Single-tube balanced heminested PCR for detecting Mycobacterium tuberculosis in smear-negative samples

A Genotyping Method for Detecting Foreign Buffalo Material in Mozzarella di Bufala Campana Cheese Using Allele-Specific- and Single-Tube Heminested-Polymerase Chain Reaction

Mozzarella di Bufala Campana (MdBC) cheese is a Protected Designation of Origin (PDO) product that is important for the economy and cultural heritage of the Campania region. Food fraud can undermine consumers' trust in this dairy product and harm the livelihood of local producers. The current methods for detecting adulteration in MdBC cheese due to the use of buffalo material from foreign countries could exhibit limitations associated with the required use of expensive equipment, time-consuming procedures, and specialized personnel. To address these limits here, we propose a rapid, reliable, and cost-effective genotyping method that can detect foreign buffalo milk in a counterpart from the PDO area and in MdBC cheese, ensuring the quality and authenticity of the latter dairy product. This method is based on dedicated allele-specific and single-tube heminested polymerase chain reaction procedures. By using allele-specific primers that are designed to detect the nucleotide g.472G>C mutation of the CSN1S1B^bt allele, we distinguished an amplicon of 330 bp in the amplification product of DNA when extracted from milk and cheese, which is specific to the material originating from foreign countries. By spiking foreign milk samples with known amounts of the counterpart from the PDO area, the sensitivity of this assay was determined to be 0.01% v/v foreign to PDO milk. Based on a rough estimate of its simplicity, reliability, and cost, this method could be a valuable tool for identifying adulterated buffalo PDO dairy products.

Performance of nested multiplex PCR assay targeting MTP40 and IS6110 gene sequences for the diagnosis of tubercular lymphadenitis

The conventional methods for diagnosis of tubercular lymphadenitis (TBLN) such as - fine needle aspiration cytology, Ziehl-Neelsen staining and culture have limitations of low sensitivity and/or specificity. So, it becomes essential to develop a rapid, sensitive, and specific method for an early diagnosis of TBLN. Therefore, the present study was conducted to evaluate nested multiplex polymerase chain reaction (nMPCR) targeting MTP40 and IS6110 gene sequences of Mycobacterium tuberculosis and Mycobacterium tuberculosis complex, respectively in 48 successive patients of TBLN and 20 random patients with non-tubercular lymph node lesions. Out of the 48 cases of TBLN, 14 (29.2%) were found to be positive by Ziehl-Neelsen staining, 15 (31.2%) were positive by culture and 43 (89.6%) cases were positive after first round of PCR while 48 (100%) cases were positive by nMPCR assay. The sensitivity and specificity of nMPCR was found to be 100% for the diagnosis of TBLN. The results thus obtained indicate that nMPCR assay is a highly sensitive and specific tool for the diagnosis of TBLN.

Performance of the BD ProbeTec ET direct detection assay for the analysis of Mycobacterium tuberculosis in respiratory and non-respiratory clinical specimens

Objectives

Early detection of Mycobacterial tuberculosis infection (MTB) is pivotal for the treatment of tuberculosis (TB).

Background

This study was performed to evaluate the performance of BD ProbeTec ET direct detection assay (DTB) against the gold standard culture technique for confirmation of MTB infection.

Methods

A total of 266 consecutive and non-duplicate clinical specimens for detection of MTB were included in this study. There were 118 respiratory and 148 non-respiratory samples. All samples were tested by microscopy for acid-fast bacillus (AFB), MTB culture and biochemical identification with simultaneous testing by DTB.

Results

A total of 88 samples (33%) were culture-positive for MTB including 39/118 respiratory, 29/99 fluid and 20/49 tissue samples. DTB sensitivity for respiratory samples was 97% and specificity was 96% with a positive predictive value (PPV) of 93% and negative predictive value (NPV) of 99%. Sensitivity of DTB in fluid samples was 80%, specificity 88%, PPV 69% and NPV 93% whereas sensitivity of DTB for tissue samples was 25%, specificity 90%, PPV 63% and NPV 63%. Of the 50 (56.8%) smear-positive samples, DTB sensitivity was 100% for respiratory, 85% for fluid and 100% for tissue samples.

