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

CRISPR-Cas12a-based detection and differentiation of Mycobacterium spp

Mycobacterium species cause several vital human diseases, including tuberculosis and non-tuberculous mycobacterial infections, which are treated with different drug regimens Therefore, accurate and rapid diagnosis is essential for effective treatment and controlling the spread of these pathogens. This study aims to develop an isothermal method combining RPA and CRISPR-Cas12a techniques, named as MyTRACK, to detect and differentiate major clinical mycobacteria at the species level. The assay has no cross-reactivity with limit of detection of 1 to 100 copies/reaction for various targeted mycobacteria. The results demonstrated 100 % specificity and 92.59 % to 100 % sensitivity in clinical isolates and were consistent with the culture technique with LPA for clinical samples. The MyTRACK assay is an effective, portable, rapid, and accurate screening method for mycobacterial detection and identification, especially in low-resource clinical settings.

Molecular Identification of Non-tuberculous Mycobacteria in Suspected Tuberculosis Cases in Central India

Introduction Mycobacterium tuberculosis complex (MTBC), the primary cause of tuberculosis (TB), must be accurately identified to implement effective patient management and control strategies. Non-tuberculous mycobacteria (NTM) in suspected TB cases can result in erroneous diagnoses and needless treatment. Objective The study aimed to identify NTM in patients suspected of TB at a tertiary care hospital in central India using molecular methods. Methods This prospective study enrolled 400 suspected pulmonary and extra-pulmonary TB patients. Patients between the age of two to 90 years, of either gender, new and previously treated cases, Culture positive, patients with immune-compromised status, patients not responding to ATT, HIV positive and negative, and willing to give consent were included in the study. Liquid culture via the Mycobacterial growth indicator tube (MGIT) system was used to culture mycobacteria from clinical samples. The SD Bioline Ag MPT64 Test (Standard Diagnostics, South Korea) and in-house multiplex-PCR (mPCR) were used to differentiate between Mycobacterium tuberculosis complex and NTM species for the molecular identification of NTM GenoType® Mycobacterium Common Mycobacteria (CM) assay kit (HAIN Life Science, Nehren, Germany) was used following the manufacturer's protocol. Results Only 59/400 (14.7%) of the samples produced a positive result in MGIT culture, indicating the presence of mycobacteria, and 85.25% of the remaining 341 samples were negative for mycobacterial growth. Further investigation of these 59 cultures with mPCR and SD Bioline Ag MPT64 test showed that 12 (20.33%) cultures were determined to be NTM, while the remaining 47 (79.67%) were identified as MTBC. Genotype characterization with GenoType® mycobacterium CM assay kit revealed that five of the 12 NTM isolates (41.67%) showed patterns that were consistent with Mycobacterium (M.) fortuitum, three (25%) showed patterns that were consistent with M. abscessus, and four (33.33%) showed patterns that were consistent with M. tuberculosis. Conclusion These results emphasize the value of molecular methods for precisely identifying mycobacterial species, particularly in suspected TB cases. The high prevalence of NTM in positive cultures emphasizes the significance of differentiating between MTBC and NTM to prevent misdiagnosis and ensure proper care. Understanding the epidemiology and clinical significance of these organisms in central India is made possible by the identification of particular NTM species.

Diagnostic Performance of Multiplex PCR for Detection of Mycobacterium tuberculosis Complex in Presumptive Pulmonary Tuberculosis Patients and Its Utility in Smear Negative Specimens

