10-14 were more likely to be seropositive to an alphavirus than adults (p < 0.001), suggesting a recent transmission period. Alphavirus and flavivirus seropositivity was detected in the youngest participants (age 5-9), providing evidence of inter-epidemic transmission. Demographic variables that were significantly different amongst those with previous infection versus those without infection included age, education level, and occupation. Behavioral and environmental variables significantly different amongst those in with previous infection to those without infection included taking animals for grazing, fishing, and recent village flooding. Experience of recent fever was also found to be a significant indicator of infection (p = 0.027). These results confirm alphavirus and flavivirus exposure in western Kenya, while illustrating significantly higher alphavirus transmission compared to previous studies.

Serologic Evidence for Influenza C and D Virus among Ruminants and Camelids, Africa, 1991-2015

Influenza D virus has been identified in America, Europe, and Asia. We detected influenza D virus antibodies in cattle and small ruminants from North (Morocco) and West (Togo and Benin) Africa. Dromedary camels in Kenya harbored influenza C or D virus antibodies, indicating a potential new host for these viruses.

An integrated study of human and animal infectious disease in the Lake Victoria crescent small-holder crop-livestock production system, Kenya

BACKGROUND

The neglected zoonotic diseases (NZD) are an understudied group that are a major cause of illness throughout the developing world. In general, little is known about the prevalence and burden of NZDs in affected communities, particularly in relation to other infectious diseases with which they are often co-endemic. We describe the design and descriptive epidemiological outputs from an integrated study of human and animal zoonotic and non-zoonotic disease in a rural farming community in western Kenya.

METHODS

This cross-sectional survey involved 2113 people, their cattle (n = 983) and pigs (n = 91). People and animals were tested for infection or exposure to a wide range of zoonotic and non-zoonotic pathogens. Prevalence estimates, with adjustment for the complex study design, were derived. Evidence for spatial clustering in exposure or infection was identified using the spatial scan statistic.

RESULTS

There was a high prevalence of human parasitism in the community, particularly with hookworm (Ancylostoma duodenale or Necator americanus) (36.3% (95% CI 32.8-39.9)), Entamoeba histolytica/dispar (30.1% (95% CI 27.5-32.8)), and Plasmodium falciparum (29.4% (95% CI 26.8-32.0)). Human infection with Taenia spp. was also prevalent (19.7% (95% CI 16.7-22.7)), while exposure to other zoonotic pathogens was comparatively rarer (Brucella spp., 0.6% (95% CI 0.2-0.9); Coxiella burnetii, 2.2% (95% CI 1.5-2.9); Rift Valley fever, 0.5% (95% CI 0.2-0.8)). A low prevalence of exposure to Brucella spp. was observed in cattle (0.26% (95% CI 0-0.56). This was higher for Rift Valley fever virus (1.4% (95% CI 0.5-2.22)) and C. burnetii (10.0% (95% CI 7.7-12.2)). The prevalence of Taenia spp. cysticercosis was 53.5% (95% CI 48.7-58.3) in cattle and 17.2% (95% CI 9.1-25.3) in pigs. Mycobacterium bovis infection was found in 2.2% of cattle (95% CI 1.3-3.2), while the prevalence of infection with Mycobacterium spp. was 8.2% (95% CI 6.8-9.6) in people.

CONCLUSION

Zoonotic infections in people and animals occur in the context of a wide range of co-endemic pathogens in a rural community in western Kenya. The wide diversity of pathogens under study provides a unique opportunity to explore the distribution and determinants of infection in a multi-pathogen, multi-host system.

Poor performance of the rapid test for human brucellosis in health facilities in Kenya

