• View in gallery

    Distribution of the nontuberculous mycobacterial species among the clinical isolates (N = 69).

  • 1.

    Griffith DE et al.2007. An official ATS/IDSA statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am J Respir Crit Care Med 175: 367416.

    • Search Google Scholar
    • Export Citation
  • 2.

    Sharma S, Sharma R, Singh B, Upadhyay V, Mani I, Tripathi M & Kumar P 2019. A prospective study of non-tuberculous mycobacterial disease among tuberculosis suspects at a tertiary care centre in north India. Indian J Med Res 150: 458467.

    • Search Google Scholar
    • Export Citation
  • 3.

    Piersimoni C & Scarparo C 2009. Extrapulmonary infections associated with nontuberculous mycobacteria in immunocompetent persons. Emerg Infect Dis 15: 13511358.

    • Search Google Scholar
    • Export Citation
  • 4.

    Jani MN, Rodrigues CS & Mehta AP 2011. The neglected and often ignored: nontuberculous mycobacteria. J Glob Infect Dis 3: 94.

  • 5.

    Park H, Jang H, Song E, Chang CL, Lee M, Jeong S, Park J, Kang B & Kim C 2005. Detection and genotyping of Mycobacterium species from clinical isolates and specimens by oligonucleotide array. J Clin Microbiol 43: 17821788.

    • Search Google Scholar
    • Export Citation
  • 6.

    Suresh P, Biswas L, Prasad V, Kumar A, Sivadas S, Khan S & Biswas R 2020. BCG infection due to MPT64-negative strain: a diagnostic challenge. Am J Trop Med Hyg 103: 10721075.

    • Search Google Scholar
    • Export Citation
  • 7.

    Shenai S, Rodrigues C & Mehta A 2010. Time to identify and define non-tuberculous mycobacteria in a tuberculosis-endemic region. Int J Tuberc Lung Dis 14: 10011008.

    • Search Google Scholar
    • Export Citation
  • 8.

    Sharma P, Singh D, Sharma K, Verma S, Mahajan S & Kanga A 2018. Are we neglecting nontuberculous mycobacteria just as laboratory contaminants? Time to reevaluate things. J Pathogens 8907629. doi: 10.1155/2018/8907629.

    • Search Google Scholar
    • Export Citation
  • 9.

    Myneedu VP, Verma AK, Bhalla M, Arora J, Reza S, Sah GC & Behera D 2013. Occurrence of non-tuberculous Mycobacterium in clinical samples—a potential pathogen. Indian J Tuberc 60: 7176.

    • Search Google Scholar
    • Export Citation
  • 10.

    Umrao J, Singh D, Zia A, Saxena S, Sarsaiya S, Singh S, Khatoon J & Dhole TN 2016. Prevalence and species spectrum of both pulmonary and extrapulmonary nontuberculous mycobacteria isolates at a tertiary care center. Int J Mycobacteriol 5: 288293.

    • Search Google Scholar
    • Export Citation
  • 11.

    Jain S, Sankar MM, Sharma N, Singh S & Chugh TD 2014. High prevalence of non-tuberculous mycobacterial disease among non-HIV infected individuals in a TB endemic country—experience from a tertiary center in Delhi, India. Pathog Glob Health 108: 118122.

    • Search Google Scholar
    • Export Citation
  • 12.

    Gopinath K & Singh S 2010. Non-tuberculous mycobacteria in TB-endemic countries: are we neglecting the danger? PLoS Negl Trop Dis 4: e615.

  • 13.

    Maurya AK, Nag VL, Kant S, Kushwaha RAS, Kumar M, Singh AK & Dhole TN 2015. Prevalence of nontuberculous mycobacteria among extrapulmonary tuberculosis cases in tertiary care centers in northern India. BioMed Res Int 465403. doi: 10.1155/2015/465403.

    • Search Google Scholar
    • Export Citation
  • 14.

