Molecular Characterization of Human Enteroviruses Detected in Children Under Five Years Old in Kenya 2009 - 2015

   Introduction:  Human enterovirus (HEVs) infection is common, with an extensive array of clinical displays ranging from asymptomatic to life-threatening. Presentation include nonspecific febrile illness often accompanied by muscle pain, sore throat, abdominal discomfort, rash, headache, encephalitis, aseptic meningitis and acute flaccid paralysis [2]. Objectives: The study objective was to investigate the natural selection and genetic variability of HEVs and to identify HEV serotypes in circulation among children below 5 years old with diarrhea in an informal settlement(Kibera) in Kenya. Methodology: Specimens (n=628) from a prospective cohort study assessing the incidence and etiology of diarrhea from 2009-2015 were analyzed. Enteric Taqman array cards (TAC) were used for initial screening where two hundred and nine (78%) tested positive for HEVs. Of these specimens, 72 (42%) had a cycle threshold (Ct) ≤30 and were tested by conventional PCR targeting the 3’ regions of the viral protein 1 (VP1) gene. A total of 48 (67%) underwent sequencing; 11 (23%) of which yielded nucleotide sequences. Phylogenetic analyses clustered the Kenyan serotypes to HEVs groups C, B and A. Evaluation of the VP1 amino acid sequences revealed numerous amino acid substitutions in relation to reference strains, which were confirmed to be due to natural selection by negative or positive selection. Conclusion: The Heterogeneous nature of stool samples is known to influence disparities in viral nucleic acid yields. TAC detected 209 of which 171 (82%) were confirmed positive for HEVs by real-time reverse transcription polymerase chain reaction (RRT-PCR), targeting the 5’ NTR regions. Therefore, the results may not be a representative of all circulating HEVs in the study area. Since this was a retrospective study of previously collected samples, it is possible that some HEVs strains may have failed to amplify

Outbreak of beriberi among African union troops in Mogadishu, Somalia

Context and Objectives: In July 2009, WHO and partners were notified of a large outbreak of unknown illness, including deaths, among African Union (AU) soldiers in Mogadishu. Illnesses were characterized by peripheral edema, dyspnea, palpitations, and fever. Our objectives were to determine the cause of the outbreak, and to design and recommend control strategies. Design, Setting, and Participants: The illness was defined as acute onset of lower limb edema, with dyspnea, chest pain, palpitations, nausea, vomiting, abdominal pain, or headache. Investigations in Nairobi and Mogadishu included clinical, epidemiologic, environmental, and laboratory studies. A case-control study was performed to identify risk factors for illness. Results: From April 26, 2009 to May 1, 2010, 241 AU soldiers had lower limb edema and at least one additional symptom; four patients died. At least 52 soldiers were airlifted to hospitals in Kenya and Uganda. Four of 31 hospitalized patients in Kenya had right-sided heart failure with pulmonary hypertension. Initial laboratory investigations did not reveal hematologic, metabolic, infectious or toxicological abnormalities. Illness was associated with exclusive consumption of food provided to troops (not eating locally acquired foods) and a high level of insecurity (e.g., being exposed to enemy fire on a daily basis). Because the syndrome was clinically compatible with wet beriberi, thiamine was administered to ill soldiers, resulting in rapid and dramatic resolution. Blood samples taken from 16 cases prior to treatment showed increased levels of erythrocyte transketolase activation coefficient, consistent with thiamine deficiency. With mass thiamine supplementation for healthy troops, the number of subsequent beriberi cases decreased with no further deaths reported. Conclusions: An outbreak of wet beriberi caused by thiamine deficiency due to restricted diet occurred among soldiers in a modern, well-equipped army. Vigilance to ensure adequate micronutrient intake must be a priority in populations completely dependent upon nutritional support from external sources

Longitudinal Patterns of Antimicrobial Resistance in Escherichia coli Isolated from Children <5 Years of Age Following Hospital Discharge in Kenya and the Impact of a 5-Day Course of Azithromycin

