Growing Challenges of Lung Infections with Non-tuberculous Mycobacteria in Immunocompromised Patients: Epidemiology and Treatment

Non-tuberculous mycobacteria (NTM) encompass numerous species that pose a serious threat to human health. NTM have emerged as opportunistic pathogens causing infections in both immunocompromised and immunocompetent individuals (Gopalaswamy et al. 2020; Chai et al. 2022). Advances in molecular diagnostics have accelerated the study of NTM species, enabling rapid and precise identification, which is crucial for timely treatment (Horne and Skerrett 2019). However, the genetic diversity of NTM species complicates understanding of their pathogenesis and resistance mechanisms (Johnson and Odell 2014; Mercaldo et al. 2023). The global burden of NTM infections is increasingly recognized, and the challenges posed by NTM require coordinated research and surveillance to address this growing public health threat.

Mycobacterium, a genus within the Actinobacteria class, comprises over 196 species, including 24 subspecies, representing a diverse group of microorganisms with unique features (Parte 2014). These rod-shaped, Gram-positive bacteria are predominantly saprophytes found in soil and water, although several species are notable pathogens in humans and animals (Mencarini et al. 2017; Desai and Hurtado 2021; Gunasingam 2022; Gu et al. 2023). NTM, first isolated by Pinner (1935), have been recognized as a distinct entity within the Mycobacterium genus, separate from the tuberculosis (TB)-causing strains. Known by various names, including mycobacteria other than TB and atypical mycobacteria, these organisms have garnered attention due to their ubiquitous presence and rising incidence worldwide (Ahmed et al. 2020). The Runyon classification, which categorizes NTM based on pigment production and growth rate, remains a cornerstone in understanding their diversity (Table 1) (Runyon 1959; Herdman and Steele 2004; Salvana et al. 2007; Abdalla et al. 2009; Tortoli 2014; Koh 2017; Tortoli et al. 2017; Sharma and Upadhyay 2020). NTM are prevalent in natural environments such as soil and water and colonize artificial water systems, posing a serious challenge to public health systems (Steglich et al. 2020). The capacity of NTM to form biofilms enhances their survival and complicates efforts to eradicate them from infected sites. Clinically, NTM is known to cause a spectrum of diseases, most notably lung infections and extrapulmonary conditions affecting the skin, soft tissues, bones, and lymph nodes (Prevots et al. 2010; Chin et al. 2020; Ratnatunga et al. 2020; Dahl et al. 2022; Bhanushali et al. 2023). Diagnosing and treating NTM infections are fraught with challenges, primarily due to their resistance to standard antibiotics and the need for long-term therapy.

A noticeable global increase in incidence and spread characterizes the epidemiology of NTM infections, however, accurate estimates of incidence are difficult due to lack of required registration (Cowman et al. 2019; Thornton et al. 2021). The global incidence of NTM lung disease ranges from 2 to 14 cases per 100,000 persons per year (Griffith et al. 2007). In the USA, coverage ranges from 1.0 to 1.8 cases per 100,000 persons, while in the UK, coverage ranges from 4 to 6.1 cases per 100,000 between 2007 and 2012 (Prevots and Marras 2015; Sharma and Upadhyay 2020). In Japan, the incidence is 13.7 cases per 100,000 people, and in the Netherlands, it is about 5.3 cases per 100,000 (Hoefsloot et al. 2013; Morimoto et al. 2014). In Australia, the estimated incidence rate for all NTM increased 2.3-fold from 11.10/100,000 in 2001 to 25.88/100,000 in 2016 (Thomson et al. 2017, 2020). An interesting observation is the higher frequency of lung diseases caused by atypical mycobacteria in populations living in coastal areas. This has been suggested to be due to environmental factors such as soil composition, water exposure, climate changes, and increased environmental exposure to trace metals in surface waters (Dahl et al. 2022). Climate change has contributed to the spread of NTM, creating alterations in temperature and precipitation patterns, influencing soil composition and water quality, and creating favorable conditions for NTM growth (Chin et al. 2020; Blanc et al. 2021; Kambali et al. 2021; Dahl et al. 2022).