Conclusion

DTB performed within acceptable limits for the rapid detection of MTB in respiratory samples compared to fluid and tissue specimens.

Diagnosis of Mycobacterium tuberculosis using molecular biology technology

OBJECTIVE

To present an integrated molecular biology dedicated system for tuberculosis diagnosis.

METHODS

One hundred and five sputum specimens from patients strongly suspected by clinical parameters of tuberculosis were studied by Ziehl-Neelsen staining, by cultivation on solid medium and by a balanced heminested fluorometric PCR system (Orange G3TB) that could preserve worker safety and produce a rather pure material free of potential inhibitors. DNA amplification was performed in a low cost tuberculosis termocycler-fluorometer. Produced double stranded DNA was flurometrically detected. The whole reaction was conducted in one single tube which would not be opened after adding the processed sample in order to minimize the risk of cross contamination with amplicons.

RESULTS

The assay was able to detect 30 bacillus per sample mL with 99.8% interassay variation coefficient. PCR was positive in 23 (21.9%) tested samples (21 of them were smear negative). In our study it showed a preliminary sensitivity of 94.5% for sputum and an overall specificity of 98.7%.

CONCLUSIONS

Total run time of the test is 4 h with 2.5 real working time. All PCR positive samples are also positive by microbiological culture and clinical criteria. Results show that it could be a very useful tool to increase detection efficiency of tuberculosis disease in low bacilus load samples. Furthermore, its low cost and friendly using make it feasible to run in poor regions.

Rapid and biosecure diagnostic test for tuberculosis

Early and rapid detection of the causative organism is necessary in tuberculosis. We present here an integrated and dedicated molecular biology system for tuberculosis diagnosis. One hundred and eighty-nine (189) biologic specimens from patients strongly suspected by clinical parameters of tuberculosis were studied by Ziehl-Neelsen staining, cultivation on a solid medium, and by a balanced heminested fluorometric PCR system (Orange G3TB) that preserves worker safety and produces a rather pure material free of potential inhibitors. DNA amplification was carried out in a low cost using a tuberculosis thermocycler-fluorometer. The double stranded DNA produced is fluorometrically detected. The whole reaction is carried out in one single tube which is never opened after adding the processed sample, thus minimizing the risk of cross contamination with amplicons. The assay is able to detect 30 bacilli/ml of sample having a 99.8 % inter-assay coefficient of variation. PCR was positive in 36 (18.9 %) tested samples (33 of them were smear-negative). In our study, it yields a preliminary overall sensitivity of 97.4 %. In addition, its overall specificity is 98.7 %. The total run time of the test is 4 h with two and a half real working hours. All PCR-positive samples also had a positive result by microbiological culture and clinical criteria. The results obtained showed that it could be a very useful tool to increase efficiency in detecting the tuberculosis disease in low bacillus inoculum samples. Furthermore, its low cost and friendly usage make it feasible to be used in regions with poor development.

Polyclonal antibody against conserved sequences of mce1A protein blocks MTB infection in macrophages

