We evaluated the in vitro activity of rifamycin derivatives, including rifampin, rifapentine, rifaximin, and rifabutin, against clinical nontuberculous mycobacteria (NTM) isolates. Of the rifamycin derivatives, rifabutin showed the lowest MICs against all NTM species, including Mycobacterium avium complex, M. abscessus, and M. kansasii.
KEYWORDS: nontuberculous mycobacteria, Mycobacterium avium complex, Mycobacterium abscessus, Mycobacterium kansasii, rifamycins, rifabutin
ABSTRACT
We evaluated the in vitro activity of rifamycin derivatives, including rifampin, rifapentine, rifaximin, and rifabutin, against clinical nontuberculous mycobacteria (NTM) isolates. Of the rifamycin derivatives, rifabutin showed the lowest MICs against all NTM species, including Mycobacterium avium complex, M. abscessus, and M. kansasii. Rifabutin also had effective in vitro activity against macrolide- and aminoglycoside-resistant NTM isolates. Rifabutin could be worth considering as a therapeutic option for NTM disease, particularly drug-resistant disease.
INTRODUCTION
The prevalence of nontuberculous mycobacteria-pulmonary disease (NTM-PD) is increasing (1, 2). Among NTM species, Mycobacterium avium complex (MAC), which is mainly composed of M. avium and M. intracellulare, is the most common pathogen, and Mycobacterium abscessus (MABS), predominantly composed of M. abscessus subsp. abscessus (here termed M. abscessus) and M. abscessus subsp. massiliense (here termed M. massiliense), is the second most common pathogen in many countries (3–5). M. kansasii also causes chronic PD (6).
For MAC- or M. kansasii-PD, guidelines recommend a macrolide-based multidrug therapy including rifampin (3). However, there are no accurate data on which of the rifamycin derivatives, including rifampin, rifapentine, rifaximin, and rifabutin, is the most effective. The guidelines for MABS-PD recommend multidrug therapy, including macrolide and intravenous amikacin as key drugs (3). However, as MABS-PD is highly drug resistant, there are only a few effective oral drugs. Therefore, treatment outcomes of NTM-PD are unsatisfactory (7–9). Recently, oral agents, such as rifamycin derivatives, particularly rifabutin, were reported to have in vitro low MIC and synergistic effects with other drugs against NTM species (10–14). However, limited data are available from studies using various clinical strains or strains resistant to key antibiotics. Therefore, we evaluated the in vitro activity of rifamycin derivatives against clinical NTM isolates, including macrolide- and amikacin-resistant isolates.
We evaluated 311 clinical isolates of five major pathogenic NTM from 311 nonduplicated patients with treatment-naive NTM-PD (Table 1). Additionally, 57 macrolide-resistant and 44 aminoglycoside-resistant NTM isolates, which were confirmed by mutation analyses to be related to macrolide or aminoglycoside resistance, were included in the analysis (15–19). All data included in this study were obtained from an Institutional Review Board-approved observational cohort at Samsung Medical Center, South Korea (ClinicalTrials.gov registration no. NCT00970801). In vitro drug susceptibility testing was performed by measuring the MIC using the broth microdilution method according to guidelines from the Clinical and Laboratory Standards Institute (20). M. peregrinum ATCC 700686, M. abscessus ATCC 19977, M. avium ATCC 700898, and M. kansasii ATCC 12478 were used as controls.
TABLE 1.