Human brucellosis is considered to be an important but typically under-diagnosed cause of febrile illness in many low and middle-income countries. In Kenya, and throughout East Africa, laboratory diagnosis for the disease is based primarily on the febrile antigen Brucella agglutination test (FBAT), yet few studies of the diagnostic accuracy of this test exist. Assessment of the performance of the FBAT is essential for its appropriate clinical use, as well as for evaluating surveillance data reported by public health systems. To assess FBAT performance, we collected sera from people with symptoms compatible with brucellosis attending two health facilities in Busia County, Kenya. Sera were tested using the FBAT and results compared with those from the Rose Bengal Test (RBT), an assay with well-known performance characteristics. Positives on either test were confirmed using the classical serum agglutination test (SAT)-Coombs test combination and a rapid IgM/IgG lateral flow immunochromatography assay (LFA). A questionnaire focussing on known risk factors for exposure to Brucella spp. was also conducted, and relationships with FBAT positivity examined using logistic regression. Out of 825 recruited individuals, 162 (19.6%) were classified as positive using the FBAT. In contrast, only eight (1.0%) were positive using the RBT. Of the 162 FBAT positives, one (0.62%) had an atypical agglutination in SAT and three (1.9%) showed low Coombs titres. Out of 148 FBAT positive individuals tested using the LFA, five (3.4%) were IgM positive and none were IgG positive. Poor or no correlation was observed between FBAT results and most established risk factors for Brucella infection. We observed substantial disagreement between the FBAT and a number of well-known serological tests, with the majority of reactive FBAT results appearing to be false positives. Poor FBAT specificity, combined with a lack of confirmatory testing, strongly suggests overdiagnosis of brucellosis is common in this low prevalence setting. This is expected to have important economic impacts on affected patients subjected to the long and likely unnecessary courses of multiple antibiotics required for treatment of the disease.

Brucellosis is a debilitating disease of people caused by infection with one of a number of different Brucella species. In almost all cases, people acquire the infection through exposure to infected animals or contaminated animal products. Human brucellosis is well known for its wide range of symptoms, and is often clinically indistinguishable from other infectious diseases, such as malaria or typhoid. Diagnosing the disease therefore typically relies on laboratory tests. A wide range of tests are available, but little is known about the accuracy of the principal test used in Government health facilities in Kenya, the febrile Brucella agglutination test (FBAT). In this study, we identified people with symptoms compatible with brucellosis attending health centres in Kenya. By comparing results from the FBAT performed on samples collected from these individuals with the results from a range of well-established diagnostic tests, we were able to show that the FBAT produces large numbers of false positive results. We expect that this leads to a high levels of overdiagnosis of brucellosis in some parts of Kenya. Treatment of the disease involves multiple weeks of multiple antibiotics, and these incorrect diagnoses may have important and unnecessary negative impacts on affected patients.

Modelling the risk of Taenia solium exposure from pork produced in western Kenya

The tapeworm Taenia solium is the parasite responsible for neurocysticercosis, a neglected tropical disease of public health importance, thought to cause approximately 1/3 of epilepsy cases across endemic regions. The consumption of undercooked infected pork perpetuates the parasite’s life-cycle through the establishment of adult tapeworm infections in the community. Reducing the risk associated with pork consumption in the developing world is therefore a public health priority. The aim of this study was to estimate the risk of any one pork meal in western Kenya containing a potentially infective T. solium cysticercus at the point of consumption, an aspect of the parasite transmission that has not been estimated before. To estimate this, we used a quantitative food chain risk assessment model built in the @RISK add-on to Microsoft Excel. This model indicates that any one pork meal consumed in western Kenya has a 0.006 (99% Uncertainty Interval (U.I). 0.0002–0.0164) probability of containing at least one viable T. solium cysticercus at the point of consumption and therefore being potentially infectious to humans. This equates to 22,282 (99% U.I. 622–64,134) potentially infective pork meals consumed in the course of one year within Busia District alone. This model indicates a high risk of T. solium infection associated with pork consumption in western Kenya and the work presented here can be built upon to investigate the efficacy of various mitigation strategies for this locality.

Taenia solium is a serious zoonotic helminth which is thought to be responsible for approximately 1/3^rd of epilepsy cases in the developing world. The work presented in this paper aimed to understand what the risk is of acquiring T. solium taeniosis from pork slaughtered and consumed in western Kenya. In order to do this we built a stochastic risk assessment model to investigate the safety of pork reaching the consumer in terms of the risk of having viable T. solium cysts in any one portion of meat consumed. We found that pork represents a high risk product in this study area and therefore control strategies are urgently needed to reduce the public health risk posed by this product.