NTM infections are influenced by host-related and environmental factors, manifesting mainly as pulmonary or disseminated infections in immunocompromised individuals (Figure 1). Pulmonary NTM infections are often linked to lung impairments from conditions like bronchiectasis, COPD, emphysema, or cancer (Kumar et al. 2024). Genetic predispositions include cystic fibrosis, α-1-anti-trypsin deficiency, interferon (IFN)-γ and interleukin (IL)-12 receptor anomalies, primary ciliary dyskinesia, and pulmonary alveolar proteinosis (Park et al. 2022). Non-genetic factors such as medications (anti-tumor necrosis factor [TNF]-α agents, cytotoxic drugs, corticosteroids), gastroesophageal reflux disease, vitamin D deficiency, rheumatoid arthritis, and allergic bronchopulmonary aspergillosis also contribute. Lady Windermere syndrome, affecting postmenopausal women, is another risk factor (Loebinger et al. 2023). Acquired immune deficiencies, such as HIV, hematologic malignancies, and autoantibodies against IFN-γ, increase mycobacteriosis risk. Environmental factors include natural settings (soil, water) and artificial ones (hot tubs, hospital facilities) harboring contaminated water and equipment. NTM's lipid-rich cell walls enable biofilm formation, resisting antibiotics and disinfectants. Their specialized growth requirements often lead to underdiagnosis in routine tests (Antczak et al. 2017; Cowman et al. 2019; Pereira et al. 2020).

Fig 1.

Risk factors contributing to NTM infections. The risk factors for NTM infection can be broadly categorized into environmental exposures, underlying health conditions, lifestyle factors, and certain procedural or occupational hazards. CGD, chronic granulomatous disease; COPD, chronic obstructive pulmonary disease; GvH, graft versus host; IFN, interferon; IL, interleukin; NTM, non-tuberculous mycobacteria; SCID, severe combined immunodeficiency.

NTM diseases manifest in forms ranging from lymph node infections to symptoms resembling aseptic meningitis. The most common manifestation is lung infections, known as non-tuberculous mycobacterial pulmonary disease (NTM-PD), predominantly caused by MAC species and M. abscessus globally (Chotmongkol et al. 2024). NTM lung diseases exhibit three primary patterns based on their pathology: TB-like diseases with or without lung cavitation typically in older male smokers with COPD; bronchiectasis, often in slender, non-smoking older women known as “Lady Windermere syndrome,” and lung inflammation resulting from continuous exposure to mycobacteria in water systems like those in residential, office, and healthcare settings (Arend et al. 2009). Patients usually present with mixed forms of these patterns, making typical classification challenging.