MIC ranges and MIC50 and MIC90 values of four rifamycin derivatives for 311 clinical NTM isolates
| NTM species (no.) | Antibiotic | No. (%) of isolates with MIC (μg/ml) of: |
MIC range (μg/ml) | MIC50 (μg/ml) | MIC90 (μg/ml) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ≤0.062 | 0.125 | 0.25 | 0.5 | 1 | 2 | 4 | 8 | 16 | 32 | 64 | >64 | |||||
| M. avium (63) | Rifampin | 2 (3.2) | 2 (3.2) | 6 (9.5) | 16 (25.4) | 8 (12.7) | 7 (11.1) | 2 (3.2) | 3 (4.8) | 11 (17.4) | 6 (9.5) | 0.25–>64 | 4 | 64 | ||
| Rifapentine | 3 (4.8) | 4 (6.3) | 22 (34.9) | 9 (14.3) | 6 (9.5) | 6 (9.5) | 5 (7.9) | 4 (6.3) | 1 (1.6) | 3 (4.8) | 0.125–>64 | 1 | 16 | |||
| Rifaximin | 1 (1.6) | 2 (3.2) | 2 (3.2) | 15 (24) | 19 (30.2) | 10 (15.9) | 4 (6.3) | 6 (9.5) | 1 (1.6) | 3 (4.8) | 0.125–>64 | 2 | 16 | |||
| Rifabutin | 33 (52.4) | 7 (11.1) | 4 (6.3) | 5 (7.9) | 9 (14.3) | 1 (1.6) | 1 (1.6) | 3 (3.2) | ≤0.062–64 | ≤0.062 | 0.25 | |||||
| M. intracellulare (58) | Rifampin | 1 (1.7) | 1 (1.7) | 1 (1.7) | 11 (19) | 41 (70.7) | 3 (5.2) | 0.25–>64 | 64 | 64 | ||||||
| Rifapentine | 1 (1.7) | 5 (8.6) | 19 (32.8) | 19 (32.8) | 9 (15.5) | 2 (3.4) | 1 (1.7) | 2 (3.4) | ≤0.062–>64 | 8 | 16 | |||||
| Rifaximin | 1 (1.7) | 2 (3.4) | 12 (20.7) | 41 (70.7) | 2 (3.4) | 8–>64 | 64 | 64 | ||||||||
| Rifabutin | 1 (1.7) | 2 (3.4) | 8 (12.7) | 26 (44.8) | 16 (28.4) | 2 (3.4) | 1 (1.7) | 2 (3.4) | ≤0.062–16 | 0.5 | 1 | |||||
| M. kansasii (58) | Rifampin | 6 (10.3) | 32 (55.2) | 9 (15.5) | 3 (5.2) | 3 (5.2) | 1 (1.7) | 2 (3.4) | 2 (3.4) | 0.5–>64 | 1 | 8 | ||||
| Rifapentine | 14 (24.1) | 30 (51.7) | 5 (8.6) | 4 (6.9) | 2 (3.4) | 1 (1.7) | 2 (3.4) | 0.125–>64 | 0.25 | 1 | ||||||
| Rifaximin | 13 (22.4) | 26 (44.8) | 10 (17.2) | 3 (5.2) | 1 (1.7) | 1 (1.7) | 2 (3.4) | 2 (3.4) | 0.25–>64 | 0.5 | 4 | |||||
| Rifabutin | 51 (87.9) | 1 (1.7) | 3 (5.2) | 1 (1.7) | 1 (1.7) | 1 (1.7) | ≤0.062–64 | ≤0.062 | ≤0.062 | |||||||
| M. abscessus (65) | Rifampin | 1 (1.5) | 64 (98.5) | 64–>64 | >64 | >64 | ||||||||||
| Rifapentine | 1 (1.5) | 3 (4.6) | 61 (93.8) | 32–>64 | >64 | >64 | ||||||||||
| Rifaximin | 1 (1.5) | 2 (3.1) | 18 (27.7) | 44 (67.7) | 4–>64 | >64 | >64 | |||||||||
| Rifabutin | 1 (1.5) | 3 (4.6) | 8 (12.3) | 25 (38.5) | 26 (40) | 2 (3.1) | 0.25–32 | 8 | 16 | |||||||
| M. massiliense (67) | Rifampin | 1 (1.5) | 1 (1.5) | 1 (1.5) | 17 (25.4) | 47 (70.1) | 0.125–>64 | >64 | >64 | |||||||
| Rifapentine | 1 (1.5) | 3 (4.5) | 4 (6) | 5 (7.5) | 33 (49.3) | 21 (31.3) | 1–>64 | 64 | >64 | |||||||
| Rifaximin | 4 (6) | 5 (7.5) | 6 (9) | 19 (28.4) | 31 (46.3) | 2 (3) | 2–>64 | 32 | 64 | |||||||