    Renaud CJ, Subramanian S, Tambyah PA & Lee EJC 2011. The clinical course of rapidly growing nontuberculous mycobacterial peritoneal dialysis infections in Asians: a case series and literature review. Nephrology (Carlton) 16: 174179.

    • Search Google Scholar
    • Export Citation
  • 15.

    Patil R, Patil T, Schenfeld L & Massoud S 2011. Mycobacterium porcinum peritonitis in a patient on continuous ambulatory peritoneal dialysis. J Gen Intern Med 26: 346348.

    • Search Google Scholar
    • Export Citation
  • 16.

    Spaulding AB, Lai YL, Zelazny AM, Olivier KN, Kadri SS, Prevots DR & Adjemian J 2017. Geographic distribution of nontuberculous mycobacterial species identified among clinical isolates in the United States, 2009–2013. Ann Am Thorac Soc 14: 16551661.

    • Search Google Scholar
    • Export Citation
 
 

 

 

 

 

 

 

Epidemiology of Nontuberculous Mycobacterial Infection in Tuberculosis Suspects

View More View Less
  • 1 Center for Nanosciences and Molecular medicine, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, Kerala, India;
  • | 2 Department of Microbiology, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, Kerala, India;
  • | 3 Department of Dermatology, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, Kerala, India;
  • | 4 Department of Respiratory Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, Kerala, India

ABSTRACT.

Nontuberculosis mycobacteria (NTM) are opportunistic pathogens that cause a wide range of illnesses. Here, the species distribution and prevalence of NTM infections in tuberculosis suspects was analyzed. A total of 7,073 specimens from pulmonary and extrapulmonary sites were analyzed, and 709 (10%) were found to be culture positive for mycobacteria. Of these, 85.2% were identified as Mycobacterium tuberculosis complex and 14.8% as NTM (65.7% rapid growers and 34.3% slow growers). Speciation of the NTM isolates (n = 69) identified 19 NTM species. M. abscessus (33.3%) and M. fortuitum (24.6%) were the most dominant NTM species isolated from the patients, followed by M. porcinum (5.8%) and M. parascrofulaceum (4.3%). We also report peritonitis caused by rapidly growing NTM among the patients undergoing continuous ambulatory peritoneal dialysis and a case of M. senegalense peritonitis. A low prevalence but high species diversity of NTM was detected in our study. The high species diversity of NTM necessitates the need to unequivocally identify mycobacterial isolates for appropriate treatment.

INTRODUCTION

Mycobacterial species other than Mycobacterium tuberculosis and Mycobacterium leprae are together referred to as nontuberculous mycobacteria (NTM).1 They are ubiquitous, environmental organisms found in soil, water, and dust and on moist hospital surfaces. Colonization of medical equipment such as endoscopes and surgical solutions has also been reported.1 NTM infections are an emerging public health problem globally, with increasing prevalence of 0.38% to 27.4% in India alone.2 More than 200 NTM species have been identified so far, of which approximately 60 species are considered as pathogenic to humans and have been found to be responsible for localized or disseminated disease.25 The spectrum of the NTM disease, the treatment options, and subsequent patient outcomes vary by the infecting NTM species. Geographic variation in both prevalence and species spectrum of NTM has been reported from across the world and also from different regions of India.14 Because susceptibility to antimicrobial agents can be predicted by knowing the NTM species, identification to the species level is of paramount importance. Clinically, pulmonary NTM disease mimics tuberculosis (TB), leading to inappropriate treatment because they are inherently resistant to antitubercular drugs.1,2,4 The patient outcomes of the NTM disease also vary greatly by the causative species.1 We have evaluated the species distribution and prevalence of NTM infections in both pulmonary and extrapulmonary specimens of TB suspects over a five 5-year period.

