This article has Open Peer Review reports available.
Frequency and clinical implications of the isolation of rare nontuberculous mycobacteria
© Kim et al.; licensee BioMed Central. 2015
Received: 11 July 2014
Accepted: 23 December 2014
Published: 9 January 2015
To date, more than 125 species of nontuberculous mycobacteria (NTM) have been identified. In this study, we investigated the frequency and clinical implication of the rarely isolated NTM from respiratory specimens.
Patients with NTM isolated from their respiratory specimens between July 1, 2010 and June 31, 2012 were screened for inclusion. Rare NTM were defined as those NTM not falling within the group of eight NTM species commonly identified at our institution: Mycobacterium avium, M. intracellulare, M. abscessus, M. massiliense, M. fortuitum, M. kansasii, M. gordonae, and M. peregrinum. Clinical, radiographic and microbiological data from patients with rare NTM were reviewed and analyzed.
During the study period, 73 rare NTM were isolated from the respiratory specimens of 68 patients. Among these, M. conceptionense was the most common (nine patients, 12.3%). The median age of the 68 patients with rare NTM was 68 years, while 39 of the patients were male. Rare NTM were isolated only once in majority of patient (64 patients, 94.1%). Among the four patients from whom rare NTM were isolated two or more times, only two showed radiographic aggravation caused by rare NTM during the follow-up period.
Most of the rarely identified NTM species were isolated from respiratory specimens only once per patient, without concomitant clinical aggravation. Clinicians could therefore observe such patients closely without invasive work-ups or treatment, provided the patients do not have decreased host immunity towards mycobacteria.
Nontuberculous mycobacteria (NTM) are defined as mycobacteria other than Mycobacterium tuberculosis complex and M. leprae. Since the recognition of NTM as possible pathogens in the 1950s [1,2], the observed occurrence of NTM lung diseases has been increasing worldwide [3-5]. This may be attributed in part to improvements in microbial diagnostic tools leading to increased isolation of NTM. Additionally, the concomitant increase in susceptible hosts such as patients with underlying lung disease or an immunocompromised state may also contribute to the observed increase in NTM lung disease [5-9].
Presently, more than 125 classes of NTM species have been identified . Furthermore, newly identified species of NTM are constantly reported owing to advances in technologies for the detection for NTM. For example, new species such as M. fragae and M. paragordonae were identified as recently as 2013 [11,12].
Although the clinical characteristics of diseases caused by commonly isolated NTM such as M. avium, M. intracellulare or M. abscessus are well known, those caused by newly recognized and rarely isolated NTM are not yet fully understood. In the present study, we investigated the frequency of rare NTM isolation and the clinical characteristics of patients with rare NTM.
Patients from whom NTM were isolated one or more times from respiratory specimens such as sputum, bronchoscopic wash fluid and bronchoalveolar lavage (BAL) fluid between July 1, 2010 and June 31, 2012 at Seoul National University Hospital, were included in the analysis. Hence, a total of 2556 NTM isolated from 1373 patients during the study period were analyzed retrospectively. The Institutional Review Board of Seoul National University Hospital approved the study protocol and waived the requirement for obtaining patient consent.
Identification of NTM species
Respiratory specimens were decontaminated with 4% sodium hydroxide (NaOH), homogenized, and concentrated by centrifugation at 3000 × g for 20 min. The processed sediments were stained using the Ziehl-Neelsen method . Concentrated specimens were cultured in MGIT tubes (Becton-Dickinson and Co.; Sparks, MD, USA) as well as in 3% Ogawa medium and observed weekly for 6 or 9 weeks after inoculation, respectively. Once cultured, M. tuberculosis and NTM were differentiated using the Gen-Probe® method (Gen-Probe; San Diego, CA, USA) . Following isolation of a suspected mycobacterial species, confirmation of NTM was performed by analyzing the sequences of three genes: 16S rRNA, rpoB, and tuf. Polymerase chain reaction (PCR) and subsequent sequence were performed and the resulting sequences were compared with those in the reference database using the basic local alignment search tool (BLAST). Mycobacterial species were identified using the 16S rRNA sequences and the algorithm described in the Clinical and Laboratory Standards Institute guidelines MM18-A .
Definition of rare NTM
For the purposes of this study, ‘rare NTM’ were defined as NTM species other than M. avium, M. intracellulare, M. abscessus, M. massiliense, M. fortuitum, M. kansasii, M. gordonae and M. peregrinum, which are the eight NTM species commonly identified at our institution.
