1
|
Park HE, Kim KM, Trinh MP, Yoo JW, Shin SJ, Shin MK. Bigger problems from smaller colonies: emergence of antibiotic-tolerant small colony variants of Mycobacterium avium complex in MAC-pulmonary disease patients. Ann Clin Microbiol Antimicrob 2024; 23:25. [PMID: 38500139 PMCID: PMC10949641 DOI: 10.1186/s12941-024-00683-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/03/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Mycobacterium avium complex (MAC) is a group of slow-growing mycobacteria that includes Mycobacterium avium and Mycobacterium intracellulare. MAC pulmonary disease (MAC-PD) poses a threat to immunocompromised individuals and those with structural pulmonary diseases worldwide. The standard treatment regimen for MAC-PD includes a macrolide in combination with rifampicin and ethambutol. However, the treatment failure and disease recurrence rates after successful treatment remain high. RESULTS In the present study, we investigated the unique characteristics of small colony variants (SCVs) isolated from patients with MAC-PD. Furthermore, revertant (RVT) phenotype, emerged from the SCVs after prolonged incubation on 7H10 agar. We observed that SCVs exhibited slower growth rates than wild-type (WT) strains but had higher minimum inhibitory concentrations (MICs) against multiple antibiotics. However, some antibiotics showed low MICs for the WT, SCVs, and RVT phenotypes. Additionally, the genotypes were identical among SCVs, WT, and RVT. Based on the MIC data, we conducted time-kill kinetic experiments using various antibiotic combinations. The response to antibiotics varied among the phenotypes, with RVT being the most susceptible, WT showing intermediate susceptibility, and SCVs displaying the lowest susceptibility. CONCLUSIONS In conclusion, the emergence of the SCVs phenotype represents a survival strategy adopted by MAC to adapt to hostile environments and persist during infection within the host. Additionally, combining the current drugs in the treatment regimen with additional drugs that promote the conversion of SCVs to RVT may offer a promising strategy to improve the clinical outcomes of patients with refractory MAC-PD.
Collapse
Affiliation(s)
- Hyun-Eui Park
- Department of Microbiology and Convergence of Medical Science, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Kyu-Min Kim
- Department of Microbiology and Convergence of Medical Science, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Minh Phuong Trinh
- Department of Microbiology and Convergence of Medical Science, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Jung-Wan Yoo
- Department of Internal Medicine, Gyeongsang National University Hospital, Jinju, 52727, Republic of Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
| | - Min-Kyoung Shin
- Department of Microbiology and Convergence of Medical Science, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea.
| |
Collapse
|
2
|
Lari N, Rindi L. High genetic heterogeneity of Mycobacterium intracellulare isolated from respiratory specimens. BMC Microbiol 2022; 22:5. [PMID: 34979921 PMCID: PMC8722163 DOI: 10.1186/s12866-021-02426-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/08/2021] [Indexed: 11/27/2022] Open
Abstract
Background M. intracellulare is a frequent causative pathogen of nontuberculous mycobacteria infection that causes infections in the respiratory tract, whose incidence is increasing in many countries. This study aimed at determining the VNTR-based genetic diversity of a collection of 39 M. intracellulare human strains isolated from respiratory specimens over the last 5 years. Results The VNTR analysis showed that M. intracellulare strains displayed a high genetic diversity, indicating that the M. intracellulare genotypes are quite heterogeneous in our geographical area. Moreover, a comparison with VNTR profiles of strains from other countries confirmed that genotypes of clinical strains of M. intracellulare are not related to geographical origin. Conclusions VNTR typing has proved to be a highly discriminatory method for better understanding the molecular epidemiology of M. intracellulare.
Collapse
Affiliation(s)
- Nicoletta Lari
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, 35/39, I-56127, Pisa, Italy
| | - Laura Rindi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, 35/39, I-56127, Pisa, Italy.
| |
Collapse
|
3
|
Comparative Evaluation of Band-Based Genotyping Methods for Mycobacterium intracellulare and Its Application for Epidemiological Analysis. Microorganisms 2020; 8:microorganisms8091315. [PMID: 32872369 PMCID: PMC7564390 DOI: 10.3390/microorganisms8091315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 11/17/2022] Open
Abstract
Mycobacterium intracellulare is a leading cause of nontuberculous mycobacterial pulmonary disease, with a rapidly increasing prevalence worldwide. This bacterium, commonly distributed in soil and water, is known to be transmitted through the environment rather than between people. Therefore, it is imperative to establish distinguishable genotyping methods to understand the clinical outcome, disease relapses, and epidemiology. Therefore, in this study, representative band-based genotyping methods were performed using M. intracellualre clinical isolates, and their Hunter-Gaston discriminatory index (HGDI) was 0.947, 0.994, and 1 for variable number tandem repetition (VNTR), VNTR-mycobacterial interspersed repetitive units, pulsed field gel electrophoresis, and repetitive sequence based-PCR, respectively. Although VNTR showed relatively low HGDI, co-infection with other M. intracellualre strains could be determined by loci showing allele diversity from 0 to 0.69. Additionally, genetic distance of clinical isolates from Gyeongnam/Korea, and other regions/countries were visualized by minimum spanning tree (MST) using the globally available VNTR profiles. The results of MST revealed that M. intracellulare isolated from patients in Gyeongnam/Korea had specific VNTR genotypes, which may be evidence of the geographic distribution of M. intracellulare specific genotypes. The comparative results of genotyping techniques and geographical characteristics in this study may provide fundamental information for the epidemiology of M. intracellulare.
