Comparative evaluation of two commercial amplification assays for direct detection of Mycobacterium tuberculosis complex in respiratory specimens.

Two commercial assays detecting the presence of Mycobacterium tuberculosis complex in clinical specimens by rRNA target amplification (Gen-Probe Amplified M. tuberculosis Direct Test [AMTD]) and PCR (Amplicor) were evaluated. The tests were applied to 327 digested, decontaminated respiratory specimens collected from 236 patients. Results were compared with those of acid-fast staining and culture. The combination of culture and clinical diagnosis was considered the "gold standard." A total of 60 specimens were collected from 27 patients with a diagnosis of pulmonary tuberculosis. Thirteen of these specimens were from patients receiving standard antituberculosis therapy and therefore were not included in the comparison. Of the remaining 47 specimens, 33 were smear positive, 40 were culture positive, 45 were AMTD positive, and 39 were Amplicor positive. After resolution of discrepant results, the overall sensitivities, specificities, and positive and negative predictive values were 77, 100, 100, and 95 for staining; 87, 100, 100, and 97.4 for culture; 95.9, 98.9, 94, and 99.2 for AMTD; and 85.4, 99.6, 97.9, and 97.1 for Amplicor, respectively. Agreement between AMTD and Amplicor assay results was 96.8%. It is concluded that although both nucleic acid amplification methods are rapid and specific for the detection of M. tuberculosis complex in respiratory specimens, AMTD appeared to be more sensitive than Amplicor.     

Evaluation of a commercial probe assay for detection of rifampin resistance inMycobacterium tuberculosis directly from respiratory and nonrespiratory clinical samples

A commercial assay (Inno-Line Probe Assay; Innogenetics, Belgium) was evaluated to determine its ability to detect rifampin resistance inMycobacterium tuberculosis directly from clinical specimens. Fifty-nine selected specimens (42 respiratory and 17 nonrespiratory) culture positive forMycobacterium tuberculosis were tested along with their corresponding isolates in culture. The results were compared with those obtained by in vitro susceptibility testing. The results of the line probe assay to detect rifampin resistance inMycobacterium tuberculosis present in clinical specimens and in cultured isolates were concordant for 58 of 59 (98.3%) isolates (95% confidence limits = 90.9–99.9%). The line probe assay failed only once, when a fecal specimen was tested; no amplification was observed due to the presence of inhibitory compounds. The most frequently observed mutation was His₅₂₆Asp (58.7%), followed by the His₅₂₆Tyr (23.9%); together, they represented 82.6% of rifampin-resistant samples. In conclusion, the Inno-Line Probe Assay is a rapid, useful method for detecting the presence ofMycobacterium tuberculosis complex and its resistance to rifampin directly from clinical specimens and culture. Moreover, since rifampin resistance is a potential marker for multidrug resistance inMycobacterium tuberculosis, this assay may constitute an important tool for the control of tuberculosis.     

Evaluation of a commercial rRNA target amplification assay for detection ofMycobacterium tuberculosis complex in respiratory specimens

Seventy-one respiratory samples were analyzed in a new commercially available target rRNA amplification assay aimed at detectingMycobacterium tuberculosis complex directly in patient specimens. The assay (Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test) correctly identified 26 of 27 samples positive forMycobacterium tuberculosis and 43 of 44 samples negative forMycobacterium tuberculosis in culture. When appropriate controls are performed, the assay also performs well with other specimens, such as tissue biopsies, lymph node or bone marrow aspirates and pleural and ascitic exudates.     

Mechanisms of mycobacterial persistence in tuberculosis

Tuberculosis is one of the world's most devastating diseases, with more than two million deaths and eight million new cases occurring annually. Mycobacterium tuberculosis evades the innate antimicrobial defenses of macrophages by inhibiting the maturation of its phagosome to a bactericidal phagolysosome. Phagosome maturation is dependent on macrophage Ca(2+) signaling, which results in the recruitment of cytosolic calmodulin (CaM) to the phagosome membrane and subsequent focal activation of CaM kinase II (CaMKII). M. tuberculosis blocks this process via inhibition of a macrophage enzyme, sphingosine kinase, which is a proximal generator of Ca(2+) signaling during phagocytosis. This results in a failure of assembly of the Ca(2+)/CaM/CaMKII signaling complex on the membrane of the mycobacterial phagosome and the bacilli's persistence and replication in a protective intracellular niche. Pharmacologic or physiologic reversal of this inhibition of macrophage Ca(2+) signaling restores the normal sequence of phagosome maturation, resulting in decreased intracellular viability of M. tuberculosis.     

