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Nguyen TQ, Heo BE, Jeon S, Ash A, Lee H, Moon C, Jang J. Exploring antibiotic resistance mechanisms in Mycobacterium abscessus for enhanced therapeutic approaches. Front Microbiol 2024; 15:1331508. [PMID: 38380095 PMCID: PMC10877060 DOI: 10.3389/fmicb.2024.1331508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/17/2024] [Indexed: 02/22/2024] Open
Abstract
Mycobacterium abscessus, a leading cause of severe lung infections in immunocompromised individuals, poses significant challenges for current therapeutic strategies due to resistance mechanisms. Therefore, understanding the intrinsic and acquired antibiotic resistance of M. abscessus is crucial for effective treatment. This review highlights the mechanisms employed by M. abscessus to sustain antibiotic resistance, encompassing not only conventional drugs but also newly discovered drug candidates. This comprehensive analysis aims to identify novel entities capable of overcoming the notorious resistance exhibited by M. abscessus, providing insights for the development of more effective therapeutic interventions.
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Affiliation(s)
- Thanh Quang Nguyen
- Division of Life Science, Department of Bio & Medical Big Data (BK21 Four Program), Research Institute of Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Bo Eun Heo
- Division of Life Science, Department of Bio & Medical Big Data (BK21 Four Program), Research Institute of Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Seunghyeon Jeon
- Division of Life Science, Department of Bio & Medical Big Data (BK21 Four Program), Research Institute of Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Anwesha Ash
- Division of Life Science, Department of Bio & Medical Big Data (BK21 Four Program), Research Institute of Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Heehyun Lee
- Division of Life Science, Department of Bio & Medical Big Data (BK21 Four Program), Research Institute of Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Cheol Moon
- Department of Clinical Laboratory Science, Semyung University, Jecheon, Republic of Korea
| | - Jichan Jang
- Division of Life Science, Department of Bio & Medical Big Data (BK21 Four Program), Research Institute of Life Science, Gyeongsang National University, Jinju, Republic of Korea
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Quang NT, Jang J. Current Molecular Therapeutic Agents and Drug Candidates for Mycobacterium abscessus. Front Pharmacol 2021; 12:724725. [PMID: 34526902 PMCID: PMC8435730 DOI: 10.3389/fphar.2021.724725] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium abscessus has been recognised as a dreadful respiratory pathogen among the non-tuberculous mycobacteria (NTM) because of misdiagnosis, prolonged therapy with poor treatment outcomes and a high cost. This pathogen also shows extremely high antimicrobial resistance against current antibiotics, including the anti-tuberculosis agents. Therefore, current chemotherapies require a long curative period and the clinical outcomes are not satisfactory. Thus, there is an urgent need for discovering and developing novel, more effective anti-M. abscessus drugs. In this review, we sum the effectiveness of the current anti-M. abscessus drugs and drug candidates. Furthermore, we describe the shortcomings and difficulties associated with M. abscessus drug discovery and development.
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Affiliation(s)
- Nguyen Thanh Quang
- Molecular Mechanisms of Antibiotics, Division of Life Science, Department of Bio and Medical Big Data (BK21 Four Program), Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - Jichan Jang
- Molecular Mechanisms of Antibiotics, Division of Life Science, Department of Bio and Medical Big Data (BK21 Four Program), Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
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Shaw LP, Doyle RM, Kavaliunaite E, Spencer H, Balloux F, Dixon G, Harris KA. Children With Cystic Fibrosis Are Infected With Multiple Subpopulations of Mycobacterium abscessus With Different Antimicrobial Resistance Profiles. Clin Infect Dis 2020; 69:1678-1686. [PMID: 30689761 PMCID: PMC6821159 DOI: 10.1093/cid/ciz069] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/21/2019] [Indexed: 12/12/2022] Open
Abstract
Background Children with cystic fibrosis (CF) can develop life-threatening infections of Mycobacterium abscessus. These present a significant clinical challenge, particularly when the strains involved are resistant to antibiotics. Recent evidence of within-patient subclones of M. abscessus in adults with CF suggests the possibility that within-patient diversity may be relevant for the treatment of pediatric CF patients. Methods We performed whole-genome sequencing (WGS) on 32 isolates of M. abscessus that were taken from multiple body sites of 2 patients with CF who were undergoing treatment at Great Ormond Street Hospital, United Kingdom, in 2015. Results We found evidence of extensive diversity within patients over time. A clustering analysis of single nucleotide variants revealed that each patient harbored multiple subpopulations, which were differentially abundant between sputum, lung samples, chest wounds, and pleural fluid. The sputum isolates did not reflect the overall within-patient diversity and did not allow for the detection of subclones with mutations previously associated with macrolide resistance (rrl 2058/2059). Some variants were present at intermediate frequencies before the lung transplants. The time of the transplants coincided with extensive variation, suggesting that this event is particularly disruptive for the microbial community, but the transplants did not clear the M. abscessus infections and both patients died as a result of these infections. Conclusions Isolates of M. abscessus from sputum do not always reflect the entire diversity present within the patient, which can include subclones with differing antimicrobial resistance profiles. An awareness of this phenotypic variability, with the sampling of multiple body sites in conjunction with WGS, may be necessary to ensure the best treatment for this vulnerable patient group.
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Affiliation(s)
- Liam P Shaw
- UCL Genetics Institute, University College London, London.,Nuffield Department of Medicine, John Radcliffe Hospital, Oxford
| | - Ronan M Doyle
- Department of Microbiology, Virology and Infection Control.,National Institute for Health Research Biomedical Research Centre
| | - Ema Kavaliunaite
- Paediatric Respiratory Medicine and Lung Transplantation, Great Ormond Street Hospital National Health Services Foundation Trust, London, United Kingdom
| | - Helen Spencer
- Paediatric Respiratory Medicine and Lung Transplantation, Great Ormond Street Hospital National Health Services Foundation Trust, London, United Kingdom
| | | | - Garth Dixon
- Department of Microbiology, Virology and Infection Control.,National Institute for Health Research Biomedical Research Centre
| | - Kathryn A Harris
- Department of Microbiology, Virology and Infection Control.,National Institute for Health Research Biomedical Research Centre
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Waters V, Ratjen F. Antibiotic treatment for nontuberculous mycobacteria lung infection in people with cystic fibrosis. Cochrane Database Syst Rev 2020; 6:CD010004. [PMID: 32521055 PMCID: PMC7389742 DOI: 10.1002/14651858.cd010004.pub5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Nontuberculous mycobacteria are mycobacteria, other than those in the Mycobacterium tuberculosis complex, and are commonly found in the environment. Nontuberculous mycobacteria species (most commonly Mycobacterium avium complex and Mycobacterium abscessus) are isolated from the respiratory tract of approximately 5% to 40% of individuals with cystic fibrosis; they can cause lung disease in people with cystic fibrosis leading to more a rapid decline in lung function and even death in certain circumstances. Although there are guidelines for the antimicrobial treatment of nontuberculous mycobacteria lung disease, these recommendations are not specific for people with cystic fibrosis and it is not clear which antibiotic regimen may be the most effective in the treatment of these individuals. This is an update of a previous review. OBJECTIVES The objective of our review was to compare antibiotic treatment to no antibiotic treatment, or to compare different combinations of antibiotic treatment, for nontuberculous mycobacteria lung infections in people with cystic fibrosis. The primary objective was to assess the effect of treatment on lung function and pulmonary exacerbations and to quantify adverse events. The secondary objectives were to assess treatment effects on the amount of bacteria in the sputum, quality of life, mortality, nutritional parameters, hospitalizations and use of oral antibiotics. SEARCH METHODS We searched the Cochrane Cystic Fibrosis Trials Register, compiled from electronic database searches and hand searching of journals and conference abstract books. Date of last search: 24 February 2020. We also searched a register of ongoing trials and the reference lists of relevant articles and reviews. Date of last search: 21 March 2019. SELECTION CRITERIA Any randomized controlled trials comparing nontuberculous mycobacteria antibiotics to no antibiotic treatment, as well as one nontuberculous mycobacteria antibiotic regimen compared to another nontuberculous mycobacteria antibiotic regimen, in individuals with cystic fibrosis. DATA COLLECTION AND ANALYSIS: Data were not collected because in the one trial identified by the search, data specific to individuals with cystic fibrosis could not be obtained from the pharmaceutical company. MAIN RESULTS One completed trial was identified by the searches, but data specific to individuals with cystic fibrosis could not be obtained from the pharmaceutical company. AUTHORS' CONCLUSIONS This review did not find any evidence for the effectiveness of different antimicrobial treatment for nontuberculous mycobacteria lung disease in people with cystic fibrosis. Until such evidence becomes available, it is reasonable for clinicians to follow published clinical practice guidelines for the diagnosis and treatment of nodular or bronchiectatic pulmonary disease due to Mycobacterium avium complex or Mycobacterium abscessus in patients with cystic fibrosis.