Collapse
|
4
|
Differential Genotyping of Mycobacterium avium Complex and Its Implications in Clinical and Environmental Epidemiology. Microorganisms 2020; 8:microorganisms8010098. [PMID: 31936743 PMCID: PMC7022546 DOI: 10.3390/microorganisms8010098] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/03/2020] [Accepted: 01/07/2020] [Indexed: 11/16/2022] Open
Abstract
In recent decades, the incidence and prevalence of nontuberculous mycobacteria (NTM) have greatly increased, becoming a major worldwide public health problem. Among numerous NTM species, the Mycobacterium avium complex (MAC) is the most predominant species, causing disease in humans. MAC is recognized as a ubiquitous microorganism, with contaminated water and soil being established sources of infection. However, the reason for the recent increase in MAC-associated disease has not yet been fully elucidated. Furthermore, human MAC infections are associated with a variety of infection sources. To improve the determination of infection sources and epidemiology of MAC, feasible and reliable genotyping methods are required to allow for the characterization of the epidemiology and biology of MAC. In this review, we discuss genotyping methods, such as pulsed-field gel electrophoresis, a variable number of tandem repeats, mycobacterial interspersed repetitive-unit-variable number of tandem repeats, and repetitive element sequence-based PCR that have been applied to elucidate the association between the MAC genotypes and epidemiological dominance, clinical phenotypes, evolutionary process, and control measures of infection. Characterizing the association between infection sources and the epidemiology of MAC will allow for the development of novel preventive strategies for the effective control of MAC infection.
Collapse
|
5
|
Cochard T, Branger M, Supply P, Sreevatsan S, Biet F. MAC-INMV-SSR: a web application dedicated to genotyping members of Mycobacterium avium complex (MAC) including Mycobacterium avium subsp. paratuberculosis strains. INFECTION GENETICS AND EVOLUTION 2019; 77:104075. [PMID: 31634642 DOI: 10.1016/j.meegid.2019.104075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/11/2019] [Accepted: 10/16/2019] [Indexed: 01/27/2023]
Abstract
Genotyping of Mycobacterium avium subsp. paratuberculosis (Map) is an indispensable tool for surveillance of this significant veterinary pathogen. For Map, multi-locus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRUs) and other variable number variable-number tandem repeats (VNTRs) was established using 8 markers. In the recent past this standard, portable, reproducible and discriminatory typing method has been frequently applied alone or in combinations with multi-locus short-sequence-repeat (MLSSR) sequencing. With the widespread use of these genotyping methods, standardization between laboratories needs to be managed, and knowledge of existing profiles and newly defined genotypes should be indexed and shared. To meet this need, a web application called "MAC-INMV-SSR database" was developed. This freely accessible service allows users to compare MLVA and MLSSR subtype data of their strains with those of existing reference strains analyzed with the same genotyping methods.
Collapse
Affiliation(s)
- Thierry Cochard
- ISP, INRA, Université de Tours, UMR 1282, 37380 Nouzilly, France
| | - Maxime Branger
- ISP, INRA, Université de Tours, UMR 1282, 37380 Nouzilly, France
| | - Philip Supply
- INSERM U1019, F-59019 Lille Cedex, France; CNRS UMR 8204, F-59019, Lille Cedex, France; Institut Pasteur de Lille, France; Univ Lille Nord de France, F-59019 Lille Cedex, France
| | - Srinand Sreevatsan
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing 48824, USA
| | - Franck Biet
- ISP, INRA, Université de Tours, UMR 1282, 37380 Nouzilly, France.
| |
Collapse
|
6
|
Yamaba Y, Ito Y, Suzuki K, Kikuchi T, Ogawa K, Fujiuchi S, Hasegawa N, Kurashima A, Higuchi T, Uchiya KI, Watanabe A, Niimi A. Moxifloxacin resistance and genotyping of Mycobacterium avium and Mycobacterium intracellulare isolates in Japan. J Infect Chemother 2019; 25:995-1000. [PMID: 31239192 DOI: 10.1016/j.jiac.2019.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/10/2019] [Accepted: 05/24/2019] [Indexed: 11/15/2022]
Abstract
BACKGROUND Although fluoroquinolones are considered as alternative therapies of pulmonary Mycobacterium avium complex (MAC) disease, the association between fluoroquinolone resistance and MAC genotypes in clinical isolates from individuals not previously treated for MAC infection is not fully clear. METHODS Totals of 154 M. avium isolates and 35 Mycobacterium intracellulare isolates were obtained from treatment-naïve patients with pulmonary MAC disease at the diagnosis of MAC infection at 8 hospitals in Japan. Their susceptibilities of moxifloxacin were determined by broth microdilution methods. Moxifloxacin-resistant isolates were examined for mutations of gyrA and gyrB. Variable numbers of tandem repeats (VNTR) assay was performed using 15 M. avium VNTR loci and 16 M. intracellulare VNTR loci. RESULTS Moxifloxacin susceptibility was categorized as resistant and intermediate for 6.5% and 16.9%, respectively, of M. avium isolates and 8.6% and 17.1% of M. intracellulare isolates. Although the isolates of both species had amino acid substitutions of Thr 96 and Thr 522 at the sites corresponding to Ser 95 in the M. tuberculosis GyrA and Gly 520 in the M. tuberculosis GyrB, respectively, these substitutions were observed irrespective of susceptibility and did not confer resistance. The VNTR assays showed revealed three clusters among M. avium isolates and two clusters among M. intracellulare isolates. No significant differences in moxifloxacin resistance were observed among these clusters. CONCLUSIONS Although resistance or intermediate resistance to moxifloxacin was observed in approximately one-fourth of M. avium and M. intracellulare isolates, this resistance was not associated with mutations in gyrA and gyrB or with VNTR genotypes.
