Validation of immune-complex enzyme immunoassays for diagnosis of pneumococcal pneumonia among adults in Kenya

The efficacy of pneumococcal vaccines in protecting against pneumococcal pneumonia can feasibly be measured only with a diagnostic technique that has a high specificity (0.98 to 1.00) and a sensitivity greatly exceeding that of blood cultures (>0.2 to 0.3). In this context immune-complex enzyme immunoassays (EIAs) offer a novel, convenient diagnostic method, and we have investigated three such assays with appropriate study populations in Kenya. Sera from 129 Kenyan adults with pneumococcal pneumonia and 97 ill controls from the same clinics, but without pneumococcal disease syndromes, were assayed with immune-complex EIAs for pneumolysin, C-polysaccharide, and mixed capsular polysaccharides (Pneumovax II). At an optical density (OD) threshold yielding a specificity of 0.95, the sensitivities (95% confidence intervals) of the assays were 0.22 (0.15 to 0.30), 0.26 (0.19 to 0.34), and 0.22 (0.15 to 0.29), respectively. For pneumolysin immune complexes, human immunodeficiency virus (HIV)-positive patients had a higher mean OD than HIV-negative patients (639 versus 321; P < 0.0001), but stratification by HIV infection status did not alter the performance of this test. Combining the results of all three EIAs did not enhance the diagnostic performances of the individual assays. In Kenyan adults the sensitivities of the immune-complex EIAs could exceed that of blood cultures only at levels of specificity that were insufficient for the performance of vaccine efficacy studies.     

Stakeholders understanding of the concept of benefit sharing in health research in Kenya: a qualitative study

Background

Large-scale whole genome sequencing (WGS) studies promise to revolutionize cancer research by identifying targets for therapy and by discovering molecular biomarkers to aid early diagnosis, to better determine prognosis and to improve treatment response prediction. Such projects raise a number of ethical, legal, and social (ELS) issues that should be considered. In this study, we set out to discover how these issues are being handled across different jurisdictions.

Methods

We examined informed consent (IC) forms from 30 cancer genome sequencing studies to assess (1) stated purpose of sample collection, (2) scope of consent requested, (3) data sharing protocols (4) privacy protection measures, (5) described risks of participation, (6) subject re-contacting, and (7) protocol for withdrawal.

Results

There is a high degree of similarity in how cancer researchers engaged in WGS are protecting participant privacy. We observed a strong trend towards both using samples for additional, unspecified research and sharing data with other investigators. IC forms were varied in terms of how they discussed re-contacting participants, returning results and facilitating participant withdrawal. Contrary to expectation, there were no consistent trends that emerged over the eight year period from which forms were collected.

Conclusion

Examining IC forms from WGS studies elucidates how investigators are handling ELS challenges posed by this research. This information is important for ensuring that while the public benefits of research are maximized, the rights of participants are also being appropriately respected.     

Diagnosis of pneumococcal pneumonia by psaA PCR analysis of lung aspirates from adult patients in Kenya

psaA is the gene encoding pneumococcal surface adhesin A (PsaA), a 37-kDa protein expressed on the surface of Streptococcus pneumoniae. PCR primers for psaA have been shown to amplify the target DNA sequence in all 90 serotypes of S. pneumoniae and in none of 67 heterologous pathogens and colonizing bacteria of the upper respiratory tract. Pathogenic bacteria identified in lung aspirate specimens cannot normally be dismissed as contaminants or colonizers, which limit the assay specificity of other respiratory tract specimens. psaA PCR analysis was evaluated in 171 lung aspirates from Kenyan adults with acute pneumonia. The limit of detection was one genome equivalent. Sensitivity, estimated in 35 culture-positive lung aspirates, was 0.83 (95% confidence interval, 0.70 to 0.95). psaA PCR analysis extended the number of identifications of S. pneumoniae in lung aspirates from 35 on culture to 61 by both methods. Of 26 new pneumococcal diagnoses, 19 were corroborated by results of blood culture or urine antigen detection. Sequences of the PCR products from 12 positive samples were identical to the psaA target gene fragment. Using an internal control for the PCR, inhibition of psaA PCR was demonstrated in 17% (8 of 47) of false-negative specimens. The results of a control PCR for the human gene beta-actin suggested that false-negative psaA PCR results are attributable to problems of specimen collection, processing, or DNA extraction in 30% of cases (14 of 47). psaA PCR analysis is a sensitive tool for diagnosis of pneumococcal pneumonia in adults.     

