Beijing clades of Mycobacterium tuberculosis are associated with differential survival in HIV-negative Russian patients.

We conducted a prospective study to establish factors associated with survival in tuberculosis patients in Russia including social, clinical and pathogen-related genetic parameters. Specifically we wished to determine whether different strains/clades of the Beijing lineage exerted a differential effect of survival. HIV-negative culture-confirmed cases were recruited during 2008-2010 across Samara Oblast and censored in December 2011. Molecular characterization was performed by a combination of spoligotyping, multilocus VNTR typing and whole genome sequencing (WGS). We analyzed 2602 strains and detected a high prevalence of Beijing family (n=1933; 74%) represented largely by two highly homogenous dominant clades A (n=794) and B (n=402) and non-A/non-B (n=737). Multivariable analysis of 1366 patients with full clinical and genotyping data showed that multi- and extensive drug resistance (HR=1.86; 95%CI: 1.52, 2.28 and HR=2.19; 95%CI: 1.55, 3.11) had the largest impact on survival. In addition older age, extensive lung damage, shortness of breath, treatment in the past and alcohol abuse reduced survival time. After adjustment for clinical and demographic predictors there was evidence that clades A and B combined were associated with poorer survival than other Beijing strains (HR=0.48; 95%CI 0.34, 0.67). All other pathogen-related factors (polymorphisms in genes plcA, plcB, plcC, lipR, dosT and pks15/1) had no effect on survival. In conclusion, drug resistance exerted the greatest effect on survival of TB patients. Nevertheless we provide evidence for the independent biological effect on survival of different Beijing family strains even within the same defined geographical population. Better understanding of the role of different strain factors in active disease and their influence on outcome is essential.

Analysis of undiagnosed tuberculosis-related deaths identified at post-mortem among HIV-infected patients in Russia: a descriptive study.

BACKGROUND: Tuberculosis remains a serious public health threat and economic burden in Russia with escalating rates of drug resistance against a background of growing HIV-epidemic. Samara Oblast is one of the regions of the Russian Federation where more than 1% of the population is affected by the HIV-epidemic; almost half of the cases are concentrated in the largely-industrial city of Togliatti with a population of 800 000. METHODS: We conducted a retrospective analysis of errors leading to death of HIV-positive patients in general health care hospitals in Togliatti, Russia, in 2008. All (n = 29) cases when tuberculosis was established at autopsy as a cause of death were included. RESULTS: Median length of hospital stay was 20 days; in 11 cases the death occurred within the first 24 hours of admission. All cases were known to be HIV-positive prior to admission, however HAART was not initiated for any case, and no relevant tests to assess severity of immunosupression were performed despite their availability. No appropriate diagnostic algorithms were applied to confirm tuberculosis. Major gaps were identified in the work of hospital and consulting physicians including insufficient records keeping. In almost all patients earlier regular HIV-relevant tests were not performed due to poor compliance of patients, many of whom abused alcohol and drugs. CONCLUSIONS: We conclude that introduction of prompt and accurate diagnostics tests, adequate treatment protocols and intensive training of physicians in management of AIDS and TB is vital. This should include reviewing standards of care for HIV-positive individuals with accompanying social problems.

Survival of civilian and prisoner drug-sensitive, multi- and extensive drug- resistant tuberculosis cohorts prospectively followed in Russia.

OBJECTIVE AND METHODS: A long-term observational study was conducted in Samara, Russia to assess the survival and risk factors for death of a cohort of non-multidrug resistant tuberculosis (non-MDRTB) and multidrug resistant tuberculosis (MDRTB) civilian and prison patients and a civilian extensive drug-resistant tuberculosis (XDRTB) cohort. RESULTS: MDRTB and XDRTB rates of 54.8% and 11.1% were identified in the region. Half (50%) of MDRTB patients and the majority of non-MDRTB patients (71%) were still alive at 5 years. Over half (58%) of the patients died within two years of establishing a diagnosis of XDRTB. In the multivariate analysis, retreatment (HR = 1.61, 95%CI 1.04, 2.49) and MDRTB (HR = 1.67, 95%CI 1.17, 2.39) were significantly associated with death within the non-MDR/MDRTB cohort. The effect of age on survival was relatively small (HR = 1.01, 95%CI 1.00, 1.02). No specific factor affected survival of XDRTB patients although median survival time for HIV-infected versus HIV-negative patients from this group was shorter (185 versus 496 days). The majority of MDRTB and XDRTB strains (84% and 92% respectively) strains belonged to the Beijing family. Mutations in the rpoB (codon 531 in 81/92; 88.8%), katG (mutation S315T in 91/92, 98.9%) and inhA genes accounted for most rifampin and isoniazid resistance respectively, mutations in the QRDR region of gyrA for most fluroquinolone resistance (68/92; 73.5%). CONCLUSIONS: Alarmingly high rates of XDRTB exist. Previous TB treatment cycles and MDR were significant risk factors for mortality. XDRTB patients' survival is short especially for HIV-infected patients. Beijing family strains comprise the majority of drug-resistant strains.