Objective  The primary objective of this study was to assess the diagnostic performance of multiplex polymerase chain reaction (mPCR) for the detection of Mycobacterium tuberculosis complex (MTBC) in presumptive pulmonary TB patients, in the setting of a tertiary level teaching hospital in central India, in comparison to liquid culture using BACTEC mycobacteria growth indicator tubes (MGIT) 960 TB system as the gold standard. The secondary objective was to assess the performance of mPCR for Ziehl Neelsen smear negative samples and ascertain the utility of this assay in smear negative samples. Materials and Methods  Sputum or bronchoalveolar lavage samples were collected from patients who were adults, aged 18 years or older, presenting with presumptive pulmonary TB, and subjected to three microbiological investigations, that is, Ziehl Neelsen staining, mycobacterial culture using mycobacterial growth indicator tubes in the BD BACTEC MGIT 960 instrument, and the mPCR. Statistical Analysis  For statistical analysis, 2 × 2 contingency tables were prepared and analyzed separately for all samples and for smear-negative samples using GraphPad and MedCalc tools. Sensitivity, specificity, positive predictive value, and negative predictive value (NPV) of mPCR were calculated by taking MGIT culture as the reference standard. Results  For all samples ( n  = 114), sensitivity of mPCR for the detection of (MTBC) was 93.48% (95% confidence interval [CI]: 82.10-98.63%), specificity was 95.59% (95% CI: 87.64-99.08%), positive predictive value (PPV) was 93.48% (95% CI: 82.54-97.75%), and NPV was 95.59% (95% CI: 87.87-98.48%). For smear negative samples ( n  = 80), sensitivity was 80.00% (95% CI: 51.91-95.67%), specificity was 98.46% (95% CI: 91.72-99.96%), PPV was 92.31% (95% CI: 62.80-98.84%), and NPV was 95.52% (95% CI: 88.57-98.33%). Conclusion  In this study, we were able to demonstrate the good performance characteristics of the mPCR for the detection of MTBC from clinical samples of patients with presumptive pulmonary tuberculosis, with MGIT liquid culture as the reference standard. It may be concluded that mPCR can be considered equivalent to MGIT culture in terms of clinical decision making and yield of positivity, owing to the good sensitivity and specificity for the detection of MTBC.

Trends and Species Diversity of Non-tuberculous Mycobacteria Isolated From Respiratiroy Samples in Northern China, 2014–2021

Background

Pulmonary non-tuberculous mycobacteria (NTM) infection has become a public health concern in China and around the world. The objective of this study was to describe the longitudinal changes in the frequency and diversity of NTM in northern China.

Methods

We retrospectively analyzed data on mycobacterium species in Beijing Chest Hospital from January 2014 to December 2021. The isolates were identified to species level by targeted DNA sequencing.

Results

After excluding duplicates, 1,755 NTM strains were analyzed, which were from 27 provinces in China over 8 years. Among all mycobacteria, the proportion of NTM increased each year, from 4.24% in 2014 to 12.68% in 2021. Overall, 39 different NTM species were identified, including 23 slow growing mycobacteria (SGM) and 16 rapid growing mycobacteria (RGM). The most common species were M. intracellulare (51.62%), M. abscessus (22.22%), M. kansasii (8.32%), M. avium (7.75%) and M. fortuitum (2.05%). The number of NTM species identified also increased each year from 9 in 2014 to 26 in 2021. Most species showed stable isolation rates over the years; however, the proportion of M. avium increased from 3.85 to 10.42% during the study period. Besides, 81 non-mycobacteria strains, including Gordonia (21 isolates), Nocardia (19 isolates) and Tsukamurella (17 isolates), etc., were also discovered.

Conclusion

The proportion of NTM and species diversity increased considerably in northern China from 2014 to 2021. M. intracellulare was the most common NTM isolated among respiratory specimens, followed by M. abscessus and M. kansasii. Rare NTM species and non-mycobacteria pathogens also need attention.

Evaluation of the MeltPro Myco Assay for the Identification of Non-Tuberculous Mycobacteria

Purpose

Methods

Results

Conclusion

Characterization of Non-tuberculous Mycobacteria by Line Probe Assay Isolated from Pulmonary Tuberculosis Suspected Patients at Rajasthan

Non-tuberculous Mycobacteria (NTM) are emerging as an important opportunistic pathogen. Since clinical presentation of NTM infection is similar to tuberculosis (TB), patients present as suspected TB or drug resistant TB. Presently in the National Tuberculosis Elimination Programme (NTEP ) NTM are not being speciated, but there is an urgent need to characterize the NTM so that appropriate treatment can be given as many species are multi-drug resistant. The purpose of the present study was to use Line Probe Assay (LPA) i.e. GenoType Mycobacterium CM/AS assay to characterize NTM for rapid early reporting and to know the pattern of NTM at Rajasthan. Sputum samples from 5000 TB and Multi Drug Resistant TB (MDRTB) suspect patients were processed and cultured on Mycobacterium Growth Indicator Tube (MGIT). Culture isolates found positive for mycobacteria in Ziehl Neelsen (ZN) staining and negative by MPT64 antigen test were then subjected for GenoType Mycobacterium CM/AS Among sputum samples from 5000 patients 1520 (30.4%) patient samples were positive for mycobacteria, among these 1488 (97.9%) were Mycobacterium tuberculosis (MTB) and 32 (2.1%) were NTM, among them 56.2% were Mycobacterium intracellulare, 21.8% Mycobacterium abscessus, 9.3% Mycobacterium fortuitum, 1% Mycobacterium simiae and 9.3% isolates showed invalid results. Incidence of NTM was very low (2.1%) among them M. intracellulare and M. abscessus were the most commonly isolated species, GenoType Mycobacterium CM/AS assay was found to be easy, rapid and reliable test giving valid results in 91% cases in 3-5 days of getting growth.