Risk factors for pneumonia in urban-dwelling HIV-infected women: a case-control study in Nairobi,Kenya

In sub-Saharan Africa, respiratory tract infections (RTI) are the leading cause of serious morbidity and mortality in HIV-infected persons. This study sought to investigate demographic, socioeconomic, and environmental risk factors for pneumonia in a cohort of HIV-infected women. The authors performed a nested case-control study in a cohort of HIV-1-infected adults followed in Nairobi, Kenya. Thirty-nine women who developed pneumonia during the follow-up period were selected as cases, and 66 women who did not develop pneumonia were randomly chosen to serve as control subjects. A questionnaire was administered in subjects' homes that assessed demographics, home environment, and socioeconomic status. Women were followed in the cohort for a median of 36.8 months (range, 27.3-39.3). Adjusting for length of follow-up period, factors associated with lower socioeconomic status (lower monthly spending [OR = 3.2; 95% CI, 1.2-8.4 per 10,000 Kenyan shilling decrease], having no savings [OR = 4.1; 95% CI, 1.4-11.9], less sturdy home construction material such as mud or cement walls [OR = 2.6; 95% CI, 1.1-5.9] or dirt floors [OR = 2.8; 95% CI, 1.0-7.6], and lack of a window in the home [OR = 5.5; 95% CI, 0.9-32.2]) and being widowed (OR = 4.3; 95% CI, 1.2-15.1) or single (OR = 3.3; 95% CI, 1.0-11.2) were associated with an increased risk of pneumonia. In multivariate analysis, widowed (AOR = 5.9; 95% CI, 1.3-26.3), single (AOR = 7.7; 95% CI, 1.6-36.4), and divorced (AOR = 4.5; 95% CI, 1.0-20.1) women, those without savings (AOR = 3.7; 95% CI, 1.2-11.7), and those living in more crowded and contagious conditions (AOR = 1.5; 95% CI, 1.1-2.1) remained at increased risk of pneumonia. If confirmed by prospective investigation, these findings could help identify persons and subpopulations of HIV-infected women with the greatest risk of pneumonia.     

Epidemiology of hepatitis B in eastern Kenya

A cross-sectional survey of outpatients attending the three distinct hospitals in the towns of Mombasa, Kilifi, and Malindi was conducted to determine the patterns of hepatitis B transmission in eastern Kenya. Of 1,533 study subjects (mean age 21.9 +/- 13.2 years; range, 4 months to 80 years), 11.4% were positive for HBsAg and 56.2% were seropositive for at least one hepatitis B marker (HBsAg, anti-HBs, or anti-HBc). Anti-delta antibody was found in 1.2% of HBsAg-positive samples. HBeAg was found in 36.0% of HBsAg-positive samples obtained from women of childbearing age. The prevalence of seropositivity for hepatitis B markers was positively correlated with age, increasing from 20% in subjects less than 4 years old to more than 80% in study subjects greater than 40 years old. On multivariate analysis, male sex was found to be associated with HBsAg positivity, and age and previous deliveries of children were associated with seropositivity for any hepatitis marker (HBsAg, anti-HBs, or anti-HBc). An effective hepatitis B immunization strategy in this region of Kenya would require vaccination early in life because a major portion of hepatitis B transmission occurs in childhood.     

