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Sur S, Patra T, Karmakar M, Banerjee A. Mycobacterium abscessus: insights from a bioinformatic perspective. Crit Rev Microbiol 2022:1-16. [PMID: 35696783 DOI: 10.1080/1040841x.2022.2082268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Mycobacterium abscessus is a nontuberculous mycobacterium, associated with broncho-pulmonary infections in individuals suffering from cystic fibrosis, bronchiectasis, and pulmonary diseases. The risk factors for transmission include biofilms, contaminated water resources, fomites, and infected individuals. M. abscessus is extensively resistant to antibiotics. To date, there is no vaccine and combination antibiotic therapy is followed. However, drug toxicities, low cure rates, and high cost of treatment make it imperfect. Over the last 20 years, bioinformatic studies on M. abscessus have advanced our understanding of the pathogen. This review integrates knowledge from the analysis of genomes, microbiomes, genomic variations, phylogeny, proteome, transcriptome, secretome, antibiotic resistance, and vaccine design to further our understanding. The utility of genome-based studies in comprehending disease progression, surveillance, tracing transmission routes, and epidemiological outbreaks on a global scale has been highlighted. Furthermore, this review underlined the importance of using computational methodologies for pinpointing factors responsible for pathogen survival and resistance. We reiterate the significance of interdisciplinary research to fight M. abscessus. In a nutshell, the outcome of computational studies can go a long way in creating novel therapeutic avenues to control M. abscessus mediated pulmonary infections.
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Affiliation(s)
- Saubashya Sur
- Postgraduate Department of Botany, Ramananda College, Bishnupur, India
| | - Tanushree Patra
- Postgraduate Department of Botany, Ramananda College, Bishnupur, India
| | - Mistu Karmakar
- Postgraduate Department of Botany, Ramananda College, Bishnupur, India
| | - Anindita Banerjee
- Postgraduate Department of Botany, Ramananda College, Bishnupur, India
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Cheng A, Sun HY, Tsai YT, Lu PL, Lee SSJ, Lee YT, Wang YC, Liu PY, Chien JY, Hsueh PR, Chang SY, Wu UI, Sheng WH, Chen YC, Chang SC. Longitudinal non-cystic fibrosis trends of pulmonary Mycobacterium abscessus disease from 2010 to 2017: spread of the "globally successful clone" in Asia. ERJ Open Res 2021; 7:00191-2020. [PMID: 33532483 PMCID: PMC7836708 DOI: 10.1183/23120541.00191-2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/30/2020] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Mycobacterium abscessus (MAB) has emerged as the predominant pulmonary non-tuberculous mycobacterial pathogen in parts of Asia, including Taiwan. The reasons for the significant increase in MAB infections in the non-cystic fibrosis (CF) populations are poorly understood. The study aimed to elucidate whether this increase is related to the spread of the globally successful clone of MAB. METHODS We performed multilocus sequence typing of 371 nonduplicated MAB pulmonary isolates from 371 patients sampled between 2010-2017 at seven hospitals across Taiwan. RESULTS In total, 183 (49.3%) isolates were M. abscessus subsp. abscessus (MAB-a), 187 (50.4%) were M. abscessus subsp. massiliense (MAB-m), and 1 (0.3%) was M. abscessus subsp. bolletii (MAB-b). MAB-a sequence type (ST)1 (23.7%) and ST127 (3.8%), followed by MAB-m ST48 (16.2%), ST117 (15.1%), ST23 (8.6%) were most common overall. Of MAB-a strains, 50 (27.3%) belonged to novel STs and 38 (10.2%) were singleton strains, while of MAB-m strains, only 10 (5.3%) were novel and 8 (2.2%) were singletons. From 2010 to 2017, the frequency of the historically dominant ST1 declined from 28.6% to 22.5%, whereas the recently emerged globally successful clonal cluster 3, ST23 and ST48, increased from 14.3% to 40.0%. CONCLUSIONS The dominance of ST1 particularly in the last 2 years of this study appears to be declining, while ST23, reported in outbreaks among CF and post-surgical cohorts across the Americas and Europe, alongside the closely related ST48, is present among non-CF populations in Taiwan. These trends need to be confirmed with further ongoing studies to track the molecular epidemiology of clinical MAB isolates worldwide.
