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author:("mutong, David")
1.  Risk Factors for Sustained Cholera Transmission, Juba County, South Sudan, 2014 
Emerging Infectious Diseases  2015;21(10):1849-1852.
We conducted a case–control study to identify risk factors for the 2014 cholera outbreak in Juba County, South Sudan. Illness was associated with traveling or eating away from home; treating drinking water and receiving oral cholera vaccination were protective. Oral cholera vaccination should be used to complement cholera prevention efforts.
PMCID: PMC4593433  PMID: 26402715
cholera; risk factors; matched case-control study; zoonoses; South Sudan; transmission; sub-Saharan Africa; epidemic; water sanitation; environmental factors; vaccine; diarrheal disease; enteric infections; Vibrio cholerae
2.  Assessing parents’ knowledge and attitudes towards seasonal influenza vaccination of children before and after a seasonal influenza vaccination effectiveness study in low-income urban and rural Kenya, 2010–2011 
BMC Public Health  2013;13:391.
Influenza vaccine is rarely used in Kenya, and little is known about attitudes towards the vaccine. From June-September 2010, free seasonal influenza vaccine was offered to children between 6 months and 10 years old in two Population-Based Infectious Disease Surveillance (PBIDS) sites. This survey assessed attitudes about influenza, uptake of the vaccine and experiences with childhood influenza vaccination.
We administered a questionnaire and held focus group discussions with parents of children of enrollment age in the two sites before and after first year of the vaccine campaign. For pre-vaccination focus group discussions, we randomly selected mothers and fathers who had an eligible child from the PBIDS database to participate. For the post-vaccination focus group discussions we stratified parents whose children were eligible for vaccination into fully vaccinated, partially vaccinated and non-vaccinated groups.
Overall, 5284 and 5755 people completed pre and post-vaccination questionnaires, respectively, in Kibera and Lwak. From pre-vaccination questionnaire results, among parents who were planning on vaccinating their children, 2219 (77.6%) in Kibera and 1780 (89.6%) in Lwak said the main reason was to protect the children from seasonal influenza. In the pre-vaccination discussions, no parent had heard of the seasonal influenza vaccine. At the end of the vaccine campaign, of 18,652 eligible children, 5,817 (31.2%) were fully vaccinated, 2,073 (11.1%) were partially vaccinated and, 10,762 (57.7%) were not vaccinated. In focus group discussions, parents who declined vaccine were concerned about vaccine safety or believed seasonal influenza illness was not severe enough to warrant vaccination. Parents who declined the vaccine were mainly too busy [251(25%) in Kibera and 95 (10.5%) in Lwak], or their child was away during the vaccination period [199(19.8%) in Kibera; 94(10.4%) in Lwak].
If influenza vaccine were to be introduced more broadly in Kenya, effective health messaging will be needed on vaccine side effects and frequency and potential severity of influenza infection.
PMCID: PMC3639236  PMID: 23617891
Seasonal influenza; Vaccination; Attitude; Parent; Children; Low-income; Kenya
4.  A Cost Effectiveness and Capacity Analysis for the Introduction of Universal Rotavirus Vaccination in Kenya: Comparison between Rotarix and RotaTeq Vaccines 
PLoS ONE  2012;7(10):e47511.
Diarrhoea is an important cause of death in the developing world, and rotavirus is the single most important cause of diarrhoea associated mortality. Two vaccines (Rotarix and RotaTeq) are available to prevent rotavirus disease. This analysis was undertaken to aid the decision in Kenya as to which vaccine to choose when introducing rotavirus vaccination.
Cost-effectiveness modelling, using national and sentinel surveillance data, and an impact assessment on the cold chain.