| Rifabutin | 1 (1.5) | 3 (4.5) | 2 (3) | 16 (23.9) | 24 (35.8) | 12 (17.9) | 9 (13.4) | ≤0.062–16 | 4 | 16 | ||||||
Table 1 shows MIC levels of rifamycin derivatives for the 311 clinical NTM isolates. In MAC, the MIC50 (≤0.062 to 0.5 μg/ml) and MIC90 (0.25 to 1 μg/ml) values of rifabutin were 16 to 256 times lower than those of other rifamycins. In M. kansasii, the MIC50 (≤0.062 μg/ml) and MIC90 (≤0.062 μg/ml) values of rifabutin were lowest among the rifamycin derivatives. However, unlike MAC and M. kansasii, MABS showed relatively higher MIC50 (32 to >64 μg/ml) and MIC90 (>64 μg/ml) values for rifampin, rifapentine, or rifaximin. Nevertheless, the MIC50 (4 to 8 μg/ml) and MIC90 (16 μg/ml) values of rifabutin for MABS remained the lowest.
Table 2 shows the MIC levels of rifamycin derivatives for macrolide (n = 57)- and aminoglycoside (n = 44)-resistant NTM. Similarly, rifabutin showed the lowest MIC50 (≤0.062 to 8 μg/ml) and MIC90 (0.5 to 16 μg/ml) values against macrolide- and aminoglycoside-resistant NTM isolates, including MAC, M. abscessus, and M. massiliense.
TABLE 2.
MIC ranges and MIC50 and MIC90 values of four rifamycin antibiotics for 57 macrolide-resistant and 44 aminoglycoside-resistant clinical NTM isolates
| NTM species (no.) | Antibiotic | No. (%) of isolates with MIC (μg/ml) of: |
MIC range (μg/ml) | MIC50 (μg/ml) | MIC90 (μg/ml) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ≤0.062 | 0.125 | 0.25 | 0.5 | 1 | 2 | 4 | 8 | 16 | 32 | 64 | >64 | |||||
| Macrolide resistant | ||||||||||||||||
| M. avium (10) | Rifampin | 1 (10) | 1 (10) | 1 (10) | 1 (10) | 2 (20) | 4 (40) | ≤0.062–>64 | 64 | >64 | ||||||
| Rifapentine | 1 (10) | 1 (10) | 1 (10) | 1 (10) | 3 (30) | 1 (10) | 2 (20) | ≤0.062–>64 | 8 | >64 | ||||||
| Rifaximin | 1 (10) | 1 (10) | 3 (30) | 1 (10) | 2 (20) | 2 (20) | ≤0.062–>64 | 4 | >64 | |||||||
| Rifabutin | 1 (10) | 3 (30) | 2 (20) | 3 (30) | 1 (10) | ≤0.062–2 | 0.5 | 2 | ||||||||
| M. intracellulare (17) | Rifampin | 2 (11.8) | 1 (5.9) | 1 (5.9) | 3 (17.6) | 10 (58.8) | ≤0.062–64 | 64 | 64 | |||||||
| Rifapentine | 1 (5.9) | 1 (5.9) | 1 (5.9) | 2 (11.8) | 8 (47.1) | 3 (17.6) | 1 (5.9) | ≤0.062–64 | 8 | 16 | ||||||
| Rifaximin | 1 (5.9) | 2 (11.8) | 1 (5.9) | 4 (23.5) | 9 (52.9) | ≤0.062–64 | 64 | 64 | ||||||||
| Rifabutin | 3 (17.6) | 2 (11.8) | 2 (11.8) | 9 (52.9) | 1 (5.9) | ≤0.062–16 | 2 | 2 | ||||||||
| M. abscessus (13) | Rifampin | 1 (7.7) | 1 (7.7) | 11 (84.6) | 32–>64 | >64 | >64 | |||||||||