Collapse
Affiliation(s)
- Yusuke Yamaba
- Department of Respiratory Medicine, Allergy and Clinical Immunology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yutaka Ito
- Department of Respiratory Medicine, Allergy and Clinical Immunology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan; Department of Respiratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
| | - Katsuhiro Suzuki
- Department of Internal Medicine, National Hospital Organization Kinki-chuo Chest Medical Center, Osaka, Japan
| | - Toshiaki Kikuchi
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kenji Ogawa
- Department of Respiratory Medicine, National Hospital Organization, Higashinagoya National Hospital, Nagoya, Japan
| | - Satoru Fujiuchi
- Department of Respiratory Medicine, National Hospital Organization, Asahikawa Medical Center, Asahikawa, Japan
| | - Naoki Hasegawa
- Center for Infectious Diseases and Infection Control, Keio University School of Medicine, Tokyo, Japan
| | - Atsuyuki Kurashima
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Takeshi Higuchi
- Laboratory for Clinical Investigation, Kyoto University Hospital, Kyoto, Japan
| | - Kei-Ichi Uchiya
- Department of Microbiology, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Akira Watanabe
- Research Division for Development of Anti-Infective Agents, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Akio Niimi
- Department of Respiratory Medicine, Allergy and Clinical Immunology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| |
Collapse
|
7
|
Kimizuka Y, Hoshino Y, Nishimura T, Asami T, Sakakibara Y, Morimoto K, Maeda S, Nakata N, Abe T, Uno S, Namkoong H, Fujiwara H, Funatsu Y, Yagi K, Fujie T, Ishii M, Inase N, Iwata S, Kurashima A, Betsuyaku T, Hasegawa N. Retrospective evaluation of natural course in mild cases of Mycobacterium avium complex pulmonary disease. PLoS One 2019; 14:e0216034. [PMID: 31022253 PMCID: PMC6483267 DOI: 10.1371/journal.pone.0216034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 04/14/2019] [Indexed: 11/23/2022] Open
Abstract
Background There is no proven management for mild cases of Mycobacterium avium complex (MAC) pulmonary disease, who do not immediately receive treatment and are managed with observation alone, because its long term-natural course, factors predictive of deterioration, and the effect of treating the disease remain unclear. Thus, we sought to investigate the natural course of mild cases of MAC pulmonary disease. Methods We conducted a multicenter retrospective study. Sixty-five patients with mild MAC pulmonary disease in whom treatment was withheld for at least 6 months after diagnosis were retrospectively recruited after a review of 747 medical records. Longitudinal changes in clinical features were evaluated by using a mixed effects model. Results Mean follow-up was 6.9 ± 5.7 years. During the follow-up period, 15 patients (23%) required treatment and 50 (77%) were managed with observation alone. At diagnosis, 65 patients had nodular bronchiectatic disease without fibrocavitary lesions. Among clinical features, mean body mass index (BMI), forced expiratory volume in 1 second as percent of forced vital capacity (%FEV1), nodular lung lesions, and bronchiectasis worsened significantly in the observation group during follow-up. In the treatment group, BMI, and %FEV1 were stable, but bronchiectasis significantly worsened. At diagnosis, the polyclonal MAC infection rate in the treatment group was higher than that in the observation group. Other microbiological factors, such as insertion sequences, did not differ significantly between the groups. Conclusions Mild MAC pulmonary disease progresses slowly but substantially without treatment. Treatment prevents the deterioration of the disease but not the progression of bronchiectasis. Polyclonal MAC infection is a predictor of disease progression.
Collapse
Affiliation(s)
- Yoshifumi Kimizuka
- Division of Pulmonary Medicine, Department of Medicine, School of Medicine, Keio University, Shinjuku, Tokyo, Japan
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Yoshihiko Hoshino
- Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
- * E-mail: (YH); (TN)
| | - Tomoyasu Nishimura
- Health Center, Keio University, Shinjuku, Tokyo, Japan
- * E-mail: (YH); (TN)
| | - Takahiro Asami
- Division of Pulmonary Medicine, Department of Medicine, School of Medicine, Keio University, Shinjuku, Tokyo, Japan
| | - Yumi Sakakibara
- Department of Integrated Pulmonology, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Kozo Morimoto
- Respiratory Disease Center, Fukujuji Hospital, Anti-tuberculosis Association, Kiyose, Tokyo, Japan
| | - Shinji Maeda
- Faculty of Pharmaceutical Sciences, Hokkaido University of Science, Sapporo, Hokkaido, Japan
| | - Noboru Nakata
- Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Takayuki Abe
- Department of Preventive Medicine and Public Health, Biostatistics Unit at Clinical and Translational Research Center, School of Medicine, Keio University, Shinjuku, Tokyo, Japan
| | - Shunsuke Uno
- Center for Infectious Diseases and Infection Control, School of Medicine, Keio University, Shinjuku, Tokyo, Japan
| | - Ho Namkoong
- Division of Pulmonary Medicine, Department of Medicine, School of Medicine, Keio University, Shinjuku, Tokyo, Japan
| | - Hiroshi Fujiwara
- Center for Infectious Diseases and Infection Control, School of Medicine, Keio University, Shinjuku, Tokyo, Japan
| | - Yohei Funatsu
- Division of Pulmonary Medicine, Department of Medicine, School of Medicine, Keio University, Shinjuku, Tokyo, Japan
| | - Kazuma Yagi
- Division of Pulmonary Medicine, Department of Medicine, School of Medicine, Keio University, Shinjuku, Tokyo, Japan
| | - Toshihide Fujie
- Department of Integrated Pulmonology, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Makoto Ishii
- Division of Pulmonary Medicine, Department of Medicine, School of Medicine, Keio University, Shinjuku, Tokyo, Japan
| | - Naohiko Inase
- Department of Integrated Pulmonology, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Satoshi Iwata
- Department of Infectious Diseases, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Atsuyuki Kurashima
- Respiratory Disease Center, Fukujuji Hospital, Anti-tuberculosis Association, Kiyose, Tokyo, Japan
| | - Tomoko Betsuyaku
- Division of Pulmonary Medicine, Department of Medicine, School of Medicine, Keio University, Shinjuku, Tokyo, Japan
| | - Naoki Hasegawa
- Center for Infectious Diseases and Infection Control, School of Medicine, Keio University, Shinjuku, Tokyo, Japan
| | | |
Collapse
|
8
|
Bakuła Z, Brzostek A, Borówka P, Żaczek A, Szulc-Kiełbik I, Podpora A, Parniewski P, Strapagiel D, Dziadek J, Proboszcz M, Bielecki J, van Ingen J, Jagielski T. Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis. Sci Rep 2018; 8:4462. [PMID: 29535391 PMCID: PMC5849605 DOI: 10.1038/s41598-018-21562-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 02/06/2018] [Indexed: 11/09/2022] Open
Abstract
Molecular epidemiological studies of Mycobacterium kansasii are hampered by the lack of highly-discriminatory genotyping modalities. The purpose of this study was to design a new, high-resolution fingerprinting method for M. kansasii. Complete genome sequence of the M. kansasii ATCC 12478 reference strain was searched for satellite-like repetitive DNA elements comprising tandem repeats. A total of 24 variable-number tandem repeat (VNTR) loci were identified with potential discriminatory capacity. Of these, 17 were used to study polymorphism among 67 M. kansasii strains representing six subtypes (I-VI). The results of VNTR typing were compared with those of pulsed-field gel electrophoresis (PFGE) with AsnI digestion. Six VNTRs i.e. (VNTR 1, 2, 8, 14, 20 and 23) allow to differentiate analyzed strains with the same discriminatory capacities as use of a 17-loci panel. VNTR typing and PFGE in conjunction revealed 45 distinct patterns, including 11 clusters with 33 isolates and 34 unique patterns. The Hunter-Gaston's discriminatory index was 0.95 and 0.66 for PFGE and VNTR typing respectively, and 0.97 for the two methods combined. In conclusion, this study delivers a new typing scheme, based on VNTR polymorphism, and recommends it as a first-line test prior to PFGE analysis in a two-step typing strategy for M. kansasii.
