Non-tuberculous mycobacteria (NTM) are close relatives of
NTM are an extremely heterogeneous group with many new species and subspecies added recently due to advances in molecular tools [2]. They show a high level of diversity of morphological, physiological, and biochemical features. Before the post-genomic era, NTM were classified by Runyon based on their growth on agar and pigment formation. According to the Runyon classification, bacteria growing on agar in less than seven days are called
The majority of NTM are saprophytic bacteria, among which a small number of species can produce diseases in humans. They are mainly opportunistic infections posing a higher risk of acquisition in immunocompromised patients and patients with pre-existing lung conditions. NTM species have been demonstrated to produce predominantly infections involving the pulmonary system, but have also been shown to cause cervical lymphadenitis in young children, disseminated diseases, skin, soft tissue, and eye infections [5, 6, 7] (figure 1).
Clinical diseases caused by non-tuberculous mycobacteria. Common and less common isolated NTM species are listed in an alphabetical order [8, 9, 10].
NTM similarly to
Diagnosis of NTM infections is complex due to environmental exposure of individuals and the necessity of distinguishing a colonizer or contaminant from a true pathogen. The diagnosis of NTM infections requires integrated clinical, radiographic, and microbiologic data. Species-level identification is very important for choosing successful treatment and it is usually achieved by molecular methods. Mass spectrometry–based methods, such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), is an alternative approach enabling identification of NTM infection etiological agents.
NTM therapy is protracted (often more than one year) and requires multidrug regimens. Treatment outcome varies by patient and is dependent on the NTM species and the host status, but often remains poor [10]. Currently used regimens represent limited efficacy and often lead to severe adverse effects. NTM are naturally resistant to disinfectants and a wide spectrum of antibiotics, including most Tb drugs, posing a major challenge for effective treatment [13]. For these reasons alternatives to antibiotic therapy treatment methods have been explored in parallel.
In the last two decades, the gradual and systematic increase of NTM disease incidence has been shown worldwide [7]. Because diagnosis is complicated and treatment is very often ineffective, NTM diseases are a growing global health problem. This article reviews the key factors contributing to the risk, diagnosis, and treatment of NTM infections.
The last two decades have shown an alarming and growing trend in the incidence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) worldwide. Studies from the United Kingdom showed that NTM infection rates increased from 0.9 to 2.9/100,000 from 1995 to 2006 [14]. The growing trend of NTM incidence in the United Kingdom was further supported by studies of Shah et al. [15]. Using a population-based approach, they found that infection rates in the United Kingdom rose from 5.6/100,000 in 2007 to 7.6/100,000 in 2012. This denoted an almost tenfold increase since 1995 [15]. In Denmark, the NTM-PD incidence rose from 0.6 to 1.5/100,000 from 2003 to 2008 [16]. Similar rates have been recorded in other European countries [17, 18, 19]. The incidence and prevalence of NTM-PD are most likely highly underestimated in most European countries since it is usually not a reportable condition [20]. Although NTM-PD is considered rare in European countries, it is imposing a high economic burden due to complex diagnosis and prolonged treatment regimens [17]. Studies from the United States suggest an annual rate of NTM-PD of 1.4 to 13.9/100,000, with higher prevalence in the Southern United States and Hawaii. Furthermore, epidemiology studies consistently confirm that NTM-PD prevalence in the USA is increasing, with estimates ranging from 2.5% to 8% per year [7, 21]. A high incidence of NTM-PD was also reported in Ontario, Canada, between 2001 and 2013: 13.33/100,000 [22]. In Asia NTM-PD infections at a rate of 14.7/100,000 were estimated in the Japanese population in 2014 [23]. Among patient populations, NTM-PD rates are more dramatic in patients with pre-existing lung diseases. The overall prevalence of NTM respiratory infections in patients with cystic fibrosis (CF) ranges from 6% to 13% [24, 25]. NTM-PD in Europe is predominantly caused by
Several closely related species have been incorporated into the MAC based on high-throughput gene sequencing [26, 27].