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Affiliation(s)
- Aristine Cheng
- Dept of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsin-Yun Sun
- Dept of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Tzu Tsai
- Dept of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Po-Liang Lu
- Dept of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Susan Shin-Jung Lee
- Dept of Internal Medicine, Dept of Pathology and Laboratory, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Yi-Tzu Lee
- Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
- Dept of Emergency Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yung-Chih Wang
- Dept of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Po-Yu Liu
- Dept of Internal Medicine, Taichung, Veterans General Hospital, Taichung, Taiwan
| | - Jung-Yien Chien
- Dept of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Po-Ren Hsueh
- Dept of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- College of Medicine, National Taiwan University, Taipei, Taiwan
- Dept of Laboratory Medicine, National Taiwan University Hospital, Taiwan
| | - Shu-Yuan Chang
- Dept of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Un-In Wu
- Dept of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wang-Huei Sheng
- Dept of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yee-Chun Chen
- Dept of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shan-Chwen Chang
- Dept of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- College of Medicine, National Taiwan University, Taipei, Taiwan
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Chin KL, Sarmiento ME, Alvarez-Cabrera N, Norazmi MN, Acosta A. Pulmonary non-tuberculous mycobacterial infections: current state and future management. Eur J Clin Microbiol Infect Dis 2020; 39:799-826. [PMID: 31853742 PMCID: PMC7222044 DOI: 10.1007/s10096-019-03771-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 11/18/2019] [Indexed: 12/11/2022]
Abstract
Currently, there is a trend of increasing incidence in pulmonary non-tuberculous mycobacterial infections (PNTM) together with a decrease in tuberculosis (TB) incidence, particularly in developed countries. The prevalence of PNTM in underdeveloped and developing countries remains unclear as there is still a lack of detection methods that could clearly diagnose PNTM applicable in these low-resource settings. Since non-tuberculous mycobacteria (NTM) are environmental pathogens, the vicinity favouring host-pathogen interactions is known as important predisposing factor for PNTM. The ongoing changes in world population, as well as socio-political and economic factors, are linked to the rise in the incidence of PNTM. Development is an important factor for the improvement of population well-being, but it has also been linked, in general, to detrimental environmental consequences, including the rise of emergent (usually neglected) infectious diseases, such as PNTM. The rise of neglected PNTM infections requires the expansion of the current efforts on the development of diagnostics, therapies and vaccines for mycobacterial diseases, which at present, are mainly focused on TB. This review discuss the current situation of PNTM and its predisposing factors, as well as the efforts and challenges for their control.
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Affiliation(s)
- Kai Ling Chin
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia.
| | - Maria E Sarmiento
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia
| | - Nadine Alvarez-Cabrera
- Center for Discovery and Innovation (CDI), Hackensack Meridian School of Medicine at Seton Hall University, Nutley, NJ, USA
| | - Mohd Nor Norazmi
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia
| | - Armando Acosta
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia.
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Comparing the Utilities of Different Multilocus Sequence Typing Schemes for Identifying Outbreak Strains of Mycobacterium abscessus subsp. massiliense. J Clin Microbiol 2019; 58:JCM.01304-19. [PMID: 31619535 DOI: 10.1128/jcm.01304-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 10/11/2019] [Indexed: 12/31/2022] Open
Abstract
Outbreaks of infections by Mycobacterium abscessus, particularly subspecies massiliense, are increasingly reported worldwide. Several multilocus sequence typing (MLST) protocols for grouping international outbreak strains have been developed but not yet directly compared. Using the three-gene (hsp65, rpoB, and secA1), seven-gene (argH, cya, glpK, gnd, murC, pta, and purH) and thirteen-gene (all of the preceding genes plus gdhA, pgm, and pknA) MLST schemes, we identified 22, 38, and 40 unique sequence types (STs), respectively, among a total of 139 nonduplicated M. abscessus isolates. Among subspecies massiliense, three-gene MLST not only clustered all outbreak strains together (in 100% agreement with the seven-gene and thirteen-gene schemes), but it also distinguished between two new STs that would have been grouped together by the seven-gene MLST but were distinct by the thirteen-gene MLST owing to differences in hsp65, rpoB, and pknA Here, we show that an abbreviated MLST may be useful for simultaneous identification of M. abscessus the subspecies level and screening M. abscessus subsp. massiliense isolates with outbreak potential.
