Different clinical features of patients with pulmonary disease caused by various Mycobacterium avium–intracellulare complex subspecies and antimicrobial susceptibility

Relationship between culture conversion and clinical outcomes in nontuberculous mycobacterial pulmonary disease: Narrative review

PURPOSE

Nontuberculous mycobacterial pulmonary disease (NTMPD) is a chronic, often progressive condition associated with a significant symptom burden and increased mortality. Goals of NTMPD treatment include microbiological eradication, symptom reduction, improved quality of life (QoL), and preventing disease progression. Antibiotics are used to reduce microbial burden, and cultures of sputum are used to guide treatment. However, it is unclear whether achieving culture-negative status (often called "culture conversion") is associated with improved clinical outcomes. Studies use a variety of measures including symptom burden, radiological status, lung function, 6-min walk test distance, QoL assessments, and mortality to evaluate clinical outcomes related to changes in how patients feel, function, and survive. There is strong interest in more clearly understanding which clinical benefits may be associated with culture conversion. As NTMPD can cause sustained structural lung damage and declines in long-term pulmonary function, it is important to have clear evidence if prevention of these morbidities is associated with culture conversion.

METHODS

This targeted literature review summarizes the published evidence regarding associations between sputum culture conversion and clinical outcomes in patients with NTMPD. Identified studies used varying definitions of culture conversion and treatment success, making interpretation of outcomes across studies challenging.

RESULTS

Although some studies suggest an association between culture conversion and aspects of clinical improvement, overall, there are currently few high-quality studies supporting a link.

CONCLUSION

Further clarification of the relationship between culture conversion and clinical outcomes would be helpful in improving clinical monitoring and therapeutic decision-making during the treatment of patients with NTMPD.

Whole-genome phylogenetic analysis of Mycobacterium avium complex from clinical respiratory samples

The Mycobacterium avium complex (MAC) is a common causative agent causing nontuberculous mycobacterial (NTM) pulmonary disease worldwide. Whole-genome sequencing was performed on a total of 203 retrospective MAC isolates from respiratory specimens. Phylogenomic analysis identified eight subspecies and species. M. avium subspecies hominissuis (MAH) was the overwhelmingly dominant species (148/203, 72.9%). The other seven identified species were M. intracellulare subsp. yongonense (18/203, 8.9%), M. intracellulare subsp. chimaera (10/203, 4.9%), M. colombiense (11/203, 5.4%), M. paraintracellulare (6/203, 3%), M. marseillense (5/203, 2.5%), M. intracellulare (3/203, 1.5%), and M. avium subspecies paratuberculosis (2/203, 1%). Significant genetic clustering was observed among MAH isolates. Notably, a large cluster (<12 SNPs) of 76 MAH isolates bearing the same sequence type was observed. The presence of closely related isolates within hospital settings raises concerns about transmission routes with environmental sources potentially playing a significant role. Based on susceptibility breakpoints that are available for clarithromycin, amikacin, linezolid, and moxifloxacin, low rates of clarithromycin (0.5%, 1/203) and amikacin (1.5%, 3/203) phenotypic resistance were observed. While linezolid and moxifloxacin resistance were 25.6% (52/2030) and 46.3% (94/203), respectively. Drug resistance-associated loci were searched for mutations linked to phenotypic drug resistance. Of the entire cohort, only one isolate was found to have a A2059G 23S rRNA (rrl) gene mutation responsible for macrolide resistance.

IMPORTANCE

Mycobacterium avium complex (MAC) infections are increasingly challenging to manage due to their complex species diversity and varied resistance patterns. This study underscores the genetic diversity within MAC, identifying at least eight species and subspecies among 203 clinical isolates, with M. avium subsp. hominissuis (MAH) being most prevalent at 72.9%. Notably, genetic clustering was observed within MAH and M. intracellulare subsp. chimaera, suggesting potential transmission routes within healthcare settings. Clarithromycin and amikacin resistance was found to be uncommon, aligning with the rarity of resistance-associated genetic mutations. These findings emphasize the need for enhanced infection control measures and routine susceptibility testing to tailor antibiotic therapies effectively.

