Biphasic MERS-CoV Incidence in Nomadic Dromedaries with Putative Transmission to Humans, Kenya, 2022-2023.

Middle East respiratory syndrome coronavirus (MERS-CoV) is endemic in dromedaries in Africa, but camel-to-human transmission is limited. Sustained 12-month sampling of dromedaries in a Kenya abattoir hub showed biphasic MERS-CoV incidence; peak detections occurred in October 2022 and February 2023. Dromedary-exposed abattoir workers (7/48) had serologic signs of previous MERS-CoV exposure.

Transmission of SARS-CoV-2 among underserved pastoralist communities in Kajiado County, Kenya: 2020-2022.

Initial transmission of severe acute respiratory syndrome virus-2 (SARS-CoV-2) was highest in densely populated regions of Kenya. Transmission gradually trickled down to the less densely populated, remote and underserved regions such as the pastoral regions of Kajiado County which are characterized by poor healthcare systems. Molecular assays that were pivotal for COVID-19 diagnosis were not available in these regions. Serology is an alternative method for retrospectively tracking the transmission of SARS-CoV-2 in such populations. Dry blood spots (DBS) were prepared from consenting patients attending six health facilities in Kajiado County from March 2020 to March 2022. Upon elution, we conducted an enzyme-linked immunosorbent assay (ELISA) for the detection of SARS-Cov-2 IgG antibodies. Of the 908 DBSs we analyzed, 706 (78%) were from female participants. The overall seropositivity to SARS-Cov-2 antibodies was 7.3% (95% CI 5.7-9.1). The elderly (over 60 years) and male participants had a high likelihood of testing positive for SAR-CoV-2 infections. Mashuru (15.6%, 14/90) and Meto (15%, 19/127) health facilities registered the highest proportion of seropositive participants. Evidence of SARS-CoV-2 transmission among pastoralists in the remote and underserved regions of Kajiado County was established by DBS sampling and serologic testing.

Antimicrobial Usage, Susceptibility Profiles, and Resistance Genes in Campylobacter Isolated from Cattle, Chicken, and Water Samples in Kajiado County, Kenya.

Campylobacter organisms are the major cause of bacterial gastroenteritis and diarrhoeal illness in man and livestock. Campylobacter is growingly becoming resistant to critically crucial antibiotics; thereby presenting public health challenge. This study aimed at establishing antimicrobial use, susceptibility profiles, and resistance genes in Campylobacter isolates recovered from chicken, cattle, and cattle-trough water samples. The study was conducted between October 2020 and May 2022 and involved the revival of cryopreserved Campylobacter isolates confirmed by PCR from a previous prevalence study in Kajiado County, Kenya. Data on antimicrobial use and animal health-seeking behaviour among livestock owners (from the same farms where sampling was done for the prevalence study) were collected through interview using a pretested semistructured questionnaire. One hundred and three isolates (29 C. coli (16 cattle isolates, 9 chicken isolates, and 4 water isolates) and 74 C. jejuni (38 cattle isolates, 30 chicken isolates, and 6 water isolates)) were assayed for phenotypic antibiotic susceptibility profile using the Kirby-Bauer disk diffusion method for ampicillin (AX), tetracycline (TE), gentamicin (GEN), erythromycin (E), ciprofloxacin (CIP), and nalidixic acid (NA). Furthermore, detection of genes conferring resistance to tetracyclines (tet (O), ß-lactams (bla OXA-61), aminoglycosides (aph-3-1), (fluoro)quinolones (gyrA), and multidrug efflux pump (cmeB) encoding resistance to multiple antibiotics was detected by mPCR and confirmed by DNA sequencing. The correlation between antibiotic use and resistance phenotypes was determined using the Pearson's correlation coefficient (r) method. Tetracyclines, aminoglycosides, and ß-lactam-based antibiotics were the most commonly used antimicrobials; with most farms generally reported using antimicrobials in chicken production systems than in cattle. The highest resistance amongst isolates was recorded in ampicillin (100%), followed by tetracycline (97.1%), erythromycin (75.7%), and ciprofloxacin (63.1%). Multidrug resistance (MDR) profile was observed in 99 of 103 (96.1%) isolates; with all the Campylobacter coli isolates displaying MDR. All chicken isolates (39/39, 100%) exhibited multidrug resistance. The AX-TE-E-CIP was the most common MDR pattern at 29.1%. The antibiotic resistance genes were detected as follows: tet (O), gyrA, cmeB, bla OXA-61 , and aph-3-1 genes were detected at 93.2%, 61.2%, 54.4%, 36.9%, and 22.3% of all Campylobacter isolates, respectively. The highest correlations were found between tet (O) and tetracycline-resistant phenotypes for C. coli (96.4%) and C. jejuni (95.8%). A moderate level of concordance was observed between the Kirby-Bauer disk diffusion method (phenotypic assay) and PCR (genotypic assay) for tetracycline in both C. coli (kappa coefficient = 0.65) and C. jejuni (kappa coefficient = 0.55). The study discloses relatively high resistance profiles and multidrug resistance to antibiotics of critical importance in humans. The evolution of the multidrug-resistantCampylobacter isolates has been linked to the use and misuse of antimicrobials. This poses a potential hazard to public and animal health, necessitating need to reduce the use of antibiotics in livestock husbandry practice coupled with stringent biosecurity measures to mitigate antimicrobial resistance.