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Affiliation(s)
- Valerie Waters
- Department of Pediatrics, Division of Infectious Diseases, Hospital for Sick Children, Toronto, Canada
| | - Felix Ratjen
- Department of Pediatrics, The Hospital for Sick Children, Toronto, Canada
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Kavaliunaite E, Harris KA, Aurora P, Dixon G, Shingadia D, Muthialu N, Spencer H. Outcome according to subspecies following lung transplantation in cystic fibrosis pediatric patients infected with Mycobacterium abscessus. Transpl Infect Dis 2020; 22:e13274. [PMID: 32129923 DOI: 10.1111/tid.13274] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/23/2020] [Accepted: 02/24/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Mycobacterium abscessus infection has been associated with variable outcomes following lung transplantation. M abscessus comprises three subspecies (M abscessus subsp abscessus, M abscessus subsp massiliense, and M abscessus subsp bolletii). We investigated whether lung transplantation outcome in cystic fibrosis (CF) patients in a single center was related to the M abscessus subspecies and genetic cluster. METHODS CF patients with chronic M abscessus infection transplanted at Great Ormond Street Hospital between 2004 and 2017 were retrospectively examined. All M abscessus isolates were identified to subspecies level by polymerase chain reaction and sequencing. Genetic cluster was determined by variable number tandem repeat profiling and whole-genome sequencing (WGS), and sequence type inferred from WGS. RESULTS Thirteen patients with chronic M abscessus infection underwent heart/lung or lung transplantation. Subspecies identification showed n = 1 with M abscessus bolletii, n = 5 with M abscessus massiliense, and n = 7 with M abscessus abscessus infection. Eight (62%) patients (one with M abscessus massiliense and seven with M abscessus abscessus) died post-lung transplant. The patient with M abscessus bolletii and three patients with M abscessus massiliense did well post-transplant. One patient with M abscessus massiliense is receiving ongoing treatment. CONCLUSIONS Dramatically worse outcomes are observed in patients infected with M abscessus subspecies abscessus, the majority of whom were infected with ST-1 and ST-26 strains. Patients infected with other M abcsessus strains can have acceptable outcomes.
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Affiliation(s)
- Ema Kavaliunaite
- Department of Cardiothoracic Transplantation, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Kathryn A Harris
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Paul Aurora
- Department of Cardiothoracic Transplantation, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Garth Dixon
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Delane Shingadia
- Department of Infectious Diseases, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Nagarajan Muthialu
- Department of Cardiothoracic Transplantation, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Helen Spencer
- Department of Cardiothoracic Transplantation, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
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Xiao G, Zhang S, Liang Z, Li G, Fang M, Liu Y, Zhang J, Ou M, He X, Zhang T, Zeng C, Liu L, Zhang G. Identification of Mycobacterium abscessus species and subspecies using the Cas12a/sgRNA-based nucleic acid detection platform. Eur J Clin Microbiol Infect Dis 2020; 39:551-558. [PMID: 31776874 DOI: 10.1007/s10096-019-03757-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/28/2019] [Indexed: 12/26/2022]
Abstract
The rapidly growing mycobacterium Mycobacterium abscessus is a clinically important organism causing pulmonary and skin diseases. The M. abscessus complex is comprised of three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii. Here, we aimed to develop a Cas12a/sgRNA-based nucleic acid detection platform to identify M. abscessus species and subspecies. By designing specific sgRNA probes targeting rpoB and erm(41), we demonstrated that M. abscessus could be differentiated from other major mycobacterial species and identified at the subspecies level. Using this platform, a total of 38 clinical M. abscessus isolates were identified, 18 as M. abscessus subsp. abscessus and 20 as M. abscessus subsp. massiliense. We concluded that the Cas12a/sgRNA-based nucleic acid detection platform provides an easy-to-use, quick, and cost-effective approach for identification of M. abscessus species and subspecies.
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Affiliation(s)
- Guohui Xiao
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, 510530, China
| | - Su Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Zhihang Liang
- School of Basic Medical Sciences, Guangdong Medical University, Dongguan, 524023, China
| | - Guanqiang Li
- Department of Laboratory Medicine, Shenzhen Longgang People's Hospital, The Chinese University of Hong Kong, Shenzhen, 518172, China
| | - Mutong Fang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Yaya Liu
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Juanjuan Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Min Ou
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Xing He
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, 510530, China
| | - Changchun Zeng
- Department of Laboratory Medicine, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen, 518110, China
| | - Lei Liu
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China.
- School of Basic Medical Sciences, Guangdong Medical University, Dongguan, 524023, China.
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Bastian I, Shephard L, Lumb R. Revised guidelines for Australian laboratories performing mycobacteriology testing. ACTA ACUST UNITED AC 2020; 44. [PMID: 31940451 DOI: 10.33321/cdi.2020.44.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/27/2021] [Indexed: 11/20/2022]
Abstract
Mycobacteriology laboratories play a key role in tuberculosis (TB) control by providing phenotypic and molecular diagnostics, by performing molecular typing to aid contact tracing, and by supporting research and similar laboratories in Australia's neighbouring countries where TB is prevalent. The National Tuberculosis Advisory Committee (NTAC) published a set of laboratory guidelines in 2006 aiming to document the infrastructure, equipment, staffing and work practices required for safe high-quality work in Australian mycobacteriology laboratories. These revised guidelines have the same aims and have been through a similar extensive consultative peer-review process involving the Mycobacterium Reference Laboratory (MRL) network, the Mycobacterium Special Interest Group (SIG) of the Australian Society for Microbiology (ASM), and other relevant national bodies. This revised document contains several significant changes reflecting the publication of new biosafety guidelines and tuberculosis standards by various national and international organisations, technology developments - such as the MPT64-based immunochromatographic tests (ICTs) and the Xpert MTB/RIF assay, and updated work practices in mycobacteriology laboratories. The biosafety recommendations affirm the latest Australian/New Zealand Standard 2243.3: 2010 and promote a biorisk assessment approach that, in addition to the risk categorisation of the organism, also considers the characteristics of the procedure being performed. Using this biorisk assessment approach, limited manipulations, such as Ziehl-Neelsen (ZN) microscopy, MPT64 ICTs, and culture inactivation/DNA extraction for molecular testing, may be performed on a positive TB culture in a PC2 laboratory with additional features and work practices. Other significant changes include recommendations on the integration of MPT64 ICTs and novel molecular tests into TB laboratory workflows to provide rapid accurate results that improve the care of TB patients. This revised document supersedes the original 2006 publication. NTAC will periodically review these guidelines and provide updates as new laboratory technologies become available.
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Affiliation(s)
- Ivan Bastian
- SA Pathology, PO Box 14, Rundle Mall, Adelaide SA 5000
| | - Lisa Shephard
- SA Pathology, PO Box 14, Rundle Mall, Adelaide SA 5000
| | - Richard Lumb
- SA Pathology, PO Box 14, Rundle Mall, Adelaide SA 5000
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Kim BJ, Kim GN, Kim BR, Shim TS, Kook YH, Kim BJ. New Mycobacteroides abscessus subsp. massiliense strains with recombinant hsp65 gene laterally transferred from Mycobacteroides abscessus subsp. abscessus: Potential for misidentification of M. abscessus strains with the hsp65-based method. PLoS One 2019; 14:e0220312. [PMID: 31518354 PMCID: PMC6743754 DOI: 10.1371/journal.pone.0220312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 07/13/2019] [Indexed: 12/05/2022] Open
Abstract
It has been reported that lateral gene transfer (LGT) events among Mycobacteroides abscessus strains are prevalent. The hsp65 gene, a chronometer gene for bacterial phylogenetic analysis, is resistant to LGT events, particularly among mycobacterial strains, rendering the hsp65-targeting method the most widely used method for mycobacterial detection. To determine the prevalence of M. abscessus strains that are subject to hsp65 LGT, we applied rpoB typing to 100 clinically isolated Korean strains of M. abscessus that had been identified by hsp65 sequence analysis. The analysis indicated the presence of 2 rough strains, showing a discrepancy between the 2 typing methods. MLST analysis based on the partial sequencing of seven housekeeping genes, erm(41) PCR and further hsp65 PCR-restriction enzyme and polymorphism analysis (PRA) were conducted to identify the two strains. The MLST results showed that the two strains belong to M. abscessus subsp. massiliense and not to M. abscessus subsp. abscessus, as indicated by the rpoB-based analysis, suggesting that their hsp65 genes are subject to LGT from M. abscessus subsp. abscessus. Further analysis of these strains using the hsp65 PRA method indicated that these strains possess a PRA pattern identical to that of M. abscessus subsp. abscessus and distinct from that of M. abscessus subsp. massiliense. In conclusion, we identified two M. abscessus subsp. massiliense rough strains from Korean patients with hsp65 genes that might be laterally transferred from M. abscessus subsp. abscessus. To the best of our knowledge, this is the first demonstration of possible LGT events associated with the hsp65 gene in mycobacteria. Our results also suggest that there is the potential for misidentification when the hsp65-based protocol is used for mycobacterial identification.