The median estimated incidence of rotavirus disease in Kenya was 3015 outpatient visits, 279 hospitalisations and 65 deaths per 100,000 children under five years of age per year. Cumulated over the first five years of life vaccination was predicted to prevent 34% of the outpatient visits, 31% of the hospitalizations and 42% of the deaths. The estimated prevented costs accumulated over five years totalled US$1,782,761 (direct and indirect costs) with an associated 48,585 DALYs. From a societal perspective Rotarix had a cost-effectiveness ratio of US$142 per DALY (US$5 for the full course of two doses) and RotaTeq US$288 per DALY ($10.5 for the full course of three doses). RotaTeq will have a bigger impact on the cold chain compared to Rotarix.
Vaccination against rotavirus disease is cost-effective for Kenya irrespective of the vaccine. Of the two vaccines Rotarix was the preferred choice due to a better cost-effectiveness ratio, the presence of a vaccine vial monitor, the requirement of fewer doses and less storage space, and proven thermo-stability.
PMCID: PMC3480384  PMID: 23115650
5.  Molecular Epidemiology of Geographically Dispersed Vibrio cholerae, Kenya, January 2009–May 2010 
Emerging Infectious Diseases  2012;18(6):925-931.
Isolates represent multiple genetic lineages, a finding consistent with multiple emergences from endemic reservoirs.
Numerous outbreaks of cholera have occurred in Kenya since 1971. To more fully understand the epidemiology of cholera in Kenya, we analyzed the genetic relationships among 170 Vibrio cholerae O1 isolates at 5 loci containing variable tandem repeats. The isolates were collected during January 2009–May 2010 from various geographic areas throughout the country. The isolates grouped genetically into 5 clonal complexes, each comprising a series of genotypes that differed by an allelic change at a single locus. No obvious correlation between the geographic locations of the isolates and their genotypes was observed. Nevertheless, geographic differentiation of the clonal complexes occurred. Our analyses showed that multiple genetic lineages of V. cholerae were simultaneously infecting persons in Kenya. This finding is consistent with the simultaneous emergence of multiple distinct genetic lineages of V. cholerae from endemic environmental reservoirs rather than recent introduction and spread by travelers.
PMCID: PMC3358164  PMID: 22607971
phenotypes; genotypes; Vibrio cholerae; cholera; characterization; molecular epidemiology; outbreaks; bacteria; Kenya
6.  Relationship of Climate, Geography, and Geology to the Incidence of Rift Valley Fever in Kenya during the 2006–2007 Outbreak 
We estimated Rift Valley fever (RVF) incidence as a function of geological, geographical, and climatological factors during the 2006–2007 RVF epidemic in Kenya. Location information was obtained for 214 of 340 (63%) confirmed and probable RVF cases that occurred during an outbreak from November 1, 2006 to February 28, 2007. Locations with subtypes of solonetz, calcisols, solonchaks, and planosols soil types were highly associated with RVF occurrence during the outbreak period. Increased rainfall and higher greenness measures before the outbreak were associated with increased risk. RVF was more likely to occur on plains, in densely bushed areas, at lower elevations, and in the Somalia acacia ecological zone. Cases occurred in three spatial temporal clusters that differed by the date of associated rainfall, soil type, and land usage.
PMCID: PMC3269292  PMID: 22302875
7.  Epidemiology of respiratory viral infections in two long-term refugee camps in Kenya, 2007-2010 
Refugees are at risk for poor outcomes from acute respiratory infections (ARI) because of overcrowding, suboptimal living conditions, and malnutrition. We implemented surveillance for respiratory viruses in Dadaab and Kakuma refugee camps in Kenya to characterize their role in the epidemiology of ARI among refugees.
From 1 September 2007 through 31 August 2010, we obtained nasopharyngeal (NP) and oropharyngeal (OP) specimens from patients with influenza-like illness (ILI) or severe acute respiratory infections (SARI) and tested them by RT-PCR for adenovirus (AdV), respiratory syncytial virus (RSV), human metapneumovirus (hMPV), parainfluenza viruses (PIV), and influenza A and B viruses. Definitions for ILI and SARI were adapted from those of the World Health Organization. Proportions of cases associated with viral aetiology were calculated by camp and by clinical case definition. In addition, for children < 5 years only, crude estimates of rates due to SARI per 1000 were obtained.
