1
|
Godmer A, Bigey L, Giai‐Gianetto Q, Pierrat G, Mohammad N, Mougari F, Piarroux R, Veziris N, Aubry A. Contribution of machine learning for subspecies identification from Mycobacterium abscessus with MALDI-TOF MS in solid and liquid media. Microb Biotechnol 2024; 17:e14545. [PMID: 39257027 PMCID: PMC11387462 DOI: 10.1111/1751-7915.14545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 07/26/2024] [Indexed: 09/12/2024] Open
Abstract
Mycobacterium abscessus (MABS) displays differential subspecies susceptibility to macrolides. Thus, identifying MABS's subspecies (M. abscessus, M. bolletii and M. massiliense) is a clinical necessity for guiding treatment decisions. We aimed to assess the potential of Machine Learning (ML)-based classifiers coupled to Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) MS to identify MABS subspecies. Two spectral databases were created by using 40 confirmed MABS strains. Spectra were obtained by using MALDI-TOF MS from strains cultivated on solid (Columbia Blood Agar, CBA) or liquid (MGIT®) media for 1 to 13 days. Each database was divided into a dataset for ML-based pipeline development and a dataset to assess the performance. An in-house programme was developed to identify discriminant peaks specific to each subspecies. The peak-based approach successfully distinguished M. massiliense from the other subspecies for strains grown on CBA. The ML approach achieved 100% accuracy for subspecies identification on CBA, falling to 77.5% on MGIT®. This study validates the usefulness of ML, in particular the Random Forest algorithm, to discriminate MABS subspecies by MALDI-TOF MS. However, identification in MGIT®, a medium largely used in mycobacteriology laboratories, is not yet reliable and should be a development priority.
Collapse
Affiliation(s)
- Alexandre Godmer
- U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi‐Paris)Sorbonne UniversitéParisFrance
- AP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Département de BactériologieGroupe Hospitalier Universitaire, Sorbonne Université, HôpitalParisFrance
| | - Lise Bigey
- U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi‐Paris)Sorbonne UniversitéParisFrance
- DER (Département d'Enseignement et de Recherche) de Biologie, ENS Paris‐SaclayUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Quentin Giai‐Gianetto
- Institut PasteurUniversité Paris Cité, Bioinformatics and Biostatistics HUBParisFrance
- Institut PasteurUniversité Paris Cité, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR CNRS 2024ParisFrance
| | - Gautier Pierrat
- AP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Département de BactériologieGroupe Hospitalier Universitaire, Sorbonne Université, HôpitalParisFrance
| | - Noshine Mohammad
- Inserm, Institut Pierre‐Louis d'Epidémiologie et de Santé Publique, IPLESP, AP‐HP, Groupe Hospitalier Pitié‐Salpêtrière, Service de Parasitologie‐ MycologieSorbonne UniversitéParisFrance
| | - Faiza Mougari
- Service de Mycobactériologie spécialisée et de référence, Centre National de Référence des Mycobactéries (Laboratoire associé), APHP GHU NordUniversité Paris Cité, INSERM IAME UMRParisFrance
| | - Renaud Piarroux
- Inserm, Institut Pierre‐Louis d'Epidémiologie et de Santé Publique, IPLESP, AP‐HP, Groupe Hospitalier Pitié‐Salpêtrière, Service de Parasitologie‐ MycologieSorbonne UniversitéParisFrance
| | - Nicolas Veziris
- U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi‐Paris)Sorbonne UniversitéParisFrance
- AP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Département de BactériologieGroupe Hospitalier Universitaire, Sorbonne Université, HôpitalParisFrance
- AP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris)Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux AntituberculeuxParisFrance
| | - Alexandra Aubry
- U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi‐Paris)Sorbonne UniversitéParisFrance
- AP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris)Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux AntituberculeuxParisFrance
| |
Collapse
|
2
|
Liu W, Li B, Chu H, Zhang Z, Luo L, Ma W, Yang S, Guo Q. Rapid detection of mutations in erm(41) and rrl associated with clarithromycin resistance in Mycobacterium abscessus complex by denaturing gradient gel electrophoresis. J Microbiol Methods 2017; 143:87-93. [PMID: 29079298 DOI: 10.1016/j.mimet.2017.10.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 10/19/2017] [Accepted: 10/20/2017] [Indexed: 12/28/2022]
Abstract
Clarithromycin resistance is increasing dramatically among Mycobacterium abscessus complex. The main resistance mechanisms are mutations in the erm(41) and rrl genes. Here we report PCR-based denaturing gradient gel electrophoresis (DGGE) as an alternative method for rapidly detection of mutations in erm(41) and rrl among M. abscessus isolates. Four primer sets targeting the full-length erm(41) gene and a 354bp fragment of the rrl gene were designed. A combination of 16 different DGGE patterns were observed for erm(41) gene, including 16 in M. abscessus subsp. abscessus and 1 in M. abscessus subsp. massiliense. Six DGGE patterns were obtained for rrl gene. Mutations in the erm(41) and rrl detected by DGGE were 100% identical to mutations detected by DNA sequencing. This is the first report to identify PCR-based DGGE as a practical, relatively inexpensive technique for rapidly detecting mutations in the erm(41) and rrl genes associated with clarithromycin resistance in M. abscessus complex.
