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1.  Insufficient quality of sputum submitted for tuberculosis diagnosis and associated factors, in Klaten district, Indonesia 
Background
Sputum smear microscopy is the standard diagnostic method for detection of smear positive pulmonary tuberculosis (TB). Insufficient quality of sputum might result in missing cases. In this study we aimed at assessing the quality of sputum in a district in Central Java and determining patient and health worker factors associated with submission of three good quality sputum samples.
Methods
In 16 health centers information was collected on the quality of sputum submitted by TB suspects, i.e. volume, color, and viscosity. TB suspects were interviewed to assess their knowledge of TB, motivation to provide sputum and whether they were informed why and how to produce a sputum sample. Health workers were interviewed to assess what information they provided to TB suspects about the reason for sputum examination, methods to produce sputum and characteristics of a good quality sputum sample. All health worker and patient factors were evaluated for association with sputum quality.
Results
Of 387 TB suspects, 294 (76.0%) could be traced and interviewed, and of 272 (70.3%) information about sputum quality was available. Of those 203 (74.6%) submitted three samples, 90 (33.1%) provided at least one good sample, and 37 (13.6%) provided three good quality sputum samples. Of the 272 TB suspects, 168 (61.8%) mentioned that information on the reason for sputum examination was provided, 66 (24.3%) remembered that they were informed about how to produce sputum and 40 (14.7%) recalled being informed about the characteristics of good quality sputum. Paramedics reported to provide often/always information on the importance of sputum examination, and when to produce sputum. Information on how to produce sputum and characteristics of a good sputum sample was less often provided. None of the studied patient characteristics or health worker factors was associated with providing good quality sputum.
Conclusion
A considerable number of TB suspects did not provide three sputum samples and a large number of sputum samples were of insufficient quality. Training of health workers in providing health education to the TB suspect about the reason for sputum examination and how to produce a good quality sputum sample should be a priority of the TB program.
doi:10.1186/1471-2466-9-16
PMCID: PMC2689165  PMID: 19426477
2.  Non-conversion of sputum culture among patients with smear positive pulmonary tuberculosis in Cameroon: a prospective cohort study 
BMC Infectious Diseases  2014;14:138.
Background
We investigated the determinants of sputum culture non-conversion following intensive phase of treatment, and assessed the effects on the outcome among patients treated for a first episode of smear positive tuberculosis (TB).
Methods
This was a prospective cohort study spanning October 2009 to May 2012, among patients treated for a first episode of smear positive pulmonary tuberculosis in the Chest service of the Yaounde Jamot Hospital, Cameroon. Logistic regressions models were used to relate baseline characteristics with non-conversion of sputum cultures after the intensive phase of treatment.
Results
A total of 953 patients were admitted to the service during the study period, including 97 (10.2%) who had a positive sputum smear at the end of the intensive phase of anti-tuberculosis treatment. Eighty-six patients with persistent of smear positive sputa at the end of intensive phase of TB treatment were included, among whom 46 (53%) had positive sputum culture for Mycobacterium tuberculosis (C+). The absence of haemoptysis [adjusted odd ratio 4.65 (95% confidence intervals: 1.14-18.95)] and current smoking [7.26 (1.59-33.23)] were the main determinants of sputum culture non-conversion. Of the 46C + patients, 7 (15%) were resistant to at least one anti-tuberculosis drug. Treatment failure rate was 28% among C + patients and 8% among C– patients (p = 0.023). The sensitivity and specificity were 78.6% and 55.4% for culture non-conversion after intensive treatment, in predicting anti-TB treatment failure.
Conclusions
Failure rate is high among patients with positive sputum culture after intensive treatment, even in the absence of multi-drug resistant bacilli. Treatment should be closely monitored in these patients and susceptibility to anti-tuberculosis drugs tested in the presence of persistent positive smears following the intensive phase of treatment.
doi:10.1186/1471-2334-14-138
PMCID: PMC3984706  PMID: 24618155
Mycobacterium tuberculosis; Culture conversion; Outcome; Cameroon
3.  Diagnosing sputum/smear-negative pulmonary tuberculosis: Does fibre-optic bronchoscopy play a significant role? 
Background:
Diagnosis of sputum/smear-negative pulmonary tuberculosis patients can be both challenging and time consuming with many patients being put on empirical anti-tubercular treatment. Fibreoptic bronchoscopy may provide a confirmative and early diagnosis in such patients.
Aims:
To assess the role of fibreoptic bronchoscopy in the diagnosis of sputum /smear-negative pulmonary tuberculosis.
Materials and Methods:
The study was conducted on 75 suspected sputum / smear-negative pulmonary tuberculosis cases attending Pulmonary Medicine Department of Mamata Medical College and Hospital, Khammam, AP. Fibreoptic bronchoscopy was performed; culture of sputum and bronchial washings for Mycobacterium tuberculosis was done by BACTEC method.
Results:
A final diagnosis of sputum /smear-negative pulmonary tuberculosis was made in 60 patients. Bronchial washings smear for acid-fast bacilli (AFB) was positive in 21 patients while culture of bronchial washings was positive in 39 patients. In 29 patients, smear or culture of bronchial washing alone contributed to the final diagnosis. Total yield of bronchoscopy in diagnosis of sputum smear negative pulmonary tuberculosis was 83.33% (50/60); bronchoscopy was the only diagnostic method in 66% cases (40/60) with bronchial washings being the only diagnostic method in 48.33%. Bronchial washings smear for AFB and histopathological evidence of caseating granuloma made immediate diagnosis possible in 48.33% (29/60) patients.
Conclusion:
Our study suggests that fibreoptic bronchoscopy can provide excellent material for diagnosis of suspected cases of Pulmonary Tuberculosis in whom smears of expectorated sputum do not reveal mycobacteria.
doi:10.4103/0970-2113.63607
PMCID: PMC2893426  PMID: 20616936
Bronchial washings; fibreoptic bronchoscopy; pulmonary tuberculosis; sputum smear negative
4.  Direct microscopy versus sputum cytology analysis and bleach sedimentation for diagnosis of tuberculosis: a prospective diagnostic study 
BMC Infectious Diseases  2010;10:276.