Rapid Identification of Mycobacterium tuberculosis Complex Using Mass Spectrometry: A Proof of Concept

Mycobacteria that form the Mycobacterium tuberculosis complex are responsible for deadly tuberculosis in animals and patients. Identification of these pathogens at the species level is of primary importance for treatment and source tracing and currently relies on DNA analysis, including whole genome sequencing (WGS), which requires a whole day. In this study, we report the unprecedented discrimination of M. tuberculosis complex species using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), with WGS as the comparative reference standard. In the first step, optimized peptide extraction applied to 36 isolates otherwise identified in five of the 11 M. tuberculosis complex variants by WGS yielded 139 MALDI-TOF spectra, which were used to identify biomarkers of interest that facilitate differentiation between variants. In a second step, 70/80 (88%) other isolates were correctly classified by an algorithm based on specific peaks. This study is the first to report a MALDI-TOF-MS method for discriminating M. tuberculosis complex mycobacteria that is easily implemented in clinical microbiology laboratories.

Non-tuberculous mycobacteria: a disease beyond TB and preparedness in India

BACKGROUND AND METHODS

Fifty-six Indian studies on NTM diseases were selected between 1981 and 2020 from various electronic databases (PubMed, EMBASE, Medline, BIOSIS preview, and Scopus) for systematic review.

RESULTS

NTM isolation rates increased from 0.9% between 2001 and 2010 to 1.6% between 2011 and 2020. Prevalence of NTM-pulmonary disease (NTM-PD) among presumptive-TB patients in India was 1.1% (395/34,829). M. avium complex (MAC) (19%) was most commonly isolated from pulmonary specimens followed by M. chelonae (10%), M. fortuitum (9.8%), and M. abscessus (8.8%). M. fortuitum (35.5%), M. chelonae (23.6%) and M. abscessus (15%) were frequently reported from extra-pulmonary specimens. Patients with NTM-PD were mostly treated with a macrolide-based three-drug regimen. Clarithromycin-based-drug regimen in combination with amikacin, ciprofloxacin and several other drugs (rifampicin, imipenem, ofloxacin, linezolid, azithromycin) was used for treatment of EP-NTM. Median duration of the treatment in NTM-PD was 12 months, (6-18 months) whereas it was 6 months (3.1-8.7 months) in EP-NTM. Treatment was successful in 45% (19/42) of NTM-PD patients and 75% (93/124) of EP-NTM patients.

CONCLUSION

It is concluded from this review that most Indian studies have published laboratory data on NTM isolation and speciation and lacked information on clinical, microbiological and radiological correlation and treatment outcome details. Future studies should address these issues while publishing on NTM diseases.

Drug susceptibiity testing of nontuberculous mycobacteria by broth microdilution method

INTRODUCTION

-Incidence of Nontuberculous mycobacteria (NTM) has been increasing in past few years. Treatment of NTM differs from Mycobacterium tuberculosis. For proper treatment, it's important to carry out Drug Susceptibility Testing of NTM. Method of DST for NTM is different from MTB and is not available in most laboratories.

METHOD

-We performed DST on 122 isolates of NTM. Amikacin, Ciprofloxacin, Trimethoprim, Doxycycline, Moxifloxacin, Clarithromycin, Minocycline and Cefoxitin were used for Rapid Growing Mycobacteria (RGM) and Rifampicin, Clarithromycin, Ethambutol, Isoniazid and Moxifloxacin for Slow Growing Mycobacteria (SGM). M. avium Complex (MAC) was tested against Clarithromycin. Minimum inhibitor concentration was calculated as recommended by standard Clinical and Laboratory Standards Institute (CLSI) and Resazurin Microtitre Assay (REMA).

RESULT

-Most of Rapid Growing Mycobacteria were sensitive to Amikacin (76.1%) and Moxifloxacin (46.47%) while Slow Growing Mycobacteria showed only 33.3% sensitivity to Rifampicin and Moxifloxacin and 42% to Clarithromycin. M. avium-intracellulare complex showed 45-50% sensitivity to Clarithromycin. Overall, 98% concordance (Kappa = 0.98; almost perfect; 95% CI = 0.966 to 0.996) was seen between standard and REMA method of DST of NTM.

