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Diagnostics Microbiology and immunology, Analytical science, Genetics and epigenetics

The Quest to Breathe Easy

At a Glance

  • Lung infections caused by non-tuberculous mycobacteria are on the rise globally
  • New research has revealed challenges including antimicrobial resistance, gene variants, and refractory disease
  • It’s important to identify causative pathogens before selecting treatment – but this sometimes presents a challenge of its own
  • Drug susceptibility testing is variable and requires good external quality assurance

Pulmonary infections caused by non-tuberculous mycobacteria (NTM), such as Mycobacterium avium complex (MAC), have significantly increased in recent years – and so has research into such diseases. The degree of attention focused on these mycobacteria, especially at the recent European Congress of Clinical Microbiology and Infectious Diseases, reflects the high level of interest in disease caused by NTM – a diverse group of opportunistic bacterial pathogens with a wide spectrum of virulence. Patients more susceptible to NTM infection include those with chronic respiratory disease, such as bronchiectasis, chronic obstructive pulmonary disease (COPD), cystic fibrosis, and idiopathic pulmonary fibrosis (1).

“NTM are intrinsically resistant to most classes of antibiotics. They require very long periods of antibiotic treatment using three, four, or five antibiotics at the same time – with treatment durations of up to one and a half to two years. Just imagine the associated toxicity – this can be a nightmare for everyone involved,” said Jakko van Ingen, head of the mycobacteriology laboratory at Radboud University Medical Center, Nijmegen, the Netherlands (2). He pointed out that NTM can pose a real problem when they cause chronic pulmonary infections in humans. “Cure rates are really poor, as low as 40 percent for M. abscessus and up to 70 percent for MAC disease. Even if you cure the patient once, there is a good chance you will see them again because the recurrence rate is around 40 percent.” He suggests that, for patients who are particularly susceptible to NTM, new treatment approaches may be warranted. “Current treatment regimens are not based on pharmacokinetic and pharmacodynamic science but rather on case series – on tradition. For all of these reasons we started our research group to use science to find better regimens with better outcomes.”

Using a “hollow fiber” in vitro model, his group has shown that many treatment methods currently in use are inadequate – some because they fail to sterilize, others because they are only effective at intolerably high doses. As a result, van Ingen’s group and many others are looking at new medications and combination therapies, as well as potentially giving old drugs new life as NTM treatments.

A global challenge

But even the best treatment for NTM disease is of no use without good diagnostics. Emmanuelle Cambau of Lariboisiere Hospital’s National Reference Centre for Mycobacteria in Paris, France, stressed the importance of correctly identifying the species and subspecies of NTM responsible for pulmonary infection and of testing for resistance mutations – particularly in the erm(41) and rrl genes – before starting a macrolide. She emphasized the need for more research to establish the difference between colonization and infection, and between relapse and reinfection. Cambau also highlighted the need for effective new antibiotics to combat infection.

Identifying the causative organism and its genetic characteristics are a key part of providing appropriate care.

Charles Daley of the University of Colorado, Denver, USA, said that treatment of NTM lung disease (NTM-LD) should be based on three factors: patient, organism, and goals of treatment. MAC lung disease treatment should include a macrolide-containing three-drug regimen administered for 12 months beyond culture conversion. Aminoglycosides may be added for cavitary or macrolide-resistant disease, and inhaled liposomal amikacin (currently only approved in the US) may be added in treatment-refractory cases. Treatment of M. abscessus LD should include at least three active drugs with inclusion of a macrolide when a non-functional erm(41) gene is present or when gene status is unknown. These conditional treatment options make it clear that identifying the causative organism and its genetic characteristics are a key part of providing appropriate care.

Reviewing some challenging or difficult cases, Miguel Santin of Bellvitge University Hospital, Barcelona, Spain, recommended an observational period for progression before starting therapy in patients with NTM-LD (nodular/bronchiectatic disease). He also advocated surgery as a reliable alternative for patients with refractory NTM-LD – but reinforced the importance of therapy following current guidelines. Prior to making a treatment decision, an observational period and appropriate testing can identify which infections are most likely to require a non-standard course of action.

The changing epidemiology of NTM

On behalf of a network of clinical microbiology laboratories from 21 Madrid hospitals (Grupo de Estudio de Micobacterias-SMMC), Jaime Esteban-Moreno reported the results of a five-year, multi-center study of NTM epidemiology. Collectively, the hospitals service a population of more than six million people, and were therefore able to include a total of 6,306 mycobacterial isolates (4,106 NTM and 2,200 tuberculosis) in their research. Although tuberculosis numbers remained stable throughout the study, NTM isolates were not – after a period of stability from 2013 to 2016, they increased from 2016 to 2017 (3). Of the total NTM isolates, MAC represented almost half; rapidly growing mycobacteria were the second-most common, followed by M. lentiflavum. Altogether, the researchers identified 63 different species.