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Affiliation(s)
- Byoung-Jun Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Ga-Na Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Bo-Ram Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Tae-Sun Shim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Yoon-Hoh Kook
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea
- * E-mail:
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Stephenson D, Perry A, Appleby MR, Lee D, Davison J, Johnston A, Jones AL, Nelson A, Bourke SJ, Thomas MF, De Soyza A, Lordan JL, Lumb J, Robb AE, Samuel JR, Walton KE, Perry JD. An evaluation of methods for the isolation of nontuberculous mycobacteria from patients with cystic fibrosis, bronchiectasis and patients assessed for lung transplantation. BMC Pulm Med 2019; 19:19. [PMID: 30665395 PMCID: PMC6341538 DOI: 10.1186/s12890-019-0781-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 01/07/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND RGM medium is an agar-based, selective culture medium designed for the isolation of nontuberculous mycobacteria (NTM) from the sputum of patients with cystic fibrosis (CF). We evaluated RGM medium for the detection of NTM in patients with CF (405 samples), bronchiectasis (323 samples) and other lung diseases necessitating lung transplantation (274 samples). METHODS In total, 1002 respiratory samples from 676 patients were included in the study. Direct culture on RGM medium, with incubation at two temperatures (30 °C and 37 °C), was compared with conventional culture of decontaminated samples for acid-fast bacilli (AFB) using both a solid medium (Löwenstein-Jensen medium) and a liquid medium (the Mycobacterial Growth Indicator Tube; MGIT). RESULTS For all three patient groups, significantly more isolates of NTM were recovered using RGM medium incubated at 30 °C than by any other method (sensitivity: 94.6% vs. 22.4% for conventional AFB culture; P < 0.0001). Significantly more isolates of Mycobacterium abscessus complex were isolated on RGM at 30 °C than by AFB culture (sensitivity: 96.1% vs. 58.8%; P < 0.0001). The recovery of Mycobacterium avium complex was also greater using RGM medium at 30 °C compared to AFB culture (sensitivity: 83% vs. 70.2%), although this difference was not statistically significant and a combination of methods was necessary for optimal recovery (P = 0.21). CONCLUSIONS In the largest study of RGM medium to date, we reaffirm its utility for isolation of NTM from patients with CF. Furthermore; we show that it also provides an effective tool for culture of respiratory samples from patients with bronchiectasis and other lung diseases.
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Affiliation(s)
- D Stephenson
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, UK.,Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - A Perry
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, UK
| | - M R Appleby
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, UK
| | - D Lee
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, UK
| | - J Davison
- Adult Bronchiectasis Service, Freeman Hospital, Newcastle upon Tyne, UK
| | - A Johnston
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - A L Jones
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - A Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - S J Bourke
- Adult Cystic Fibrosis Centre, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - M F Thomas
- Paediatric Respiratory Unit, Great North Children's Hospital, Newcastle upon Tyne, UK
| | - A De Soyza
- Adult Bronchiectasis Service, Freeman Hospital, Newcastle upon Tyne, UK
| | - J L Lordan
- Cardiopulmonary Transplant Service, Freeman Hospital, Newcastle upon Tyne, UK
| | - J Lumb
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, UK
| | - A E Robb
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, UK
| | - J R Samuel
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, UK
| | - K E Walton
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, UK
| | - J D Perry
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, UK. .,Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK.
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10
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Sabin AP, Ferrieri P, Kline S. Mycobacterium abscessus Complex Infections in Children: A Review. Curr Infect Dis Rep 2017; 19:46. [PMID: 28983867 PMCID: PMC5821427 DOI: 10.1007/s11908-017-0597-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW Infections in children with Mycobacterium abscessus complex represent a particular challenge for clinicians. Increasing incidence of these infections worldwide has necessitated focused attention to improve both diagnostic as well as treatment modalities. Published medical literature was reviewed, with emphasis on material published in the past 5 years. RECENT FINDINGS Increasing availability of new diagnostic tools, such as matrix-assisted laser desorption ionization-time of flight mass spectrometry and custom PCRs, has provided unique insights into the subspecies within the complex and improved diagnostic certainty. Microbiological review of all recent isolates at the University of Minnesota Medical Center was also conducted, with description of the antimicrobial sensitivity patterns encountered in our center, and compared with those published from other centers in the recent literature. A discussion of conventional antimicrobial treatment regimens, alongside detailed description of the relevant antimicrobials, is derived from recent publications. Antimicrobial therapy, combined with surgical intervention in some cases, remains the mainstay of pediatric care. Ongoing questions remain regarding the transmission mechanics, immunologic vulnerabilities exploited by these organisms in the host, and the optimal antimicrobial regimens necessary to enable a reliable cure. Updated treatment guidelines based on focused clinical studies in children and accounting especially for the immunocompromised children at greatest risk are very much needed.
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Affiliation(s)
- Arick P Sabin
- Department of Medicine, Division of Infectious Diseases and International Medicine, University of Minnesota Medical School, 420 Delaware Street SE, MMC # 250, Minneapolis, MN, 55455, USA
| | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology and Department of Pediatrics, Division of Infectious Diseases, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Susan Kline
- Department of Medicine, Division of Infectious Diseases and International Medicine, University of Minnesota Medical School, 420 Delaware Street SE, MMC # 250, Minneapolis, MN, 55455, USA.
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11
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Kim BJ, Kim GN, Kim BR, Shim TS, Kook YH, Kim BJ. Phylogenetic analysis of Mycobacterium massiliense strains having recombinant rpoB gene laterally transferred from Mycobacterium abscessus. PLoS One 2017; 12:e0179237. [PMID: 28604829 PMCID: PMC5467896 DOI: 10.1371/journal.pone.0179237] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/25/2017] [Indexed: 11/18/2022] Open
Abstract
Recent multi locus sequence typing (MLST) and genome based studies indicate that lateral gene transfer (LGT) events in the rpoB gene are prevalent between Mycobacterium abscessus complex strains. To check the prevalence of the M. massiliense strains subject to rpoB LGT (Rec-mas), we applied rpoB typing (711 bp) to 106 Korean strains of M. massiliense infection that had already been identified by hsp65 sequence analysis (603 bp). The analysis indicated 6 smooth strains in M. massiliense Type I (10.0%, 6/60) genotypes but no strains in M. massiliense Type II genotypes (0%, 0/46), showing a discrepancy between the 2 typing methods. Further MLST analysis based on the partial sequencing of seven housekeeping genes, argH, cya, glpK, gnd, murC, pta and purH, as well as erm(41) PCR proved that these 6 Rec-mas strains consisted of two distinct genotypes belonging to M. massiliense and not M. abscessus. The complete rpoB sequencing analysis showed that these 6 Rec-mas strains have an identical hybrid rpoB gene, of which a 478 bp partial rpoB fragment may be laterally transferred from M. abscessus. Notably, five of the 6 Rec-mas strains showed complete identical sequences in a total of nine genes, including the seven MLST genes, hsp65, and rpoB, suggesting their clonal propagation in South Korea. In conclusion, we identified 6 M. massiliense smooth strains of 2 phylogenetically distinct genotypes with a specific hybrid rpoB gene laterally transferred from M. abscessus from Korean patients. Their clinical relevance and bacteriological traits remain to be elucidated.
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Affiliation(s)
- Byoung-Jun Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Ga-Na Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Bo-Ram Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Tae-Sun Shim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Yoon-Hoh Kook
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea
- * E-mail:
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Al-Momani H, Perry A, Jones R, Bourke S, Doe S, Perry J, Anderson A, Forrest T, Forrest I, Griffin M, Brodlie M, Pearson J, Ward C. Nontuberculous mycobacteria in gastrostomy fed patients with cystic fibrosis. Sci Rep 2017; 7:46546. [PMID: 28436419 PMCID: PMC5402269 DOI: 10.1038/srep46546] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 03/22/2017] [Indexed: 11/09/2022] Open
Abstract
Multi-drug resistant Mycobacterium abscessus complex (MABSC) is a form of Nontuberculous mycobacteria (NTM) of special, international concern in Cystic Fibrosis (CF). We hypothesised that gastric juice and percutaneous endoscopic gastrostomy (PEG) feeding devices might yield MABSC isolates. Gastric juice and sputa from sixteen adult PEG fed CF patients and five replaced PEG tubes were studied. Bacterial and fungal isolates were cultured. Mycobacterium were identified by rpoB, sodA and hsp65 gene sequencing and strain typed using variable number tandem repeat. Bacteria and/or fungi grew from all gastric juice, sputa and PEG samples. MABSC were detected in 7 patients. Five had MABSC in their sputum. Two had an identical MABSC strain in their sputum and gastric juice and one had the same strain isolated from their PEG tube and sputum. Two patients who were sputum sample negative had MABSC isolated in their gastric juice or PEG tube. MABSC were therefore identified for the first time from a gastric sample in a minority of patients. We conclude that gastric juice and PEG-tubes may be a potential source of MABSC isolates in CF patients, and these findings warrant further study.