CONCLUSION

-Rapid growers showed good sensitivity to Amikacin and Moxifloxacin, while only one third SGM showed sensitivity to Rifampicin, Moxifloxacin and Clarithromycin. For proper management of NTM of eastern Rajasthan its important to know the DST profile in our area to initiate empirical therapy till the results of specific patient are available. REMA was found to give excellent concordance with standard method.

GenSeizer: a Multiplex PCR-Based Targeted Gene Sequencing Platform for Rapid and Accurate Identification of Major Mycobacterium Species

Mycobacterium tuberculosis and nontuberculous mycobacterium (NTM) infections often exhibit similar clinical symptoms. Timely and effective treatment relies on the rapid and accurate identification of species and resistance genotypes. In this study, a new platform (GenSeizer), which combines bioinformatics analysis of a large data set and multiplex PCR-based targeted gene sequencing, was developed to identify 10 major Mycobacterium species that cause pulmonary, as well as extrapulmonary, human diseases. The simultaneous detection of certain erm(41) and rrl resistance genotypes in M. abscessus was also feasible. This platform was specific and sensitive and exhibited no cross-reactivity among reference strains and a detection limit of 5 DNA copies or 50 CFU Mycobacterium/ml. In a blind comparison, GenSeizer and multigene sequencing showed 100% agreement in the ability to identify 88 clinical Mycobacterium isolates. The resistance genotypes, confirmed by whole-genome sequencing of 30 M. abscessus strains, were also correctly identified by GenSeizer 100% of the time. These results indicate that GenSeizer is an efficient, reliable platform for detecting major pathogenic Mycobacterium species.

Mycobacterium chelonae bacteraemia in a patient with myasthenia gravis receiving long-term steroid therapy

Non-tuberculous mycobacteria (NTM) are ubiquitous environmental organisms found in soil and water. Infections caused by NTM are increasing with conditions ranging from harmless colonization to invasive infections, the latter being more common in immunocompromised hosts. In this report, we present a case of bacteraemia caused by Mycobacterium chelonae, a rapidly growing NTM belonging to Class IV in the Runyon classification, in a 71-year-old male with ocular myasthenia gravis undergoing treatment with oral prednisolone. Gram staining of these organisms from blood culture can be easily overlooked or confused with diptheroids. Detection of Gram-positive bacilli should prompt Ziehl–Neelsen staining to distinguish diphtheroids from rapidly growing mycobacteria in immunosuppressed patients. In addition, speciation and antimicrobial susceptibility testing are of paramount importance in such cases as there is considerable variation in the resistance patterns between different species of NTM. Line probe assay provides a rapid and reliable method for identification of NTM to the species level, which can guide treatment with appropriate antibiotics. This case report highlights the importance of early detection of such cases so as to optimize management and improve patient outcomes.

Pulmonary non-tuberculous mycobacterial infections: current state and future management

Currently, there is a trend of increasing incidence in pulmonary non-tuberculous mycobacterial infections (PNTM) together with a decrease in tuberculosis (TB) incidence, particularly in developed countries. The prevalence of PNTM in underdeveloped and developing countries remains unclear as there is still a lack of detection methods that could clearly diagnose PNTM applicable in these low-resource settings. Since non-tuberculous mycobacteria (NTM) are environmental pathogens, the vicinity favouring host-pathogen interactions is known as important predisposing factor for PNTM. The ongoing changes in world population, as well as socio-political and economic factors, are linked to the rise in the incidence of PNTM. Development is an important factor for the improvement of population well-being, but it has also been linked, in general, to detrimental environmental consequences, including the rise of emergent (usually neglected) infectious diseases, such as PNTM. The rise of neglected PNTM infections requires the expansion of the current efforts on the development of diagnostics, therapies and vaccines for mycobacterial diseases, which at present, are mainly focused on TB. This review discuss the current situation of PNTM and its predisposing factors, as well as the efforts and challenges for their control.

Epidemiology and risk factors associated with NTM pulmonary and extrapulmonary infections in a high tuberculosis endemic Region

Introduction

Non-tuberculous mycobacteria, although identified as pathogenic to humans long time ago, are emerging as the new threat in the past two decades. Even in tuberculosis endemic country such as India, they are being isolated from the clinical specimens more often than previously. This change in trend is of concern, because they are often misdiagnosed as Mycobacterium tuberculosis or even as drug-resistant tuberculosis.

Objectives

A prospective, observational study was planned to identify the frequency and risk factors associated with pulmonary and extrapulmonary non-tuberculous mycobacterial (NTM) infections. Agreement between two commercially available molecular systems, namely GenoType Mycobacteria CM assay and matrix-assisted laser desorption/ionisation time of flight mass spectrometry (MALDI TOF MS) used in the identification of mycobacterial species is also analysed.