| Rifapentine | 2 (15.4) | 2 (15.4) | 9 (69.2) | 32–>64 | >64 | >64 | ||||||||||
| Rifaximin | 3 (23) | 3 (23) | 3 (23) | 4 (30.8) | 16–>64 | 64 | >64 | |||||||||
| Rifabutin | 5 (38.5) | 3 (23) | 4 (30.8) | 1 (9) | 2–16 | 4 | 8 | |||||||||
| M. massiliense (17) | Rifampin | 3 | 2 (11.8) | 12 (70.6) | 32–>64 | >64 | >64 | |||||||||
| Rifapentine | 2 (11.8) | 4 (23.5) | 11 (64.7) | 16–>64 | >64 | >64 | ||||||||||
| Rifaximin | 2 (11.8) | 3 (17.6) | 1 (5.9) | 4 (23.5) | 2 (11.8) | 5 (29.4) | 4–>64 | 32 | >64 | |||||||
| Rifabutin | 1 (5.9) | 1 (5.9) | 7 (41.8) | 2 (11.8) | 4 (23.5) | 2 (11.8) | 0.5–16 | 2 | 16 | |||||||
| Aminoglycoside resistant | ||||||||||||||||
| M. avium (12) | Rifampin | 1 (8.3) | 5 (41.7) | 1 (8.3) | 1 (8.3) | 1 (8.3) | 3 (25) | 1–64 | 2 | 64 | ||||||
| Rifapentine | 7 (58.3) | 1 (8.3) | 1 (8.3) | 1 (8.3) | 2 (16.7) | 0.5–8 | 0.5 | 8 | ||||||||
| Rifaximin | 2 (16.7) | 3 (25) | 2 (16.7) | 2 (16.7) | 1 (8.3) | 2 (16.7) | 0.25–16 | 1 | 16 | |||||||
| Rifabutin | 7 (58.3) | 1 (8.3) | 1 (8.3) | 3 (25) | ≤0.062–0.5 | ≤0.062 | 0.5 | |||||||||
| M. intracellulare (17) | Rifampin | 1 (5.9) | 2 (11.8) | 5 (29.4) | 8 (47.1) | 1 (5.9) | 0.5–>64 | 32 | 64 | |||||||
| Rifapentine | 1 (5.9) | 1 (5.9) | 3 (17.6) | 5 (29.4) | 3 (17.6) | 3 (17.6) | 1 (5.9) | ≤0.062–32 | 4 | 16 | ||||||
| Rifaximin | 1 (5.9) | 1 (5.9) | 1 (5.9) | 4 (23.5) | 3 (17.6) | 5 (29.4) | 2 (11.8) | 0.25–>64 | 32 | >64 | ||||||
| Rifabutin | 2 (11.8) | 3 (17.6) | 6 (35.3) | 2 (11.8) | 1 (5.9) | 2 (11.8) | 1 (5.9) | ≤0.062–8 | 0.5 | 4 | ||||||
| M. abscessus (9) | Rifampin | 9 (100) | >64 | >64 | >64 | |||||||||||
| Rifapentine | 1 (11.1) | 8 (88.9) | 64–>64 | >64 | >64 | |||||||||||
| Rifaximin | 2 (22.2) | 7 | 32–64 | 64 | 64 | |||||||||||
| Rifabutin | 6 (66.7) | 2 (22.2) | 1 (11.1) | 4–16 | 4 | 16 | ||||||||||
| M. massiliense (6) | Rifampin | 6 (100) | >64 | >64 | >64 | |||||||||||
| Rifapentine | 3 (50) | 3 (50) | 64–>64 | >64 | >64 | |||||||||||
| Rifaximin | 5 (83.3) | 1 (16.6) | 64–>64 | >64 | >64 | |||||||||||
| Rifabutin | 1 (16.7) | 1 (16.7) | 2 (33.3) | 2 (33.3) | 2–16 | 8 | 16 | |||||||||
We examined the in vitro activity of rifamycin derivatives against major pathogenic NTM species, including macrolide- and aminoglycoside-resistant NTM. Among the various rifamycin antibiotics, rifabutin showed the greatest effect in vitro for major NTM species regardless of resistance to key antibiotics, such as macrolides or aminoglycosides. Our data suggest that rifabutin is a therapeutic option for NTM-PD, particularly drug-resistant disease.