THE STUDY

The current descriptive study was performed with the specimens that were received for tubercular diagnosis during 2015 to 2020. Patient demographic details collected included comorbidities, histopathology reports, treatment, and outcome. A total of 7,073 pulmonary and extrapulmonary clinical specimens were analyzed in this study. Approximately 2 to 10 mL of the specimens were collected from pulmonary and extrapulmonary sites. Pulmonary samples included sputum, bronchoalveolar lavage, and lung tissue. Extrapulmonary samples were cerebrospinal fluid, urine, ascitic fluid, lymphnode, pleural fluid, synovial fluid, and pus swab. The specimens from non-sterile sites with commensal bacterial flora were subjected to digestion and decontamination using N-acetyl-L-cysteine and sodium hydroxide (NALC/NaOH). To detect the presence of acid-fast bacteria, all clinical samples were subjected to smear microscopy by Ziehl-Neelsen and auramine-rhodamine fluorescence staining. Mycobacterial cultures were performed in BACTEC MGIT960 (BD Diagnostics, Sparks, MD) automated system. Positive culture tubes were subjected to rapid immunochromatographic assay, SD Bioline MPT64 Card assay (Standard Diagnostics, Seoul, Korea) to differentiate between Mycobacterium tuberculosis complex and NTM.6 Isolates negative for MPT64 antigen were identified as NTM. NTM isolates were speciated by PCR followed by Sanger sequencing of 16S-23S intergenic spacer region using the primer pair Myco-F(5'TGGATCCGACGAAGTCGTAACAAGG-3') and Myco-R (5'ATGCTCGCAACCACTATCCA-3'). Of the 7073 individual patient samples cultured, 709 (10%) were positive for mycobacteria. Among the 709 mycobacterial isolates, 105 (14.8%) were found to be NTM and 604 (85.2%) were identified as M. tuberculosis complex by the MPT64 Rapid Card test (Standard Diagnostics). The overall prevalence of NTM among TB suspects was 1.4% (105 of 7,073) and 65.7% (69 of 105) of the isolates were rapidly growing mycobacteria (RGM) (Table 1). The proportion of NTM among the mycobacterial isolates was low (14.8%) and remained static throughout the study period. Infection rates were found to be 49.5% in men and 50.5% in women. The median age of the patients with NTM infection was 55 years (range: 20–75 years). Of the 105 NTM isolates, 63 (60%) were isolated from the extrapulmonary sites and 42 (40%) from pulmonary specimens (Table 2). Among the 42 pulmonary infections, only 24 (57.1%) cases fulfilled the American Thoracic Society criteria for NTM disease. Past history of TB was documented in 17 (16.2%) cases, of which 88% were of pulmonary involvement. Among these 17 cases, two were on antitubercular treatment at presentation and another two were considered relapse of M. tuberculosis infection. Of the 26 cases of soft tissue involvement, 11 cases were postoperative infections. In-hospital mortality was seen in two cases with underlying conditions such as chronic kidney disease and malignancy. Diabetes was the most common (23.8%) risk factor associated with the NTM infections. The other underlying risk factors were malignancy (18.1%), chemotherapy (11.4%), chronic liver disease (11.4%), chronic kidney disease (11.4%), transplant (5.7%), and chronic obstructive pulmonary disorder (5.7%) (Table 3).

Table 1

Profile of mycobacterial culture

CulturesNo. of samples (%)
No. of samples subjected to MGIT culture7,073
Mycobacterium-positive cultures709 (10)
MTBC604 (85.2)
NTM105 (14.8)
Pulmonary NTM42 (40)
Extrapulmonary NTM63 (60)
NTM rapid growers69 (65.7)
NTM slow growers36 (34.3)

MGIT = mycobacterial growth indication tube; MTBC = Mycobacterium tuberculosis complex; NTM = nontuberculosis mycobacteria.

Table 2

Specimen-wise distribution of nontuberculosis mycobacteria isolates

Sample no.OrganismTotalAscitic fluidBALCSFCervical nodeFNAPleural fluidPusSputumTissueUrine
1M. abscessus23174812
2M. arupense211
3M. chelonae11
4M. chimaera11
5M. colombiense11
6M. europaeum11
7M. fortuitum17311723
8M. goodie211
9M. gordonae11
10M. intracellulare321
11M. kansasii11
12M. lentiflavum11
13M. marseillense11
14M. parascrofulaceum312
15M. peregrinum11
16M. porcinum431
17M. senegalense3111
18M. shigaense11
19M. simiae22
Total69814111192635

BAL = bronchoalveolar lavage; CSF = cerebrospinal fluid; FNA = fine needle aspiration.

