1
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Kim D, Shin JI, Yoo IY, Jo S, Chu J, Cho WY, Shin SH, Chung YJ, Park YJ, Jung SH. GenoMycAnalyzer: a web-based tool for species and drug resistance prediction for Mycobacterium genomes. BMC Genomics 2024; 25:387. [PMID: 38643090 PMCID: PMC11031912 DOI: 10.1186/s12864-024-10320-3] [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: 03/04/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Drug-resistant tuberculosis (TB) is a major threat to global public health. Whole-genome sequencing (WGS) is a useful tool for species identification and drug resistance prediction, and many clinical laboratories are transitioning to WGS as a routine diagnostic tool. However, user-friendly and high-confidence automated bioinformatics tools are needed to rapidly identify M. tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM), detect drug resistance, and further guide treatment options. RESULTS We developed GenoMycAnalyzer, a web-based software that integrates functions for identifying MTBC and NTM species, lineage and spoligotype prediction, variant calling, annotation, drug-resistance determination, and data visualization. The accuracy of GenoMycAnalyzer for genotypic drug susceptibility testing (gDST) was evaluated using 5,473 MTBC isolates that underwent phenotypic DST (pDST). The GenoMycAnalyzer database was built to predict the gDST for 15 antituberculosis drugs using the World Health Organization mutational catalogue. Compared to pDST, the sensitivity of drug susceptibilities by the GenoMycAnalyzer for first-line drugs ranged from 95.9% for rifampicin (95% CI 94.8-96.7%) to 79.6% for pyrazinamide (95% CI 76.9-82.2%), whereas those for second-line drugs ranged from 98.2% for levofloxacin (95% CI 90.1-100.0%) to 74.9% for capreomycin (95% CI 69.3-80.0%). Notably, the integration of large deletions of the four resistance-conferring genes increased gDST sensitivity. The specificity of drug susceptibilities by the GenoMycAnalyzer ranged from 98.7% for amikacin (95% CI 97.8-99.3%) to 79.5% for ethionamide (95% CI 76.4-82.3%). The incorporated Kraken2 software identified 1,284 mycobacterial species with an accuracy of 98.8%. GenoMycAnalyzer also perfectly predicted lineages for 1,935 MTBC and spoligotypes for 54 MTBC. CONCLUSIONS GenoMycAnalyzer offers both web-based and graphical user interfaces, which can help biologists with limited access to high-performance computing systems or limited bioinformatics skills. By streamlining the interpretation of WGS data, the GenoMycAnalyzer has the potential to significantly impact TB management and contribute to global efforts to combat this infectious disease. GenoMycAnalyzer is available at http://www.mycochase.org .
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Affiliation(s)
- Doyoung Kim
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jeong-Ih Shin
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Integrated Research Center for Genomic Polymorphism, Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - In Young Yoo
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sungjin Jo
- Department of Laboratory Medicine, Eunpyeong St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jiyon Chu
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | | | | | - Yeun-Jun Chung
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Integrated Research Center for Genomic Polymorphism, Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Departments of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeon-Joon Park
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seung-Hyun Jung
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea.
- Integrated Research Center for Genomic Polymorphism, Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea.
- Departments of Biochemistry, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seoch-Gu, Seoul, 06591, Republic of Korea.
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2
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Romagnoli CL, Conceição EC, Machado E, Barreto LBPF, Sharma A, Silva NM, Marques LE, Juliano MA, da Silva Lourenço MC, Digiampietri LA, Suffys PN, Leão SC, Viana-Niero C. Description of new species of Mycobacterium terrae complex isolated from sewage at the São Paulo zoological park foundation in Brazil. Front Microbiol 2024; 15:1335985. [PMID: 38322314 PMCID: PMC10844392 DOI: 10.3389/fmicb.2024.1335985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/02/2024] [Indexed: 02/08/2024] Open
Abstract
Five mycobacterial isolates from sewage were classified as members of the genus Mycobacterium but presented inconclusive species assignments. Thus, the isolates (MYC017, MYC098, MYC101, MYC123 and MYC340) were analyzed by phenotypical, biochemical, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and genomic features to clarify their taxonomic position. Phenotypic analysis and biochemical tests did not distinguish these isolates from other non-pigmented mycobacteria. In contrast, MALDI-TOF MS analysis showed that isolates were not related to any previously described Mycobacterium species. Comparative genomic analysis showed values of ANI and dDDH between 81.59-85.56% and 24.4-28.8%, respectively, when compared to the genomes of species of this genus. In addition, two (MYC101 and MYC123) presented indistinguishable protein spectra from each other and values of ANI = 98.57% and dDDH = 97.3%, therefore being considered as belonging to the same species. Phylogenetic analysis grouped the five isolates within the Mycobacterium terrae complex (MTC) but in a specific subclade and separated from the species already described and supported by 100% bootstrap value, confirming that they are part of this complex but different from earlier described species. According to these data, we propose the description of four new species belonging to the Mycobacterium genus: (i) Mycobacterium defluvii sp. nov. strain MYC017T (= ATCC TSD-296T = JCM 35364T), (ii) Mycobacterium crassicus sp. nov. strain MYC098T (= ATCC TSD-297T = JCM 35365T), (iii) Mycobacterium zoologicum sp. nov. strain MYC101T (= ATCC TSD-298T = JCM 35366T) and MYC123 (= ATCC BAA-3216 = JCM 35367); and (iv) Mycobacterium nativiensis sp. nov. strain MYC340T (= ATCC TSD-299T = JCM 35368T).
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Affiliation(s)
- Camila Lopes Romagnoli
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Emilyn Costa Conceição
- Laboratório de Bacteriologia e Bioensaios em Micobactérias, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Edson Machado
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Leonardo Bruno Paz Ferreira Barreto
- Laboratório de Bacteriologia e Bioensaios em Micobactérias, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Abhinav Sharma
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Natalia Maria Silva
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Lucas Evangelista Marques
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Maria Cristina da Silva Lourenço
- Laboratório de Bacteriologia e Bioensaios em Micobactérias, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Philip Noel Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Sylvia Cardoso Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Cristina Viana-Niero
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
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3
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Tagliani E, Kohl TA, Ghodousi A, Groenheit R, Holicka Y, Niemann S, Maurer FP, Cirillo DM, Cambau E. Appeal from the European tuberculosis reference laboratory network (ERLTB-Net) for improving the diagnosis of infections due to nontuberculous mycobacteria. Clin Microbiol Infect 2024; 30:4-6. [PMID: 37321396 DOI: 10.1016/j.cmi.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/28/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023]
Affiliation(s)
- Elisa Tagliani
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany; National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Arash Ghodousi
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ramona Groenheit
- National and WHO Supranational Reference Laboratory for Tuberculosis, Public Health Agency of Sweden, Solna, Sweden
| | - Yen Holicka
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany; National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Florian P Maurer
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Emmanuelle Cambau
- Université Paris Cité, IAME Inserm UMR 1137, Service de Mycobactériologie Spécialisée et de Référence, Laboratoire Associé Du CNR des Mycobactéries et de La Résistance des Mycobactéries Aux Antituberculeux (CNR-MyRMA) APHP GHU Paris Nord, Hôpital Bichat, Paris, France.
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4
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Singh N, Khare R, Mazumder S. Mycobacterium senegalense Infection in Kidney Transplant Patient with Diabetes, Memphis, Tennessee, USA. Emerg Infect Dis 2024; 30:192-194. [PMID: 38147514 PMCID: PMC10756380 DOI: 10.3201/eid3001.231013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
Fewer than 30 cases of Mycobacterium senegalense infection have been reported. We report a complicated case of M. senegalense infection in Memphis, Tennessee, in the southeastern United States. The patient's comorbidities of past organ transplant and insulin-dependent diabetes required delicate consideration of those health conditions to guide treatment.
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5
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Kiselinova M, Naesens L, Huis In ’t Veld D, Boelens J, Van Braeckel E, Vande Weygaerde Y, Callens S. Management Challenges of Extrapulmonary Nontuberculous Mycobacterial Infection: A Single-Center Case Series and Literature Review. Pathogens 2023; 13:12. [PMID: 38276158 PMCID: PMC10819148 DOI: 10.3390/pathogens13010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
Extrapulmonary nontuberculous mycobacterial (NTM) disease remains largely enigmatic, yet these mycobacteria are increasingly acknowledged as important opportunistic pathogens in humans. Traditionally, NTM infections have been identified across various anatomical locations, with the respiratory system being the most affected and best understood. Historically, extrapulmonary NTM infection was predominantly associated with HIV/AIDS, with Mycobacterium avium lymphadenopathy being the most commonly reported. Today, however, because of the expanding utilization of immunosuppressive therapies and the demographic shift towards an aging population, an increasing number of NTM infections are expected and seen. Hence, a heightened index of suspicion is essential, necessitating a multifaceted approach to identification and drug sensitivity testing to improve treatment outcomes. In extrapulmonary NTM management, expert consultation is strongly recommended to determine the most efficacious treatment regimen, as individualized, patient-tailored therapies are often required. Furthermore, the economic burden of NTM disease is considerable, accompanied by high rates of hospitalization. To optimize the management of these intricate infections, there is an urgent need for comprehensive data on incidence, prevalence, and outcomes. This case-based series delves into the intricate nature of extrapulmonary NTM infections, focusing on both rapid and slow-growing NTM species, and explores therapeutic options, resistance mechanisms, and host-related immunological factors.