The pathogenesis of Mycobacterium tuberculosis is largely due to its ability to enter and survive within human macrophages. It is suggested that a specific protein namely mammalian cell entry protein is involved in the pathogenesis and the specific gene for this protein mce1A has been identified in several pathogenic organisms such as Rickettsia, Shigella, Escherichia coli, Helicobacter, Streptomyces, Klebsiella, Vibrio, Neisseria, Rhodococcus, Nocardioides, Saccharopolyspora erthyrae, and Pseudomonas. Analysis of mce1 operons in the above mentioned organisms through bioinformatics tools has revealed the presence of unique sequences (conserved regions) suggesting that these sequences may be involved in the process of infection. Presently, the mce1A full-length (1,365 bp) region from Mycobacterium bovis and its conserved regions (303 bp) were cloned in to an expression vector and the purified expressed proteins of molecular weight ~47 and ~11 kDa, respectively, were injected to rabbits to raise the polyclonal antibodies. The purified polyclonal antibodies were checked for their ability to inhibit the Mycobacterium infection in cultured human macrophages. In macrophage invasion assay, when antibody added at high concentration, decrease in viable counts was observed in all cell cultures within the first 5 days after infection, where the intracellular bacterial CFU obtained from the infected MTB increased by the 3rd day at low concentration of antibody. The macrophage invasion assay has indicated that the purified antibodies of mce1A conserved region can inhibit the infection of Mycobacterium.

Analysis of sequence diversity among IS6110 sequence of Mycobacterium tuberculosis: possible implications for PCR based detection

The IS6110 belongs to the family of insertion sequences (IS) of the IS3 category. This insertion sequence was reported to be specific for Mycobacterium tuberculosis complex and hence is extensively exploited for laboratory detection of the agent of tuberculosis and for epidemiological investigations based on polymerase chain reaction. IS6110 is 1361-bp long and within this sequence different regions have been utilized as targets in the identification of M. tuberculosis by PCR. However, the results are not always consistent, specific and sensitive. In recent years, a few clinical investigations raised concerns over IS6110 specificity and sensitivity in the diagnosis of tuberculosis due to false-positive (homology with other target DNA besides M. tuberculosis) or false negative (due to absence of copies of IS6110) results with IS6110 specific primers. To unravel the variations in IS6110 sequences, an insilico analysis of IS6110 sequence of different strains of M. tuberculosis was carried out. Our results of comparative analysis of IS6110 insertion sequences of M. tuberculosis complex suggests that, IS6110 insertion sequences harbored variations in its sequence, which is evident from the phylogenetic analysis. Importantly, IS6110 sequence has divergence within the copies of same strain and formed different clusters. A list of IS6110 specific primers used in various clinical investigation of tuberculosis was obtained from the literature and their performance scrutinized. Our study emphasizes the need to develop PCR assays (multiplex format) targeting more than one region of the genome of M. tuberculosis.

Comparative evaluation of two polymerase chain reactions targeting different genomic regions to detect Mycobacterium tuberculosis in sputum

PURPOSE

Tuberculosis remains an important health problem all over the world, especially in resource poor settings like India. The Ziehl-Neelsen (ZN) staining of sputum smear is still the method of choice in the diagnosis of tuberculosis in spite of its low sensitivity and specificity. This paper evaluates comparison of two different polymerase chain reaction (PCR) assays with sputum smear findings to detect Mycobacterium tuberculosis.

MATERIALS AND METHODS

A total of 191 sputum samples were collected from 84 patients attending a tertiary care hospital, who were suspected of having pulmonary tuberculosis, were examined by PCR targeting two different genomic regions, namely, TRC 4 by non-nested format and IS6110 insertion element by nested format in comparison to ZN staining of sputum smears.

RESULTS

Among the patients tested, 20.24% (Mid-p 95%CI: 31.5-52.4) were smear positive, 7.14% (Mid-p 95%CI: 2.94-14.26) were positive by TRC 4 PCR and 41.67% (Mid-p 95%CI: 12.7-29.8) were positive by IS6110 nested PCR (nPCR). The median age of overall positive cases was 42 years. Among the nPCR positives, the median for age of rural and peri-urban community was 46 and 32 years, respectively. The kappa coefficient between smear findings and TRC4 PCR findings was 0.27 and an agreement of 0.83 was observed (Z = 2.99; one-tailed P = 0.001). TRC 4 PCR picked two unique positives that were negative by smear and IS6110 nPCR.

