Are We Neglecting Nontuberculous Mycobacteria Just as Laboratory Contaminants? Time to Reevaluate Things

Rapid and accurate identification and differentiation of Mycobacterium tuberculosis and non-tuberculous mycobacteria using PCR kits available in a high-burden setting

Infections caused by mycobacteria, including Mycobacterium tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM), are a major public health issue worldwide. An accurate diagnosis of mycobacterial species is a challenge for surveillance and treatment, particularly in high-burden settings usually associated with low- and middle-income countries. In this study, we analyzed the clinical performance of two commercial PCR kits designed for the identification and differentiation of MTBC and NTM, available in a high-burden setting such as Ecuador. A total of 109 mycobacteria isolates were included in the study, 59 of which were previously characterized as M. tuberculosis and the other 59 as NTM. Both kits displayed great clinical performance for the identification of M. tuberculosis, with 100% sensitivity. On the other hand, for NTM, one of the kits displayed a good clinical performance with a sensitivity of 94.9% (CI 95%: 89-100%), while the second kit had a reduced sensitivity of 77.1% (CI 95%: 65-89%). In conclusion, one of the kits is a fast and reliable tool for the identification and discrimination of MTBC and NTM from clinical isolates.

Surgical site infections by atypical mycobacteria: prevalence and species characterization using MALDI-TOF and molecular LCD chip array

BACKGROUND

Surgical site infection (SSI) is a post-operative complication of high concern with adverse impact on patient prognosis and public health systems. Recently, SSI pathogens have experienced a change in microbial profile with increasing reports of non-tuberculous mycobacteria (NTM) as important pathogens.

AIM

of the study The study aimed to detect the prevalence of NTM among cases with SSIs and describe their species using matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) and PCR-based microarray.

METHODS

The study was conducted with 192 pus samples collected from patients with SSI. Mycobacterial investigations were done in the form of Ziehl-Neelsen (ZN) smears for acid-fast bacilli, automated mycobacterial culture to isolate mycobacteria, followed by immunochromatography test to predict NTM. NTM-positive cultures were tested by MALDI -TOF MS and PCR-based microarray to reach species-level identification.

RESULTS

Mycobacterial growth was found in 11/192 samples (5.7%) and identified as 4 NTM and 7 M. tuberculosis isolates with prevalence of 2.1% and 3.64%, respectively. The NTM species were described by MALDI-TOF as M. abscessus, M. porcinum, M. bacteremicum, and M. gordonae. Microarray agreed with MALDI-TOF in identifying one isolate (M. abscessus), while two isolates were classified as belonging to broad groups and one isolate failed to be identified.

CONCLUSIONS

The prevalence of NTM among SSI was found to be low, yet have to be considered in the diagnosis of mycobacteria. Employing advanced technologies in diagnosis is recommended to guide for appropriate treatment.

In silico analysis of promoter regions to identify regulatory elements in TetR family transcriptional regulatory genes of Mycobacterium colombiense CECT 3035

Background

Mycobacterium colombiense is an acid-fast, non-motile, rod-shaped mycobacterium confirmed to cause respiratory disease and disseminated infection in immune-compromised patients, and lymphadenopathy in immune-competent children. It has virulence mechanisms that allow them to adapt, survive, replicate, and produce diseases in the host. To tackle the diseases caused by M. colombiense, understanding of the regulation mechanisms of its genes is important. This paper, therefore, analyzes transcription start sites, promoter regions, motifs, transcription factors, and CpG islands in TetR family transcriptional regulatory (TFTR) genes of M. colombiense CECT 3035 using neural network promoter prediction, MEME, TOMTOM algorithms, and evolutionary analysis with the help of MEGA-X.

Results

The analysis of 22 protein coding TFTR genes of M. colombiense CECT 3035 showed that 86.36% and 13.64% of the gene sequences had one and two TSSs, respectively. Using MEME, we identified five motifs (MTF1, MTF2, MTF3, MTF4, and MTF5) and MTF1 was revealed as the common promoter motif for 100% TFTR genes of M. colombiense CECT 3035 which may serve as binding site for transcription factors that shared a minimum homology of 95.45%. MTF1 was compared to the registered prokaryotic motifs and found to match with 15 of them. MTF1 serves as the binding site mainly for AraC, LexA, and Bacterial histone-like protein families. Other protein families such as MATP, RR, σ-70 factor, TetR, LytTR, LuxR, and NAP also appear to be the binding candidates for MTF1. These families are known to have functions in virulence mechanisms, metabolism, quorum sensing, cell division, and antibiotic resistance. Furthermore, it was found that TFTR genes of M. colombiense CECT 3035 have many CpG islands with several fragments in their CpG islands. Molecular evolutionary genetic analysis showed close relationship among the genes.