An integrated approach to rapid diagnosis of tuberculosis and multidrug resistance using liquid culture and molecular methods in Russia.

OBJECTIVE: To analyse the feasibility, cost and performance of rapid tuberculosis (TB) molecular and culture systems, in a high multidrug-resistant TB (MDR TB) middle-income region (Samara, Russia) and provide evidence for WHO policy change. METHODS: Performance and cost evaluation was conducted to compare the BACTEC MGIT 960 system for culture and drug susceptibility testing (DST) and molecular systems for TB diagnosis, resistance to isoniazid and rifampin, and MDR TB identification compared to conventional Lowenstein-Jensen culture assays. FINDINGS: 698 consecutive patients (2487 sputum samples) with risk factors for drug-resistant tuberculosis were recruited. Overall M. tuberculosis complex culture positivity rates were 31.6% (787/2487) in MGIT and 27.1% (675/2487) in LJ (90.5% and 83.2% for smear-positive specimens). In total, 809 cultures of M. tuberculosis complex were isolated by any method. Median time to detection was 14 days for MGIT and 36 days for LJ (10 and 33 days for smear positive specimens) and indirect DST in MGIT took 9 days compared to 21 days on LJ. There was good concordance between DST on LJ and MGIT (96.8% for rifampin and 95.6% for isoniazid). Both molecular hybridization assay results correlated well with MGIT DST results, although molecular assays generally yielded higher rates of resistance (by approximately 3% for both isoniazid and rifampin). CONCLUSION: With effective planning and logistics, the MGIT 960 and molecular based methodologies can be successfully introduced into a reference laboratory setting in a middle incidence country. High rates of MDR TB in the Russian Federation make the introduction of such assays particularly useful.

Performance of the Genotype MTBDRPlus assay in the diagnosis of tuberculosis and drug resistance in Samara, Russian Federation.

BACKGROUND: Russia is a high tuberculosis (TB) burden country with a high prevalence of multidrug resistant tuberculosis (MDRTB). Molecular assays for detection of MDRTB on clinical specimens are not widely available in Russia. RESULTS: We performed an evaluation of the GenoType MTBDRplus assay (HAIN Lifescience GmbH, Germany) on a total of 168 sputum specimens from individual patients at a public health laboratory in Central Russia, as a model of a middle income site in a region with high levels of drug resistance. Phenotypic drug resistance tests (DST) were performed on cultures derived from the same sputum specimens using the BACTEC 960 liquid media system.Interpretable GenoType MTBDRplus results were obtained for 154(91.7%) specimens with readability rates significantly higher in sputum specimens graded 2+ and 3+ compared to 1+ (RR = 1.17 95%CI 1.04-1.32). The sensitivity and specificity of the assay for the detection of rifampicin (RIF) and isoniazid (INH) resistance and MDR was 96.2%, 97.4%, 97.1% and 90.7%, 83.3%, 88.9% respectively. Mutations in codon 531 of the rpoB gene and codon 315 of the katG gene dominated in RIF and INH resistant strains respectively. Disagreements between phenotypical and molecular tests results (12 samples) could be explained by the presence of rare mutations in strains circulating in Russia and simultaneous presence of resistant and sensitive bacilli in sputum specimens (heteroresistance). CONCLUSION: High sensitivity, short turnaround times and the potential for screening large numbers of specimens rapidly, make the GenoType MTBDRplus assay suitable as a first-line screening assay for drug resistant TB.

Rates of latent tuberculosis in health care staff in Russia.

BACKGROUND: Russia is one of 22 high burden tuberculosis (TB) countries. Identifying individuals, particularly health care workers (HCWs) with latent tuberculosis infection (LTBI), and determining the rate of infection, can assist TB control through chemoprophylaxis and improving institutional cross-infection strategies. The objective of the study was to estimate the prevalence and determine the relative risks and risk factors for infection, within a vertically organised TB service in a country with universal bacille Calmette-Guérin (BCG) vaccination. METHODS AND FINDINGS: We conducted a cross-sectional study to assess the prevalence of and risk factors for LTBI among unexposed students, minimally exposed medical students, primary care health providers, and TB hospital health providers in Samara, Russian Federation. We used a novel in vitro assay (for gamma-interferon [IFN-gamma]) release to establish LTBI and a questionnaire to address risk factors. LTBI was seen in 40.8% (107/262) of staff and was significantly higher in doctors and nurses (39.1% [90/230]) than in students (8.7% [32/368]) (relative risk [RR] 4.5; 95% confidence interval [CI] 3.1-6.5) and in TB service versus primary health doctors and nurses: respectively 46.9% (45/96) versus 29.3% (34/116) (RR 1.6; 95% CI 1.1-2.3). There was a gradient of LTBI, proportional to exposure, in medical students, primary health care providers, and TB doctors: respectively, 10.1% (24/238), 25.5% (14/55), and 55% (22/40). LTBI was also high in TB laboratory workers: 11/18 (61.1%). CONCLUSIONS: IFN-gamma assays have a useful role in screening HCWs with a high risk of LTBI and who are BCG vaccinated. TB HCWs were at significantly higher risk of having LTBI. Larger cohort studies are needed to evaluate the individual risks of active TB development in positive individuals and the effectiveness of preventive therapy based on IFN-gamma test results.

