Nontuberculous Mycobacteria—Overview

ABSTRACT

Nontuberculous mycobacteria (NTM) are emerging pathogens that affect both immunocompromised and immunocompetent patients. The development of molecular methods has allowed the characterization of new species and the identification of NTM to the precise species and subspecies levels. The incidence and prevalence of NTM lung disease are increasing worldwide, and this syndrome accounts for the majority of clinical cases of NTM disease. Common causative organisms of pulmonary infection are the slowly growing mycobacteria Mycobacterium avium complex and Mycobacterium kansasii and the rapidly growing mycobacteria, including Mycobacterium abscessus complex. NTM lung disease often affects elderly people with chronic lung disease and may be a manifestation of a complex genetic disorder determined by interactions among multiple genes, as well as environmental exposures. To be diagnosed with NTM lung disease, patients should meet all clinical and microbiologic criteria, but the decision to start treatment is complex, requiring careful individualized analysis of risks and benefits. Clinicians should be alert to the unique aspects of NTM lung disease, including the need for proper diagnosis, the availability of advanced molecular methods for species and subspecies identification, and the benefits and limitations of recommended treatments.

INTRODUCTION

The term nontuberculous mycobacteria (NTM) generally refers to mycobacteria other than the Mycobacterium tuberculosis complex and M. leprae (1). NTM are ubiquitous in the environment, including household water, natural water sources, and soil (2). Human disease due to NTM is classified into four distinct clinical syndromes: chronic pulmonary disease, lymphadenitis, cutaneous disease, and disseminated disease. Of these, chronic pulmonary disease is the syndrome most commonly encountered clinically (1).

Most NTM disease is assumed to originate from environmental NTM (2). Of the many possible sources of infection, airborne NTM may play an important role in respiratory disease (1). NTM are quite resistant to commonly used water disinfectants, such as chlorine, and the ability of NTM to persist in urban water supplies may therefore be contributing to the increasing prevalence of NTM lung disease in many countries (2). Unlike with pulmonary tuberculosis, person-to-person transmission is considered an unlikely source for NTM respiratory disease for most patients (1), although evidence for this type of transmission has been reported for cystic fibrosis (CF) patients infected with M. abscessus complex (MABC) (3, 4). Ingestion is likely to be an important source of infection for children with NTM cervical lymphadenitis and for the majority of human immunodeficiency virus-infected patients, in whom M. avium dissemination begins as gastrointestinal colonization (1). Direct inoculation of NTM organisms from water or some other material is likely to be a source of infection for those with skin and soft tissue infections (1).

EPIDEMIOLOGY

Early on, NTM were classified by Runyon according to their growth rates on solid culture medium and pigment formation. Types I, II, and III, slowly growing mycobacteria, took 7 days or more to grow and were told apart by their coloration. If pigment was produced only on exposure to light, they were photochromogens (type I); if pigment was produced even if grown in the dark, they were scotochromogens (type II); if they were not strongly pigmented, they were nonphotochromogens (type III). Rapidly growing mycobacteria (type IV) grew in less than 7 days but more slowly than most bacteria. Slowly growing mycobacteria include the M. avium complex (MAC), M. kansasii, M. xenopi, M. malmoense, and M. szulgai, whereas rapidly growing mycobacteria include MABC and the M. fortuitum complex (Table 1).

TABLE 1.

Classification of NTM commonly causing human disease

Slowly growing mycobacteria	Rapidly growing mycobacteria
Runyon group I, photochromogens	Runyon group IV
M. kansasii	M. abscessus complex
M. marinum	M. chelonae
M. simiae	M. fortuitum complex
Runyon group II, scotochromogens	M. peregrinum
M. scrofulaceum
M. szulgai
M. gordonae
Runyon group III, nonchromogens
M. avium complex
M. ulcerans
M. xenopi
M. malmoense
M. terrae complex
M. haemophilum
M. genavense

The incidence and prevalence of NTM lung disease continue to increase worldwide (5, 6). Among the more than 150 officially recognized NTM species, the most frequent human pathogens are MAC, MABC, and M. kansasii. However, M. xenopi and M. malmoense are the predominant organisms found in some geographical areas (7). Correct identification of clinical NTM isolates is important because NTM species differ in their clinical relevance, which is defined by the percentage of patients with a positive NTM culture who ultimately meet the diagnostic criteria of NTM disease (8). Even among patients with a positive respiratory culture for an NTM species commonly associated with lung infection, only 25 to 60% meet the criteria for NTM pulmonary disease (6). Isolation of MAC, MABC, M. kansasii, M. malmoense, M. xenopi, and M. szulgai from respiratory specimens indicates a relatively high probability of true NTM lung disease, whereas less virulent species, such as M. gordonae, M. terrae, and M. fortuitum complex, are usually contaminants rather than causative agents of true NTM lung disease (6, 8).

