Anti-tuberculosis drug resistance in Nairobi, Kenya

Background: Drug resistant tuberculosis (TB) which is a state when Mycobaterium tuberculosis (MTB) organisms are resistant to antimicrobial agents at the levels attainable in blood and tissue pose a serious threat to TB control programs. Limited information exists on the exact prevalence of resistance to anti-tuberculosis drugs in populations with high rates of tuberculosis and HIV co-infection such as those in Nairobi, Kenya. Setting: A cross sectional study was conducted among new and previously treated consecutive sputum smear positive pulmonary tuberculosis (PTB) patients of 14 years and older at 16 diagnostic and treatment facilities in Nairobi, Kenya, between February and August 2010. Objective: To determine the magnitude of drug resistance to first line antituberculosis drugs among MTB isolates obtained from a study addressing the diagnosis and epidemiology of drug resistant tuberculosis in Nairobi, Kenya. Methods: Sputum samples from patients with bacteriologically confirmed PTB on microscopy were cultured on Lowenstein Jensen (LJ) media. Participants were offered diagnostic testing and counselling for HIV testing. Strains of MTB complex from Lowenstein Jensen (LJ) slopes were subjected to drug susceptibility testing (DST) to isoniazid (H), rifampicin (R), streptomycin (S), and ethambutol (E) using the proportional method on the Mycobacterium Growth Indicator Tube (MGIT) conventional method. Results: A total of 595 TB patients had their MTB strains DST done. Of the 568 (95.4%) patients who had valid results for analysis, 369 were new and 199 previously treated. About eighty five percent and seventy seven percent of the strains from new patients and previously treated patients were fully sensitive to all the drugs tested respectively. Any resistance to isoniazid, streptomycin, ethambutol and rifampicin was 10.3%, 4.3%, 5.1% and 0.81% respectively among new patients. Among previously treated patients any resistance to isoniazid, streptomycin, ethambutol and rifampicin was 18.1%, 10.5%, 7.03% and 9.04% respectively. The prevalence of MDR TB defined as resistant to at least both isoniazid and rifampicin was 0.54% and 8.54% among new and previously treated patients respectively. Conclusion: The study found high levels of drug resistant TB in Nairobi compared to other previous studies done in the country. MDR TB in Kenya is now a reality and the situation in Nairobi being the largest cosmopolitant city is worrying. The upword trend of MDR TB in Nairobi is course of concern. This calls for urgent concerted efforts to address the problem especially the strenghthening of the implementation of the comprehensive framework of the DOTS-Plus strategy for appropriate management of MDR-TB

Diversity of Mycobacterium tuberculosis strains in Nairobi, Kenya

Setting: Tuberculosis (TB) patients attending 16 public health facilities in Nairobi, Kenya. Objective: To determine the Mycobacterium tuberculosis (M.tuberculosis) strain families circulating in Nairobi, Kenya. Methods: Sputum specimens from consecutive new and previously treated smear positive pulmonary TB patients were collected between February and August 2010 and cultured on Lowenstein9Jensen media. Spoligotyping was done on DNA extracted from the first isolate of each patient. The international spoligotype data base (SpolDB4) was used to group isolates into strain families. Results: Fourty seven different strain families were identified from 536 isolates. The principal groups were; CAS1_KILI 96/536 (17%), T1 69/536 (12%), Beijing 65/536 (12%), LAM9 46/536 (9% ), LAM3 & S/Conversant 37/536 (7% ), LAM11_ZWE 26/536 (5%), CAS1_DELHI 24/536 (4%) and T2 24/536 (4%). Others identified and are found in the SpolDB4 were 113/536 (21%). A possible new M.tuberculosis strain family was identified with 21/536 (4%) isolates which was designated as Nairobi subtype. Others identified not previously included in the SpolDB4 accounted for 15/536 (3%). Conclusion: We found a diverse array of M.tuberculosis strain families which could be indicative of a cosmopolitant polulation with frequent migration that may suggest that the dorminant strain families may have been present in the population for an extended period of time or on going transmision of closely related strains families. The emergence of the Beijing strains poses a serious threat to TB control due to its high virulence and frequent association with multidrug resistance. We therefore call for strenghthening efforts on early case finding through enhanced public health education campains and provision of accessible diagnostic services with enhanced treatment compliance

