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

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.)

Comprehensive transcriptome of the maize stalk borer, Busseola fusca, from multiple tissue types, developmental stages, and parasitoid wasp exposures

International audienc

AfriMTE and AfriCOMET : Empowering COMET to Embrace Under-resourced African Languages

Despite the progress we have recorded in scaling multilingual machine translation (MT) models and evaluation data to several under-resourced African languages, it is difficult to measure accurately the progress we have made on these languages because evaluation is often performed on n-gram matching metrics like BLEU that often have worse correlation with human judgments. Embedding-based metrics such as COMET correlate better; however, lack of evaluation data with human ratings for under-resourced languages, complexity of annotation guidelines like Multidimensional Quality Metrics (MQM), and limited language coverage of multilingual encoders have hampered their applicability to African languages. In this paper, we address these challenges by creating high-quality human evaluation data with a simplified MQM guideline for error-span annotation and direct assessment (DA) scoring for 13 typologically diverse African languages. Furthermore, we develop AfriCOMET, a COMET evaluation metric for African languages by leveraging DA training data from high-resource languages and African-centric multilingual encoder (AfroXLM-Roberta) to create the state-of-the-art evaluation metric for African languages MT with respect to Spearman-rank correlation with human judgments (+0.406)

Community based initiatives to mainstream climate change adaptation into disaster risk reduction: evidence from the Hunter Valley (Australia)

In Australia, local communities often enact Community-Based Initiatives (CBIs) to respond to climate change through Climate Change Adaptation (CCA). CBIs can also be integrated into the Disaster Risk Reduction (DRR) agenda. The paper explores the extent to which CBIs promote the mainstreaming of CCA into DRR. Primary data were obtained from interviews with representatives of CBIs and supporting organisations in three local governments of the Hunter Valley (New South Wales, Australia). Findings show that CBIs recognise the potential contribution of climate change in modifying the local hazard profile. CBIs mainstream CCA into DRR by following four approaches: environmental and social justice; sustainability and transition; ecosystem-based approach; and adaptive planning. Partnerships were identified both among CBIs and between CBIs and City Councils; however, conflicts between CBIs, City Councils and business actors emerged, and a lack of commitment by multi-level governments in responding to climate change was revealed. The findings show that CBIs consider CCA and DRR within a broad everyday context related to vulnerability and local development. But we argue that assigning responsibility for climate change issues to CBIs is not a panacea and should not be the only local climate change response. Instead, CBIs need to be included in a larger and long-term commitment by actors that possess access to resources, such as higher levels of government. The paper provides a local Australian perspective on the effectiveness of mainstreaming CCA into DRR and furthers the conversation for the benefit of other communities facing similar challenges