Background
Diagnostic options for pulmonary tuberculosis in resource-poor settings are commonly limited to smear microscopy. We investigated whether bleach concentration by sedimentation and sputum cytology analysis (SCA) increased the positivity rate of smear microscopy for smear-positive tuberculosis.
Methods
We did a prospective diagnostic study in a Médecins Sans Frontières-supported hospital in Mindouli, Republic of Congo. Three sputum samples were obtained from 280 consecutive pulmonary tuberculosis suspects, and were processed according to WHO guidelines for direct smear microscopy. The remainder of each sputum sample was homogenised with 2.6% bleach, sedimented overnight, smeared, and examined blinded to the direct smear result for acid-fast bacilli (AFB). All direct smears were assessed for quality by SCA. If a patient produced fewer than three good-quality sputum samples, further samples were requested. Sediment smear examination was performed independently of SCA result on the corresponding direct smear. Positivity rates were compared using McNemar's test.
Results
Excluding SCA, 43.2% of all patients were diagnosed as positive on direct microscopy of up to three samples. 47.9% were diagnosed on sediment microscopy, with 48.2% being diagnosed on direct microscopy, sediment microscopy, or both. The positivity rate increased from 43.2% to 47.9% with a case definition of one positive smear (≥1 AFB/100 high power fields) of three, and from 42.1% to 43.9% with two positive smears. SCA resulted in 87.9% of patients producing at least two good-quality sputum samples, with 75.7% producing three or more. Using a case definition of one positive smear, the incremental yield of bleach sedimentation was 14/121, or 11.6% (95% CI 6.5-18.6, p = 0.001) and in combination with SCA was 15/121, or 12.4% (95% CI 7.1-19.6, p = 0.002). Incremental yields with two positive smears were 5/118, or 4.2% (95% CI 1.4-9.6, p = 0.062) and 7/118, or 5.9% (95% CI 2.4-11.8, p = 0.016), respectively.
Conclusions
The combination of bleach sedimentation and SCA resulted in significantly increased microscopy positivity rates with a case definition of either one or two positive smears. Implementation of bleach sedimentation led to a significant increase in the diagnosis of smear-positive patients. Implementation of SCA did not result in significantly increased diagnosis of tuberculosis, but did result in improved sample quality. Requesting extra sputum samples based on SCA results, combined with bleach sedimentation, could significantly increase the detection of smear-positive patients if routinely implemented in resource-limited settings where gold standard techniques are not available. We recommend that a pilot phase is undertaken before routine implementation to determine the impact in a particular context.
doi:10.1186/1471-2334-10-276
PMCID: PMC2946302  PMID: 20858253
5.  SIMPLE MEASURES ARE AS EFFECTIVE AS INVASIVE TECHNIQUES IN THE DIAGNOSIS OF PULMONARY TUBERCULOSIS IN MALAWI 
Setting
Detection of smear-positive pulmonary tuberculosis (PTB) cases is vital for tuberculosis control. Methods to augment sputum collection are available but their additional benefit is uncertain in resource-limited settings.
Objective
To compare the diagnostic yields using five methods to obtain sputum from adults diagnosed with smear-negative PTB in Malawi.
Design
Self-expectorated sputum was collected under supervision for microscopy and mycobacterial culture in the study laboratory. Confirmed smear-negative patients, provided physiotherapy-assisted sputum and induced sputum followed, the next morning, by gastric washing and bronchoalveolar-lavage samples.
Results
150 patients, diagnosed with smear-negative PTB by the hospital service, were screened. 39 (26%) were smear-positive from supervised self-expectorated sputum examined in the study laboratory. The remaining 111 confirmed smear-negative patients were enrolled; 89% were HIV positive. Seven additional smear-positive cases were diagnosed using the augmented sputum collection techniques. No differences were observed in the numbers of cases detected using the different methods. 44 (95.6%) of the 46 smear-positive cases could be detected from self-expectorated and physiotherapy-assisted samples
Conclusions
For countries like Malawi, the best use of limited resources to detect smear-positive PTB cases would be to improve the quality of self-expectorated sputum collection and microscopy. The additional diagnostic yield using bronchoalveolar-lavage after induced sputum is limited.
PMCID: PMC2873674  PMID: 19105886
Induced sputum; gastric washings; physiotherapy; BAL; HIV
6.  A Pilot Study of Short-Duration Sputum Pretreatment Procedures for Optimizing Smear Microscopy for Tuberculosis 
PLoS ONE  2009;4(5):e5626.
Background
Direct sputum smear microscopy for tuberculosis (TB) lacks sensitivity for the detection of acid fast bacilli. Sputum pretreatment procedures may enhance sensitivity. We did a pilot study to compare the diagnostic accuracy and incremental yield of two short-duration (<1 hour) sputum pretreatment procedures to optimize direct smears among patients with suspected TB at a referral hospital in India.
Methodology/Findings
Blinded laboratory comparison of bleach and universal sediment processing (USP) pretreated centrifuged auramine smears to direct Ziehl-Neelsen (ZN) and direct auramine smears and to solid (Loweinstein-Jensen (LJ)) and liquid (BACTEC 460) culture. 178 pulmonary and extrapulmonary TB suspects were prospectively recruited during a one year period. Thirty six (20.2%) were positive by either solid or liquid culture. Direct ZN smear detected 22 of 36 cases and direct auramine smears detected 26 of 36 cases. Bleach and USP centrifugation detected 24 cases each, providing no incremental yield beyond direct smears. When compared to combined culture, pretreated smears were not more sensitive than direct smears (66.6% vs 61.1 (ZN) or 72.2 (auramine)), and were not more specific (92.3% vs 93.0 (ZN) or 97.2 (auramine).