CONCLUSION

The non-nested TRC 4 PCR showed inability for accurate detection of M. tuberculosis in sputum samples. The study concluded that the nPCR targeting IS6110 is superior and more sensitive than TRC 4 PCR.

Comparative evaluation of nested PCR and conventional smear methods for the detection of Mycobacterium tuberculosis in sputum samples

BACKGROUND

With 1.8 million new cases each year, India carries 20% of the global burden of tuberculosis, a situation that is now further exacerbated with the emergence of drug resistance. The current diagnostic technique suggested by the Government of India's Revised National Tuberculosis Control Programme is Ziehl-Neelsen staining of a sputum smear. This technique is known to be inadequate.

OBJECTIVE

The aim of this study was to evaluate nested PCR (nPCR) in the detection of pulmonary tuberculosis in sputum samples in comparison with conventional smear findings, in an effort to improve detection rates from those obtained by the smear-alone approach.

STUDY DESIGN

Patients attending a tertiary-care hospital (situated in a rural area of Vellore district) with clinical suspicion of pulmonary tuberculosis were prospectively recruited from mid-April 2009 to mid-December 2009 and investigated. The sputum samples were stained by Ziehl-Neelsen staining for smear examination. DNA extracted from concentrated sputum was tested by nPCR, targeting the IS6110 sequence in the Mycobacterium tuberculosis genome.

RESULTS

Among 84 patients tested (median age 45.5 years), 80.95% were from the rural community and 19.05% were from the peri-urban community. Seventeen patients (20.24%; mid-p 95% CI 31.5, 52.4) tested positive by the smear examination and 35 (41.67%; mid-p 95% CI 12.7, 29.8) tested positive by nPCR. The difference in detection rates was statistically significant (chi(2) = 9.02; p = 0.002). The kappa coefficient between smear findings and nPCR findings was 0.47, which was a statistically significant agreement (Z = 4.91; p < 0.0001).

CONCLUSION

This report describes the molecular detection of M. tuberculosis in patients' sputum samples tested by the nPCR format, using IS6110 as a target sequence. A high prevalence of pulmonary tuberculosis was identified by the nPCR assay, which was shown to have a significantly higher detection rate than conventional smear staining.

Development of a real-time qPCR method for detection and enumeration of Mycobacterium spp. in surface water

A real-time quantitative PCR method was developed for the detection and enumeration of Mycobacterium spp. from environmental samples and was compared to two other methods already described. The results showed that our method, targeting 16S rRNA, was more specific than the two previously published real-time quantitative PCR methods targeting another 16S rRNA locus and the hsp65 gene (100% versus 44% and 91%, respectively).

Peptide nucleic acid array for detection of point mutations in hepatitis B virus associated with antiviral resistance

The detection of antiviral-resistant hepatitis B virus (HBV) mutations is important for monitoring the response to treatment and for effective treatment decisions. We have developed an array using peptide nucleic acid (PNA) probes to detect point mutations in HBV associated with antiviral resistance. PNA probes were designed to detect mutations associated with resistance to lamivudine, adefovir, and entecavir. The PNA array assay was sensitive enough to detect 10(2) copies/ml. The PNA array assay was able to detect mutants present in more than 5% of the virus population when the total HBV DNA concentration was greater than 10(4) copies/ml. We analyzed a total of 68 clinical samples by this assay and validated its usefulness by comparing results to those of the sequencing method. The PNA array correctly identified viral mutants and has high concordance (98.3%) with direct sequencing in detecting antiviral-resistant mutations. Our results showed that the PNA array is a rapid, sensitive, and easily applicable assay for the detection of antiviral-resistant mutation in HBV. Thus, the PNA array is a useful and powerful diagnostic tool for the detection of point mutations or polymorphisms.