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Affiliation(s)
- H Al-Momani
- Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - A Perry
- Department of Microbiology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, UK
| | - R Jones
- Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - S Bourke
- Adult Cystic Fibrosis Centre and Northern Oesophago-Gastric Unit Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, UK
| | - S Doe
- Adult Cystic Fibrosis Centre and Northern Oesophago-Gastric Unit Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, UK
| | - J Perry
- Department of Microbiology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, UK
| | - A Anderson
- Adult Cystic Fibrosis Centre and Northern Oesophago-Gastric Unit Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, UK
| | - T Forrest
- Adult Cystic Fibrosis Centre and Northern Oesophago-Gastric Unit Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, UK
| | - I Forrest
- Adult Cystic Fibrosis Centre and Northern Oesophago-Gastric Unit Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, UK
| | - M Griffin
- Adult Cystic Fibrosis Centre and Northern Oesophago-Gastric Unit Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, UK
| | - M Brodlie
- Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - J Pearson
- Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - C Ward
- Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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13
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Waters V, Ratjen F. Antibiotic treatment for nontuberculous mycobacteria lung infection in people with cystic fibrosis. Cochrane Database Syst Rev 2016; 12:CD010004. [PMID: 28000919 PMCID: PMC6464024 DOI: 10.1002/14651858.cd010004.pub4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Nontuberculous mycobacteria are mycobacteria, other than those in the Mycobacterium tuberculosis complex, and are commonly found in the environment. Nontuberculous mycobacteria species (most commonly Mycobacterium avium complex and Mycobacterium abscessus) are isolated from the respiratory tract of approximately 5% to 40% of individuals with cystic fibrosis; they can cause lung disease in people with cystic fibrosis leading to more a rapid decline in lung function and even death in certain circumstances. Although there are guidelines for the antimicrobial treatment of nontuberculous mycobacteria lung disease, these recommendations are not specific for people with cystic fibrosis and it is not clear which antibiotic regimen may be the most effective in the treatment of these individuals. This is an update of a previous review. OBJECTIVES The objective of our review was to compare antibiotic treatment to no antibiotic treatment, or to compare different combinations of antibiotic treatment, for nontuberculous mycobacteria lung infections in people with cystic fibrosis. The primary objective was to assess the effect of treatment on lung function and pulmonary exacerbations and to quantify adverse events. The secondary objectives were to assess treatment effects on the amount of bacteria in the sputum, quality of life, mortality, nutritional parameters, hospitalizations and use of oral antibiotics. SEARCH METHODS We searched the Cochrane Cystic Fibrosis Trials Register, compiled from electronic database searches and hand searching of journals and conference abstract books. Date of last search: 02 September 2016.We also searched a register of ongoing trials and the reference lists of relevant articles and reviews. Date of last search: 03 November 2016. SELECTION CRITERIA Any randomized controlled trials comparing nontuberculous mycobacteria antibiotics to no antibiotic treatment, as well as one nontuberculous mycobacteria antibiotic regimen compared to another nontuberculous mycobacteria antibiotic regimen, in individuals with cystic fibrosis. DATA COLLECTION AND ANALYSIS: Data were not collected because in the one trial identified by the search, data specific to individuals with cystic fibrosis could not be obtained from the pharmaceutical company. MAIN RESULTS One completed trial was identified by the searches, but data specific to individuals with cystic fibrosis could not be obtained from the pharmaceutical company. AUTHORS' CONCLUSIONS This review did not find any evidence for the effectiveness of different antimicrobial treatment for nontuberculous mycobacteria lung disease in people with cystic fibrosis. Until such evidence becomes available, it is reasonable for clinicians to follow published clinical practice guidelines for the diagnosis and treatment of nodular or bronchiectatic pulmonary disease due to Mycobacterium avium complex or Mycobacterium abscessus in patients with cystic fibrosis.
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Affiliation(s)
- Valerie Waters
- Hospital for Sick ChildrenDepartment of Pediatrics, Division of Infectious Diseases555 University AvenueTorontoONCanadaM5G 1X8
| | - Felix Ratjen
- The Hospital for Sick ChildrenDepartment of Pediatrics555 University AvenueTorontoONCanadaM5G 1XB
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14
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Al-Momani H, Perry A, Stewart CJ, Jones R, Krishnan A, Robertson AG, Bourke S, Doe S, Cummings SP, Anderson A, Forrest T, Griffin SM, Brodlie M, Pearson J, Ward C. Microbiological profiles of sputum and gastric juice aspirates in Cystic Fibrosis patients. Sci Rep 2016; 6:26985. [PMID: 27245316 PMCID: PMC4887896 DOI: 10.1038/srep26985] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/11/2016] [Indexed: 02/08/2023] Open
Abstract
Gastro-Oesophageal Reflux (GOR) is a key problem in Cystic Fibrosis (CF), but the relationship between lung and gastric microbiomes is not well understood. We hypothesised that CF gastric and lung microbiomes are related. Gastric and sputum cultures were obtained from fifteen CF patients receiving percutaneous endoscopic gastrostomy feeding. Non-CF gastric juice data was obtained through endoscopy from 14 patients without lung disease. Bacterial and fungal isolates were identified by culture. Molecular bacterial profiling used next generation sequencing (NGS) of the 16S rRNA gene. Cultures grew bacteria and/or fungi in all CF gastric juice and sputa and in 9/14 non-CF gastric juices. Pseudomonas aeruginosa(Pa) was present in CF sputum in 11 patients, 4 had identical Pa strains in the stomach. NGS data from non-CF gastric juice samples were significantly more diverse compared to CF samples. NGS showed CF gastric juice had markedly lower abundance of normal gut bacteria; Bacteroides and Faecalibacterium, but increased Pseudomonas compared with non-CF. Multivariate partial least squares discriminant analysis demonstrated similar bacterial profiles of CF sputum and gastric juice samples, which were distinct from non-CF gastric juice. We provide novel evidence suggesting the existence of an aerodigestive microbiome in CF, which may have clinical relevance.
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Affiliation(s)
- H Al-Momani
- Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne. NE2 4HH, UK
| | - A Perry
- Department of Microbiology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK
| | - C J Stewart
- Northumbria University, Ellison Place, Newcastle-upon-Tyne NE1 8ST, UK
| | - R Jones
- Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne. NE2 4HH, UK
| | - A Krishnan
- Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne. NE2 4HH, UK
| | - A G Robertson
- Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne. NE2 4HH, UK
| | - S Bourke
- Adult Cystic Fibrosis Centre and Northern Oesophago-Gastric Unit, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK
| | - S Doe
- Adult Cystic Fibrosis Centre and Northern Oesophago-Gastric Unit, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK
| | - S P Cummings
- School of Science and Engineering, Teesside University, Middlesbrough, TS1 3BA, UK
| | - A Anderson
- Adult Cystic Fibrosis Centre and Northern Oesophago-Gastric Unit, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK
| | - T Forrest
- Adult Cystic Fibrosis Centre and Northern Oesophago-Gastric Unit, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK
| | - S M Griffin
- Adult Cystic Fibrosis Centre and Northern Oesophago-Gastric Unit, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK
| | - M Brodlie
- Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne. NE2 4HH, UK
| | - J Pearson
- Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne. NE2 4HH, UK
| | - C Ward
- Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne. NE2 4HH, UK
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15
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Evaluation of Various Culture Media for Detection of Rapidly Growing Mycobacteria from Patients with Cystic Fibrosis. J Clin Microbiol 2016; 54:1797-1803. [PMID: 27098962 DOI: 10.1128/jcm.00471-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/16/2016] [Indexed: 11/20/2022] Open
Abstract
Isolation of nontuberculous mycobacteria (NTM) from the sputum of patients with cystic fibrosis (CF) is challenging due to overgrowth by rapidly growing species that colonize the lungs of patients with CF. Extended incubation on Burkholderia cepacia selective agar (BCSA) has been recommended as an expedient culture method for the isolation of rapidly growing NTM in this setting. The aim of this study was to assess five selective media designed for the isolation of Burkholderia cepacia complex, along with two media designed for the isolation of mycobacteria (rapidly growing mycobacteria [RGM] medium and Middlebrook 7H11 agar), for their abilities to isolate NTM. All seven media were challenged with 147 isolates of rapidly growing mycobacteria and 185 isolates belonging to other species. RGM medium was then compared with the most selective brand of BCSA for the isolation of NTM from 224 sputum samples from patients with CF. Different agars designed for the isolation of B. cepacia complex varied considerably in their inhibition of other bacteria and fungi. RGM medium supported the growth of all isolates of mycobacteria and was more selective than any other medium. NTM were recovered from 17 of 224 sputum samples using RGM medium, compared with only 7 samples using the most selective brand of BCSA (P = 0.023). RGM medium offers a superior option, compared to other selective agars, for the isolation of rapidly growing mycobacteria from the sputum of patients with CF. Furthermore, the convenience of using RGM medium enables routine screening for rapidly growing NTM in all submitted sputum samples from patients with CF.
