Identification of group B respiratory syncytial viruses that lack the 60-nucleotide duplication after six consecutive epidemics of total BA dominance at coastal Kenya

Respiratory syncytial virus BA genotype has reportedly replaced other group B genotypes worldwide. We report the observation of three group B viruses, all identical in G sequence but lacking the BA duplication, at a coastal district hospital in Kenya in early 2012. This follows a period of six consecutive respiratory syncytial virus (RSV) epidemics with 100% BA dominance among group B isolates. The new strains appear only distantly related to BA variants and to previously circulating SAB1 viruses last seen in the district in 2005, suggesting that they were circulating elsewhere undetected. These results are of relevance to an understanding of RSV persistence

Determination of carnivores prey base by scat analysis in Samburu community group ranches in Kenya

This study determined the prey base for four main carnivores found in Samburu community group ranches and grazing area, Lion (Panthera leo), Leopard (Panthera pardus), Wild dog (Lycaon pictus) and Hyaena (Crocuta crocuta, and Hyaena hyaena). A total of 96 scat samples including, 8 from Lion, 16 Leopards’, 2 Wild dogs’, and 70 Hyaenas’ were collected, identified and microscopically analyzed for prey hair characterisation. At least 50 different hairs from every scat sample were mounted on slides and microscopically characterized using details from reference hairs. Hairs from 18 depredated species both domestic and wild ungulates were recovered from the scat samples. Predated species were identified, as either domestic (Cow, Sheep, Goat, Donkey, and Camel) or wild ungulate prey (Grant’s gazelle, plain Zebra, Grevy’s Zebra, Impala, Waterbuck, Dikdik, Eland, lesser Kudu, greater Kudu, Baboon, rock Hyraxes, Elephant and Oryx). The carnivores showed a relatively high kill of wild ungulate prey compared to domestic prey. Camel was the most preferred domestic animal by both the Lion and the leopard, while wild Dog and Hyaena preferred cow and donkey respectively. Grevy’s zebra contributed highest to the lion’s diet while the Plain zebra was most preferred by the leopard. Both the hyaena and the Wild dog had a preference for the waterbuck. The Hyaena had the highest domestic depredation, while all the other big cats depredated more on wild ungulatesKey words: Scat, group ranch, domestic, wild ungulate, prey, depredation

Investigation of extramammary sources of Group B Streptococcus reveals its unusual ecology and epidemiology in camels

Camels are vital to food production in the drylands of the Horn of Africa, with milk as their main contribution to food security. A major constraint to camel milk production is mastitis, inflammation of the mammary gland. The condition negatively impacts milk yield and quality as well as household income. A leading cause of mastitis in dairy camels is Streptococcus agalactiae, or group B Streptococcus (GBS), which is also a commensal and pathogen of humans and cattle. It has been suggested that extramammary reservoirs for this pathogen may contribute to the occurrence of mastitis in camels. We explored the molecular epidemiology of GBS in camels using a cross-sectional study design for sample collection and phenotypic, genomic and phylogenetic analysis of isolates. Among 88 adult camels and 93 calves from six herds in Laikipia County, Kenya, GBS was detected in 20% of 50 milk samples, 25% of 152 nasal swabs, 8% of 90 oral swabs and 3% of 90 rectal swabs, but not in vaginal swabs. Per camel herd, two to four sequence types (ST) were identified using Multi Locus Sequence Typing (MLST). More than half of the isolates belonged to ST617 or its single-locus variant, ST1652, with these STs found across all sample types. Capsular serotype VI was detected in 30 of 58 isolates. In three herds, identical STs were detected in milk and swab samples, suggesting that extramammary sources of GBS may contribute to the maintenance and spread of GBS within camel herds. This needs to be considered when developing prevention and control strategies for GBS mastitis. The high nasal carriage rate, low recto-vaginal carriage rate, and high prevalence of serotype VI for GBS in camels are in stark contrast to the distribution of GBS in humans and in cattle and reveal hitherto unknown ecological and molecular features of this bacterial species

The Effect of Antibiotic Exposure and Specimen Volume on the Detection of Bacterial Pathogens in Children With Pneumonia.