In-house nucleic acid amplification tests for the detection of Mycobacterium tuberculosis in sputum specimens: meta-analysis and meta-regression

BACKGROUND

More than 200 studies related to nucleic acid amplification (NAA) tests to detect Mycobacterium tuberculosis directly from clinical specimens have appeared in the world literature since this technology was first introduced. NAA tests come as either commercial kits or as tests designed by the reporting investigators themselves (in-house tests). In-house tests vary widely in their accuracy, and factors that contribute to heterogeneity in test accuracy are not well characterized. Here, we used meta-analytical methods, including meta-regression, to identify factors related to study design and assay protocols that affect test accuracy in order to identify those factors associated with high estimates of accuracy.

RESULTS

By searching multiple databases and sources, we identified 2520 potentially relevant citations, and analyzed 84 separate studies from 65 publications that dealt with in-house NAA tests to detect M. tuberculosis in sputum samples. Sources of heterogeneity in test accuracy estimates were determined by subgroup and meta-regression analyses. Among 84 studies analyzed, the sensitivity and specificity estimates varied widely; sensitivity varied from 9.4% to 100%, and specificity estimates ranged from 5.6% to 100%. In the meta-regression analysis, the use of IS6110 as a target, and the use of nested PCR methods appeared to be significantly associated with higher diagnostic accuracy.

CONCLUSION

Estimates of accuracy of in-house NAA tests for tuberculosis are highly heterogeneous. The use of IS6110 as an amplification target, and the use of nested PCR methods appeared to be associated with higher diagnostic accuracy. However, the substantial heterogeneity in both sensitivity and specificity of the in-house NAA tests rendered clinically useful estimates of test accuracy difficult. Future development of NAA-based tests to detect M. tuberculosis from sputum specimens should take into consideration these findings in improving accuracy of in-house NAA tests.

Análise de diferentes primers utilizados na PCR visando ao diagnóstico da tuberculose no Estado do Amazonas

INTRODUÇÃO: Há diferentes primers sendo testados para a detecção do DNA do Mycobacterium tuberculosis. A acuidade da reação em cadeia da polimerase (PCR) depende da existência da seqüência alvo no bacilo e de os testes serem realizados em cepas isoladas ou em amostras clínicas. OBJETIVO: Verificar a presença das seqüências de DNA alvo mais relatadas na literatura para o diagnóstico da tuberculose em amostras clínicas usando como controle positivo as respectivas cepas de M. tuberculosis isoladas. MÉTODO: Oitenta e uma amostras clínicas de pacientes com suspeita de tuberculose foram submetidas à baciloscopia e cultivo. A técnica de PCR foi realizada nas amostras clínicas e cepas isoladas com primers específicos para os seguintes alvos: IS6110, 65 kDa, 38 kDa e MPB64. RESULTADOS: Em 24 amostras com baciloscopia e cultivo negativos, a PCR também foi negativa com todos os primers testados. Em 19 amostras com baciloscopia positiva e nas cepas isoladas obteve-se 100% de resultados positivos nas PCR, exceto nas PCR em amostras clínicas com os primers para a seqüência MPB64 (89,4%). Em 38 amostras com baciloscopia negativa e cultivo positivo, as PCR tiveram resultados variáveis, sendo que os primers específicos que amplificam o fragmento de 123 pb da seqüência IS6110 foram os que forneceram os maiores percentuais de positividade (92,1%), concordância diagnóstica (0,9143), co-positividade (94,7%) e co-negatividade (100%). CONCLUSÃO: As seqüências IS6110, 38 kDa, MPB64 e 65 kDa foram encontradas no genoma de todas as cepas de M. tuberculosis isoladas desses pacientes do Estado do Amazonas. O protocolo utilizado no processamento das amostras clínicas e os primers específicos utilizados para amplificação do fragmento de 123 pb da seqüência IS6110 demonstraram maior eficiência no diagnóstico da tuberculose pulmonar (paucibacilar) em comparação com a literatura.