Collapse
Affiliation(s)
- Zofia Bakuła
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Paulina Borówka
- Department of Anthropology, University of Łódź, Łódź, Poland
| | - Anna Żaczek
- Department of Biochemistry and Cell Biology, University of Rzeszów, Rzeszów, Poland
| | | | - Agata Podpora
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paweł Parniewski
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Małgorzata Proboszcz
- Department of Internal Medicine, Pulmonary Diseases and Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Jacek Bielecki
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tomasz Jagielski
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| |
Collapse
|
9
|
Adachi T, Ichikawa K, Inagaki T, Moriyama M, Nakagawa T, Ogawa K, Hasegawa Y, Yagi T. Molecular typing and genetic characterization of Mycobacterium avium subsp. hominissuis isolates from humans and swine in Japan. J Med Microbiol 2016; 65:1289-1295. [PMID: 27624954 DOI: 10.1099/jmm.0.000351] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium avium subsp. hominissuis (MAH) causes disease in both humans and swine; however, the genetic variations in MAH isolates are unclear. The aim of this study was to elucidate the genetic variations in MAH isolates from humans and swine in Japan. We analysed the 16S-23S rDNA internal transcribed spacer (ITS) sequence and variable number of tandem repeats (VNTRs) using the Mycobacterium avium tandem repeat loci, prevalence of ISMav6 and clarithromycin resistance for MAH isolates from patients with pulmonary MAC (pMAC) disease (n=69), and HIV-seropositive and blood culture-positive (HIV-MAC) patients (n=28) and swine (n=23). In the minimum spanning tree based on VNTR analysis, swine MAC isolates belonged to a cluster distinguishable from that of human pMAC isolates. Isolates from HIV-MAC were scattered throughout both clusters. The three major distinct sequevars, Mav-A, Mav-B and Mav-F, were determined according to 16S-23S rDNA ITS sequence analysis in addition to three new sequevars, Mav-Q, Mav-R and Mav-S. Mav-A and Mav-F comprised the majority of human pMAC strains; in contrast, Mav-B predominated in swine isolates. Distribution of ITS sequevars in the minimum spanning tree based on VNTR analysis showed similar clusters of isolates from different origins, i.e. human pMAC, HIV-MAC and swine. These results, together with ISMav6 possession and clarithromycin resistance, revealed the genetic diversity of MAH strains recovered from humans and swine. Molecular epidemiology and genetic characterization in the present study showed the distinctive genetic evolutionary lineage of MAH strains isolated from human pMAC diseases and swine.
Collapse
Affiliation(s)
- Takashi Adachi
- Department of Pulmonary Medicine, National Hospital Organization, Higashinagoya National Hospital, 5-101 Umemorizaka, Meito-ku, Nagoya, Aichi 468-8620, Japan.,Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8560, Japan
| | - Kazuya Ichikawa
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8560, Japan
| | - Takayuki Inagaki
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8560, Japan
| | - Makoto Moriyama
- Department of Pharmacy, National Hospital Organization, Toyohashi Medical Center, Toyohashi 440-8510, Japan
| | - Taku Nakagawa
- Department of Pulmonary Medicine, National Hospital Organization, Higashinagoya National Hospital, 5-101 Umemorizaka, Meito-ku, Nagoya, Aichi 468-8620, Japan
| | - Kenji Ogawa
- Department of Pulmonary Medicine, National Hospital Organization, Higashinagoya National Hospital, 5-101 Umemorizaka, Meito-ku, Nagoya, Aichi 468-8620, Japan
| | - Yoshinori Hasegawa
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8560, Japan
| | - Tetsuya Yagi
- Department of Infectious Diseases, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8560, Japan
| |
Collapse
|
10
|
Variable-Number Tandem-Repeat Analysis of Respiratory and Household Water Biofilm Isolates of "Mycobacterium avium subsp. hominissuis" with Establishment of a PCR Database. J Clin Microbiol 2016; 54:891-901. [PMID: 26739155 DOI: 10.1128/jcm.02409-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/28/2015] [Indexed: 11/20/2022] Open
Abstract
"Mycobacterium aviumsubsp.hominissuis" is an important cause of pulmonary disease. It is acquired from environmental sources, but there is no methodology for large population studies. We evaluated the potential of variable-number tandem-repeat (VNTR) analysis. Clinical and household biofilmM. aviumisolates underwent molecular identification. Testing for IS901was done to separateM. aviumsubsp.aviumfromM. aviumsubsp.hominissuis VNTR types were defined using VNTR loci, and subtyping was performed using 3'hsp65and internal transcribed spacer (ITS) sequencing. Forty-nine VNTR types and eight subtypes ofM. aviumsubsp.hominissuis(IS901negative) were identified among 416 isolates ofM. aviumfrom 121 patients and 80 biofilm sites. Of those types, 67% were found only among patient isolates, 11% only among household water isolates, and 23% among both. Of 13 VNTR types that included ≥4 patients, the majority (61.5%) represented geographic clustering (same city). Most VNTR types with multiple patients belonged to the same 3'hsp65sequence code (sequevar). A total of 44 isolates belonging to fourM. aviumsubsp.hominissuisVNTR types (8%), including three with the rare Mav-F ITS sequence and 0/8 subspecies, produced amplicons with IS901PCR primers. By sequencing, all 44 amplicons were not IS901but ISMav6, which was recently observed in Japan but had not been previously described among U.S. isolates. VNTR analysis ofM. aviumsubsp.hominissuisisolates is easier and faster than pulsed-field gel electrophoresis. Seven VNTR loci separated 417 isolates into 49 types. No isolates ofM. aviumsubsp.aviumwere identified. The distributions of the VNTR copy numbers, the allelic diversity, and the low prevalence of ISMav6 differed from the findings for respiratory isolates reported from Japan.
