Approximately 10 to 15% of tuberculosis (TB) cases in India are estimated to have extrapulmonary disease, and due to a lack of diagnostic means, they often remain untreated. The early detection of Mycobacterium tuberculosis and multidrug resistance is a priority in TB diagnosis to improve the successful treatment rate of TB and reduce transmission. The Xpert MTB/RIF (Xpert) test, recently endorsed by the World Health Organization for the detection of pulmonary TB, was evaluated to test its utility in 547 patients with suspected extrapulmonary tuberculosis. Five hundred forty-seven extrapulmonary specimens were split and processed simultaneously for both culture (solid and liquid) and Xpert testing. For culture, the sensitivity was low, 53% (150/283 specimens). Xpert sensitivity and specificity results were assessed in comparison to a composite reference standard made up of smear and culture results and clinical, radiological, and histological findings. The sensitivity of the Xpert assay was 81% (228/283 specimens) (64% [89/138] for smear-negative cases and 96% [139/145] for smear-positive cases), with a specificity of 99.6%. The sensitivity was found to be high for the majority of specimen types (63 to 100%) except for cerebrospinal fluid, the sensitivity of which was 29% (2/7 specimens). The Xpert test correctly identified 98% of phenotypic rifampin (RIF)-resistant cases and 94% of phenotypic RIF-susceptible cases. Sequencing of the 6 discrepant samples resolved 3 of them, resulting in an increased specificity of 98%. In conclusion, the results of this study suggest that the Xpert test also shows good potential for the diagnosis of extrapulmonary TB and that its ease of use makes it applicable for countries where TB is endemic.India has the world's largest burden of tuberculosis (TB), accounting for one-fifth of the global TB incidence. The global annual incidence estimate is 9.4 million cases, of which 1.98 million cases are from India (10). TB remains the largest infectious killer disease affecting adults in developing countries (1). In India, TB disproportionately involves the young. Almost 50% of multidrug-resistant TB (MDR-TB) (resistant to at least rifampin [RIF] and isoniazid) cases worldwide are estimated to occur in China and India (21). TB manifests clinically as pulmonary or extrapulmonary tuberculosis (EPTB), with the former being more common. In India, 10 to 15% of TB cases are estimated to be cases of EPTB (which affects mainly the lymph nodes, meninges, kidney, spine, and growing ends of the bones), with a 25 to 50% case mortality rate within months. In this situation, not only rapid TB case detection but also the early determination of MDR status is important. The major challenge in the diagnosis of EPTB is the frequently atypical clinical presentation simulating other inflammatory and neoplastic conditions, which frequently results in a delay or deprivation of treatment. Therefore, a high index of suspicion is necessary to make an early diagnosis, and quite often, more than one procedure is ne...

Rationale: The Xpert MTB/RIF is an automated molecular test for Mycobacterium tuberculosis that estimates bacterial burden by measuring the threshold-cycle (Ct) of its M. tuberculosis-specific real-time polymerase chain reaction. Bacterial burden is an important biomarker for disease severity, infection control risk, and response to therapy. Objectives: Evaluate bacterial load quantitation by Xpert MTB/RIF compared with conventional quantitative methods. Methods: Xpert MTB/RIF results were compared with smear-microscopy, semiquantiative solid culture, and time-to-detection in liquid culture for 741 patients and 2,008 samples tested in a multisite clinical trial. An internal control real-time polymerase chain reaction was evaluated for its ability to identify inaccurate quantitative Xpert MTB/RIF results. Measurements and Main Results: Assays with an internal control Ct greater than 34 were likely to be inaccurately quantitated; this represented 15% of M. tuberculosis-positive tests. Excluding these, decreasing M. tuberculosis Ct was associated with increasing smear microscopy grade for smears of concentrated sputum pellets (r s ¼ 20.77) and directly from sputum (r s ¼ 20.71). A Ct cutoff of approximately 27.7 best predicted smear-positive status. The association between M. tuberculosis Ct and time-to-detection in liquid culture (r s ¼ 0.68) and semiquantitative colony counts (r s ¼ 20.56) was weaker than smear. Tests of paired same-patient sputum showed that highviscosity sputum samples contained 332 more M. tuberculosis than nonviscous samples. Comparisons between the grade of the acid-fast bacilli smear and Xpert MTB/RIF quantitative data across study sites enabled us to identify a site outlier in microscopy. Conclusions: Xpert MTB/RIF quantitation offers a new, standardized approach to measuring bacterial burden in the sputum of patients with tuberculosis.Keywords: tuberculosis; molecular diagnostics; diagnostic techniques and procedures; diagnosis; clinical trial Measurements of bacterial load have long played an important role in tuberculosis diagnostics. Semiquantitative or quantitative measures of the number of Mycobacterium tuberculosis bacilli present within a clinical sample have been clinically useful for determining disease severity, assessing transmission risk, or monitoring therapy (1-3). Quantitative readouts have also aided in the investigation of potentially false-positive results (4-6).The Xpert MTB/RIF (Cepheid, Sunnyvale, CA) assay simultaneously detects the presence of M. tuberculosis and its susceptibility to the important first-line drug rifampin in less than 2 hours (7). The assay is contained in a small plastic cartridge, and it is run on the GeneXpert platform (Cepheid), a diagnostic The Xpert MTB/RIF assay is a rapid diagnostic test for tuberculosis and rifampin resistance. A number of studies have examined the sensitivity and specificity of the assay in various clinical settings and with various sample types. The test can also provide an estimate of the bacterial load present in the s...