Phenotypic amikacin resistance may not indicate poor response to amikacin in Mycobacterium avium complex pulmonary disease

When using amikacin to treat Mycobacterium avium complex pulmonary disease (MAC-PD), a minimum inhibitory concentration resistance breakpoint of ≥64 mcg/mL is recommended. We explored whether amikacin resistance characterized by phenotypic drug susceptibility testing was associated with clinical outcomes or mutational resistance in a retrospective cohort of patients with MAC-PD. Despite little aminoglycoside exposure, amikacin resistance was common in our MAC-PD patients but was not associated with worse outcomes or rrs gene mutations.

Treatment outcomes and relapse in patients with Mycobacterium avium-intracellulare complex pulmonary disease

The treatment responses and outcomes in patients with Mycobacterium avium-intracellulare complex pulmonary disease (MAC-PD) remain uncertain. This retrospective study was conducted in Taiwan between 2011 and 2020. A microbiological cure was defined as the requirement for a minimum of three consecutive negative cultures following culture conversion that continued until the completion of anti-MAC treatment. A total of 97 patients with MAC-PD were enrolled in this study. The sputum smear-negative conversion rate was 40% (19/47). Thirty (31%) patients achieved sputum culture-negative conversion rates within 3 years after treatment initiation. All patients with negative sputum culture conversion rates achieved microbiological cure. Patients treated with a macrolide + rifamycin + ethambutol (M + R + EMB)-based regimen had a higher microbiological cure rate than the other patients (39% vs 17%, P = 0.023). Patients with persistently positive sputum smears after 6 months of treatment had a lower microbiological cure rate than those with negative sputum smears (6% vs 44%, P < 0.001). Among 30 patients with microbiological cure, the median time from sputum culture conversion to treatment completion was 221.5 (0-483) days, and the 1-year relapse rate was 17%. Treatment with the M + R + EMB-based regimen was associated with a higher microbiological cure rate, and patients with persistently positive sputum smears after 6 months of treatment had a lower microbiological cure rate. IMPORTANCE The treatment responses and outcomes in patients with Mycobacterium avium-intracellulare complex pulmonary disease (MAC-PD) remain uncertain. In this study, patients with MAC-PD treated with a macrolide + rifamycin + ethambutol (M + R + EMB)-based regimen had a higher microbiological cure rate than those treated with other regimens. After 6 months of treatment, patients with persistently positive sputum smears had a lower microbiological cure rate than those with negative sputum smears. Among patients with microbiological cure, the median time from sputum culture conversion to treatment completion was 221.5 days (range, 0-483), and the 1-year relapse rate was 17%.

The factors associated with mortality and progressive disease of nontuberculous mycobacterial lung disease: a systematic review and meta-analysis

This systematic review and meta-analysis aimed to comprehensively evaluate the factors associated with mortality and progressive disease in NTM-LD patients. We conducted a literature search to identify the eligible studies, dated between January 1, 2007, and April 12, 2021. Forty-one studies with total 10,452 patients were included. The overall all-cause mortality rate was 20% (95% CI 17-24%). The overall rates of clinical and radiographic progressive disease were 46% (95% CI 39-53%) and 43% (95% CI 31-55%), respectively. Older age, male sex, history of TB, diabetes, chronic heart disease, malignancy, systemic immunosuppression, chronic liver disease, presence of cavity, consolidative radiologic features, acid-fast bacillus (AFB) smear positivity, hypoalbuminemia, anemia, increasing platelet count, high CRP, and high ESR were significantly associated with increased all-cause mortality, whereas increasing body mass index (BMI), hemoptysis, and treatment with rifamycin regimen (in M. xenopi) were significantly associated with decreased all-cause mortality in multivariable analysis. History of TB, Aspergillus co-infection, cough, increased sputum, weight loss, presence of cavity, and AFB smear positivity were significantly associated with increased clinical progression with treatment, while older age and low BMI were significantly associated with decreased clinical progression in multivariable analysis. Older age, interstitial lung disease, presence of cavity, consolidative radiologic feature, anemia, high CRP, and leukocytosis were significantly associated with increased radiographic progression after adjusting for covariates. Older age, history of tuberculosis, presence of cavity, consolidative radiologic features, AFB smear positivity, anemia, and high C-reactive protein were common significant factors associated with the all-cause mortality and clinical or radiographic progressive disease of NTM-LD. These factors are thought to directly affect NTM-LD related mortality. The future prediction models for the prognosis of NTM-LD should be established considering these factors.