Collapse
|
11
|
Genetic diversity of clinical Mycobacterium avium subsp. hominissuis and Mycobacterium intracellulare isolates causing pulmonary diseases recovered from different geographical regions. INFECTION GENETICS AND EVOLUTION 2015; 36:250-255. [PMID: 26435330 DOI: 10.1016/j.meegid.2015.09.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/09/2015] [Accepted: 09/29/2015] [Indexed: 11/22/2022]
Abstract
Mycobacterium avium complex (MAC) infections are increasing annually in many countries. MAC strains are the most common nontuberculous mycobacterial pathogens isolated from respiratory samples and predominantly consist of two species, Mycobacterium avium and Mycobacterium intracellulare. The aim of this study was to analyze the molecular epidemiology and genetic backgrounds of clinical MAC isolates collected from The Netherlands, Germany, United States, Korea and Japan. Variable numbers of tandem repeats (VNTR) analysis was used to examine the genetic relatedness of clinical isolates of M. avium subsp. hominissuis (n=261) and M. intracellulare (n=116). Minimum spanning tree and unweighted pair group method using arithmetic averages analyses based on the VNTR data indicated that M. avium subsp. hominissuis isolates from Japan shared a high degree of genetic relatedness with Korean isolates, but not with isolates from Europe or the United States, whereas M. intracellulare isolates did not show any specific clustering by geographic origin. The findings from the present study indicate that strains of M. avium subsp. hominissuis, but not M. intracellulare, exhibit geographical differences in genetic diversity and imply that MAC strains may have different sources, routes of transmission and perhaps clinical manifestations.
Collapse
|
12
|
Sun Z, Li W, Xu S, Huang H. The discovery, function and development of the variable number tandem repeats in different Mycobacterium species. Crit Rev Microbiol 2015; 42:738-58. [PMID: 26089025 DOI: 10.3109/1040841x.2015.1022506] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The method of genotyping by variable number tandem repeats (VNTRs) facilitates the epidemiological studies of different Mycobacterium species worldwide. Until now, the VNTR method is not fully understood, for example, its discovery, function and classification. The inconsistent nomenclature and terminology of VNTR is especially confusing. In this review, we first describe in detail the VNTRs in Mycobacterium tuberculosis (M. tuberculosis), as this pathogen resulted in more deaths than any other microbial pathogen as well as for which extensive studies of VNTRs were carried out, and then we outline the recent progress of the VNTR-related epidemiological research in several other Mycobacterium species, such as M. abscessus, M. africanum, M. avium, M. bovis, M. canettii, M. caprae, M. intracellulare, M. leprae, M. marinum, M. microti, M. pinnipedii and M. ulcerans from different countries and regions. This article is aimed mainly at the practical notes of VNTR to help the scientists in better understanding and performing this method.
Collapse
Affiliation(s)
- Zhaogang Sun
- a Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing Key Laboratory for Drug Resistance Tuberculosis Research , Beijing , China and
| | - Weimin Li
- b Beijing Chest Hospital, National Tuberculosis Clinical Laboratory, Capital Medical University , Beijing , China
| | - Shaofa Xu
- b Beijing Chest Hospital, National Tuberculosis Clinical Laboratory, Capital Medical University , Beijing , China
| | - Hairong Huang
- b Beijing Chest Hospital, National Tuberculosis Clinical Laboratory, Capital Medical University , Beijing , China
| |
Collapse
|
13
|
Association between polyclonal and mixed mycobacterial Mycobacterium avium complex infection and environmental exposure. Ann Am Thorac Soc 2014; 11:45-53. [PMID: 24251904 DOI: 10.1513/annalsats.201309-297oc] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
RATIONALE Polyclonal and mixed mycobacterial Mycobacterium avium complex (MAC) infection is observed in pulmonary MAC disease. Human living environments contain multiple species or genotypes of nontuberculous mycobacterial strains and are considered sources of infection. OBJECTIVES To investigate the association of environmental exposure with polyclonal and mixed mycobacterial infection in pulmonary MAC disease after adjustments for potential confounding diseases and conditions and radiographic findings. METHODS We collected two separate sputum samples from 102 patients and single sputum samples from 18 patients in whom the second MAC strain was not isolated in our prospective cohort of pulmonary MAC disease. MAC isolates from sputum samples and patients' residential soils were used for variable number of tandem repeats (VNTR) analyses. Polyclonal and mixed mycobacterial MAC infections were defined as having different VNTR genotypes and other mycobacterial species, respectively. Monoclonal MAC infection was defined as all isolates showing a single VNTR genotype. Associations of the type of infection with clinical and radiographic findings and environmental exposure were measured. MEASUREMENTS AND MAIN RESULTS Polyclonal and mixed mycobacterial MAC and monoclonal infections were observed in 42 and 78 patients, respectively. By stepwise regression analysis, patients with polyclonal and mixed mycobacterial MAC infections were associated with history of asthma (odds ratio [OR], 11.56; 95% confidence interval [CI], 1.41-255.77; P = 0.021), high soil exposure (≥2 h/wk; OR, 4.31; 95% CI, 1.72-11.45; P < 0.01), shower use in a bathroom (OR, 4.57; 95% CI, 1.28-23.23; P = 0.018), and swimming in a pool (OR, 9.69; 95% CI, 1.21-206.92; P < 0.01). CONCLUSIONS Environmental exposure was associated with polyclonal and mixed mycobacterial MAC infection in pulmonary MAC disease.