MAC is the most common etiology of NTM lung disease worldwide (5, 6) and was originally composed of two species, M. avium and M. intracellulare, which cannot be differentiated through traditional physical and biochemical tests (1). Most laboratories and studies report these species as MAC because they are considered to be highly similar, and the clinical features of patients who are infected with these two species are considered indistinguishable (1). With the development of molecular identification methods, several new species closely related to M. intracellulare have been identified: M. chimaera, M. colombiense, M. arosiense, M. vulneris, M. marseillense, M. timonense, M. bouchedurhonense, M. mantenii, M. yongonense, and “M. indicus pranii” (9). Information regarding the exact proportion and clinical relevance of these different species among MAC clinical isolates is still limited. Some reports have suggested that patients with M. intracellulare lung disease exhibit a more severe and advanced clinical presentation at the time of diagnosis and have a worse prognosis in terms of disease progression and treatment response than patients with M. avium lung disease (10). In addition, M. chimaera was reported to be less virulent than M. avium and M. intracellulare (11, 12), and rates of recurrence of MAC lung disease after successful treatment completion are different among MAC species (12).

Mycobacterium kansasii is another slowly growing NTM and the second most common cause of NTM lung disease in some European countries, including the United Kingdom (7). Traditionally, M. kansasii has been considered the most virulent NTM species, and the presence of a single M. kansasii isolate in a sputum sample has been believed to be clinically significant (1), although this has not been definitely established (13).

MABC is the most important source of pulmonary infections caused by rapidly growing mycobacteria in patients with chronic lung diseases, such as bronchiectasis and CF (1, 14). Currently, MABC is divided into three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii (15). Of the three subspecies, M. abscessus subsp. abscessus is the most common pathogen (45% to 65%), followed by M. abscessus subsp. massiliense (20% to 55%) and M. abscessus subsp. bolletii (1% to 18%) (16). The rates of response to antibiotic therapy are different for each of these subspecies (17). Therefore, precise species or subspecies identification of NTM clinical isolates, including MAC and MABC, is becoming increasingly important for managing patients with NTM lung disease.

Approximately 90% of NTM infections involve the pulmonary system; the rest involve lymph nodes, skin and soft tissue, and bones (18, 19). Less frequently reported are keratitis, otitis media, central nervous system infection, and disseminated infection (18, 19) (Table 2).

TABLE 2.

Pulmonary and extrapulmonary disease caused by NTM

Disease	Common etiology
Pulmonary disease	M. avium complex
	M. abscessus complex
	M. kansasii
	M. malmoense
	M. xenopi
Lymphadenitis	M. avium complex
	M. scrofulaceum
	M. malmoense
	M. hemophilum
Skin, soft tissue infecton	M. abscessus complex
	M. chelonae
	M. fortuitum complex
	M. marinum
	M. ulcerans
Bone infection	M. avium complex
	M. xenopi
	M. marinum
	M. kansasii
	M. abscessus complex
	M. fortuitum complex

PATHOGENESIS

Despite the fact that NTM are widespread in the environment and that exposure to these organisms is inevitable, NTM lung disease is relatively uncommon, suggesting that normal host defense mechanisms are sufficient to prevent NTM infection and that patients who develop NTM lung disease likely have specific susceptibility factors that make them vulnerable to these infections. Many diseases associated with structural lung damage, such as CF, non-CF bronchiectasis, primary ciliary dyskinesia, chronic obstructive pulmonary disease, previous tuberculosis, and pneumoconiosis, have been recognized as predisposing patients to NTM lung disease (20, 21). An immunosuppressed status, related to, for example, human immunodeficiency virus infection, transplantation, or use of tumor necrosis factor alpha inhibitor, is also associated with NTM disease (21). Additionally, uncommon defects in the interleukin-12/interferon gamma axis and anti-interferon gamma autoantibody may lead to disseminated NTM infection (22, 23).

However, some patients with no known overt genetic or immunologic defects develop NTM lung disease. These patients are typically postmenopausal women who have a unique body morphotype, that is, a slender marfanoid body habitus (scoliosis, pectus excavatum, and mitral valve prolapse) (24), and certain immunophenotypes, such as altered serum adipokine levels and mucociliary dysfunction (25, 26). A recent whole-exome sequencing study found an increased prevalence of genetic mutations controlling immune function, ciliary function, connective tissue, and the CF transmembrane conductance regulator in patients with NTM lung disease compared with healthy controls (27). These data suggest that NTM lung disease in otherwise healthy persons is a manifestation of a complex genetic disorder determined by interactions among multiple genes, as well as environmental exposures.