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16
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Inducible and Acquired Clarithromycin Resistance in the Mycobacterium abscessus Complex. PLoS One 2015; 10:e0140166. [PMID: 26448181 PMCID: PMC4598034 DOI: 10.1371/journal.pone.0140166] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 08/17/2015] [Indexed: 11/19/2022] Open
Abstract
PURPOSE Clarithromycin was considered the cornerstone for the treatment of Mycobacterium abscessus complex infections. Genetic resistance mechanisms have been described and many experts propose amikacin as an alternative. Nevertheless, clarithromycin has several advantages; therefore, it is necessary to identify the non-functional erm(41) allele to determine the most suitable treatment. The aims of this study were to characterize the molecular mechanisms of clarithromycin resistance in a collection of Mycobacterium abscessus complex isolates and to verify the relationship between these mechanisms and the antibiogram. MATERIALS AND METHODS Clinical isolates of M. abscessus complex (n = 22) from 16 patients were identified using four housekeeping genes (rpoB, secA1, sodA and hsp65), and their genetic resistance was characterized by studying erm(41) and rrl genes. Nine strains were recovered from the clinical isolates and subjected to E-test and microdilution clarithromycin susceptibility tests, with readings at 3, 7 and 14 days. RESULTS We classified 11/16 (68.8%) M. abscessus subsp. abscessus, 4/16 (25.0%) M. abscessus subsp. bolletii, and 1/16 (6.3%) M. abscessus subsp. massiliense. T28 erm(41) allele was observed in 8 Mycobacterium abscessus subps. abscessus and 3 Mycobacterium abscessus subsp. bolletii. One strain of M. abscessus subsp. bolletii had an erm(41) gene truncated and was susceptible to clarithromycin. No mutations were observed in rrl gene first isolates. In three patients, follow-up of initial rrl wild-type strains showed acquired resistance. CONCLUSIONS Most clinical isolates of M. abscessus complex had inducible resistance to clarithromycin and total absence of constitutive resistance. Our findings showed that the acquisition of resistance mutations in rrl gene was associated with functional and non-functional erm(41) gene. Caution is needed when using erm(41) sequencing alone to identify M. abscessus subspecies. This study reports an acquired mutation at position 2057 of rrl gene, conferring medium-low clarithromycin constitutive resistance.
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17
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New Real-Time PCR Assays for Detection of Inducible and Acquired Clarithromycin Resistance in the Mycobacterium abscessus Group. J Clin Microbiol 2015; 53:3430-7. [PMID: 26269619 DOI: 10.1128/jcm.01714-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/01/2015] [Indexed: 11/20/2022] Open
Abstract
Members of the Mycobacterium abscessus group (MAG) cause lung, soft tissue, and disseminated infections. The oral macrolides clarithromycin and azithromycin are commonly used for treatment. MAG can display clarithromycin resistance through the inducible erm(41) gene or via acquired mutations in the rrl (23S rRNA) gene. Strains harboring a truncation or a T28C substitution in erm(41) lose the inducible resistance trait. Phenotypic detection of clarithromycin resistance requires extended incubation (14 days), highlighting the need for faster methods to detect resistance. Two real-time PCR-based assays were developed to assess inducible and acquired clarithromycin resistance and tested on a total of 90 clinical and reference strains. A SYBR green assay was designed to distinguish between a full-length and truncated erm(41) gene by temperature shift in melting curve analysis. Single nucleotide polymorphism (SNP) allele discrimination assays were developed to distinguish T or C at position 28 of erm(41) and 23S rRNA rrl gene mutations at position 2058 and/or 2059. Truncated and full-size erm(41) genes were detected in 21/90 and 69/90 strains, respectively, with 64/69 displaying T at nucleotide position 28 and 5/69 containing C at that position. Fifteen isolates showed rrl mutations conferring clarithromycin resistance, including A2058G (11 isolates), A2058C (3 isolates), and A2059G (1 isolate). Targeted sequencing and phenotypic assessment of resistance concurred with molecular assay results. Interestingly, we also noted cooccurring strains harboring an active erm(41), inactive erm(41), and/or acquired mutational resistance, as well as slowly growing MAG strains and also strains displaying an inducible resistance phenotype within 5 days, long before the recommended 14-day extended incubation.
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18
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O'Driscoll C, Konjek J, Heym B, Fitzgibbon MM, Plant BJ, Ní Chróinín M, Mullane D, Lynch-Healy M, Corcoran GD, Schaffer K, Rogers TR, Prentice MB. Molecular epidemiology of Mycobacterium abscessus complex isolates in Ireland. J Cyst Fibros 2015; 15:179-85. [PMID: 26072272 DOI: 10.1016/j.jcf.2015.05.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 05/17/2015] [Accepted: 05/17/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND The Mycobacterium abscessus complex are the rapidly growing mycobacteria (RGM) most commonly causing lung disease, especially in cystic fibrosis (CF) patients. Ireland has the world's highest CF incidence. The molecular epidemiology of M. abscessus complex in Ireland is unreported. METHODS We performed rpoB gene sequencing and multi-locus sequence typing (MLST) on M. abscessus complex strains isolated from thirty-six patients in 2006-2012 (eighteen known CF patients). RESULTS Twenty-eight strains (78%) were M. abscessus subsp. abscessus, eight M. abscessus subsp. massiliense, none were M. abscessus subsp. bolletii. Sequence type 1 (ST1) and ST26 (M. abscessus subsp. abscessus) were commonest. Seven M. abscessus subsp. abscessus STs (25%) were novel (two with novel alleles). Seven M. abscessus subsp. massiliense STs were previously reported (88%), including two ST23, the globally successful clone. In 2012, of 552 CF patients screened, eleven were infected with M. abscessus complex strains (2%). CONCLUSIONS The most prevalent M. abscessus subsp. abscessus and M. abscessus subsp. massiliense strains in Ireland belong to widely-distributed STs, but there is evidence of high M. abscessus subsp. abscessus diversity.
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Affiliation(s)
- C O'Driscoll
- Department of Microbiology, Cork University Hospital, Cork, Ireland
| | - J Konjek
- EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Biévre, 78180 Montigny-le-Bretonneux, France
| | - B Heym
- EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Biévre, 78180 Montigny-le-Bretonneux, France; APHP Hôpitaux Universitaires Paris Ile-de-France Ouest, Service de Microbiologie, Hôpital Ambroise Paré, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France
| | - M M Fitzgibbon
- Irish Mycobacteria Reference Laboratory, St. James Hospital, Dublin, Ireland
| | - B J Plant
- Cork Adult Cystic Fibrosis Centre, University College Cork, Cork University Hospital, Wilton, Cork, Ireland
| | - M Ní Chróinín
- Department of Paediatrics, Cork University Hospital, Wilton, Cork, Ireland
| | - D Mullane
- Department of Paediatrics, Cork University Hospital, Wilton, Cork, Ireland
| | - M Lynch-Healy
- Department of Microbiology, Cork University Hospital, Cork, Ireland
| | - G D Corcoran
- Department of Microbiology, Cork University Hospital, Cork, Ireland
| | - K Schaffer
- Department of Microbiology, St. Vincent's University Hospital, Dublin, Ireland
| | - T R Rogers
- Irish Mycobacteria Reference Laboratory, St. James Hospital, Dublin, Ireland
| | - M B Prentice
- Department of Microbiology, Cork University Hospital, Cork, Ireland; Department of Pathology, University College Cork, Cork, Ireland; Department of Microbiology, University College Cork, Cork, Ireland.
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19
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Preece CL, Perry A, Gray B, Kenna DT, Jones AL, Cummings SP, Robb A, Thomas MF, Brodlie M, O'Brien CJ, Bourke SJ, Perry JD. A novel culture medium for isolation of rapidly-growing mycobacteria from the sputum of patients with cystic fibrosis. J Cyst Fibros 2015; 15:186-91. [PMID: 26002312 DOI: 10.1016/j.jcf.2015.05.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/01/2015] [Accepted: 05/02/2015] [Indexed: 12/22/2022]
Abstract
BACKGROUND Isolation of mycobacteria from the sputum of patients with cystic fibrosis (CF) is challenging due to the overgrowth of cultures by other bacteria and fungi. In this setting, Burkholderia cepacia selective agar (BCSA) has been recommended as a convenient and effective culture medium for the isolation of rapidly-growing, non-tuberculous mycobacteria (NTM). A novel selective culture medium (RGM medium) was evaluated for the isolation of rapidly-growing NTM from the sputum of children and adults with CF. METHODS A total of 118 isolates of rapidly-growing mycobacteria and 98 other bacteria and fungi were inoculated onto RGM medium. These were assessed for growth at 30°C over a seven day period. A total of 502 consecutive sputum samples were collected from 210 patients with CF. Each sample was homogenized and cultured onto RGM medium and also onto BCSA. Cultures were incubated for 10days at 30°C. RESULTS Of 118 isolates of mycobacteria all but one grew well on RGM medium, whereas 94% of other bacteria and fungi were inhibited. A total of 55 sputum samples (from 33 distinct patients) yielded NTM using a combination of both RGM and BCSA (prevalence: 15.7%). NTM were recovered from 54 sputum samples using RGM medium compared with only 17 samples using BCSA (sensitivity 98% vs. 31%; P≤0.0001). A total of 419 isolates of non-mycobacteria were recovered from sputum samples on BCSA compared with 46 on RGM medium. CONCLUSIONS RGM medium offers a simple and effective culture method for the isolation of rapidly-growing mycobacteria from sputum samples from patients with CF without decontamination of samples. RGM medium allows for the systematic screening of all sputum samples routinely referred for culture from patients with CF.