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Affiliation(s)
- Maja Kiselinova
- Department of General Internal Medicine, Ghent University Hospital, 9000 Ghent, Belgium; (L.N.); (S.C.)
| | - Leslie Naesens
- Department of General Internal Medicine, Ghent University Hospital, 9000 Ghent, Belgium; (L.N.); (S.C.)
| | - Diana Huis In ’t Veld
- Department of General Internal Medicine, Ghent University Hospital, 9000 Ghent, Belgium; (L.N.); (S.C.)
| | - Jerina Boelens
- Department of Microbiology, Ghent University Hospital, 9000 Ghent, Belgium;
| | - Eva Van Braeckel
- Department of Respiratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium (Y.V.W.)
- Department of Internal Medicine and Paediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | | | - Steven Callens
- Department of General Internal Medicine, Ghent University Hospital, 9000 Ghent, Belgium; (L.N.); (S.C.)
- Department of Internal Medicine and Paediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
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6
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Gramegna A, Misuraca S, Lombardi A, Premuda C, Barone I, Ori M, Amati F, Retucci M, Nazzari E, Alicandro G, Ferrarese M, Codecasa L, Bandera A, Aliberti S, Daccò V, Blasi F. Treatable traits and challenges in the clinical management of non-tuberculous mycobacteria lung disease in people with cystic fibrosis. Respir Res 2023; 24:316. [PMID: 38104098 PMCID: PMC10725605 DOI: 10.1186/s12931-023-02612-1] [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: 09/05/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023] Open
Abstract
INTRODUCTION Over the last ten years an increasing prevalence and incidence of non-tuberculous mycobacteria (NTM) has been reported among patients with cystic fibrosis (CF) Viviani (J Cyst Fibros, 15(5):619-623, 2016). NTM pulmonary disease has been associated with negative clinical outcomes and often requires pharmacological treatment. Although specific guidelines help clinicians in the process of diagnosis and clinical management, the focus on the multidimensional assessment of concomitant problems is still scarce. MAIN BODY This review aims to identify the treatable traits of NTM pulmonary disease in people with CF and discuss the importance of a multidisciplinary approach in order to detect and manage all the clinical and behavioral aspects of the disease. The multidisciplinary complexity of NTM pulmonary disease in CF requires careful management of respiratory and extra-respiratory, including control of comorbidities, drug interactions and behavioral factors as adherence to therapies. CONCLUSIONS The treatable trait strategy can help to optimize clinical management through systematic assessment of all the aspects of the disease, providing a holistic treatment for such a multi-systemic and complex condition.
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Affiliation(s)
- Andrea Gramegna
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy.
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy.
| | - Sofia Misuraca
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Andrea Lombardi
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
- Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Chiara Premuda
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Ivan Barone
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Margherita Ori
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Francesco Amati
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072, Milan, Italy
- Respiratory Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089, Milan, Italy
| | - Mariangela Retucci
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
- Healthcare Professions Department, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Erica Nazzari
- Cystic Fibrosis Center, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milan, Italy
| | - Gianfranco Alicandro
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Maurizio Ferrarese
- Regional TB Reference Centre, Villa Marelli Institute, Niguarda Hospital, Milan, Italy
| | - Luigi Codecasa
- Regional TB Reference Centre, Villa Marelli Institute, Niguarda Hospital, Milan, Italy
| | - Alessandra Bandera
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
- Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Aliberti
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072, Milan, Italy
- Respiratory Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089, Milan, Italy
| | - Valeria Daccò
- Cystic Fibrosis Center, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milan, Italy
| | - Francesco Blasi
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
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7
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Honda JR. Environmental Sources and Transmission of Nontuberculous Mycobacteria. Clin Chest Med 2023; 44:661-674. [PMID: 37890909 DOI: 10.1016/j.ccm.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
The field of environmental nontuberculous mycobacteria (NTM) is benefiting from a new era of genomics that has catapulted our understanding of preferred niches, transmission, and outbreak investigations. The ability to forecast environmental features that promote or reduce environmental NTM prevalence will greatly improve with coordinated environmental sampling and by elevating the necessity for uniform disease notifications. Studies that synergize environmental biology, isolate notifications, and comparative genomics in prospective, longitudinal studies, particularly during climate changes and weather events, will be useful to solve longstanding NTM public health quandaries.
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Affiliation(s)
- Jennifer R Honda
- Department of Cellular and Molecular Biology, University of Texas Health Science Center at Tyler, 11937 US Hwy 271, BMR Building, Tyler, TX 75708, USA.
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8
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Calado Nogueira de Moura V, Nguyen MVH, Hunkins JJ, Daley CL, Khare R. In vitro susceptibility patterns for slowly growing non-tuberculous mycobacteria in the USA from 2018 to 2022. J Antimicrob Chemother 2023; 78:2849-2858. [PMID: 37864515 PMCID: PMC10689928 DOI: 10.1093/jac/dkad317] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/22/2023] [Indexed: 10/23/2023] Open
Abstract
BACKGROUND Treatment of slowly growing non-tuberculous mycobacteria (SGM) is challenging. In vitro antimicrobial susceptibility testing (AST) is needed to optimize a multidrug regimen but requires weeks to result. Aggregated AST patterns, or an antibiogram, of SGM would be helpful to providers. OBJECTIVES We aggregated and analysed human SGM isolates sent to our laboratory from across the USA between 2018 and 2022 to describe their in vitro susceptibility patterns and construct an antibiogram. METHODS SGM isolates' species/subspecies and mutations in rrs or rrl were identified by a line probe assay. AST was done primarily by broth microdilution and interpreted using the latest CLSI guideline. Mutational and AST results for SGM with ≥15 isolates were collated and analysed with descriptive statistics. RESULTS There were 32 different species/subspecies of SGM from 10 131 isolates between January 2018 and December 2022 from across the USA, 80% of which were from organisms in Mycobacterium avium complex (MAC). Most specimens were sputum and came from Florida (2892). MAC ranged from 94% to 100% susceptible to clarithromycin, 64% to 91% to amikacin, 2% to 31% to linezolid, and 4% to 41% to moxifloxacin. Non-MAC SGM ranged from 82% to 100% susceptible to clarithromycin, 49% to 100% to amikacin, and 76% to 100% to rifabutin, but susceptibilities to other antimicrobials varied widely. WT rrs and rrl predicted >96% of phenotypic non-resistance to amikacin and clarithromycin, respectively, whereas mutant genotypes predicted >90% of phenotypic resistance. CONCLUSIONS Most SGM are likely to be susceptible to clarithromycin and amikacin, complementing their treatment guidance by mycobacterial experts. Molecular identification of resistant genotypes is accurate and helpful. This antibiogram for SGM will help providers.
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Affiliation(s)
| | - Minh-Vu H Nguyen
- Division of Mycobacterial and Respiratory Infections, Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Joshua J Hunkins
- Department of Immunology and Microbiology, University of Colorado, Aurora, CO, USA
| | - Charles L Daley
- Division of Mycobacterial and Respiratory Infections, Department of Medicine, National Jewish Health, Denver, CO, USA
- Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Reeti Khare
- Advanced Diagnostics Laboratories, National Jewish Health, Denver, CO, USA
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9
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English J, Newberry F, Hoyles L, Patrick S, Stewart L. Genomic analyses of Bacteroides fragilis: subdivisions I and II represent distinct species. J Med Microbiol 2023; 72. [PMID: 37910167 DOI: 10.1099/jmm.0.001768] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Introduction. Bacteroides fragilis is a Gram-negative anaerobe that is a member of the human gastrointestinal microbiota and is frequently found as an extra-intestinal opportunistic pathogen. B. fragilis comprises two distinct groups - divisions I and II - characterized by the presence/absence of genes [cepA and ccrA (cfiA), respectively] that confer resistance to β-lactam antibiotics by either serine or metallo-β-lactamase production. No large-scale analyses of publicly available B. fragilis sequence data have been undertaken, and the resistome of the species remains poorly defined.Hypothesis/Gap Statement. Reclassification of divisions I and II B. fragilis as two distinct species has been proposed but additional evidence is required.Aims. To investigate the genomic diversity of GenBank B. fragilis genomes and establish the prevalence of division I and II strains among publicly available B. fragilis genomes, and to generate further evidence to demonstrate that B. fragilis division I and II strains represent distinct genomospecies.Methodology. High-quality (n=377) genomes listed as B. fragilis in GenBank were included in pangenome and functional analyses. Genome data were also subject to resistome profiling using The Comprehensive Antibiotic Resistance Database.Results. Average nucleotide identity and phylogenetic analyses showed B. fragilis divisions I and II represent distinct species: B. fragilis sensu stricto (n=275 genomes) and B. fragilis A (n=102 genomes; Genome Taxonomy Database designation), respectively. Exploration of the pangenome of B. fragilis sensu stricto and B. fragilis A revealed separation of the two species at the core and accessory gene levels.Conclusion. The findings indicate that B. fragilis A, previously referred to as division II B. fragilis, is an individual species and distinct from B. fragilis sensu stricto. The B. fragilis pangenome analysis supported previous genomic, phylogenetic and resistome screening analyses collectively reinforcing that divisions I and II are two separate species. In addition, it was confirmed that differences in the accessory genes of B. fragilis divisions I and II are primarily associated with carbohydrate metabolism and suggest that differences other than antimicrobial resistance could also be used to distinguish between these two species.