The pathogenesis of NTM-PD is complex, taking months or years to develop, complicating diagnosis and often making it hard to trace the infection source (Wilińska and Szturmowicz 2010; Ratnatunga et al. 2020). Bacteria enter via the respiratory system, colonizing bronchial epithelial cells (Figure 2). The host activates airway clearance mechanisms, but if bacteria persist, they face the innate and acquired immune responses. Fibronectin-binding proteins on bacterial surfaces allow adhesion to the respiratory epithelium via integrin receptors (Honda et al. 2015). Colonizing mycobacteria undergo phenotypic changes, enhancing macrophage conquest. Their ability to inhibit inflammatory cytokine production and form biofilms compromise the immune response, allowing colonization and invasion of bronchial epithelial cells. Mycobacteria present in the macrophages can be killed or maintained within them by inducing NTM genes, inhibiting macrophage functions, lymphocyte proliferation, and causing macrophage destruction and apoptosis (Honda et al. 2015). Activated macrophages produce reactive oxygen and nitrogen species against mycobacteria. Inflammatory response results from cytokine production by activated macrophages and secretion of IL-12 leads to T cell differentiation into Th1 cells. Macrophages also stimulate natural killer (NK) cells with cytotoxic properties. Dendritic cells, M cells, and neutrophils also participate in phagocytosis (Horne and Skerrett 2019). During a specific immune response, T lymphocytes recognize bacterial antigens and transform into effector CD4⁺ and CD8⁺ T cells (Nair et al. 2016; Ndlovu and Marakalala 2016; Torrelles and Schlesinger 2017; Li et al. 2021). Antigens presented by antigen-presenting cells through MHC class II molecules are recognized by CD4⁺ Th1 lymphocytes, producing IFN-γ to enhance antigen presentation and macrophage killing. CD8⁺ Tc (cytotoxic) lymphocytes recognize antigens through MHC class I molecules, leading to apoptosis of infected host cells. Tc lymphocytes release cytokines like IFN-γ, mediating the immune response. γ/δ T lymphocytes also recognize antigens without MHC C involvement (Shu et al. 2020). When a pathogen evades the host's immune response, it can persist long-term. For M. tuberculosis, mechanisms enabling persistence include granuloma formation, which contain the bacteria and prevent clearance, and enter a dormant state to evade immune surveillance. M. tuberculosis also manipulates the host's immune response by modulating cytokine and chemokine production, influencing granuloma macrophages to undergo transformation to other morphological forms conducive to bacterial survival (Etna et al. 2014; Guler et al. 2021). Granulomas consist of a collection of organized immune cells, and using modern genetic techniques (e.g., parallel ssRNAseq), a high degree of heterogeneity between different granulomas has been shown (Cooper et al. 2024). Host–pathogen interactions modulate the processes leading to the formation of a wide spectrum of granuloma structures even within a single human host. From a histological point of view, in TB frequently the most central part of the granuloma is an acellular caseous necrotic region containing mycobacteria, while it is also possible to form other types of granulomas, which may not have a necrotic area and are composed primarily of macrophages and a few lymphocytes (Guirado and Schlesinger 2013). Macrophages play a key role in the formation of granulomas, and they represent a significant amount of the granuloma cell population, forming the inner layers of the granuloma and acting as a central skeleton that facilitates the organization of other cell types around it. Macrophages undergo “epithelial differentiation,” tightly assembling together to form the granuloma. Epithelial macrophages are a key component of tuberculoid granulomas, accompanied by “conventional” macrophages, foam macrophages, and multinucleated giant cells (Cronan 2022). Other cell types are also identified in the granuloma structure: neutrophils, dendritic cells, eosinophils, mast cells, T and B lymphocytes, NK cells and innate lymphoid cells, and even fibroblasts, and endothelial and epithelial cells, most of which are found in the periphery of the granuloma (Cronan 2022; Weeratunga et al. 2024). NTM mycobacteria are less virulent than M. tuberculosis but can pose serious threats to immunocompromised individuals, such as those with HIV/AIDS or undergoing immunosuppressive therapy (Varma-Basil and Bose 2019). Studies on human leukemia monocytic cell line Tohoku Hospital Pediatrics-1 (THP-1) infected with various NTM strains show that NTMs adopt different strategies to manipulate host defenses for long-term persistence (Sousa et al. 2019). Key factors include phagosome acidification, nitric oxide (NO) production, and cell death. Some strains are cleared within 24 h (M. smegmatis and M. fortuitum), while others replicate (M. avium and M. fortuitum). A study using human cells (THP-1, monocyte-derived macrophages, and alveolar macrophages) infected with various NTM found that macrophage infectivity and virulence vary among NTM species and isolates. Some NTMs evade antibacterial peptides like LL-37 through modified phospholipids, representing a novel virulence mechanism (Honda et al. 2020).

Fig 2.

Immune mechanisms accompanying mycobacterial infection. GM-CSF, granulocyte-macrophage colony-stimulating factor; IFN, interferon; IL, interleukin; MCAF, monocyte chemotactic and activating factor; MIF, migration inhibitory factor; RNS, reactive nitrogen species; ROS, reactive oxygen species; TNF, tumor necrosis factor.

In 2007, the American Thoracic Society (ATS) and the Infectious Diseases Society of America (IDSA) issued a statement outlining the criteria for the diagnosis and treatment of pulmonary diseases related to NTM-PD (Griffith et al. 2007; Daley et al. 2020a). According to these guidelines, the diagnosis is based on clinical symptoms, radiological findings, and microbiological results. Clinical indicators include respiratory symptoms (chronic or recurrent cough, sputum production, shortness of breath) and systemic symptoms (fatigue, weight loss, fever, chest pain). Radiological confirmation of infection is required through chest X-rays showing nodular or cavitary opacities, or high-resolution computer tomography showing bronchiectasis with numerous small nodules. Microbiological criteria include at least two positive culture results from independent sputum samples or one positive culture from bronchial washings, bronchoalveolar lavage, or histopathological examination with a positive lung biopsy, and at least one sputum or bronchial wash positive for NTM in culture (Griffith et al. 2007; Daley et al. 2020a). Identification mainly relies on acid-fast bacilli staining (e.g., Ziehl-Neelsen method and fluorescence) and testing using molecular diagnostic tools like GeneExpert. Samples are cultured on media suitable for NTM growth: Löwenstein–Jensen, Middlebrook, and Dubos (Sharma and Upadhyay 2020). NTM species identification uses biochemical tests, now being phased out for modern techniques. High-performance liquid chromatography identifies slow-growing NTM but is less specific for rapidly growing species. Molecular methods have revolutionized identification, including Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), real-time PCR, gene probes, linear probe hybridization, DNA sequencing, and Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF-MS). Several readymade DNA sequencing systems are available, but some species are genetically similar, complicating diagnosis. Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF)'s effectiveness also depends on the available sequence library (Pennington et al. 2021).