Use of allele-specific amplification and analysis of conformation polymorphism for detecting rifampicin resistance of clinical strains ofMycobacterium tuberculosis

Analysis of 90 clinical strains ofM. tuberculosis demonstrated the possibility of using allele-specific amplification for detecting mutations determining rifampicin resistance. Successive use of two allele-specific primers helped us to detect 85% resistant strains. Other strains were studied using conformation polymorphism analysis of single-stranded DNA fragments. Consecutive use of two assays correctly identified 98% resistant strains. Translated fromByulleten' Eksperimental'noi Biologii i Meditsiny, Vol. 128, No. 11, pp. 555–558, November, 1999     

Clinical evaluation of a commercial ligase-based gene amplification method for detection ofMycobacterium tuberculosis

The purpose of this study was to evaluate the clinical usefulness of a commercial ligase-based gene amplification method (LCxMycobacterium tuberculosis test; Abbott Laboratories, USA) for detection ofMycobacterium tuberculosis. The tuberculosis infection rate among clinical samples was 10.6%. The sensitivity, specificity, and positive and negative predictive values were 23.5%, 100%, 100%, and 91.7%, respectively, with the fluorochrome auramine stain; 32.4%, 100%, 100%, and 92.6%, respectively, with culture; and 76.5%, 95.8%, 68.4% and 97.2%, respectively, with the gene amplification method. When only samples from patients without current or previous treatment were studied, the sensitivity was 36.4% with the auramine stain, 63.6% with culture, and 100% with the gene amplification assay. The mean treatment time for culture-negative and assay-negative samples was greater than that of culture-negative and assay-positive samples. The LCxMycobacterium tuberculosis test is a sensitive method for detection and identification ofMycobacterium tuberculosis. It produces few false-positive results. However, as it can remain positive after the culture becomes negative, it is not recommended for evaluation of treatment efficiency.     

Phylogenetic reconstruction within Mycobacterium tuberculosis Beijing genotype in northwestern Russia

A selection of genetic markers was used to study the evolution of Mycobacterium tuberculosis Beijing family strains in northwestern Russia. A total of 221 of 434 epidemiologically unlinked isolates studied in 1996-2001 belonged to the Beijing family as determined by standard spoligotyping (signals 35-43). Ninety-six percent of these Beijing isolates ("typical") were closely related in IS6110-RFLP (D > 0.85) while 9 remaining isolates (2 different profiles, "atypical") were more distant from the rest (D = 0.6-0.7). Further analysis was performed on a selection of 12 typical and both atypical Beijing strains with different IS6110-RFLP profiles (2 isolates each). All 28 Beijing isolates studied had the KatG 463Leu allele, an intact mtp40 fragment of the mpcA gene, and an identical structure of the DR locus (15 DVRs) with an upstream IS6110 copy in opposite orientation. The IS6110-RFLP based neighbor-joining (distance) and quartet-puzzling (maximum-likelihood) trees showed that the branch lengths were considerably longer for atypical Beijing strains. Typical Beijing strains had the 1.02 kb Rv3135 PPE-family gene and two IS1547 copies (iplA and iplB) one of them (iplB) disrupted by IS6110 insertion. Atypical Beijing strains had the 1.97 kb Rv3135 gene and a single intact IS1547/iplA copy. We suggest that the M. tuberculosis Beijing family strains currently circulating in the northwest of Russia are relatively ancient and thus appear to be endemic in this region since evolutionarily distant time. The prevalent typical Beijing strains (96%) are likely to be of monophyletic origin and their ongoing dissemination has started recently: these strains differ in rapidly evolving IS6110-RFLP but have identical structure of other polymorphic genome regions studied. The atypical Beijing strains (4%) are evolutionary older; they probably had a common (unknown) ancestor with typical Beijing strains.     