Conclusions/Significance
Short duration sputum pretreatment with bleach and USP centrifugation did not increase yield as compared to direct sputum smears. Further work is needed to confirm this in a larger study and also determine if longer duration pre-treatment might be effective in optimizing smear microscopy for TB.
doi:10.1371/journal.pone.0005626
PMCID: PMC2680966  PMID: 19461963
7.  Value of third sputum smear for detection of pulmonary tuberculosis in HIV infected patients 
Infectious Disease Reports  2012;4(2):e35.
We evaluated diagnostic yield of third sputum smear in patients co infected with HIV for detection of pulmonary tuberculosis (TB). Among 139 pulmonary tuberculosis cases confirmed with positive sputum culture, diagnostic yield of first smear of sputum with acid fast staining was 81.9%. Incremental yield of 2nd and 3rd samples was 11.7% and 6.3% respectively. So two sputum smears may be enough for primary evaluation of HIV infected patients suspected to TB.
doi:10.4081/idr.2012.e35
PMCID: PMC3892638  PMID: 24470949
tuberculosis; HIV; diagnosis; pulmonary infection; sputum.
8.  Effect of Diagnostic and Treatment Delay on the Risk of Tuberculosis Transmission in Shenzhen, China: An Observational Cohort Study, 1993–2010 
PLoS ONE  2013;8(6):e67516.
Introduction
To understand better the risk of tuberculosis transmission with increasing delay in tuberculosis treatment, we undertook a retrospective cohort study in Shenzhen, China.
Methods
All pulmonary tuberculosis cases in the Shenzhen tuberculosis surveillance database from 1993–2010 were included. Sputum smear positivity and presence of pulmonary cavity were used as proxies for risk of tuberculosis transmission.
Results
Among 48,441pulmonary tuberculosis cases, 70% presented with symptoms of pulmonary TB, 62% were sputum smear positive, and 21% had a pulmonary cavity on chest x-ray. 95.3% of patients self-presented for evaluation of illness after a median 58 days of delay after symptoms began. The proportion presenting sputum smear positive (p<0.001) and with a pulmonary cavity (p<0.001) increased significantly with increasing duration of delay.
Conclusions
Delayed diagnosis and treatment of tuberculosis is associated with a significantly increased risk of pulmonary sputum smear positivity and pulmonary cavity. To decrease risk of transmission, treatment delay needs to be reduced further.
doi:10.1371/journal.pone.0067516
PMCID: PMC3694886  PMID: 23826313
9.  Diagnostic accuracy of same-day microscopy versus standard microscopy for pulmonary tuberculosis: a systematic review and meta-analysis 
The Lancet infectious diseases  2012;13(2):10.1016/S1473-3099(12)70232-3.
Summary
Background
Sputum smear microscopy is the most widely available diagnostic test for pulmonary tuberculosis in countries with a high burden of the disease. Improving its accuracy is crucial to achievement of case-detection targets established by the Millennium Development Goals. Unfortunately, many patients are unable to submit all of the specimens needed for examination or to return for treatment because standard sputum collection and reporting requires several clinic visits. To inform policy recommendations by a WHO-convened Expert Group, we aimed to assess the accuracy of sputum smear examination with strategies for obtaining sputum on 1 day compared with strategies for obtaining sputum over 2 days.
Methods
We did a systematic review and meta-analysis of research articles comparing the accuracy of front-loaded or same-day microscopy and standard sputum smear microscopy for diagnosis of culture-confirmed pulmonary tuberculosis. We searched Medline, Embase, Biosis, and Web of Science for articles published between Jan 1, 2005, and Feb 14, 2012. Two investigators identified eligible articles and extracted data for individual study sites. We generated pooled summary estimates (95% CIs) for sensitivity and specificity by use of random-effects meta-analysis when four or more studies were available.
Findings
We identified eight relevant studies from five articles enrolling 7771 patients with suspected tuberculosis in low-income countries. Compared with the standard approach of examination of two smears with Ziehl-Neelsen light microscopy over 2 days, examination of two smears taken on the same day had much the same sensitivity (64% [95% CI 60 to 69] for standard microscopy vs 63% [58 to 68] for same-day microscopy) and specificity (98% [97 to 99] vs 98% [97 to 99]). We noted similar results for studies employing light-emitting diode fluorescence microscopy and for studies examining three smears, whether they were compared with two-smear strategies or with one another.
Interpretation
Same-day sputum smear microscopy is as accurate as standard smear microscopy. Data from tuberculosis programmes are needed to document the changes required in the health system to successfully implement the strategy and understand its effects.
doi:10.1016/S1473-3099(12)70232-3
PMCID: PMC3836432  PMID: 23099183
10.  The effect of HIV and antiretroviral therapy on characteristics of pulmonary tuberculosis in northern Malawi: a cross-sectional study 
BMC Infectious Diseases  2014;14:107.
Background
HIV infection reduces the likelihood that individuals with pulmonary tuberculosis are smear positive and that they have cavitatory disease. Antiretroviral therapy (ART) may shift the pattern of disease to be more similar to that of HIV negative patients. This would aid diagnosis- which often depends on sputum smears – but would also increase infectiousness. We assessed the effect of HIV and ART on smear positivity and cavitatory disease in laboratory-confirmed pulmonary TB patients.
Methods
Three sputum samples were collected per pulmonary TB suspect and were examined using microscopy and culture. Chest radiographs were available for a subset of patients as part of another study. The effect of HIV and ART status on sputum smear positivity and lung cavitation were evaluated using multivariable logistic regression.
Results
Of 1024 laboratory-confirmed pulmonary TB patients who were identified between January 2005 and December 2011, 766 had HIV and ART status available. Positive sputum smears were significantly more common among HIV negative individuals than HIV positive individuals (adjusted OR = 2.91, 95% CI 1.53 – 5.55). Compared to those HIV positive but not on ART, patients on ART were more likely to be smear positive (adjusted OR = 2.33, 95% CI 1.01 – 5.39) if they had been on ART ≤ 6 months, but only slightly more likely to be smear positive (adjusted OR = 1.43, 95% CI 0.68 – 2.99) if they were on ART > 6 months. HIV negative patients were more likely than HIV positive patients to have cavitatory disease (adjusted OR = 1.97, 95% CI 1.20 – 3.23). Patients on ART > 6 months had a slight increase in cavitatory disease compared to HIV positive patients not on ART (adjusted OR = 1.68, CI 0.78 – 3.63).