One-tube semi-nested PCR-ELISA for the detection of human cytomegalovirus DNA sequences; comparison with hybridization-based and semi-nested-based PCR-ELISA procedures

Amplification of DNA targets by polymerase chain reaction (PCR) followed by their colorimetric detection in an enzyme-linked immunosorbent assay (ELISA) is increasingly used in both immunological research and clinical practice. Several methods for the labeling and detection of amplified DNA sequences have been previously described. In this study, we compared the conventional hybridization-based PCR-ELISA with a modified semi-nested and one-tube semi-nested PCR-ELISA for the detection of human cytomegalovirus (HCMV) DNA. Amplified DNA sequences were labeled with biotin and 2,4-dinitrophenyl (DNP), and detected by DNP-specific monoclonal antibody conjugated to alkaline phosphatase. Using a cloned HCMV DNA as a template, we found that the one-tube semi-nested PCR-ELISA gave a strong positive response when 20 copies of the template were used, whereas both the hybridization-based and the semi-nested-based PCR-ELISA required at least 200 template copies. The claim of higher sensitivity and robustness of the one-tube semi-nested assay was also supported by the analysis of plasma samples from patients treated for HCMV infection. Since the modified one-tube semi-nested PCR-ELISA is quick, sensitive and easy-to-perform, it can be used with advantage in routine identification of DNA targets in clinical and other specimens.

Rapid detection of pulmonary tuberculosis using the BDProbeTEC ET Mycobacterium tuberculosis Complex Direct Detection Assay (DTB)

The ability to rapidly detect tubercle bacilli in respiratory secretions was determined for the BDProbeTEC ET Mycobacterium tuberculosis Complex Direct Detection Assay in comparison with the acid-fast smear (AFS). A total of 267 respiratory specimens obtained from 89 patients were evaluated. The DTB assay was positive in 70 of 78 culture positive specimens (89.7%) and 12 of 177 culture negative specimens (6.8%). The AFS was positive in 33 of 78 culture positive specimens (42.3%) and 3 of 186 culture negative specimens (1.6%). The sensitivity, specificity, positive predictive value, and negative predictive value of DTB assay were 89.7%, 93.7%, 85.4%, and 95.7%, respectively. The sensitivity of a single DBT (74.4%) was 2.1-times greater than three AFS (35.9%). The greater cost of the DTB assay compared to the AFS was compensated by its valuable information for the diagnosis and control of tuberculosis. These results demonstrated the clinical usefulness of the DTB assay for the rapid diagnosis of tuberculosis in respiratory specimens.

Simultaneous identification of Mycobacterium genus and Mycobacterium tuberculosis complex in clinical samples by 5'-exonuclease fluorogenic PCR

Early diagnosis of tuberculosis and screening of other mycobacteria is required for the appropriate management of patients. We have therefore developed a 5'-exonuclease fluorogenic PCR assay in a single-tube balanced heminested format that simultaneously detects Mycobacterium tuberculosis complex (MTC) and members of the Mycobacterium genus (MYC) using the 16S ribosomal DNA target directly on clinical samples. One hundred twenty-seven clinical samples (65 smear negative and 62 smear positive) with a positive culture result from 127 patients were tested, including 40 negative control specimens. The finding of both a positive MTC and probe value and a positive MYC probe value confirmed the presence of MTC or mycobacteria with a 100% positive predictive value. However, a negative value for MTC or MYC did not discount the presence of mycobacteria in the specimen. Interestingly, the addition of the MYC probe allowed the diagnosis of an additional 7% of patients with tuberculosis and rapid screening of nontuberculous mycobacteria (NTM). Thus, over 75% of the patients were diagnosed with mycobacterial disease by PCR. The sensitivity was much higher on smear-positive samples (90.3%) than smear-negative samples (49.2%) and was slightly higher for MTC than NTM samples. With regard to the origin of the sample, MTC pulmonary samples gave better results than others. In conclusion, we believe this test may be useful for the rapid detection of mycobacteria in clinical samples and may be a valuable tool when used together with conventional methods and the clinical data available.