The nearly ubiquitous presence of NTM in the environment and overlap of bacterial and human habitation makes NTM species perfect candidates for opportunistic pathogens. Natural environmental niches of NTM are lakes, streams, rivers, seawater, and soil [4]. Until recently, it was believed that the environment was the only possible source of NTM infection. NTM are believed to be naturally transmitted to human-engineered and household environments mainly through water distribution systems. For example, MAC bacteria are frequently isolated from tap water and bathrooms, the end-points of water distribution systems [12]. Particularly, shower-head biofilms have been shown to be enriched in NTM compared to main stream water [37, 38]. Significantly, MAC-based infection was shown to be more prevalent in patients whose bathrooms were contaminated with MAC bacteria. Furthermore, genotyping studies showed that clinical isolates are identical to environmental ones [12]. NTM were also found in other human-engineered environments involving water, such as swimming pools, hot tubs, rainwater tanks, cooling towers, and hospital faucets and ice machines [4]. Other common reservoirs of NTM present in the household are garden and potting soil and house dust. Interestingly, in Europe MAC bacteria and other NTM were isolated more frequently from soil than water or biofilms [12]. As an effect of their relatively hydrophobic surface, NTM are readily aerosolized. It is conceivable that aerosols formed by NTM arising from shower heads, soil, dust, and pool water can be infection sources. Survival of NTM in the environment is facilitated by the ability of these bacteria to form biofilms on surfaces. Furthermore, NTM have been shown to live within free-living amoebae where they can be protected from extreme environmental conditions [4]. This hypothesis was based on the observation that amoebae and mycobacteria are frequently isolated from the same environmental niches such as freshwater, soil, and municipal potable water systems [39]. Further, several studies demonstrated that NTM have the ability to invade amoebae and live intracellularly as endosymbionts. They can survive both within trophozoites and within cysts and replicate inside protozoa [39, 40]. However, direct evidence of the presence of mycobacteria in naturally infected amoebae remains scarce [41].Thus, this hypothesis requires further evaluation.
The environment is also the source of
Food products are another possible source of NTM exposure. Several studies have shown the presence of
Although household water plays an important role in spreading NTM infection, it does not explain the global increase of infections caused by these microorganisms. Most likely, other transmission routes must exist. This is further supported by the fact that the isolation of
Sources of non-tuberculous mycobacteria [4, 12, 41, 42, 44, 47, 48]
Natural environment |
---|
Lakes, streams, rivers, ground water and seawater |
Soil and dust from soil |
Amoebae |
Aquatic insects |
Plumbing systems |
Tap water, shower heads, and faucets |
Swimming pools, hot tubs, footbaths, hydrotherapy pools |
Ice machines |
Humidifiers |
Dialysis centers |
Heater-cooler units |
Potting and garden soil |
Aquarium water |
Food products |
Rainwater tanks and cooling towers |
Though exposure to NTM through contact with shower water, soil, or dust is common in human everyday life, clinical disease manifestation occurs only in some individuals. Prominent risk factors for acquiring pulmonary NTM infections are genetic and acquired lung diseases causing defects in lung structural and functional integrity such as CF, chronic obstructive pulmonary disease (COPD), non-CF bronchiectasis, pneumoconiosis, post-radiotherapy fibrosis, chronic pulmonary aspiration, allergic bronchopulmonary aspergillosis, previous pulmonary tuberculosis, and lung cancer [49, 50]. Additionally, genetic defects in genes related to immune responses, cystic fibrosis transmembrane conductance regulator (CFTR), cilia, and connective tissue have been found more frequently in patients with pulmonary NTM disease compared with control groups [47].
Another risk factor group includes elderly white postmenopausal women with a distinct physical phenotype characterized by slender build, pectus excavatumor scoliosis, and mitral valve prolapse: described as “Lady Windermere syndrome” [51]. Similar characteristics have been also described for men as “Lord Windermere syndrome” [52]. Primary and acquired immunodeficiencies including Mendelian susceptibility to mycobacterial disease (MSMD), severe combined immunodeficiency (SCID), acquired immunodeficiency syndrome (AIDS), and hematological malignancies pose significant risks for acquiring NTM infections. Another threat is associated with immunomodulatory drugs used in autoimmune diseases and cancer treatment. Similarly, TNF therapy applied in rheumatoid arthritis patients increases the risk of NTM disease [50, 53]. Host age and gender are also significant risk factors in acquiring NTM infections. Most studies worldwide have found older patients (≥ 65 years) and women in a higher preponderance of NTM infections [7, 54]. It is worth noting that low body mass index and low nutrient intake were associated with susceptibility to pulmonary NTM disease [47]. The above-mentioned risk factors and more for acquiring NTM infection are summarized in figure 2.
Predisposing factors for non-tuberculous mycobacterial diseases [47, 50].
Diagnostic criteria are summarized in several guidelines [10, 55, 56, 57]. The diagnosis of NTM-PD should be based on integrated clinical, radiographic, and microbiologic data. The most important factor is excluding contaminants or colonizers and other diseases such as tuberculosis. In histological examination, cell granulomatosis caused by NTM infections is indistinguishable from tuberculosis.