Clinical and radiographic characteristics
Demographic, clinical and radiographic data of the patients from whom rare NTM were isolated were reviewed. Demographic data including age, gender, and smoking habits; past medical history of tuberculosis (TB), measles, pertussis, and sinusitis; comorbidities including malignancy, diabetes mellitus, cerebrovascular disease, rheumatic disease, inflammatory bowel disease, gastroesophageal reflux disease, and underlying lung disease; clinical data for self-reported symptoms; and findings of the physical examinations, were all thoroughly reviewed. The characteristics and distribution of lung lesions were analyzed based on chest computed tomography (CT) by two pulmonologists (J.K. and J.J.Y.), who were aware of the patients’ NTM results. Patients from whom rare NTM were isolated more than once were analyzed separately.
Common NTM isolated from respiratory specimens during the study period
NTM commonly isolated from respiratory specimens during the study period
Mycobacterium avium complex
Mycobacterium abscessus complex
Rare NTM isolated during the study period
Rare NTM species isolated from respiratory specimens during the study period
Failed species identification‡
Characteristics of the patient cohort from whom rare NTM were isolated
Demographics and clinical characteristics of the patient cohort from whom rare NTM were isolated
Age (year), median (range)
Body Mass Index (kg/m2), median (range)
Past medical history
Previous history of TB
Inflammatory bowel disease
Underlying lung disease
Interstitial lung disease
Steroid (5–10 mg daily)*
Other immunomodulatory drugs*
Radiographic findings in patient cohort with rare NTM
Right upper lobe
Right middle lobe
Right lower lobe
Left upper lobe
Left lower lobe
Multilobar (≥3 lobes with abnormalities)
Upper lobe cavitary pattern
Nodular bronchiectatic pattern
Clinical course of four patients from whom rare NTM were isolated more than once
Clinical characteristics of four patients from whom rare NTM were isolated more than once
Isolated NTM (number of times isolated)
Progression of radiographic lesions
• History of tuberculous cervical lymphadenitis
• Nodules and subsegmental atelectasis
M. conceptionense (2)
• Not definite
• Undergoing jejunostomy (due to lye ingestion)
• Consolidations and branching opacities
M. abscessus (2)
• Increase in number of multiple centrilobular nodules and extent of bronchiectasis
• Bipolar I disorder
M. goodii (2)
Clarithromycin, Rifampin, Ethambutol, Moxifloxacin
(Sep. 2007–Oct. 2009)
• Bronchiectasis and nodules
M. phocaicum (1)
• Not definite
• Coronary artery disease
M. mageritense (1)
• History of pulmonary TB
• Nodules, consolidations, fluid-containing cavity
M. chimaera (3)
• New centrilobular nodules and patchy consolidation
New NTM are constantly reported, while the lung diseases arising from these new organisms are reported at a similarly rapid rate [16-19]. Consequently, clinicians inevitably encounter patients who present with unfamiliar and rarely identified NTM.
In the present study, various species of rarely identified NTM were isolated from respiratory specimens. M. conceptionense was the most frequently isolated rare NTM. This species was reported to cause infections of the skin and subcutaneous fat following surgical procedures in immunocompetent patients [20-22]. Moreover, another study demonstrated that this NTM may be a lung pathogen . However, in our study, for the patient from whom M. conceptionense was isolated at two separate time points, neither aggravation of the symptoms nor progression of radiographic lesions was identified.
Other rare NTM species isolated from patients in the present study (M. lentiflavum, M. mageritense, M. chimaera and M. xenopi) may also cause lung diseases [16,18,19,23]. However, yet other rare NTM isolated from these patients, such as M. kumamotonense and M. celatum, have generally been considered to be misidentifications or a result of culture contamination, and are thus deemed to be clinically non-pathogenic organisms [24,25].
NTM classified as rarely isolated NTM in this study may prove common in other geographic regions. For example, M. xenopi is commonly identified in southern Ontario, South East England and Europe [26,27], but rarely in Australia, South America, USA and Asia [28,29]. However, in this study performed in South Korea, M. xenopi was isolated only once.
Despite their pathogenic potential, among the patients from whom rare NTM were identified, rare NTM were isolated only once in the majority of patients (64/68). Once-off isolation of the majority of the rare NTM suggests limited clinical significance of these NTM. Additionally, the observation that only one of the three patients from whom rare NTM were isolated two or more times without co-infection with common NTM showed evidence of radiographic aggravation, further substantiates the minimal clinical significance of rare NTM.