Collapse
Affiliation(s)
- Weijia Liu
- Tongji University School of Medicine, Shanghai 200092, China
| | - Bing Li
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Haiqing Chu
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.
| | - Zhemin Zhang
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.
| | - Liulin Luo
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Wei Ma
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shiyi Yang
- Tongji University School of Medicine, Shanghai 200092, China
| | - Qi Guo
- Tongji University School of Medicine, Shanghai 200092, China
| |
Collapse
|
3
|
Evaluation of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Mycobacterium abscessus Subspecies According to Whole-Genome Sequencing. J Clin Microbiol 2016; 54:2982-2989. [PMID: 27682129 DOI: 10.1128/jcm.01151-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/19/2016] [Indexed: 12/22/2022] Open
Abstract
This study was undertaken to evaluate the utility of matrix-assisted laser desorption ionization-time of flight mass spectrometry with the Vitek MS Plus system for identifying Mycobacterium abscessus subspecies in order to facilitate more rapid and appropriate therapy. A total of 175 clinical M. abscessus strains were identified by whole-genome sequencing analysis: 139 Mycobacterium abscessus subsp. abscessus and 36 Mycobacterium abscessus subsp. massiliense The research-use-only (RUO) Saramis Knowledge Base database v.4.12 was modified accordingly by adding 40 M. abscessus subsp. abscessus and 19 M. abscessus subsp. massiliense reference spectra to construct subspecies SuperSpectra. A blind test, used to validate the remaining 116 isolates, yielded 99.1% (n = 115) reliability and only 0.9% (n = 1) error for subspecies identification. Among the two subspecies SuperSpectra, two specific peaks were found for M. abscessus subsp. abscessus and four specific peaks were found for M. abscessus subsp. massiliense Our study is the first to report differential peaks 3,354.4 m/z and 6,711.1 m/z, which were specific for M. abscessus subsp. massiliense Our research demonstrates the capacity of the Vitek MS RUO Saramis Knowledge Base database to identify M. abscessus at the subspecies level. Moreover, it validates the potential ease and accuracy with which it can be incorporated into the IVD system for the identification of M. abscessus subspecies.
Collapse
|
4
|
Luo L, Li B, Chu H, Huang D, Zhang Z, Zhang J, Gui T, Xu L, Zhao L, Sun X, Xiao H. Characterization of Mycobacterium Abscessus Subtypes in Shanghai of China: Drug Sensitivity and Bacterial Epidemicity as well as Clinical Manifestations. Medicine (Baltimore) 2016; 95:e2338. [PMID: 26817866 PMCID: PMC4998240 DOI: 10.1097/md.0000000000002338] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/22/2015] [Accepted: 11/27/2015] [Indexed: 02/05/2023] Open
Abstract
The aim of the study was to investigate the epidemic characteristics of Mycobacterium abscessus in Shanghai.Fifty-five strains from 55 M. abscessus pulmonary disease patients were isolated. Drug sensitivity was measured by a broth microdilution method. Subtypes of M. abscessus were identified by DNA sequencing. Multilocus sequence typing (MLST), mining spanning tree (MST), and pulsed-field gel electrophoresis (PFGE) were used to analyze sequence types (ST) and clonal complexes (CC). Clinical manifestations were assessed by CT imaging.We identified 42 A isolates, 11 M, and 2 B-subtypes. A and M were highly sensitive to tigecycline and amikacin (97.6-100%). The A-type easily developed drug resistance against clarithromycin. Both types were highly resistance to sulfonamides, moxifloxacin, doxycycline, imipenem, and tobramycin. MLST analysis identified 41 STs including 32 new STs. The MST algorithm distributed 55 isolates into 12 separate CC. The PFGE analysis exhibited 53 distinct restriction patterns and the M-type was closely clustered according to their ST and CC numbers. CT imaging showed that tree-in-bud and patch shadow were commonly observed in M-type, whereas pulmonary cavities were often found in A-type infection patients (P < 0.001).ST1 in A and ST23 in M-type were the main epidemic strains in Shanghai. The M-type appeared to be prone to epidemic nosocomial transmission.