We tested specimens from 1815 ILI and 4449 SARI patients (median age = 1 year). Proportion positive for virus were AdV, 21.7%; RSV, 12.5%; hMPV, 5.7%; PIV, 9.4%; influenza A, 9.7%; and influenza B, 2.6%; 49.8% were positive for at least one virus. The annual rate of SARI hospitalisation for 2007-2010 was 57 per 1000 children per year. Virus-positive hospitalisation rates were 14 for AdV; 9 for RSV; 6 for PIV; 4 for hMPV; 5 for influenza A; and 1 for influenza B. The rate of SARI hospitalisation was highest in children < 1 year old (156 per 1000 child-years). The ratio of rates for children < 1 year and 1 to < 5 years old was 3.7:1 for AdV, 5.5:1 for RSV, 4.4:1 for PIV, 5.1:1 for hMPV, 3.2:1 for influenza A, and 2.2:1 for influenza B. While SARI hospitalisation rates peaked from November to February in Dadaab, no distinct seasonality was observed in Kakuma.
Respiratory viral infections, particularly RSV and AdV, were associated with high rates of illness and make up a substantial portion of respiratory infection in these two refugee settings.
PMCID: PMC3398263  PMID: 22251705
8.  Risk Factors for Severe Rift Valley Fever Infection in Kenya, 2007 
A large Rift Valley fever (RVF) outbreak occurred in Kenya from December 2006 to March 2007. We conducted a study to define risk factors associated with infection and severe disease. A total of 861 individuals from 424 households were enrolled. Two hundred and two participants (23%) had serologic evidence of acute RVF infection. Of these, 52 (26%) had severe RVF disease characterized by hemorrhagic manifestations or death. Independent risk factors for acute RVF infection were consuming or handling products from sick animals (odds ratio [OR] = 2.53, 95% confidence interval [CI] = 1.78–3.61, population attributable risk percentage [PAR%] = 19%) and being a herdsperson (OR 1.77, 95% CI = 1.20–2.63, PAR% = 11%). Touching an aborted animal fetus was associated with severe RVF disease (OR = 3.83, 95% CI = 1.68–9.07, PAR% = 14%). Consuming or handling products from sick animals was associated with death (OR = 3.67, 95% CI = 1.07–12.64, PAR% = 47%). Exposures related to animal contact were associated with acute RVF infection, whereas exposures to mosquitoes were not independent risk factors.
PMCID: PMC2913492  PMID: 20682901
9.  Pathologic Studies on Suspect Animal and Human Cases of Rift Valley Fever from an Outbreak in Eastern Africa, 2006–2007 
Rift Valley fever (RVF) is an important viral zoonotic disease in Africa with periodic outbreaks associated with severe disease, death, and economic hardship. During the 2006–2007 outbreaks in Eastern Africa, postmortem and necropsy tissue samples from 14 animals and 20 humans clinically suspected of RVF were studied with histopathologic evaluation and immunohistochemical (IHC) assays. Six animal and 11 human samples had IHC evidence of Rift Valley fever virus (RVFV) antigens. We found that extensive hepatocellular necrosis without prominent inflammatory cell infiltrates is the most distinctive histopathologic change in liver tissues infected with RVFV. Pathologic studies on postmortem tissue samples can help establish the diagnosis of RVF, differentiating from endemic diseases with clinical manifestations similar to RVF, such as malaria, leptospirosis, or yellow fever.