The limited clinical importance of the frequent one-time isolation of rare NTM presented in this study underscores the importance of the current ATS/IDSA diagnostic guidelines, which require repeated isolation of an NTM in the appropriate clinical setting . Clinicians confronted with rare NTM could observe the patients for a while watching whether the same species of NTM would be isolated again or not.
To fully appreciate these results, a limitation of this study should be noted: species level identification was not performed on all NTM isolated from respiratory specimens. A prospective study including species identification of all NTM isolated during the certain period would likely confirm the findings of the current study.
Rarely identified NTM isolated from respiratory specimens have limited clinical importance in most cases. Clinicians who treat patients with rarely identified NTM could therefore observe them closely without any intensive work-ups or treatment being required, provided that these patients do not present with decreased host immunity towards mycobacteria.
This work was supported by grant number 800–20120025 from the Seoul National University College of Medicine (Seoul, Republic of Korea). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
- Tsukamura M, Kita N, Shimoide H, Arakawa H, Kuze A. Studies on the epidemiology of nontuberculous mycobacteriosis in Japan. Am Rev Respir Dis. 1988;137:1280–4.View ArticlePubMedGoogle Scholar
- O'Brien RJ, Geiter LJ, Snider DE. The epidemiology of nontuberculous mycobacterial diseases in the United States: results from a national survey. Am Rev Respir Dis. 1987;135:1007–14.PubMedGoogle Scholar
- Henry MT, Inamdar LO, Riordain D, Schweiger M, Watson JP. Nontuberculous mycobacteria in non-HIV patients: epidemiology, treatment and response. Eur Respir J. 2004;23:741–6.View ArticlePubMedGoogle Scholar
- Martin-Casabona N, Bahrmand AR, Bennedsen J, Thomsen VO, Curcio M, Fauville-Dufaux M, et al. Non-tuberculous mycobacteria: patterns of isolation; a multicountry retrospective survey. Int J Tuberc Lung Dis. 2004;8:1186–93.PubMedGoogle Scholar
- Wolinsky E. Nontuberculous mycobacteria and associated diseases. Am Rev Respir Dis. 1979;119:107–59.PubMedGoogle Scholar
- Falkinham 3rd JO. Ecology of nontuberculous mycobacteria–where do human infections come from? Semin Respir Crit Care Med. 2013;34:95–102.View ArticlePubMedGoogle Scholar
- Jouanguy E, Altare F, Lamhamedi S, Revy P, Emile JF, Newport M, et al. Interferon-r receptor deficiency in an infant with fatal bacille Calmette-Guerin infection. N Engl J Med. 1996;335:1956–61.View ArticlePubMedGoogle Scholar
- Dorman SE, Holland SM. Interferon-r and interleukin-12 pathway defects and human disease. Cytokine Growth Factor Rev. 2000;11:321–33.View ArticlePubMedGoogle Scholar
- Holland SM. Immune deficiency presenting as mycobacterial infection. Clin Rev Immunol. 2001;20:121–37.Google Scholar
- McNabb A, Eisler D, Adie K, Amos M, Rodrigues M, Stephens G, et al. Assessment of Partial Sequencing of the 65-Kilodalton Heat Shock Protein Gene (hsp65) for Routine Identification of Mycobacterium Species Isolated from Clinical Sources. J Clin Microbiol. 2004;42:3000–11.View ArticlePubMedPubMed CentralGoogle Scholar
- Ramos JP, Campos CE, Caldas PC, Ferreira NV, da Silva MV, Redner P, et al. Mycobacterium fragae sp. nov., a non-chromogenic species isolated from human respiratory specimens. Int J Syst Evol Microbiol. 2013;63:2583–7.View ArticlePubMedGoogle Scholar
- Kim BJ, Hong SH, Kook YH, Kim BJ. Mycobacterium paragordonae sp. nov., a slowly growing, scotochromogenic species closely related to Mycobacterium gordonae. Int J Syst Evol Microbiol. 2014;64:39–45.View ArticlePubMedGoogle Scholar
- Griffith D, Aksamit T, Brown-Elliott B, Catanzaro A, Daley CL, Gordin F, et al. An official ATS/IDSA statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am J Respir Crit Care Med. 2007;175:367–416.View ArticlePubMedGoogle Scholar