Conclusions
HIV infection is associated with less smear positivity and cavitation in pulmonary TB patients. Among HIV positive patients, the use of ART shifts the presentation of disease towards that seen in HIV-negative individuals, which facilitates diagnosis but which also could increase infectiousness.
doi:10.1186/1471-2334-14-107
PMCID: PMC3941771  PMID: 24568242
Smear positivity; Cavitation; HIV; ART; Infectiousness; Culture; Malawi
11.  Validation of a Clinical-Radiographic Score to Assess the Probability of Pulmonary Tuberculosis in Suspect Patients with Negative Sputum Smears 
PLoS ONE  2011;6(4):e18486.
Background
Clinical suspects of pulmonary tuberculosis in which the sputum smears are negative for acid fast bacilli represent a diagnostic challenge in resource constrained settings. Our objective was to validate an existing clinical-radiographic score that assessed the probability of smear-negative pulmonary tuberculosis (SNPT) in high incidence settings in Peru.
Methodology/Principal Findings
We included in two referral hospitals in Lima patients with clinical suspicion of pulmonary tuberculosis and two or more negative sputum smears. Using a published but not externally validated score, patients were classified as having low, intermediate or high probability of pulmonary tuberculosis. The reference standard for the diagnosis of tuberculosis was a positive sputum culture in at least one of 2 liquid (MGIT or Middlebrook 7H9) and 1 solid (Ogawa) media. Prevalence of tuberculosis was calculated in each of the three probability groups.
684 patients were included. 184 (27.8%) had a diagnosis of pulmonary tuberculosis. The score did not perform well in patients with a previous history of pulmonary tuberculosis. In patients without, the prevalence of tuberculosis was 5.1%, 31.7% and 72% in the low, intermediate and high probability group respectively. The area under de ROC curve was 0.76 (95% CI 0.72–0.80) and scores ≥6 had a positive LR of 10.9.
Conclusions/Significance
In smear negative suspects without previous history of tuberculosis, the clinical-radiographic score can be used as a tool to assess the probability of pulmonary tuberculosis and to guide the decision to initiate or defer treatment or to requesting additional tests.
doi:10.1371/journal.pone.0018486
PMCID: PMC3071732  PMID: 21483690
12.  False-Positive Gen-Probe Direct Mycobacterium tuberculosis Amplification Test Results for Patients with Pulmonary M. kansasii and M. avium Infections 
Journal of Clinical Microbiology  1999;37(1):175-178.
The Gen-Probe Amplified Mycobacterium Tuberculosis Direct (MTD) test has been approved for use in the United States for the rapid diagnosis of pulmonary tuberculosis in patients with acid-fast smear-positive sputum samples since 1996. Four patients infected with human immunodeficiency virus and one chronic pulmonary-disease patient seen in our institutions with abnormal chest radiographs and fluorochrome stain-positive sputa were evaluated for tuberculosis, including performance of the MTD test on expectorated sputum samples. Three of these five patients’ sputa were highly smear-positive (i.e., more than 100 bacilli per high-power field), while two patient’s sputa contained 1 to 10 bacilli per field. MTD results on sputum specimens from these patients ranged from 43,498 to 193,858 relative light units (RLU). Gen-Probe has defined values of at least 30,000 RLU as indicative of a positive test, i.e., the presence of Mycobacterium tuberculosis RNA. Four of the patients’ sputum cultures yielded growth of M. kansasii within 6 to 12 days, and the fifth produced growth of M. avium only. One patient’s culture contained both M. kansasii and M. avium, but none of the initial or follow-up cultures from these five patients revealed M. tuberculosis. However, subsequent cultures from three of the patients again revealed M. kansasii. During the period of this study, in which MTD tests were performed on smear-positive sputum specimens from 82 patients, four of seven patients with culture-proven M. kansasii pulmonary infections yielded one or more false-positive MTD tests. The MTD sensitivity observed in this study was 93.8%, and the specificity was 85.3%. Five cultures of M. kansasii (including three of these patients’ isolates and M. kansasii ATCC 12478), and cultures of several other species were examined at densities of 105 to 107 viable CFU/ml by the MTD test. All five isolates of M. kansasii and three of three isolates of M. simiae yielded false-positive test results, with readings of 75,191 to 335,591 RLU. These findings indicate that low-level false-positive MTD results can occur due to the presence of M. kansasii, M. avium, and possibly other Mycobacterium species other than M. tuberculosis in sputum. Low-level positive MTD results of 30,000 to 500,000 RLU should be interpreted in light of these findings. It remains to be determined if the enhanced MTD test (MTD 2) recently released by Gen-Probe will provide greater specificity than that observed in this report with its first-generation test.
PMCID: PMC84200  PMID: 9854086
13.  Fiberoptic bronchoscopy for the rapid diagnosis of smear-negative pulmonary tuberculosis 
BMC Infectious Diseases  2012;12:141.
Background
This study was aimed to investigate the diagnostic value of fiberoptic bronchoscopy (FOB) with chest high-resolution computed tomography (HRCT) for the rapid diagnosis of active pulmonary tuberculosis (PTB) in patients suspected of PTB but found to have a negative sputum acid-fast bacilli (AFB) smear.
Methods
We evaluated the diagnostic accuracy of results from FOB and HRCT in 126 patients at Gangnam Severance Hospital (Seoul, Korea) who were suspected of having PTB.
Results
Of 126 patients who had negative sputum AFB smears but were suspected of having PTB, 54 patients were confirmed as having active PTB. Hemoptysis was negatively correlated with active PTB. Tree-in-bud appearance on HRCT was significantly associated with active PTB. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of FOB alone was 75.9%, 97.2%, 95.3%, and 84.3%, respectively, for the rapid diagnosis of active PTB. The combination of FOB and HRCT improved the sensitivity to 96.3% and the NPV to 96.2%.
