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Calvet-Seral J, Crespo-Yuste E, Mathys V, Rodriguez-Villalobos H, Ceyssens PJ, Martin A, Gonzalo-Asensio J. Targeted Chromosomal Barcoding Establishes Direct Genotype-Phenotype Associations for Antibiotic Resistance in Mycobacterium abscessus. Microbiol Spectr 2023; 11:e0534422. [PMID: 36988496 PMCID: PMC10269753 DOI: 10.1128/spectrum.05344-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/04/2023] [Indexed: 03/30/2023] Open
Abstract
A bedaquiline-resistant Mycobacterium abscessus isolate was sequenced, and a candidate mutation in the atpE gene was identified as responsible for the antibiotic resistance phenotype. To establish a direct genotype-phenotype relationship of this mutation which results in a Asp-to-Ala change at position 29 (D29A), we developed a recombineering-based method consisting of the specific replacement of the desired mutation in the bacterial chromosome. As surrogate bacteria, we used two M. abscessus bedaquiline-susceptible strains: ATCC 19977 and the SL541 clinical isolate. The allelic exchange substrates used in recombineering carried either the sole D29A mutation or a genetic barcode of silent mutations in codons flanking the D29A mutation. After selection of bedaquiline-resistant M. abscessus colonies transformed with both substrates, we obtained equivalent numbers of recombinants. These resistant colonies were analyzed by allele-specific PCR and Sanger sequencing, and we demonstrated that the presence of the genetic barcode was linked to the targeted incorporation of the desired mutation in its chromosomal location. All recombinants displayed the same MIC to bedaquiline as the original isolate, from which the D29A mutation was identified. Finally, to demonstrate the broad applicability of this method, we confirmed the association of bedaquiline resistance with the atpE A64P mutation in analysis performed in independent M. abscessus strains and by independent researchers. IMPORTANCE Antimicrobial resistance (AMR) threatens the effective prevention and treatment of an ever-increasing range of infections caused by microorganisms. On the other hand, infections caused by Mycobacterium abscessus affect people with chronic lung diseases, and their incidence has grown alarmingly in recent years. Further, these bacteria are known to easily develop AMR to the few therapeutic options available, making their treatment long-lasting and challenging. The recent introduction of new antibiotics against M. abscessus, such as bedaquiline, makes us anticipate a future when a plethora of antibiotic-resistant strains will be isolated and sequenced. However, in the era of whole-genome sequencing, one of the challenges is to unequivocally assign a biological function to each identified polymorphism. Thus, in this study, we developed a fast, robust, and reliable method to assign genotype-phenotype associations for putative antibiotic-resistant polymorphisms in M. abscessus.
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Affiliation(s)
- Juan Calvet-Seral
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Facultad de Medicina, Universidad de Zaragoza IIS-Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Estefanía Crespo-Yuste
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Facultad de Medicina, Universidad de Zaragoza IIS-Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Vanessa Mathys
- Unit of Human Bacterial Diseases, Sciensano, Brussels, Belgium
| | - Hector Rodriguez-Villalobos
- Cliniques Universitaires Saint-Luc, Microbiology Department, Université Catholique de Louvain, Brussels, Belgium
| | | | - Anandi Martin
- Institute of Experimental and Clinical Research, Université Catholique de Louvain, Woluwe-Saint-Lambert, Belgium
- Syngulon, Seraing, Belgium
| | - Jesús Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Facultad de Medicina, Universidad de Zaragoza IIS-Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Zaragoza, Spain
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Detection of Mixed Populations of Clarithromycin-Susceptible and -Resistant Mycobacterium abscessus Strains. J Clin Microbiol 2022; 60:e0169421. [PMID: 35313731 DOI: 10.1128/jcm.01694-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clarithromycin resistance in Mycobacterium abscessus subsp. abscessus, massiliense, and bolletii occurs through induction of erm(41) or mutations in rrl (23S rRNA) genes. Phenotypic detection of clarithromycin resistance is hindered by the need for extended incubation as well as co-occurrence of mixed populations of M. abscessus with different susceptibility profiles. We developed a quantitative EvaGreen-based droplet digital PCR (ddPCR) scheme for rapid detection of full-length or truncated erm(41) and a probe based ddPCR screening assay for assessment of 23S rRNA rrl mutational resistance. We tested 100 M. abscessus strains, synthetic mixes with different susceptibility profiles, and 13 positive MGIT samples. Truncated and full-length erm(41) genes were detected in 27/100 and 73/100 strains and 4/13 and 9/13 MGIT samples, respectively yielding a sensitivity and specificity of 100%. Clarithromycin resistance mutations in rrl were detected in 26/100 isolates, i.e., A2058G (18/100), A2058C (7/100), and A2059G (1/100), and in 3/13 MGIT samples, i.e., A2058G (2/13) and A2059G (1/13). A screening assay of rrl ddPCR (A2058A/A2058G probes) showed 100% sensitivity in detecting the wild type or A2058G mutation as well as identifying samples requiring further testing. Upon inclusion of additional ddPCR assays, we were able to detect A2058C and A2059G clarithromycin resistance-conferring mutations in the rrl gene. Our ddPCR scheme can differentiate between full-length and truncated erm(41) and identify clarithromycin resistance-conferring mutations in the rrl gene from clinical isolates and positive MGIT samples as well as deconvolute and quantitate mixed populations of M. abscessus with different clarithromycin resistance traits.
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Orujyan D, Narinyan W, Rangarajan S, Rangchaikul P, Prasad C, Saviola B, Venketaraman V. Protective Efficacy of BCG Vaccine against Mycobacterium leprae and Non-Tuberculous Mycobacterial Infections. Vaccines (Basel) 2022; 10:vaccines10030390. [PMID: 35335022 PMCID: PMC8952781 DOI: 10.3390/vaccines10030390] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/16/2022] [Accepted: 03/02/2022] [Indexed: 02/06/2023] Open
Abstract
The genus mycobacterium includes several species that are known to cause infections in humans. The microorganisms are classified into tuberculous and non-tuberculous based on their morphological characteristics, defined by the dynamic relationship between the host defenses and the infectious agent. Non-tuberculous mycobacteria (NTM) include all the species of mycobacterium other than the ones that cause tuberculosis (TB). The group of NTM contains almost 200 different species and they are found in soil, water, animals—both domestic and wild—milk and food products, and from plumbed water resources such as sewers and showerhead sprays. A systematic review of Medline between 1946 and 2014 showed an 81% decline in TB incidence rates with a simultaneous 94% increase in infections caused by NTM. Prevalence of infections due to NTM has increased relative to infections caused by TB owing to the stringent prevention and control programs in Western countries such as the USA and Canada. While the spread of typical mycobacterial infections such as TB and leprosy involves human contact, NTM seem to spread easily from the environment without the risk of acquiring from a human contact except in the case of M. abscessus in patients with cystic fibrosis, where human transmission as well as transmission through fomites and aerosols has been recorded. NTM are opportunistic in their infectious processes, making immunocompromised individuals such as those with other systemic infections such as HIV, immunodeficiencies, pulmonary disease, or usage of medications such as long-term corticosteroids/TNF-α inhibitors more susceptible. This review provides insight on pathogenesis, treatment, and BCG vaccine efficacy against M. leprae and some important NTM infections.