- Bergmann JS, Yuoh G, Fish G, Wood GL. Clinical evaluation of the enhanced Gen-Probe Amplifi ed Mycobacterium Tuberculosis Direct Test for rapid diagnosis of tuberculosis in prison inmates. J Clin Microbiol. 1999;37:1419–25.PubMedPubMed CentralGoogle Scholar
- Performance standards for antimicrobial susceptibility testing; 18th informational supplement. In Book Performance standards for antimicrobial susceptibility testing; 18th informational supplement (Editor ed.^eds.). pp. M100-S118. City: Clinical and Laboratory Standards Institute; 2008:M100-S118.Google Scholar
- Cohen-Bacrie S, David M, Stremler N, Dubus JC, Rolain JM, Drancourt M. Mycobacterium chimaera pulmonary infection complicating cystic fibrosis: a case report. J Med Case Rep. 2011;5:473.View ArticlePubMedPubMed CentralGoogle Scholar
- Martinez-Gonzalez DFJ, Navarro-Ortega D, Muñoz C, Martí-Obiol R, Borrás-Salvador R. Achalasia and mycobacterium goodii pulmonary infection. Pediatr Infect Dis J. 2011;30:447–8.View ArticlePubMedGoogle Scholar
- Kim SY, Kim MS, Chang HE, Yim JJ, Lee JH, Song SH, et al. Pulmonary Infection Caused by Mycobacterium conceptionense. Emerg Infect Dis. 2012;1:174–6.View ArticleGoogle Scholar
- Jeong BH, Song JU, Kim W, Han SG, Ko Y, Song J, et al. Nontuberculous mycobacterial lung disease caused by Mycobacterium lentiflavumin a patient with bronchiectasis. Tuberc Respir Dis. 2013;74:187.View ArticleGoogle Scholar
- Liao CH, Lai CC, Huang YT, Chou CH, Hsu HL, Hsueh PR. Subcutaneous abscess caused by Mycobacterium conceptionense in an immunocompetent patient. J Infect. 2009;58:308–9.View ArticlePubMedGoogle Scholar
- Yang HJ, Yim HW, Lee MY, Ko KS, Yoon HJ. Mycobacterium conceptionense infection complicating face rejuvenation with fat grafting. J Med Microbiol. 2011;60:371–4.View ArticlePubMedGoogle Scholar
- Lee KH, Heo ST, Choi SW, Park da H, Kim YR, Yoo SJ. Three cases of postoperative septic arthritis caused by Mycobacterium conceptionense in the shoulder joints of immunocompetent patients. J Clin Microbiol. 2014;52:1013–5.View ArticlePubMedPubMed CentralGoogle Scholar
- Carrillo MC, Patsios D, Wagnetz U, Jamieson F, Marras TK. Comparison of the spectrum of radiologic and clinical manifestations of pulmonary disease caused by Mycobacterium avium complex and Mycobacterium xenopi. Can Assoc Radiol J. 2014;65:207–13.View ArticlePubMedGoogle Scholar
- Rodríguez-Aranda A, Jimenez MS, Yubero J, Chaves F, Rubio-Garcia R, Palenque E, et al. Misindentification of Mycobacterium kumamotonense as M. tuberculosis. Emerg Infect Dis. 2010;7:1178–80.View ArticleGoogle Scholar
- Tjhie JH, van Belle AF, Dessens-Kroon M, van Soolingen D. Misidentification and Diagnostic Delay Caused by a False-Positive Amplified Mycobacterium tuberculosis Direct Test in an Immunocompetent Patient with a Mycobacterium celatum Infection. J Clin Microbiol. 2001;39:2311–2.View ArticlePubMedPubMed CentralGoogle Scholar
- Andrejak C, Thomsen VO, Johansen IS, Riis A, Benfield TL, Duhaut P, et al. Nontuberculous pulmonary mycobacteriosis in Denmark: incidence and prognostic factors. Am J Respir Crit Care Med. 2010;181:514–21.View ArticlePubMedGoogle Scholar
- Brode SK, Jamieson FB, Ng R, Campitelli MA, Kwong JC, Paterson JM, et al. Risk of mycobacterial infections associated with rheumatoid arthritis in ontario, Canada. Chest. 2014;146:563–72.View ArticlePubMedGoogle Scholar
- Hoefsloot W, van Ingen J, Andrejak C, Angeby K, Bauriaud R, Bemer P, et al. The geographic diversity of nontuberculous mycobacteria isolated from pulmonary samples: an NTM-NET collaborative study. Eur Respir J. 2013;42:1604–13.View ArticlePubMedGoogle Scholar
- Wang HX, Yue J, Han M, Yang JH, Gao RL, Jing LJ, et al. Nontuberculous mycobacteria: susceptibility pattern and prevalence rate in Shanghai from 2005 to 2008. Chin Med J. 2010;123:184–7.PubMedGoogle Scholar
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.