CLINICAL PRESENTATION AND DIAGNOSTIC CRITERIA

The isolation of NTM remains a challenge for clinicians. Because NTM exist naturally in the environment, isolation of NTM from nonsterile respiratory specimens does not necessarily mean that they are the causative agents of lung disease; rather, such recovery of NTM may reflect colonization or transient infection without the induction of disease, or it may result from contamination of the respiratory specimens (1). Diagnosis of NTM lung disease requires the clinician to integrate clinical, radiographic, and microbiological data, particularly as the symptoms, such as chronic cough, sputum, hemoptysis, fatigue, malaise, and weight loss, are often nonspecific and may also reflect underlying lung disease, such as bronchiectasis and chronic obstructive lung disease. Therefore, symptomatic patients with compatible radiographic findings must meet specific microbiological criteria in order to be diagnosed with NTM lung disease (1).

NTM lung disease has two major different radiographic manifestations: the fibrocavitary form and the nodular bronchiectatic form (1). The fibrocavitary form has cavitary lesions predominantly in the upper lobes, with radiographic findings similar to those of pulmonary tuberculosis (Fig. 1); this manifestation frequently develops in older men with a history of smoking and underlying lung disease, such as previous tuberculosis and chronic obstructive pulmonary disease, and is associated with relatively rapid disease progression. The other form of NTM lung disease is nodular bronchiectatic disease, which can present as multifocal bronchiectasis, clusters of small nodules, and branching linear structures that frequently involve the right middle lobe and the lingular segment of the left upper lobe (Fig. 2).

FIGURE 1.

Fibrocavitary form of Mycobacterium intracellulare lung disease in a 62-year-old male patient. The patient underwent antituberculosis treatment and a right upper lobectomy at 30 years of age. Chest computed tomography shows a large cavity in the right upper lung field. Note the emphysema in both lungs.

FIGURE 2.

Nodular bronchiectatic form of Mycobacterium abscessus lung disease in a 63-year-old female patient. Chest computed tomography shows severe bronchiectasis in the right middle lobe and in the lingular segment of the left upper lobe. Note the multiple small nodules and tree-in-bud appearance suggesting bronchiolitis in both lungs.

The diagnostic criteria from the American Thoracic Society and the Infectious Disease Society of America are widely used to diagnose NTM lung disease (1). Clinical findings should include pulmonary symptoms and compatible radiographic evidence (nodular or cavitary opacities) and high-resolution computed tomography findings (multifocal bronchiectasis with multiple small nodules). Microbiological criteria include two positive sputum cultures, one positive bronchial wash or lavage sample, or other evidence of NTM, such as lung biopsy samples that are culture positive for NTM and that have histological features consistent with the presence of mycobacteria (1). These criteria fit well for MAC, MABC, and M. kansasii infections; however, there is insufficient information regarding other forms of NTM disease to be certain that these diagnostic criteria are universally applicable to all types of NTM respiratory pathogens (1, 8) (Table 3).

TABLE 3.

Diagnostic criteria of NTM lung disease^a

Clinical (both required)

1. Pulmonary symptoms, nodular or cavitary opacities on chest radiograph, or a high-resolution computed tomography scan that shows multifocal bronchiectasis with multiple small nodulesAND2. Appropriate exclusion of other diagnoses

Microbiologic

1. Positive culture results from at least two separate expectorated sputum samples. If the results are nondiagnostic, consider repeat sputum AFB smears and cultures.OR2. Positive culture result from at least one bronchial wash or lavageOR3. Transbronchial or other lung biopsy with mycobacterial histopathologic features (granulomatous inflammation or AFB) and positive culture for NTM or biopsy showing mycobacterial histopathologic features (granulomatous inflammation or AFB) and one or more sputum or bronchial washings that are culture positive for NTM4. Expert consultation should be obtained when NTM are recovered that are either infrequently encountered or that usually represent environmental contamination.5. Patients who are suspected of having NTM lung disease but do not meet the diagnostic criteria should be monitored until the diagnosis is firmly established or excluded.6. Making the diagnosis of NTM lung disease does not, per se, necessitate the institution of therapy, which is a decision based on potential risks and benefits of therapy for individual patients.

^a Reprinted from reference 1 with permission of the American Thoracic Society. Copyright © 2016 American Thoracic Society.

LABORATORY DIAGNOSIS

Acid-fast bacillus (AFB) staining cannot differentiate between M. tuberculosis and NTM. However, many commercial kits for nucleic acid amplification tests are available to differentiate NTM from M. tuberculosis in AFB smear-positive respiratory samples (8, 28).

Both liquid and solid media are used for mycobacterial culture (1). Cultures grown on solid media allow for the observation of colony morphology, growth rates, species categorization based on pigmentation, and quantitation of the infecting organism. Liquid systems are more sensitive and reduce the delay in the detection of NTM, but they are prone to contamination by other microorganisms and bacterial overgrowth (8, 28).