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Nontuberculous Mycobacterial Resistance to Antibiotics and Disinfectants: Challenges Still Ahead. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8168750. [PMID: 35257011 PMCID: PMC8898113 DOI: 10.1155/2022/8168750] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Accepted: 02/16/2022] [Indexed: 12/11/2022]
Abstract
The mortality incidence from nontuberculous mycobacteria (NTM) infections has been steadily developing globally. These bacterial agents were once thought to be innocent environmental saprophytic that are only dangerous to patients with defective lungs or the immunosuppressed. Nevertheless, the emergence of highly resistant NTM to different antibiotics and disinfectants increased the importance of these agents in the health system. Currently, NTM frequently infect seemingly immunocompetent individuals at rising rates. This is of concern as the resistant NTM are difficult to control and treat. The details behind this NTM development are only beginning to be clarified. The current study will provide an overview of the most important NTM resistance mechanisms to not only antibiotics but also the most commonly used disinfectants. Such evaluations can open new doors to improving control strategies and reducing the risk of NTM infection. Moreover, further studies are crucial to uncover this association.
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Zhang C, Sun L, Wang D, Li Y, Zhang L, Wang L, Peng J. Advances in antimicrobial resistance testing. Adv Clin Chem 2022; 111:1-68. [DOI: 10.1016/bs.acc.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Bordin A, Pandey S, Coulter C, Syrmis M, Pardo C, Hackett H, Bell SC, Wainwright CE, Nimmo GR, Jennison AV, Clark JE, Whiley DM. Rapid macrolide and amikacin resistance testing for Mycobacterium abscessus in people with cystic fibrosis. J Med Microbiol 2021; 70. [PMID: 33909552 DOI: 10.1099/jmm.0.001349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Introduction. Mycobacterium abscessus complex (MABSC) is an environmental organism and opportunistic pathogen. MABSC pulmonary infections in people with cystic fibrosis are of growing clinical concern. Resistance data guide the use of macrolides and amikacin in MABSC pulmonary disease treatment. MABSC can acquire resistance against macrolides or amikacin via 23S or 16S rRNA gene mutations, respectively.Gap Statement. Current culture-based methods for MABSC detection and antibiotic resistance characterization are typically prolonged, limiting their utility to directly inform treatment or clinical trials. Culture-independent molecular methods may help address this limitation.Aim. To develop real-time PCR assays for characterization of key 23S or 16S rRNA gene mutations associated with constitutive resistance in MABSC.Methodology. We designed two real-time PCR assays to detect the key 23S and 16S rRNA gene mutations. The highly conserved nature of rRNA genes was a major design challenge. To reduce potential cross-reactivity, primers included non-template bases and targeted single-nucleotide polymorphisms unique to MABSC. We applied these assays, as well as a previously developed real-time PCR assay for MABSC detection, to 968 respiratory samples from people with cystic fibrosis. The results from the molecular methods were compared to those for gold standard culture methods and 23S and 16S rRNA gene sequencing.Results.The real-time PCR MABSC detection assay provided a sensitivity of 83.8 % and a specificity of 97.8 % compared to culture. The results from the real-time PCR resistance detection assays were mostly concordant (>77.4 %) with cultured isolate sequencing. The real-time PCR resistance detection assays identified several samples harbouring both resistant and susceptible MABSC, while culture-dependent methods only identified susceptible MABSC in these samples.Conclusion. Using the molecular methods described here, results for health care providers or researchers could be available days or weeks earlier than is currently possible via culture-based antibiotic susceptibility testing.
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Affiliation(s)
- Amanda Bordin
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Sushil Pandey
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Christopher Coulter
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Melanie Syrmis
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia.,The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Carolyn Pardo
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Hazel Hackett
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Scott C Bell
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,The Prince Charles Hospital, Department of Thoracic Medicine, Brisbane, Queensland, Australia
| | - Claire E Wainwright
- Respiratory and Sleep Medicine Department, Queensland Children's Hospital, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Graeme R Nimmo
- Central Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Amy V Jennison
- Forensic and Scientific Services, Queensland Health, Brisbane, Queensland, Australia
| | - Julia E Clark
- Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - David M Whiley
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia.,Central Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
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Guo Q, Wei J, Zou W, Li Q, Qian X, Zhu Z. Antimicrobial susceptibility profiles of Mycobacterium abscessus complex isolates from respiratory specimens in Shanghai, China. J Glob Antimicrob Resist 2021; 25:72-76. [PMID: 33689828 DOI: 10.1016/j.jgar.2021.02.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/27/2021] [Accepted: 02/21/2021] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES The aim of this study was to compare the antibiotic susceptibility profiles of Mycobacterium abscessus complex (MABC) isolates and to investigate the relationship between susceptibility profiles and genetic mechanisms of macrolide resistance. METHODS More than 200 isolates collected from respiratory specimens between 2014 and 2018 were randomly analysed in this study. Minimum inhibitory concentrations (Mics) of ten potential antimicrobial agents were determined by the microplate alamarBlue assay. RESULTS We identified 43 MABC isolates, including 32 M. abscessus subsp. abscessus (M. abscessus) (6 from immunocompromised patients) and 11 M. abscessus subsp. massiliense (M. massiliense). The majority of MABC isolates were susceptible to amikacin (96.9% and 100.0% for M. abscessus and M. massiliense, respectively), linezolid (96.9% and 100.0%, respectively), cefoxitin (100.0% and 100.0%, respectively), imipenem (90.6% and 72.7%, respectively) and tobramycin (90.6% and 72.7%, respectively). The resistance rates to clarithromycin and doxycycline in isolates of M. abscessus (68.8% and 100.0%) were significantly higher than those in isolates of M. massiliense (18.2% and 63.6%) (P < 0.05), whereas the percentage of tobramycin-resistant isolates among M. abscessus (9.4%) was significantly lower than among M. massiliense (27.3%) (P = 0.007). Sequencing analyses showed significant differences between erm(41) of M. abscessus and M. massiliense. CONCLUSION Mycobacterium abscessus is the dominant pathogen of pulmonary MABC infections in our hospital. Aminoglycosides (amikacin and tobramycin), β-lactams (cefoxitin and imipenem) and linezolid exhibited potent inhibitory activity against MABC in vitro. The erm(41) gene may be a promising marker to predict macrolide susceptibility for M. abscessus.