Environmental predictors of bovine Eimeria infection in western Kenya

Eimeriosis is caused by a protozoan infection affecting most domestic animal species. Outbreaks in cattle are associated with various environmental factors in temperate climates but limited work has been done in tropical settings. The objective of this work was to determine the prevalence and environmental factors associated with bovine Eimeria spp. infection in a mixed farming area of western Kenya. A total of 983 cattle were sampled from 226 cattle-keeping households. Faecal samples were collected directly from the rectum via digital extraction and analysed for the presence of Eimeria spp. infection using the MacMaster technique. Individual and household level predictors of infection were explored using mixed effects logistic regression. The prevalence of individual animal Eimeria infection was 32.8% (95% CI 29.9-35.9). A positive linear relationship was found between risk of Eimeria infection and increasing temperature (OR = 1.4, 95% CI 1.06-1.86) and distance to areas at risk of flooding (OR = 1.49, 95% CI 1.17-1.91). There was weak evidence of non-linear relationship between Eimeria infection and the proportion of the area around a household that was classified as swamp (OR = 1.12, 95% CI 0.87-1.44; OR (quadratic term) = 0.85, 95% CI 0.73-1.00), and the sand content of the soil (OR = 1.18, 95% CI 0.91-1.53; OR (quadratic term) = 1.1, 95% CI 0.99-1.23). The risk of animal Eimeria spp. infection is influenced by a number of climatic and soil-associated conditions.

The Sero-epidemiology of Coxiella burnetii in Humans and Cattle, Western Kenya: Evidence from a Cross-Sectional Study

Evidence suggests that the intracellular bacterial pathogen Coxiella burnetii (which causes Q fever) is widespread, with a near global distribution. While there has been increasing attention to Q fever epidemiology in high-income settings, a recent systematic review highlighted significant gaps in our understanding of the prevalence, spatial distribution and risk factors for Q fever infection across Africa. This research aimed to provide a One Health assessment of Q fever epidemiology in parts of Western and Nyanza Provinces, Western Kenya, in cattle and humans. A cross-sectional survey was conducted: serum samples from 2049 humans and 955 cattle in 416 homesteads were analysed for C. burnetii antibodies. Questionnaires covering demographic, socio-economic and husbandry information were also administered. These data were linked to environmental datasets based on geographical locations (e.g., land cover). Correlation and spatial-cross correlation analyses were applied to assess the potential link between cattle and human seroprevalence. Multilevel regression analysis was used to assess the relationships between a range of socio-economic, demographic and environmental factors and sero-positivity in both humans and animals. The overall sero-prevalence of C. burnetii was 2.5% in humans and 10.5% in cattle, but we found no evidence of correlation between cattle and human seroprevalence either within households, or when incorporating spatial proximity to other households in the survey. Multilevel modelling indicated the importance of several factors for exposure to the organism. Cattle obtained from market (as opposed to those bred in their homestead) and those residing in areas with lower precipitation levels had the highest sero-prevalence. For humans, the youngest age group had the highest odds of seropositivity, variations were observed between ethnic groups, and frequent livestock contact (specifically grazing and dealing with abortion material) was also a risk factor. These results illustrate endemicity of C. burnetii in western Kenya, although prevalence is relatively low. The analysis indicates that while environmental factors may play a role in cattle exposure patterns, human exposure patterns are likely to be driven more strongly by livestock contacts. The implication of livestock markets in cattle exposure risks suggests these may be a suitable target for interventions.

Seroepidemiological Study of Interepidemic Rift Valley Fever Virus Infection Among Persons with Intense Ruminant Exposure in Madagascar and Kenya

In this cross-sectional seroepidemiological study we sought to examine the evidence for circulation of Rift Valley fever virus (RVFV) among herders in Madagascar and Kenya. From July 2010 to June 2012, we enrolled 459 herders and 98 controls (without ruminant exposures) and studied their sera (immunoglobulin G [IgG] and IgM through enzyme-linked immunosorbent assay [ELISA] and plaque reduction neutralization test [PRNT] assays) for evidence of previous RVFV infection. Overall, 59 (12.9%) of 459 herders and 7 (7.1%) of the 98 controls were positive by the IgG ELISA assay. Of the 59 ELISA-positive herders, 23 (38.9%) were confirmed by the PRNT assay (21 from eastern Kenya). Two of the 21 PRNT-positive study subjects also had elevated IgM antibodies against RVFV suggesting recent infection. Multivariate modeling in this study revealed that being seminomadic (odds ratio [OR] = 6.4, 95% confidence interval [CI] = 2.1–15.4) was most strongly associated with antibodies against RVFV. Although we cannot know when these infections occurred, it seems likely that some interepidemic RVFV infections are occurring among herders. As there are disincentives regarding reporting RVFV outbreaks in livestock or wildlife, it may be prudent to conduct periodic, limited, active seroepidemiological surveillance for RVFV infections in herders, especially in eastern Kenya.