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Affiliation(s)
- Jamie English
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
| | - Fiona Newberry
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Lesley Hoyles
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Sheila Patrick
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
- Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Linda Stewart
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
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10
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Modesto M, Ngom-Bru C, Scarafile D, Bruttin A, Pruvost S, Sarker SA, Ahmed T, Sakwinska O, Mattarelli P, Duboux S. Bifidobacterium longum subsp. iuvenis subsp. nov., a novel subspecies isolated from the faeces of weaning infants. Int J Syst Evol Microbiol 2023; 73. [PMID: 37851001 DOI: 10.1099/ijsem.0.006013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023] Open
Abstract
The species
Bifidobacterium longum
currently comprises four subspecies:
B. longum
subsp.
longum
,
B. longum
subsp.
infantis
,
B. longum
subsp.
suis
and
B. longum
subsp.
suillum
. Recently, several studies on
B. longum
suggested the presence of a separate clade containing four strains isolated from infants and one from rhesus macaque. These strains shared a phylogenetic similarity to
B. longum
subsp.
suis
DSM 20210T and
B. longum
subsp.
suillum
JCM1995T [average nucleotide identity (ANI) of 98.1 %) while showed an ANI of 96.5 % with both
B. longum
subsp.
infantis
and
B. longum
subsp.
longum
. The current work describes five novel additional
B. longum
strains isolated from Bangladeshi weaning infants and demonstrates their common phylogenetic origin with those of the previously proposed separated clade. Based on polyphasic taxonomic approach comprising loci multilocus sequence analysis and whole genome multilocus sequence typing, all ten examined strains have been confirmed as a distinct lineage within the species
B. longum
with
B. longum
subsp.
suis
and
B. longum
subsp.
suillum
as closest subspecies. Interestingly, these strains are present in weaning infants and primates as opposed to their closest relatives which have been typically isolated from pig and calves. These strains, similarly to
B. longum
subsp.
infantis
, show a common capacity to metabolize the human milk oligosaccharide 3-fucosyllactose. Moreover, they harbour a riboflavin synthesis operon, which differentiate them from their closest subspecies,
B. longum
subsp.
suis
and
B. longum
subsp.
suillum
. Based on the consistent results from genotypical, ecological and phenotypical analyses, a novel subspecies with the name
Bifidobacterium longum
subsp. iuvenis, with type strain NCC 5000T (=LMG 32752T=CCOS 2034T), is proposed.
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Affiliation(s)
- Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 42, 40127 Bologna, Italy
| | - Catherine Ngom-Bru
- Nestlé Research, Société des Produits Nestlé SA, 1000 Lausanne 26, Switzerland
| | - Donatella Scarafile
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 42, 40127 Bologna, Italy
| | - Anne Bruttin
- Nestlé Research, Société des Produits Nestlé SA, 1000 Lausanne 26, Switzerland
| | - Solenn Pruvost
- Nestlé Research, Société des Produits Nestlé SA, 1000 Lausanne 26, Switzerland
| | - Shafiqul Alam Sarker
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Olga Sakwinska
- Nestlé Research, Société des Produits Nestlé SA, 1000 Lausanne 26, Switzerland
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 42, 40127 Bologna, Italy
| | - Stéphane Duboux
- Nestlé Research, Société des Produits Nestlé SA, 1000 Lausanne 26, Switzerland
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11
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Byrne A, Bissonnette N, Ollier S, Tahlan K. Investigating in vivo Mycobacterium avium subsp. paratuberculosis microevolution and mixed strain infections. Microbiol Spectr 2023; 11:e0171623. [PMID: 37584606 PMCID: PMC10581078 DOI: 10.1128/spectrum.01716-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's Disease (JD) in ruminants, which is responsible for significant economic loss to the global dairy industry. Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with genetically distinct strains of a pathogen, whereas within-host changes in an infecting strain leading to genetically distinguishable progeny is called microevolution. The two processes can influence host-pathogen dynamics, disease progression and outcomes, but not much is known about their prevalence and impact on JD. Therefore, we obtained up to 10 MAP isolates each from 14 high-shedding animals and subjected them to whole-genome sequencing. Twelve of the 14 animals examined showed evidence for the presence of MSIs and microevolution, while the genotypes of MAP isolates from the remaining two animals could be attributed solely to microevolution. All MAP isolates that were otherwise isogenic had differences in short sequence repeats (SSRs), of which SSR1 and SSR2 were the most diverse and homoplastic. Variations in SSR1 and SSR2, which are located in ORF1 and ORF2, respectively, affect the genetic reading frame, leading to protein products with altered sequences and computed structures. The ORF1 gene product is predicted to be a MAP surface protein with possible roles in host immune modulation, but nothing could be inferred regarding the function of ORF2. Both genes are conserved in Mycobacterium avium complex members, but SSR1-based modulation of ORF1 reading frames seems to only occur in MAP, which could have potential implications on the infectivity of this pathogen. IMPORTANCE Johne's disease (JD) is a major problem in dairy animals, and concerns have been raised regarding the association of Mycobacterium avium subsp. paratuberculosis (MAP) with Crohn's disease in humans. MAP is an extremely slow-growing bacterium with low genome evolutionary rates. Certain short sequence repeats (SSR1 and SSR2) in the MAP chromosome are highly variable and evolve at a faster rate than the rest of the chromosome. In the current study, multiple MAP isolates with genetic variations such as single-nucleotide polymorphisms, and more noticeably, diverse SSRs, could simultaneously infect animals. Variations in SSR1 and SSR2 affect the products of the respective genes containing them. Since multiple MAP isolates can infect the same animal and the possibility that the pathogen undergoes further changes within the host due to unstable SSRs, this could provide a compensative mechanism for an otherwise slow-evolving pathogen to increase phenotypic diversity for overcoming host responses.
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Affiliation(s)
- Alexander Byrne
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada
| | - Séverine Ollier
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
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12
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Wetzstein N, Kohl TA, Diricks M, Mas-Peiro S, Holubec T, Kessel J, Graf C, Koch B, Herrmann E, Vehreschild MJGT, Hogardt M, Niemann S, Stephan C, Wichelhaus TA. Clinical characteristics and outcome of Mycobacterium chimaera infections after cardiac surgery: systematic review and meta-analysis of 180 heater-cooler unit-associated cases. Clin Microbiol Infect 2023; 29:1008-1014. [PMID: 36918144 DOI: 10.1016/j.cmi.2023.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/13/2023] [Accepted: 03/05/2023] [Indexed: 03/14/2023]
Abstract
OBJECTIVES Since 2013, heater-cooler unit (HCU) associated Mycobacterium chimaera infections linked to a global outbreak have been described. These infections were characterised by high morbidity and mortality due to delayed diagnosis, as well as challenges in antimycobacterial and surgical therapy. This study aimed to investigate the clinical characteristics and outcome of published cases of HCU-associated M. chimaera infections. METHODS We searched PubMed and the Web of Science until 15 June 2022 for case reports, case series, and cohort studies, without language restriction, on patients with M. chimaera infection and a prior history of cardiac surgery. In this systematic review of case reports, no risk of bias assessment could be performed. Clinical, microbiological, and radiological features were recorded. Logistic regression and time-to-event analyses were performed to identify the potential factors associated with better survival. RESULTS One hundred eighty patients from 54 publications were included. Most patients underwent surgical aortic valve (67.0%; 118/176 of patients with available data) or combined aortic valve and root replacement (15.3%; 27/176). The median period between the time point of surgery and the first symptoms was 17 months (interquartile range 13-26 months). The overall case fatality rate was 45.5% (80/176), with a median survival of 24 months after the initiation of antimycobacterial therapy or diagnosis. A reoperation (including the removal or exchange of foreign material) was associated with better survival in multivariate logistic regression (OR 0.32 for lethal events; 95% CI 0.12-0.79; p 0.015) and in time-to-event analysis (p 0.0094). DISCUSSION This systematic review and meta-analysis confirm the high overall mortality of HCU -associated disseminated M. chimaera infections after cardiac surgery. A reoperation seems to be associated with better survival. Physicians have to stay aware of this infection, as patients might still be present today due to the long latency period.
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Affiliation(s)
- Nils Wetzstein
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.
| | - Thomas A Kohl
- The German Centre for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Germany; Molecular and Experimental Mycobacteriology, Research Centre Borstel, Borstel, Germany
| | - Margo Diricks
- The German Centre for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Germany; Molecular and Experimental Mycobacteriology, Research Centre Borstel, Borstel, Germany
| | - Silvia Mas-Peiro
- Department of Internal Medicine, Cardiology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Tomas Holubec
- Department of Cardiovascular Surgery, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johanna Kessel
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Christiana Graf
- Department of Internal Medicine, Gastroenterology and Hepatology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Benjamin Koch
- Department of Internal Medicine, Nephrology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Eva Herrmann
- Institute of Biostatistics and Mathematical Modelling, Goethe University, Frankfurt am Main, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Michael Hogardt
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Stefan Niemann
- The German Centre for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Germany; Molecular and Experimental Mycobacteriology, Research Centre Borstel, Borstel, Germany
| | - Christoph Stephan
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Thomas A Wichelhaus
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
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13
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Zhao F, Feng Y, Wang C, Xie Y, Zhou D, Xiao Y, Zong Z. Complete Genome Sequence of Mycobacterium marinum Strain 050012 Isolated from Infected Skin Tissue. Microbiol Resour Announc 2023:e0017423. [PMID: 37125927 DOI: 10.1128/mra.00174-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
We report the complete genome sequence of a Mycobacterium marinum strain, which was isolated from skin tissue of a wound infection. This strain was subjected to short- and long-read sequencing. Its complete genome contains a single 6,393,703-bp circular chromosome. Phylogenomic analysis of all M. marinum genomes assigned this strain to cluster I.