Definitive diagnosis of NTM infections should be supported by repeated isolation of NTM from several specimens from the patient or a single specimen if it is collected aseptically from a sterile body site [10]. Thus, mycobacterial culture remains the gold standard of diagnosis. The isolation of mycobacteria, especially slow-growing species, is difficult, because some species require special micronutrients (e.g.,
For direct identification from clinical material, a nucleic acid amplification test (NAAT) and real-time PCR are used. Direct probe hybridization assays (e.g., AccuProbe) allow identification of
Whole-genome sequencing (WGS) is a promising tool which, besides identification at the species level, enables biomarker discovery [30]. WGS requires high DNA purity and quantity but additionally provides information about antibiotic resistance and is valid for epidemiologic purposes. Next-generation sequencing (NGS) technology is expensive and is not widely available in clinical laboratories but its role will likely increase after further validation and standardization.
Molecular methods of mycobacteria identification are technically demanding and expensive, and not available in most clinical laboratories. As an alternative, mass spectrometry techniques- MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) is used as a reliable, rapid, and cost-effective method, but this technique requires a cultivation step. Microorganism identification is based on a spectral fingerprint produced by extracted proteins. Over the last decade, MALDI-TOF MS has been used with increasing frequency in routine clinical laboratories worldwide.
Sample preparation for MALDI-TOF analysis is relatively uncomplicated; however, the lipid-rich cell envelope of mycobacteria makes it necessary to disrupt the cells before protein extraction. Different methods have been tested, including use of a special inactivation step and mechanical disruption with glass or zirconia beads [67, 68]. Recently, a method consisting of sequential freezing and mechanical cell disruption significantly improved the identification score of NTM isolates [69].
Cao et al. performed a meta-analysis of 19 studies that used MALDI-TOF for identification of clinical pathogenic mycobacteria. Among 2,593
Two major commercial MALDI-TOF MS identification systems—bioMérieux and Bruker—for identification of NTM were compared in the study of Brown-Elliot et al. [71]. Two large clinical laboratories in the USA utilizing different systems (VITEK bioMérieux with v3.0 Knowledge Base and Bruker Biotyper system with RUO Mycobacteria Library v5.0.0) performed identification of the same NTM isolates. The clinical isolates were previously sequenced and were analyzed as blind samples. Out of 244 isolates, Bruker Biotyper system identified 92% and bioMérieux 95% of NTM strains, to at least complex/group level. The Biotyper and bioMérieux systems identified 62% and 57%, respectively, either to the species or subspecies level. The species differentiation in
MALDI-TOF spectra of protein extracts of
Apart from protein fingerprint, lipid profiles of mycobacteria obtained by MALDI-TOF mass spectrometry have strong potential and could be used for rapid species identification [75], but this technique is currently not applied in routine clinical microbiology (however, it could be adapted in reference laboratories). Methods used for identification of NTM species are summarized in table 2.
Methods used for identification of non-tuberculous mycobacterial species [57, 63, 76]
Culture-independent | Culture-dependent | ||
---|---|---|---|
Method | Limitation | Method | Limitation |
Histology | Cell granulomatosis indistinguishable | Phenotypic methods | Time consuming, does not allow |
from Tb | -Biochemical testing | identification of the newly described | |
species | |||
Smear microscopy | NTM not distinguishable from Mtb | Chemotaxonomical methods | Not available in all clinical laboratories |
-HPLC of mycolic acids | |||
Nucleic acid amplification test | Using for excluding Mtb | Direct probe hybridization assay | Limited number of species |
-Commercial NAAT | |||
Real-time PCR | Low sensitivity, limited range of species | Line probe assay | Limited number of species |
– in-house methods | -Commercial test | ||
Serological testing | Cross-reactivity | 16S DNA sequencing | Limited discriminatory power |
Multigene sequencing | Expensive, not available in clinical | ||
-Whole genome sequencing | laboratories | ||
Highly trained staff | |||
MALDI-TOF MS | Database content; quality of protein extracts |
As recommended by several guidelines [10, 55, 56], macrolide-based multidrug regimens guided by susceptibility testing results are the main therapeutic options for NTM infections. The use of multidrug therapy is fundamental to avoid drug resistance. In general, treatment involves the administration of clarithromycin or azithromycin in combination with at least two other antibiotics for no less than 18 months or 12 months after culture conversion [10, 55]. For lung infections with MAC, azithromycin, which is preferentially used over clarithromycin, is combined with rifampicin and ethambutol [55].