Table 3

Demographic details of the patients (N = 105) with nontuberculosis mycobacteria infections

ParameterNo. of patients (%)
Gender
 Male52 (49.5)
 Female53 (50.5)
Age group
 1 to 204 (3.8)
 21 to 4015 (14.3)
 41 to 6046 (43.8)
 61 to 8037 (35.2)
 Above 803 (2.9)
Risk factors
 Diabetes25 (23.8)
 Malignancy19 (18.1)
 Chemotherapy12 (11.4)
 Chronic liver disease12 (11.4)
 Chronic kidney disease12 (11.4)
 Transplant6 (5.7)
 Chronic obstructive pulmonary disease6 (5.7)
 Others13 (13.3)

Of the 105 NTM isolates, speciation by sequencing was performed for 69 isolates, identifying 19 NTM species, with M. abscessus (33.3%) and M. fortuitum (24.6%) being the most common (Figure 1). Emergence of peritonitis due to NTM in patients undergoing continuous ambulatory peritoneal dialysis (CAPD) was found in eight cases. All the eight cases were caused by RGM, three each by M. porcinum and M. fortuitum and one each by M. abscessus and M. senegalense.

Figure 1.
Figure 1.

Distribution of the nontuberculous mycobacterial species among the clinical isolates (N = 69).

Citation: The American Journal of Tropical Medicine and Hygiene 105, 5; 10.4269/ajtmh.21-0095

DISCUSSION

Pulmonary NTM infections most often are misdiagnosed as infections caused by M. tuberculosis complex because the clinical, radiological, and microscopic findings of both are similar and may lead to unwarranted or inappropriate therapy.1,4,7 Here, we have analyzed the prevalence and species distribution of NTM in TB suspects. We found a low prevalence (1.4%) of NTM among TB suspects, which is in agreement with four previous studies from India that reported a prevalence of 0.38%, 0.77%, 1.0%, and 1.2% respectively.2,79 However, two Indian studies using the MGIT960 system reported a higher prevalence of 2.98% and 5.6%, respectively.10,11 A study from India found 17.6% of MDR pulmonary TB and 12.4% of extrapulmonary TB cases were due to NTM.12 Another Indian study found that 30.8% of pulmonary NTM cases had history of TB disease. The same study also found that 92.3% of the NTM infections were previously diagnosed as pulmonary or extrapulmonary TB.11 The proportion of NTM infections with previous history of TB is in the range of 30.8% to 94% in India.2,4,7,8,11 NTM infection rates in this study were found to be similar in both men and women, which was not in agreement with recently published studies from India.2,8,10 Older age (> 50 years) was found to be a risk factor for NTM infections, which is in concordance with other Indian studies.2,8,10 Notably, HIV was not documented as a risk factor in our study. Previous Indian studies have reported HIV as a risk factor in 0% to 2% in patients with NTM infection.11,13

Speciation of the NTM isolates identified 19 NTM species with M. abscessus and M. fortuitum as the most commonly isolated NTM species. Previous Indian studies have also reported M. abscessus and M. fortuitum as the most predominant species.10,13 However, two recent Indian studies have reported M. intracellularae as the commonest NTM isolate.2,8 We have documented the emergence of peritonitis due to NTM in patients undergoing CAPD. A previous study in an Asian population found that 3% of peritonitis in patients on CAPD was caused by rapid-growing NTM (80% due to M. abscessus) with high rates (80%) of catheter loss and increased three month mortality (40%).14 Notably, M. porcinum peritonitis has been reported only once,15 whereas M. senegalense peritonitis is being reported for the first time in the literature. In our study, we have observed a very low prevalence of Mycobacterium avium species. In silico amplification analysis of the primers used in this study for speciation of the NTM has shown amplification of 271 bp for the MAC species: M. avium, Mycobacterium intracellulare, Mycobacterium chimaera, Mycobacterium colombiense, Mycobacterium bouchedurhonense, Mycobacterium marseillense, and Mycobacterium timonense. In our sequence analysis, we have detected the MAC species M. intracellurae (4.3%), M. chimaera (1.4%), M. marseillense (1.4%), and M. colombiense (1.4%). Our data indicate that the lower incidence of M. avium in our study population could likely be due to the variations in the geographic distribution of NTM species. For example, in the United States M. avium complex was the most common species found in the south, whereas the incidence of M. abscessus/M. chelonae was considerably higher in the west.16