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In Vitro Synergism of Rifabutin with Clarithromycin, Imipenem, and Tigecycline against the Mycobacterium abscessus Complex. Antimicrob Agents Chemother 2019; 63:AAC.02234-18. [PMID: 30670428 DOI: 10.1128/aac.02234-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/16/2019] [Indexed: 11/20/2022] Open
Abstract
Infections caused by the difficult-to-treat bacterium Mycobacterium abscessus are increasing in frequency. Rifabutin, in contrast to rifampin, appears to be active in vitro against M. abscessus, especially against clarithromycin-resistant strains. However, explorations for potential synergy between rifabutin and available antimicrobials are currently limited. In vitro synergism between rifabutin and 10 antimicrobials was evaluated in 31 mycobacterial strains by the checkerboard method. The fractional inhibitory concentration index (FICI) was calculated for each rifabutin-based combination. The colony morphology was recorded. Molecular methods for determination of the M. abscessus subspecies and analysis of macrolide resistance were performed by sequencing of the secA1, rpoB, hsp65, erm(41), and rrl genes. Rifabutin yielded an MIC50 of 16 mg/liter (range, 2 to 32 mg/liter) against 26 clinical M. abscessus isolates (comprising 13 M. abscessus subsp. abscessus and 13 M. abscessus subsp. massiliense isolates) and 5 reference strains, including M. abscessus subsp. abscessus ATCC 19977, M. abscessus subsp. bolletii BCRC 16915, M. abscessus subsp. massiliense BCRC 16916, M. chelonae ATCC 35752, and M. peregrinum ATCC 700686. Significant synergism, classified by an FICI of ≤0.5, was demonstrated for the combinations of rifabutin and imipenem in 100% of M. abscessus subsp. abscessus and 69% of M. abscessus subsp. massiliense isolates, and significant synergism for rifabutin and tigecycline was demonstrated in 77% of M. abscessus subsp. abscessus and 69% of M. abscessus subsp. massiliense isolates. Among the 6 clarithromycin-resistant (MICs ≥ 8 mg/liter) M. abscessus subsp. abscessus isolates, the combination of rifabutin and clarithromycin was 100% synergistic. Rifabutin showed promising in vitro synergism with first-line anti-M. abscessus agents, especially for macrolide-resistant M. abscessus subsp. abscessus isolates.
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Kham-Ngam I, Chetchotisakd P, Ananta P, Chaimanee P, Reechaipichitkul W, Lulitanond V, Namwat W, Faksri K. Differentiation between persistent infection/colonization and re-infection/re-colonization of Mycobacterium abscessus isolated from patients in Northeast Thailand. INFECTION GENETICS AND EVOLUTION 2018; 68:35-42. [PMID: 30521865 DOI: 10.1016/j.meegid.2018.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/20/2018] [Accepted: 12/01/2018] [Indexed: 01/15/2023]
Abstract
Mycobacterium abscessus can cause true infection or be present in the host as a harmless colonist. The ability of M. abscessus to cause disease and develop drug resistance is known to have a genetic basis. We aimed to differentiate between persistent infection and reinfection using multilocus sequence typing (MLST) and to study the genetic diversity of M. abscessus relative to multi-organ infection and drug resistance in Northeast Thailand. DNA was extracted from 62 M. abscessus isolates (24 cases). The following genes were sequenced: argH, cya, glpK, gnd, murC, pta, purH and rpoB. Drug susceptibility tests were performed using broth microdilution. Subspecies classification and phylogeny were determined. Among the 24 cases (62 isolates), 19 cases (49 isolates) were of true NTM infection and 5 cases (13 isolates) examples of colonization. Two subspecies, M. abscessus subsp. massiliense (12 cases, 32 isolates) and M. abscessus subsp. abscessus (12 cases, 30 isolates) were identified. The major sequence type (ST) was ST227. Two clonal groups among patients were found; clonal cluster I (5 cases, 8 isolates) and clonal cluster II (2 cases, 4 isolates) but no epidemiological link was apparent. Reinfection (2 cases with different clones of M. abscessus strains; >9 SNPs different) and persistent infection (14 cases with the same clone; <6 SNPs) were distinguished based on a phylogeny. Based on these SNP cutoff values, 3 cases of persistent colonization (same strain through time) and 2 cases of re-colonization (different strains through time) were identified. M. abscessus subsp. abscessus was significantly associated with clarithromycin resistance (p < .001) and multi-organ infection (p = .03). Molecular epidemiology based on MLST can be used to differentiate between reinfection vs persistent infection, persistent colonization vs re-colonization. ST227 was the main epidemic strain in Northeast Thailand.