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Affiliation(s)
- Feifei Zhao
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Feng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
| | - Chengcheng Wang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Xie
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Dan Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yuling Xiao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
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14
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Kotimoole C, Antil N, Kasaragod S, Behera S, Arvind A, Reiling N, Flo T, Prasad T. Development of a spectral library for the discovery of altered genomic events in Mycobacterium avium associated with virulence using mass spectrometry-based proteogenomic analysis. Mol Cell Proteomics 2023; 22:100533. [PMID: 36948415 PMCID: PMC10149365 DOI: 10.1016/j.mcpro.2023.100533] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 02/02/2023] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
Mycobacterium avium is one of the prominent disease-causing bacteria in humans. It causes lymphadenitis, chronic and extrapulmonary, and disseminated infections in adults, children, and immunocompromised patients. M. avium has ∼4,500 predicted protein-coding regions on average, which can help discover several variants at the proteome level. Many of them are potentially associated with virulence; thus, identifying such proteins can be a helpful feature in developing panel-based theranostics. In line with such a long-term goal, we carried out an in-depth proteomic analysis of M. avium with both data-dependent and data-independent acquisition methods. Further, a set of proteogenomic investigations were carried out using i) a protein database for Mycobacterium tuberculosis, ii) a M. avium genome six-frame translated database, and iii) a variant protein database of M. avium. A search of mass spectrometry data against M. avium protein database resulted in identifying 2,954 proteins. Further, proteogenomic analyses aided in identifying 1,301 novel peptide sequences and correcting translation start sites for 15 proteins. Ultimately, we created a spectral library of M. avium proteins, including novel genome search-specific peptides and variant peptides detected in this study. We validated the spectral library by a data-independent acquisition of the M. avium proteome. Thus, we present an M. avium spectral library of 29,033 peptide precursors supported by 0.4 million fragment ions for further use by the biomedical community.
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Affiliation(s)
- ChinmayaNarayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Neelam Antil
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Sandeep Kasaragod
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - SantoshKumar Behera
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Anjana Arvind
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Norbert Reiling
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Parkallee 22, D-23845 Borstel, Germany; German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany
| | - TrudeHelen Flo
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Kunnskapssenteret, 424.04.035, Øya, Norway
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15
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Draft Genome Sequence of a Mycobacterium chelonae subsp. bovis Strain Isolated from a Baikal Seal (Pusa sibirica) in Captivity. Microbiol Resour Announc 2023; 12:e0113522. [PMID: 36840582 PMCID: PMC10019254 DOI: 10.1128/mra.01135-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Mycobacterium chelonae is a nontuberculous mycobacterium that causes infections in various animals, including humans. In this study, we report the draft genome sequence of M. chelonae subsp. bovis strain NJB1701, which was isolated from a Baikal seal (Pusa sibirica) in captivity in Japan.
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16
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Hunkins JJ, de-Moura VCN, Eddy JJ, Daley CL, Khare R. In vitro susceptibility patterns for rapidly growing nontuberculous mycobacteria in the United States. Diagn Microbiol Infect Dis 2023; 105:115882. [PMID: 36610383 DOI: 10.1016/j.diagmicrobio.2022.115882] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/01/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Antimicrobial susceptibility testing for rapidly growing mycobacteria (RGM) is uncommon or only performed in large reference laboratories. Here we developed a cumulative antibiogram for 14 RGM using the largest sample size to date (N = 3860). All RGM showed 82% to 100% susceptibility to amikacin. Mycobacterium abscessus showed low percentages of susceptibility to most antimicrobials; of antimicrobials without interpretations, the minimum inhibitory concentration-90 for clofazimine was low (≤0.5mg/L). All three subspecies had ≤2.6% rrl resistance mutations, however intact erm(41) was detected in 70% to100% of M. abscessus abscessus and bolletii. Mycobacterium chelonae had a similar susceptibility pattern to M. abscessus subsp. massiliense and Mycobacterium immunogenum except that it was susceptible to tobramycin (87%). Mycobacterium fortuitum complex and similar organisms showed higher frequency of susceptibility to fluoroquinolones, beta-lactams, linezolid, and trimethoprim/sulfamethoxazole. Although relatively small published RGM antibiograms showed substantial variance, a comprehensive antibiogram can help influence treatment and monitoring patterns of resistance.
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Affiliation(s)
- Joshua-J Hunkins
- Department of Immunology and Microbiology, University of Colorado, Aurora, CO, USA
| | | | - Jared-J Eddy
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Charles-L Daley
- Department of Medicine, National Jewish Health, Denver, CO, USA; Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Reeti Khare
- Advanced Diagnostics Laboratories, National Jewish Health, Denver, CO, USA; Department of Medicine, National Jewish Health, Denver, CO, USA.
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17
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Paiola M, Dimitrakopoulou D, Pavelka MS, Robert J. Amphibians as a model to study the role of immune cell heterogeneity in host and mycobacterial interactions. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 139:104594. [PMID: 36403788 DOI: 10.1016/j.dci.2022.104594] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
Mycobacterial infections represent major concerns for aquatic and terrestrial vertebrates including humans. Although our current knowledge is mostly restricted to Mycobacterium tuberculosis and mammalian host interactions, increasing evidence suggests common features in endo- and ectothermic animals infected with non-tuberculous mycobacteria (NTMs) like those described for M. tuberculosis. Importantly, most of the pathogenic and non-pathogenic NTMs detected in amphibians from wild, farmed, and research facilities represent, in addition to the potential economic loss, a rising concern for human health. Upon mycobacterial infection in mammals, the protective immune responses involving the innate and adaptive immune systems are highly complex and therefore not fully understood. This complexity results from the versatility and resilience of mycobacteria to hostile conditions as well as from the immune cell heterogeneity arising from the distinct developmental origins according with the concept of layered immunity. Similar to the differing responses of neonates versus adults during tuberculosis development, the pathogenesis and inflammatory responses are stage-specific in Xenopus laevis during infection by the NTM M. marinum. That is, both in human fetal and neonatal development and in tadpole development, responses are characterized by hypo-responsiveness and a lower capacity to contain mycobacterial infections. Similar to a mammalian fetus and neonates, T cells and myeloid cells in Xenopus tadpoles and axolotls are different from the adult immune cells. Fetal and amphibian larval T cells, which are characterized by a lower T cell receptor (TCR) repertoire diversity, are biased toward regulatory function, and they have distinct progenitor origins from those of the adult immune cells. Some early developing T cells and likely macrophage subpopulations are conserved in adult anurans and mammals, and therefore, they likely play an important role in the host-pathogen interactions from early stages of development to adulthood. Thus, we propose the use of developing amphibians, which have the advantage of being free-living early in their development, as an alternative and complementary model to study the role of immune cell heterogeneity in host-mycobacteria interactions.
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Affiliation(s)
- Matthieu Paiola
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Dionysia Dimitrakopoulou
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Martin S Pavelka
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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18
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Maranha A, Costa M, Ripoll-Rozada J, Manso JA, Miranda V, Mendes VM, Manadas B, Macedo-Ribeiro S, Ventura MR, Pereira PJB, Empadinhas N. Self-recycling and partially conservative replication of mycobacterial methylmannose polysaccharides. Commun Biol 2023; 6:108. [PMID: 36707645 PMCID: PMC9883506 DOI: 10.1038/s42003-023-04448-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/10/2023] [Indexed: 01/29/2023] Open
Abstract
The steep increase in nontuberculous mycobacteria (NTM) infections makes understanding their unique physiology an urgent health priority. NTM synthesize two polysaccharides proposed to modulate fatty acid metabolism: the ubiquitous 6-O-methylglucose lipopolysaccharide, and the 3-O-methylmannose polysaccharide (MMP) so far detected in rapidly growing mycobacteria. The recent identification of a unique MMP methyltransferase implicated the adjacent genes in MMP biosynthesis. We report a wide distribution of this gene cluster in NTM, including slowly growing mycobacteria such as Mycobacterium avium, which we reveal to produce MMP. Using a combination of MMP purification and chemoenzymatic syntheses of intermediates, we identified the biosynthetic mechanism of MMP, relying on two enzymes that we characterized biochemically and structurally: a previously undescribed α-endomannosidase that hydrolyses MMP into defined-sized mannoligosaccharides that prime the elongation of new daughter MMP chains by a rare α-(1→4)-mannosyltransferase. Therefore, MMP biogenesis occurs through a partially conservative replication mechanism, whose disruption affected mycobacterial growth rate at low temperature.