A novel repeat sequence-based PCR (rep-PCR) using specific repeat sequences of Mycobacterium intracellulare as a DNA fingerprinting

Repetitive sequence-based PCR (rep-PCR) is a potential epidemiological technique that can provide high-throughput genotype fingerprints of heterogeneous Mycobacterium strains rapidly. Previously published rep-PCR primers, which are based on nucleotide sequences of Gram-negative bacteria may have low specificity for mycobacteria. Moreover, it was difficult to ensure the continuity of the study after the commercial rep-PCR kit was discontinued. Here, we designed a novel rep-PCR for Mycobacterium intracellulare, a major cause of nontuberculous mycobacterial pulmonary disease with frequent recurrence. We screened the 7,645 repeat sequences for 200 fragments from the genome of M. intracellulare ATCC 13950 in silico, finally generating five primers with more than 90% identity for a total of 226 loci in the genome. The five primers could make different band patterns depending on the genome of three different M. intracellulare strains using an in silico test. The novel rep-PCR with the five primers was conducted using 34 bacterial samples of 7 species containing 25 M. intracellulare clinical isolates, compared with previous published rep-PCRs. This shows distinguished patterns depending on species and blotting assay for 6 species implied the sequence specificity of the five primers. The Designed rep-PCR had a 95-98% of similarity value in the reproducibility test and showed 7 groups of fingerprints in M. intracellulare strains. Designed rep-PCR had a correlation value of 0.814 with VNTR, reference epidemiological method. This study provides a promising genotype fingerprinting method for tracing the recurrence of heterogeneous M. intracellulare.

Identification and drug susceptibility testing of the subspecies of Mycobacterium avium complex clinical isolates in mainland China

OBJECTIVES

The Mycobacterium avium complex (MAC), comprising a series of subspecies, has a worldwide distribution, with differences in drug susceptibility among subspecies. This study aimed to assess the composition of MAC and susceptibility differences among subspecies in mainland China.

METHODS

A total of 287 MAC clinical strains were included in the study. Multitarget sequences were applied to accurately identify subspecies, and a microdilution method was used to evaluate minimum inhibitory concentrations (MICs) among subspecies using Sensititre SLOMYCO plates.

RESULTS

Mycobacterium intracellular (N = 169), Mycobacterium avium (N = 52), Mycobacterium chimaera (N = 22), Mycobacterium marseillense (N = 25), Mycobacterium colombiense (N = 14), Mycobacterium yongonense (N = 4), Mycobacterium vulneris (N = 3) and Mycobacterium timonense (N = 2) were isolated from MAC. Clarithromycin, amikacin and rifabutin showed lower MIC₅₀ and MIC₉₀ values than other drugs, and the resistance rates of clarithromycin, amikacin, linezolid and moxifloxacin were 6.3%, 10.5%, 51.9% and 46.3%, respectively. The resistance rates of clarithromycin and moxifloxacin in the initial treatment group were significantly lower than those in the retreatment group (4.09% vs. 12.94%; 30.41% vs. 75.29%; P < 0.05). Drug susceptibility differences were observed in clarithromycin and moxifloxacin among the five major subspecies (P < 0.05); however, those statistically significant differences disappeared when MACs were divided into two groups according to previous anti-tuberculosis (anti-TB) treatment history.

CONCLUSION

This study revealed that MAC, primarily comprising M. intracellulare, was susceptible to clarithromycin, amikacin and rifabutin. Drug susceptibility among subspecies did not exhibit intrinsic differences in our study. Previous anti-TB treatment patients are more resistant to drugs; thus, attention should be given to those patients in the clinic.