GenoType mycobacterium assay for identification of mycobacterial species isolated from human clinical samples by using liquid medium

Attenuated tuberculin skin test responses associated with Mycobacterium intracellulare sputum colonization in an adolescent TB prevalence survey in Western Kenya

INTRODUCTION

Exposure to Non-tuberculous Mycobacteria (NTM) varies regionally and may partly explain the disparate outcomes of BCG vaccination and tuberculosis (TB) susceptibility.

METHODS

We examined NTM sputum colonization, associations with clinical characteristics, and tuberculin skin test (TST) responses in an adolescent TB prevalence survey.

RESULTS

Among 5004 adolescents screened, 2281 (45.5 %) were evaluated further. TB and NTM prevalence rates were 0.3 % and 8.0 %, respectively. Among 418 NTM isolates, 103 were unidentifiable, and 315 (75 %) comprised 15 species, the most frequent being M. intracellulare (MAC) (108, 26 %), M. scrofulaceum (96, 23 %) and M. fortuitum (51, 12 %). "NTM colonized" adolescents had less frequent chronic cough and night sweats (adjusted odds ratio [aOR] 0.62, 95 % confidence interval [CI] 0.44-0.87and aOR 0.61, CI 0.42-0.89 respectively), and lower TST induration (median 11 mm (interquartile range [IQR] 0-16) vs 13 mm (IQR 6-17; p = 0.006)) when compared to "NTM not colonized" participants. MAC, but not M. scrofulaceum or M. fortuitum, was associated with decreased TST induration (median 7.5 mm (IQR 0-15) vs 13 mm (IQR 6-17) among "MAC colonized" vs "not colonized", p = 0.001).

CONCLUSION

We observed high NTM prevalence rates with species-specific associations with TST induration, consistent with a model of species-dependent heterologous immunity among mycobacteria.

Recent technological advancements in tuberculosis diagnostics - A review

Early diagnosis and on-time effective treatment are indispensable for Tuberculosis (TB) control - a life threatening infectious communicable disease. The conventional techniques for diagnosing TB normally take two to three weeks. This delay in diagnosis and further increase in detection complexity due to the emerging risks of XDR-TB (Extensively drug Resistant-TB) and MDR-TB (Multidrug Resistant-TB) are evoking interest of researchers in the field of developing rapid TB detection techniques such as biosensing and other point-of-care (POC) techniques. Biosensing technologies along with the collaboration with nanotechnology have enormous potential to boost the MTB detection and for overall management in clinical diagnosis. A diverse range of portable, sensitive and rapid biosensors based on different signal transducer principles and with different biomarkers detection capabilities have been developed for TB detection in the early stages. Further, a lot of progress has been achieved over the years in developing various point-of-care diagnostic tools including non-molecular methods and molecular techniques. The objective of this study is to present a succinct review of the available TB detection techniques that are either in use or under development. The focus of this review is on the current developments occurred in nano-biosensing technologies. A synopsis of ameliorations in different non-molecular diagnostic tools and progress in the field of molecular techniques along with the role of emerging Lab-on-Chip technology for diagnosing and mitigating the TB consequences have also been presented.

Mycobacterium diagnostics: from the primitive to the promising

The field of clinical microbiology has been revolutionised by genomic and proteomic methods, which have facilitated more rapid diagnosis and characterisation of infection in many cases. In contrast, mycobacteriological evolution has tended to retain the traditional methods of smear microscopy for detection of acid-fast bacilli to indicate mycobacteria, along with culture, and in synergy with more modern molecular methods. Thus, efforts have been focused on reducing the time to diagnosis of infection, while increasing the amount of diagnostic information available, including more definitive speciation, and more rapid susceptibility test results. Although smear microscopy remains a mainstay for the laboratory-based diagnosis of mycobacterial infection, molecular testing has vastly reduced the time needed for identification of Mycobacterium tuberculosis in particular, when compared with traditional culture-based techniques. Molecular methods may also yield antimicrobial susceptibility results through testing for the most common resistance-inducing mutations to some of the antimicrobial agents of choice. However, the diversity of resistance mutations already characterised suggests that these currently-available molecular detection systems should be accompanied by culture-based susceptibility testing. This review compares the efficacy of microscopic, phenotypic, proteomic and genotypic methods available for mycobacterial diagnosis. The diversity of methods currently in use reflects the complexity of this area of diagnostic microbiology.