BACKGROUND.: Antibiotic exposure and specimen volume are known to affect pathogen detection by culture. Here we assess their effects on bacterial pathogen detection by both culture and polymerase chain reaction (PCR) in children. METHODS.: PERCH (Pneumonia Etiology Research for Child Health) is a case-control study of pneumonia in children aged 1-59 months investigating pathogens in blood, nasopharyngeal/oropharyngeal (NP/OP) swabs, and induced sputum by culture and PCR. Antibiotic exposure was ascertained by serum bioassay, and for cases, by a record of antibiotic treatment prior to specimen collection. Inoculated blood culture bottles were weighed to estimate volume. RESULTS.: Antibiotic exposure ranged by specimen type from 43.5% to 81.7% in 4223 cases and was detected in 2.3% of 4863 controls. Antibiotics were associated with a 45% reduction in blood culture yield and approximately 20% reduction in yield from induced sputum culture. Reduction in yield of Streptococcus pneumoniae from NP culture was approximately 30% in cases and approximately 32% in controls. Several bacteria had significant but marginal reductions (by 5%-7%) in detection by PCR in NP/OP swabs from both cases and controls, with the exception of S. pneumoniae in exposed controls, which was detected 25% less frequently compared to nonexposed controls. Bacterial detection in induced sputum by PCR decreased 7% for exposed compared to nonexposed cases. For every additional 1 mL of blood culture specimen collected, microbial yield increased 0.51% (95% confidence interval, 0.47%-0.54%), from 2% when volume was ≤1 mL to approximately 6% for ≥3 mL. CONCLUSIONS.: Antibiotic exposure and blood culture volume affect detection of bacterial pathogens in children with pneumonia and should be accounted for in studies of etiology and in clinical management

Investigation of extramammary sources of Group B Streptococcus reveals its unusual ecology and epidemiology in camels

Camels are vital to food production in the drylands of the Horn of Africa, with milk as their main contribution to food security. A major constraint to camel milk production is mastitis, inflammation of the mammary gland. The condition negatively impacts milk yield and quality as well as household income. A leading cause of mastitis in dairy camels is Streptococcus agalactiae, or group B Streptococcus (GBS), which is also a commensal and pathogen of humans and cattle. It has been suggested that extramammary reservoirs for this pathogen may contribute to the occurrence of mastitis in camels. We explored the molecular epidemiology of GBS in camels using a cross-sectional study design for sample collection and phenotypic, genomic and phylogenetic analysis of isolates. Among 88 adult camels and 93 calves from six herds in Laikipia County, Kenya, GBS was detected in 20% of 50 milk samples, 25% of 152 nasal swabs, 8% of 90 oral swabs and 3% of 90 rectal swabs, but not in vaginal swabs. Per camel herd, two to four sequence types (ST) were identified using Multi Locus Sequence Typing (MLST). More than half of the isolates belonged to ST617 or its single-locus variant, ST1652, with these STs found across all sample types. Capsular serotype VI was detected in 30 of 58 isolates. In three herds, identical STs were detected in milk and swab samples, suggesting that extramammary sources of GBS may contribute to the maintenance and spread of GBS within camel herds. This needs to be considered when developing prevention and control strategies for GBS mastitis. The high nasal carriage rate, low recto-vaginal carriage rate, and high prevalence of serotype VI for GBS in camels are in stark contrast to the distribution of GBS in humans and in cattle and reveal hitherto unknown ecological and molecular features of this bacterial species

ANTIINFLAMMATORY PROPERTIES OF DICHLOROMETHANE: METHANOLIC LEAF EXTRACTS OF CAESALPINIA VOLKENSII AND MAYTENUS OBSCURA IN ANIMAL MODELS

Objective: Inflammation is the reaction to injury of the living tissues. Conventional medication of inflammation is expensive and arguably associated with various severe adverse effects hence the need to develop herbal agents that are effective as alternative. Caesalpinia volkensii and Maytenus obscura are plants that grow in Mbeere County of Eastern region of Kenya. This study was designed to evaluate the anti-inflammatory activity of C. volkensii and M. obscura plants. Methods: Experimental animals were divided in to four groups; normal group, diseased negative control group, diseased reference group and diseased experimental groups. Inflammation was inducted into the mice using carrageenan. The experimental groups were treated with leaf extracts of the plants at concentration of 50 mg/kg, 100 mg/kg and 150 mg/kg. Anti-inflammatory activities in rats were compared with diclofenac (15 mg/kg) as the standard conventional drug. Results: The leaf extracts of C. volkensii reduced the paw edema by between 6.50%-13.42% while the extracts of M. obscura reduced it by between 4.94%-22.36%. Diclofenac reduced the paw edema by between 4.11%-10.47%. Conclusion: The phytochemical screening results showed that the extracts of C. volkensii had flavonoids, steroids and phenolics while the leaf extracts M. obscura had phenolics, terpenoids and saponins. Flavonoids, saponins and phenolics have been associated with anti-inflammatory activities. Therefore, the study has established that the DCM: methanolic leaf extracts of Caesalpinia volkensii and Maytenus obscura are effective in management of inflammation