Thesis (Master's)--University of Washington, 2023Introduction: Antimicrobial resistance (AMR) is a growing concern worldwide, especially among gram-negative bacteria. One gram-negative species, E. coli, is responsible for most deaths attributed to AMR, especially in sub-Saharan Africa. Hospitalization is a time of increased exposure to pathogens and antibiotics. However, there is limited data on the burden of AMR post-hospital discharge and factors associated with the occurrence of extended-spectrum β-lactamase (ESBL) - producing E. coli within communities.Methods: A sequential cross-sectional data analysis from E. coli isolated from fecal samples collected from children <60 months old in Homabay and Kisii counties of Western Kenya. Fecal samples were collected at hospital discharge, and at three-month and six-month follow-ups. Fecal samples from each unique child were cultured in triplicate for E. coli. If E. coli was isolated from at least one of the samples tested in triplicate, the child was considered to have a positive E. coli culture. Any unique child with E. coli isolated at enrollment with antimicrobial susceptibility testing (AST) results was included in our analysis. We evaluated changes in the proportion of AMR to twelve selected antibiotics over six months following hospital discharge and determined AMR decline by comparing the proportion of AMR between discharge and three months and between three- and six-months post-discharge. We also determined the occurrence of ESBL-producing E. coli at six months post-hospital discharge. We conducted a univariate analysis to determine the burden of AMR post-hospital discharge and a Multivariate Poisson regression to evaluate the association between the occurrence of ESBL-producing E. coli at six months post-hospital discharge and selected risk factors. We then conducted a sensitivity analysis to examine differences in phenotypic AMR among isolates detected at discharge, three months, and six months post-hospital discharge. Results: 406 unique children were enrolled in the study, and all had E. coli isolated at the discharge time point. Most of the children (323, or 80%) had E. coli isolated at each time point (discharge, month three, and month six). E. coli isolates were predominantly from males (59.5%) and the median age of the included children was 19 months (IQR 23 months) at enrollment. Most children were hospitalized for at least three days, were of low socio-economic status (65.2%), and were HIV unexposed (84%).   There was a statistically significant decline in the proportional non-susceptibility to all antibiotics from hospital discharge to three months. The proportion of non-susceptibility isolates between three months and six months was not statistically significant for most antibiotics, except for ceftazidime 0.58 (0.36 - 0.95, p0.031), gentamicin 0.44 (0.30 - 0.63, p<0.001), and ESBL-producing E. coli 0.55 (0.32 - 0.94, p0.029). Non-susceptibility to ampicillin (AMP) and trimethoprim-sulfamethoxazole (TMP/SMX) remained highest at the end of follow-up at month six (72% and 84%, respectively). Carriage of ESBL-producing E. coli dropped from 44% at hospital discharge to 11% at six months post-hospital discharge. There were no statistically significant risk factors associated with the occurrence of ESBL-producing E. coli at six months post-hospital discharge. Conclusions: At hospital discharge, non-susceptibility to E. coli remained high, suggesting that exposure to antibiotics in the hospital is a driver of AMR in these children. Non-susceptibility to all antibiotics significantly declined up to three months post-discharge suggesting that when antibiotic pressure associated with illness and hospitalization is removed, AMR emergence also stabilizes. ESBL-producing E. coli remained stable up to six months post-hospital discharge. There were no significant correlates of ESBL-producing E. coli at six months post-hospital discharge among the risk factors examined. Overall, these findings highlight the urgent need for facility-based interventions, including increased surveillance, antibiotic stewardship, and other control measures, to reduce the spread of antimicrobial-resistant bacteria in sub-Saharan Africa

The contribution of respiratory pathogens to fatal and non-fatal respiratory hospitalizations: a pilot study of Taqman Array Cards (TAC) in Kenya

