Population structure, biogeography and transmissibility of Mycobacterium tuberculosis.

Mycobacterium tuberculosis is a clonal pathogen proposed to have co-evolved with its human host for millennia, yet our understanding of its genomic diversity and biogeography remains incomplete. Here we use a combination of phylogenetics and dimensionality reduction to reevaluate the population structure of M. tuberculosis, providing an in-depth analysis of the ancient Indo-Oceanic Lineage 1 and the modern Central Asian Lineage 3, and expanding our understanding of Lineages 2 and 4. We assess sub-lineages using genomic sequences from 4939 pan-susceptible strains, and find 30 new genetically distinct clades that we validate in a dataset of 4645 independent isolates. We find a consistent geographically restricted or unrestricted pattern for 20 groups, including three groups of Lineage 1. The distribution of terminal branch lengths across the M. tuberculosis phylogeny supports the hypothesis of a higher transmissibility of Lineages 2 and 4, in comparison with Lineages 3 and 1, on a global scale. We define an expanded barcode of 95 single nucleotide substitutions that allows rapid identification of 69 M. tuberculosis sub-lineages and 26 additional internal groups. Our results paint a higher resolution picture of the M. tuberculosis phylogeny and biogeography.

Population-based resistance of Mycobacterium tuberculosis isolates to pyrazinamide and fluoroquinolones: results from a multicountry surveillance project.

BACKGROUND: Pyrazinamide and fluoroquinolones are essential antituberculosis drugs in new rifampicin-sparing regimens. However, little information about the extent of resistance to these drugs at the population level is available. METHODS: In a molecular epidemiology analysis, we used population-based surveys from Azerbaijan, Bangladesh, Belarus, Pakistan, and South Africa to investigate resistance to pyrazinamide and fluoroquinolones among patients with tuberculosis. Resistance to pyrazinamide was assessed by gene sequencing with the detection of resistance-conferring mutations in the pncA gene, and susceptibility testing to fluoroquinolones was conducted using the MGIT system. FINDINGS: Pyrazinamide resistance was assessed in 4972 patients. Levels of resistance varied substantially in the surveyed settings (3·0-42·1%). In all settings, pyrazinamide resistance was significantly associated with rifampicin resistance. Among 5015 patients who underwent susceptibility testing to fluoroquinolones, proportions of resistance ranged from 1·0-16·6% for ofloxacin, to 0·5-12·4% for levofloxacin, and 0·9-14·6% for moxifloxacin when tested at 0·5 µg/mL. High levels of ofloxacin resistance were detected in Pakistan. Resistance to moxifloxacin and gatifloxacin when tested at 2 µg/mL was low in all countries. INTERPRETATION: Although pyrazinamide resistance was significantly associated with rifampicin resistance, this drug may still be effective in 19-63% of patients with rifampicin-resistant tuberculosis. Even though the high level of resistance to ofloxacin found in Pakistan is worrisome because it might be the expression of extensive and unregulated use of fluoroquinolones in some parts of Asia, the negligible levels of resistance to fourth-generation fluoroquinolones documented in all survey sites is an encouraging finding. Rational use of this class of antibiotics should therefore be ensured to preserve its effectiveness. FUNDING: Bill & Melinda Gates Foundation, United States Agency for International Development, Global Alliance for Tuberculosis Drug Development.

Health system delay in treatment of multidrug resistant tuberculosis patients in Bangladesh.

BACKGROUND: Bangladesh is one of the 27 high burden countries for multidrug resistant tuberculosis listed by the World Health Organization. Delay in multidrug resistant tuberculosis treatment may allow progression of the disease and affect the attempts to curb transmission of drug resistant tuberculosis. The main objective of this study was to investigate the health system delay in multidrug resistant tuberculosis treatment in Bangladesh and to explore the factors related to the delay. METHODS: Information related to the delay was collected as part of a previously conducted case-control study. The current study restricts analysis to patients with multidrug resistant tuberculosis who were diagnosed using rapid diagnostic methods (Xpert MTB/RIF or the line probe assay). Information was collected by face-to-face interviews and through record reviews from all three Government hospitals providing multidrug resistant tuberculosis services, from September 2012 to April 2013. Multivariable regression analysis was performed using Bootstrap variance estimators. Definitions were as follows: Provider delay: time between visiting a provider for first consultation on MDR-TB related symptom to visiting a designated diagnostic centre for testing; Diagnostic delay: time from date of diagnostic sample provided to date of result; Treatment initiation delay: time between the date of diagnosis and date of treatment initiation; Health system delay: time between visiting a provider to start of treatment. Health system delay was derived by adding provider delay, diagnostic delay and treatment initiation delay. RESULTS: The 207 multidrug resistant tuberculosis patients experienced a health system delay of median 7.1 weeks. The health system delay consists of provider delay (median 4 weeks), diagnostic delay (median 5 days) and treatment initiation delay (median 10 days). Health system delay (Coefficient: 37.7; 95 %; CI 15.0-60.4; p 0.003) was associated with the visit to private practitioners for first consultation. CONCLUSIONS: Diagnosis time for multidrug resistant tuberculosis was fast using the rapid tests. However, some degree of delay was present in treatment initiation, after diagnosis. The most effective way to reduce health system delay would be through strategies such as engaging private practitioners in multidrug resistant tuberculosis control.