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Affiliation(s)
- Irin Kham-Ngam
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
| | | | - Pimjai Ananta
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Clinical Microbiology Unit, Srinagarind Hospital, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Prajaub Chaimanee
- Clinical Microbiology Unit, Srinagarind Hospital, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Wipa Reechaipichitkul
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Viraphong Lulitanond
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
| | - Wises Namwat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand.
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Carneiro MDS, Nunes LDS, David SMMD, Barth AL. Lack of association between rrl and erm(41) mutations and clarithromycin resistance in Mycobacterium abscessus complex. Mem Inst Oswaldo Cruz 2017; 112:775-778. [PMID: 29091138 PMCID: PMC5661901 DOI: 10.1590/0074-02760170080] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/06/2017] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Mycobacterium abscessus complex (MABC) includes species with high resistance rates among mycobacterial pathogens. In fact, MABC infections may not respond to clarithromycin treatment, which has historically been very effective against MABC infection. Molecular markers have been proposed to detect both acquired (rrl polymorphisms) and inducible (erm(41) polymorphisms) clarithromycin resistance in MABC isolates. OBJECTIVES This study aimed to evaluate the susceptibility profile and molecular markers of clarithromycin resistance in MABC. METHODS The clarithromycin susceptibility profile was determined by broth microdilution with reads on days 3, 5, 7 and 14. Mutations in the rrl and erm(41) genes were evaluated by polymerase chain reaction (PCR) using specific primers, followed by sequencing. FINDINGS A total of 14 M. abscessus subsp. abscessus isolates and 28 M. abscessus subsp. massiliense isolates were evaluated, and clarithromycin resistance was observed in all isolates for up to three days of incubation. None of the 42 isolates exhibited a point mutation in the rrl gene, while all the isolates had a T28 polymorphism in the erm(41) gene. Moreover, all 28 M. abscessus subsp. massiliense isolates had a deletion in the erm(41) gene. MAIN CONCLUSIONS While all the MABC isolates exhibited acquired clarithromycin resistance, no isolates exhibited a point mutation in the rrl gene in this study. The M. abscessus subsp. massiliense isolates demonstrated clarithromycin resistance, which is an uncommon phenotype. The molecular data for the rrl and erm(41) genes were not consistent with the phenotypic test results of clarithromycin susceptibility, indicating a lack of correlation between molecular clarithromycin resistance markers for both acquired and inducible resistance.
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Affiliation(s)
- Maiara Dos Santos Carneiro
- Universidade Federal do Rio Grande do Sul, Faculdade de Farmácia, Programa de Pós-Graduação em Ciências Farmacêuticas, Porto Alegre, RS, Brasil.,Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Laboratório de Pesquisa em Resistência Bacteriana, Porto Alegre, RS, Brasil
| | - Luciana de Souza Nunes
- Universidade Federal do Pampa, Uruguaiana, RS, Brasil.,Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Laboratório de Pesquisa em Resistência Bacteriana, Porto Alegre, RS, Brasil
| | | | - Afonso Luis Barth
- Universidade Federal do Rio Grande do Sul, Faculdade de Farmácia, Programa de Pós-Graduação em Ciências Farmacêuticas, Porto Alegre, RS, Brasil.,Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Laboratório de Pesquisa em Resistência Bacteriana, Porto Alegre, RS, Brasil
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Ribeiro GM, Matsumoto CK, Real F, Teixeira D, Duarte RS, Mortara RA, Leão SC, de Souza Carvalho-Wodarz C. Increased survival and proliferation of the epidemic strain Mycobacterium abscessus subsp. massiliense CRM0019 in alveolar epithelial cells. BMC Microbiol 2017; 17:195. [PMID: 28903728 PMCID: PMC5598063 DOI: 10.1186/s12866-017-1102-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/05/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Outbreaks of infections caused by rapidly growing mycobacteria have been reported worldwide generally associated with medical procedures. Mycobacterium abscessus subsp. massiliense CRM0019 was obtained during an epidemic of postsurgical infections and was characterized by increased persistence in vivo. To better understand the successful survival strategies of this microorganism, we evaluated its infectivity and proliferation in macrophages (RAW