Collapse
MESH Headings
- Anti-Bacterial Agents/therapeutic use
- Bacterial Typing Techniques
- China/epidemiology
- DNA Barcoding, Taxonomic
- Electrophoresis, Gel, Pulsed-Field
- Female
- Humans
- Male
- Microbial Sensitivity Tests
- Middle Aged
- Multilocus Sequence Typing
- Mycobacterium Infections, Nontuberculous/drug therapy
- Mycobacterium Infections, Nontuberculous/epidemiology
- Mycobacterium Infections, Nontuberculous/microbiology
- Nontuberculous Mycobacteria/classification
- Nontuberculous Mycobacteria/drug effects
- Nontuberculous Mycobacteria/isolation & purification
- Pneumonia, Bacterial/drug therapy
- Pneumonia, Bacterial/epidemiology
- Pneumonia, Bacterial/microbiology
- Retrospective Studies
- Tomography, X-Ray Computed
Collapse
Affiliation(s)
- Liulin Luo
- From the Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine (LL); Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine (BL, HC, ZZ, JZ, TG, LX, LZ); Department of Clinical Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine (DH); Department of Radiology, Shanghai Pulmonary Hospital, Tongji University School of Medicine (XS); and Department of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China (HX)
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Suzuki H, Yoshida S, Yoshida A, Okuzumi K, Fukusima A, Hishinuma A. A novel cluster of Mycobacterium abscessus complex revealed by matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS). Diagn Microbiol Infect Dis 2015; 83:365-70. [DOI: 10.1016/j.diagmicrobio.2015.08.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/16/2015] [Accepted: 08/21/2015] [Indexed: 10/23/2022]
|
6
|
Kim BJ, Shim TS, Yi SY, Kim HC, Kim BR, Lee SY, Kook YH, Kim BJ. Mycobacterium massiliense Type II genotype leads to higher level of colony forming units and TNF-α secretion from human monocytes than Type I genotype. APMIS 2015; 123:895-902. [PMID: 26303945 DOI: 10.1111/apm.12436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/19/2015] [Indexed: 12/21/2022]
Abstract
Recently, we introduced a novel Mycobacterium massiliense Type II genotype from Korean patients, in which all isolates showed only a rough (R) colony morphotype. In this study, we sought to compare clinical factors and virulence potentials of two genotypes of M. massiliense, Type I and Type II. Patients infected with Type II tend to be younger at infection than those infected with Type I (56.7 vs 62.3, p = 0.051). Type II was more significantly related to R colony type than Type I (34.1% vs 94.1%, p < 0.001). The Type II strain showed significantly more colony forming units (CFUs) and higher levels of TNF-α secretion in infection of human monocytes than the Type I strain. The challenge of extracted glycopeptidolipid (GPL) into human monocytes indicated that the loss of GPL from the cell wall of the Type II genotype led to a higher level of TNF-α secretion in a toll-like receptor 2(TLR2)-dependent manner. Taken together, our data suggest that the M. massiliense Type II genotype shows higher virulence than Type I, which may be due to the induction of TNF-α via the loss of GPL from the Type II cell wall.
Collapse
Affiliation(s)
- Byoung-Jun Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Korea
| | - Tae Sun Shim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Su-Yeon Yi
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Korea
| | - Ho-Cheol Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Bo-Ram Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Korea
| | - So-Young Lee
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Korea
| | - Yoon-Hoh Kook
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Korea
| |
Collapse
|
7
|
Kim K, Hong SH, Kim BJ, Kim BR, Lee SY, Kim GN, Shim TS, Kook YH, Kim BJ. Separation of Mycobacterium abscessus into subspecies or genotype level by direct application of peptide nucleic acid multi-probe- real-time PCR method into sputa samples. BMC Infect Dis 2015; 15:325. [PMID: 26259717 PMCID: PMC4531893 DOI: 10.1186/s12879-015-1076-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/31/2015] [Indexed: 11/30/2022] Open
Abstract
Background Recently, we introduced a novel peptide nucleic acid (PNA) multi-probe real time PCR method targeting the hsp65 gene (hsp65 PNA RT-PCR) to distinguish Mycobacterium abscessus groups. Methods Here, we evaluated the usefulness of the hsp65 PNA RT-PCR for the direct identification of the M. abscessus group at the subspecies and genotype levels from sputa samples. The method was applied to total sputa DNA from 60 different patients who were identified as having mycobacterial infections via rpoB PCR restriction analysis of the same cultures. Results The hsp65 PNA RT-PCR method had higher sensitivity than the multi-probe real-time PCR assay targeting hsp65 (HMPRT-PCR) for the detection of M. abscessus from sputum [96.7 % (29/30 samples) vs. 70 % (21/30 samples); 100 % specificity]. Conclusions These results suggest that the PNA-based method is feasible for the detection of M. abscessus members not only from cultures but also directly from sputa. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-1076-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kijeong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 156-756, Republic of Korea.