Materials and Methods

NTM isolated from pulmonary and extrapulmonary clinical specimens over a period of 1½ year was included in the study. Patient demographics were collected, and the risk factors associated with NTM infections were analyzed. NTM grown on culture was speciated using GenoType Mycobacteria CM assay (HAIN Life Sciences, Germany) and MALDI TOF MS (bioMerieux, France). Drug-susceptibility tests were done for rapid-growing NTM using E-test (bioMerieux, France).

Results

Eight hundred and fifty-four mycobacteria were isolated from 5009 specimens processed during the study period. Out of the mycobacteria grown, 74 (8.7%) were NTM and 780 (91.3%) were Mycobacterium tuberculosis complex. The NTM isolated from pulmonary specimens were 46 (62.16%) and from extrapulmonary sources were 28 (37.84%). The most common species isolated from pulmonary specimens was Mycobacterium intracellulare and from extrapulmonary specimens was Mycobacterium abscessus. Concordance between the two commercial assays used for the identification was 96.49%. The most common risk factor associated with pulmonary NTM was previous lung pathology, while with extrapulmonary NTM infection was previous surgical intervention. Drug-susceptibility tests for rapid growers showed amikacin and clarithromycin as the most active drugs in vitro.

Conclusions

NTM plays a significant role in causing pulmonary and extrapulmonary infections even in our part of the country with high endemicity of tuberculosis. NTM has emerged as important pathogens even in the immunocompetent patients. There is a need for rapid diagnosis and susceptibility testing of NTM to aid physicians administer timely and appropriate treatment to the patients.

Cas12a/Guide RNA-Based Platform for Rapid and Accurate Identification of Major Mycobacterium Species

Mycobacterium tuberculosis infection and nontuberculous mycobacteria (NTM) infections exhibit similar clinical symptoms; however, the therapies for these two types of infections are different. Therefore, the rapid and accurate identification of M. tuberculosis and NTM species is very important for the control of tuberculosis and NTM infections. In the present study, a Cas12a/guide RNA (gRNA)-based platform was developed to identify M. tuberculosis and most NTM species. By designing species-specific gRNA probes targeting the rpoB sequence, a Cas12a/gRNA-based platform successfully identified M. tuberculosis and six major NTM species (Mycobacterium abscessus, Mycobacterium intracellulare, Mycobacterium avium, Mycobacterium kansasii, Mycobacterium gordonae, and Mycobacterium fortuitum) without cross-reactivity. In a blind assessment, a total of 72 out of 73 clinical Mycobacterium isolates were correctly identified, which is consistent with previous rpoB sequencing results. These results suggest that the Cas12a/gRNA-based platform is a promising tool for the rapid, accurate, and cost-effective identification of both M. tuberculosis and NTM species.

Nontuberculous mycobacteria: A report of eighteen cases from a tertiary care center in India

Context

Nontuberculous mycobacteria (NTM) are ubiquitous mycobacteria present in environment and generally affect patients with either structural lung disease or immunosuppression and commonly involve lungs, lymph node, or skin.

Materials and Methods

Between July 2016 and February 2019, 18 cases of NTM were diagnosed and their relevant clinical, diagnostic, and treatment details were recorded after taking informed consent.

Results

We report 18 cases of NTM involving lungs (n = 11), skin and soft tissue (n = 3), joint (n = 2), genitourinary (n = 1), and central nervous system (n = 1). History of immunosuppression was present in two patients, whereas history of some form of intervention was seen in six patients. Mycobacterium fortuitum group (n = 5) was the most commonly isolated organism, followed by Mycobacterium avium complex (n = 4), Mycobacterium abscessus (n = 3), Mycobacterium kansasii (n = 2), and Mycobacterium chelonae (n = 1). In two patients, M. chelonae and M. abscessus were isolated in succession. Of these 18 patients, clinical response was present in 15 of the patients. Diagnosis and treatment of NTM in resource limited settings is extremely challenging.

Conclusion

Most of the patients with NTM are misdiagnosed and are treated as tuberculosis in India, sometimes with a multidrug resistance regimen, which results in significant morbidity and mortality. We present these cases to shed some light on the epidemiology of NTM in this part of India.