Conclusions
FOB is a useful tool in the rapid diagnosis of active PTB with a high sensitivity, specificity, PPV and NPV in sputum smear-negative PTB-suspected patients. HRCT improves the sensitivity of FOB when used in combination with FOB in sputum smear-negative patients suspected of having PTB.
doi:10.1186/1471-2334-12-141
PMCID: PMC3507815  PMID: 22726571
14.  Survival among Patients with HIV Infection and Smear-Negative Pulmonary Tuberculosis - United States, 1993–2006 
PLoS ONE  2012;7(10):e47855.
Background
In patients with HIV and tuberculosis (TB) in resource-constrained settings, smear-negative disease has been associated with higher mortality than smear-positive disease. Higher reported mortality may be due to misdiagnosis, diagnostic delays, or because smear-negative disease indicates more advanced immune suppression.
Methods
We analyzed culture-confirmed, pulmonary TB among patients with TB and HIV in the United States from 1993–2008 to calculate prevalence ratios (PRs) for smear-negative disease by demographic and clinical characteristics. Allowing two years for treatment outcome to be reported, we determined hazard ratios (HRs) for survival by smear status, adjusted for significant covariates on patients before 2006.
Results
Among 16,710 cases with sputum smear results, 6,739 (39%) were sputum smear-negative and 9,971 (58%) were sputum smear-positive. The prevalence of smear-negative disease was lower in male patients (PR: 0.89, 95% confidence interval [CI]: 0.86–0.93) and in those who were homeless (PR: 0.92, CI: 0.87–0.97) or used alcohol excessively (PR: 0.91, CI: 0.87–0.95), and higher in persons diagnosed while incarcerated (PR: 1.20, CI: 1.13–1.27). Patients with smear-negative disease had better survival compared to patients with smear-positive disease, both before (HR: 0.82, CI: 0.75–0.90) and after (HR: 0.81, CI: 0.71–0.92) the introduction of combination anti-retroviral therapy.
Conclusions
In the United States, smear-negative pulmonary TB in patients with HIV was not associated with higher mortality, in contrast to what has been documented in high TB burden settings. Smear-negative TB can be routinely and definitively diagnosed in the United States, whereas high-burden countries often rely solely on AFB-smear microscopy. This difference could contribute to diagnostic and treatment delays in high-burden countries, possibly resulting in higher mortality.
doi:10.1371/journal.pone.0047855
PMCID: PMC3479118  PMID: 23110113
15.  Comparison of acid-fast stain and culture for Mycobacterium tuberculosis in pre- and post-bronchoscopy sputum and bronchoalveolar lavage in HIV-infected patients with atypical chest X-ray in Ethiopia 
Annals of Thoracic Medicine  2007;2(4):154-157.
BACKGROUND:
Smear-negative tuberculosis occurs more frequently in human immunodeficiency virus (HIV)-infected patients than in non-HIV-infected patients. Besides, there are substantial numbers of patients who cannot produce sputum, making the diagnosis of pulmonary tuberculosis (PTB) difficult.
AIMS:
To evaluate the relative yield of pre- and post-bronchoscopy sputum and bronchoalveolar lavage (BAL) in ‘sputum smear’-negative, HIV-positive patients.
SETTINGS:
A tertiary care referral hospital in Addis Ababa.
MATERIALS AND METHODS:
Acid-fast stain (AFS) using the concentration technique was done on 85 pre-bronchoscopy sputum and 120 BAL samples. Direct AFS was done on all BAL and 117 post-bronchoscopy sputum samples. Culture for Mycobacterium tuberculosis (MTB) was done for all sputa and BAL.
RESULTS:
MTB was isolated from 26 (21.7%), 23 (19.7%) and 13 (15.3%) of BAL, post- and pre-bronchoscopy sputum cultures respectively. AFS on pre-bronchoscopy sputum using concentration technique and direct AFS on BAL together detected 11 (41%) of the 27 culture-positive cases. In patients who could produce sputum, the sensitivity of pre-bronchoscopy sputum culture (13/85, 15.3%) was comparable to BAL (12/85, 14%) and post-bronchoscopy sputum (12/85, 14%). In patients who could not produce sputum, however, both BAL (12/35, 40%) and post-bronchoscopy sputum (12/32, 31.4%) detected significantly more patients than those who could produce sputum (P=0.002, P=0.028 respectively).
CONCLUSION:
In HIV-infected patients, AFS by concentration method on pre-bronchoscopy sputum and direct AFS on BAL in patients who cannot produce sputum are the preferred methods of making a rapid diagnosis. BAL culture seems to add little value in patients who can produce sputum; therefore, bronchoscopy should be deferred under such circumstances.
doi:10.4103/1817-1737.36549
PMCID: PMC2732096  PMID: 19727366
Acid-fast stain; bronchoalveolar lavage; concentration technique; M. tuberculosis; post-bronchoscopy; pre-bronchoscopy
16.  Evaluation of in-house PCR for diagnosis of smear-negative pulmonary tuberculosis in Kampala, Uganda 
BMC Research Notes  2012;5:487.
Background
Nucleic acid amplification tests (NAATs) have offered hope for rapid diagnosis of tuberculosis (TB). However, their efficiency with smear-negative samples has not been widely studied in low income settings. Here, we evaluated in-house PCR assay for diagnosis of smear-negative TB using Lowenstein-Jensen (LJ) culture as the baseline test. Two hundred and five pulmonary TB (PTB) suspects with smear-negative sputum samples, admitted on a short stay emergency ward at Mulago Hospital in Kampala, Uganda, were enrolled. Two smear-negative sputum samples were obtained from each PTB suspect and processed simultaneously for identification of MTBC using in-house PCR and LJ culture.