Collapse
|
14
|
Zhao X, Wang Y, Pang Y. Antimicrobial susceptibility and molecular characterization of Mycobacterium intracellulare in China. INFECTION GENETICS AND EVOLUTION 2014; 27:332-8. [PMID: 25131955 DOI: 10.1016/j.meegid.2014.07.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/24/2014] [Accepted: 07/29/2014] [Indexed: 10/24/2022]
Abstract
Mycobacterium avium complex (MAC) is the most common non-tuberculosis mycobacterial pathogen isolated from respiratory samples, mainly including two species, Mycobacterium avium (M. avium) and Mycobacterium intracellulare (M. intracellulare). Although these two species belong to the same group, M. avium and M. intracellulare reveal significantly differences in pathogenicity and biology. Nevertheless, little is known regarding the drug resistant details profile of M. avium or M. intracellulare instead of MAC. Here, we examined the antimicrobial susceptibility profiles of 52 clinical M. intracellulare isolates against fourteen antimicrobial agents, which are widely selected for the treatment of nontuberculous mycobacteria (NTM) infection. The drug susceptibility test revealed that clarithromycin (47/52, 90.4%), rifampicin (41/52, 78.8%) and capreomycin (40/52, 76.9%) revealed highly antimicrobial activities against M. intracellulare isolates in vitro. Furthermore, all clarithromycin resistant isolates harbored mutations in the 23S rRNA gene, and the percentage of amikacin resistant ones with mutation in the rrs gene is 62.5% (10/16). The Hunter-Gaston Discriminatory Index (HGDI) value for the 16-loci Variable Number of Tandem Repeat (VNTR) typing of M. intracellulare isolates was 0.994, and M. intracellulare resistance to moxifloxacin was significantly more commonly found in clustered strains than in nonclustered strains (χ(2)=5.551, P=0.040). In conclusion, our data demonstrated that clarithromycin and capreomycin revealed highly antimicrobial activities against M. intracellulare isolates, and clarithromycin and amikacin resistance could be detected more readily and rapidly using molecular scanning of corresponding drug target than conventional drug susceptibility testing. We also found that infection by clustered strains was significantly associated with resistance to moxifloxacin.
Collapse
Affiliation(s)
- Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Yufeng Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yu Pang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| |
Collapse
|
15
|
Leão C, Canto A, Machado D, Sanches IS, Couto I, Viveiros M, Inácio J, Botelho A. Relatedness of Mycobacterium avium subspecies hominissuis clinical isolates of human and porcine origins assessed by MLVA. Vet Microbiol 2014; 173:92-100. [PMID: 25085520 DOI: 10.1016/j.vetmic.2014.06.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 05/16/2014] [Accepted: 06/28/2014] [Indexed: 11/26/2022]
Abstract
Mycobacterium avium subsp. hominissuis (MAH) is an important opportunistic pathogen, infecting humans and animals, notably pigs. Several methods have been used to characterize MAH strains. RFLP and PFGE typing techniques have been used as standard methods but are technically demanding. In contrast, the analysis of VNTR loci is a simpler, affordable and highly reliable PCR-based technique, allowing a numerical and reproductive digitalization of typing data. In this study, the analysis of Mycobacterium avium tandem repeats (MATRs) loci was adapted to evaluate the genetic diversity of epidemiological unrelated MAH clinical strains of human (n=28) and porcine (n=69) origins, collected from diverse geographical regions across mainland Portugal. These MAH isolates were found to be genetically diverse and genotypes are randomly distributed across the country. Some of the human strains shared identical VNTR profiles with porcine isolates. Our study shows that the VNTR genotyping using selected MATR loci is a useful analysis technique for assessing the genetic diversity of MAH isolates from Portugal. This typing method could be successfully applied in other countries toward the implementation of a worldwide open-access database of MATR-VNTR profiles of MAH isolates, allowing a better assessment of the global epidemiology traits of this important pathogenic species.
Collapse
Affiliation(s)
- Célia Leão
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV, IP), Estrada de Benfica 701, 1549-011 Lisboa, Portugal; Centro de Recursos Microbiológicos (CREM), Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Ana Canto
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV, IP), Estrada de Benfica 701, 1549-011 Lisboa, Portugal
| | - Diana Machado
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical da Universidade Nova deLisboa (IHMT/UNL), Rua da Junqueira, 100, 1349-008 Lisboa, Portugal
| | - Ilda Santos Sanches
- Centro de Recursos Microbiológicos (CREM), Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Isabel Couto
- Centro de Recursos Microbiológicos (CREM), Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal; Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical da Universidade Nova deLisboa (IHMT/UNL), Rua da Junqueira, 100, 1349-008 Lisboa, Portugal
| | - Miguel Viveiros
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical da Universidade Nova deLisboa (IHMT/UNL), Rua da Junqueira, 100, 1349-008 Lisboa, Portugal
| | - João Inácio
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV, IP), Estrada de Benfica 701, 1549-011 Lisboa, Portugal; School of Pharmacy and Biomolecular Sciences, University of Brighton, Lewes Road, Brighton BN2 4GJ, United Kingdom.
| | - Ana Botelho
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV, IP), Estrada de Benfica 701, 1549-011 Lisboa, Portugal.