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Affiliation(s)
- Ana Maranha
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342IIIUC - Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Mafalda Costa
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Jorge Ripoll-Rozada
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal ,grid.507090.b0000 0004 5303 6218Present Address: Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, Spain
| | - José A. Manso
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Vanessa Miranda
- grid.10772.330000000121511713Bioorganic Chemistry Group, Instituto de Tecnologia Química Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Vera M. Mendes
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Sandra Macedo-Ribeiro
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - M. Rita Ventura
- grid.10772.330000000121511713Bioorganic Chemistry Group, Instituto de Tecnologia Química Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Pedro José Barbosa Pereira
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Nuno Empadinhas
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342IIIUC - Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
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19
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Li Y, Liu C, Ma A, He W, Qiu Q, Zhao Y, Li Y. Identification and drug susceptibility testing of the subspecies of Mycobacterium avium complex clinical isolates in mainland China. J Glob Antimicrob Resist 2022; 31:90-97. [PMID: 35660663 DOI: 10.1016/j.jgar.2022.05.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 10/25/2021] [Accepted: 05/29/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES The Mycobacterium avium complex (MAC), comprising a series of subspecies, has a worldwide distribution, with differences in drug susceptibility among subspecies. This study aimed to assess the composition of MAC and susceptibility differences among subspecies in mainland China. METHODS A total of 287 MAC clinical strains were included in the study. Multitarget sequences were applied to accurately identify subspecies, and a microdilution method was used to evaluate minimum inhibitory concentrations (MICs) among subspecies using Sensititre SLOMYCO plates. RESULTS Mycobacterium intracellular (N = 169), Mycobacterium avium (N = 52), Mycobacterium chimaera (N = 22), Mycobacterium marseillense (N = 25), Mycobacterium colombiense (N = 14), Mycobacterium yongonense (N = 4), Mycobacterium vulneris (N = 3) and Mycobacterium timonense (N = 2) were isolated from MAC. Clarithromycin, amikacin and rifabutin showed lower MIC50 and MIC90 values than other drugs, and the resistance rates of clarithromycin, amikacin, linezolid and moxifloxacin were 6.3%, 10.5%, 51.9% and 46.3%, respectively. The resistance rates of clarithromycin and moxifloxacin in the initial treatment group were significantly lower than those in the retreatment group (4.09% vs. 12.94%; 30.41% vs. 75.29%; P < 0.05). Drug susceptibility differences were observed in clarithromycin and moxifloxacin among the five major subspecies (P < 0.05); however, those statistically significant differences disappeared when MACs were divided into two groups according to previous anti-tuberculosis (anti-TB) treatment history. CONCLUSION This study revealed that MAC, primarily comprising M. intracellulare, was susceptible to clarithromycin, amikacin and rifabutin. Drug susceptibility among subspecies did not exhibit intrinsic differences in our study. Previous anti-TB treatment patients are more resistant to drugs; thus, attention should be given to those patients in the clinic.
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Affiliation(s)
- Yuanchun Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.
| | - Chunfa Liu
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Aijing Ma
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wencong He
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qian Qiu
- Research Institute of Tuberculosis, Chongqing Public Health Medical Center, Southwest University, Chongqing, China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Yanming Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.
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20
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Behra PRK, Pettersson BMF, Ramesh M, Das S, Dasgupta S, Kirsebom LA. Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA. BMC Genomics 2022; 23:704. [PMID: 36243697 PMCID: PMC9569102 DOI: 10.1186/s12864-022-08927-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Mycobacterium genus encompasses at least 192 named species, many of which cause severe diseases such as tuberculosis. Non-tuberculosis mycobacteria (NTM) can also infect humans and animals. Some are of emerging concern because they show high resistance to commonly used antibiotics while others are used and evaluated in bioremediation or included in anticancer vaccines. RESULTS We provide the genome sequences for 114 mycobacterial type strains and together with 130 available mycobacterial genomes we generated a phylogenetic tree based on 387 core genes and supported by average nucleotide identity (ANI) data. The 244 genome sequences cover most of the species constituting the Mycobacterium genus. The genome sizes ranged from 3.2 to 8.1 Mb with an average of 5.7 Mb, and we identified 14 new plasmids. Moreover, mycobacterial genomes consisted of phage-like sequences ranging between 0 and 4.64% dependent on mycobacteria while the number of IS elements varied between 1 and 290. Our data also revealed that, depending on the mycobacteria, the number of tRNA and non-coding (nc) RNA genes differ and that their positions on the chromosome varied. We identified a conserved core set of 12 ncRNAs, 43 tRNAs and 18 aminoacyl-tRNA synthetases among mycobacteria. CONCLUSIONS Phages, IS elements, tRNA and ncRNAs appear to have contributed to the evolution of the Mycobacterium genus where several tRNA and ncRNA genes have been horizontally transferred. On the basis of our phylogenetic analysis, we identified several isolates of unnamed species as new mycobacterial species or strains of known mycobacteria. The predicted number of coding sequences correlates with genome size while the number of tRNA, rRNA and ncRNA genes does not. Together these findings expand our insight into the evolution of the Mycobacterium genus and as such they establish a platform to understand mycobacterial pathogenicity, their evolution, antibiotic resistance/tolerance as well as the function and evolution of ncRNA among mycobacteria.
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Affiliation(s)
- Phani Rama Krishna Behra
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
| | - B. M. Fredrik Pettersson
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
| | - Malavika Ramesh
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
| | - Sarbashis Das
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
| | - Santanu Dasgupta
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
| | - Leif A. Kirsebom
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
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Evaluation of MALDI Biotyper Mycobacteria Library for Identification of Nontuberculous Mycobacteria. J Clin Microbiol 2022; 60:e0021722. [PMID: 35969171 PMCID: PMC9491183 DOI: 10.1128/jcm.00217-22] [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: 11/20/2022] Open
Abstract
The Bruker Biotyper matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) platform was assessed on its ability to accurately identify 314 nontuberculous mycobacteria (NTM) representing 73 species. All NTM isolates, representing 183 rapidly growing and 131 slowly growing organisms, were previously identified by Sanger DNA sequencing of the full-length 16S rRNA gene, and region V of the rpoB gene. An optimized version of the Bruker bead-beating procedure for protein extraction of NTM isolates was used to ensure high quality spectra for all NTM isolates, including less frequently encountered species. NTM spectra were analyzed using Bruker's research use only, Mycobacteria Library v6.0, supplemented by the MicrobeNet database. Identification of NTM by MALDI-TOF had an accuracy of 94% (296/314). The identification accuracy for rapidly growing mycobacteria was higher at 99% (182/183) than it was for slowly growing mycobacteria at 87% (114/131). While MALDI-TOF performed well against Sanger sequencing of the 16S rRNA gene alone, there were 11 species that required additional sequencing of rpoB. Most discrepancies between MALDI-TOF and sequencing results are likely due to underrepresentation of some species in the libraries used. Overall, the results of this study support Bruker's MALDI-TOF platform as an accurate and reliable method for the identification of NTM.
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Schmidt V, Köhler H, Heenemann K, Möbius P. Mycobacteriosis in Various Pet and Wild Birds from Germany: Pathological Findings, Coinfections, and Characterization of Causative Mycobacteria. Microbiol Spectr 2022; 10:e0045222. [PMID: 35852339 PMCID: PMC9430480 DOI: 10.1128/spectrum.00452-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/27/2022] [Indexed: 12/02/2022] Open
Abstract
A total of 50 birds diagnosed with mycobacteriosis were examined for pathomorphological lesions, coinfections, and causative agents. Mycobacterial species were identified and isolates differentiated using multilocus sequence typing (MLST) and mycobacterial interspersed repetitive-unit variable-number of tandem-repeat (MIRU-VNTR) analysis. Possible associations between mycobacterial species, pathomorphological findings, coinfections, bird orders, and husbandry conditions were evaluated statistically. Mycobacteria were isolated from 34 birds (13 of 22 Psittaciformes, 12 of 18 Passeriformes, five of six Columbiformes, and four other orders) belonging to 26 species in total. Mycobacterium genavense (Mg) was cultured from 15 birds, Mycobacterium avium subsp. avium (Maa) from 20 birds, and Mycobacterium avium subsp. hominissuis (Mah) from three birds; hence, four birds had mixed infections. About equal numbers of psittacines and passerines were infected with Ma and Mg. The genetic diversity differed; Mg isolates belonged to one MLST type, Maa to six, and Mah to three combined genotypes. Several coinfections were detected; viruses and/or endoparasites affected 44%, fungi 38%, and bacteria 29% of the birds. Pathological findings and mycobacteriosis-affected organs were independent of coinfections. Overall, gross pathological findings were more often seen in mycobacteriosis caused by Ma (95%) compared with Mg (66%). Organ distribution of mycobacteriosis was independent of the mycobacterial species. Pathomorphological changes were seen in the small intestine of 71% and the lung of 65% of the birds, suggesting oral or pulmonal ingestion of mycobacteria. There were no associations between mycobacterial species and bird orders or bird husbandry conditions. Not only Mg, but also Maa and Mah, were clearly identified as primary cause of mycobacteriosis in pet birds. IMPORTANCE In this study, the causative agents and confounding factors of mycobacteriosis in a set of pet and some wild birds from Germany were examined. Not only Mycobacterium genavense, but also M. avium subsp. avium and M. avium subsp. hominissuis, contributed to mycobacteriosis in these birds. Various coinfections did not affect the manifestation of mycobacteriosis. Due to different gross necropsy findings, however, a different pathogenicity of the two species was assumed. New strains of M. avium subsp. hominissuis originating from birds were identified and characterized, which is important for epidemiological studies and for understanding the zoonotic role of this pathogen, as the subsp. hominissuis represents an increasing public health concern. The study provides some evidence of correlation between M. avium subsp. avium genotypes and virulence which will have to be confirmed by broader studies.