Characterisation of rpsL, rrs and embB mutations associated with streptomycin and ethambutol resistance in Mycobacterium tuberculosis

In order to characterise molecular mechanisms of first-line drug resistance in Mycobacterium tuberculosis and to evaluate the use of molecular markers of resistance (gene point mutations), we analysed 66 multi-drug-resistant (MDR) isolates from Latvian tuberculosis patients. They were all resistant to rifampin (RIF), isoniazid (INH) and streptomycin (SM), and 33 were resistant to ethambutol (EMB). Enzymatic digestion by MboII and nucleotide sequencing of the rpsL gene fragment detected a single nucleotide substitution K43R in 40 (61%) of the 66 SM-resistant M. tuberculosis isolates. Of the other 26 SM-resistant isolates, 16 (24%) had mutations at positions 513A-->C and 516C-->T of the rrs gene and 10 (15%) had the wild-type sequence. The single-stranded DNA conformation polymorphism (SSCP) method was used to detect mutations in the embB gene associated with EMB resistance. Substitutions in the embB gene were found by SSCP analysis in 15 (45%) and by sequencing in 17 (52%) of the 33 EMB-resistant isolates. Surprisingly, SSCP revealed a nucleotide mutation at codon M306 in five (15%) of 33 in vitro EMB-susceptible MDR isolates.     

Comparison of in-house PCR with conventional techniques and Cobas Amplicor M. tuberculosis kit for detection of Mycobacterium tuberculosis

PURPOSE: Polymerase chain reaction (PCR) assay, introduced as a fast and sensitive diagnostic method, is useful in detecting Mycobacterium tuberculosis. The purpose of this study was to evaluate the usefulness of in-house PCR assay in the detection of Mycobacterium tuberculosis by comparing PCR results with conventional diagnostic techniques and Cobas Amplicor M. tuberculosis kit. MATERIALS AND METHODS: We retrospectively assessed the diagnostic yield of in-house PCR method employed for the amplification IS6110 sequences in 2,973 specimens. We also compared in-house PCR with Cobas Amplicor M. tuberculosis kit in 120 specimens collected from June to July 2006. Routine acid-fast stain (AFS) and culture assay were also performed and analyzed. RESULTS: Of 2,973 cases, 2,832 cases (95.3%) showed consistent results between in house PCR, AFS and culture methods, whereas 141 (4.7%) displayed inconsistent results. The sensitivities, specificities, and positive and negative predictive values of each method were as follows: 77.5%, 99.7%, 95.5%, and 98.0%, respectively for PCR; 49.2%, 100%, 100%, and 95.7%, respectively, for AFS method; and 80.7%, 100%, 100%, and 98.3%, respectively, for culture assay. Consistent results between PCR and Cobas Amplicor M. tuberculosis kit were shown in 109 cases (90.8%). The sensitivities, specificities, and positive and negative predictive values of each method were as follows: 81.3%, 98.9%, 96.3%, and 93.5% respectively for PCR and 71.9%, 100%, 100%, and 90.7%, respectively, for Cobas Amplicor kit. CONCLUSION: In-house PCR and Cobas Amplicor kit show high sensitivity and specificity, and are reliable tests in the diagnosis of tuberculosis.     

Sarcoid-like lesions associated with the immune restoration inflammatory syndrome in AIDS: absence of polymerase chain reaction detection of Mycobacterium tuberculosis in granulomas isolated by laser capture microdissection

Highly active antiretroviral therapy (HAART)-treated human immunodeficiency virus (HIV)-positive patients can develop granulomatous lesions within the first few weeks of initiating therapy. This immune syndrome, called immune restoration inflammatory syndrome (IRIS), can induce sarcoid-like lesions in tissues. The pathogenesis of these granulomas is currently unknown because no pathogen has been identified to date in the lesions using morphological and/or microbiological approaches. However, the role of certain microbes, such as Mycobacterium tuberculosis, is still debated. The aim of this study was to look for the presence of M. tuberculosis in sarcoid-like lesions occurring in 14 AIDS patients treated with HAART. We used the PCR DNA amplification method in granulomas microdissected from sections stained by hematoxylin–eosin from formalin-fixed, paraffin-embedded specimens. Results were compared to those obtained from microdissected tuberculosis (TB) granulomas (15 patients) and from microdissected sarcoidosis granulomas (12 patients). M. tuberculosis DNA was undetectable from the microdissected sarcoid-like granulomas, whereas DNA from M. tuberculosis was isolated in all the microdissected TB granulomas and was absent in the microdissected sarcoidosis granulomas. Taken together, these data showed that M. tuberculosis DNA is not associated with the presence of sarcoid-like lesions occurring in HIV-positive patients treated with HAART.     