Factors related to previous tuberculosis treatment of patients with multidrug-resistant tuberculosis in Bangladesh.

OBJECTIVE: Previous tuberculosis (TB) treatment status is an established risk factor for multidrug-resistant TB (MDR-TB). This study explores which factors related to previous TB treatment may lead to the development of multidrug resistant in Bangladesh. DESIGN: We previously conducted a large case-control study to identify risk factors for developing MDR-TB in Bangladesh. Patients who had a history of previous TB treatment, either MDR-TB or non-MDR-TB, were interviewed about their previous treatment episode. This study restricts analysis to the strata of patients who have been previously treated for TB. Information was collected through face-to-face interviews and record reviews. Unadjusted and multivariable logistic regression was used for data analysis. SETTING: Central-level, district-level and subdistrict-level hospitals in rural and urban Bangladesh. RESULTS: The strata of previously treated patients include a total of 293 patients (245 current MDR-TB; 48 non-MDR-TB). Overall, 54% of patients received previous TB treatment more than once, and all of these patients were multidrug resistant. Patients with MDR-TB were more likely to have experienced the following factors: incomplete treatment (OR 4.3; 95% CI 1.7 to 10.6), adverse reactions due to TB treatment (OR 8.2; 95% CI 3.2 to 20.7), hospitalisation for symptoms associated with TB (OR 16.9; CI 1.8 to 156.2), DOTS (directly observed treatment, short-course) centre as treatment unit (OR 6.4; CI 1.8 to 22.8), supervised treatment (OR 3.8; CI 1.6 to 9.5); time-to-treatment centre (OR 0.984; CI 0.974 to 0.993). CONCLUSIONS: Incomplete treatment, hospitalisation for TB treatment and adverse reaction are the factors related to previous TB treatment of patients with MDR-TB. Although the presence of supervised treatment (DOT), less time-to-treatment centres and being treated in DOTS centres were relatively higher among the patients with MDR-TB compared with patients without MDR-TB, these findings include information of their most recent TB treatment episode only. Most (64.5%) of the patients with MDR-TB had received TB treatment more than once.

The Multi-Drug Resistant Tuberculosis Diagnosis and Treatment Cascade in Bangladesh.

OBJECTIVES: To determine, in areas supported by BRAC, Bangladesh i) the pre-diagnosis and pre-treatment attrition among presumptive and confirmed Multi-Drug Resistant Tuberculosis (MDR-TB) patients and ii) factors associated with attrition. METHODS: This was a retrospective cohort study involving record review. Presumptive MDR-TB patients from peripheral microscopy centres serving 60% of the total population of Bangladesh were included in the study. Attrition and turnaround time for MDR-TB diagnosis by Xpert MTB/RIF and treatment initiation were calculated between July 2012 and June 2014. RESULTS: Of 836 presumptive MDR-TB patients referred from 398 peripheral microscopy centres, 161 MDR-TB patients were diagnosed. The number of diagnosed MDR-TB patients was less than country estimates of MDR-TB patients (2000 cases) during the study period. Among those referred, pre-diagnosis and pre-treatment attrition was 17% and 21% respectively. Median turnaround time for MDR-TB testing, result receipt and treatment initiation was four, zero and five days respectively. Farmers (RR=2.3, p=0.01) and daily wage laborers (RR=2.1, p=0.04) had twice the risk of having pre-diagnosis attrition. Poor record-keeping and unreliable upkeep of presumptive MDR-TB patient databases were identified as challenges at the peripheral microscopy centres. CONCLUSION: There was a low proportion of pre-diagnosis and pre-treatment attrition in patients with presumptive and confirmed MDR-TB under programmatic conditions. However, the recording and reporting system did not detect all presumptive MDR-TB patients, highlighting the need to improve the system in order to prevent morbidity, mortality and transmission of MDR-TB in the community.

Knowledge and attitude of key community members towards tuberculosis: mixed method study from BRAC TB control areas in Bangladesh.