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Affiliation(s)
- Clair L Preece
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK; Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Audrey Perry
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK
| | - Bethany Gray
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK
| | - Dervla T Kenna
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, London, UK
| | - Amanda L Jones
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Stephen P Cummings
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Ali Robb
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK
| | - Matthew F Thomas
- Paediatric Respiratory Unit, Great North Children's Hospital, Newcastle upon Tyne NE1 4LP, UK
| | - Malcolm Brodlie
- Paediatric Respiratory Unit, Great North Children's Hospital, Newcastle upon Tyne NE1 4LP, UK
| | - Christopher J O'Brien
- Paediatric Respiratory Unit, Great North Children's Hospital, Newcastle upon Tyne NE1 4LP, UK
| | - Stephen J Bourke
- Adult Cystic Fibrosis Centre, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK
| | - John D Perry
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK; Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK.
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20
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Syrmis MW, Pandey S, Tolson C, Carter R, Congdon J, Sloots T, Coulter C, Whiley D. Identification of Mycobacterium abscessus complex and M. abscessus subsp. massiliense culture isolates by real-time assays. J Med Microbiol 2015; 64:790-794. [PMID: 25976000 DOI: 10.1099/jmm.0.000085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Melanie W Syrmis
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Health Services, Queensland, Australia.,Queensland Children's Medical Research Institute, Queensland, Australia.,University of Queensland, Queensland, Australia
| | - Sushil Pandey
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland, Australia
| | - Carla Tolson
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland, Australia
| | - Robyn Carter
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland, Australia
| | - Jake Congdon
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland, Australia
| | - Theo Sloots
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Health Services, Queensland, Australia.,Queensland Children's Medical Research Institute, Queensland, Australia.,University of Queensland, Queensland, Australia
| | - Christopher Coulter
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland, Australia
| | - David Whiley
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Health Services, Queensland, Australia.,Queensland Children's Medical Research Institute, Queensland, Australia.,University of Queensland, Queensland, Australia
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21
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Steindor M, Nkwouano V, Mayatepek E, Mackenzie CR, Schramm D, Jacobsen M. Rapid detection and immune characterization of Mycobacterium abscessus infection in cystic fibrosis patients. PLoS One 2015; 10:e0119737. [PMID: 25742660 PMCID: PMC4351040 DOI: 10.1371/journal.pone.0119737] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/15/2015] [Indexed: 11/18/2022] Open
Abstract
Cystic fibrosis patients are highly susceptible to infections with non-tuberculous mycobacteria. Especially Mycobacterium abscessus infections are common but reliable diagnosis is hampered by non-specific clinical symptoms and insensitive mycobacterial culture. In the present study we established novel methods for rapid detection and immune characterization of Mycobacterium abscessus infection in cystic fibrosis patients. We performed Mycobacterium abscessus specific DNA-strip- and quantitative PCR-based analyses of non-cultured sputum samples to detect and characterize Mycobacterium abscessus infections. Concomitantly in vitro T-cell reactivation with purified protein derivatives (PPDs) from different mycobacterial species was used to determine Mycobacterium abscessus specific T-cell cytokine expression of infected cystic fibrosis patients. Four of 35 cystic fibrosis patients (11.4%) were Mycobacterium abscessus culture positive and showed concordant DNA-strip-test results. Quantitative PCR revealed marked differences of mycobacterial burden between cystic fibrosis patients and during disease course. Tandem-repeat analysis classified distinct Mycobacterium abscessus strains of infected cystic fibrosis patients and excluded patient-to-patient transmission. Mycobacterium abscessus specific T-cells were detected in the blood of cystic fibrosis patients with confirmed chronic infection and a subgroup of patients without evidence of Mycobacterium abscessus infection. Comparison of cytokine expression and phenotypic markers revealed increased proportions of CD40L positive T-cells that lack Interleukin-2 expression as a marker for chronic Mycobacterium abscessus infections in cystic fibrosis patients. Direct sputum examination enabled rapid diagnosis and quantification of Mycobacterium abscessus in cystic fibrosis patients. T-cell in vitro reactivation and cytokine expression analyses may contribute to diagnosis of chronic Mycobacterium abscessus infection.
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Affiliation(s)
- Mathis Steindor
- Department of General Pediatrics, Neonatology, and Pediatric Cardiology, University Children’s Hospital, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Vanesa Nkwouano
- Department of General Pediatrics, Neonatology, and Pediatric Cardiology, University Children’s Hospital, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Ertan Mayatepek
- Department of General Pediatrics, Neonatology, and Pediatric Cardiology, University Children’s Hospital, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Colin R. Mackenzie
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Dirk Schramm
- Department of General Pediatrics, Neonatology, and Pediatric Cardiology, University Children’s Hospital, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Marc Jacobsen
- Department of General Pediatrics, Neonatology, and Pediatric Cardiology, University Children’s Hospital, Heinrich Heine University, 40225 Duesseldorf, Germany
- * E-mail:
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Waters V, Ratjen F. Antibiotic treatment for nontuberculous mycobacteria lung infection in people with cystic fibrosis. Cochrane Database Syst Rev 2014:CD010004. [PMID: 25470304 DOI: 10.1002/14651858.cd010004.pub3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Nontuberculous mycobacteria are mycobacteria, other than those in the Mycobacterium tuberculosis complex, and are commonly found in the environment. Nontuberculous mycobacteria species (most commonly Mycobacterium avium complex and Mycobacterium abscessus) are isolated from the respiratory tract of approximately 5% to 20% of individuals with cystic fibrosis; they can cause lung disease in people with cystic fibrosis leading to more a rapid decline in lung function and even death in certain circumstances. Although there are guidelines for the antimicrobial treatment of nontuberculous mycobacteria lung disease, these recommendations are not specific for people with cystic fibrosis and it is not clear which antibiotic regimen may be the most effective in the treatment of these patients. OBJECTIVES The objective of our review was to compare antibiotic treatment to no antibiotic treatment, or to compare different combinations of antibiotic treatment, for nontuberculous mycobacteria lung infections in people with cystic fibrosis. The primary objective was to assess the effect of treatment on lung function and pulmonary exacerbations and to quantify adverse events. The secondary objectives were to assess treatment effects on the amount of bacteria in the sputum, quality of life, mortality, nutritional parameters, hospitalizations and use of oral antibiotics. SEARCH METHODS We searched the Cochrane Cystic Fibrosis Trials Register, compiled from electronic database searches and hand searching of journals and conference abstract books. Date of last search: 13 November 2014.We also searched a register of ongoing trials and the reference lists of relevant articles and reviews. Date of last search: 24 September 2014. SELECTION CRITERIA Any randomized controlled trials comparing nontuberculous mycobacteria antibiotics to no antibiotic treatment, as well as one nontuberculous mycobacteria antibiotic regimen compared to another nontuberculous mycobacteria antibiotic regimen, in individuals with cystic fibrosis. DATA COLLECTION AND ANALYSIS Data were not collected because no completed trials were identified by the searches. MAIN RESULTS No completed trials were identified by the searches, but one ongoing trial was identified, which may be eligible for inclusion in this review when completed. AUTHORS' CONCLUSIONS This review did not find any evidence for the effectiveness of different antimicrobial treatment for nontuberculous mycobacteria lung disease in people with cystic fibrosis. Until such evidence becomes available, it is reasonable for clinicians to follow the American Thoracic Society guidelines for the diagnosis and treatment of nodular or bronchiectatic pulmonary disease due to Mycobacterium avium complex or Mycobacterium abscessus in patients with cystic fibrosis.
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Affiliation(s)
- Valerie Waters
- Department of Pediatrics, Division of Infectious Diseases, Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada.
