Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya.

BACKGROUND: Livestock systems have been proposed as a reservoir for antimicrobial-resistant (AMR) bacteria and AMR genetic determinants that may infect or colonise humans, yet quantitative evidence regarding their epidemiological role remains lacking. Here, we used a combination of genomics, epidemiology and ecology to investigate patterns of AMR gene carriage in Escherichia coli, regarded as a sentinel organism. METHODS: We conducted a structured epidemiological survey of 99 households across Nairobi, Kenya, and whole genome sequenced E. coli isolates from 311 human, 606 livestock and 399 wildlife faecal samples. We used statistical models to investigate the prevalence of AMR carriage and characterise AMR gene diversity and structure of AMR genes in different host populations across the city. We also investigated household-level risk factors for the exchange of AMR genes between sympatric humans and livestock. RESULTS: We detected 56 unique acquired genes along with 13 point mutations present in variable proportions in human and animal isolates, known to confer resistance to nine antibiotic classes. We find that AMR gene community composition is not associated with host species, but AMR genes were frequently co-located, potentially enabling the acquisition and dispersal of multi-drug resistance in a single step. We find that whilst keeping livestock had no influence on human AMR gene carriage, the potential for AMR transmission across human-livestock interfaces is greatest when manure is poorly disposed of and in larger households. CONCLUSIONS: Findings of widespread carriage of AMR bacteria in human and animal populations, including in long-distance wildlife species, in community settings highlight the value of evidence-based surveillance to address antimicrobial resistance on a global scale. Our genomic analysis provided an in-depth understanding of AMR determinants at the interfaces of One Health sectors that will inform AMR prevention and control.

Coxiella burnetii serostatus in dromedary camels (Camelus dromedarius) is associated with the presence of C. burnetii DNA in attached ticks in Laikipia County, Kenya.

AIMS: Q fever is a globally distributed, neglected zoonotic disease of conservation and public health importance, caused by the bacterium Coxiella burnetii. Coxiella burnetii normally causes subclinical infections in livestock, but may also cause reproductive pathology and spontaneous abortions in artiodactyl species. One such artiodactyl, the dromedary camel (Camelus dromedarius), is an increasingly important livestock species in semi-arid landscapes. Ticks are naturally infected with C. burnetii worldwide and are frequently found on camels in Kenya. In this study, we assessed the relationship between dromedary camels' C. burnetii serostatus and whether the camels were carrying C. burnetii PCR-positive ticks in Kenya. We hypothesized that there would be a positive association between camel seropositivity and carrying C. burnetii PCR-positive ticks. METHODS AND RESULTS: Blood was collected from camels (N = 233) from three herds, and serum was analysed using commercial ELISA antibody test kits. Ticks were collected (N = 4354), divided into pools of the same species from the same camel (N = 397) and tested for C. burnetii and Coxiella-like endosymbionts. Descriptive statistics were used to summarize seroprevalence by camel demographic and clinical variables. Univariate logistic regression analyses were used to assess relationships between serostatus (outcome) and tick PCR status, camel demographic variables, and camel clinical variables (predictors). Camel C. burnetii seroprevalence was 52%. Across tick pools, the prevalence of C. burnetii was 15% and Coxiella-like endosymbionts was 27%. Camel seropositivity was significantly associated with the presence of a C. burnetii PCR-positive tick pool (OR: 2.58; 95% CI: 1.4-5.1; p = 0.0045), increasing age class, and increasing total solids. CONCLUSIONS: The role of ticks and camels in the epidemiology of Q fever warrants further research to better understand this zoonotic disease that has potential to cause illness and reproductive losses in humans, livestock, and wildlife.

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.

Evidence of Histoplasma capsulatum seropositivity and exploration of risk factors for exposure in Busia county, western Kenya: Analysis of the PAZ dataset.