Role of GenoType(®) Mycobacterium Common Mycobacteria/Additional Species Assay for Rapid Differentiation Between Mycobacterium tuberculosis Complex and Different Species of Non-Tuberculous Mycobacteria

Background:

Mycobacterium tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM) may or may not have same clinical presentations, but the treatment regimens are always different. Laboratory differentiation between MTBC and NTM by routine methods are time consuming and cumbersome to perform. We have evaluated the role of GenoType^® Mycobacterium common mycobacteria/additional species (CM/AS) assay for differentiation between MTBC and different species of NTM in clinical isolates from tuberculosis (TB) cases.

Materials and Methods:

A total of 1080 clinical specimens were collected from January 2010 to June 2012. Diagnosis was performed by Ziehl-Neelsen staining followed by culture in BacT/ALERT 3D system (bioMerieux, France). A total of 219 culture positive clinical isolates (BacT/ALERT^® MP cultures) were selected for differentiation by p-nitrobenzoic acid (PNB) sensitivity test as and BIO-LINE SD Ag MPT64 TB test considering as the gold standard test. Final identification and differentiation between MTBC and different species of NTM were further confirmed by GenoType^® Mycobacterium CM/AS assay (Hain Lifescience, Nehren, Germany).

Results:

Out of 219 BacT/ALERT^® MP culture positive isolates tested by PNB as 153 MTBC (69.9%) and by GenoType^® Mycobacterium CM/AS assay as 159 (72.6%) MTBC and remaining 60 (27.4%) were considered as NTM species. The GenoType^® Mycobacterium CM/AS assay was proved 99.3% sensitive and 98.3% specific for rapid differentiation of MTBC and NTM. The most common NTM species were; Mycobacterium fortuitum 20 (33.3%) among rapid growing mycobacteria and Mycobacterium intracellulare 11 (18.3%) among slow growing mycobacteria.

Conclusion:

The GenoType^® Mycobacterium assay makes rapid and accurate identification of NTM species as compared with different phenotypic and molecular diagnostic tool and helps in management of infections caused by different mycobacteria.

Evaluation of the speed-oligo direct Mycobacterium tuberculosis assay for molecular detection of mycobacteria in clinical respiratory specimens

We present the first evaluation of a novel molecular assay, the Speed-oligo Direct Mycobacterium tuberculosis (SO-DMT) assay, which is based on PCR combined with a dipstick for the detection of mycobacteria and the specific identification of M. tuberculosis complex (MTC) in respiratory specimens. A blind evaluation was carried out in two stages: first, under experimental conditions on convenience samples comprising 20 negative specimens, 44 smear- and culture-positive respiratory specimens, and 11 sputa inoculated with various mycobacterium-related organisms; and second, in the routine workflow of 566 fresh respiratory specimens (4.9% acid-fast bacillus [AFB] smear positives, 7.6% MTC positives, and 1.8% nontuberculous mycobacteria [NTM] culture positives) from two Mycobacterium laboratories. SO-DMT assay showed no reactivity in any of the mycobacterium-free specimens or in those with mycobacterium-related organisms. Compared to culture, the sensitivity in the selected smear-positive specimens was 0.91 (0.92 for MTC and 0.90 for NTM), and there was no molecular detection of NTM in a tuberculosis case or vice versa. With respect to culture and clinical data, the sensitivity, specificity, and positive and negative predictive values for the SO-DMT system in routine specimens were 0.76 (0.93 in smear positives [1.0 for MTC and 0.5 for NTM] and 0.56 in smear negatives [0.68 for MTC and 0.16 for NTM]), 0.99, 0.85 (1.00 in smear positives and 0.68 in smear negatives), and 0.97, respectively. Molecular misidentification of NTM cases occurred when testing 2 gastric aspirates from two children with clinically but not microbiologically confirmed lung tuberculosis. The SO-DMT assay appears to be a fast and easy alternative for detecting mycobacteria and differentiating MTC from NTM in smear-positive respiratory specimens.