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Grants
- Clinic for Birds and Reptiles, University of Leipzig, Germany
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Jena, Germany
- Institute for Virology, University of Leipzig, Germany
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Anmial Health), Jena, Germany
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Affiliation(s)
- Volker Schmidt
- Clinic for Birds and Reptiles, University of Leipzig, Leipzig, Germany
| | - Heike Köhler
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institute (Federal Research Institute for Animal Health), Jena, Germany
| | | | - Petra Möbius
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institute (Federal Research Institute for Animal Health), Jena, Germany
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Zangl L, Schäffer S, Daill D, Friedrich T, Gessl W, Mladinić M, Sturmbauer C, Wanzenböck J, Weiss SJ, Koblmüller S. A comprehensive DNA barcode inventory of Austria's fish species. PLoS One 2022; 17:e0268694. [PMID: 35679240 PMCID: PMC9182252 DOI: 10.1371/journal.pone.0268694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/04/2022] [Indexed: 11/19/2022] Open
Abstract
Austria is inhabited by more than 80 species of native and non-native freshwater fishes. Despite considerable knowledge about Austrian fish species, the latest Red List of threatened species dates back 15 years and a systematic genetic inventory of Austria's fish species does not exist. To fulfill this deficit, we employed DNA barcoding to generate an up-to-date and comprehensive genetic reference database for Austrian fish species. In total, 639 newly generated cytochrome c oxidase subunit 1 (COI) sequences were added to the 377 existing records from the BOLD data base, to compile a near complete reference dataset. Standard sequence similarity analyses resulted in 83 distinct clusters almost perfectly reflecting the expected number of species in Austria. Mean intraspecific distances of 0.22% were significantly lower than distances to closest relatives, resulting in a pronounced barcoding gap and unique Barcode Index Numbers (BINs) for most of the species. Four cases of BIN sharing were detected, pointing to hybridization and/or recent divergence, whereas in Phoxinus spp., Gobio spp. and Barbatula barbatula intraspecific splits, multiple BINs and consequently cryptic diversity were observed. The overall high identification success and clear genetic separation of most of the species confirms the applicability and accuracy of genetic methods for bio-surveillance. Furthermore, the new DNA barcoding data pinpoints cases of taxonomic uncertainty, which need to be addressed in further detail, to more precisely assort genetic lineages and their local distribution ranges in a new National Red-List.
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Affiliation(s)
- Lukas Zangl
- Institute of Biology, University of Graz, Graz, Austria
- Universalmuseum Joanneum, Studienzentrum Naturkunde, Graz, Austria
| | | | - Daniel Daill
- Institute of Biology, University of Graz, Graz, Austria
- Consultants in Aquatic Ecology and Engineering—blattfisch e.U., Wels, Austria
| | - Thomas Friedrich
- Institute of Hydrobiology and Aquatic Ecosystem Management, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Marija Mladinić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Josef Wanzenböck
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
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Mizzi R, Plain KM, Whittington R, Timms VJ. Global Phylogeny of Mycobacterium avium and Identification of Mutation Hotspots During Niche Adaptation. Front Microbiol 2022; 13:892333. [PMID: 35602010 PMCID: PMC9121174 DOI: 10.3389/fmicb.2022.892333] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/06/2022] [Indexed: 12/27/2022] Open
Abstract
Mycobacterium avium is separated into four subspecies: M. avium subspecies avium (MAA), M. avium subspecies silvaticum (MAS), M. avium subspecies hominissuis (MAH), and M. avium subspecies paratuberculosis (MAP). Understanding the mechanisms of host and tissue adaptation leading to their clinical significance is vital to reduce the economic, welfare, and public health concerns associated with diseases they may cause in humans and animals. Despite substantial phenotypic diversity, the subspecies nomenclature is controversial due to high genetic similarity. Consequently, a set of 1,230 M. avium genomes was used to generate a phylogeny, investigate SNP hotspots, and identify subspecies-specific genes. Phylogeny reiterated the findings from previous work and established that Mycobacterium avium is a species made up of one highly diverse subspecies, known as MAH, and at least two clonal pathogens, named MAA and MAP. Pan-genomes identified coding sequences unique to each subspecies, and in conjunction with a mapping approach, mutation hotspot regions were revealed compared to the reference genomes for MAA, MAH, and MAP. These subspecies-specific genes may serve as valuable biomarkers, providing a deeper understanding of genetic differences between M. avium subspecies and the virulence mechanisms of mycobacteria. Furthermore, SNP analysis demonstrated common regions between subspecies that have undergone extensive mutations during niche adaptation. The findings provide insights into host and tissue specificity of this genetically conserved but phenotypically diverse species, with the potential to provide new diagnostic targets and epidemiological and therapeutic advances.
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Affiliation(s)
- Rachel Mizzi
- Farm Animal Health, School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Karren M Plain
- Farm Animal Health, School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia.,Microbiology and Parasitology Research, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Richard Whittington
- Farm Animal Health, School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Verlaine J Timms
- Neilan Laboratory of Microbial and Molecular Diversity, College of Engineering, Science and Environment, The University of Newcastle, Newcastle, NSW, Australia
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25
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Complete Genome Sequence of Mycobacterium fortuitum subsp. fortuitum JCM 6387, a Type Strain of Human-Pathogenic Mycobacteria Showing Inducible Macrolide Resistance. Microbiol Resour Announc 2022; 11:e0006022. [PMID: 35357161 PMCID: PMC9022504 DOI: 10.1128/mra.00060-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Mycobacterium fortuitum subsp. fortuitum is a rapidly growing mycobacterial species for which pathogenic features are unclear. Here, we report the complete genome sequence of the Mycobacterium fortuitum subsp. fortuitum type strain. This sequence will provide essential information for future comparative genome studies of this mycobacterium.
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26
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Parker HA, Forrester L, Kaldor CD, Dickerhof N, Hampton MB. Antimicrobial Activity of Neutrophils Against Mycobacteria. Front Immunol 2021; 12:782495. [PMID: 35003097 PMCID: PMC8732375 DOI: 10.3389/fimmu.2021.782495] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/06/2021] [Indexed: 12/21/2022] Open
Abstract
The mycobacterium genus contains a broad range of species, including the human pathogens M. tuberculosis and M. leprae. These bacteria are best known for their residence inside host cells. Neutrophils are frequently observed at sites of mycobacterial infection, but their role in clearance is not well understood. In this review, we discuss how neutrophils attempt to control mycobacterial infections, either through the ingestion of bacteria into intracellular phagosomes, or the release of neutrophil extracellular traps (NETs). Despite their powerful antimicrobial activity, including the production of reactive oxidants such as hypochlorous acid, neutrophils appear ineffective in killing pathogenic mycobacteria. We explore mycobacterial resistance mechanisms, and how thwarting neutrophil action exacerbates disease pathology. A better understanding of how mycobacteria protect themselves from neutrophils will aid the development of novel strategies that facilitate bacterial clearance and limit host tissue damage.
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Affiliation(s)
| | | | | | | | - Mark B. Hampton
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
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Comparative Genomics of Mycobacterium avium Complex Reveals Signatures of Environment-Specific Adaptation and Community Acquisition. mSystems 2021; 6:e0119421. [PMID: 34665012 PMCID: PMC8525567 DOI: 10.1128/msystems.01194-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nontuberculous mycobacteria, including those in the Mycobacterium avium complex (MAC), constitute an increasingly urgent threat to global public health. Ubiquitous in soil and water worldwide, MAC members cause a diverse array of infections in humans and animals that are often multidrug resistant, intractable, and deadly. MAC lung disease is of particular concern and is now more prevalent than tuberculosis in many countries, including the United States. Although the clinical importance of these microorganisms continues to expand, our understanding of their genomic diversity is limited, hampering basic and translational studies alike. Here, we leveraged a unique collection of genomes to characterize MAC population structure, gene content, and within-host strain dynamics in unprecedented detail. We found that different MAC species encode distinct suites of biomedically relevant genes, including antibiotic resistance genes and virulence factors, which may influence their distinct clinical manifestations. We observed that M. avium isolates from different sources—human pulmonary infections, human disseminated infections, animals, and natural environments—are readily distinguished by their core and accessory genomes, by their patterns of horizontal gene transfer, and by numerous specific genes, including virulence factors. We identified highly similar MAC strains from distinct patients within and across two geographically distinct clinical cohorts, providing important insights into the reservoirs which seed community acquisition. We also discovered a novel MAC genomospecies in one of these cohorts. Collectively, our results provide key genomic context for these emerging pathogens and will facilitate future exploration of MAC ecology, evolution, and pathogenesis. IMPORTANCE Members of the Mycobacterium avium complex (MAC), a group of mycobacteria encompassing M. avium and its closest relatives, are omnipresent in natural environments and emerging pathogens of humans and animals. MAC infections are difficult to treat, sometimes fatal, and increasingly common. Here, we used comparative genomics to illuminate key aspects of MAC biology. We found that different MAC species and M. avium isolates from different sources encode distinct suites of clinically relevant genes, including those for virulence and antibiotic resistance. We identified highly similar MAC strains in patients from different states and decades, suggesting community acquisition from dispersed and stable reservoirs, and we discovered a novel MAC species. Our work provides valuable insight into the genomic features underlying these versatile pathogens.