Whole Genome Sequencing for Rapid Characterization of Rabies Virus Using Nanopore Technology.

Genomic data can be used to track the transmission and geographic spread of infectious diseases. However, the sequencing capacity required for genomic surveillance remains limited in many low- and middle-income countries (LMICs), where dog-mediated rabies and/or rabies transmitted by wildlife such as vampire bats pose major public health and economic concerns. We present here a rapid and affordable sample-to-sequence-to-interpretation workflow using nanopore technology. Protocols for sample collection and the diagnosis of rabies are briefly described, followed by details of the optimized whole genome sequencing workflow, including primer design and optimization for multiplex polymerase chain reaction (PCR), a modified, low-cost sequencing library preparation, sequencing with live and offline base calling, genetic lineage designation, and phylogenetic analysis. Implementation of the workflow is demonstrated, and critical steps are highlighted for local deployment, such as pipeline validation, primer optimization, inclusion of negative controls, and the use of publicly available data and genomic tools (GLUE, MADDOG) for classification and placement within regional and global phylogenies. The turnaround time for the workflow is 2-3 days, and the cost ranges from $25 per sample for a 96 sample run to $80 per sample for a 12 sample run. We conclude that setting up rabies virus genomic surveillance in LMICs is feasible and can support progress toward the global goal of zero dog-mediated human rabies deaths by 2030, as well as enhanced monitoring of wildlife rabies spread. Moreover, the platform can be adapted for other pathogens, helping to build a versatile genomic capacity that contributes to epidemic and pandemic preparedness.

The impact of livestock interventions on nutritional outcomes of children younger than 5 years old and women in Africa: a systematic review and meta-analysis.

Background: Nutrition-sensitive livestock interventions have the potential to improve the nutrition of communities that are dependent on livestock for their livelihoods by increasing the availability and access to animal-source foods. These interventions can also boost household income, improving purchasing power for other foods, as well as enhance determinants of health. However, there is a lack of synthesized empirical evidence of the impact and effect of livestock interventions on diets and human nutritional status in Africa. Objective: To review evidence of the effectiveness of nutrition-sensitive livestock interventions in improving diets and nutritional status in children younger than 5 years old and in pregnant and lactating women. Methods: Following PRISMA guidelines, we conducted a systematic review and meta-analysis of published studies reporting on the effect of livestock interventions on maternal and child nutrition in Africa. Data were extracted, synthesized, and summarized qualitatively. Key outcomes were presented in summary tables alongside a narrative summary. Estimation of pooled effects was undertaken for experimental studies with nutritional outcomes of consumption of animal-source foods (ASFs) and minimum dietary diversity (MDD). Fixed effects regression models and pooled effect sizes were computed and reported as odds ratios (ORs) together with their 95% confidence intervals (CI). Results: After the screening, 29 research papers were included in the review, and of these, only 4 were included in the meta-analysis. We found that nutrition-sensitive livestock interventions have a significant positive impact on the consumption of ASFs for children < 5 years (OR = 5.39; 95% CI: 4.43-6.56) and on the likelihood of meeting minimum dietary diversity (OR = 1.89; 95% CI: 1.51-2.37). Additionally, the impact of livestock interventions on stunting, wasting, and being underweight varied depending on the type of intervention and duration of the program/intervention implementation. Therefore, because of this heterogeneity in reporting metrics, the pooled estimates could not be computed. Conclusion: Nutrition-sensitive livestock interventions showed a positive effect in increasing the consumption of ASFs, leading to improved dietary diversity. However, the quality of the evidence is low, and therefore, more randomized controlled studies with consistent and similar reporting metrics are needed to increase the evidence base on how nutrition-sensitive livestock interventions affect child growth outcomes.

Draft genome of a clinical Pseudomonas qingdaonensis isolate from a hospitalized patient at Kenyatta National Hospital, Kenya.

The first draft genome of Pseudomonas qingdaonensis, a gram-negative bacteria isolated from hospitalized patients in Kenya, is presented in this study. The genome was assembled using nanopore MinION readings, yielding an assembly of 8,857,650 base pairs made up of 5(five) contigs. The genome sequence of Pseudomonas qingdaonensis will help researchers better grasp its genetics. Furthermore, the data can be a valuable resource for comparative genomics and future research in this novel species.

Draft genome sequences of three emerging beta-lactamase-producing Escherichia coli in the camel production system in Northern Kenya.