Newer Diagnostic Tests and their Application in Pediatric TB

The diagnosis of childhood tuberculosis is a challenge due to the pauci-bacillary nature of infection and the difficulty in obtaining appropriate sample. In the past 2-3 decades, many new tests were introduced for the diagnosis of tuberculosis (TB) and some of them have been evaluated for their application in pediatric tuberculosis as well. There is an attempt to improve smear microscopy by introducing light-emitting diode (LED) fluorescence microscopy and there are also some automated digital microscopy platforms under evaluation. Introduction of automated liquid culture platform along with rapid molecular based identification methods have considerably reduced the time delay in mycobacterial culture. Recent addition of many nucleic acid amplification platforms like Amplicor PCR, Genprobe, Xpert MTB/Rif, line probe assays, loop mediated isothermal amplification etc are also been found to be useful. Latest techniques like microarray and gene sequencing are also being used in clinical laboratories with variable results. Indirect methods of TB diagnosis like T cell based assays including tuberculin skin test and interferon-gamma release assays have their role primarily in the diagnosis of latent TB. Biomarkers are the latest addition in the battery of TB diagnostic tests facilitating diagnosis using easily accessible samples like urine, blood and breath of patients. Many biomarkers are still under evaluation and some of them are found to have a potential role as promising diagnostic tests of future.

Rapid identification of mycobacteria from positive MGIT broths of primary cultures by MALDI-TOF mass spectrometry

Background

Rapid identification of mycobacteria is important for timely treatment and the implementation of public health measures. The MGIT system ensures rapid detection of mycobacteria, but identification is usually delayed by days to weeks due to further subculture on solid medium. Matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS) was demonstrated to effectively identify mycobacteria isolates subcultured from solid or liquid media. Reports of identification directly from MGIT broths of both sterile and non-sterile clinical specimens, omitting the subculture step, were limited and not satisfactory before. Our identification method dramatically shortened delay from detection to identification of mycobacteria.

Methodology

We assessed the performance of the Vitek MS IVD version 3.0 for direct identification of NTM and M.tuberculosis from primary MGIT cultures, and assessed two sample preparation methods.

Results

Direct identification of NTM from positive MGIT broths, using MALDI-TOF VITEK MS with IVD v.3.0, generated high rates of acceptable results reaching 96.4% (80/83), and up to 100% (83/83) for sample preparations including a 0.1% SDS washing step. The sensitivity of VITEK MS to identify M.tuberculosis from MGIT tubes was 58/72 (80.6%), when using immunochromatography (ICA) test as gold standard. A characteristic colony clumping, wool-like appearance was observed in 48, and all 58 (100%) were correctly identified as M.tuberculosis using MALDI-TOF. The detection rate of M.tuberculosis complex was low (10/24, 41.6%) in the 24 MGIT tubes that was polymicrobial. Our method significantly reduced both the reagent cost and turnaround time.

Conclusions

Based on a simplified protocol, we showed that MALDI-TOF MS can be used for rapid identification of NTM directly from primary MGIT cultures within the routine clinical laboratory workflow. However, we recommend an initial ICA test to screen for M.tuberculosis complex, due to a low identification rate of M. tuberculosis in the presence of polymicrobial cultures using MALDI-TOF.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid identification of Mycobacterium abscessus

BACKGROUND

Nontuberculous mycobacteria are increasingly being implicated in infections and have become an important cause of health care associated infections. Mycobacterium abscessus, a rapidly growing mycobacteria, is of particular concern as it tends to be resistant to commonly used therapeutic options. Conventional phenotypic methods for speciation of mycobacteria are time consuming, labor intensive and not always reliable. Molecular methods require expertise and are expensive. The study was used to evaluate the use of matrix associated laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as a means of rapid identification of M. abscessus.

METHODS

35 isolates of rapidly growing Mycobacterium from an outbreak of surgical site infections at a tertiary care hospital were identified using phenotypic methods. The mycobacterial isolates were inactivated and an extraction protocol was followed. These isolates were then analyzed by MALDI biotyper (Bruker Daltonics) using biotyper software 4.0 and the mycobacterial reference database v 2.0.

RESULTS

All 35 isolates were identified as M. abscessus by MALDI biotyper but the scores obtained according to guidelines of the company were lower than previous studies with only 23 out of the 35 isolates having scores of greater 1.8 which was described as the minimum score to be achieved for reliable identification.

CONCLUSION

MALDI-TOF MS offers a rapid and inexpensive method for identification of Mycobacteria; however, the scores obtained in our study were lower than reported in other studies.

Genotyping and drug susceptibility testing of mycobacterial isolates from population-based tuberculosis prevalence survey in Ghana

Background

Mycobacterium tuberculosis complex (MTBC) and Non-tuberculosis Mycobacterium (NTM) infections differ clinically, making rapid identification and drug susceptibility testing (DST) very critical for infection control and drug therapy. This study aims to use World Health Organization (WHO) approved line probe assay (LPA) to differentiate mycobacterial isolates obtained from tuberculosis (TB) prevalence survey in Ghana and to determine their drug resistance patterns.