| | - Seok-Hyun Hong
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Byoung-Jun Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Bo-Ram Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - So-Young Lee
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Ga-Na Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Tae Sun Shim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Yoon-Hoh Kook
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Bum-Joon Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| |
Collapse
|
8
|
Jung SY, Kim BG, Kwon D, Park JH, Youn SK, Jeon S, Um HY, Kwon KE, Kim HJ, Jung HJ, Choi E, Park BJ. An outbreak of joint and cutaneous infections caused by non-tuberculous mycobacteria after corticosteroid injection. Int J Infect Dis 2015; 36:62-9. [PMID: 26026822 DOI: 10.1016/j.ijid.2015.05.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 04/13/2015] [Accepted: 05/16/2015] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES An outbreak of joint and cutaneous infections among patients who had been injected at a single clinic in South Korea was investigated. METHODS In this retrospective case-control study, 61 cases were diagnosed based on symptoms and signs of septic arthritis or cutaneous infection that developed after injections at the clinic between April and September 2012; 64 controls were investigated by administering questionnaires on risk factors and analyzing the clinic medical records. An environmental investigation was performed, and clinical specimens of the cases were analyzed by pulsed-field gel electrophoresis. RESULTS All cases were injected with triamcinolone. A greater number of triamcinolone injections (adjusted odds ratio 4.3, 95% confidence interval 1.5-12.1 for six or more visits, compared with one or two visits) was associated with the development of an infection. In the clinic, only the triamcinolone injection was prepared by mixing with lidocaine and normal saline, and an alcohol swab was prepared using boiled tap water by members of the clinic staff. Although injected medications and environmental cultures were not found to be responsible, a single strain of Mycobacterium massiliense was isolated from the affected sites of 16 cases. CONCLUSIONS Repeated injection of triamcinolone contaminated with NTM from the clinic environment may have caused this post-injection outbreak.
Collapse
Affiliation(s)
- Sun-Young Jung
- Korea Institute of Drug Safety and Risk Management (KIDS), Boryung Bldg, 136 Changgyeonggung-ro, Jongno-Gu, Seoul 110-750, South Korea
| | - Bong Gi Kim
- Korea Institute of Drug Safety and Risk Management (KIDS), Boryung Bldg, 136 Changgyeonggung-ro, Jongno-Gu, Seoul 110-750, South Korea
| | - Donghyok Kwon
- Division of Epidemic Intelligence Service, Korea Centers for Disease Control and Prevention (KCDC), Osong-eup, Cheongwon-gun, Chungcheongbuk-do, South Korea
| | - Ji-Hyuk Park
- Department of Preventive Medicine, Dongguk University College of Medicine, Gyeongju-si, Gyeongsangbuk-do, South Korea
| | - Seung-Ki Youn
- Division of Epidemic Intelligence Service, Korea Centers for Disease Control and Prevention (KCDC), Osong-eup, Cheongwon-gun, Chungcheongbuk-do, South Korea
| | - Semi Jeon
- Division of Tuberculosis and Bacterial Respiratory Infection, Center for Infectious Diseases, Korea National Institute of Health (KNIH), Osong-eup, Cheongwon-gun, Chungcheongbuk-do, South Korea
| | - Hye-Yeon Um
- Korea Institute of Drug Safety and Risk Management (KIDS), Boryung Bldg, 136 Changgyeonggung-ro, Jongno-Gu, Seoul 110-750, South Korea
| | - Kyoung-Eun Kwon
- Korea Institute of Drug Safety and Risk Management (KIDS), Boryung Bldg, 136 Changgyeonggung-ro, Jongno-Gu, Seoul 110-750, South Korea
| | - Hyun-Jung Kim
- Korea Institute of Drug Safety and Risk Management (KIDS), Boryung Bldg, 136 Changgyeonggung-ro, Jongno-Gu, Seoul 110-750, South Korea
| | - Hyun-Joo Jung
- Korea Institute of Drug Safety and Risk Management (KIDS), Boryung Bldg, 136 Changgyeonggung-ro, Jongno-Gu, Seoul 110-750, South Korea
| | - Eunmi Choi
- Korea Institute of Drug Safety and Risk Management (KIDS), Boryung Bldg, 136 Changgyeonggung-ro, Jongno-Gu, Seoul 110-750, South Korea
| | - Byung-Joo Park
- Korea Institute of Drug Safety and Risk Management (KIDS), Boryung Bldg, 136 Changgyeonggung-ro, Jongno-Gu, Seoul 110-750, South Korea; Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea.