and BMDM) and alveolar epithelial cells (A549). For that, we assessed the following parameters, for both M. abscessus CRM0019 as well as the reference strain M. abscessus ATCC 19977: internalization, intracellular survival for up 3 days, competence to subvert lysosome fusion and the intracellular survival after cell reinfection. RESULTS CRM0019 and ATCC 19977 strains showed the same internalization rate (approximately 30% after 6 h infection), in both A549 and RAW cells. However, colony forming units data showed that CRM0019 survived better in A549 cells than the ATCC 19977 strain. Phagosomal characteristics of CRM0019 showed the bacteria inside tight phagosomes in A549 cells, contrasting to the loosely phagosomal membrane in macrophages. This observation holds for the ATCC 19977 strain in both cell types. The competence to subvert lysosome fusion was assessed by acidification and acquisition of lysosomal protein. For M. abscessus strains the phagosomes were acidified in all cell lines; nevertheless, the acquisition of lysosomal protein was reduced by CRM0019 compared to the ATCC 19977 strain, in A549 cells. Conversely, in macrophages, both M. abscessus strains were located in mature phagosomes, however without bacterial death. Once recovered from macrophages M. abscessus could establish a new intracellular infection. Nevertheless, only CRM0019 showed a higher growth rate in A549, increasing nearly 10-fold after 48 and 72 h. CONCLUSION M. abscessus CRM0019 creates a protective and replicative niche in alveolar epithelial cells mainly by avoiding phagosome maturation. Once recovered from infected macrophages, CRM0019 remains infective and displays greater intracellular growth in A549 cells compared to the ATCC 19977 strain. This evasion strategy in alveolar epithelial cells may contribute to the long survival of the CRM0019 strain in the host and thus to the inefficacy of in vivo treatment.
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Affiliation(s)
- Giovanni Monteiro Ribeiro
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Cristianne Kayoko Matsumoto
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Fernando Real
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil.,Laboratoire Entrée muqueuse du VIH et Immunité muqueuse, Department Infection, Immunité et Inflammation, Institut Cochin, Paris, France
| | - Daniela Teixeira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Rafael Silva Duarte
- Laboratório de Micobactérias, Instituto de Microbiologia Professor Paulo de Góes, Cidade Universitária, Rio de Janeiro, Brazil
| | - Renato Arruda Mortara
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Sylvia Cardoso Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Cristiane de Souza Carvalho-Wodarz
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil. .,Department of Drug Delivery, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany.
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Everall I, Nogueira CL, Bryant JM, Sánchez-Busó L, Chimara E, Duarte RDS, Ramos JP, Lima KVB, Lopes ML, Palaci M, Kipnis A, Monego F, Floto RA, Parkhill J, Leão SC, Harris SR. Genomic epidemiology of a national outbreak of post-surgical Mycobacterium abscessus wound infections in Brazil. Microb Genom 2017; 3:e000111. [PMID: 28884021 PMCID: PMC5562415 DOI: 10.1099/mgen.0.000111] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/28/2017] [Indexed: 11/18/2022] Open
Abstract
An epidemic of post-surgical wound infections, caused by a non-tuberculous mycobacterium, has been on-going in Brazil. It has been unclear whether one or multiple lineages are responsible and whether their wide geographical distribution across Brazil is due to spread from a single point source or is the result of human-mediated transmission. 188 isolates, collected from nine Brazilian states, were whole genome sequenced and analysed using phylogenetic and comparative genomic approaches. The isolates from Brazil formed a single clade, which was estimated to have emerged in 2003. We observed temporal and geographic structure within the lineage that enabled us to infer the movement of sub-lineages across Brazil. The genome size of the Brazilian lineage was reduced relative to most strains in the three subspecies of Mycobacterium abscessus and contained a novel plasmid, pMAB02, in addition to the previously described pMAB01 plasmid. One lineage, which emerged just prior to the initial outbreak, is responsible for the epidemic of post-surgical wound infections in Brazil. Phylogenetic analysis indicates that multiple transmission events led to its spread. The presence of a novel plasmid and the reduced genome size suggest that the lineage has undergone adaptation to the surgical niche.