There are limitations of our study. First, although the primers used in our study were able to identify M. abscessus at the species level, unambiguous identification of all subspecies of M. abscessus could not be achieved due to significant heterogenicity observed in the target sequence. Second, because the growth rate of mycobacterial species determines the shift in the predominant mycobacterial population by the end of reporting period in liquid-based culture systems such as MGIT, we could have missed MTB populations in mixed infections. It is expected that the NTM, especially RGM with its fast growth rate, will overgrow MTB, which has a slow growth rate.

We report the emergence of peritonitis caused by rapidly growing NTM among CAPD patients and a case of M. senegalense peritonitis. The low prevalence but high species diversity of NTM identified in our study suggests a need for urgent and accurate characterization of NTM for proper treatment and management of patients.

ACKNOWLEDGMENTS

We are grateful to Amrita Centre for Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, for infrastructural and financial support. We thank Sanu Babu, Department of Microbiology, for providing technical assistance in conducting the study. The American Society of Tropical Medicine and Hygiene (ASTMH) assisted with publication expenses.

REFERENCES

  • 1.

    Griffith DE et al.2007. An official ATS/IDSA statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am J Respir Crit Care Med 175: 367416.

    • Search Google Scholar
    • Export Citation
  • 2.

    Sharma S, Sharma R, Singh B, Upadhyay V, Mani I, Tripathi M & Kumar P 2019. A prospective study of non-tuberculous mycobacterial disease among tuberculosis suspects at a tertiary care centre in north India. Indian J Med Res 150: 458467.

    • Search Google Scholar
    • Export Citation
  • 3.

    Piersimoni C & Scarparo C 2009. Extrapulmonary infections associated with nontuberculous mycobacteria in immunocompetent persons. Emerg Infect Dis 15: 13511358.

    • Search Google Scholar
    • Export Citation
  • 4.

    Jani MN, Rodrigues CS & Mehta AP 2011. The neglected and often ignored: nontuberculous mycobacteria. J Glob Infect Dis 3: 94.

  • 5.

    Park H, Jang H, Song E, Chang CL, Lee M, Jeong S, Park J, Kang B & Kim C 2005. Detection and genotyping of Mycobacterium species from clinical isolates and specimens by oligonucleotide array. J Clin Microbiol 43: 17821788.

    • Search Google Scholar
    • Export Citation
  • 6.

    Suresh P, Biswas L, Prasad V, Kumar A, Sivadas S, Khan S & Biswas R 2020. BCG infection due to MPT64-negative strain: a diagnostic challenge. Am J Trop Med Hyg 103: 10721075.

    • Search Google Scholar
    • Export Citation
  • 7.

    Shenai S, Rodrigues C & Mehta A 2010. Time to identify and define non-tuberculous mycobacteria in a tuberculosis-endemic region. Int J Tuberc Lung Dis 14: 10011008.

    • Search Google Scholar
    • Export Citation
  • 8.

    Sharma P, Singh D, Sharma K, Verma S, Mahajan S & Kanga A 2018. Are we neglecting nontuberculous mycobacteria just as laboratory contaminants? Time to reevaluate things. J Pathogens 8907629. doi: 10.1155/2018/8907629.

    • Search Google Scholar
    • Export Citation
  • 9.