Contains fulltext : 177998.pdf (publisher's version ) (Open Access)BACKGROUND: Respiratory diseases cause substantial morbidity and mortality worldwide, with sub-Saharan Africa bearing the greatest burden. Identifying etiologies of respiratory disease is important to inform cost effective treatment, prevention and control strategies. Testing for all of the different pathogens that are potentially associated with respiratory illnesses is challenging. We piloted the use of a multi-pathogen respiratory Taqman Array Cards (TAC) to identify pathogens in respiratory samples collected from non-fatal and fatal cases and their matched asymptomatic controls. METHODS: This is a case control study comparing viral and bacterial pathogens detected among non-fatal and fatal cases to those detected among age and time matched asymptomatic controls. We used McNemar's test to compare proportions of pathogens detected among cases (non-fatal and fatal) to their matched asymptomatic controls. We used Mann-Whitney test to compare the distribution of median Cycle threshold (Ct) values among non-fatal and fatal cases to their corresponding asymptomatic controls. RESULTS: There were 72 fatal and 72 non-fatal cases matched to 72 controls. We identified at least one pathogen in 109/144 (76%) cases and 59/72 (82%) controls. For most pathogens, the median Ct values were lower among cases (fatal and non-fatal) compared to asymptomatic controls. CONCLUSIONS: Similar rates of pathogen detection among cases and controls make interpretation of results challenging. Ct-values might be helpful in interpreting clinical relevance of detected pathogens using multi-pathogen diagnostic tools

Prevalence and risk factors associated with asymptomatic Plasmodium falciparum infection and anemia among pregnant women at the first antenatal care visit: A hospital based cross-sectional study in Kwale County, Kenya.

BackgroundPrevalence of Prevalence of malaria in pregnancy (MiP) in Kenya ranges from 9% to 18%. We estimated the prevalence and factors associated with MiP and anemia in pregnancy (AiP) among asymptomatic women attending antenatal care (ANC) visits.MethodsWe performed a cross-sectional study among pregnant women attending ANC at Msambweni Hospital, between September 2018 and February 2019. Data was collected and analyzed in Epi Info 7. Descriptive statistics were calculated and we compared MiP and AiP in asymptomatic cases to those without either condition. Adjusted prevalence Odds odds ratios (aPOR) and 95% confidence intervals (CI) were calculated to identify factors associated with asymptomatic MiP and AiP.ResultsWe interviewed 308 study participants; their mean age was 26.6 years (± 5.8 years), mean gestational age was 21.8 weeks (± 6.0 weeks), 173 (56.2%) were in the second trimester of pregnancy, 12.9% (40/308) had MiP and 62.7% had AiP. Women who were aged ≤ 20 years had three times likelihood of developing MiP (aPOR = 3.1 Cl: 1.3-7.35) compared to those aged >20 years old. The likelihood of AiP was higher among women with gestational age ≥ 16 weeks (aPOR = 3.9, CI: 1.96-7.75), those with parasitemia (aPOR = 3.3, 95% CI: 1.31-8.18), those in third trimester of pregnancy (aPOR = 2.6, 95% CI:1.40-4.96) and those who reported eating soil as a craving during pregnancy (aPOR = 1.9, 95%CI:1.15-3.29).ConclusionsMajority of the women had asymptomatic MiP and AiP. MiP was observed in one tenth of all study participants. Asymptomatic MiP was associated with younger age while AiP was associated with gestational age parasitemia, and soil consumption as a craving during pregnancy

Additional file 1: Figure S1. of The contribution of respiratory pathogens to fatal and non-fatal respiratory hospitalizations: a pilot study of Taqman Array Cards (TAC) in Kenya

Schematic diagram of the two versions of Taqman array cards (TAC) used in the study. Table S1. Viral and bacterial pathogens detected using Taqman array cards (TAC) among non-fatal and fatal cases and asymptomatic controls, by age group, western Kenya, 2009-11. Table S2. Distribution of respiratory pathogens among cases (non-fatal and fatal) and corresponding asymptomatic controls in rural western Kenya, 2009-11. (DOCX 614 kb

Available laboratory results for cases referred for admission to AKUH-N (n = 33).

1<p>Aga Khan Laboratories- Nairobi, Kenya.</p>2<p>Center for Disease Control and Prevention Laboratories-Nairobi, Kenya.</p>3<p>Kenya Medical Research Institute-Kisumu, Kenya.</p>4<p>Walter Reed Army Medical Laboratories-Nairobi, Kenya.</p>5<p>National Influenza Center, Nairobi, Kenya.</p