BACKGROUND: Bangladesh National Tuberculosis (TB) Control Programme adopted a number of strategies to facilitate TB diagnosis and treatment. 'Advocacy, Communication and Social Mobilization' (ACSM) was one of the key strategies implemented by BRAC (Bangladesh Rural Advancement Committee, a non-governmental development organization) TB control program. The purpose of this study is to assess the knowledge and attitudes of the key community members (KCMs) participated in ACSM in BRAC TB control areas. METHODS: This study combined quantitative and qualitative methods using a mixed method approach. KCMs in three districts with low TB case detection rates were targeted to assess the ACSM program. The quantitative survey using a multi-stage random-sampling strategy was conducted among 432 participants. The qualitative study included in-depth interviews (IDIs) of a sub sample of 48 respondents. For quantitative analysis, descriptive statistics were reported using frequencies, percentages, and Chi square tests, while thematic analysis was used for qualitative part. RESULTS: Most (99%) of the participants had heard about TB, and almost all knew that TB is a contagious yet curable disease. More than half (53%) of the KCMs had good knowledge regarding TB, but BRAC workers were found to be more knowledgeable compared to other KCMs. However, considerable knowledge gaps were observed among BRAC community health workers. Qualitative results revealed that the majority of the KCMs were aware about the signs, symptoms and transmission pathways of TB and believed that smoking and addiction were the prime causes of transmission of TB. The knowledge about child TB was poor even among BRAC health workers. Stigma associated with TB was not uncommon. Almost all respondents expressed that young girls diagnosed with TB. CONCLUSIONS: This study finding has revealed varying levels of knowledge and mixed attitudes about TB among the KCMs. It also provides insight on the poor knowledge regarding child TB and indicate that despite the significant success of the TB program stigma is yet prevalent in the community. Future ACSM activities should engage community members against stigma and promote child TB related information for further improvement of BRAC TB Control Programme.

Factors associated with poor knowledge among adults on tuberculosis in Bangladesh: results from a nationwide survey.

INTRODUCTION: In 2012, Bangladesh continues to be one of the 22 high tuberculosis (TB) burden countries in the world. Although free diagnosis and management for TB is available throughout the country, case notification rate/100,000 population for new smear positive (NSP) cases under the national TB control programme (NTP) remained at around 70/100,000 population and have not changed much since 2006. Knowledge on TB disease, treatment and its management could be an important predictor for utilization of TB services and influence case detection under the NTP. Our objective is to describe knowledge of TB among newly diagnosed TB cases and community controls to assess factors associated with poor knowledge in order to identify programmatic implications for control measures. METHODS: Embedded in TB prevalence survey 2007-2009, we included 240 TB cases from the TB registers and 240 persons ≥ 15 years of age randomly selected from the households where the survey was implemented. All participants were interviewed using a structured, pre-tested questionnaire to evaluate their TB knowledge. Regression analyses were done to assess associations with poor knowledge of TB. RESULTS: Our survey documented that overall there was fair knowledge in all domains investigated. However, based on the number of correct answers to the questionnaires, community controls showed significantly poorer knowledge than the TB cases in the domains of TB transmission (80% vs. 88%), mode of transmission (67% vs. 82%), knowing ≥ 1 suggestive symptoms including cough (78% vs. 89%), curability of TB (90% vs. 98%) and availability of free treatment (75% vs. 95%). Community controls were more likely to have poor knowledge of TB issues compared to the TB cases even after controlling for other factors such as education and occupation in a multivariate model (OR 3.46, 95% CI: 2.00-6.09). CONCLUSIONS: Knowledge on various aspects of TB and TB services varies significantly between TB cases and community controls in Bangladesh. The overall higher levels of knowledge in TB cases could identify them as peer educators in ongoing communication approaches to improve care seeking behavior of the TB suspects in the community and hence case detection.

Development of multidrug resistant tuberculosis in Bangladesh: a case-control study on risk factors.

OBJECTIVE: To determine the risk factors for developing multidrug resistant tuberculosis in Bangladesh. METHODS: This case-control study was set in central, district and sub-district level hospitals of rural and urban Bangladesh. Included were 250 multidrug resistant tuberculosis (MDR-TB) patients as cases and 750 drug susceptible tuberculosis patients as controls. We recruited cases from all three government hospitals treating MDR-TB in Bangladesh during the study period. Controls were selected randomly from those local treatment units that had referred the cases. Information was collected through face-to-face interviews and record reviews. Unadjusted and multivariable logistic regression were used to analyse the data. RESULTS: Previous treatment history was shown to be the major contributing factor to MDR-TB in univariate analysis. After adjusting for other factors in multivariable analysis, age group "18-25" (OR 1.77, CI 1.07-2.93) and "26-45" (OR 1.72, CI 1.12-2.66), some level of education (OR 1.94, CI 1.32-2.85), service and business as occupation (OR 2.88, CI 1.29-6.44; OR 3.71, CI 1.59-8.66, respectively), smoking history (OR 1.58, CI 0.99-2.5), and type 2 diabetes (OR 2.56 CI 1.51-4.34) were associated with MDR-TB. Previous treatment was not included in the multivariable analysis as it was correlated with multiple predictors. CONCLUSION: Previous tuberculosis treatment was found to be the major risk factor for MDR-TB. This study also identified age 18 to 45 years, some education up to secondary level, service and business as occupation, past smoking status, and type 2 diabetes as comorbid illness as risk factors. National Tuberculosis programme should address these risk factors in MDR-TB control strategy. The integration of MDR-TB control activities with diabetes and tobacco control programmes is needed in Bangladesh.