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Affiliation(s)
- Qian Guo
- Department of Clinical Laboratory, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, People's Republic of China; Department of Molecular Biology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, People's Republic of China
| | - Jianhao Wei
- Department of Clinical Laboratory, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, People's Republic of China
| | - Wenda Zou
- Department of Reproductive Medicine Center, The Affiliated Zhuzhou Hospital, Xiang Ya Medical College, Central South University (CSU), Zhuzhou 412007, People's Republic of China
| | - Qiongxian Li
- Department of Clinical Laboratory, Nanhua County Center for Disease Control and Prevention, Chuxiong, Yunnan 675200, People's Republic of China
| | - Xueqin Qian
- Department of Clinical Laboratory, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, People's Republic of China
| | - Zhaoqin Zhu
- Department of Clinical Laboratory, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, People's Republic of China.
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8
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Sharma MK, La Y, Janella D, Soualhine H. A real-time PCR assay for rapid identification of inducible and acquired clarithromycin resistance in Mycobacterium abscessus. BMC Infect Dis 2020; 20:944. [PMID: 33302900 PMCID: PMC7730737 DOI: 10.1186/s12879-020-05686-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/04/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium abscessus is a rapidly growing mycobacteria involved in severe infections of the lung, skin, or soft tissue. Macrolides such as clarithromycin are the recommended first line drugs for treatment of M. abscessus infections. However, M. abscessus has dual mechanisms of resistance to macrolides, making treatment by macrolides difficult. A functional erm(41) gene confers for inducible resistance while acquired mutations on the 23S rRNA rrl gene confer for constitutive resistance. METHODS We have developed a real-time PCR assay to detect both inducible and acquired resistance to clarithromycin, and compared the results to traditional erm(41) and rrl sequencing and phenotypic susceptibility testing using Sensititre™ plates. RESULTS Of the total 126 M. abscessus isolates tested, truncated erm(41) was found in 23/126 (18.3%) of the samples, 27/126 (21.4%) had a T28C mutation in erm(41), and 2/126 (1.6%) had an acquired A2058C mutation in rrl. The phenotypic results correlated with the expected sequencing results in 121/126 samples (96%). Phenotypic testing compared to real-time PCR resolved 2 of these discrepancies by showing the existence of both erm(41) alleles in the isolates that sequencing missed. One culture was found to be mixed with two M. abscessus subsp. as per hsp65 sequencing and 2 isolates had discordance between molecular and phenotypic results. It was presumed that 3 isolates showed discrepancy between sequencing and real-time PCR, but one culture was mixed and other 2 detected both alleles by real-time PCR leading to 100% concordance when compared to sequencing. CONCLUSION In conclusion, real-time PCR is more accurate for detection of both acquired and induced clarithromycin resistance, specifically when mixed genic profiles are present in a sample.
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Affiliation(s)
- Meenu Kaushal Sharma
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, R3E 3R2, Winnipeg, Canada.
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada.
| | - Yanni La
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Debra Janella
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, R3E 3R2, Winnipeg, Canada
| | - Hafid Soualhine
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, R3E 3R2, Winnipeg, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
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9
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Treatment for Mycobacterium abscessus complex-lung disease. J Formos Med Assoc 2020; 119 Suppl 1:S58-S66. [PMID: 32527504 DOI: 10.1016/j.jfma.2020.05.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/17/2020] [Accepted: 05/20/2020] [Indexed: 12/29/2022] Open
Abstract
Nontuberculous mycobacterial infections and colonization are becoming more prevalent worldwide. Mycobacterium abscessus complex (MABC) is one of the predominant pathogens capable of a wide spectrum of infections, with 50% of infections involving the lungs. The decision to commence treatment is determined according to the severity of the disease, risk of progressive disease, presence of comorbidities, and goals of treatment. MABC is resistant to standard antituberculous agents and has variable drug susceptibility across different geographical locations, therefore, antibiotic susceptibility testing of all clinically significant isolates is crucial for selecting a treatment strategy. Pulmonary infections due to MABC is difficult to cure using the currently recommended regimens from the American Thoracic Society and British Thoracic Society. Macrolides are the cornerstone of treatment, but the efficacy of macrolide-based chemotherapy may be compromised by resistance. Despite the introduction of new drugs for treatment, treatment outcomes remain unsatisfactory. The combination of surgical resection of limited lung disease regions with a multidrug, macrolide-based therapy offers the optimal chance of achieving clinical cure of the disease. This review focuses on medical treatment of MABC-lung disease and the efficacy of new agents, such as clofazimine, amikacin inhalation therapy, tigecycline and linezolid, for treating MABC-lung disease.
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Daniel-Wayman S, Abate G, Barber DL, Bermudez LE, Coler RN, Cynamon MH, Daley CL, Davidson RM, Dick T, Floto RA, Henkle E, Holland SM, Jackson M, Lee RE, Nuermberger EL, Olivier KN, Ordway DJ, Prevots DR, Sacchettini JC, Salfinger M, Sassetti CM, Sizemore CF, Winthrop KL, Zelazny AM. Advancing Translational Science for Pulmonary Nontuberculous Mycobacterial Infections. A Road Map for Research. Am J Respir Crit Care Med 2020; 199:947-951. [PMID: 30428263 DOI: 10.1164/rccm.201807-1273pp] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Shelby Daniel-Wayman
- 1 Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases
| | - Getahun Abate
- 2 Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, Saint Louis University, Saint Louis, Missouri
| | - Daniel L Barber
- 3 T Lymphocyte Biology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases
| | - Luiz E Bermudez
- 4 Department of Biomedical Sciences and.,5 Department of Microbiology, Oregon State University, Corvallis, Oregon
| | - Rhea N Coler
- 6 Infectious Disease Research Institute, Seattle, Washington.,7 Department of Global Health, University of Washington, Seattle, Washington
| | - Michael H Cynamon
- 8 Veterans Administration Medical Center, Syracuse, New York.,9 State University of New York Upstate Medical Center, Syracuse, New York
| | - Charles L Daley
- 10 Division of Mycobacterial and Respiratory Infections, Department of Medicine
| | | | - Thomas Dick
- 12 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,13 Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey
| | - R Andres Floto
- 14 Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Steven M Holland
- 16 Division of Intramural Research, National Institute of Allergy and Infectious Diseases
| | - Mary Jackson
- 17 Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - Richard E Lee
- 18 Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Eric L Nuermberger
- 19 Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,20 Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Kenneth N Olivier
- 21 Laboratory of Chronic Airway Infection, Pulmonary Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, and
| | - Diane J Ordway
- 17 Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - D Rebecca Prevots
- 1 Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases
| | - James C Sacchettini
- 22 Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Max Salfinger
- 23 Mycobacteriology and Pharmacokinetics Laboratories, National Jewish Health, Denver, Colorado.,24 College of Public Health, University of South Florida, Tampa, Florida
| | - Christopher M Sassetti
- 25 Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts; and
| | - Christine F Sizemore
- 26 Tuberculosis, Leprosy, and other Mycobacterial Diseases Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Kevin L Winthrop
- 15 OHSU-PSU School of Public Health and.,27 Division of Infectious Disease, Department of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Adrian M Zelazny
- 28 Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland