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Brown-Elliott BA, Philley JV, Benwill JL, Wallace RJ. Current Opinions in the Treatment of Pulmonary Nontuberculous Mycobacteria in Non-Cystic Fibrosis Patients: Mycobacterium abscessus Group, Mycobacterium avium Complex, and Mycobacterium kansasii. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2014. [DOI: 10.1007/s40506-014-0032-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Harris KA, Underwood A, Kenna DTD, Brooks A, Kavaliunaite E, Kapatai G, Tewolde R, Aurora P, Dixon G. Whole-genome sequencing and epidemiological analysis do not provide evidence for cross-transmission of mycobacterium abscessus in a cohort of pediatric cystic fibrosis patients. Clin Infect Dis 2014; 60:1007-16. [PMID: 25452595 PMCID: PMC4357290 DOI: 10.1093/cid/ciu967] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
We have not been able to demonstrate cross-transmission of Mycobacterium abscessus within our hospital, except between siblings who had intense contact in the home environment. The role of the environment in the acquisition of M. abscessus infection requires further investigation. Background. Mycobacterium abscessus has emerged as a major pathogen in cystic fibrosis (CF) patients and has been associated with poor clinical outcomes, particularly following lung transplant. We investigated the acquisition of this bacterium in a cohort of pediatric CF patients. Methods. Demographic and patient location data were used to uncover epidemiological links between patients with genetically related strains of M. abscessus that had been previously typed by variable-number tandem repeat profiling. Whole-genome sequencing was applied to 27 M. abscessus isolates from the 20 patients in this cohort to provide definitive data on the genetic relatedness of strains. Results. Whole-genome sequencing data demonstrated that M. abscessus isolates from 16 patients were unrelated, differing by at least 34 single-nucleotide polymorphisms (SNPs) from any other isolate, suggesting that independent acquisition events have occurred. Only 2 clusters of very closely related (<25 SNPs) isolates from different patients were seen. The first cluster contained 8 isolates, differing by a maximum of 17 SNPs, from a sibling pair who had intense exposure to each other both inside and outside the hospital. The second cluster contained 3 isolates, differing by a maximum of 24 SNPs, from 2 individuals with no apparent epidemiological links. Conclusions. We have not demonstrated cross-transmission of M. abscessus within our hospital, except between 1 sibling pair. Alternative routes of acquisition of M. abscessus infection, in particular the environment, require further investigation.
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Affiliation(s)
- Kathryn A Harris
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital NHS Foundation Trust National Institute for Health Research Biomedical Research Centre at Great Ormond Street Hospital for Children NHS Foundation Trust and University College London
| | - Anthony Underwood
- Bioinformatics Unit, Infectious Disease Informatics, Microbiology Services (Colindale), Public Health England
| | - Dervla T D Kenna
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Reference Microbiology Services, Public Health England
| | - Anthony Brooks
- UCL Genomics, University College London, Institute of Child Health
| | - Ema Kavaliunaite
- Paediatric Respiratory Medicine and Lung Transplantation, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Georgia Kapatai
- Bioinformatics Unit, Infectious Disease Informatics, Microbiology Services (Colindale), Public Health England
| | - Rediat Tewolde
- Bioinformatics Unit, Infectious Disease Informatics, Microbiology Services (Colindale), Public Health England
| | - Paul Aurora
- Paediatric Respiratory Medicine and Lung Transplantation, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Garth Dixon
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital NHS Foundation Trust National Institute for Health Research Biomedical Research Centre at Great Ormond Street Hospital for Children NHS Foundation Trust and University College London
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Harris KA, Kenna DTD. Mycobacterium abscessus infection in cystic fibrosis: molecular typing and clinical outcomes. J Med Microbiol 2014; 63:1241-1246. [PMID: 25106861 DOI: 10.1099/jmm.0.077164-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium abscessus is a significant pathogen in the cystic fibrosis patient population. PCR amplification and sequencing can provide accurate subspecies identification, and can predict macrolide susceptibility, which is becoming increasingly important for patient management. Molecular techniques for further typing of isolates provide tools for the ongoing investigations into the clinical impact of particular M. abscessus strains. Whole-genome sequencing is likely to be the only technique that provides sufficient resolution for investigating transmission events between patients.
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Affiliation(s)
- Kathryn A Harris
- Microbiology, Virology and Infection Control Department, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Dervla T D Kenna
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, London, UK
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26
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ZOU ZIYING, LIU YUAN, ZHU BING, ZENG PING. Direct identification of Mycobacterium abscessus through 16S rDNA sequence analysis and a citrate utilization test: A case report. Exp Ther Med 2014; 8:115-117. [PMID: 24944608 PMCID: PMC4061238 DOI: 10.3892/etm.2014.1705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 04/15/2014] [Indexed: 11/06/2022] Open
Abstract
A growing number of nontuberculous mycobacteria infection cases, especially those caused by rapidly growing mycobacteria (RGM), have been reported in the past decade. Conventional methods for mycobacteria diagnosis are inefficient and easily lead to misdiagnosis. New detection methods, such as gene sequencing, have been reported but are not widely used. The aim of the present case report was to provide a quick and exact method of identifying Myobacterium abscessus (M. abscessus) infections. The particular case reported in this study initially manifested as hyperglycemia and papules in the right leg. Routine cultures for fungus were repeatedly negative. However, cultures of the purulent material under aerobic cultivation for five days yielded a rapidly growing, nontuberculous mycobacterium. A Ziehl-Neelsen staining of this mycobacterium revealed the presence of acid-fast bacilli that were finally identified as M. abscessus through 16S rDNA sequence analysis and a citrate utilization test. The current report may help other clinicians to make a quick and accurate diagnosis of RGM infection.
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Jeon SM, Lim NR, Kwon SJ, Shim TS, Park MS, Kim BJ, Kim SH. Analysis of species and intra-species associations between the Mycobacterium abscessus complex strains using pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). J Microbiol Methods 2014; 104:19-25. [PMID: 24918987 DOI: 10.1016/j.mimet.2014.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 05/30/2014] [Accepted: 05/30/2014] [Indexed: 10/25/2022]
Abstract
PFGE and MLST showed that the strains of M. massiliense hsp65 II-1 were clearly separated from the strains of M. massiliense hsp65 I or II-2 as well as the strains of M. abscessus or M. bolletii; thus, M. massiliense hsp6 5II-1 might represent an additional subspecies of M. massiliense.
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Affiliation(s)
- Se-Mi Jeon
- Division of Tuberculosis and Bacterial Respiratory Infections, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Chungbuk, Republic of Korea
| | - Na-Ra Lim
- Division of Tuberculosis and Bacterial Respiratory Infections, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Chungbuk, Republic of Korea
| | - Seung-Jik Kwon
- Division of Tuberculosis and Bacterial Respiratory Infections, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Chungbuk, Republic of Korea
| | - Tae-Sun Shim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, Republic of Korea
| | - Mi-Sun Park
- Division of Tuberculosis and Bacterial Respiratory Infections, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Chungbuk, Republic of Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute, Cancer Research Institute and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Seong-Han Kim
- Division of Tuberculosis and Bacterial Respiratory Infections, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Chungbuk, Republic of Korea.
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Jeon S, Lim N, Kwon S, Shim T, Park M, Kim BJ, Kim S. Molecular Typing of Mycobacterium intracellulare Using Pulsed-Field Gel Electrophoresis, Variable-Number Tandem-Repeat Analysis, Mycobacteria Interspersed Repetitive-Unit-Variable-Number Tandem Repeat Typing, and Multilocus Sequence Typing: Molecular Characterization and Comparison of Each Typing Methods. Osong Public Health Res Perspect 2014; 5:119-30. [PMID: 25180144 PMCID: PMC4147213 DOI: 10.1016/j.phrp.2014.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 04/27/2014] [Accepted: 04/28/2014] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVES Mycobacterium intracellulare is the major causative agent of nontuberculous mycobacteria-related pulmonary infections. The strain typing of M. intracellulare is important for the treatment and control of its infections. We compared the discrimination capacity and effective value of four different molecular typing methods. METHODS Antibiotic susceptibility testing, hsp65 and rpoB sequencing, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), mycobacteria interspersed repetitive-unit-variable-number tandem-repeat analysis (MIRU-VNTR), and VNTR assay targeting 44 M. intracellulare isolates obtained from patients with pulmonary infections were performed. RESULTS All the antibiotic susceptibility patterns had no association with the molecular and sequence types tested in this study; however, the molecular and sequence types were related with each other. PFGE gave best results for discriminatory capacity, followed by VNTR, MLST, and MIRU-VNTR. CONCLUSION The high discriminatory power of PFGE, VNTR, and MLST is enough for differentiating between reinfection and relapse, as well as for other molecular epidemiological usages. The MLST could be regarded as a representative classification method, because it showed the clearest relation with the sequence types.
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Affiliation(s)
- Semi Jeon
- Division of Tuberculosis and Bacterial Respiratory Infections, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Osong, Korea
| | - Nara Lim
- Division of Tuberculosis and Bacterial Respiratory Infections, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Osong, Korea
| | - Seungjik Kwon
- Division of Tuberculosis and Bacterial Respiratory Infections, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Osong, Korea
| | - Taesun Shim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, Korea
| | - Misun Park
- Division of Tuberculosis and Bacterial Respiratory Infections, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Osong, Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Korea ; Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea ; Liver Research Institute, College of Medicine, Seoul National University, Seoul, Korea
| | - Seonghan Kim
- Division of Tuberculosis and Bacterial Respiratory Infections, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Osong, Korea
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Abstract
Survival has improved in patients with cystic fibrosis (CF), in part because of aggressive antimicrobial management. Two multidrug-resistant environmental bacteria, the Burkholderia cepacia group and nontuberculous mycobacteria, have emerged. Improving genomic and proteomic technologies are allowing better identification of bacteria and fungi found in the CF lung and detection of viral agents that may be associated with pulmonary exacerbations. Anaerobic bacteria and Streptococcus angionsus group organisms may play a role in chronic CF lung infections. The diversity of organisms declines perhaps as a result of aggressive antimicrobial therapy, and an apex predator, Pseudomonas aeruginosa, may emerge in many patients with CF.