Conclusion

We believe these findings will provide a better understanding of the regulation of TFTR genes in M. colombiense CECT 3035 involved in vital processes such as cell division, pathogenesis, and drug resistance and are likely to provide insights for drug development important to tackle the diseases caused by this mycobacterium. We believe this is the first report of in silico analyses of the transcriptional regulation of M. colombiense TFTR genes.

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.

Prevalence and speciation of non-tuberculous mycobacteria among pulmonary and extrapulmonary tuberculosis suspects in South India

BACKGROUND AND OBJECTIVES

Non tuberculous mycobacteria (NTM) is an emerging opportunistic pathogen increasing globally and indistinguishable from tuberculosis (TB), which remains a challenge particularly in developing countries. This study aimed to identify the prevalence and diversity of NTM among both pulmonary TB (PTB) and extrpulmonary TB (EPTB) clinical isolates from south India.

METHODOLOGY

A total of 7633 specimens from TB suspects (PTB, n = 4327 and EPTB, n = 3306) were collected during the study period (July 2018-March 2020) in a tertiary care hospital. The study specimens were subjected to Ziehl Neelsen (ZN) staining and Auramine phenol (AP) staining followed by Lowenstein-Jensen (LJ) and mycobacteria growth indicator tube (MGIT) culture. The MPT64 immunochromatographic test (ICT) was performed among mycobacterial cultures and ICT negative isolates were subjected to Line Probe Assay (LPA). In addition, 53 (PTB, 48 and EPTB, 5) NTM MGIT positive cultures were collected from Intermediate Reference Laboratory (IRL), Puducherry and subjected to LPA for speciation.

RESULTS

Of the 7633 TB suspects, 0.6% were diagnosed as NTM diseases and 5.5% with Mycobacterium tuberculosis (MTBC). NTM infection was observed among 0.7% (31/4327) of PTB and 0.4% (14/3306) of EPTB. MTBC was detected among 6.1% (264/4327) of PTB and 4.6% (153/3306) of EPTB. Among 98 NTM cultures, 80.6% of isolates were recovered from PTB and 19.4% from EPTB specimens. Among pulmonary specimens, Mycobacterium intracellulare (26.6%), Mycobacterium abscessus (17.7%) and Mycobacterium kansasii (12.7%) were the most frequently detected species, while Mycobacterium intracellulare (21.1%), Mycobacterium scrofulaceum (15.8%) and Mycobacterium fortuitum (10.5%) were common in extrapulmonary specimens.

CONCLUSION

The frequency of NTM infection among TB suspects was low at a South Indian tertiary care hospital. The most predominant NTM species isolated from both pulmonary and extrapulmonary specimens was M. intracellulare.

Detection of clinically important non tuberculous mycobacteria (NTM) from pulmonary samples through one-step multiplex PCR assay

Background

The burden of non-tuberculous mycobacterial (NTM) disease is increasing worldwide but still its diagnosis is delayed and it is mistaken as multidrug-resistant tuberculosis (MDR-TB).The present study was performed to develop a multiplex PCR assay for detection and identification of clinically most common NTM to the species level from pulmonary samples.

Results

Out of 50 isolates, 26 were identified as Mycobacterium kansasii (MK), 20 were identified as Mycobacterium abscessus (MA) and 4 were identified as Mycobacterium avium complex (MAC) through multiplex PCR and further confirmed by sequencing.

Conclusion

Our study showed that multiplex PCR assay is a simple, convenient, and reliable technique for detection and differential identification of major NTM species.

Nontuberculous mycobacterial infections in a Brazilian pediatric population: a seven-year survey

The aim of this study was to describe the frequency of nontuberculous mycobacteria (NTM) isolation and their related outcomes among pediatric patients of a Brazilian university hospital from 2012 to 2019. NTM were identified in different clinical samples by microbiological culture and molecular-based methods. NTM were isolated from 14 patients, out of whom four (27%) were infected and were treated accordingly. Two were infected with Mycobacterium avium complex (MAC), two with M. abscessus complex (MABSC) and one with M. intracellulare. Two patients had cystic fibrosis-related lung disease and improved after successful NTM eradication. One patient was HIV-positive and died. One patient had severe combined immunodeficiency (SCID)-related pneumonia and is currently being followed-up. We conclude that NTM frequency in our center was low among pediatric patients. Whether this is inherent to Brazilian patients, due to the broad coverage of the Bacille Calmette-Guérin (BCG) vaccine in Brazil, or a result of underdiagnosis remains to be elucidated.

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.