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Affiliation(s)
- Izzy Everall
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Christiane Lourenço Nogueira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
| | - Josephine M Bryant
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Erica Chimara
- Núcleo de Tuberculose e Micobacterioses, Instituto Adolfo Lutz Av. Dr. Arnaldo, 666 9o andar São Paulo, SP, Brazil
| | - Rafael da Silva Duarte
- Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Brazil
| | | | | | - Maria Luíza Lopes
- Bacteriology and Mycology Section, Instituto Evandro Chagas, Para, Brazil
| | - Moises Palaci
- Nucleo de Doencas Infecciosas, Universidade Federal do Espirito Santo, Brazil
| | - Andre Kipnis
- Departamento de Microbiologia, Universidade Federal de Goiás, Brazil
| | - Fernanda Monego
- Departamento de Medicina Veterinária, Universidade Federal do Paraná, Brazil
| | - R. Andres Floto
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Sylvia Cardoso Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
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Mougari F, Guglielmetti L, Raskine L, Sermet-Gaudelus I, Veziris N, Cambau E. Infections caused by Mycobacterium abscessus: epidemiology, diagnostic tools and treatment. Expert Rev Anti Infect Ther 2016; 14:1139-1154. [PMID: 27690688 DOI: 10.1080/14787210.2016.1238304] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Mycobacterium abscessus is an emerging mycobacteria that is responsible for lung diseases and healthcare-associated extrapulmonary infections. Recent findings support its taxonomic status as a single species comprising 3 subspecies designated abscessus, bolletii and massiliense. We performed a review of English-language publications investigating all three of these subspecies. Areas covered: Worldwide, human infections are often attributable to environmental contamination, although the isolation of M. abscessus in this reservoir is very rare. Basic research has demonstrated an association between virulence and cell wall components and cording, and genome analysis has identified gene transfer from other bacteria. The bacteriological diagnosis of M. abscessus is based on innovative tools combining molecular biology and mass spectrometry. Genotypic and phenotypic susceptibility testing are required to predict the success of macrolide (clarithromycin or azithromycin)-based therapeutic regimens. Genotyping methods are helpful to assess relapse and cross-transmission and to search for a common source. Treatment is not standardised, and outcomes are often unsatisfactory. Expert commentary: M. abscessus is still an open field in terms of clinical and bacteriological research. Further knowledge of its ecology and transmission routes, as well as host-pathogen interactions, is required. Because the number of human cases is increasing, it is also necessary to identify more active treatments and perform clinical trials to assess standard effective regimens.
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Affiliation(s)
- Faiza Mougari
- a Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA) , Assistance publique-Hôpitaux de Paris (APHP) , Paris , France.,b AP-HP, Hôpital Lariboisière-Fernand Widal , Service de Bactériologie , Paris , France.,c IAME, UMR 1137, INSERM , Université Paris Diderot, Sorbonne Paris Cité , Paris , France
| | - Lorenzo Guglielmetti
- a Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA) , Assistance publique-Hôpitaux de Paris (APHP) , Paris , France.,b AP-HP, Hôpital Lariboisière-Fernand Widal , Service de Bactériologie , Paris , France.,d Sorbonne Universités, UPMC Université Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses, CIMI, team E13 (Bacteriology) , Paris , France.,e INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, CIMI, team E13 (Bacteriology) , Paris , France
| | - Laurent Raskine
- a Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA) , Assistance publique-Hôpitaux de Paris (APHP) , Paris , France.,b AP-HP, Hôpital Lariboisière-Fernand Widal , Service de Bactériologie , Paris , France
| | - Isabelle Sermet-Gaudelus
- f AP-HP, Groupe Hospitalier Necker-Enfants Malades , Centre de Ressources et de Compétences pour la Mucoviscidose (CRCM) et Centre de Formation de Traitement à Domicile Chez l'Enfant (CFTDE) , Paris , France
| | - Nicolas Veziris
- a Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA) , Assistance publique-Hôpitaux de Paris (APHP) , Paris , France.,d Sorbonne Universités, UPMC Université Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses, CIMI, team E13 (Bacteriology) , Paris , France.,e INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, CIMI, team E13 (Bacteriology) , Paris , France.,g AP-HP, Hôpital Pitié-Salpêtrière , Laboratory of Bacteriology , Paris , France
| | - Emmanuelle Cambau