HighlightsThis study examined long-term trends in antibiotic resistance on a national scale in India.Colistin-resistant Klebsiella pneumoniae and Escherichia coli strains have emerged in India.In 2014, the prevalence of carbapenem-resistant E. coli was11.5%, the highest reported to date globally.

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An inhA promoter mutation could be considered as a marker for the determination of ETH resistance in India, where the use of LPA is being expanded.

BackgroundUnsuccessful treatment outcomes among patients with multi-/extensively- drug resistant tuberculosis (TB) have hampered efforts involved in eradicating this disease. In order to better understand the etiology of this disease, we aimed to determine whether single or multiple strains of Mycobacterium tuberculosis (MTB) are localized within lung cavities of patients suffering from chronic progressive TB.Methodology/FindingsMultiple cavity isolates from lung of 5 patients who had undergone pulmonary resection surgery were analyzed on the basis of their drug susceptibility profile, and genotyped by spoligotyping and 24-loci MIRU-VNTR. The patients past history including treatment was studied. Three of the 5 patients had extensive drug resistant TB. Heteroresistance was also reported within different cavity isolates of the lung. Both genotyping methods reported the presence of clonal population of MTB strain within different cavities of the each patient, even those reporting heteroresistance. Four of the 5 patients were infected with a population of the Beijing genotype. Post-surgery they were prescribed a drug regimen consisting of cycloserine, a fluoroquinolone and an injectable drug. A 6 month post-surgery follow-up reported only 2 patients with positive clinical outcome, showing sputum conversion.ConclusionIdentical spoligotype patterns and MIRU-VNTR profiles between multiple cavities of each patient, characterize the presence of clonal population of MTB strains (and absence of multiple MTB infection).

Light-emitting diode fluorescence microscopy is being scaled up for tuberculosis control, but fading of auramine-stained slides could compromise external quality assurance. We stored auramine-stained slides and reexamined them over time. Slides stored in all environments faded quickly, with significant changes in the proportion of positive slides in as little as 1 week.Fluorescence microscopy (FM) can increase sensitivity and decrease the time required for sputum smear examination compared to Ziehl-Neelsen (ZN) staining and light microscopy (6). Low-cost, robust light-emitting diode (LED) microscopes have facilitated the expansion of FM into low-resource settings (2, 3), and in 2010, the World Health Organization (WHO) recommended that LED FM be phased in to replace ZN microscopy for tuberculosis (TB) diagnosis (9). As part of FM expansion, a system for external quality assurance (EQA) is needed and is currently being developed (9). While many EQA programs for ZN microscopy involve saving a sample of ZNstained smears for blinded rereading by a centralized reference laboratory (1, 8), fluorochrome-based stains fade over time (4). However, there is a wide spectrum of opinion regarding the rate of fading and its effect on the sensitivity of fluorochromestained smears. To generate evidence for the development of EQA strategies for LED FM, we examined the effect of storing auramine-stained slides at different temperatures and in different environments on the concordance of smear readings over time.All of the specimens submitted for mycobacterial diagnostics at Hinduja Hospital and Medical Research Centre, Mumbai, India, had an extra slide prepared and stained with auramine O-KMnO 4 (HiMedia, Mumbai, India). These smears were examined by two independent microscopists using a Lumin LED objective lens attachment (LW Scientific) in conjunction with an LED FM evaluation (5). A subset of slides was selected for storage and inclusion in this study. The sample was enriched with low-positive smears as follows: approximately 25% scanty, 25% 1ϩ, 25% 2ϩ, 15% 3ϩ, and 10% negative. All included smears had been identically scored by the two microscopists on initial reading. A total of 330 slides were allocated to one of four storage environments, darkness at room temperature (22°C), darkness in a humidified incubator (30°C), darkness in a refrigerator (4°C), and light at room temperature (22°C). Sixty slides in each of the 3 dark environments (closed slide boxes) were read monthly, 30 additional slides in all 4 environments were read weekly, and 30 slides were stored in the dark at room temperature and read once after 3 months. All slides were reread by both original microscopists during routine daily work and recorded as negative, scant, 1ϩ, 2ϩ, or 3ϩ. Blinding, reassortment, and restorage were performed by an unblinded researcher not involved in smear reading. Smear examination results were dichotomized as positive/negative, with smears read as scanty, 1ϩ, 2ϩ, or 3ϩ considered positive.In all of the storage environments, there wa...

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