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Yoon HJ, Chung MJ, Koh WJ, Jhun BW, Moon SM. Computed tomographic findings of macrolide-resistant Mycobacterium massiliense pulmonary disease and changes after antibiotic treatment. Medicine (Baltimore) 2019; 98:e16826. [PMID: 31490369 PMCID: PMC6738990 DOI: 10.1097/md.0000000000016826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The purpose of this study was to present the computed tomographic (CT) findings of lung abnormalities in macrolide-resistant Mycobacterium massiliense pulmonary disease and its changes in follow-up CT after antibiotic treatment.Chest CT scans of patients with macrolide-resistant M massiliense pulmonary disease (n = 19) were retrospectively reviewed. Patients were treated with multidrug therapy, and sputum examinations were performed. Follow-up CT scans obtained during antibiotic treatment after detection of macrolide resistance were also reviewed, if available (n = 13). The CT scores at detection of macrolide resistance and at the last follow-up periods were also compared.Of all patients with macrolide-resistant M massiliense pulmonary disease, 2 (11%) patients achieved sputum culture conversion during the follow-up period. The most common CT findings of M massiliense pulmonary disease at detection of macrolide resistance were bronchiectasis and bronchiolitis (n = 19, 100%), followed by consolidation (n = 16, 84%), cavities (n = 11, 58%), and nodules (n = 6, 32%). On the last follow-up CT, overall CT scores were increased in 8 (62%) of 13 patients, and total mean CT score was significantly increased (P = .021). For each CT pattern, the cavity showed the greatest increase in CT score (P = .027), followed by bronchiectasis (P = .038).Common CT findings of macrolide-resistant M massiliense pulmonary disease were similar to those of pulmonary disease caused by other species of nontuberculous mycobacteria at presentation. However, in macrolide-resistant M massiliense pulmonary disease, serial CT scans showed deterioration with cavitary and bronchiectatic change in most patients despite multidrug antibiotic therapy.
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Affiliation(s)
- Hyun Jung Yoon
- Department of Radiology, Samsung Medical Center, Sungkyunkwan University School of Medicine
- Department of Radiology, Veterans Health Service Medical Center
| | - Myung Jin Chung
- Department of Radiology, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul
| | - Seong Mi Moon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Korea
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12
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Kwon YS, Daley CL, Koh WJ. Managing antibiotic resistance in nontuberculous mycobacterial pulmonary disease: challenges and new approaches. Expert Rev Respir Med 2019; 13:851-861. [PMID: 31256694 DOI: 10.1080/17476348.2019.1638765] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Introduction: The incidence and prevalence rates of nontuberculous mycobacterial (NTM) pulmonary disease have been continuously increasing worldwide. However, the rate of successful treatment of this disease greatly needs improving, particularly when intrinsic (natural) drug resistance and acquired drug resistance in NTM pulmonary disease are associated with poor outcomes for patients. Areas covered: This review covers the major pathogens that cause NTM pulmonary disease caused by Mycobacterium avium complex, Mycobacterium abscessus, and Mycobacterium kansasii; the key drugs and recommended regimens used in the treatment of NTM pulmonary disease; the factors that contribute to resistance to the key drugs, including genetic factors and monotherapy; and the treatment strategies, including revised antibiotic regimens and surgery, that can be used to treat drug-resistant NTM pulmonary disease. Expert opinion: To avoid and overcome drug resistance in NTM pulmonary disease, the appropriate guideline-based treatments are essential, and clinical studies to evaluate new or repurposed drugs are urgently needed.
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Affiliation(s)
- Yong-Soo Kwon
- Department of Internal Medicine, Chonnam National University Hospital , Gwangju , South Korea
| | - Charles L Daley
- Division of Mycobacterial and Respiratory Infections, National Jewish Health , Denver , CO , USA
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine , Seoul , South Korea
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13
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Daniel-Wayman S, Shallom S, Azeem N, Olivier KN, Zelazny AM, Prevots DR. Amikacin exposure and susceptibility of macrolide-resistant Mycobacterium abscessus. ERJ Open Res 2019; 5:00154-2018. [PMID: 31149626 PMCID: PMC6536947 DOI: 10.1183/23120541.00154-2018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 04/15/2019] [Indexed: 11/27/2022] Open
Abstract
Mycobacterium abscessus is associated with antibiotic resistance and poor treatment outcomes. We described within-patient changes in M. abscessus resistance to clarithromycin and amikacin. Patients with amikacin exposure and a >50-month interval between M. abscessus isolates were identified. Antimicrobial susceptibility testing was performed on the first and last isolates by broth microdilution, and genetic markers of resistance were identified. 16 patients were identified with a median amikacin exposure of 2.3 years (range 0.6–8.6 years). 15 patients also received macrolides (median 7.2 years, range 1.3–10.7 years). All initial isolates were resistant to clarithromycin (minimum inhibitory concentration (MIC) ≥8 µg·mL−1). Two patients had later susceptible isolates, which were of a different subspecies (M. abscessus subsp. massiliense) than the initial isolates (M. abscessus subsp. abscessus). All initial isolates were susceptible or intermediately resistant to amikacin, and only one patient had a resistant final isolate (MIC >64 µg·mL−1), accompanied by an A→G mutation at position 1408 of the 16S ribosomal RNA. Forced expiratory volume in 1 s decreased significantly over the study period, while smear quantity and the proportions of patients with elevated C-reactive protein or cavitary lesions all increased significantly. Despite prolonged, mostly inhaled amikacin exposure, development of amikacin resistance was uncommon in this patient population; however, disease progression continued. Patients with long-term amikacin treatment rarely develop resistance but their disease continues to progresshttp://bit.ly/2V7k0kH
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Affiliation(s)
- Shelby Daniel-Wayman
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shamira Shallom
- Dept of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Nabila Azeem
- Dept of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth N Olivier
- Laboratory of Chronic Airway Infection, Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrian M Zelazny
- Dept of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - D Rebecca Prevots
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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14
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Whole-Genome Sequencing for Predicting Clarithromycin Resistance in Mycobacterium abscessus. Antimicrob Agents Chemother 2018; 63:AAC.01204-18. [PMID: 30397069 DOI: 10.1128/aac.01204-18] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/25/2018] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium abscessus is emerging as an important pathogen in chronic lung diseases, with concern regarding patient-to-patient transmission. The recent introduction of routine whole-genome sequencing (WGS) as a replacement for existing reference techniques in England provides an opportunity to characterize the genetic determinants of resistance. We conducted a systematic review to catalogue all known resistance-determining mutations. This knowledge was used to construct a predictive algorithm based on mutations in the erm(41) and rrl genes which was tested on a collection of 203 sequentially acquired clinical isolates for which there were paired genotype/phenotype data. A search for novel resistance-determining mutations was conducted using a heuristic algorithm. The sensitivity of existing knowledge for predicting resistance in clarithromycin was 95% (95% confidence interval [CI], 89 to 98%), and the specificity was 66% (95% CI, 54 to 76%). The subspecies alone was a poor predictor of resistance to clarithromycin. Eight potential new resistance-conferring single nucleotide polymorphisms (SNPs) were identified. WGS demonstrated probable resistance-determining SNPs in regions that the NTM-DR line probe cannot detect. These mutations are potentially clinically important, as they all occurred in samples that were predicted to be inducibly resistant and for which a macrolide would therefore currently be indicated. We were unable to explain all resistance, raising the possibility of the involvement of other as yet unidentified genes.