Treatment for NTM infections is extremely long, with an average duration of 18 to 24 months. The drugs and regimens are difficult to tolerate and the therapy often causes severe adverse effects which lead to treatment discontinuation or patient nonadherence [81]. Therefore, in less severe cases health professionals may choose no treatment option, and patients are kept under observation. Treatment outcome highly depends on NTM species and host health status, but usually remains poor. Whereas around 50–80% of patients with MAC pulmonary disease achieve sputum conversion [82, 83], the cure rate for lung infections caused by
In summary, the main reasons for the high failure rate of NTM infection treatment include the limited number of effective therapeutics, lengthy treatment duration, and potential for severe adverse effects. Therefore, there is an urgent need for new, more efficacious and safer regimens, as well as drugs with new modes of action. Only a few therapeutics are currently under development for NTM infections and most of them are repurposed and reformulated existing antibiotics, usually compounds from Tb or malaria treatment [11].
As environmental bacteria, NTM are subjected to constant selective pressure from their antimicrobial-producing neighbors residing within the same niches. Therefore, NTM have developed multiple resistance mechanisms, which allow them to survive in hostile environments. Natural resistance, inducible resistance, and mutational resistance are three different resistance mechanisms by which NTM demonstrate low susceptibility to antibiotics. There have been several excellent reviews on NTM resistance mechanisms; therefore we will give only a brief summary here [88, 89]. Major factors contributing to natural resistance of NTM are a highly impermeable cell envelope, the ability to form biofilms, and expression of efflux pumps. Another mechanism of natural resistance identified in NTM is connected with polymorphism in the target gene of an antimicrobial mechanism of action. Amino acid change in the DNA gyrase GyrA of
Several alternative approaches beyond standard antibiotic therapy are under current investigation for NTM treatment. Antimicrobial peptides (AMP) are short peptides (20-60 amino acids), produced by microorganisms, humans, and other mammals. These compounds possess broad- spectrum activity against pathogenic bacteria and their mode of action is complex and diverse. AMP with anti-mycobacterial activity have been found in humans, bacteria, mycobacteriophages, and synthetically produced peptides [98]. They have been shown to display either bactericidal or bacteriostatic activity against mycobacteria. Human origin AMP such as cathelicidins, defensins, granulysins, and lactoferricins have activities against
Another therapeutic option for NTM infection treatment is bacteriophages, viruses able to kill bacteria. Bacteriophages do not infect human cells and are specific for a strain or a species of bacteria and are effective even against multidrug-resistant strains. The phages can lyse bacteria at the site of infection and may be administered in combination with antibiotics. To avoid immune response of the host, nonpathogenic phages should be selected for therapy. The main limitations of phage therapy are the potential of developing bacterial resistance to phages, the difficult process of phage selection, and proper formulation of phage preparation. The major obstacles to using phage therapy have been recently reviewed [101]. Though the first therapeutic use of phages took place 100 years ago [102], the data concerning mycobacteria are limited. It is estimated that about 4,200 bacteriophages can infect
Iron chelators have been proposed as a potential strategy to treat mycobacterial infections. Mycobacteria, like other pathogens, need iron for proliferation and survival. Iron plays a pivotal role as a co-factor of many enzymes involved in bacterial growth and is also needed for bacterial virulence [105]. A few studies reported that adding iron chelators not only decreased
Nitric oxide (NO) inhalation has also been proposed as a potential treatment for NTM infections. NO possesses potent antimicrobial activity against bacteria, viruses, and fungi
Host–directed therapies are based on stimulating or modulating of immune responses to better combat mycobacteria or reduce disease symptoms. Cytokines such as IFN-γ, IL-12, GM-CSF as well as autoantibodies against IFN-γ have been tested on mice models and human patients [111]. Another strategy would involve inducing autophagy of intracellular pathogens [99]. All these host-directed therapies still need more fundamental studies as well as clinical trials to assess their real efficacy.
Major prophylactic actions should be focused on blocking NTM transmission and developing preventive vaccines against these bacteria. NTM are environmental bacteria, and the most important preventive measure is to decrease their transmission through soil and water. Due to the extreme resistance of mycobacteria to disinfectants, chlorination is not sufficient to kill these microorganisms in water supply systems [47]. Therefore, more appropriate water treatment procedures effective against these opportunistic bacteria should be developed. Another prophylactic action could be the use of enhanced ventilation in swimming pools to lower the risk of ingestion of aerosolized biofilms formed in closed indoor areas [112]. Workers with occupational risk, exposed to soil and dust particles, should wear masks and gloves.
Currently, there are no vaccines available for NTM diseases. The BCG vaccine used against Tb may have some protection against extra-pulmonary NTM infections. There is evidence that BCG vaccination protects from NTM lymphadenitis in children, and is associated with some protection against
Increasing incidence of NTM infections, especially in industrialized countries, is alarming. As opportunistic pathogens,