Results
Seventy two PTB suspects (35%, 72/205) were LJ culture positive while 128 (62.4%, 128/205) were PCR-positive. The sensitivity and specificity of in-house PCR for diagnosis of smear-negative PTB were 75% (95% CI 62.6-85.0) and 35.9% (95% CI 27.2-45.3), respectively. The positive and negative predictive values were 39% (95% CI 30.4-48.2) and 72.4% (95% CI 59.1-83.3), respectively, while the positive and negative likelihood ratios were 1.17 (95% CI 0.96-1.42) and 0.70 (95% CI 0.43-1.14), respectively. One hundred and seventeen LJ culture-negative suspects (75 PCR-positive and 42 PCR-negative) were enrolled for follow-up at 2 months. Of the PCR-positive suspects, 45 (60%, 45/75) were still alive, of whom 29 (64.4%, 29/45) returned for the follow-up visit; 15 (20%, 15/75) suspects died while another 15 (20%, 15/75) were lost to follow-up. Of the 42 PCR-negative suspects, 22 (52.4%, 22/42) were still alive, of whom 16 (72.7%, 16/22) returned for follow-up; 11 (26.2%, 11/42) died while nine (21.4%, 9/42) were lost to follow-up. Overall, more PCR-positive suspects were diagnosed with PTB during follow-up visits but the difference was not statistically significant (27.6%, 8/29 vs. 25%, 4/16, p = 0.9239). Furthermore, mortality was higher for the PCR-negative suspects but the difference was also not statistically significant (26.2% vs. 20% p = 0.7094).
Conclusion
In-house PCR correlates poorly with LJ culture for diagnosis of smear-negative PTB. Therefore, in-house PCR may not be adopted as an alternative to LJ culture.
doi:10.1186/1756-0500-5-487
PMCID: PMC3497582  PMID: 22947399
Pulmonary tuberculosis; Smear-negative TB; HIV-infected; HIV-TB co-infection; CD4 cell counts; Nucleic acid amplification tests; In-house PCR; Lowenstein-Jensen culture; Sensitivity; Specificity; Resource limited settings
17.  Design of the Anti-tuberculosis Drugs induced Adverse Reactions in China National Tuberculosis Prevention and Control Scheme Study (ADACS) 
BMC Public Health  2010;10:267.
Background
More than 1 million tuberculosis (TB) patients are receiving the standard anti-TB treatment provided by China National Tuberculosis Prevention and Control Scheme (CNTS) in China every year. Adverse reactions (ADRs) induced by anti-TB drugs could both do harm to patients and lead to anti-TB treatment failure. The ADACS aimed to explore ADRs' incidences, prognoses, economical and public health impacts for TB patients and TB control, and build a DNA bank of TB patients.
Methods/Design
Multiple study designs were adopted. Firstly, a prospective cohort with 4488 sputum smears positive pulmonary tuberculosis patients was established. Patients were followed up for 6-9 months in 52 counties of four regions. Those suspected ADRs should be checked and confirmed by Chinese State Food and Drug Administration (SFDA). Secondly, if the suspected ADR was anti-TB drug induced liver injury (ATLI), a nested case-control study would be performed which comprised choosing a matched control and doing a plus questionnaire inquiry. Thirdly, health economical data of ADRs would be collected to analyze financial burdens brought by ADRs and cost-effectiveness of ADRs' treatments. Fourthly, a drop of intravenous blood for each patient was taken and saved in FTA card for DNA banking and genotyping. Finally, the demographic, clinical, environmental, administrative and genetic data would be merged for the comprehensive analysis.
Discussion
ADACS will give an overview of anti-TB drugs induced ADRs' incidences, risk factors, treatments, prognoses, and clinical, economical and public health impacts for TB patients applying CNTS regimen in China, and provide suggestions for individualized health care and TB control policy.
doi:10.1186/1471-2458-10-267
PMCID: PMC2893093  PMID: 20492672
18.  Use of the flexible fibreoptic bronchoscope in diagnosis of sputum-negative pulmonary tuberculosis. 
Thorax  1982;37(8):598-601.
In four years' use of the flexible fibreoptic bronchoscope in diagnosing sputum-negative pulmonary tuberculosis, of 275 patients with tuberculosis suspected from chest radiographic appearances, 89 (32.4%) were shown to have active disease. In 60 (67.4%) of these patients the diagnosis was made from samples obtained through the fibreoptic bronchoscope (56 from bronchial brushings, four from transbronchial biopsy samples). Of the 56 positive bronchial brushings, 35 were positive on direct smear and 21 only on culture. Transbronchial biopsy exclusively accounted for only four of the 60 positive diagnoses. In the remaining 29 patients, the diagnosis was made from further sputum or biopsy specimens in 15, from the response to treatment in 12, and at necropsy in two. In six of 10 patients with military tuberculosis, bronchial brushings were positive on direct smear.
PMCID: PMC459382  PMID: 6817441
19.  Induced sputum and bronchoscopy in the diagnosis of pulmonary tuberculosis 
Thorax  2002;57(12):1010-1014.
Background: Previous studies suggest that bronchoscopy and a single induced sputum sample are equally effective for diagnosing pulmonary tuberculosis.
Methods: In a prospective study of subjects with possibly active pulmonary tuberculosis, the diagnostic yield of three induced sputum tests was compared with that of bronchoscopy. Subjects either produced no sputum or (acid fast) smear negative sputum. Bronchoscopy was only performed if at least two induced sputum samples were smear negative.
Results: Of 129 subjects who completed all tests, 27 (21%) had smear negative and culture positive specimens, 14 (52%) on bronchoscopy and 26 (96%) on induced sputum (p<0.005). One patient was culture positive on bronchoscopy alone compared with 13 on induced sputum alone; 13 were culture positive on both tests. Induced sputum positivity was strikingly more prevalent when chest radiographic appearances showed any features of active tuberculosis (20/63, 32%) than when appearances suggested inactivity (1/44, 2%; p<0.005). Induced sputum costs were about one third those of bronchoscopy, and the ratio of costs of the two tests per case of tuberculosis diagnosed could be as much as 1:6.