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15
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Khosravi AD, Mirsaeidi M, Farahani A, Tabandeh MR, Mohajeri P, Shoja S, Hoseini Lar KhosroShahi SR. Prevalence of nontuberculous mycobacteria and high efficacy of d-cycloserine and its synergistic effect with clarithromycin against Mycobacterium fortuitum and Mycobacterium abscessus. Infect Drug Resist 2018; 11:2521-2532. [PMID: 30573983 PMCID: PMC6290872 DOI: 10.2147/idr.s187554] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background The prevalence of pulmonary disease caused by nontuberculous mycobacteria (NTM) is reportedly on the rise in the world. Some of the species are resistant to various antibiotics; hence, limited treatment options are available. The aims of this study were to investigate the prevalence of NTM and to determine the effect of d-cycloserine against Mycobacterium fortuitum and Mycobacterium abscessus isolated from clinical specimens to find out the synergistic effect of d-cycloserine and clarithromycin. Methods A total of 95 nonduplicate pulmonary isolates of NTM were collected from three major Regional Tuberculosis (TB) Centers. NTM isolates were identified by conventional tests and PCR sequence analysis of the rpoB gene. PCR sequencing of erm-41 was performed for detecting the inducible resistance to macrolides. In vitro susceptibilities and activities of d-cycloserine-clarithromycin combinations were accessed using the broth microdilution method. Results Among 714-positive acid-fast bacilli from TB-suspected cases, 95 isolates were identified as NTM (13.3%). The prevalence of identified isolates was as follows: M. fortuitum 46 (48.4%), Mycobacterium simiae 16 (16.8%), Mycobacterium kansasii 15 (15.7%), M. abscessus 7 (7.3%), Mycobacterium thermoresistibile 4 (4.2%), Mycobacterium elephantis 3 (3.2%), Mycobacterium porcinum 2 (2.1%), and Mycobacterium chimaera 2 (2.1%). In addition, rpoB sequence analysis could identify all NTM isolates. The effect of d-cycloserine was better than that of clarithromycin. The synergistic effect of d-cycloserine with clarithromycin was observed for six (100%) and five (71.5%) strains of M. fortuitum and M. abscessus, respectively. Conclusion In the present study, we demonstrated a wide range of NTM in processed samples from different provinces of Iran. Our observations indicated that d-cycloserine was very active against M. abscessus and M. fortuitum; hence, d-cycloserine, either alone or in combination with clarithromycin, may be promising for the treatment of M. abscessus- and M. fortuitum-associated diseases.
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Affiliation(s)
- Azar Dokht Khosravi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran, .,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Mehdi Mirsaeidi
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Abbas Farahani
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran, .,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Mohammad Reza Tabandeh
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Parviz Mohajeri
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.,Nosocomial Infection Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Saeed Shoja
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for the Rapid Detection of Antimicrobial Resistance Mechanisms and Beyond. Clin Microbiol Rev 2018; 32:32/1/e00037-18. [PMID: 30487165 DOI: 10.1128/cmr.00037-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been successfully applied in recent years for first-line identification of pathogens in clinical microbiology because it is simple to use, rapid, and accurate and has economic benefits in hospital management. The range of clinical applications of MALDI-TOF MS for bacterial isolates is increasing constantly, from species identification to the two most promising applications in the near future: detection of antimicrobial resistance and strain typing for epidemiological studies. The aim of this review is to outline the contribution of previous MALDI-TOF MS studies in relation to detection of antimicrobial resistance and to discuss potential future challenges in this field. Three main approaches are ready (or almost ready) for clinical use, including the detection of antibiotic modifications due to the enzymatic activity of bacteria, the detection of antimicrobial resistance by analysis of the peak patterns of bacteria or mass peak profiles, and the detection of resistance by semiquantification of bacterial growth in the presence of a given antibiotic. This review provides an expert guide for MALDI-TOF MS users to new approaches in the field of antimicrobial resistance detection, especially possible applications as a routine diagnostic tool in microbiology laboratories.
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17
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Ryan K, Byrd TF. Mycobacterium abscessus: Shapeshifter of the Mycobacterial World. Front Microbiol 2018; 9:2642. [PMID: 30443245 PMCID: PMC6221961 DOI: 10.3389/fmicb.2018.02642] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/16/2018] [Indexed: 01/23/2023] Open
Abstract
In this review we will focus on unique aspects of Mycobacterium abscessus (MABS) which we feel earn it the designation of "shapeshifter of the mycobacterial world." We will review its emergence as a distinct species, the recognition and description of MABS subspecies which are only now being clearly defined in terms of pathogenicity, its ability to exist in different forms favoring a saprophytic lifestyle or one more suitable to invasion of mammalian hosts, as well as current challenges in terms of antimicrobial therapy and future directions for research. One can see in the various phases of MABS, a species transitioning from a free living saprophyte to a host-adapted pathogen.