Multiplex real-time PCR assay and melting curve analysis for identifying Mycobacterium tuberculosis complex and nontuberculous mycobacteria

A multiplex real-time PCR assay and melting curve analysis for identifying 23 mycobacterial species was developed and evaluated using 77 reference strains and 369 clinical isolates. Concordant results were obtained for all 189 (100%) isolates of the Mycobacterium tuberculosis complex and 169 (93.9%) isolates of nontuberculous mycobacteria. Our results showed that this multiplex real-time PCR assay is an effective tool for the mycobacterial identification from cultures.

Diagnosis of tuberculosis in an era of HIV pandemic: a review of current status and future prospects

HIV and tuberculosis co-infection interact in fundamentally important ways. This interaction is evident patho-physiologically, clinically and epidemiologically. There are several differences between HIV-infected and HIV-uninfected patients with tuberculosis (TB) that have practical diagnostic implications. TB is more likely to be disseminated in nature and more difficult to diagnose by conventional diagnostic procedures as immunosuppression progresses. As TB rates continue to increase in HIV-endemic regions, improved diagnostic techniques merit consideration as TB-control strategies. There is a need to develop more user friendly techniques, which can be adapted for use in the high-burden and low-income countries. This review focuses on the diagnostic challenges in HIV-TB co-infection with an update on the current techniques and future prospects in an era of HIV pandemic.

Biochip system for rapid and accurate identification of mycobacterial species from isolates and sputum

The accurate detection of mycobacterial species from isolates and clinical samples is important for pathogenic diagnosis and treatment and for disease control. There is an urgent need for the development of a rapid, simple, and accurate detection method. We established a biochip assay system, including a biochip, sample preparation apparatus, hybridization instrument, chip washing machine, and laser confocal scanner equipped with interpretation software for automatic diagnosis. The biochip simultaneously identified 17 common mycobacterial species by targeting the differences in the 16S rRNA. The system was assessed with 64 reference strains and 296 Mycobacterium tuberculosis and 243 nontuberculous mycobacterial isolates, as well as 138 other bacteria and 195 sputum samples, and then compared to DNA sequencing. The entire biochip assay took 6 h. The concordance rate between the biochip assay and the DNA sequencing results was 100%. In conclusion, the biochip system provides a simple, rapid, reliable, and highly accurate clinical assay for determination of mycobacterial species in a 6-h procedure, from either culture isolates or sputum samples, allowing earlier pathogen-adapted antimicrobial therapy in patients.

Identification of nontuberculous mycobacteria in clinical samples using molecular methods: a 3-year study

Nontuberculous mycobacteria (NTM) are being increasingly isolated in clinical laboratories and present technical and therapeutic challenges. In the present study, we report our experience with the identification of NTM received from 12 Lisbon hospitals over a 3-year period using GenoType Mycobacterium (CM/AS) assays (HAIN Lifescience GmbH, Nehren, Germany). Together, the two kits identified 96.6% of all NTM isolates tested. Among the 18 NTM species identified, Mycobacterium avium complex was the most frequent, although it accounted for only 34% of all NTM. Introducing these methods for the rapid identification of NTM highlights the importance of NTM as potential pathogens and assisted the selection of adequate therapy.

Identification of non-tuberculous mycobacteria: utility of the GenoType Mycobacterium CM/AS assay compared with HPLC and 16S rRNA gene sequencing

Non-tuberculous mycobacteria (NTM) causing clinical disease have become increasingly common and more diverse. A new reverse line probe assay, GenoType Mycobacterium CM/AS (Hain Lifescience), was evaluated for identification of a broad range of NTM. It was compared with phenotypic (HPLC) and molecular (DNA probes, in-house real-time multiplex species-specific PCR, 16S rRNA gene PCR and sequencing) identification techniques, which together provided the reference 'gold standard'. A total of 131 clinical isolates belonging to 31 Mycobacterium species and 19 controls, including 5 non-Mycobacterium species, was used. Concordant results between the GenoType Mycobacterium assay and the reference identification were obtained in 119/131 clinical isolates (90.8 %). Identification of Mycobacterium abscessus and Mycobacterium lentiflavum by the assay was problematic. The GenoType Mycobacterium assay enables rapid identification of a broad range of potentially clinically significant Mycobacterium species, but some species require further testing to differentiate or confirm ambiguous results.