Lung granulomas from Mycobacterium tuberculosis/HIV-1 co-infected patients display decreased in situ TNF production

Tuberculosis/HIV-1 co-infection is responsible for thousands of deaths each year, and previous studies have reported that co-infected individuals display major morphological alterations in tissue granulomas. The purpose of this study was to evaluate immunohistopathological characteristics in lung tissues from pulmonary TB/HIV-1-co-infected individuals. Following autopsy, tuberculosis-positive HIV-1-negative cases displayed granulomas with normal architecture, mainly composed of a mononuclear infiltrate with typical epithelioid, as well as giant cells, and exhibiting caseous necrosis. In contrast, lesions from the TB/HIV-1-co-infected group showed extensive necrosis, poorly formed granulomas, and a marked presence of polymorphonuclear cells. More importantly, TNF staining was greatly reduced in the TB/HIV-1-co-infected individuals. Our data suggest that HIV-1 infection alters the organization of pulmonary granulomas by modulating TNF and, possibly, cell trafficking, leading to an impaired anti-tuberculosis response.     

Tyrosine phosphatase MptpA of Mycobacterium tuberculosis inhibits phagocytosis and increases actin polymerization in macrophages

Protein tyrosine phosphatases from several microorganisms have been shown to play a role as virulence factors by modifying the phosphorylation/dephosphorylation equilibrium in cells of their host. Two tyrosine phosphatases, MptpA and MptpB, secreted by Mycobacterium tuberculosis, have been identified. Expression of MptpA is upregulated upon infection of monocytes, but its role in host cells has not been elucidated. A eukaryotic expression vector containing the mptpA cDNA has been transfected into macrophages. We report that MptpA reduced phagocytosis of mycobacteria, opsonized zymosan or zymosan, but had no effect on phagocytosis of IgG-coated particles. We also noted that the presence of F-actin at the surface of phagosomes containing opsonized zymosan was significantly increased in cells expressing MptpA. In the presence of recombinant MptpA, the process of actin polymerization at the surface of isolated phagosomes was increased; this was not the case in the presence of the phosphatase-dead mutant MptpA(C11S). MptpA had no effect when IgG-coated particles were present inside isolated phagosomes. These results indicate that, like other tyrosine phosphatases of pathogens, MptpA plays a role in phagocytosis and actin polymerization. However, MptpA had no effect on IgG particles, suggesting that its putative substrate(s) is not linked to the signaling pathways of Fcgamma receptors.     

Comparison of the mycobacteria growth indicator tube with solid culture for the detection of tuberculosis complex mycobacteria from blood

Aim of this study

The aim of this study was to compare the mycobacteria growth indicator tube and solid culture for recovery of complex tuberculosis mycobacteria from blood.

Patients and methods

One hundred and twenty-five specimens from 67 Djiboutian patients with a positive serologic diagnosis of HIV and fever were collected in an Isolator^® tube. After centrifugation and washing with phosphate-buffer, smears were prepared from the pellet for auramin staining. The remaining sediment was suspended in 1 ml of buffer. One half was inoculated into two MGIT (incubation at 30 and 37 °C into Bactec 960) and the other onto two Loewenstein–Jensen and two Coletsos medium (incubation at 30 and 37 °C).

Results

Eight cultures were contaminated: three on solid medium and MGIT simultaneously, five in MGIT only (three coagulase negative staphylococci, five enterobacteria). Fourteen strains of M. tuberculosis (six patients) and three M. canettii (two patients) (12 on solid media and MGIT, five in MGIT only) were recovered. The mean time to detection was 32.8 days for solid medium and 20.4 days for MGIT. Of a total of 25 patients with culture-proven tuberculosis, two patients had a positive blood culture only, six had blood and other specimens positive culture, 17 had a non blood specimens positive culture only.