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Affiliation(s)
- Keenan Ryan
- Department of Pharmacy, University of New Mexico Hospital, Albuquerque, NM, United States
| | - Thomas F. Byrd
- Department of Medicine, The University of New Mexico School of Medicine, Albuquerque, NM, United States
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18
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Hydroalcoholic Extract and Ethyl Acetate Fraction of Bixa orellana Leaves Decrease the Inflammatory Response to Mycobacterium abscessus Subsp. massiliense. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2018; 2018:6091934. [PMID: 30369954 PMCID: PMC6189676 DOI: 10.1155/2018/6091934] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 08/18/2018] [Indexed: 12/18/2022]
Abstract
The incidence of infections caused by rapidly growing mycobacteria (RGM), especially Mycobacterium abscessus subsp. massiliense (Mabs), is increasing worldwide. Severe infections are associated with abscess formation and strong inflammatory response. This study evaluated the antimicrobial and anti-inflammatory activities of a hydroalcoholic extract (BoHE) and ethyl acetate fraction (BoEA) of Bixa orellana leaves. Antimicrobial activity was evaluated by broth microdilution to determine the minimum inhibitory (MIC) and the minimum bactericidal (MBC) concentrations. Cytotoxicity was evaluated using erythrocytes and RAW 264.7 cells. Nitric oxide (NO) was assayed in stimulated RAW 264.7 cells, and inflammatory cell migration and acute toxicity were evaluated in a Mabs-induced peritonitis mouse model. The compounds present in BoEA were identified by high performance liquid chromatography and mass spectrometry (HPLC-MS). The MIC and MBC values were 2.34 mg/mL and 37.5 mg/mL for BoHE and 0.39 mg/mL and 6.25 mg/mL for BoEA. The extracts did not induce significant toxicity in erythrocytes and RAW 264.7 cells. High levels of NO induced by Mabs were decreased by treatment with both extracts. The anti-inflammatory activity was confirmed in vivo by significant reduction of the cell migration to the peritoneum following BoHE and BoEA pretreatment. Animals treated with BoHE or BoEA did not show signs of acute toxicity in stomach, liver, and kidney. The chemical characterization of BoEA (the most active extract) revealed that kaempferol-3-O-coumaroyl glucose is its major component. The extract of B. orellana may be effective for treating infections caused by Mabs.
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19
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Huh HJ, Kim SY, Jhun BW, Shin SJ, Koh WJ. Recent advances in molecular diagnostics and understanding mechanisms of drug resistance in nontuberculous mycobacterial diseases. INFECTION GENETICS AND EVOLUTION 2018; 72:169-182. [PMID: 30315892 DOI: 10.1016/j.meegid.2018.10.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 01/31/2023]
Abstract
Accumulating evidence suggests that human infections caused by nontuberculous mycobacteria (NTM) are increasing worldwide, indicating that NTM disease is no longer uncommon in many countries. As a result of an increasing emphasis on the importance of differential identification of NTM species, several molecular tools have recently been introduced in clinical and experimental settings. These advances have led to a much better understanding of the diversity of NTM species with regard to clinical aspects and the potential factors responsible for drug resistance that influence the different outcomes of NTM disease. In this paper, we review currently available molecular diagnostics for identification and differentiation of NTM species by summarizing data from recently applied methods, including commercially available assays, and their relevant strengths and weaknesses. We also highlight drug resistance-associated genes in clinically important NTM species. Understanding the basis for different treatment outcomes with different causative species and drug-resistance mechanisms will eventually improve current treatment regimens and facilitate the development of better control measures for NTM diseases.
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Affiliation(s)
- Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
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20
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Mougari F, Loiseau J, Veziris N, Bernard C, Bercot B, Sougakoff W, Jarlier V, Raskine L, Cambau E. Evaluation of the new GenoType NTM-DR kit for the molecular detection of antimicrobial resistance in non-tuberculous mycobacteria. J Antimicrob Chemother 2017; 72:1669-1677. [PMID: 28333340 DOI: 10.1093/jac/dkx021] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/12/2017] [Indexed: 11/13/2022] Open
Abstract
Objectives Non-tuberculous mycobacteria (NTM) are emerging pathogens causing difficult-to-treat infections. We tested a new assay (GenoType NTM-DR) that detects natural and acquired resistance mechanisms to macrolides and aminoglycosides in frequently isolated NTM species. Methods Performance was assessed on 102 isolates including reference strains [16 Mycobacterium avium , 10 Mycobacterium intracellulare , 8 Mycobacterium chimaera , 15 Mycobacterium chelonae and 53 Mycobacterium abscessus (including subsp. abscessus isolates, 18 with a t28 in erm(41) and 10 with a c28, 13 subsp. bolletii isolates and 12 subsp. massiliense isolates)]. Genotypes were determined by PCR sequencing of erm(41) and rrl for clarithromycin resistance and of the 1400-1480 rrs region for aminoglycoside resistance. Phenotypes were determined by MIC microdilution. Results GenoType NTM-DR yielded results concordant with Sanger sequencing for 100/102 (98%) isolates. The erm(41) genotypic pattern was accurately identified for M. abscessus isolates . Mutations in rrl were detected in 15 isolates (7 M. avium complex, 5 M. abscessus and 3 M. chelonae ) with acquired clarithromycin resistance harbouring rrl mutations (a2057c, a2058g, a2058t or a2059c). Mutations in rrs were detected in five isolates with amikacin resistance harbouring the rrs mutation a1408g. In two isolates, the NTM-DR test revealed an rrl mutation (initial sequencing being WT), which was confirmed by re-sequencing. The test results were concordant with phenotypic susceptibility testing in 96/102 (94.1%) isolates, with four clarithromycin-resistant and two amikacin-resistant isolates not harbouring mutations. Conclusions The GenoType NTM-DR test is efficient in detecting mutations predictive of antimicrobial resistance in M. avium complex, M. abscessus and M. chelonae.