We report the draft genome sequences and annotation of three beta-lactamase-producing Escherichia coli ( E.coli) strains isolated from fecal samples of healthy camels in Laikipia county, Kenya. This data adds to the online genome resources to support the ongoing antimicrobial resistance surveillance in the livestock-wildlife interface.

Sero - epidemiology of brucellosis in people and their livestock: A linked human - animal cross-sectional study in a pastoralist community in Kenya.

Background: Brucellosis is associated with massive livestock production losses and human morbidity worldwide. Efforts to control brucellosis among pastoralist communities are limited by scarce data on the prevalence and risk factors for exposure despite the high human-animal interactions in these communities. This study simultaneously assessed the seroprevalence of brucellosis and associated factors of exposure among pastoralists and their livestock in same households. Methods: We conducted a cross-sectional study in pastoralist communities in Marsabit County - Kenya. A total of 1,074 women and 225 children participated and provided blood samples. Blood was also drawn from 1,876 goats, 322 sheep and 189 camels. Blood samples were collected to be screened for the presence of anti-Brucella IgG antibodies using indirect IgG Enzyme-Linked Immunosorbent Assay (ELISA) kits. Further, Individual, household and herd-level epidemiological information were captured using a structured questionnaire. Group differences were compared using the Pearson's Chi-square test, and p-values < 0.05 considered statistically significant. Generalized mixed-effects multivariable logistic human and animal models using administrative ward as the random effect was used to determine variables correlated to the outcome. Results: Household-level seropositivity was 12.7% (95% CI: 10.7-14.8). The individual human seroprevalence was 10.8% (9.1-12.6) with higher seroprevalence among women than children (12.4 vs. 3.1%, p < 0.001). Herd-level seroprevalence was 26.1% (23.7-28.7) and 19.2% (17.6-20.8) among individual animals. Goats had the highest seroprevalence 23.1% (21.2 - 25.1), followed by sheep 6.8% (4.3-10.2) and camels 1.1% (0.1-3.8). Goats and sheep had a higher risk of exposure OR = 3.8 (95% CI 2.4-6.7, p < 0.001) and 2.8 (1.2-5.6, p < 0.007), respectively relative to camels. Human and animal seroprevalence were significantly associated (OR = 1.8, [95%CI: 1.23-2.58], p = 0.002). Herd seroprevalence varied by household head education (OR = 2.45, [1.67-3.61, p < 0.001]) and herd size (1.01, [1.00-1.01], p < 0.001). Conclusions: The current study showed evidence that brucellosis is endemic in this pastoralist setting and there is a significant association between animal and human brucellosis seropositivity at household level representing a potential occupational risk. Public health sensitization and sustained human and animal brucellosis screening are required.

Endemicity of Coxiella burnetii infection among people and their livestock in pastoral communities in northern Kenya.

Background: Coxiella burnetti can be transmitted to humans primarily through inhaling contaminated droplets released from infected animals or consumption of contaminated dairy products. Despite its zoonotic nature and the close association pastoralist communities have with their livestock, studies reporting simultaneous assessment of C. burnetti exposure and risk-factors among people and their livestock are scarce. Objective: This study therefore estimated the seroprevalence of Q-fever and associated risk factors of exposure in people and their livestock. Materials and methods: We conducted a cross-sectional study in pastoralist communities in Marsabit County in northern Kenya. A total of 1,074 women and 225 children were enrolled and provided blood samples for Q-fever testing. Additionally, 1,876 goats, 322 sheep and 189 camels from the same households were sampled. A structured questionnaire was administered to collect individual- and household/herd-level data. Indirect IgG ELISA kits were used to test the samples. Results: Household-level seropositivity was 13.2% [95% CI: 11.2-15.3]; differences in seropositivity levels among women and children were statistically insignificant (p = 0.8531). Lactating women had higher odds of exposure, odds ratio (OR) = 2.4 [1.3-5.3], while the odds of exposure among children increased with age OR = 1.1 [1.0-1.1]. Herd-level seroprevalence was 83.7% [81.7-85.6]. Seropositivity among goats was 74.7% [72.7-76.7], while that among sheep and camels was 56.8% [51.2-62.3] and 38.6% [31.6-45.9], respectively. Goats and sheep had a higher risk of exposure OR = 5.4 [3.7-7.3] and 2.6 [1.8-3.4], respectively relative to camels. There was no statistically significant association between Q-fever seropositivity and nutrition status in women, p = 0.900 and children, p = 1.000. We found no significant association between exposure in people and their livestock at household level (p = 0.724) despite high animal exposure levels, suggesting that Q-fever exposure in humans may be occurring at a scale larger than households. Conclusion: The one health approach used in this study revealed that Q-fever is endemic in this setting. Longitudinal studies of Q-fever burden and risk factors simultaneously assessed in human and animal populations as well as the socioeconomic impacts of the disease and further explore the role of environmental factors in Q-fever epidemiology are required. Such evidence may form the basis for designing Q-fever prevention and control strategies.