Care seeking in tuberculosis: results from a countrywide cluster randomised survey in Bangladesh.

OBJECTIVES: To explore systematically the care seeking trajectories of tuberculosis (TB) cases up to four subsequent places of care and to assess the type of services provided at each place. METHODS: TB cases detected actively during the 2007-2009 national TB prevalence survey and passively under the routine programme in the same period were interviewed by administering a standardised questionnaire. Care seeking and services provided up to four subsequent points were explored. Care seeking was further explored by categorising the providers into formal, informal and 'self-care' groups. RESULTS: A total of 273 TB cases were included in this study, of which 33 (12%) were detected during the survey and 240 (88%) from the TB registers. Out of the 118 passively detected cases who first sought care from an informal provider, 52 (44.1%) remained in the informal sector at the second point of care. Similarly, out of the 52, 17 (32.7%) and out of the 17, 5 (29.4%) remained in the informal sector at the third and fourth subsequent points of care, respectively. All the 33 actively detected cases had 'self-care' at the first point, and 27 (81.8%) remained with 'self-care' up to the fourth point of care. Prescribing drugs (59-99%) was the major type of care provided by the formal and informal care providers at each point and was limited to the non-existent practice of investigation or referrals. CONCLUSIONS: Free TB services are still underutilised by TB cases and informal caregivers remained the major care providers for such cases in Bangladesh. In order to improve case detection, it is necessary that the National Tuberculosis Programme immediately takes effective initiatives to engage all types of care providers, particularly informal providers who are the first point of care for the majority of the TB suspects.

Training of community healthcare providers and TB case detection in Bangladesh.

BACKGROUND: For several years, BRAC (previously known as the Bangladesh Rural Advancement Committee) has been assisting with national TB control efforts in Bangladesh and has especially focused on training of community healthcare personnel. This study attempts to determine whether there is any association between a community-based TB training programme in peri-urban Dhaka and TB case finding within the same catchment area. METHODS: This was a cross-sectional retrospective study using laboratory sputum registers and annual BRAC training reports. RESULTS: Between 2005 and 2010, there were 536 training activities for community healthcare providers with 9037 people trained. Numbers of patients attending laboratories with suspected TB increased from 8211 in 2004 (before training) to 10 961 in 2005 (start of training) with the proportion diagnosed with smear-positive TB increasing from 7.1% to 11.2%. Thereafter, the numbers with suspected and diagnosed TB remained similar up to 2010. The most important sources of referral of patients for investigation were community health volunteers and self-referring patients accounting for 58% of all patients. CONCLUSION: In this operational research study in peri-urban Dhaka, there was an initial increase in TB case finding with numbers then reaching a plateau despite continued training activities. Further prospective evaluation is required to understand these phenomena.

Effectiveness of involving the private medical sector in the National TB Control Programme in Bangladesh: evidence from mixed methods.

OBJECTIVES: In Bangladesh, private healthcare is common and popular, regardless of income or area of residence, making the private sector an important player in health service provision. Although the private sector offers a good range of health services, tuberculosis (TB) care in the private sector is poor. We conducted research in Dhaka, between 2004 and 2008, to develop and evaluate a public-private partnership (PPP) model to involve private medical practitioners (PMPs) within the National TB Control Programme (NTP)'s activities. Since 2008, this PPP model has been scaled up in two other big cities, Chittagong and Sylhet. This paper reports the results of this development, evaluation and scale-up. DESIGN: Mixed method, observational study design. We used NTP service statistics to compare the TB control outcomes between intervention and control areas. To capture detailed insights of PMPs and TB managers about the process and outcomes of the study, we conducted in-depth interviews, focus group discussions and workshops. SETTING: Urban setting, piloted in four areas in Dhaka city; later scaled up in other areas of Dhaka and in two major cities. FINDINGS: The partnership with PMPs yielded significantly increased case finding of sputum smear-positive TB cases. Between 2004 and 2010, 703 participating PMPs referred 3959 sputum smear-positive TB cases to the designated Directly Observed Treatment, Short-course (DOTS) centres, contributing about 36% of all TB cases in the project areas. There was a steady increase in case notification rates in the project areas following implementation of the partnership. CONCLUSIONS: The PPP model was highly effective in improving access and quality of TB care in urban settings.