- a Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA) , Assistance publique-Hôpitaux de Paris (APHP) , Paris , France.,b AP-HP, Hôpital Lariboisière-Fernand Widal , Service de Bactériologie , Paris , France.,c IAME, UMR 1137, INSERM , Université Paris Diderot, Sorbonne Paris Cité , Paris , France
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11
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Antibiotic susceptibility of diverse Mycobacterium abscessus complex strains in New South Wales, Australia. Pathology 2016; 47:678-82. [PMID: 26517625 DOI: 10.1097/pat.0000000000000327] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Members of the Mycobacterium abscessus complex are emerging pathogens of increasing importance, causing both respiratory and soft tissue infections, but precise speciation is problematic. This study was performed to examine the subspecies and antibiotic susceptibility of M. abscessus complex isolates collected during 2013 at the statewide New South Wales Mycobacterium Reference Laboratory (NSW MRL), Australia. Mycobacterium abscessus subsp. abscessus accounted for more than half of all M. abscessus isolates (n = 24, 57.1%), and M. abscessus subsp. massiliense comprised the remainder of the isolates (n = 18, 42.9%). There were no M. abscessus subsp. bolletii isolates. The prevalence of antibiotic resistance to all antibiotics, apart from amikacin was high, with 26.3% of isolates being reliably susceptible to only amikacin. Most M. abscessus subsp. abscessus isolates (80%) demonstrated inducible clarithromycin resistance whereas the majority of M. abscessus subsp. massiliense isolates (94.4%) remained susceptible to clarithromycin. There was a good correlation between the erm(41) genotype and clarithromycin susceptibility results after 14 days of incubation for most isolates with only three exceptions. Further studies correlating in vitro susceptibility profiles with clinical outcomes of M. abscessus infections treated with combination antimicrobial therapy are warranted.
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Bernut A, Viljoen A, Dupont C, Sapriel G, Blaise M, Bouchier C, Brosch R, de Chastellier C, Herrmann JL, Kremer L. Insights into the smooth-to-rough transitioning inMycobacterium bolletiiunravels a functional Tyr residue conserved in all mycobacterial MmpL family members. Mol Microbiol 2015; 99:866-83. [DOI: 10.1111/mmi.13283] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2015] [Indexed: 01/23/2023]
Affiliation(s)
- Audrey Bernut
- Centre National de la Recherche Scientifique FRE3689; Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé; Université de Montpellier; 1919 route de Mende 34293 Montpellier France
| | - Albertus Viljoen
- Centre National de la Recherche Scientifique FRE3689; Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé; Université de Montpellier; 1919 route de Mende 34293 Montpellier France
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, Inserm, U1104, CNRS UMR7280; 13288 Marseille France
| | - Christian Dupont
- Centre National de la Recherche Scientifique FRE3689; Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé; Université de Montpellier; 1919 route de Mende 34293 Montpellier France
| | - Guillaume Sapriel
- UMR1173; INSERM; Université de Versailles St Quentin; 2 avenue de la Source de la Bièvre 78180 Montigny le Bretonneux France
| | - Mickaël Blaise
- Centre National de la Recherche Scientifique FRE3689; Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé; Université de Montpellier; 1919 route de Mende 34293 Montpellier France
| | | | - Roland Brosch
- Institut Pasteur, Unité de Pathogénomique Mycobactérienne Intégrée; 25 rue du Dr. Roux 75724 Paris France
| | - Chantal de Chastellier
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, Inserm, U1104, CNRS UMR7280; 13288 Marseille France
| | - Jean-Louis Herrmann
- UMR1173; INSERM; Université de Versailles St Quentin; 2 avenue de la Source de la Bièvre 78180 Montigny le Bretonneux France
| | - Laurent Kremer
- Centre National de la Recherche Scientifique FRE3689; Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé; Université de Montpellier; 1919 route de Mende 34293 Montpellier France
- INSERM; CPBS; 34293 Montpellier France
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13