Situational analysis of leishmaniases research in Kenya

Leishmania spp are protozoan parasites of the Trypanosomatidae family that cause disease in humans and animals. In general, infections with these parasites can be divided into three main forms namely, cutaneous, mucocutaneous, and visceral leishmaniases. The disease is prevalent in many tropical and subtropical regions of the world, where it is transmitted via the bite of an infected sand fly. Leishmaniasis has been known to be endemic in parts of Kenya from as far back as early in the 20th century. These endemic areas include Turkana, Baringo, Kitui, Machakos, Meru, West Pokot and Elgeyo Marakwet districts which have been reported to be endemic for kala-azar. Recent outbreaks of VL have been reported in the previously non-endemic districts of Wajir and Mandera in North Eastern Kenya between May 2000 and August 2001. The vector for VL in Kenya is Phlebotomus martini though other vectors including P. orientalis have been reported. Baringo district is the only foci reported where both VL and CL are known to occur in Kenya. The aetiological agents for CL which include L. major which has been reported in Baringo; L. tropica in Laikipia, Samburu, Isiolo, Nakuru and Nyandarua districts while L. aethiopica has been reported in the Mt Elgon area. In Kenya, P. duboscqi, P. guggisbergi have been shown to be the vectors of L. major and L. tropica, respectively, while P. pediffer, P. longipes and P. elgonensis have been implicated as vectors of L. aethiopica. Since 1980, the Kenya Medical Research Institute (KEMRI) has spearheaded research on leishmaniases research in Kenya focusing on various aspects including characterization of Leishmania species, biology, and ecology of sand fly vectors, development of biological strategies for sand fly control, identification of animal reservoirs, diagnosis, new treatment strategies, new chemotherapeutic agents, and vaccine-related studies. KEMRI, a founding partner of the Drugs for Neglected Disease Initiative (DNDi), whose overall aim is to address lack of new or improved drugs for neglected diseases (which include leishmaniases, malaria, trypanosomiasis and Chagas disease) has made major contributions in leishmaniases research and control in Kenya and the eastern Africa region.     

Molecular epidemiology of measles virus in Kenya

Measles causes significant morbidity and mortality globally. Many countries have embarked on immunization programs to control and prevent measles outbreaks and eventually to eliminate endemic measles. Kenya is currently in the outbreak control and prevention stage for measles. Measles virus genotyping is important for molecular epidemiological purposes, including the documentation of the elimination of endemic measles virus strains from a country, and mapping of transmission pathways. In this study, we collected clinical specimens from measles outbreak cases in 2002 in Kenya for measles virus genotyping. We were able to isolate and/or detect measles virus in 10 cases from 5 of the 8 provinces in Kenya. All these Kenyan measles strains were determined to be genotype D4 strains when compared to the standard World Health Organization-designated measles virus reference strains. Interestingly, the Kenyan D4 strains clustered into two distinct D4 subgroups. In addition, the inclusion of other published D4 measles strains in this analysis indicated that there are four distinct D4 clusterings, or subgroups: Montreal-like, India-like, Johannesburg-like, and Ethiopia-like. This is the first measles molecular epidemiology study in Kenya and establishes the current endemic measles strain as genotype D4. Importantly, this study shows that the Kenyan D4 strains are distinct from the B3 measles strain found in West Africa and the D4 strains reported in Ethiopia.     

Characterization of multidrug-resistant typhoid outbreaks in Kenya

We characterized by antibiotic susceptibility, plasmid analysis, incompatibility grouping, and pulsed-field gel electrophoresis (PFGE) of XbaI- and SpeI-digested DNA 102 Salmonella enterica serovar Typhi (serovar Typhi) isolated from recent outbreaks of typhoid in three different parts of Kenya. Only 13.7% were fully susceptible, whereas another 82.4% were resistant to each of the five commonly available drugs: ampicillin, chloramphenicol, and tetracycline (MICs of >256 microg/ml); streptomycin (MIC, >1,024 microg/ml); and cotrimoxazole (MIC of >32 microg/ml). Resistance to these antibiotics was encoded on a 110-kb self-transferable plasmid of IncHI1 incompatibility group. The MICs of nalidixic acid (MIC, 8 to 16 micro g/ml) and ciprofloxacin (MIC of 0.25 to 0.38 micro g/ml) for 41.7% of the 102 serovar Typhi isolates were 5- and 10-fold higher, respectively, than for sensitive strains. Amplification by PCR and sequencing of the genes coding for gyrase (gyrA and gyrB) and topoisomerase IV (parE and parC) within the quinolone resistance-determining region revealed that the increase in the MICs of the quinolones had not resulted from any significant mutation. Analysis of genomic DNA from both antimicrobial agent-sensitive and multidrug-resistant serovar Typhi by PFGE identified two distinct subtypes that were in circulation in the three different parts of Kenya. As the prevalence of multidrug-resistant serovar Typhi increases, newer, more expensive, and less readily available antimicrobial agents will be required for the treatment of typhoid in Kenya.     