BACKGROUND: Despite recognition of histoplasmosis as a disease of national public health concern in Kenya, the burden of Histoplasma capsulatum in the general population remains unknown. This study examined the human seroprevalence of anti-Histoplasma antibody and explored associations between seropositivity and demographic and environmental variables, in Busia county, western Kenya. METHODOLOGY: Biobanked serum samples and associated data, from a previous cross-sectional survey, were examined. Latex agglutination tests to detect the presence of anti-Histoplasma antibody were performed on serum samples from 670 survey respondents, representing 178 households within 102 sub-locations. Potential epidemiologic risk factors for H. capsulatum exposure were explored using multi-level multivariable logistic regression analysis with household and sub-location included as random effects. PRINCIPAL FINDINGS: The apparent sample seroprevalence of anti-Histoplasma antibody was 15.5% (n = 104/670, 95% Confidence Interval (CI) 12.9-18.5%). A multivariable logistic regression model identified increased odds of H. capsulatum seropositivity in respondents reporting rats within the household within the previous 12 months (OR = 2.99 90% CI 1.04-8.55, p = 0.04). Compared to respondents aged 25-34 years, the odds of seropositivity were higher in respondents aged 15-24 years (OR = 2.70 90% CI 1.04-6.97, p = 0.04). CONCLUSIONS: The seroprevalence result provides a baseline for sample size approximations for future epidemiologic studies of the burden of H. capsulatum exposure in Busia county. The final model explored theoretically plausible risk factors for H. capsulatum exposure in the region. A number of factors may contribute to the complex epidemiological picture impacting H. capsulatum exposure status at the human-animal-environment interface in western Kenya. Focussed H. capsulatum research is warranted to determine the contextual significance of identified associations, and in representative sample populations.

Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape.

Quantitative evidence for the risk of zoonoses and the spread of antimicrobial resistance remains lacking. Here, as part of the UrbanZoo project, we sampled Escherichia coli from humans, livestock and peri-domestic wildlife in 99 households across Nairobi, Kenya, to investigate its distribution among host species in this rapidly developing urban landscape. We performed whole-genome sequencing of 1,338 E. coli isolates and found that the diversity and sharing patterns of E. coli were heavily structured by household and strongly shaped by host type. We also found evidence for inter-household and inter-host sharing and, importantly, between humans and animals, although this occurs much less frequently. Resistome similarity was differently distributed across host and household, consistent with being driven by shared exposure to antimicrobials. Our results indicate that a large, epidemiologically structured sampling framework combined with WGS is needed to uncover strain-sharing events among different host populations in complex environments and the major contributing pathways that could ultimately drive the emergence of zoonoses and the spread of antimicrobial resistance.

Evidence of exposure to C. burnetii among slaughterhouse workers in western Kenya.

Q fever, caused by C. burnetii, has been reported in slaughterhouse workers worldwide. The most reported risk factor for seropositivity is the workers' role in the slaughterhouse. This study examined the seroprevalence and risk factors for antibodies to C. burnetii in slaughterhouse workers in western Kenya to fill a data gap relating to this emerging disease in East Africa. Individuals were recruited from all consenting slaughterhouses in the study area between February and November 2012. Information was collected from participating workers regarding demographic data, animals slaughtered and role in the slaughterhouse. Sera samples were screened for antibodies to C. burnetii using a commercial ELISA and risk factors associated with seropositivity were identified using multi-level logistic regression analysis. Slaughterhouse workers (n = 566) were recruited from 84 ruminant slaughterhouses in western Kenya. The seroprevalence of antibodies to C. burnetii was 37.1% (95% Confidence Interval (CI) 33.2-41.2%). The risk factors identified for C. burnetii seropositivity included: male workers compared to female workers, odds ratio (OR) 5.40 (95% CI 1.38-21.22); slaughtering cattle and small ruminants compared to those who only slaughtered cattle, OR 1.52 (95% CI 1.06-2.19). In addition, specific roles in the slaughterhouse were associated with increased odds of being seropositive, including cleaning the slaughterhouse, OR 3.98 (95% CI 1.39-11.43); cleaning the intestines, OR 3.24 (95% CI 1.36-7.73); and flaying the carcass OR 2.63 (95% CI 1.46-4.75) compared to being the slaughterman or foreman. We identified that slaughterhouse workers have a higher seroprevalence of antibodies to C. burnetii compared to published values in the general population from the same area. Slaughterhouse workers therefore represent an occupational risk group in this East African setting. Workers with increased contact with the viscera and fluids are at higher risk for exposure to C. burnetii. Education of workers may reduce transmission, but an alternative approach may be to consider the benefits of vaccination in high-risk groups.

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.