Methods

A retrospective study was conducted whereby a total of 361 mycobacterial isolates were differentiated and their drug resistance patterns determined using GenoType Mycobacterium Assays: MTBC and CM/AS for differentiating MTBC and NTM as well MTBDRplus and NTM-DR for DST of MTBC and NTM respectively.

Results

Out of 361 isolates, 165 (45.7%) MTBC and 120 (33.2%) NTM (made up of 14 different species) were identified to the species levels whiles 76 (21.1%) could not be completely identified. The MTBC comprised 161 (97.6%) Mycobacterium tuberculosis and 4 (2.4%) Mycobacterium africanum. Isoniazid and rifampicin monoresistant MTBC isolates were 18/165 (10.9%) and 2/165(1.2%) respectively whiles 11/165 (6.7%) were resistant to both drugs. Majority 42/120 (35%) of NTM were M. fortuitum. DST of 28 M. avium complex and 8 M. abscessus complex species revealed that all were susceptible to macrolides (clarithromycin, azithromycin) and aminoglycosides (kanamycin, amikacin, and gentamicin).

Conclusion

Our research signifies an important contribution to TB control in terms of knowledge of the types of mycobacterium species circulating and their drug resistance patterns in Ghana.

Electronic supplementary material

The online version of this article (10.1186/s12879-017-2853-3) contains supplementary material, which is available to authorized users.

Investigation and management of an outbreak of multispecies mycobacteriosis in Australian lungfish (Neoceratodus fosteri) including the use of triple antibiotic treatment

Disease due to non-tuberculous mycobacteria (NTM) is common in fish. Current recommendations focus on outbreak management by depopulating entire fish stocks and disinfecting tanks. Treatment is not advocated. Treatment may be appropriate, however, where individual, valuable fish are concerned. ZSL London Zoo managed an outbreak of mycobacteriosis in a valuable group of imported F1 captive-bred Australian lungfish (Neoceratodus fosteri) by depopulation, isolation, extensive testing and daily oral antibiotic treatment. Four species of Mycobacterium (M. marinum, M. fortuitum, M. chelonae and M. peregrinum) were involved in this outbreak, each with unique antibiotic sensitivities. Triple therapy with rifampicin, doxycycline and enrofloxacin for 8 months was the most effective antibiotic combination, resulting in full disease resolution. No side effects were noted and, more than 18 months post-treatment, no recurrence had occurred. This is the first report of mycobacterial disease in lungfish and the first report of a polymycobacterial outbreak in fish involving these four species of Mycobacterium. This report demonstrates the value of extensive isolation and identification. Also, as therapies currently advised in standard texts did not reflect the antibiotic sensitivity of the NTM found in the fish reported here, we recommend that antibiotic treatment should always be based on sensitivity testing.

Comparative evaluation of the AdvanSure Mycobacteria GenoBlot assay and the GenoType Mycobacterium CM/AS assay for the identification of non-tuberculous mycobacteria

In this study, to assess the performance of the AdvanSure Mycobacteria GenoBlot assay (AdvanSure assay), we compared its performance with that of the GenoType Mycobacterium CM/AS assay (GenoType assay) for the identification of non-tuberculous mycobacteria (NTM). Twenty-four reference strains and 103 consecutive clinical NTM isolates were analysed. The accuracy rates for the 24 reference strains were 87.5 and 95.8 % for the AdvanSure and GenoType assays, respectively. For the 103 clinical isolates, a 91.3 % (94/103) concordance rate was observed between the two assays. The majority (7/9) of discrepancies were isolates identified as Mycobacterium avium complex (MAC) by only the AdvanSure assay. All of these isolates except one were confirmed as MAC by sequence-based typing. The AdvanSure assay showed comparable performance to the GenoType assay and can be useful as a routine method for NTM identification in the clinical setting, especially where MAC is the main cause of NTM infection.

[Identification of mycobacteria to the species level by molecular methods in the Public Health Laboratory of Bogotá, Colombia]

INTRODUCTION

Global epidemiology of non-tuberculous mycobacteria (NTM) is unknown due to the fact that notification is not required in many countries, however the number of infection reports and outbreaks caused by NTM suggest a significant increase in the last years. Traditionally, mycobacteria identification is made through biochemical profiles which allow to differentiate M. tuberculosis from NTM, and in some cases the mycobacteria species. Nevertheless, these methods are technically cumbersome and time consuming. On the other hand, the introduction of methods based on molecular biology has improved the laboratory diagnosis of NTM.