Differentiation of tuberculosis strains in a population with mainly Beijing-family strains.

A high prevalence of tuberculosis (TB) isolates that are genetically homogenous and from the Beijing family has been reported in Russia. To map TB transmission caused by these strains, new genotyping systems are needed. Mycobacterial interspersed repetitive units (MIRUs) offer the possibility of rapid PCR-based typing with comparable discrimination to IS6110 restriction fragment length polymorphism techniques. Spoligotyping and detection of IS6110 insertion in the dnaA-dnaN region were used to identify Beijing strains in 187 Mycobacterium tuberculosis isolates from Samara, Russia. The Beijing isolates were analyzed by using 12-MIRU and 3-exact tandem repeats (ETR) loci and by an expanded set of 10 additional variable number tandem repeats loci. The expanded set of 25 MIRUs provided better discrimination than the original set of 15 (Hunter-Gaston diversity index 0.870 vs. 0.625). Loci MIRU 26, 1982, and 3232 were the most polymorphic in Beijing isolates.

Health-systems efficiency in the Russian Federation: tuberculosis control.

OBJECTIVE: To conduct a comprehensive assessment of the case-mix of patients admitted to tuberculosis hospitals and the reasons for their admission in four Russian regions: Ivanovo, Orel, Samara and Vladimir. We also sought to quantify the extent to which efficiency could be improved by reducing hospitalization rates and re-profiling hospital beds available in the tuberculosis-control system. METHODS: We used a standard questionnaire to determine how beds were being used and who was using the beds in tuberculosis facilities in four Russian regions. Data were collected to determine how 4306 tuberculosis beds were utilized as well as on the socioeconomic and demographic indicators, clinical parameters and reasons for hospitalization for 3352 patients. FINDINGS: Of the 3352 patients surveyed about 70% were male; the average age was 40; and rates of unemployment, disability and alcohol misuse were high. About one-third of beds were occupied by smear-positive or culture-positive tuberculosis patients; 20% were occupied by tuberculosis patients who were smear-negative and/or culture-negative; 20% were occupied by patients who no longer had tuberculosis; and 20% were unoccupied. If clinical and public health admission criteria were applied then < 50% of admissions would be justified and < 50% of the current number of beds would be required. Up to 85% of admissions and beds were deemed to be necessary when social problems and poor access to outpatient care were considered along with clinical and public health admission criteria. CONCLUSION: Much of the Russian Federation's large tuberculosis hospital infrastructure is unnecessary when clinical and public health criteria are used, but the large hospital infrastructure within the tuberculosis-control system has an important social support function. Improving the efficiency of the system will require the reform of health-system norms and regulations as they relate to resource allocation and clinical care and implementation of lower-cost approaches to case management for patients with social problems. Additionally, closer attention will need to be paid to the management of staff numbers in the tuberculosis system.

Drug-resistant tuberculosis, clinical virulence, and the dominance of the Beijing strain family in Russia.