Conclusion

MGIT processed into Bactec 960 is a viable tool for the detection of complexe tuberculosis mycobacteria from blood and the high-frequency of these mycobacteremia in HIV infected patients from country where the prevalence of tuberculosis is high is confirmed. However, the cost/benefit ratio of this bacteriologic diagnosis had to be evaluated in developping country.     

Evaluation of the enhanced amplified Mycobacterium tuberculosis direct test for direct detection of Mycobacterium tuberculosis complex in respiratory specimens.

OBJECTIVE: To evaluate the performance of the enhanced Mycobacterium Tuberculosis Direct Test (E-MTD), for the direct detection of M tuberculosis complex (MTBC) in respiratory specimens. DESIGN: Two hundred seventy-four respiratory specimens from 151 patients in respiratory isolation were tested with the E-MTD, and the results were compared with the results of mycobacterial smear, culture, and the earlier form of the test, MTD-1. RESULTS: Forty-one specimens were culture positive for mycobacteria (20 MTBC and 21 nontuberculous mycobacteria), 23 of which were smear positive (16 MTBC, 7 nontuberculous mycobacteria). Twenty-four specimens were positive by E-MTD, and 21 were positive by MTD-1. Of the 20 MTBC culture-positive specimens, 19 were positive by the E-MTD and 19 were positive by the MTD-1. The remaining specimens were MTBC negative by all methods. After resolution of discrepancies, the sensitivity, specificity, and positive and negative predictive values were 95.2%, 100%, 100%, 99.6% for the MTD-1 and 95.2%, 98.8%, 87.0%, and 99.6%, for the E-MTD. For the E-MTD smear-positive and smear-negative specimens, these same values were 93.8%, 100%, 100%, and 87.5% and 100%, 98.8%, 62.5%, and 100%, respectively. CONCLUSION: The results suggest that the E-MTD is a reliable method for the direct detection of MTBC in smear-positive respiratory specimens.     

Growth of recombinant Mycobacterium tuberculosis H37Ra in mouse macrophages

Mycobacterium tuberculosis H37Rv and H37Ra were derived from the same parental strain but differ strikingly in their virulence for experimental animals. Transfer of genetic material between these closely related strains resulted in the isolation of a number of recombinant H37Ra clones bearing the in vivo growth-promoting ivg locus of H37Rv. The recombinant strain was phagocytosed by murine peritoneal macrophages infected in vivo or in vitro and their intracellular growth rates were compared with the vector control. The intracellular growth of the recombinant was significantly faster than the vector control, but substantially slower than the wild-type H37Rv control, regardless of the method used to infect the macrophages. The slower intracellular growth observed for the recombinant strains was not due to a genetically induced metabolic defect, since they grew in synthetic liquid medium at rates equal to those observed for both H37Rv and H37Ra. Peritoneal macrophage monolayers provide a rapid and convenient assay by which to screen H37Ra recombinants for the presence of putative virulence genes.     

Simultaneous detection of respiratory viruses in children with acute respiratory infection using two different multiplex reverse transcription-PCR assays

A 4-tube multiplex RT-PCR (mRT-PCR), which showed higher sensitivity over conventional methods, was previously developed for the diagnosis of 14 viral pathogens of the respiratory tract. Herein the mRT-PCR was compared to the commercial Luminex mPCR-microsphere flow cytometry assay (Resplex II) which allows the detection of 12 different viruses. Eleven different viruses were identified in 91 nasopharyngeal swabs of children with acute respiratory infection, influenza A (IAV) and B, respiratory syncytial virus (RSV), human rhinovirus (hRhV), human echovirus, parainfluenza viruses (PIV) 1, 2, 3 and 4, human metapneumovirus (hMPV), and human coronavirus NL63. The results of the two techniques showed 53 and 40 positive patients by the Resplex II assay and mRT-PCR, respectively, with a concordance in 35 positive and 33 negative patients (74.7%). Individual RT-PCR tests were performed to control viruses not simultaneously detected by the two multiplex assays. The major virus misdiagnosed by mRT-PCR was IAV whereas the major viruses misdiagnosed by Resplex II were PIV1, 3 and 4. The mRT-PCR remains a simple, rapid, and specific assay for the specific detection of respiratory viruses, and can be easily implemented with standards in clinical laboratories at a low cost.