Adenosine deaminase activity in bronchoalveolar lavage in Turkish patients with smear negative pulmonary tuberculosis

The sputum smear-negative patients have been a diagnostic challenge for health professionals. Adenosine deaminase (ADA) activity has been shown to rise in various body fluids of patients with tuberculosis (Tb). A prospective clinical trial was conducted to determine the diagnostic value of ADA activity in bronchoalveolar lavage (BAL) in sputum smear-negative subjects highly suggestive for pulmonary Tb. Nineteen (M/F: 15/4, mean age 46.8 +/- 16.5 years) sputum smear-negative patients highly suggestive for pulmonary Tb constituted Group I. Acid fast bacilli (AFB) grew on sputum and/or BAL culture of all subjects in this group. Twenty-nine patients (M/F: 19/10, mean age 55.7 +/- 8.0 years) with non-tuberculous pulmonary diseases constituted Group II. Ten of them had interstitial lung disease, nine lung cancer, five pneumonia and five COPD. Twelve subjects (M/F: 7/5, mean age 48.4 +/- 12.8 years) constituted the controls (Group III) undergoing fiberoptic bronchoscopy (FOB) for various indications and the lungs were found to be normal eventually. Albumin and ADA activity levels were measured in plasma and BAL in all the subjects. LocalADA was calculated. PlasmaADA and BALADA of Group I was significantly higher (P < 0.001) than that of the other groups. LocalADA was also the highest in Group I when compared with the others (P < 0.001) but that of Group II was also higher (P < 0.01) when compared with controls. With a cut-off value derived from the control subjects, sensitivity of BALADA was 100% and specificity 85.3%. Sputum PCR results are available in a couple of days whereas that of BALADA are available in a couple of hours and BALADA costs cheaper than PCR in our country. Therefore, we conclude that BALADA may be a useful, cheaper and faster diagnostic test in sputum smear-negative patients highly suggestive for pulmonary Tb. LocalADA need not be calculated as it is also significantly higher in Group II subjects and thus not as reliable as BALADA.

Rapid detection of smear-negative Mycobacterium tuberculosis by PCR and sequencing for rifampin resistance with DNA extracted directly from slides

Conventional methods for identification of Mycobacterium tuberculosis from culture can take 6 weeks. To facilitate the rapid detection of M. tuberculosis and to assess the risks of drug resistance, we developed a technique of eluting DNA directly from sputum slides and performing PCR for the detection of M. tuberculosis DNA, followed by sequencing the rpoB gene to detect rifampin resistance. This entire process requires only 48 h. Forty-seven sputum specimens submitted for microscopy for detection of acid-fast bacilli (AFB) and for mycobacterial culture and susceptibility testing were assessed after elution from the slides and extraction. M. tuberculosis-specific DNA was amplified in a nested PCR with previously described primers (primers rpo95-rpo293 and rpo105-rpo273), followed by analysis on a 4% agarose gel for a 168-bp product. Automated sequencing was performed, and the sequences were aligned against a database for detection of anomalies in the rpoB gene (codons 511 to 533) which indicate rifampin resistance. Of the 47 sputum specimens tested, 51% (24 of 47) were culture positive (time to positive culture, 2 to 6 weeks). Smears for AFB were positive for 58% (14 of 24) of the specimens and were negative for 42% (10 of 24) of the specimens. All 24 culture-positive sputum specimens (14 microscopy-positive and 10 microscopy-negative sputum specimens) were positive by PCR with eluates from the smears. Forty-nine percent (23 of 47) of the sputum specimens were negative for M. tuberculosis by smear, culture, and PCR. Of the isolates from the culture-positive samples, five were rifampin resistant by sequencing; all five were also rifampin resistant by in vitro susceptibility testing. Of these rifampin-resistant M. tuberculosis isolates, two were microscopy negative for AFB. Patients who are negative for AFB and culture positive for M. tuberculosis can now be identified within a day, allowing institution of therapy and reducing isolation time and medical costs.