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Affiliation(s)
| | | | - Nicolas Veziris
- National Reference Center for Mycobacteria and Antimycobacterial Resistance, Paris, France.,APHP, Hôpital Pitié-Salpêtrière, Bactériologie-Hygiène, 75013 Paris, France.,CR7, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Universités, UPMC Université Paris 06, CIMI, Team E13 (Bacteriology), Paris, France
| | - Christine Bernard
- National Reference Center for Mycobacteria and Antimycobacterial Resistance, Paris, France.,APHP, Hôpital Pitié-Salpêtrière, Bactériologie-Hygiène, 75013 Paris, France.,CR7, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Universités, UPMC Université Paris 06, CIMI, Team E13 (Bacteriology), Paris, France
| | | | - Wladimir Sougakoff
- National Reference Center for Mycobacteria and Antimycobacterial Resistance, Paris, France.,APHP, Hôpital Pitié-Salpêtrière, Bactériologie-Hygiène, 75013 Paris, France.,CR7, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Universités, UPMC Université Paris 06, CIMI, Team E13 (Bacteriology), Paris, France
| | - Vincent Jarlier
- National Reference Center for Mycobacteria and Antimycobacterial Resistance, Paris, France.,APHP, Hôpital Pitié-Salpêtrière, Bactériologie-Hygiène, 75013 Paris, France.,CR7, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Universités, UPMC Université Paris 06, CIMI, Team E13 (Bacteriology), Paris, France
| | - Laurent Raskine
- National Reference Center for Mycobacteria and Antimycobacterial Resistance, Paris, France.,APHP, Hôpital Lariboisière, Laboratory of Bacteriology, Paris, France
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21
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Clinical Characteristics and Treatment Outcomes of Patients with Acquired Macrolide-Resistant Mycobacterium abscessus Lung Disease. Antimicrob Agents Chemother 2017; 61:AAC.01146-17. [PMID: 28739795 DOI: 10.1128/aac.01146-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/20/2017] [Indexed: 01/14/2023] Open
Abstract
Macrolide antibiotics are mainstays in the treatment of lung disease due to the Mycobacterium abscessus complex. Although previous studies have reported development of acquired macrolide resistance in this species, limited data are available on the outcomes of lung disease due to macrolide-resistant Mycobacterium abscessus subsp. abscessus This study evaluated the clinical features, treatment outcomes, and molecular characteristics of macrolide-resistant isolates of M. abscessus subsp. abscessus We performed a retrospective review of medical records and genetic analysis of clinical isolates from 13 patients who had acquired macrolide-resistant M. abscessus subsp. abscessus lung disease between November 2006 and March 2016. Eleven (85%) patients had the nodular bronchiectatic form of the disease, and two (15%) patients had the fibrocavitary form. When acquired macrolide resistance was detected, 10 (77%) patients were on antibiotic therapy for M. abscessus subsp. abscessus, and three (23%) patients were on therapy for lung disease due to other nontuberculous mycobacteria. The median treatment duration after detecting resistance was 24.0 months (interquartile range, 16.0 to 43.0 months). Treatment outcomes were poor, and final sputum culture conversion was achieved in only one (8%) patient, after resectional surgery. All 13 clinical isolates demonstrated point mutations at position 2058 (n = 10) or 2059 (n = 3) of the 23S rRNA gene, which resulted in acquired macrolide resistance. This study indicates that treatment outcomes are very poor after the development of acquired macrolide resistance in patients with M. abscessus subsp. abscessus lung disease. Thus, more effective measures are needed to prevent development and effectively treat macrolide-resistant M. abscessus subsp. abscessus lung disease.
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Jeong SH, Kim SY, Huh HJ, Ki CS, Lee NY, Kang CI, Chung DR, Peck KR, Shin SJ, Koh WJ. Mycobacteriological characteristics and treatment outcomes in extrapulmonary Mycobacterium abscessus complex infections. Int J Infect Dis 2017; 60:49-56. [PMID: 28522316 DOI: 10.1016/j.ijid.2017.05.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/30/2017] [Accepted: 05/10/2017] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES The differentiation between Mycobacterium abscessus subspecies abscessus (M. abscessus) and Mycobacterium abscessus subspecies massiliense (M. massiliense) and determination of the presence of inducible resistance to macrolide antibiotics are important factors in the management of patients with Mycobacterium abscessus complex (MABC) infections. Unlike pulmonary MABC infections, little information on extrapulmonary MABC infections is available. METHODS The molecular identification of clinical isolates was performed, and the clinical characteristics and treatment outcomes of 20 consecutive patients with extrapulmonary MABC infections were assessed. RESULTS M. abscessus and M. massiliense each caused 10 (50%) of the cases. Eight (80%) M. abscessus isolates that had inducible resistance to clarithromycin harbored an intact erm(41) gene of the T28 variant, whereas two (20%) M. abscessus isolates had the C28 erm(41) variant and were susceptible to clarithromycin. All M. massiliense isolates had a truncated erm(41) gene and were susceptible to clarithromycin. The drug susceptibility profiles other than clarithromycin were similar for the M. abscessus and M. massiliense isolates. Of the 20 patients, 17 (85%) showed a favorable outcome, including all patients with M. massiliense infection and 70% (7/10) of patients with M. abscessus infection. Favorable outcomes were associated with M. massiliense and M. abscessus isolates with a non-functional erm(41) gene (p=0.049). CONCLUSIONS Precise species and subspecies identification and the determination of macrolide susceptibility are recommended for the optimal treatment of extrapulmonary MABC infections.
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Affiliation(s)
- Suk Hyeon Jeong
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Chang-Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Cheol-In Kang
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Doo Ryeon Chung
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
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Clinical Characteristics and Treatment Outcomes of Patients with Macrolide-Resistant Mycobacterium massiliense Lung Disease. Antimicrob Agents Chemother 2017; 61:AAC.02189-16. [PMID: 27872066 DOI: 10.1128/aac.02189-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/15/2016] [Indexed: 11/20/2022] Open
Abstract
Macrolide antibiotics are cornerstones in the treatment of Mycobacterium massiliense lung disease. Despite the emergence of resistance, limited data on macrolide-resistant M massiliense lung disease are available. This study evaluated the clinical features and treatment outcomes of patients and the molecular characteristics of macrolide-resistant M massiliense isolates. We performed a retrospective review of medical records and genetic analyses of clinical isolates from 15 patients who had macrolide-resistant M massiliense lung disease between September 2005 and February 2015. Nine patients (60%) had the nodular bronchiectatic form of the disease, and six (40%) had the fibrocavitary form. Before the detection of macrolide resistance, three patients (20%) were treated with macrolide monotherapy, four (27%) with therapy for presumed Mycobacterium avium complex infections, and eight (53%) with combination antibiotic therapy for M massiliense lung disease. The median treatment duration after the detection of resistance was 18.7 months (interquartile range, 11.2 to 39.8 months). Treatment outcomes were poor, with a favorable outcome being achieved for only one patient (7%), who underwent surgery in addition to antibiotic therapy. The 1-, 3-, and 5-year mortality rates were 7, 13, and 33%, respectively. Of the 15 clinical isolates, 14 (93%) had point mutations at position 2058 (n = 9) or 2059 (n = 5) of the 23S rRNA gene, resulting in macrolide resistance. Our study indicates that treatment outcomes are poor and mortality rates are high after the development of macrolide resistance in patients with M massiliense lung disease. Thus, preventing the development of macrolide resistance should be a key consideration during treatment.
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Koh WJ, Jeong BH, Kim SY, Jeon K, Park KU, Jhun BW, Lee H, Park HY, Kim DH, Huh HJ, Ki CS, Lee NY, Kim HK, Choi YS, Kim J, Lee SH, Kim CK, Shin SJ, Daley CL, Kim H, Kwon OJ. Mycobacterial Characteristics and Treatment Outcomes in Mycobacterium abscessus Lung Disease. Clin Infect Dis 2016; 64:309-316. [DOI: 10.1093/cid/ciw724] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 10/24/2016] [Indexed: 01/28/2023] Open
Abstract
Abstract
Background
Treatment outcomes of patients with Mycobacterium abscessus subspecies abscessus lung disease are poor, and the microbial characteristics associated with treatment outcomes have not been studied systematically. The purpose of this study was to identify associations between microbial characteristics and treatment outcomes in patients with M. abscessus lung disease.