Portal hypertension in Nairobi, Kenya

Previous reports have suggested that idiopathic portal hypertension, a condition quite distinct from tropical splenomegaly syndrome, occurs in Kenya. In the present study patients with oesophageal varices were allocated to diagnostic groups on the basis of liver histology and results of splenoportovenography , and these groups were then compared for prevalence of hepatitis B markers, immunoglobulin levels and results of enzyme-linked immunosorbant assay (ELISA) for S. mansoni infection. 85 patients with oesophageal varices were studied. 29.4% had histological evidence of Schistosoma mansoni infection, 20% had cirrhosis and in 25.9% liver histology was non-diagnostic and the portal vein was radiologically shown to be patent. A comparison of clinical findings, serological data and parasitological investigations suggested that this latter group was a distinct one, and did no result from failure of histological diagnosis of cirrhosis or schistosomiasis. It is likely that these patients had idiopathic portal hypertension. In 82 normal controls, the carrier rate of hepatitis B surface antigen (HBsAg) was 12.2%, 59.8% had antibody to HBsAg (anti-HBs) and 7.3% showed antibody to core antigen (anti-HBc) as the only viral marker. 58.3% of the cirrhotics and 26.7% of patients with probable idiopathic portal hypertension were HbsAg positive. The implications of these results, and limited data on hepatitis Be antigen and antibody are discussed.     

Markers in HIV associated tuberculosis in Kenya

Tuberculosis is one of the most frequent opportunistic infections in HIV-infected patients in developing countries. In some instances, manifestations of pulmonary tuberculosis precede all other HIV related signs and symptoms because of the high virulence of M. tuberculosis. In order to characterise the interaction between these two pathogens, clinical and immunological parameters in pulmonary tuberculosis patients with and without HIV infection were compared. Amongst newly diagnosed pulmonary tuberculosis patients the association of some of these changes with the clinical outcome were evaluated. Of these, 44% were co-infected with HIV. Pulmonary tuberculosis patients with HIV-1 presented more frequently with lymphadenopathy and diarrhoea than those without HIV-1. Peripheral blood CD4+ counts were significantly lower in patients with pulmonary tuberculosis with HIV-1 than those with pulmonary tuberculosis alone, P= 0.0292. Low CD4+ lymphocyte counts, lymphadenopathy and BCG scar absence could serve as indicators of HIV-1 infection in pulmonary tuberculosis (PTB) patients.     

Global update: Kenya

In Uganda, medical researchers at Makerere University in Kampala compared data on 280 HIV-seropositive people with HIV infection symptoms and CD4 lymphocyte counts less than 300, who took 150 IU/day oral interferon alpha, with 280 matched controls who took a placebo to learn whether low-dose oral interferon alpha benefits symptomatic HIV-infected patients. The study lasted 5 months. Mortality, progression of HIV infection, ability to care for oneself, symptoms, body weight, and CD4 lymphocyte counts were similar in both case and control groups. No one reverted to HIV seronegative. The findings of a smaller study in 1990 conducted by the Kenyan Medical Research Institute showed that low doses of oral interferon alpha began to alleviate AIDS symptoms within days after beginning treatment and completely alleviated symptoms in all patients within 8-10 weeks. The study reported that 18 patients reverted to HIV seronegativity. It did not have a control group. THe study lasted at least 10 weeks and consisted of 199 symptomatic and 5 asymptomatic patients. Based on the findings of the Uganda study, the World Health Organization has decided that low-dose oral interferon alpha does not help HIV-seropositive individuals and cannot rid the body of HIV.     

Enterotoxin-like factors of Aeromonas species isolated in Kenya

Three out of thirteen Aeromonas strains tested have a heat-labile enterotoxin-like factor which does not cross-react with cholera toxin serologically, but evokes fluid accumulation in the gut of infant mouse, and causes Chinese Hamster Ovary cell elongation.