Treatment of NTM infections is complex and involves prolonged multidrug regimens, ranging from 3 months to 4 months for skin and soft tissue infections to over 12 months for lung and disseminated infections. Treatment often results in significant side effects and is poorly tolerated, especially in patients with coexisting diseases. New drugs used in multidrug-resistant TB, such as bedaquiline, pretomanid, and delamanid, are being tested for effectiveness against NTM. Guidelines for managing NTM-PD follow recommendations from ATS/European Respiratory Society (ERS)/European Society of Clinical Microbiology and Infectious Diseases (ESCMID)/IDSA, which are based on expert opinions, observational studies, and controlled trials, as well as the British Thoracic Society (Haworth et al. 2017a; Daley et al. 2020b). Antibiotic therapy is the primary treatment approach, with regimens tailored based on the NTM species, disease severity, and drug susceptibility results (Pathak et al. 2022). For slow-growing mycobacteria, a typical regimen includes rifampicin or rifabutin, ethambutol, and a macrolide for 12 months, with amikacin or streptomycin added for severe cases during the first 3 months (Larsson et al. 2017). Treatment for fast-growing mycobacteria depends on in vitro sensitivity tests. Recovery rates from these infections vary from 34% to 65%, with recurrence rates of up to 48% (Taylor and Mitchell 2023). Current guidelines recommend continuing antibiotic therapy for at least 12 months after a negative culture conversion to minimize recurrence risk (Shulha et al. 2019; Daley et al. 2020c). If antibiotic response is poor, if there is macrolide resistance, or if severe symptoms like coughing up blood occur, surgical treatment is advised (Desai and Hurtado 2017; Haworth et al. 2017b). Surgery is used in NTM pulmonary disease management to improve cure rates, especially in patients with focal lesions, and must be preceded by thorough radiological examination and/or biopsy (Lu et al. 2018). NTM infections, primarily affecting the lungs (80%–90% of cases), show varied lesion images on computed tomography scans and X-rays, influenced by the patient's immune status and preexisting lung diseases (Jamal and Hammer 2022). Surgical outcomes differ by institution. For example, a study from Seoul National University Hospital reported postoperative complications in 13.4% of NTM-PD patients, with adverse outcomes linked to factors such as female gender and preoperative positive mycobacterial cultures. In contrast, a study from Osaka, Japan, noted a 20% adverse outcome rate with a high rate of negative sputum culture conversion (Fukushima et al. 2020; Kim et al. 2021, 2023). Addressing antibiotic resistance is crucial for managing NTM-PD, as resistant strains lead to low culture conversion rates and high 5-year mortality (van der Laan et al. 2022). An innovative approach in NTM-LD t herapy involved using three bacteriophage strains to treat M. abscessus infection in a teenager with cystic fibrosis at Great Ormond Street Hospital in London. Phage therapy successfully eliminated the pathogen without cytotoxic effects, unlike traditional chemotherapeutics. However, phage therapy has significant limitations. Bacteriophages are highly specific to particular bacterial strains, requiring the screening of over 10,000 phage strains, with two genetically modified, to find three actives against M. abscessus. The therapy did not yield the same results against different M. abscessus strains in other patients. Thus, while phage therapy shows promise, its need for a highly individualized approach limits its widespread use in the near future (Dedrick et al. 2019; Laudone et al. 2021). An interesting solution is using liposomes as carriers for antibiotics, addressing the poor penetration of drugs into macrophages and cells targeted by pathogens and biofilms, including NTM.