Because treatments and outcomes differ depending on the NTM species, the accurate identification of NTM species is very important (8, 28). Traditional biochemical tests or high-performance liquid chromatography for NTM identification have been replaced by molecular methods such as line probe hybridization, PCR-restriction fragment length polymorphism analysis, real-time PCR, DNA sequencing, and matrix-assisted laser desorption ionization–time of flight spectrometry (8, 28). Gene sequencing is the reference method for the identification of NTM species and may be performed for uncommonly encountered species or for precise identification at the subspecies level (8, 28). Sequencing of the 16S rRNA gene allows discrimination at the species level or to the complex level, such as for MABC. However, single-target sequencing cannot be used to accurately differentiate species, and for a higher level of discrimination, up to the subspecies level, sequencing of several key targets, such as hsp65, rpoB, and the 16S-23S internal transcribed spacer, is needed (8, 28).

Drug susceptibility testing (DST) for NTM is difficult and controversial because of discrepancies between in vitro susceptibility and in vivo clinical outcomes (29). DST is performed using the broth microdilution method according to a standardized protocol from the Clinical and Laboratory Standards Institute (30), and among slowly growing mycobacteria, clear correlations have been established for macrolides and amikacin in MAC lung disease and for rifampin in M. kansasii lung disease (31, 32). Macrolide resistance in MAC is caused by mutations in the macrolide binding site of 23S rRNA (31, 32); macrolide susceptibility testing for all MAC isolates is advised, and clarithromycin is recommended as the class agent for testing macrolides because clarithromycin and azithromycin share cross-resistance and similar patterns of organism susceptibility (30). Rifampin and clarithromycin are the currently recommended drugs for primary susceptibility testing for M. kansasii (30).

For rapidly growing mycobacteria, the agents that should be tested are amikacin, cefoxitin, ciprofloxacin, clarithromycin, doxycycline (or minocycline), imipenem, linezolid, moxifloxacin, trimethoprim-sulfamethoxazole, and tobramycin (30). In addition, unless resistance is recognized earlier, it is recommended that the final reading for clarithromycin be performed after at least 14 days to detect inducible macrolide resistance in rapidly growing mycobacteria, especially M. abscessus (30). Inducible macrolide resistance was recently discovered in M. abscessus, with altered resistance to clarithromycin observed during in vitro DST after prolonged incubation (susceptible at day 3 but resistant at day 14) or after preincubation in macrolide-containing media (30). This inducible resistance to clarithromycin is due to a functioning erythromycin ribosomal methylase gene, erm(41), which is present in most strains of M. abscessus subsp. abscessus but not in M. abscessus subsp. massiliense (33).

TREATMENT

A diagnosis of NTM lung disease does not necessitate the initiation of antibiotic therapy against NTM species (1). Instead, this decision should be made based on the potential risks and benefits for individual patients of a prolonged course of treatment with multiple antibiotics. Initiation of NTM treatment should be individualized based on disease type, comorbid conditions, and age. Because the presence of cavitary disease is associated with higher mortality, patients with fibrocavitary disease usually require immediate treatment (34–36). Conversely, nodular bronchiectatic disease tends to occur in the absence of significant comorbidity and progresses very slowly (34–36). Therefore, early treatment of mild and indolent nodular bronchiectatic disease may not be advisable due to adverse effects from the long-term use of many drugs (34–36). Because a microbiological cure can be difficult to achieve in a substantial proportion of patients, other treatment goals, including improving patient quality of life, may be more appropriate (1).

Once the decision has been made to initiate treatment for NTM lung disease, the treatment regimens should be formulated according to established guidelines, understanding that a substantial proportion of the current guidelines rely upon expert opinion rather than randomized clinical trials (34–36). However, adherence to the current guidelines for treating NTM lung disease is poor (37).

CONCLUSIONS

NTM are emerging pathogens that affect both immunocompromised and immunocompetent patients, and the development of molecular methods has allowed the characterization of new species and the identification of NTM to the precise species and subspecies levels. The incidence and prevalence of NTM lung disease are increasing worldwide, and this syndrome accounts for the majority of clinical cases of NTM disease. Common causative agents of pulmonary infection are the slowly growing mycobacteria MAC and M. kansasii and the rapidly growing mycobacteria, including MABC. NTM lung disease often affects elderly people with chronic lung disease and may be a manifestation of a complex genetic disorder determined by interactions among multiple genes, as well as environmental exposures. To be diagnosed with NTM lung disease, patients should meet all clinical and microbiologic criteria, but the decision to start treatment is complex, requiring careful individualized analysis of risks and benefits. Clinicians should be alert to the unique aspects of NTM lung disease, including the need for proper diagnosis, the availability of advanced molecular methods for species and subspecies identification, and the benefits and limitations of recommended treatments.