| |
Collapse
|
9
|
Development of a peptide nucleic acid-based multiprobe real-time PCR method targeting the hsp65 gene for differentiation among Mycobacterium abscessus strains. J Clin Microbiol 2015; 53:1403-5. [PMID: 25653415 DOI: 10.1128/jcm.03424-14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recently, the need to distinguish between members of the Mycobacterium abscessus group has gained increasing attention. Here, we introduced a novel peptide nucleic acid (PNA) real-time PCR method targeting the hsp65 gene in order to distinguish between four subspecies within the M. abscessus group (M. abscessus and 3 types of M. massiliense).
Collapse
|
10
|
Yoshida S, Arikawa K, Tsuyuguchi K, Kurashima A, Harada T, Nagai H, Suzuki K, Iwamoto T, Hayashi S. Investigation of the population structure of Mycobacterium abscessus complex strains using 17-locus variable number tandem repeat typing and the further distinction of Mycobacterium massiliense hsp65 genotypes. J Med Microbiol 2015; 64:254-261. [PMID: 25596119 DOI: 10.1099/jmm.0.000016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium abscessus complex is a significant pathogen in patients with non-cystic fibrosis (non-CF). Nevertheless, there is little description of the genetic diversity of this species. The aims of this study were to investigate the distribution of M. abscessus complex isolated from respiratory specimens by variable number tandem repeat (VNTR) typing. The results of 104 clinical isolates from 104 non-CF patients were compared using PFGE, hsp65 genotypes and clarithromycin susceptibility. The allelic diversity (Hunter-Gaston Discriminatory Index) of the 17 loci examined by VNTR typing was high (0.977). We determined that C28 sequevar erm(41) genotypes and clarithromycin-acquired resistance isolates were scattered in the minimum spanning tree. Intriguingly, VNTR typing and PFGE were highly congruent and revealed that there were clear examples of grouping of isolates from different individuals amongst both M. abscessus and M. massiliense, and showed five clusters of distinct identical isolates. Within these clusters, M. massiliense hsp65 type I formed three different clusters. Although the distribution of M. massiliense hsp65 type II-1 was low (9.3 %), M. massiliense hsp65 type II-1 isolates separated from clusters contained hsp65 type I isolates. Thus, M. massiliense hsp65 genotypes could be discriminated by analysing VNTRs with sufficient genetic distance for intra-species-level discrimination.
Collapse
Affiliation(s)
- Shiomi Yoshida
- Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, 1180 Nagasone-cho, Kita-ku Sakai, Osaka 591-8555, Japan
| | - Kentaro Arikawa
- Department of Microbiology, Kobe Institute of Health, 4-6 Minatojima-nakamachi, Chuo-ku Kobe, Hyogo 650-0046, Japan
| | - Kazunari Tsuyuguchi
- Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, 1180 Nagasone-cho, Kita-ku Sakai, Osaka 591-8555, Japan
| | - Atsuyuki Kurashima
- Clinical Research Advisor, Japan Anti-Tuberculosis Association, Fukujuji Hospital, 3-1-24 Matsuyama, Kiyose, Tokyo 204-0022, Japan
| | - Toshiyuki Harada
- Center for Respiratory Diseases, Japan Community Health Care Organization Hokkaido Hospital, 8-3-18 Ichijyo, Nakanoshima, Toyohira-ku Sapporo, Hokkaido 062-8618, Japan
| | - Hideaki Nagai
- Center for Respiratory Diseases, National Hospital Organization Tokyo National Hospital, 3-1-2 Takeoka, Kiyose, Tokyo 204-8585, Japan
| | - Katsuhiro Suzuki
- Internal Medicine, National Hospital Organization Kinki-chuo Chest Medical Center, 1180 Nagasone-cho, Kita-ku Sakai, Osaka 591-8555, Japan
| | - Tomotada Iwamoto
- Department of Microbiology, Kobe Institute of Health, 4-6 Minatojima-nakamachi, Chuo-ku Kobe, Hyogo 650-0046, Japan
| | - Seiji Hayashi
- Internal Medicine, National Hospital Organization Kinki-chuo Chest Medical Center, 1180 Nagasone-cho, Kita-ku Sakai, Osaka 591-8555, Japan
| |
Collapse
|