Detecting Mycobacterium tuberculosis in Bactec MGIT 960 cultures by inhouse IS6110-based PCR assay in routine clinical practice

BACKGROUND/PURPOSE

Diagnosis of tuberculosis is challenging because the current methods are time-consuming and laborious. We have developed a method combining the Bactec MGIT 960 rapid culture system with the IS6110-based PCR for rapid diagnosis of tuberculosis.

METHODS

A total of 1745 samples from 712 patients treated at the Tri-Service General Hospital, Taipei, Taiwan between June and August 2005 were tested. An aliquot of positive Bactec MGIT 960 culture fluids was Kinyoun stained, and the samples positive for Kinyoun staining were directly assayed by the IS6110-based PCR. The same samples were also examined by the conventional methods for identification of Mycobacterium tuberculosis complex.

RESULTS

One hundred and four samples from 62 patients were positive according to the Bactec MGIT 960 system. Among these, 59 (56.7%) were positive and 45 (43.3%) were negative according to the IS6110-based PCR. Compared with the conventional identification methods, the IS6110-based PCR assay correctly identified all 59 M. tuberculosis isolates and gave negative results for all nontuberculosis mycobacteria. The mean turnaround time for M. tuberculosis identification by this combined method was 6.41 days for smear-positive and 14.33 days for smear-negative specimens. The sensitivity of the IS6110-based PCR assay was determined to be 5 cells or 0.1 pg of mycobacterial DNA.

CONCLUSION

The combined use of the automated Bactec MGIT 960 system and the IS6110-based PCR assay is sensitive and rapid for the detection of M. tuberculosis complex, and we recommend that this method be used routinely for identification of mycobacteria in clinical laboratories.

Assessment of cross-reactivity between Mycobacterium bovis and M. kansasii ESAT-6 and CFP-10 at the T-cell epitope level

Cross-reactivity between Mycobacterium kansasii ESAT-6 and CFP-10 homologues and their M. bovis counterparts can confound the interpretation of immunodiagnostic tests for tuberculosis. M. kansasii is a nontuberculous mycobacterial species cultured from skin test-positive cattle in Great Britain. Using peptides derived from M. bovis and M. kansasii ESAT-6 and CFP-10 regions that differ between these species, we investigated the species specificity and cross-reactivity at the level of individual bovine T-cell epitopes. Our results demonstrated that all peptides tested are fully cross-reactive, with the exception of one ESAT-6-derived peptide that harbored an M. bovis-specific epitope(s) when it was recognized in the context of bovine leukocyte antigen (BoLA)-DQ but that was cross-reactive with its M. kansasii homologues when it was restricted by BoLA-DR. This observation further highlights that prediction of species specificity by comparing sequence identity/homology alone is not sufficient and that individuals with diverse major histocompatibility complex constellations need to be tested to characterize the cross-reactivity or species specificity of peptide-based reagents.

Evaluation of the GenoType Mycobacteria Direct assay for detection of Mycobacterium tuberculosis complex and four atypical mycobacterial species in clinical samples

We evaluated GenoType Mycobacteria Direct (GTMD), a novel commercial assay based on nucleic acid sequence-based amplification technology, for the detection of Mycobacterium tuberculosis complex, M. avium, M. intracellulare, M. kansasii, and M. malmoense directly from clinical specimens. A total of 134 respiratory and extrapulmonary samples from 65 patients were processed. Sensitivity, specificity, positive predictive, and negative predictive values for GTMD were 92, 100, 100, and 77%, respectively. The GMTD technique is useful, reliable, and rapid when used during the normal routine of a clinical laboratory.

