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Wetzstein N, Diricks M, Anton TB, Andres S, Kuhns M, Kohl TA, Schwarz C, Lewin A, Kehrmann J, Kahl BC, Schmidt A, Zimmermann S, Jansson MK, Baron SA, Schulthess B, Hogardt M, Friesen I, Niemann S, Wichelhaus TA. Clinical and genomic features of Mycobacterium avium complex: a multi-national European study. Genome Med 2024; 16:86. [PMID: 38982539 PMCID: PMC11232273 DOI: 10.1186/s13073-024-01359-8] [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: 01/25/2024] [Accepted: 06/28/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND The Mycobacterium avium complex (MAC) comprises the most frequent non-tuberculous mycobacteria (NTM) in Central Europe and currently includes twelve species. M. avium (MAV), M. intracellulare subsp. intracellulare (MINT), and M. intracellulare subsp. chimaera (MCH) are clinically most relevant. However, the population structure and genomic landscape of MAC linked with potential pathobiological differences remain little investigated. METHODS Whole genome sequencing (WGS) was performed on a multi-national set of MAC isolates from Germany, France, and Switzerland. Phylogenetic analysis was conducted, as well as plasmids, resistance, and virulence genes predicted from WGS data. Data was set into a global context with publicly available sequences. Finally, detailed clinical characteristics were associated with genomic data in a subset of the cohort. RESULTS Overall, 610 isolates from 465 patients were included. The majority could be assigned to MAV (n = 386), MCH (n = 111), and MINT (n = 77). We demonstrate clustering with less than 12 SNPs distance of isolates obtained from different patients in all major MAC species and the identification of trans-European or even trans-continental clusters when set into relation with 1307 public sequences. However, none of our MCH isolates clustered closely with the heater-cooler unit outbreak strain Zuerich-1. Known plasmids were detected in MAV (325/1076, 30.2%), MINT (62/327, 19.0%), and almost all MCH-isolates (457/463, 98.7%). Predicted resistance to aminoglycosides or macrolides was rare. Overall, there was no direct link between phylogenomic grouping and clinical manifestations, but MCH and MINT were rarely found in patients with extra-pulmonary disease (OR 0.12 95% CI 0.04-0.28, p < 0.001 and OR 0.11 95% CI 0.02-0.4, p = 0.004, respectively) and MCH was negatively associated with fulfillment of the ATS criteria when isolated from respiratory samples (OR 0.28 95% CI 0.09-0.7, p = 0.011). With 14 out of 43 patients with available serial isolates, co-infections or co-colonizations with different strains or even species of the MAC were frequent (32.6%). CONCLUSIONS This study demonstrates clustering and the presence of plasmids in a large proportion of MAC isolates in Europe and in a global context. Future studies need to urgently define potential ways of transmission of MAC isolates and the potential involvement of plasmids in virulence.
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Affiliation(s)
- Nils Wetzstein
- Department of Internal Medicine, Infectious Diseases, Goethe University, University Hospital, Theodor-Stern-Kai 7, FrankfurtFrankfurt Am Main, 60590, Germany.
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.
| | - Margo Diricks
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Thomas B Anton
- Department of Internal Medicine, Infectious Diseases, Goethe University, University Hospital, Theodor-Stern-Kai 7, FrankfurtFrankfurt Am Main, 60590, Germany
| | - Sönke Andres
- 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
| | - Martin Kuhns
- 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
| | - 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
| | - Carsten Schwarz
- Division of Cystic Fibrosis, CF Center Westbrandenburg, Campus Potsdam, Klinikum Potsdam, Potsdam, Germany
| | - Astrid Lewin
- Unit Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Barbara C Kahl
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Annika Schmidt
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Institute for Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany
| | - Stefan Zimmermann
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Moritz K Jansson
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Sophie A Baron
- Faculté de Médecine Et de Pharmacie, IRD, APHM, Aix Marseille Univ, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Bettina Schulthess
- National Reference Laboratory for Mycobacteria, Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Michael Hogardt
- Institute of Medical Microbiology and Infection Control, Goethe University, University Hospital, FrankfurtFrankfurt Am Main, Germany
- German National Consiliary Laboratory On Cystic Fibrosis Bacteriology, Frankfurt Am Main, Germany
| | - Inna Friesen
- 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
| | - 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
| | - Thomas A Wichelhaus
- Institute of Medical Microbiology and Infection Control, Goethe University, University Hospital, FrankfurtFrankfurt Am Main, Germany
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Brown-Elliott BA, Wallace RJ, Wengenack NL, Workman SD, Cameron ADS, Bush G, Hughes MD, Melton S, Gonzalez-Ramirez B, Rodriguez E, Somayaji K, Klapperich C, Viers M, Bolaji AJ, Rempel E, Alexander DC. Emergence of Inducible Macrolide Resistance in Mycobacterium chelonae Due to Broad-Host-Range Plasmid and Chromosomal Variants of the Novel 23S rRNA Methylase Gene, erm(55). J Clin Microbiol 2023; 61:e0042823. [PMID: 37347171 PMCID: PMC10358161 DOI: 10.1128/jcm.00428-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/31/2023] [Indexed: 06/23/2023] Open
Abstract
Macrolides are a mainstay of therapy for infections due to nontuberculous mycobacteria (NTM). Among rapidly growing mycobacteria (RGM), inducible macrolide resistance is associated with four chromosomal 23S rRNA methylase (erm) genes. Beginning in 2018, we detected high-level inducible clarithromycin resistance (MICs of ≥16μg/mL) in clinical isolates of Mycobacterium chelonae, an RGM species not previously known to contain erm genes. Using whole-genome sequencing, we identified a novel plasmid-mediated erm gene. This gene, designated erm(55)P, exhibits <65% amino acid identity to previously described RGM erm genes. Two additional chromosomal erm(55) alleles, with sequence identities of 81% to 86% to erm(55)P, were also identified and designated erm(55)C and erm(55)T. The erm(55)T is part of a transposon. The erm(55)P allele variant is located on a putative 137-kb conjugative plasmid, pMchErm55. Evaluation of 133 consecutive isolates from 2020 to 2022 revealed 5 (3.8%) with erm(55). The erm(55)P gene was also identified in public data sets of two emerging pathogenic pigmented RGM species: Mycobacterium iranicum and Mycobacterium obuense, dating back to 2008. In both species, the gene appeared to be present on plasmids homologous to pMchErm55. Plasmid-mediated macrolide resistance, not described previously for any NTM species, appears to have spread to multiple RGM species. This has important implications for antimicrobial susceptibility guidelines and treatment of RGM infections. Further spread could present serious consequences for treatment of other macrolide-susceptible RGM. Additional studies are needed to determine the transmissibility of pMchErm55 and the distribution of erm(55) among other RGM species.