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Hasan NA, Davidson RM, Epperson LE, Kammlade SM, Beagle S, Levin AR, de Moura VC, Hunkins JJ, Weakly N, Sagel SD, Martiniano SL, Salfinger M, Daley CL, Nick JA, Strong M. Population Genomics and Inference of Mycobacterium avium Complex Clusters in Cystic Fibrosis Care Centers, United States. Emerg Infect Dis 2021; 27:2836-2846. [PMID: 34670648 PMCID: PMC8544995 DOI: 10.3201/eid2711.210124] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Mycobacterium avium complex (MAC) species constitute most mycobacteria infections in persons with cystic fibrosis (CF) in the United States, but little is known about their genomic diversity or transmission. During 2016–2020, we performed whole-genome sequencing on 364 MAC isolates from 186 persons with CF from 42 cystic fibrosis care centers (CFCCs) across 23 states. We compared isolate genomes to identify instances of shared strains between persons with CF. Among persons with multiple isolates sequenced, 15/56 (27%) had >1 MAC strain type. Genomic comparisons revealed 18 clusters of highly similar isolates; 8 of these clusters had patients who shared CFCCs, which included 27/186 (15%) persons with CF. We provide genomic evidence of highly similar MAC strains shared among patients at the same CFCCs. Polyclonal infections and high genetic similarity between MAC isolates are consistent with multiple modes of acquisition for persons with CF to acquire MAC infections.
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Meehan CJ, Barco RA, Loh YHE, Cogneau S, Rigouts L. Reconstituting the genus Mycobacterium. Int J Syst Evol Microbiol 2021; 71:004922. [PMID: 34554081 PMCID: PMC8549266 DOI: 10.1099/ijsem.0.004922] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/18/2021] [Indexed: 11/23/2022] Open
Abstract
The definition of a genus has wide-ranging implications both in terms of binomial species names and also evolutionary relationships. In recent years, the definition of the genus Mycobacterium has been debated due to the proposed split of this genus into five new genera (Mycolicibacterium, Mycolicibacter, Mycolicibacillus, Mycobacteroides and an emended Mycobacterium). Since this group of species contains many important obligate and opportunistic pathogens, it is important that any renaming of species does not cause confusion in clinical treatment as outlined by the nomen periculosum rule (56a) of the Prokaryotic Code. In this study, we evaluated the proposed and original genus boundaries for the mycobacteria, to determine if the split into five genera was warranted. By combining multiple approaches for defining genus boundaries (16S rRNA gene similarity, amino acid identity index, average nucleotide identity, alignment fraction and percentage of conserved proteins) we show that the original genus Mycobacterium is strongly supported over the proposed five-way split. Thus, we propose that the original genus label be reapplied to all species within this group, with the proposed five genera potentially used as sub-genus complex names.
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Affiliation(s)
- Conor J. Meehan
- BCCM/ITM Mycobacterial Culture Collection, Institute of Tropical Medicine, Antwerp, Belgium
- School of Chemistry and Biosciences, University of Bradford, Bradford, UK
| | - Roman A. Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
| | - Yong-Hwee E. Loh
- Norris Medical Library, University of Southern California, Los Angeles, California, USA
| | - Sari Cogneau
- BCCM/ITM Mycobacterial Culture Collection, Institute of Tropical Medicine, Antwerp, Belgium
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- BCCM/ITM Mycobacterial Culture Collection, Institute of Tropical Medicine, Antwerp, Belgium
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
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Abstract
This minireview provides an updated overview of taxonomic changes for the genus Mycobacterium, with a focus on new species identified from humans or those associated with human disease for the period of 2018 to 2019.
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Intracellular localization of the mycobacterial stressosome complex. Sci Rep 2021; 11:10060. [PMID: 33980893 PMCID: PMC8115616 DOI: 10.1038/s41598-021-89069-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/19/2021] [Indexed: 11/09/2022] Open
Abstract
Microorganisms survive stresses by alternating the expression of genes suitable for surviving the immediate and present danger and eventually adapt to new conditions. Many bacteria have evolved a multiprotein "molecular machinery" designated the "Stressosome" that integrates different stress signals and activates alternative sigma factors for appropriate downstream responses. We and others have identified orthologs of some of the Bacillus subtilis stressosome components, RsbR, RsbS, RsbT and RsbUVW in several mycobacteria and we have previously reported mutual interactions among the stressosome components RsbR, RsbS, RsbT and RsbUVW from Mycobacterium marinum. Here we provide evidence that "STAS" domains of both RsbR and RsbS are important for establishing the interaction and thus critical for stressosome assembly. Fluorescence microscopy further suggested co-localization of RsbR and RsbS in multiprotein complexes visible as co-localized fluorescent foci distributed at scattered locations in the M. marinum cytoplasm; the number, intensity and distribution of such foci changed in cells under stressed conditions. Finally, we provide bioinformatics data that 17 (of 244) mycobacteria, which lack the RsbRST genes, carry homologs of Bacillus cereus genes rsbK and rsbM indicating the existence of alternative σF activation pathways among mycobacteria.
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Santos-Pérez JL, Delgado-Mainar P, Toro-Rueda C, Baquero-Artigao F. Infección de herida quirúrgica por Mycobacterium senegalense en paciente pediátrico. Enferm Infecc Microbiol Clin 2021; 39:259-261. [DOI: 10.1016/j.eimc.2020.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/05/2020] [Accepted: 08/09/2020] [Indexed: 11/29/2022]
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Tateishi Y, Ozeki Y, Nishiyama A, Miki M, Maekura R, Fukushima Y, Nakajima C, Suzuki Y, Matsumoto S. Comparative genomic analysis of Mycobacterium intracellulare: implications for clinical taxonomic classification in pulmonary Mycobacterium avium-intracellulare complex disease. BMC Microbiol 2021; 21:103. [PMID: 33823816 PMCID: PMC8025370 DOI: 10.1186/s12866-021-02163-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/18/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Mycobacterium intracellulare is a representative etiological agent of emerging pulmonary M. avium-intracellulare complex disease in the industrialized countries worldwide. The recent genome sequencing of clinical strains isolated from pulmonary M. avium-intracellulare complex disease has provided insight into the genomic characteristics of pathogenic mycobacteria, especially for M. avium; however, the genomic characteristics of M. intracellulare remain to be elucidated. RESULTS In this study, we performed comparative genomic analysis of 55 M. intracellulare and related strains such as M. paraintracellulare (MP), M. indicus pranii (MIP) and M. yonogonense. Based on the average nucleotide identity, the clinical M. intracellulare strains were phylogenetically grouped in two clusters: (1) the typical M. intracellulare (TMI) group, including ATCC13950 and virulent M.i.27 and M.i.198 that we previously reported, and (2) the MP-MIP group. The alignment of the genomic regions was mostly preserved between groups. Plasmids were identified between groups and subgroups, including a plasmid common among some strains of the M.i.27 subgroup. Several genomic regions including those encoding factors involved in lipid metabolism (e.g., fadE3, fadE33), transporters (e.g., mce3), and type VII secretion system (genes of ESX-2 system) were shown to be hypermutated in the clinical strains. M. intracellulare was shown to be pan-genomic at the species and subspecies levels. The mce genes were specific to particular subspecies, suggesting that these genes may be helpful in discriminating virulence phenotypes between subspecies. CONCLUSIONS Our data suggest that genomic diversity among M. intracellulare, M. paraintracellulare, M. indicus pranii and M. yonogonense remains at the subspecies or genovar levels and does not reach the species level. Genetic components such as mce genes revealed by the comparative genomic analysis could be the novel focus for further insight into the mechanism of human pathogenesis for M. intracellulare and related strains.
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Affiliation(s)
- Yoshitaka Tateishi
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.
| | - Yuriko Ozeki
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Akihito Nishiyama
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Mari Miki
- Department of Respiratory Medicine, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Ryoji Maekura
- Department of Respiratory Medicine, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
- Graduate School of Health Care Sciences, Jikei Institute, Osaka, Japan
| | - Yukari Fukushima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Kampus C Jl. Mulyorejo, Surabaya, Indonesia
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Wibberg D, Price-Carter M, Rückert C, Blom J, Möbius P. Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes. Microorganisms 2020; 9:microorganisms9010070. [PMID: 33383865 PMCID: PMC7823733 DOI: 10.3390/microorganisms9010070] [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: 12/01/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium avium (M. a.) subsp. paratuberculosis (MAP) is a worldwide-distributed obligate pathogen in ruminants causing Johne’s disease. Due to a lack of complete subtype III genome sequences, there is not yet conclusive information about genetic differences between strains of cattle (MAP-C, type II) and sheep (MAP-S) type, and especially between MAP-S subtypes I, and III. Here we present the complete, circular genome of MAP-S/type III strain JIII-386 (DE) closed by Nanopore-technology and its comparison with MAP-S/type I closed genome of strain Telford (AUS), MAP-S/type III draft genome of strain S397 (U.S.), twelve closed MAP-C strains, and eight closed M.-a.-complex-strains. Structural comparative alignments revealed clearly the mosaic nature of MAP, emphasized differences between the subtypes and the higher diversity of MAP-S genomes. The comparison of various genomic elements including transposases and genomic islands provide new insights in MAP genomics. MAP type specific phenotypic features may be attributed to genes of known large sequence polymorphisms (LSPSs) regions I–IV and deletions #1 and #2, confirmed here, but could also result from identified frameshifts or interruptions of various virulence-associated genes (e.g., mbtC in MAP-S). Comprehensive core and pan genome analysis uncovered unique genes (e.g., cytochromes) and genes probably acquired by horizontal gene transfer in different MAP-types and subtypes, but also emphasized the highly conserved and close relationship, and the complex evolution of M.-a.-strains.