| |
Collapse
|
16
|
Taga S, Yagi T, Uchiya K, Shibata Y, Hamaura H, Nakagawa T, Hayashi Y, Nikai T, Ogawa K. Recurrence of pulmonary Mycobacterium avium complex disease due to endogenous reactivation. JMM Case Rep 2014. [DOI: 10.1099/jmmcr.0.000935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shu Taga
- Department of Respiratory Medicine and Allergology, Okayama City Hospital, 6‐10 Amase, Kita‐ku, Okayama, Okayama 700‐8557, Japan
| | - Tetsuya Yagi
- Department of Infectious Diseases, Nagoya University Hospital, 65 Tsurumai‐cho, Showa‐ku, Nagoya, Aichi 466‐8550, Japan
| | - Kei‐ichi Uchiya
- Department of Microbiology, Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tenpaku‐ku, Nagoya, Aichi 468‐8503, Japan
| | - Yuichi Shibata
- Department of Clinical Research, National Hospital Organization, Higashinagoya National Hospital, 5-101, Umemorizaka, Meito-ku, Nagoya, Aichi 465-8620, Japan
- Department of Microbiology, Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tenpaku‐ku, Nagoya, Aichi 468‐8503, Japan
| | - Hiromitsu Hamaura
- Department of Clinical Research, National Hospital Organization, Higashinagoya National Hospital, 5-101, Umemorizaka, Meito-ku, Nagoya, Aichi 465-8620, Japan
- Department of Microbiology, Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tenpaku‐ku, Nagoya, Aichi 468‐8503, Japan
| | - Taku Nakagawa
- Department of Pulmonary Medicine, National Hospital Organization, Higashinagoya National Hospital, 5‐101, Umemorizaka, Meito‐ku, Nagoya, Aichi 465‐8620, Japan
- Department of Clinical Research, National Hospital Organization, Higashinagoya National Hospital, 5-101, Umemorizaka, Meito-ku, Nagoya, Aichi 465-8620, Japan
| | - Yuta Hayashi
- Department of Pulmonary Medicine, National Hospital Organization, Higashinagoya National Hospital, 5‐101, Umemorizaka, Meito‐ku, Nagoya, Aichi 465‐8620, Japan
| | - Toshiaki Nikai
- Department of Microbiology, Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tenpaku‐ku, Nagoya, Aichi 468‐8503, Japan
| | - Kenji Ogawa
- Department of Pulmonary Medicine, National Hospital Organization, Higashinagoya National Hospital, 5‐101, Umemorizaka, Meito‐ku, Nagoya, Aichi 465‐8620, Japan
- Department of Clinical Research, National Hospital Organization, Higashinagoya National Hospital, 5-101, Umemorizaka, Meito-ku, Nagoya, Aichi 465-8620, Japan
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Muwonge A, Oloya J, Kankya C, Nielsen S, Godfroid J, Skjerve E, Djønne B, Johansen TB. Molecular characterization of Mycobacterium avium subspecies hominissuis isolated from humans, cattle and pigs in the Uganda cattle corridor using VNTR analysis. INFECTION GENETICS AND EVOLUTION 2013; 21:184-91. [PMID: 24270015 DOI: 10.1016/j.meegid.2013.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 11/08/2013] [Accepted: 11/12/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND Members of the Mycobacterium avium complex (MAC) cause disease in both human and animals. Their ubiquitous nature makes them both successful microbes and difficult to source track. The precise characterization of MAC species is a fundamental step in epidemiological studies and evaluating of possible reservoirs. This study aimed at identifying and characterizing Mycobacterium avium subsp. hominissuis isolated from human, slaughter cattle and pigs in various parts of the Uganda cattle corridor (UCC) at two temporal points using variable number of tandem repeat (VNTR) analysis. METHODS A total of 46 M. avium isolates; 31 from 997 pigs, 12 from 43 humans biopsies and three from 61 cattle lesions were identified to subspecies level using IS1245 and IS901 PCR, thereafter characterized using VNTR. Twelve loci from two previously described VNTR methods were used and molecular results were analyzed and interpreted using Bionumerics 6.1. PRINCIPAL FINDINGS 37 of the isolates were identified as M. avium subsp. hominissuis and four as M. avium subsp. avium, while five could not be differentiated, possibly due to mixed infection. There was distinct clustering that coincides with the temporal and spatial differences of the isolates. The isolates from humans and cattle in the North Eastern parts of the UCC shared identical VNTR genotypes. The panel of loci gave an overall discriminatory power of 0.88. Some loci were absent in several isolates, probably reflecting differences in isolates from Uganda/Africa compared to isolates previously analyzed by these methods in Europe and Asia. CONCLUSIONS The findings indicate a molecular difference between M. avium subsp. hominissuis isolates from pigs in Mubende and cattle and human in the rest of the UCC. Although human and cattle shared VNTR genotypes in the North Eastern parts of the UCC, it is most likely a reflection of a shared environmental source.
Collapse
Affiliation(s)
- Adrian Muwonge
- Department of Food Safety and Infection Biology, Center for Epidemiology and Biostatistics, Norwegian School of Veterinary Science, P.O. Box 8146 Dep., 0033 Oslo, Norway; The Roslin Institute, College of Medicine and Veterinary Medicine, University of Edinburgh, Easter Bush, Roslin, Midlothian EH25 9RG, United Kingdom.