Conclusions: In subjects investigated for possibly active or inactive tuberculosis who produce no sputum or have smear negative sputum, the most cost effective strategy is to perform three induced sputum tests without bronchoscopy. Induced sputum testing carries a high risk of nosocomial tuberculosis unless performed in respiratory isolation conditions. The cost benefits shown could be lost if risk management measures are not observed.
doi:10.1136/thorax.57.12.1010
PMCID: PMC1758793  PMID: 12454293
20.  Value of Examining Multiple Sputum Specimens in the Diagnosis of Pulmonary Tuberculosis 
Journal of Clinical Microbiology  1998;36(2):467-469.
To objectively assess the value of examining multiple sputum specimens in maximizing the sensitivity of detection of Mycobacterium tuberculosis, we retrospectively reviewed the acid-fast bacillus smear and culture results of patients diagnosed with culture-proven pulmonary tuberculosis (TB) at Hennepin County Medical Center between 1986 and 1996. Two hundred and forty six persons were diagnosed with pulmonary TB in the time period analyzed. In 93% of these cases (229 of 246) the laboratory diagnosis was made by detection of M. tuberculosis in sputum specimens; however, only 52% (120 of 229) of these patients had at least three sputum specimens submitted to the laboratory at the time of diagnosis. Of the patients from whom at least three specimens were collected, 47% (56 of 120) had at least one smear-positive specimen; the third or later specimen submitted was the first smear-positive specimen for 13% (7 of 56) of these persons but was the first culture-positive specimen for only 7% (4 of 56). Of the 64 patients with smear-negative specimens, for only 5% (3 of 64) was the third or subsequent specimen submitted the first from which M. tuberculosis was recovered. This data indicates that, in our institution, the overwhelming majority of culture-proven pulmonary TB cases are diagnosed from the first or second sputum specimen submitted to the laboratory and that only rarely is a third specimen of diagnostic value.
PMCID: PMC104561  PMID: 9466760
21.  Smear microscopy and culture conversion rates among smear positive pulmonary tuberculosis patients by HIV status in Dar es Salaam, Tanzania 
BMC Infectious Diseases  2010;10:210.
Background
Tanzania ranks 15th among the world's 22 countries with the largest tuberculosis burden and tuberculosis has continued to be among the major public health problems in the country. Limited data, especially in patients co infected with HIV, are available to predict the duration of time required for a smear positive pulmonary tuberculosis patient to achieve sputum conversion after starting effective treatment. In this study we assessed the sputum smear and culture conversion rates among HIV positive and HIV negative smear positive pulmonary tuberculosis patients in Dar es Salaam
Methods
The study was a prospective cohort study which lasted for nine months, from April to December 2008
Results
A total of 502 smear positive pulmonary tuberculosis patients were recruited. HIV test results were obtained for 498 patients, of which 33.7% were HIV positive.
After two weeks of treatment the conversion rate by standard sputum microscopy was higher in HIV positive(72.8%) than HIV negative(63.3%) patients by univariate analysis(P = 0.046), but not in multivariate analysis. Also after two weeks of treatment the conversion rate by fluorescence microscopy was higher in HIV positive (72.8%) than in HIV negative(63.2%) patients by univariate analysis (P = 0.043) but not in the multivariate analysis. The conversion rates by both methods during the rest of the treatment period (8, 12, and 20 weeks) were not significantly different between HIV positive and HIV negative patients.
With regards to culture, the conversion rate during the whole period of the treatment (2, 8, 12 and 20 weeks) were not significantly different between HIV positive and HIV negative patients.
Conclusion
Conversion rates of standard smear microscopy, fluorescence microscopy and culture did not differ between HIV positive and HIV negative pulmonary tuberculosis patients.
doi:10.1186/1471-2334-10-210
PMCID: PMC2918607  PMID: 20637077
22.  Risk factors in patients with AFB smear-positive sputum who receive inappropriate antituberculous treatment 
Background
Acid-fast bacilli (AFB) smear-positive sputum is usually an initial clue in the diagnosis of pulmonary tuberculosis (TB); however, the test is not disease-specific. Nontuberculous mycobacterium-related colonization or lung disease often has AFB smear-positive sputum results, and physicians may prescribe unnecessary antituberculous drugs for these patients. The aim of this study was to analyze the clinical characteristics of patients with AFB smear-positive sputum who received unnecessary anti-TB treatment.
Methods and patients
From January 2008 to July 2011, we retrospectively enrolled 97 patients with AFB smear-positive sputum who did not have pulmonary TB according to mycobacterial cultures and clinical judgment. We analyzed the clinical and radiographic features of the patients who received inappropriate and unnecessary anti-TB treatment. Preliminary analyses of chisquare and Fisher’s exact tests were applied to determine factors unlikely to be associated with the independent variables. The relationship between independent covariates was then analyzed using multivariate logistic regression.
Results
Of the 97 enrolled patients, 25 (25.8%) were diagnosed with pulmonary TB and prescribed anti-TB drugs (mostly a combination of isoniazid, rifampicin, ethambutol, and pyrazinamide). The other 72 (74.2%) patients were not initially diagnosed with pulmonary TB and were classified as the control group. Compared to the control group, the patients who received inappropriate anti-TB treatment had more chronic cough as presentation symptom and heavy AFB Ziehl–Neelsen staining in sputum (>10/100 fields, grading 2+ to 4+). There were no significant differences in the radiographic analysis between the two groups.
Conclusion
Among the patients with AFB smear-positive sputum that did not have pulmonary TB, chronic cough and heavy AFB staining (2+ to 4+) were risk factors for the inappropriate administration of unnecessary anti-TB treatment.
doi:10.2147/DDDT.S39247
PMCID: PMC3563317  PMID: 23386785
AFB smear-positive sputum; Mycobacterium tuberculosis; antituberculous treatment
23.  Fiberoptic bronchoscopy, as a valuable diagnostic option in sputum negative pulmonary tuberculosis: A prospective study 
Context:
World Health Organization recommends bacteriological confirmation of pulmonary tuberculosis (PTB) by the detection of acid-fast bacilli (AFB) in respiratory specimens. However about 40-60% of patients with PTB suspected clinically or radiologically may fail to produce sputum, or when it is available, AFB may be negative on repeated smear examination. These sputum smear negative patients and those who fail to produce any sputum can be diagnosed by flexible fiberoptic bronchoscopy.