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Burns JL, Rolain JM. Culture-based diagnostic microbiology in cystic fibrosis: can we simplify the complexity? J Cyst Fibros 2013; 13:1-9. [PMID: 24094376 DOI: 10.1016/j.jcf.2013.09.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/16/2013] [Accepted: 09/17/2013] [Indexed: 10/26/2022]
Abstract
Cystic fibrosis (CF) diagnostic microbiology has evolved from a focus on Staphylococcus aureus as primary pathogen to identification of the contribution of Pseudomonas aeruginosa and other non-fermenting gram negatives; studies of the lung microbiome have added new complexity. This review summarizes state-of-the art culture methods and makes recommendations for addition of non-culture based methods in the diagnostic laboratory. Plating on selective media is recommended, with organism identification by matrix assisted laser desorption-time of flight mass spectroscopy and real-time polymerase chain reaction (PCR) supplanting both biochemical identification and other less accurate and more time-consuming molecular methods. Conventional antibiotic susceptibility testing, possibly at less frequent intervals, remains the standard but more CF-relevant methods may arise in the future. There is a role for direct identification of organisms in clinical samples using quantitative real-time PCR, next generation sequencing, and metagenomic studies for the re-examination of samples that do not yield traditional CF pathogens.
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Affiliation(s)
- Jane L Burns
- Seattle Children's Hospital, University of Washington School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Seattle, WA, USA.
| | - Jean-Marc Rolain
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
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New rapid scheme for distinguishing the subspecies of the Mycobacterium abscessus group and identifying Mycobacterium massiliense isolates with inducible clarithromycin resistance. J Clin Microbiol 2013; 51:2943-9. [PMID: 23804391 DOI: 10.1128/jcm.01132-13] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium abscessus (M. abscessus sensu lato, or the M. abscessus group) comprises three closely related taxa whose taxonomic statuses are under revision, i.e., M. abscessus sensu stricto, Mycobacterium bolletii, and Mycobacterium massiliense. We describe here a simple, robust, and cost-effective PCR-based method for distinguishing among M. abscessus, M. massiliense, and M. bolletii. Based on the M. abscessus ATCC 19977(T) genome, regions that discriminated between M. abscessus and M. massiliense were identified through array-based comparative genomic hybridization. A typing scheme using PCR primers designed for four of these locations was applied to 46 well-characterized clinical isolates comprising 29 M. abscessus, 15 M. massiliense, and 2 M. bolletii isolates previously identified by multitarget sequencing. Interestingly, 2 isolates unequivocally identified as M. massiliense were shown to have a full-length erm(41) gene instead of the expected gene deletion and showed inducible clarithromycin resistance after 14 days. We propose using this PCR-based typing scheme combined with erm(41) PCR for straightforward identification of M. abscessus, M. massiliense, and M. bolletii and the assessment of inducible clarithromycin resistance. This method can be easily integrated into a routine workflow to provide subspecies-level identification within 24 h after isolation of the M. abscessus group.
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Waters V, Ratjen F. Antibiotic treatment for nontuberculous mycobacteria lung infection in people with cystic fibrosis. Cochrane Database Syst Rev 2012; 12:CD010004. [PMID: 23235684 DOI: 10.1002/14651858.cd010004.pub2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Nontuberculous mycobacteria are mycobacteria, other than those in the Mycobacterium tuberculosis complex, and are commonly found in the environment. Nontuberculous mycobacteria species (most commonly Mycobacterium avium complex and Mycobacterium abscessus) are isolated from the respiratory tract of approximately 5% to 20% of individuals with cystic fibrosis; they can cause lung disease in people with cystic fibrosis leading to more a rapid decline in lung function and even death in certain circumstances. Although there are guidelines for the antimicrobial treatment of nontuberculous mycobacteria lung disease, these recommendations are not specific for people with cystic fibrosis and it is not clear which antibiotic regimen may be the most effective in the treatment of these patients. OBJECTIVES The objective of our review was to compare antibiotic treatment to no antibiotic treatment, or to compare different combinations of antibiotic treatment, for nontuberculous mycobacteria lung infections in people with cystic fibrosis. The primary objective was to assess the effect of treatment on lung function and pulmonary exacerbations and to quantify adverse events. The secondary objectives were to assess treatment effects on the amount of bacteria in the sputum, quality of life, mortality, nutritional parameters, hospitalizations and use of oral antibiotics. SEARCH METHODS We searched the Cochrane Cystic Fibrosis Trials Register, compiled from electronic database searches and hand searching of journals and conference abstract books. Date of last search: 19 July 2012.We also searched a register of ongoing trials and the reference lists of relevant articles and reviews. Date of last search: 10 August 2012. SELECTION CRITERIA Any randomized controlled trials comparing nontuberculous mycobacteria antibiotics to no antibiotic treatment, as well as one nontuberculous mycobacteria antibiotic regimen compared to another nontuberculous mycobacteria antibiotic regimen, in individuals with cystic fibrosis. DATA COLLECTION AND ANALYSIS Data were not collected because no completed trials were identified by the searches. MAIN RESULTS No completed trials were identified by the searches, but one ongoing trial was identified, which may be eligible for inclusion in this review when completed. AUTHORS' CONCLUSIONS This review did not find any evidence for the effectiveness of different antimicrobial treatment for nontuberculous mycobacteria lung disease in people with cystic fibrosis. Until such evidence becomes available, it is reasonable for clinicians to follow the American Thoracic Society guidelines for the diagnosis and treatment of nodular or bronchiectatic pulmonary disease due to Mycobacterium avium complex or Mycobacterium abscessus in patients with cystic fibrosis.
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Affiliation(s)
- Valerie Waters
- Department of Pediatrics, Division of Infectious Diseases, Hospital for Sick Children, Toronto, Canada.
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Kim BJ, Yi SY, Shim TS, Do SY, Yu HK, Park YG, Kook YH, Kim BJ. Discovery of a novel hsp65 genotype within Mycobacterium massiliense associated with the rough colony morphology. PLoS One 2012; 7:e38420. [PMID: 22693637 PMCID: PMC3367924 DOI: 10.1371/journal.pone.0038420] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 05/09/2012] [Indexed: 11/19/2022] Open
Abstract
So far, genetic diversity among strains within Mycobacterium massiliense has rarely been studied. To investigate the genetic diversity among M. massiliense, we conducted phylogenetic analysis based on hsp65 (603-bp) and rpoB (711-bp) sequences from 65 M. massiliense Korean isolates. We found that hsp65 sequence analysis could clearly differentiate them into two distinct genotypes, Type I and Type II, which were isolated from 35 (53.8%) and 30 patients (46.2%), respectively. The rpoB sequence analysis revealed a total of four genotypes (R-I to R-IV) within M. massiliense strains, three of which (R-I, R-II and R-III) correlated with hsp65 Type I, and other (R-IV), which correlated with Type II. Interestingly, genotyping by the hsp65 method agreed well with colony morphology. Despite some exceptions, Type I and II correlated with smooth and rough colonies, respectively. Also, both types were completely different from one another in terms of MALDI-TOF mass spectrometry profiles of whole lipid. In addition, we developed PCR-restriction analysis (PRA) based on the Hinf I digestion of 644-bp hsp65 PCR amplicons, which enables the two genotypes within M. massiliense to be easily and reliably separated. In conclusion, two distinct hsp65 genotypes exist within M. massiliense strains, which differ from one another in terms of both morphology and lipid profile. Furthermore, our data indicates that Type II is a novel M. massiliense genotype being herein presented for the first time. The disparity in clinical traits between these two hsp65 genotypes needs to be exploited in the future study.
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Affiliation(s)
- Byoung-Jun Kim
- Department of Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Su-Yeon Yi
- Department of Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Tae-Sun Shim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, Republic of Korea
| | - Seung Yeon Do
- Department of Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hee-Kyung Yu
- Korean Institute of Tuberculosis, Korean National Tuberculosis Association, Chungcheongbuk-Do, Republic of Korea
| | - Young-Gil Park
- Korean Institute of Tuberculosis, Korean National Tuberculosis Association, Chungcheongbuk-Do, Republic of Korea
| | - Yoon-Hoh Kook
- Department of Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
- * E-mail:
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34
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Molecular fingerprinting of Mycobacterium abscessus strains in a cohort of pediatric cystic fibrosis patients. J Clin Microbiol 2012; 50:1758-61. [PMID: 22403419 DOI: 10.1128/jcm.00155-12] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Forty-one Mycobacterium abscessus complex isolates from 17 pediatric cystic fibrosis (CF) patients were typed using a novel variable-number tandem repeat (VNTR) scheme and an automated repetitive-PCR (rep-PCR) system. Both VNTR and rep-PCR typing methods differentiate between members of the M. abscessus complex. The isolates from individual patients are indistinguishable, and the data strongly suggest that individual CF patients are persistently infected with one strain and also suggests that different CF patients can harbor the same strain.
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