| | - James Oloya
- Department of Epidemiology and Biostatistics/Population Health, College of Public Health, 132 Coverdell Center, University of Georgia Athens, GA 30602-7396, USA
| | - Clovice Kankya
- Department of Veterinary Public Health, School of Veterinary Medicine, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Sigrun Nielsen
- Norwegian Veterinary Institute, P.O. Box 750, N-0106 Oslo, Norway
| | - Jacques Godfroid
- Department of Food Safety and Infection Biology, Section of Arctic Veterinary Medicine, Norwegian School of Veterinary Science, Stakkevollveien 23, 9010 Tromsø, Norway
| | - Eystein Skjerve
- Department of Food Safety and Infection Biology, Center for Epidemiology and Biostatistics, Norwegian School of Veterinary Science, P.O. Box 8146 Dep., 0033 Oslo, Norway
| | - Berit Djønne
- Norwegian Veterinary Institute, P.O. Box 750, N-0106 Oslo, Norway
| | - Tone B Johansen
- Norwegian Veterinary Institute, P.O. Box 750, N-0106 Oslo, Norway
| |
Collapse
|
19
|
Fujita K, Ito Y, Hirai T, Maekawa K, Imai S, Tatsumi S, Niimi A, Iinuma Y, Ichiyama S, Mishima M. Genetic relatedness of Mycobacterium avium-intracellulare complex isolates from patients with pulmonary MAC disease and their residential soils. Clin Microbiol Infect 2013; 19:537-41. [DOI: 10.1111/j.1469-0691.2012.03929.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
20
|
Mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) genotyping of mycobacterium intracellulare for strain comparison with establishment of a PCR-based database. J Clin Microbiol 2012; 51:409-16. [PMID: 23175249 DOI: 10.1128/jcm.02443-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Strain comparison is important to population genetics and to evaluate relapses in patients with Mycobacterium avium complex (MAC) lung disease, but the "gold standard" of pulsed-field gel electrophoresis (PFGE) is time-consuming and complex. We used variable-number tandem repeats (VNTR) for fingerprinting of respiratory isolates of M. intracellulare from patients with underlying bronchiectasis, to establish a nonsequence-based database for population analysis. Different genotypes identified by PFGE underwent species identification using a 16S rRNA gene multiplex PCR. Genotypes of M. intracellulare were confirmed by internal transcribed spacer 1 (ITS1) sequencing and characterized using seven VNTR primers. The pattern of VNTR amplicon sizes and repeat number defined each specific VNTR type. Forty-two VNTR types were identified among 84 genotypes. PFGE revealed most isolates with the same VNTR type to be clonal or exhibit similar grouping of bands. Repetitive sequence-based PCR (rep-PCR) showed minimal pattern diversity between VNTR types compared to PFGE. Fingerprinting of relapse isolates from 31 treated patients using VNTR combined with 16S multiplex PCR unambiguously and reliably distinguished different genotypes from the same patient, with results comparable to those of PFGE. VNTR for strain comparison is easier and faster than PFGE, is as accurate as PFGE, and does not require sequencing. Starting with a collection of 167 M. intracellulare isolates, VNTR distinguished M. intracellulare into 42 clonal groups. Comparison of isolates from different geographic areas, habitats, and clinical settings is now possible.
Collapse
|
21
|
Broukhanski G, Simor A, Pillai DR. Defining criteria to interpret multilocus variable-number tandem repeat analysis to aid Clostridium difficile outbreak investigation. J Med Microbiol 2011; 60:1095-1100. [PMID: 21474615 DOI: 10.1099/jmm.0.029819-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PFGE is currently the North American standard for surveillance for Clostridium difficile but lacks discriminatory power to aid outbreak investigation. A further limitation to PFGE is the high baseline rate of the epidemic North American pulsotype (NAP) 1 strain in hospitals. Multilocus variable-number tandem repeat analysis (MLVA) appears to have superior discriminatory power but criteria to define clonality have not been set. We conducted surveillance for toxin-positive C. difficile infection (CDI) at a single academic health sciences centre between September 2009 and April 2010. Seventy-four patient specimens resulting in 86 discrete CDI episodes were subjected to PFGE and MLVA. Results were analysed using Bionumerics software to generate phylogenetic trees and coupled to patient demographic data. Amongst the NAP1 strains, two distinct clusters were identified by MLVA using 90 % similarity as a cut-off by Manhattan distance-based clustering, four clusters using 95 % and seven clusters using 97 %. Population analysis conducted on multiple colonies (n = 25) demonstrated that 1-3 % difference in MLVA types was typical for a single individual. Typing was also conducted in the context of institutional outbreaks (n = 42, three outbreaks) in order to determine clusters within the NAP1 strain. By combining longitudinal surveillance with epidemiological information, single specimen population analysis and typing in the context of institutional outbreaks, we conclude that the use of the Manhattan distance-based clustering with a cut-off of 95-97 % is capable of distinguishing outbreak clones from sporadic isolates.
Collapse
Affiliation(s)
- George Broukhanski
- Ontario Agency for Health Protection and Promotion, Toronto, Ontario, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Simor
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Dylan R Pillai
- Ontario Agency for Health Protection and Promotion, Toronto, Ontario, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
22
|
Dauchy FA, Dégrange S, Charron A, Dupon M, Xin Y, Bébéar C, Maugein J. Variable-number tandem-repeat markers for typing Mycobacterium intracellulare strains isolated in humans. BMC Microbiol 2010; 10:93. [PMID: 20350295 PMCID: PMC2861668 DOI: 10.1186/1471-2180-10-93] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Accepted: 03/29/2010] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Mycobacterium intracellulare, a species of the Mycobacterium avium complex, may be the cause of severe lung, lymphatic node, skin and bone/joint infections, as well as bacteriemia. The goal of this work was to identify Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) markers and to study their variability in a collection of isolates of M. intracellulare collected in humans. We studied 61 isolates collected in humans between 2001 and 2008, as well as the reference strain, M. intracellulare ATCC 13950. RESULTS We identified 45 MIRU-VNTR candidates, of which 17 corresponded to the MIRU-VNTR identified in the genome of M. intracellulare ATCC 13950. Among the 45 potential MIRU-VNTR, seven were selected for use in a MIRU-VNTR assay applied to our collection of isolates. Forty-four patterns were found by MIRU-VNTR typing and the discriminatory power of the assay was high with a Hunter-Gaston diversity index of 0.98. We do not have evidence of a particular distribution of MIRU-VNTR polymorphism according to clinical situation. CONCLUSIONS Our results suggest that MIRU-VNTR typing could be used for molecular epidemiological studies applied to M. intracellulare.
Collapse
Affiliation(s)
- Frédéric-Antoine Dauchy
- Service de Maladies Infectieuses et Tropicales, Hôpital Pellegrin, Université Victor Segalen Bordeaux 2, 33076 Bordeaux, France.
| | | | | | | | | | | | | |
Collapse
|