CONTEXT: Tuberculosis and multidrug-resistant tuberculosis is a serious public health problem in Russia. OBJECTIVE: To address the extent of "Beijing strain" transmission in the prison/civil sectors and the association of drug resistance, clinical, and social factors with the Beijing genotype. DESIGN AND SETTING: Cross-sectional population-based molecular epidemiological study of all civilian and penitentiary tuberculosis facilities in the Samara region, Russia. PATIENTS: Consecutively recruited patients with bacteriologically proven tuberculosis (n = 880). MAIN OUTCOME MEASURE: Proportion of Beijing strains and association with drug resistance, human immunodeficiency virus infection, imprisonment, radiological, clinical, and other social factors. RESULTS: Beijing-family strains (identified by spoligotyping and composed of 2 main types by mycobacterial interspersed repetitive unit analysis) were predominant: 586/880 (66.6%; 95% confidence interval [CI], 63.4%-69.7%) with a significantly higher prevalence in the prison population (rate ratio [RR], 1.3; 95% CI, 1.2-1.5) and those aged younger than 35 years (RR, 1.2; 95% CI, 1.0-1.3). Comparable proportions were co-infected with the human immunodeficiency virus ( approximately 10%), concurrent hepatitis B and C (21.6%), drank alcohol ( approximately 90%), smoked ( approximately 90%), and had a similar sexual history. Drug resistance was nearly 2-fold higher in patients infected with Beijing strains compared with non-Beijing strains: multidrug resistance (RR, 2.4; 95% CI, 1.9-3.0), for isoniazid (RR, 1.8; 95% CI, 1.5-2.1), for rifampicin (RR, 2.2; 95% CI, 1.7-2.7), for streptomycin (RR, 1.9; 95% CI, 1.5-2.3), and for ethambutol (RR, 2.2; 95% CI, 1.6-3.2). Univariate analysis demonstrated that male sex (odds ratio [OR], 1.5; 95% CI, 1.1-1.9), advanced radiological abnormalities (OR, 3.3; 95% CI, 1.3-8.4), homelessness (OR, 5.6; 95% CI, 1.1-6.3), and previous imprisonment (OR, 2.0; 95% CI, 1.5-2.7) were strongly associated with Beijing-strain family disease. Multivariate analysis supported previous imprisonment to be a risk factor (OR, 2.0; 95% CI, 1.4-3.3) and night sweats to be less associated (OR 0.7; 95% CI, 0.5-1.0) with Beijing-strain disease. CONCLUSIONS: Drug resistance and previous imprisonment but not human immunodeficiency virus co-infection were significantly associated with Beijing-strain infection. There was evidence that Beijing isolates caused radiologically more advanced disease.

Antimicrobial prescribing patterns for respiratory diseases including tuberculosis in Russia: a possible role in drug resistance?

BACKGROUND: Inappropriate antibiotic prescribing exposes patients to the risk of side effects and encourages the development of drug resistance across antimicrobial groups used for respiratory infections including tuberculosis (TB). AIM: Determine among Russian general practitioners and specialists: (1) sources of antimicrobial prescribing information; (2) patterns of antimicrobial prescribing for common respiratory diseases and differences between primary and specialist physicians; (3) whether drug resistance in TB might be linked to over-prescribing of anti-TB drugs for respiratory conditions. METHODS: Point-prevalence cross-sectional survey involving all 28 primary care, general medicine and TB treatment institutions in Samara City, Russian Federation. In this two-stage study, a questionnaire was used to examine doctors' antimicrobial (including TB drugs) prescribing habits, sources of prescribing information, management of respiratory infections and a case scenario ('common cold'). This was followed by a case note review of actual prescribing for consecutive patients with respiratory diseases at three institutions. RESULTS: Initial questionnaires were completed by 81.3% (425/523) of physicians with 78.4% working in primary care. Most doctors used standard textbooks to guide their antimicrobial practice but 80% made extensive use of pharmaceutical company information. A minority of 1.7% would have inappropriately prescribed antibiotics for the case and 0.8-1.8% of respondents would have definitely prescribed TB drugs for non-TB conditions. Of the 495 respiratory cases, 25% of doctors prescribed an antibiotic for a simple upper respiratory tract infection and of 8 patients with a clinical diagnosis of TB, 4 received rifampicin monotherapy alone. Ciprofloxacin was widely but inappropriately used. CONCLUSION: Doctors rely on information provided by pharmaceutical companies; there was inappropriate antibiotic prescribing.

Rifampin- and multidrug-resistant tuberculosis in Russian civilians and prison inmates: dominance of the beijing strain family.

Consecutive patient cultures (140) of Mycobacteriium tuberculosis were collected from five Russian civilian and prison tuberculosis laboratories and analyzed for rifampin (rpoB) and isoniazid resistance (inhA, katG, ahpC); transmission of Beijing family isolates; and the importance of prison and previous therapy in drug resistance. Rifampin, isoniazid, and multidrug resistance occurred in 58.2%, 51.6%, and 44.7% of cultures, respectively; 80% of prison cultures were rifampin resistant. Spoligotyping and variable number tandem repeat (VNTR) fingerprinting divided the isolates into 43 groups. Spoligotyping demonstrated that a high proportion (68.1%) of patients were infected with Beijing family strains and that most (69.1%) were rifampin resistant; the highest proportion (81.6%) occurred in prison. One VNTR subgroup (42435) comprised 68 (72.3%) of the Beijing isolates with a small number of IS6110 types; 50 (73.5%) were rifampin resistant. Rifampin-resistant Beijing isolates are dominant within the patient population, especially among prisoners, and threaten treatment programs.