While liposomes are widely used for various applications, they have not been extensively used in mycobacterial infection therapy. The only approved liposomal therapeutic for treatment-resistant Mycobacterium avium complex pulmonary disease (MAC-PD) in the USA, EU, and Japan is a liposomal inhalation suspension of amikacin (ALIS). ALIS, composed of dipalmitoylphosphatidylcholine and cholesterol, is designed to provide strong antibacterial activity against MAC, targeted delivery to infection sites, and penetration into intracellular spaces, including macrophages and biofilms (Shirley 2019; Hoy 2021; Winthrop et al. 2021; Morimoto et al. 2024).

The search for new chemotherapeutic agents with antitubercular effects is a direct approach. Several new antibiotics, including novel benzimidazoles like SPR719 and EJMCh-6, have shown potency in lab tests against various NTM species (e.g., M. ulcerans, M. marinum, M. chimaera, M. avium, M. abscessus) (Pidot et al. 2021; Quang and Jang 2021; Aragaw et al. 2022). Studies on SPR720 for MAC-PD have entered phase 2a trials but were suspended by the U.S. Food and Drug Administration. Additionally, delamanid and pretomanid, two new anti-TB drugs, are being considered for M. abscessus, though further research is needed to confirm their effectiveness (Kumar et al. 2022). Investigating drug administration through inhalation offers an alternative to antibiotics, such as NO or granulocyte-macrophage colony-stimulating factor (GM-CSF). Studies with NTM-PD patients showed that inhaling 160 ppm of NO for 50 min, three times daily, 5 days a week for 3 weeks, improved clinical symptoms and reduced NTM presence in sputum cultures (Flume et al. 2023). Inhaling GM-CSF could also be beneficial for NTM therapy. Macrophages activated by GM-CSF can better combat NTM. Monocyte-derived macrophages in bronchiectatic airways are less effective at killing NTM compared with resident alveolar macrophages due to limited GM-CSF exposure. Treatment with GM-CSF may enhance the ability of these macrophages to eliminate NTM, even when standard antibiotics fail (Hisert et al. 2023). In 2023, the clinical trial with 32 NTM-PD patients treated with inhaled GM-CSF (300 μg/day for 48 weeks) showed a 25% culture conversion rate, mainly in M. avium complex cases (Thomson et al. 2023).

The role of the M. bovis Bacillus Calmette-Guérin (BCG) vaccine in NTM therapy remains under investigation, aiming to establish long-lived memory T cells. Before modern HIV treatments, disseminated infections from NTM, especially M. avium complex, were more frequent, highlighting the role of CD4⁺ T cells in defending against mycobacterial infections (Verma et al. 2020). In studies on immunocompromised mice, the BCG vaccine reduced the bacterial burden in the lungs and spleen. DNA plasmids and recombinant BCG vaccines encoding specific mycobacterial genes have shown promising effects against M. avium (Orujyan et al. 2022). Abate et al. (2019) demonstrated that BCG immunization induces cross-reactive T cells inhibiting intracellular replication of M. avium and M. abscessus, increasing IL-17 and IFN-γ production. However, a study with 1000 participants at Seoul National University Hospital found that BCG was not protective against NTM-PD progression (Kwak et al. 2022). This might be influenced by the number of BCG doses. In most countries, only one dose is given shortly after birth, or revaccination is carried out at a later age, as was the case in South Korea, Singapore, Taiwan, and Malaysia; however, these countries withdrew from this practice now (Tam and Leung 2000). Meanwhile, in Turkey, full immunization includes up to five doses: at birth, at 2 months after birth, at 6–7 years of age, at 11–12 years of age, and at 16–17 years of age (Verma et al. 2020). Further research is therefore necessary, both in vitro and cohort studies, which will improve our knowledge on how BCG vaccination affects NTM infections/outcome and the persistence of NTM in the human host.

The increasing prevalence of NTM infections requires a comprehensive understanding of their epidemiology, etiology, and clinical manifestations. Current diagnostic methods often fail to accurately identify NTM infections, delaying treatment and leading to poor outcomes. Thus, developing more sensitive and specific diagnostic tools is critical for early detection. Treating NTM infections also presents significant challenges. Current regimens, while sometimes effective, often fail and are associated with side effects. Drug resistance further threatens treatment efficacy, underscoring the urgent need for novel therapeutics that improve efficacy and reduce adverse effects. Future research should prioritize understanding NTM pathogenesis and drug resistance mechanisms and identifying new therapeutic targets.