PMCID: PMC2913495  PMID: 20682904
10.  An Investigation of a Major Outbreak of Rift Valley Fever in Kenya: 2006–2007 
An outbreak of Rift Valley fever (RVF) occurred in Kenya during November 2006 through March 2007. We characterized the magnitude of the outbreak through disease surveillance and serosurveys, and investigated contributing factors to enhance strategies for forecasting to prevent or minimize the impact of future outbreaks. Of 700 suspected cases, 392 met probable or confirmed case definitions; demographic data were available for 340 (87%), including 90 (26.4%) deaths. Male cases were more likely to die than females, Case Fatality Rate Ratio 1.8 (95% Confidence Interval [CI] 1.3–3.8). Serosurveys suggested an attack rate up to 13% of residents in heavily affected areas. Genetic sequencing showed high homology among viruses from this and earlier RVF outbreaks. Case areas were more likely than non-case areas to have soil types that retain surface moisture. The outbreak had a devastatingly high case-fatality rate for hospitalized patients. However, there were up to 180,000 infected mildly ill or asymptomatic people within highly affected areas. Soil type data may add specificity to climate-based forecasting models for RVF.
PMCID: PMC2913496  PMID: 20682900
11.  Rift Valley Fever Outbreak in Livestock in Kenya, 2006–2007 
We analyzed the extent of livestock involvement in the latest Rift Valley fever (RVF) outbreak in Kenya that started in December 2006 and continued until June 2007. When compared with previous RVF outbreaks in the country, the 2006–07 outbreak was the most extensive in cattle, sheep, goats, and camels affecting thousands of animals in 29 of 69 administrative districts across six of the eight provinces. This contrasted with the distribution of approximately 700 human RVF cases in the country, where over 85% of these cases were located in four districts; Garissa and Ijara districts in Northeastern Province, Baringo district in Rift Valley Province, and Kilifi district in Coast Province. Analysis of livestock and human data suggests that livestock infections occur before virus detection in humans, as supported by clustering of human RVF cases around livestock cases in Baringo district. The highest livestock morbidity and mortality rates were recorded in Garissa and Baringo districts, the same districts that recorded a high number of human cases. The districts that reported RVF in livestock for the first time in 2006/07 included Kitui, Tharaka, Meru South, Meru central, Mwingi, Embu, and Mbeere in Eastern Province, Malindi and Taita taveta in Coast Province, Kirinyaga and Murang'a in Central Province, and Baringo and Samburu in Rift Valley Province, indicating that the disease was occurring in new regions in the country.
PMCID: PMC2913503  PMID: 20682907
12.  Using a Field Quantitative Real-Time PCR Test To Rapidly Identify Highly Viremic Rift Valley Fever Cases▿  
Journal of Clinical Microbiology  2009;47(4):1166-1171.
Approximately 8% of Rift Valley fever (RVF) cases develop severe disease, leading to hemorrhage, hepatitis, and/or encephalitis and resulting in up to 50% of deaths. A major obstacle in the management of RVF and other viral hemorrhagic fever cases in outbreaks that occur in rural settings is the inability to rapidly identify such cases, with poor prognosis early enough to allow for more-aggressive therapies. During an RVF outbreak in Kenya in 2006 to 2007, we evaluated whether quantitative real-time reverse transcription-PCR (qRT-PCR) could be used in the field to rapidly identify viremic RVF cases with risk of death. In 52 of 430 RVF cases analyzed by qRT-PCR and virus culture, 18 died (case fatality rate [CFR] = 34.6%). Levels of viremia in fatal cases were significantly higher than those in nonfatal cases (mean of 105.2 versus 102.9 per ml; P < 0.005). A negative correlation between the levels of infectious virus particles and the qRT-PCR crossover threshold (CT) values allowed the use of qRT-PCR to assess prognosis. The CFR was 50.0% among cases with CT values of <27.0 (corresponding to 2.1 × 104 viral RNA particles/ml of serum) and 4.5% among cases with CT values of ≥27.0. This cutoff yielded 93.8% sensitivity and a 95.5% negative predictive value; the specificity and positive predictive value were 58% and 50%, respectively. This study shows a correlation between high viremia and fatality and indicates that qRT-PCR testing can identify nearly all fatal RVF cases.
PMCID: PMC2668310  PMID: 19171680

Results 1-12 (12)