Spatial-temporal distribution and sequence diversity of Group A human respiratory syncytial viruses in Kenya preceding the emergence of ON1 genotype

Background Human respiratory syncytial virus (HRSV) is a major cause of severe viral acute respiratory illness and contributes significantly to severe pneumonia cases in Africa. Little is known about its spatial–temporal distribution as defined by its genetic diversity. Methods A retrospective study conducted utilizing archived nasopharyngeal specimens from patients attending outpatient clinics in hospitals located in five demographically and climatically distinct regions of Kenya; Coast, Western, Highlands, Eastern and Nairobi. The viral total RNA was extracted and tested using multiplex real time RT-PCR (reverse transcriptase polymerase chain reaction). A segment of the G-gene was amplified using one-step RT-PCR and sequenced by Sanger di-deoxy method. Bayesian analysis of phylogeny was utilized and subsequently median joining methods for haplotype network reconstruction. Results Three genotypes of HRSVA were detected; GA5 (14.0%), GA2 (33.1%), and NA1 (52.9%). HRSVA prevalence varied by location from 33% to 13.2% in the Highlands and the Eastern regions respectively. The mean nucleotide diversity (Pi[π]) varied by genotype: highest of 0.018 for GA5 and lowest of 0.005 for NA1. A total of 58 haplotypes were identified (GA5 10; GA2 20; NA1 28). These haplotypes were introduced into the population locally by single haplotypes and additional subsidiary seeds amongst the GA2 and the NA1 haplotypes. Conclusions HRSVA was found across all the regions throughout the study period and comprised three genotypes; GA5, GA2, and NA1 genotypes. The genotypes were disproportionately distributed across the regions with GA5 gradually increasing toward the Western zones and decreasing toward the Eastern zones of the country

Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages

Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.We thank S. Lecher, S. Li and J. Zallet for technical support. Calculations were performed at the sciCORE scientific computing core facility at the University of Basel. This work was supported by the Swiss National Science Foundation (grants 310030_166687 (S.G.) and 320030_153442 (M.E.) and Swiss HIV Cohort Study grant 740 to L.F.), the European Research Council (309540-EVODRTB to S.G.), TB-PAN-NET (FP7-223681 to S.N.), PathoNgenTrace projects (FP7-278864-2 to S.N.), SystemsX.ch (S.G.), the German Center for Infection Research (DZIF; S.N.), the Novartis Foundation (S.G.), the Natural Science Foundation of China (91631301 to Q.G.), and the National Institute of Allergy and Infectious Diseases (5U01-AI069924-05) of the US National Institutes of Health (M.E.)

Climate change responses among the Maasai Community in Kenya

© 2017, Springer Science+Business Media B.V. The impacts of climate change to the dryland areas of East Africa are especially strong, especially if it is considered that these areas have weak institutions and governance systems. Climate change has also affected many rural communities in a severe way, reducing crop yields and sometimes causing crop failure. In Kenya and Tanzania, where drylands cover over around 80 and 50% of their respective land areas, rural populations have been especially affected. Among them is the tribal group of the Maasai, legendary nomad warriors, who have been suffering from persistent droughts and the negative impacts on their cattle herds. This paper describes how climate change affects the Maasai communities in Kenya and the changes seen in their habits and diet, in order to adapt to a changing climate

Contemporary challenges of participatory field research for land use change analyses: examples from Kenya

This article discusses the evolution of participatory methods and their benefits and pitfalls in contributing to land use and land cover change (LULCC) analyses. Participation has become a practical means of developing a more complete assessment of societal change by bringing local people’s narratives and understandings to bear on the interpretation of data collected using more extractive methods, such as the household survey, or data collected remotely, such as satellite images. Their methodological value lies in their ability to provide insights into the local mediation of external political, economic, and cultural processes. However, the realization of these contributions to LULCC analysis requires sensitivity to community differentiation, competing narratives of change, and the broader social context in which participatory forums take place. Examples from Kenya suggest that participatory feedback workshops present distinct empirical advantages that allow researchers to develop an understanding of critical intersections of social and environmental change through a dialogical process whereby participants themselves frame the central categories and change processes