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Caierão J, Paiva JACD, Sampaio JLM, Silva MGD, Santos DRDS, Coelho FS, Fonseca LDS, Duarte RS, Armstrong DT, Regua-Mangia AH. Multilocus enzyme electrophoresis analysis of rapidly-growing mycobacteria: an alternative tool for identification and typing. Int J Infect Dis 2015; 42:11-16. [PMID: 26603643 DOI: 10.1016/j.ijid.2015.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/15/2015] [Accepted: 11/15/2015] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVES Rapidly growing mycobacteria (RGM) have emerged as important pathogens in clinical settings, associated with esthetic procedures and postsurgical infections, pulmonary infections among cystic fibrosis patients, and other structural pulmonary diseases. Microorganisms belonging to Mycobacterium abscessus-Mycobacterium chelonae and to Mycobacterium fortuitum groups have frequently been associated with outbreaks and various epidemics. In the present study, RGM strains were characterized in order to investigate molecular markers based on proteomic analysis. METHODS Multilocus enzyme electrophoresis (MLEE) was used for species identification and clonal analysis of RGM recovered from postsurgical wound infections during an epidemic. The study included 30M. abscessus subsp. bolletii clinical isolates, most belonging to the BRA100 clone (epidemic in Rio de Janeiro city), as well as 16 RGM ATCC reference strains. RESULTS Molecular typing allowed the detection of diversity in the studied population and revealed species-specific isoenzymatic patterns. Additionally, the clonal relationship among M. abscessus subsp. bolletii outbreak isolates, as examined using MLEE, was markedly consistent. CONCLUSIONS Isoenzymatic characterization was found to be a useful molecular tool to identify RGM species and to determine the relatedness among closely related M. abscessus subsp. bolletii isolates. This may be considered a powerful approach for epidemiological studies on RGM.
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Affiliation(s)
- Juliana Caierão
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre, Rio Grande do Sul, Brazil
| | - José Augusto Cardoso Dias Paiva
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, CCS, Bloco I, Cidade Universitária - Rio de Janeiro, RJ 21941-902, Brazil
| | | | - Marlei Gomes da Silva
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, CCS, Bloco I, Cidade Universitária - Rio de Janeiro, RJ 21941-902, Brazil
| | | | - Fabrice Santana Coelho
- Hospital Pedro Ernesto, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leila de Souza Fonseca
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, CCS, Bloco I, Cidade Universitária - Rio de Janeiro, RJ 21941-902, Brazil
| | - Rafael Silva Duarte
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, CCS, Bloco I, Cidade Universitária - Rio de Janeiro, RJ 21941-902, Brazil.
| | | | - Adriana Hamond Regua-Mangia
- Departamento de Ciências Biológicas, Escola Nacional de Saúde Pública Sergio Arouca/FIOCRUZ, Rio de Janeiro, Brazil
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14
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Nunes-Costa D, Alarico S, Dalcolmo MP, Correia-Neves M, Empadinhas N. The looming tide of nontuberculous mycobacterial infections in Portugal and Brazil. Tuberculosis (Edinb) 2015; 96:107-19. [PMID: 26560840 DOI: 10.1016/j.tube.2015.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/27/2015] [Accepted: 09/16/2015] [Indexed: 01/15/2023]
Abstract
Nontuberculous mycobacteria (NTM) are widely disseminated in the environment and an emerging cause of infectious diseases worldwide. Their remarkable natural resistance to disinfectants and antibiotics and an ability to survive under low-nutrient conditions allows NTM to colonize and persist in man-made environments such as household and hospital water distribution systems. This overlap between human and NTM environments afforded new opportunities for human exposure, and for expression of their often neglected and underestimated pathogenic potential. Some risk factors predisposing to NTM disease have been identified and are mainly associated with immune fragilities of the human host. However, infections in apparently immunocompetent persons are also increasingly reported. The purpose of this review is to bring attention to this emerging health problem in Portugal and Brazil and to emphasize the urgent need for increased surveillance and more comprehensive epidemiological data in both countries, where such information is scarce and seriously thwarts the adoption of proper preventive strategies and therapeutic options.
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Affiliation(s)
- Daniela Nunes-Costa
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Susana Alarico
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | | | - Margarida Correia-Neves
- ICVS - Health and Life Sciences Research Institute, University of Minho, Braga, Portugal; ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Nuno Empadinhas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal.
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15
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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.
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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
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