Methods
Sixty-seven consecutive patients with M. abscessus lung disease undergoing antibiotic treatment for ≥12 months between January 2002 and December 2012 were included. Morphotypic and genetic analyses were performed on isolates from 44 patients.
Results
Final sputum conversion to culture negative occurred in 34 (51%) patients. Compared to isolates from 24 patients with persistently positive cultures, pretreatment isolates from 20 patients with final negative conversion were more likely to exhibit smooth colonies (9/20, 45% vs 2/24, 8%; P = .020), susceptibility to clarithromycin (7/20, 35% vs 1/24, 4%; P = .015), and be of the C28 sequevar with regard to the erm(41) gene (6/20, 30% vs 1/24, 4%; P = .035). Mycobacterium abscessus lung disease recurred in 5 (15%) patients after successful completion of antibiotic therapy. Genotypic analysis revealed that most episodes (22/24, 92%) of persistently positive cultures during antibiotic treatment and all cases of microbiologic recurrence after treatment completion were caused by different M. abscessus genotypes within a patient.
Conclusions
Precise identification to the subspecies level and analysis of mycobacterial characteristics could help predict treatment outcomes in patients with M. abscessus lung disease. Treatment failures and recurrences are frequently associated with multiple genotypes, suggesting reinfection.
Clinical Trials Registration
NCT00970801.
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Affiliation(s)
- Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Byeong-Ho Jeong
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Kyeongman Jeon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Hyun Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Hye Yun Park
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Dae Hun Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics
| | | | | | - Hong Kwan Kim
- Department of Thoracic Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul
| | - Yong Soo Choi
- Department of Thoracic Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul
| | - Jhingook Kim
- Department of Thoracic Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul
| | | | | | - Sung Jae Shin
- Department of Microbiology, Yonsei University College of Medicine, Seoul, South Korea
| | - Charles L Daley
- Division of Mycobacterial and Respiratory Infections, Department of Medicine, National Jewish Health, Denver, Colorado
| | - Hojoong Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - O Jung Kwon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine
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Abstract
Pulmonary infections are the most frequent diseases caused by nontuberculous mycobacteria (NTM). Common causative organisms of pulmonary infection are slowly growing mycobacteria including Mycobacterium avium complex and Mycobacterium kansasii, and rapidly growing mycobacteria including Mycobacterium abscessus complex. Clinical concern has been raised over the increasing incidence of NTM lung disease combined with the poor treatment outcomes of these chronic infectious diseases. Since treatment guidelines of the American Thoracic Society/Infectious Disease Society of America were published in 2007 there have been continuous efforts to improve the outcomes of NTM lung disease, albeit slowly and with limitations. Here, we focus on recent advances in the antibiotic treatment of NTM lung disease.
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Affiliation(s)
- Young Ae Kang
- a Division of Pulmonology, Department of Internal Medicine , Severance Hospital, Institute of Chest Diseases, Yonsei University College of Medicine , Seoul , South Korea
| | - Won-Jung Koh
- b Division of Pulmonary and Critical Care Medicine, Department of Medicine , Samsung Medical Center, Sungkyunkwan University School of Medicine , Seoul , South Korea
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Stout JE, Koh WJ, Yew WW. Update on pulmonary disease due to non-tuberculous mycobacteria. Int J Infect Dis 2016; 45:123-34. [PMID: 26976549 DOI: 10.1016/j.ijid.2016.03.006] [Citation(s) in RCA: 221] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/06/2016] [Accepted: 03/08/2016] [Indexed: 01/01/2023] Open
Abstract
Non-tuberculous mycobacteria (NTM) are emerging worldwide as significant causes of chronic pulmonary infection, posing a number of challenges for both clinicians and researchers. While a number of studies worldwide have described an increasing prevalence of NTM pulmonary disease over time, population-based data are relatively sparse and subject to ascertainment bias. Furthermore, the disease is geographically heterogeneous. While some species are commonly implicated worldwide (Mycobacterium avium complex, Mycobacterium abscessus), others (e.g., Mycobacterium malmoense, Mycobacterium xenopi) are regionally important. Thoracic computed tomography, microbiological testing with identification to the species level, and local epidemiology must all be taken into account to accurately diagnose NTM pulmonary disease. A diagnosis of NTM pulmonary disease does not necessarily imply that treatment is required; a patient-centered approach is essential. When treatment is required, multidrug therapy based on appropriate susceptibility testing for the species in question should be used. New diagnostic and therapeutic modalities are needed to optimize the management of these complicated infections.
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Affiliation(s)
- Jason E Stout
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Box 102359-DUMC, Durham, NC 27710, USA.
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Wing Wai Yew
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong, China
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28
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Clonal Diversification and Changes in Lipid Traits and Colony Morphology in Mycobacterium abscessus Clinical Isolates. J Clin Microbiol 2015; 53:3438-47. [PMID: 26292297 DOI: 10.1128/jcm.02015-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 07/29/2015] [Indexed: 11/20/2022] Open
Abstract
The smooth-to-rough colony morphology shift in Mycobacterium abscessus has been implicated in loss of glycopeptidolipid (GPL), increased pathogenicity, and clinical decline in cystic fibrosis (CF) patients. However, the evolutionary phenotypic and genetic changes remain obscure. Serial isolates from nine non-CF patients with persistent M. abscessus infection were characterized by colony morphology, lipid profile via thin-layer chromatography and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), sequencing of eight genes in the GPL locus, and expression level of fadD23, a key gene involved in the biosynthesis of complex lipids. All 50 isolates were typed as M. abscessus subspecies abscessus and were clonally related within each patient. Rough isolates, all lacking GPL, predominated at later disease stages, some showing variation within rough morphology. While most (77%) rough isolates harbored detrimental mutations in mps1 and mps2, 13% displayed previously unreported mutations in mmpL4a and mmpS4, the latter yielding a putative GPL precursor. Two isolates showed no deleterious mutations in any of the eight genes sequenced. Mixed populations harboring different GPL locus mutations were detected in 5 patients, demonstrating clonal diversification, which was likely overlooked by conventional acid-fast bacillus (AFB) culture methods. Our work highlights applications of MALDI-TOF MS beyond identification, focusing on mycobacterial lipids relevant in virulence and adaptation. Later isolates displayed accumulation of triacylglycerol and reduced expression of fadD23, sometimes preceding rough colony onset. Our results indicate that clonal diversification and a shift in lipid metabolism, including the loss of GPL, occur during chronic lung infection with M. abscessus. GPL loss alone may not account for all traits associated with rough morphology.
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