Aims:
Our study was an attempt to analyze the role of fiberoptic bronchoscopy in sputum smear negative PTB patients with respect to their association with clinical and radiological profile.
Materials and Methods:
In this prospective, open label, observational study, 40 cases of sputum smear negative PTB were subjected to bronchoscopic examination after taking informed consent and samples like bronchial aspirate, bronchoalveolar lavage and post bronchoscopy sputum were collected. The data was analysed and the results were given in percentage.
Results:
Out of the total 40 patients, overall diagnosis was confirmed in 24 (60%) patients. Of these 24 patients, 17 patients were confirmed for PTB whereas 7 had other diagnoses.
Conclusion:
The study concludes that fiberoptic bronchoscopy is a useful tool in diagnosing sputum smear negative PTB patients with respect to their association with clinical and radiological profile, and also identifies individuals at a higher risk for progression of disease, at an early stage despite not meeting routine bacteriological criteria for confirmation of PTB.
doi:10.4103/2229-516X.106355
PMCID: PMC3678692  PMID: 23776825
AFB-negative; pulmonary tuberculosis; AFB-negative sputum; fiberoptic bronchoscopy; pulmonary tuberculosis
24.  Genotype MTBDRplus for Direct Detection of Mycobacterium tuberculosis and Drug Resistance in Strains from Gold Miners in South Africa 
Journal of Clinical Microbiology  2012;50(4):1189-1194.
GenoType MTBDRplus is a molecular assay for detection of Mycobacterium tuberculosis and drug resistance. Assay performance as applied directly to consecutive unselected sputum samples has not been established. The objective of this study was to determine the accuracy of the MTBDRplus test for direct detection of M. tuberculosis (in sputum) and for drug resistance in consecutively submitted sputum samples. In this cross-sectional study in South Africa, one sputum specimen from each person suspected of having pulmonary tuberculosis was tested by smear microscopy, direct MTBDRplus, and Mycobacterial Growth Indicator Tube (MGIT) culture with MGIT drug susceptibility testing. MGIT results were the reference standard. We tested 2,510 sputum samples, and 529 (21.1%) were positive for M. tuberculosis by MGIT. Direct MTBDRplus identified M. tuberculosis in 256 of 529 specimens (sensitivity, 48.4%; 95% confidence interval [CI], 44.1, 52.7). The sensitivity of MTBDRplus for M. tuberculosis detection by sputum smear status was as follows: smear negative, 13.7% (95% CI, 9.8, 18.4); smear scanty, 46.2% (95% CI, 19.2, 74.9); smear 1+, 69.1% (95% CI, 55.2, 80.9); smear 2+, 86.3% (95% CI, 73.7, 94.3); smear 3+, 89.8% (95% CI, 83.7, 94.2). Direct MTBDRplus testing was negative for 1,594/1,612 sputum samples that were culture negative for M. tuberculosis (specificity, 98.9%; 95% CI, 98.2, 99.3). For specimens positive for M. tuberculosis by MTBDRplus, this assay's sensitivity and specificity for rifampin resistance were 85.7% (95% CI, 57.2, 98.2) and 96.6% (95% CI, 93.2, 98.6) and for isoniazid resistance they were 62.1% (95% CI, 42.3, 79.3) and 97.9% (95% CI, 94.8, 99.4). For sputum testing, the sensitivity of MTBDRplus is directly related to the specimen's bacillary burden. Our results support recommendations that the MTBDRplus test not be used for direct testing of smear-negative or paucibacillary sputum samples.
doi:10.1128/JCM.05723-11
PMCID: PMC3318561  PMID: 22238443
25.  Use of a Molecular Diagnostic Test in AFB Smear Positive Tuberculosis Suspects Greatly Reduces Time to Detection of Multidrug Resistant Tuberculosis 
PLoS ONE  2012;7(2):e31563.
Background
The WHO has recommended the implementation of rapid diagnostic tests to detect and help combat M/XDR tuberculosis (TB). There are limited data on the performance and impact of these tests in field settings.
Methods
The performance of the commercially available Genotype MTBDRplus molecular assay was compared to conventional methods including AFB smear, culture and drug susceptibility testing (DST) using both an absolute concentration method on Löwenstein-Jensen media and broth-based method using the MGIT 960 system. Sputum specimens were obtained from TB suspects in the country of Georgia who received care through the National TB Program.
Results
Among 500 AFB smear-positive sputum specimens, 458 (91.6%) had both a positive sputum culture for Mycobacterium tuberculosis and a valid MTBDRplus assay result. The MTBDRplus assay detected isoniazid (INH) resistance directly from the sputum specimen in 159 (89.8%) of 177 specimens and MDR-TB in 109 (95.6%) of 114 specimens compared to conventional methods. There was high agreement between the MTBDRplus assay and conventional DST results in detecting MDR-TB (kappa = 0.95, p<0.01). The most prevalent INH resistance mutation was S315T (78%) in the katG codon and the most common rifampicin resistance mutation was S531L (68%) in the rpoB codon. Among 13 specimens from TB suspects with negative sputum cultures, 7 had a positive MTBDRplus assay (3 with MDR-TB). The time to detection of MDR-TB was significantly less using the MTBDRplus assay (4.2 days) compared to the use of standard phenotypic tests (67.3 days with solid media and 21.6 days with broth-based media).
Conclusions
Compared to conventional methods, the MTBDRplus assay had high accuracy and significantly reduced time to detection of MDR-TB in an area with high MDR-TB prevalence. The use of rapid molecular diagnostic tests for TB and drug resistance should increase the proportion of patients promptly placed on appropriate therapy.
doi:10.1371/journal.pone.0031563
PMCID: PMC3276512  PMID: 22347495

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