    Myneedu VP, Verma AK, Bhalla M, Arora J, Reza S, Sah GC & Behera D 2013. Occurrence of non-tuberculous Mycobacterium in clinical samples—a potential pathogen. Indian J Tuberc 60: 7176.

    • Search Google Scholar
    • Export Citation
  • 10.

    Umrao J, Singh D, Zia A, Saxena S, Sarsaiya S, Singh S, Khatoon J & Dhole TN 2016. Prevalence and species spectrum of both pulmonary and extrapulmonary nontuberculous mycobacteria isolates at a tertiary care center. Int J Mycobacteriol 5: 288293.

    • Search Google Scholar
    • Export Citation
  • 11.

    Jain S, Sankar MM, Sharma N, Singh S & Chugh TD 2014. High prevalence of non-tuberculous mycobacterial disease among non-HIV infected individuals in a TB endemic country—experience from a tertiary center in Delhi, India. Pathog Glob Health 108: 118122.

    • Search Google Scholar
    • Export Citation
  • 12.

    Gopinath K & Singh S 2010. Non-tuberculous mycobacteria in TB-endemic countries: are we neglecting the danger? PLoS Negl Trop Dis 4: e615.

  • 13.

    Maurya AK, Nag VL, Kant S, Kushwaha RAS, Kumar M, Singh AK & Dhole TN 2015. Prevalence of nontuberculous mycobacteria among extrapulmonary tuberculosis cases in tertiary care centers in northern India. BioMed Res Int 465403. doi: 10.1155/2015/465403.

    • Search Google Scholar
    • Export Citation
  • 14.

    Renaud CJ, Subramanian S, Tambyah PA & Lee EJC 2011. The clinical course of rapidly growing nontuberculous mycobacterial peritoneal dialysis infections in Asians: a case series and literature review. Nephrology (Carlton) 16: 174179.

    • Search Google Scholar
    • Export Citation
  • 15.

    Patil R, Patil T, Schenfeld L & Massoud S 2011. Mycobacterium porcinum peritonitis in a patient on continuous ambulatory peritoneal dialysis. J Gen Intern Med 26: 346348.

    • Search Google Scholar
    • Export Citation
  • 16.

    Spaulding AB, Lai YL, Zelazny AM, Olivier KN, Kadri SS, Prevots DR & Adjemian J 2017. Geographic distribution of nontuberculous mycobacterial species identified among clinical isolates in the United States, 2009–2013. Ann Am Thorac Soc 14: 16551661.

    • Search Google Scholar
    • Export Citation

Author Notes

Address correspondence to Anil Kumar, Department of Microbiology, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi-682041, Kerala, India, E-mail: vanilkumar@aims.amrita.edu or Lalitha Biswas, Center for Nanosciences and Molecular medicine, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi-682041, Kerala, India, E-mail: lalithabiswas@aims.amrita.edu.

Authors’ addresses: Parasmal Suresh, Center for Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India, E-mail: parassureshjn@gmail.com. Anil Kumar, Microbiology, Amrita Institute of Medical Sciences, Ponekara, Kochi, Kerala, India, E-mail: vanilkumar@aims.amrita.edu. Raja Biswas and Lalitha Biswas, Center for Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India, E-mails: rajabiswas@aims.amrita.edu and lalithabiswas@aims.amrita.edu. Gopikrishnan Anjaneyan, Department of Dermatology, Amrita Institute of Medical Sciences, Kochi, Kerala, India, E-mail: gopi19430@aims.amrita.edu. Divya Vijayakumar and Swathy Thulasidharan, Department of Microbiology, Amrita Institute of Medical Sciences and Research Centre, Kochi, Kerala, India, E-mails: divarchives@gmail.com and swathy.thulasidharan@gmail.com. Akhilesh Kunoor, Department of Respiratory Medicine, Amrita Institute of Medical Sciences and Research Centre, Kochi, Kerala, India, E-mail: akhileshk@aims.amrita.edu.

Save