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Affiliation(s)
- Barbara A. Brown-Elliott
- Mycobacteria/Nocardia Research Laboratory, University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Richard J. Wallace
- Mycobacteria/Nocardia Research Laboratory, University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Nancy L. Wengenack
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sean D. Workman
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | | | - Georgie Bush
- Mycobacteria/Nocardia Research Laboratory, University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - M. Dolores Hughes
- Mycobacteria/Nocardia Research Laboratory, University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Stephanie Melton
- Mycobacteria/Nocardia Research Laboratory, University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Bibiana Gonzalez-Ramirez
- Mycobacteria/Nocardia Research Laboratory, University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Eliana Rodriguez
- Mycobacteria/Nocardia Research Laboratory, University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Kavya Somayaji
- Mycobacteria/Nocardia Research Laboratory, University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | | | - Mary Viers
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ayooluwa J. Bolaji
- Cadham Provincial Laboratory, Diagnostic Services, Shared Health, Winnipeg, Manitoba, Canada
| | - Emma Rempel
- Cadham Provincial Laboratory, Diagnostic Services, Shared Health, Winnipeg, Manitoba, Canada
| | - David C. Alexander
- Cadham Provincial Laboratory, Diagnostic Services, Shared Health, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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Sabin AP, Ferrieri P, Kline S. Mycobacterium abscessus Complex Infections in Children: A Review. Curr Infect Dis Rep 2017; 19:46. [PMID: 28983867 PMCID: PMC5821427 DOI: 10.1007/s11908-017-0597-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW Infections in children with Mycobacterium abscessus complex represent a particular challenge for clinicians. Increasing incidence of these infections worldwide has necessitated focused attention to improve both diagnostic as well as treatment modalities. Published medical literature was reviewed, with emphasis on material published in the past 5 years. RECENT FINDINGS Increasing availability of new diagnostic tools, such as matrix-assisted laser desorption ionization-time of flight mass spectrometry and custom PCRs, has provided unique insights into the subspecies within the complex and improved diagnostic certainty. Microbiological review of all recent isolates at the University of Minnesota Medical Center was also conducted, with description of the antimicrobial sensitivity patterns encountered in our center, and compared with those published from other centers in the recent literature. A discussion of conventional antimicrobial treatment regimens, alongside detailed description of the relevant antimicrobials, is derived from recent publications. Antimicrobial therapy, combined with surgical intervention in some cases, remains the mainstay of pediatric care. Ongoing questions remain regarding the transmission mechanics, immunologic vulnerabilities exploited by these organisms in the host, and the optimal antimicrobial regimens necessary to enable a reliable cure. Updated treatment guidelines based on focused clinical studies in children and accounting especially for the immunocompromised children at greatest risk are very much needed.
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Affiliation(s)
- Arick P Sabin
- Department of Medicine, Division of Infectious Diseases and International Medicine, University of Minnesota Medical School, 420 Delaware Street SE, MMC # 250, Minneapolis, MN, 55455, USA
| | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology and Department of Pediatrics, Division of Infectious Diseases, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Susan Kline
- Department of Medicine, Division of Infectious Diseases and International Medicine, University of Minnesota Medical School, 420 Delaware Street SE, MMC # 250, Minneapolis, MN, 55455, USA.
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van Ingen J, Kuijper EJ. Drug susceptibility testing of nontuberculous mycobacteria. Future Microbiol 2015; 9:1095-110. [PMID: 25340838 DOI: 10.2217/fmb.14.60] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Diseases caused by nontuberculous mycobacteria are emerging in many settings. With an increased number of patients needing treatment, the role of drug susceptibility testing is again in the spotlight. This articles covers the history and methodology of drug susceptibility tests for nontuberculous mycobacteria, but focuses on the correlations between in vitro drug susceptibility, pharmacokinetics and in vivo outcomes of treatment. Among slow-growing nontuberculous mycobacteria, clear correlations have been established for macrolides and amikacin (Mycobacterium avium complex) and for rifampicin (Mycobacterium kansasii). Among rapid-growing mycobacteria, correlations have been established in extrapulmonary disease for aminoglycosides, cefoxitin and co-trimoxazole. In pulmonary disease, correlations are less clear and outcomes of treatment are generally poor, especially for Mycobacterium abscessus. The clinical significance of inducible resistance to macrolides among rapid growers is an important topic. The true role of drug susceptibility testing for nontuberculous mycobacteria still needs to be addressed, preferably within clinical trials.
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Affiliation(s)
- Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, The Netherlands
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