Colonization Density of the Upper Respiratory Tract as a Predictor of Pneumonia-Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus, and Pneumocystis jirovecii.

BACKGROUND.: There is limited information on the association between colonization density of upper respiratory tract colonizers and pathogen-specific pneumonia. We assessed this association for Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus, and Pneumocystis jirovecii. METHODS.: In 7 low- and middle-income countries, nasopharyngeal/oropharyngeal swabs from children with severe pneumonia and age-frequency matched community controls were tested using quantitative polymerase chain reaction (PCR). Differences in median colonization density were evaluated using the Wilcoxon rank-sum test. Density cutoffs were determined using receiver operating characteristic curves. Cases with a pathogen identified from lung aspirate culture or PCR, pleural fluid culture or PCR, blood culture, and immunofluorescence for P. jirovecii defined microbiologically confirmed cases for the given pathogens. RESULTS.: Higher densities of H. influenzae were observed in both microbiologically confirmed cases and chest radiograph (CXR)-positive cases compared to controls. Staphylococcus aureus and P. jirovecii had higher densities in CXR-positive cases vs controls. A 5.9 log10 copies/mL density cutoff for H. influenzae yielded 86% sensitivity and 77% specificity for detecting microbiologically confirmed cases; however, densities overlapped between cases and controls and positive predictive values were poor (<3%). Informative density cutoffs were not found for S. aureus and M. catarrhalis, and a lack of confirmed case data limited the cutoff identification for P. jirovecii. CONCLUSIONS.: There is evidence for an association between H. influenzae colonization density and H. influenzae-confirmed pneumonia in children; the association may be particularly informative in epidemiologic studies. Colonization densities of M. catarrhalis, S. aureus, and P. jirovecii are unlikely to be of diagnostic value in clinical settings

Socio-economic determinants of disease progression among HIV infected adults in Kenya

BACKGROUND: Socioeconomic determinants have been shown to have an effect on the progression of HIV disease evidenced by studies carried out largely in developed countries. Knowledge of these factors could inform on prioritization of populations during scale up of highly active antiretroviral therapy (HAART) constrained health systems. The objective of this study was to identify socioeconomic correlates of HIV disease progression in an adult Kenyan population. METHODS: We analysed data from 312 HIV positive individuals, drawn from a cohort enrolled in a randomized clinical trial investigating the effectiveness of Acyclovir in the prevention of HIV transmission among serodiscordant couples. In this study we included individuals with CD4 counts ≥ 350 cells/mm(3) and World Health Organization (WHO), clinical stage one or two. The exposure variables measured were: - daily household income available for expenditure, age, gender, housing type and level of formal education. We used a composite outcome of disease progression to WHO clinical stage 3 or 4 or a laboratory outcome of CD4 count below 350 cells/mm(3) after two years of follow-up. Logistic regression was used to determine associations of variables that were found to be significant at univariate analysis, and to control for potential confounders. RESULTS: Seventy eight (25 %) individuals reported HIV disease progression. Majority (79.9 %) were female. The median age was 30 year and 93.6 % had attained a primary level of education. Median CD4 at enrolment into the clinical trial was 564 cells/mm(3); those who had disease progression were enrolled with a significantly (p < 0.001) lower CD4 count. Daily household income available for expenditure adjusted for CD4 count at enrolment was associated significantly (p = 0.04) with HIV disease progression. Disease progression was five times more likely to occur in study subjects with daily income available for expenditure of less than US$1 compared to those with more than US$ 5 available for daily expenditure [adjusted Odds Ratio 4.6 (95 % Confidence Interval 1.4–14.4)]. Disease progression was not associated with age, gender, type of housing or level of education attained (p < 0.05). CONCLUSION: Populations with low household incomes should be considered vulnerable to disease progression and should therefore be prioritized during the scale up of HAART for treatment as prevention