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Affiliation(s)
- Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, 33501 Bielefeld, Germany; (D.W.); (C.R.)
| | - Marian Price-Carter
- AgResearch, Hopkirk Research Institute, Grasslands Research Centre, Palmerston North 4442, New Zealand;
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Bielefeld University, 33501 Bielefeld, Germany; (D.W.); (C.R.)
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Gießen, D-35390 Gießen, Germany;
| | - Petra Möbius
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, 07743 Jena, Germany
- Correspondence: ; Tel.: +49-(0)3641-8042280
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Chang CL, Chen LC, Yu CJ, Hsueh PR, Chien JY. Different clinical features of patients with pulmonary disease caused by various Mycobacterium avium–intracellulare complex subspecies and antimicrobial susceptibility. Int J Infect Dis 2020; 98:33-40. [DOI: 10.1016/j.ijid.2020.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 11/15/2022] Open
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Bannantine JP, Conde C, Bayles DO, Branger M, Biet F. Genetic Diversity Among Mycobacterium avium Subspecies Revealed by Analysis of Complete Genome Sequences. Front Microbiol 2020; 11:1701. [PMID: 32849358 PMCID: PMC7426613 DOI: 10.3389/fmicb.2020.01701] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/29/2020] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium avium comprises four subspecies that contain both human and veterinary pathogens. At the inception of this study, twenty-eight M. avium genomes had been annotated as RefSeq genomes, facilitating direct comparisons. These genomes represent strains from around the world and provided a unique opportunity to examine genome dynamics in this species. Each genome was confirmed to be classified correctly based on SNP genotyping, nucleotide identity and presence/absence of repetitive elements or other typing methods. The Mycobacterium avium subspecies paratuberculosis (Map) genome size and organization was remarkably consistent, averaging 4.8 Mb with a variance of only 29.6 kb among the 13 strains. Comparing recombination events along with the larger genome size and variance observed among Mycobacterium avium subspecies avium (Maa) and Mycobacterium avium subspecies hominissuis (Mah) strains (collectively termed non-Map) suggests horizontal gene transfer occurs in non-Map, but not in Map strains. Overall, M. avium subspecies could be divided into two major sub-divisions, with the Map type II (bovine strains) clustering tightly on one end of a phylogenetic spectrum and Mah strains clustering more loosely together on the other end. The most evolutionarily distinct Map strain was an ovine strain, designated Telford, which had >1,000 SNPs and showed large rearrangements compared to the bovine type II strains. The Telford strain clustered with Maa strains as an intermediate between Map type II and Mah. SNP analysis and genome organization analyses repeatedly demonstrated the conserved nature of Map versus the mosaic nature of non-Map M. avium strains. Finally, core and pangenomes were developed for Map and non-Map strains. A total of 80% Map genes belonged to the Map core genome, while only 40% of non-Map genes belonged to the non-Map core genome. These genomes provide a more complete and detailed comparison of these subspecies strains as well as a blueprint for how genetic diversity originated.
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Affiliation(s)
- John P Bannantine
- USDA-Agricultural Research Service, National Animal Disease Center, Ames, IA, United States
| | - Cyril Conde
- INRAE, Université de Tours, ISP, Nouzilly, France
| | - Darrell O Bayles
- USDA-Agricultural Research Service, National Animal Disease Center, Ames, IA, United States
| | | | - Franck Biet
- INRAE, Université de Tours, ISP, Nouzilly, France
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Feature of Adhesins Produced by Human Clinical Isolates of Mycobacterium intracellulare, Mycobacterium intracellulare subsp. chimaera and Closely Related Species. Microorganisms 2020; 8:microorganisms8081154. [PMID: 32751435 PMCID: PMC7465531 DOI: 10.3390/microorganisms8081154] [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: 07/07/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 01/09/2023] Open
Abstract
The Mycobacterium avium complex includes two closely related species, Mycobacterium avium and Mycobacterium intracellulare. They are opportunistic pathogens in humans and responsible for severe disease in a wide variety of animals. Yet, little is known about factors involved in their pathogenicity. Here, we identified, purified and characterized adhesins belonging to the heparin-binding hemagglutinin (HBHA) and laminin-binding protein (LBP) family from M. intracellulare ATCC13950 and examined clinical isolates from patients with different pathologies associated with M. intracellulare infection for the presence and conservation of HBHA and LBP. Using a recombinant derivative strain of M. intracellulare ATCC13950 producing green fluorescent protein and luciferase, we found that the addition of heparin inhibited mycobacterial adherence to A549 cells, whereas the addition of laminin enhanced adherence. Both HBHA and LBP were purified by heparin-Sepharose chromatography and their methylation profiles were determined by mass spectrometry. Patients with M. intracellulare infection mounted strong antibody responses to both proteins. By using PCR and immunoblot analyses, we found that both proteins were highly conserved among all 17 examined clinical M. intracellulare isolates from patients with diverse disease manifestations, suggesting a conserved role of these adhesins in M. intracellulare virulence in humans and their potential use as a diagnostic tool.
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Behra PRK, Pettersson BMF, Ramesh M, Dasgupta S, Kirsebom LA. Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members. Sci Rep 2019; 9:19259. [PMID: 31848383 PMCID: PMC6917791 DOI: 10.1038/s41598-019-55464-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/12/2019] [Indexed: 11/09/2022] Open
Abstract
Nontuberculous mycobacteria, NTM, are of growing concern and among these members of the Mycobacterium mucogenicum (Mmuc) and Mycobacterium neoaurum (Mneo) clades can cause infections in humans and they are resistant to first-line anti-tuberculosis drugs. They can be isolated from different ecological niches such as soil, tap water and ground water. Mycobacteria, such as Mmuc and Mneo, are classified as rapid growing mycobacteria, RGM, while the most familiar, Mycobacterium tuberculosis, belongs to the slow growing mycobacteria, SGM. Modern “omics” approaches have provided new insights into our understanding of the biology and evolution of this group of bacteria. Here we present comparative genomics data for seventeen NTM of which sixteen belong to the Mmuc- and Mneo-clades. Focusing on virulence genes, including genes encoding sigma/anti-sigma factors, serine threonine protein kinases (STPK), type VII (ESX genes) secretion systems and mammalian cell entry (Mce) factors we provide insight into their presence as well as phylogenetic relationship in the case of the sigma/anti-sigma factors and STPKs. Our data further suggest that these NTM lack ESX-5 and Mce2 genes, which are known to affect virulence. In this context, Mmuc- and Mneo-clade members lack several of the genes in the glycopeptidolipid (GLP) locus, which have roles in colony morphotype appearance and virulence. For the M. mucogenicum type strain, MmucT, we provide RNASeq data focusing on mRNA levels for sigma factors, STPK, ESX proteins and Mce proteins. These data are discussed and compared to in particular the SGM and fish pathogen Mycobacterium marinum. Finally, we provide insight into as to why members of the Mmuc- and Mneo-clades show resistance to rifampin and isoniazid, and why MmucT forms a rough colony morphotype.
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Affiliation(s)
- Phani Rama Krishna Behra
- Department of Cell and Molecular Biology, Box 596, BMC, Uppsala University, SE 751 24, Uppsala, Sweden
| | - B M Fredrik Pettersson
- Department of Cell and Molecular Biology, Box 596, BMC, Uppsala University, SE 751 24, Uppsala, Sweden
| | - Malavika Ramesh
- Department of Cell and Molecular Biology, Box 596, BMC, Uppsala University, SE 751 24, Uppsala, Sweden
| | - Santanu Dasgupta
- Department of Cell and Molecular Biology, Box 596, BMC, Uppsala University, SE 751 24, Uppsala, Sweden
| | - Leif A Kirsebom
- Department of Cell and Molecular Biology, Box 596, BMC, Uppsala University, SE 751 24, Uppsala, Sweden.
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Clusters of nontuberculous mycobacteria linked to water sources at three Veterans Affairs medical centers. Infect Control Hosp Epidemiol 2019; 41:320-330. [DOI: 10.1017/ice.2019.342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
AbstractObjective:To characterize nontuberculous mycobacteria (NTM) associated with case clusters at 3 medical facilities.Design:Retrospective cohort study using molecular typing of patient and water isolates.Setting:Veterans Affairs Medical Centers (VAMCs).Methods:Isolation and identification of NTM from clinical and water samples using culture, MALDI-TOF, and gene population sequencing to determine species and genetic relatedness. Clinical data were abstracted from electronic health records.Results:An identical strain of Mycobacterium conceptionense was isolated from 41 patients at VA Medical Centers (VAMCs A, B, and D), and from VAMC A’s ICU ice machine. Isolates were initially identified as other NTM species within the M. fortuitum clade. Sequencing analyses revealed that they were identical M. conceptionense strains. Overall, 7 patients (17%) met the criteria for pulmonary or nonpulmonary infection with NTM, and 13 of 41 (32%) were treated with effective antimicrobials regardless of infection or colonization status. Separately, a M. mucogenicum patient strain from VAMC A matched a strain isolated from a VAMC B ICU ice machine. VAMC C, in a different state, had a 4-patient cluster with Mycobacterium porcinum. Strains were identical to those isolated from sink-water samples at this facility.Conclusion:NTM from hospital water systems are found in hospitalized patients, often during workup for other infections, making attribution of NTM infection problematic. Variable NTM identification methods and changing taxonomy create challenges for epidemiologic investigation and linkage to environmental sources.
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