Diagnostic moderne de la tuberculose

Microscopic examination of sputum smears (search for acid-fast bacilli or AFB) is the most rapid procedure for diagnosis of contagious tuberculosis. Gene amplification is not yet reliable for direct detection of M. tuberculosis in clinical specimens that are AFB smear-negative. Culture (3 to 8 weeks on Lowenstein-Jensen medium or 1 to 4 weeks in liquid media) remains essential to identify AFB and conduct antibiotic susceptibility testing. AFB from culture can be identified in a few hours by molecular approaches with specific DNA probes. Results of susceptibility testing, even in liquid media, are not available until 2 to 4 weeks after the recovery of specimens, although mutations of the rpoB and katG 315 genes, which confer resistance to rifampin and isoniazid, can be detected within hours by molecular hybridization with specific probes fixed on strips. Immunologic tests that measure the interferon gamma produced by sensitized lymphocytes are promising tools for the diagnosis of latent tuberculosis.

Evaluation of the new GenoType Mycobacterium assay for identification of mycobacterial species

The new commercial assay GenoType Mycobacterium, intended for the identification of mycobacteria, was evaluated with a panel of 197 strains belonging to 86 different taxa. The system, which relies on solid-phase reverse hybridization, is composed of two different kits: GenoType CM for the identification of more frequently detected mycobacterial species and GenoType AS for less common species. The sensitivity and specificity were 97.9% and 92.4% for the CM kit and 99.3% and 99.4% for the AS kit. Our results show that the system may represent a useful tool to substantially enlarge the number of mycobacteria that can be reliably identified in clinical laboratories.

Mycobacteria in drinking water distribution systems: ecology and significance for human health

In contrast to the notorious pathogens Mycobacterium tuberculosis and M. leprae, the majority of the mycobacterial species described to date are generally not considered as obligate human pathogens. The natural reservoirs of these non-primary pathogenic mycobacteria include aquatic and terrestrial environments. Under certain circumstances, e.g., skin lesions, pulmonary or immune dysfunctions and chronic diseases, these environmental mycobacteria (EM) may cause disease. EM such as M. avium, M. kansasii, and M. xenopi have frequently been isolated from drinking water and hospital water distribution systems. Biofilm formation, amoeba-associated lifestyle, and resistance to chlorine have been recognized as important factors that contribute to the survival, colonization and persistence of EM in water distribution systems. Although the presence of EM in tap water has been linked to nosocomial infections and pseudo-infections, it remains unclear if these EM provide a health risk for immunocompromised people, in particular AIDS patients. In this regard, control strategies based on maintenance of an effective disinfectant residual and low concentration of nutrients have been proposed to keep EM numbers to a minimum in water distribution systems.

Activity of rifampin against Mycobacterium tuberculosis in a reference center

Rifampin is a bactericidal antibiotic that acts both on extra- and intracellular bacilli. It inhibits RNA synthesis by binding to the beta-subunit in the RNA polymerase. A study was conducted on rifampin resistance from 1993 to 2002 with 1,794 Mycobacterium tuberculosis strains submitted to Mycobacteria Reference Center, Córdoba, Spain. A total of 1,460 of these strains came from pulmonary specimens and 235 from extrapulmonary specimens. All strains were identified by conventional morphological, bacteriological, biochemical, genetic, and chromatographic methods. For 99 strains, the source was not indicated. Initially, the BACTEC 460 TB system was used for antibiotic sensitivity testing. Since 1996, the ESP II system was also used. The strains ATCC27294 (sensitive to streptomycin, rifampin, ethambutol, and isoniazid) and ATCC38838 (resistant to rifampin) were used as controls. The resistance degree detected was 10.03%, of which 1.2% and 8.7% corresponded to primary and secondary resistances, respectively. A total of 137 strains showed multiresistance. The surveillance of resistance and of the potential factors that may lead to an increase in resistance is thus warranted.

The genetics of nontuberculous mycobacterial infection

The molecular aetiology of familial susceptibility to disseminated mycobacterial disease, usually involving weakly pathogenic strains of mycobacteria, has now been elucidated in more than 30 families. Mutations have been identified in five genes in the interleukin-12-dependent interferon-gamma pathway, highlighting the importance of this pathway in human mycobacterial immunity. Knowledge derived from the study of these rare patients contributes to our understanding of the immune response to common mycobacterial pathogens such as Mycobacterium tuberculosis and Mycobacterium leprae, which remain major public health problems globally. This knowledge can be applied to the rational development of novel therapies and vaccines for these important mycobacterial diseases.