Interestingly, we found that the MIC50 (1 to 2 μg/ml) and MIC90 (16 μg/ml) values of rifapentine and rifaximin in M. avium were lower than those of rifampin (4 and 64 μg/ml, respectively) and that the MIC50 (8 μg/ml) and MIC90 (16 μg/ml) values of rifapentine in M. intracellulare were lower than those of rifampin (64 and >64 μg/ml, respectively). However, in MABS, all rifamycin antibiotics except rifabutin had very high MIC50 (32 to >64 μg/ml) and MIC90 (64 to >64 μg/ml) values. These findings indicate that rifamycin antibiotics, except rifabutin, have different in vitro activities for each NTM species and that rifapentine or rifaximin is a treatment option for NTM-PD, particularly MAC.
NTM-PD caused by macrolide- and aminoglycoside-resistant strains is difficult to treat (21, 22). Several oral agents, such as bedaquiline, clofazimine, and linezolid, were recently reported to have low in vitro MICs against NTM and were suggested for use in maintenance therapy. However, data are limited, and drugs such as linezolid can have severe side effects. In these contexts, as rifabutin had lower MIC50 and MIC90 values for macrolide- and aminoglycoside-resistant NTM, our results suggest that rifabutin is appropriate as a treatment for both drug-susceptible and drug-resistant NTM-PD.
Mycobacterial cell walls are less permeable than the outer membranes of other Gram-negative bacteria because of their higher lipid content (23, 24). The cell wall of M. chelonae, a mycobacterium classified as the same species as MABS until the early 1990s, was reported to be 10 to 20 times less permeable than M. tuberculosis, and, due to the structural specificity of this cell wall, MABS is considered resistant to rifamycins (25–27). In addition, MABS has intrinsic rifamycin resistance, whereby rifamycin is inactivated through metabolism by ADP-ribosyltransferase MABS_0591 (28–30).
Rifabutin is considered a new candidate antibiotic for MABS-PD (27). In a recent study of more than 2,700 U.S. Food and Drug Administration-approved drugs, rifabutin was effective against MABS, and recent data showed that rifabutin had synergistic effects with several antibiotics and no antagonism (10, 27). After the initial report that rifabutin was effective against MABS, several studies confirmed the MICs of rifabutin for clinical MABS isolates, and these MIC50 and MIC90 values were not significantly different from our result. Most recently, Chew et al. tested 218 M. abscessus isolates, including 146 respiratory isolates, and reported that the MIC50 and MIC90 of rifabutin were 16 and 32 μg/ml, respectively (12, 31). In addition, it was reported that rifabutin is effective for MABS in mice, zebrafish, and macrophage infection models (13, 14, 32). However, there are limited data on the in vitro activity of rifabutin using large sample sizes and various types of clinical NTM strains.
In summary, rifabutin showed effective in vitro activity against clinical NTM isolates regardless of macrolide or aminoglycoside resistance.
ACKNOWLEDGMENTS
This research was supported by a grant from the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (HI20C0017), and was also supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education (NRF-2020R1I1A1A01066970 to D.H.K.).
We express our heartfelt gratitude and respect to Won-Jung Koh for giving us invaluable guidance and unfailing support from the very beginning of this research. Won-Jung Koh passed away in August 2019. We dedicate this work to his memory.
We have no conflicts of interest to declare.
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