OBJECTIVE

To establish the NTM frequency in positive cultures for acid-fast bacilli (AAFB) which were sent to Laboratorio de Salud Pública de Bogotá over a 12 month period.

MATERIALS AND METHODS

A total of 100 positive cultures for acid-fast bacilli from public and private hospitals from Bogotá were identified by both biochemical methods and the molecular methods PRA (PCR-restriction enzyme analysis) and multiplex-PCR. Furthermore, low prevalence mycobacteria species and non-interpretable results were confirmed by 16SrDNA sequentiation analysis.

RESULTS

Identification using the PRA method showed NMT occurrence in 11% of cultures. In addition, this molecular methodology allowed to detect the occurrence of more than one mycobacteria in 4% of the cultures. Interestingly, a new M. kubicae pattern of PCR-restriction analysis is reported in our study.

CONCLUSION

Using a mycobacteria identification algorithm, which includes the molecular method PRA, improves the diagnostic power of conventional methods and could help to advance both NTM epidemiology knowledge and mycobacteriosis control.

Prevalence of nontuberculous mycobacteria among extrapulmonary tuberculosis cases in tertiary care centers in Northern India

The reports of nontuberculous mycobacteria (NTM) associated with extrapulmonary diseases are increasing in tertiary care hospitals. Despite a significant increase in knowledge about NTM infections, they still represent a diagnostic and therapeutic challenge. The aim of this study is to know the prevalence of NTN among extrapulmonary tuberculosis cases in tertiary care centers in Northern India. A total of 227 culture positive isolates from 756 cases were tested for niacin production and catalase assay. BIO-LINE SD Ag MPT64 TB test and final identification and differentiation between MTBC and different species of NTM were further confirmed by GenoType Mycobacterium CM/AS assay. 71 cases (9.3%) were positive for AFB by ZN staining and 227 cases (30.1%) were positive for mycobacteria by culture. Niacin production and catalase activity were negative in 62/227 (27.4%) strains and after using a panel of different biochemicals and final confirmation by GenoType Mycobacterium CM assay. Out of 227 cultures tested, 165 (72.6%) strains were confirmed as M. tuberculosis complex, and 62 (27.4%) were confirmed as NTM. The most common NTM species identified were M. fortuitum 17 (27.5%) and M. intracellulare 13 (20.9%). The rapid identification of NTM species may help in targeted therapy and management of the diseases.

Evaluation of the Speed-Oligo Mycobacteria assay for the identification of nontuberculous mycobacteria

Nontuberculous mycobacteria (NTM) causing human infectious disease have become increasingly common. Rapid and accurate identification to the species level is, therefore, critical. The Speed-Oligo Mycobacteria assay is an oligochromatographic method that was made available recently for the identification and differentiation of mycobacteria. The present study aimed to evaluate the performance of the Speed-Oligo Mycobacteria assay for the identification of NTM. We examined a total of 62 strains (9 type strains, 19 reference strains and 34 clinical isolates) belonging to 13 different species (Mycobacterium intracellulare, M. fortuitum, M. gordonae, M. kansasii, M. marinum, M. peregrinum, M. scrofulaceum, M. abscessus, M. bovis BCG, M. chelonae, M. avium, M. malmoense and M. xenopi). The Speed-Oligo Mycobacteria assay was performed according to the manufacturer's instructions. Discrepant results between Speed-Oligo Mycobacteria and the original identification were reassessed by the Speed-Oligo Mycobacteria assay and resolved by the GenoType Mycobacterium CM assay and by sequencing of 16S rRNA and protein-encoding genes. We found 93.5 % (58/62) concordance for the identification of NTM as compared with the original identification. Three strains were erroneously identified by Speed-Oligo Mycobacteria: one M. kansasii strain was identified as Mycobacterium tuberculosis complex, and one M. chelonae strain and one M. peregrinum strain were both identified as Mycobacterium abscessus. Moreover, one M. chelonae strain was not identified by Speed-Oligo Mycobacteria since it did not react with any species-specific probe. For these strains, sequencing of the genes hsp65, 16S rRNA and rpoB and the GenoType Mycobacterium CM assay were performed. The Speed-Oligo Mycobacteria assay can be a useful tool for the rapid and easy identification of the most common NTM. If applied in clinical practice it could reduce diagnostic delays and contribute to correct clinical and better management of infections caused by NTM.