Esteban-Moreno and his colleagues plan further studies to establish the clinical significance of the increase in NTM isolates. “We need to know more about the epidemiology because there is no mandatory reporting of NTM infections in Spain. Our take-home message is that NTM isolates are increasing in frequency – now, we need to know more about the patients to find out whether these represent colonization or true clinical infections.” He believes that several factors may be responsible for the identified increase, including a growth in the number of susceptible patients with chronic lung disease or environmental factors.

Effective and inexpensive NTM identification

In the five-year study, the researchers identified NTM isolates using commercial molecular biology systems – namely, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). But they’re not the only group that sees the potential of MALDI-TOF MS. Katrien Vandebroek and her colleagues at Ziekenhuis Oost-Limburg, Genk, Belgium, found the technique to be an effective and inexpensive tool for the identification of NTM species (4). To reach this conclusion, they grew eight strains of the bacteria on Löwenstein-Jensen agar and used MALDI-TOF MS to identify them; all eight were correctly identified. They also achieved correct identification in 89.8 percent of Mycobacterial Growth Indicator Tube (MGIT) clones. Identification of positive MGITs from clinical samples proved more difficult; however, using a higher MGIT volume for protein extraction improved performance to 92 percent. Some hurdles still remain, of course. Not every species is equally easy to identify; in Vandebroek’s study, the M. chimaera-intracellulare group proved most difficult. Coinfections were also noted to interfere with MALDI-TOF MS identification. Nevertheless, the technique’s accessibility and utility offers promise for future research and diagnosis.

A call for quality assurance

The reliability and reproducibility of drug susceptibility testing (DST) of NTM isolates needs to be improved, according to Vladyslav Nikolayevskyy, the author of a recent study on the subject (5). Nikolayevskyy, of Public Health England, London, UK, presented a multi-center pilot study of a novel external quality assurance (EQA) scheme for NTM susceptibility testing. The study employed a structured questionnaire, followed by a pilot EQA round using identical panels of 10 well-characterized Mycobacterium avium and Mycobacterium abscessus isolates.

Inter-laboratory reproducibility for NTM phenotypic DST is insufficient, highlighting the need for expanding EQA schemes to clinically relevant NTM.

The panels were sent to 22 participating laboratories to be tested for susceptibility to clarithromycin, moxifloxacin, amikacin, linezolid, and doxycycline. EQA results were received from 16 laboratories using the broth microdilution method. Essential agreement ranged from 78.8 (amikacin) to 96.2 percent (linezolid) for M. avium, and from 76.0 (amikacin) to 100 percent (doxycycline) for M. abscessus. Categorical agreement ranged from 56.8 (moxifloxacin) to 100 percent (clarithromycin) for M. avium, and from 53.6 (linezolid) to 100 percent (doxycycline) for M. abscessus. These results show that inter-laboratory reproducibility for NTM phenotypic DST is insufficient, highlighting the need for expanding EQA schemes to clinically relevant NTM.

“The take-home message is that, as things currently stand, the reproducibility can be considered suboptimal,” said Nikolayevskyy. “This is very important for laboratory accreditation – every laboratory needs to demonstrate that they are proficient and that they participate in external quality assessment schemes [...] There has been a lot of interest [in these results] not only from the UK, but also from the EU, continental Europe, and globally. Drug susceptibility testing is being increasingly used because the prevalence of NTM is increasing globally.”

Although rapid advances are being made in the understanding, diagnosis, and treatment of NTM disease, there are still clear gaps in our ability to tackle this increasing threat. With this research and more, those working to combat the disease hope that, soon, every patient will receive a rapid and accurate diagnosis – and a treatment tailored to their specific pathogen.

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  1. CS Haworth et al., “British Thoracic Society guidelines for the management of non-tuberculous mycobacterial pulmonary disease (NTM-PD)”, Thorax, 72, ii1 (2017). PMID: 29054853.
  2. J van Ingen, “Kill ’em all! The quest for an antibiotic regimen that cures nontuberculous mycobacterial disease”. Presented at the 29th European Congress of Clinical Microbiology and Infectious Diseases; 13–16 April, 2019; Amsterdam, Netherlands.
  3. K Vandebroek et al., “MALDI-TOF MS: a performant, easy and inexpensive tool for the identification of non-tuberculous mycobacteria”. Presented at the 29th European Congress of Clinical Microbiology and Infectious Diseases; 13–16 April, 2019; Amsterdam, Netherlands. Abstract #P0432.
  4. M Kaelin et al., “Diversity of non-tuberculous mycobacteria in heating/cooling devices: results from prospective surveillance”. Presented at the 29th European Congress of Clinical Microbiology and Infectious Diseases; 13–16 April, 2019; Amsterdam, Netherlands. Abstract #P2637.
  5. V Nikolayevskyy et al., “Novel external quality assurance scheme for drug susceptibility testing of non-tuberculous mycobacteria: a multi-centre pilot study”. Presented at the 29th European Congress of Clinical Microbiology and Infectious Diseases; 13–16 April, 2019; Amsterdam, Netherlands. Abstract #P0983.

About the Author

Ian Mason

A writer specializing in medicine and science for both medical and lay publications. He is based in Surrey, UK.

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