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Gross JE, Caceres S, Poch K, Epperson LE, Hasan NA, Jia F, Calado Nogueira de Moura V, Strand M, Lipner EM, Honda JR, Strong M, Davidson RM, Daley CL, Nick JA. Prospective healthcare-associated links in transmission of nontuberculous mycobacteria among people with cystic fibrosis (pHALT NTM) study: Rationale and study design. PLoS One 2023; 18:e0291910. [PMID: 38117792 PMCID: PMC10732400 DOI: 10.1371/journal.pone.0291910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/07/2023] [Indexed: 12/22/2023] Open
Abstract
BACKGROUND Healthcare-associated acquisition and transmission of nontuberculous mycobacteria (NTM) among people with cystic fibrosis (pwCF) has been described, and remains a concern for both patients and providers. This report describes the design of a prospective observational study utilizing the standardized epidemiologic investigation toolkit for healthcare-associated links in transmission of NTM among pwCF. METHODS This is a parallel multi-site study of pwCF who have infections with respiratory NTM isolates and receive healthcare within a common CF Care Center. Participants have a history of one or more NTM positive airway cultures and have been identified as having NTM infections suggestive of a possible outbreak within a single Center, based on NTM isolate genomic analysis. Participants are enrolled in the study over a 3-year period. Primary endpoints are identification of shared healthcare-associated source(s) among pwCF in a Center, identification of healthcare environmental dust and water biofilm NTM isolates that are genetically highly-related to respiratory isolates, and identification of common home of residence watersheds among pwCF infected with clustered isolates. Secondary endpoints include characterization of healthcare-associated transmission and/or acquisition modes and settings as well as description of incidence and prevalence of healthcare-associated environmental NTM species/subspecies by geographical region. DISCUSSION We hypothesize that genetically highly-related isolates of NTM among pwCF cared for at the same Center may arise from healthcare sources including patient-to-patient transmission and/or acquisition from health-care environmental dust and/or water biofilms. This study design utilizes a published, standardized, evidence-based epidemiologic toolkit to facilitate confidential, independent healthcare-associated NTM outbreak investigations within CF Care Centers. This study will facilitate real-time, rapid detection and mitigation of healthcare-associated NTM outbreaks to reduce NTM risk, inform infection prevention and control guidelines, and characterize the prevalence and origin of NTM outbreaks from healthcare-associated patient-to-patient transmission and/or environmental acquisition. This study will systematically characterize human disease causing NTM isolates from serial collection of healthcare environmental dust and water biofilms and define the most common healthcare environmental sources harboring NTM biofilms. TRIAL REGISTRATION ClinicalTrials.gov NCT05686837.
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Affiliation(s)
- Jane E. Gross
- Department of Pediatrics, National Jewish Health, Denver, CO, United States of America
- Department of Medicine, National Jewish Health, Denver, CO, United States of America
| | - Silvia Caceres
- Department of Medicine, National Jewish Health, Denver, CO, United States of America
| | - Katie Poch
- Department of Medicine, National Jewish Health, Denver, CO, United States of America
| | - L. Elaine Epperson
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States of America
| | - Nabeeh A. Hasan
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States of America
| | - Fan Jia
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States of America
| | | | - Matthew Strand
- Division of Biostatistics, National Jewish Health, Denver, CO, United States of America
| | - Ettie M. Lipner
- Epidemiology and Population Studies Unit, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, United States of America
| | - Jennifer R. Honda
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States of America
| | - Michael Strong
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States of America
| | - Rebecca M. Davidson
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States of America
| | - Charles L. Daley
- Department of Medicine, National Jewish Health, Denver, CO, United States of America
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Jerry A. Nick
- Department of Medicine, National Jewish Health, Denver, CO, United States of America
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
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2
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Baird T, Bell S. Cystic Fibrosis-Related Nontuberculous Mycobacterial Pulmonary Disease. Clin Chest Med 2023; 44:847-860. [PMID: 37890921 DOI: 10.1016/j.ccm.2023.06.008] [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
Non-tuberculous mycobacteria (NTM) infection is a major cause of morbidity in people with cystic fibrosis (pwCF) with rates of infection increasing worldwide. Accurate diagnosis and decisions surrounding best management remain challenging. Treatment guidelines have been developed to assist physicians in managing NTM in pwCF, but involve prolonged and complex mycobacterial regimens, often associated with significant toxicity. Fortunately, current management and outcomes of NTM in CF are likely to evolve due to improved understanding of disease acquisition, better diagnostics, emerging antimycobacterial therapies, and the widespread uptake of cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies.
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Affiliation(s)
- Timothy Baird
- Department of Respiratory Medicine, Sunshine Coast University Hospital, Sunshine Coast, Queensland, Australia; Sunshine Coast Health Institute, Sunshine Coast, Queensland, Australia; University of the Sunshine Coast, Sunshine Coast, Queensland, Australia.
| | - Scott Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Queensland, Australia; Children's Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Australia; Translational Research Institute, Brisbane, Queensland, Australia; Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia
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3
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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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4
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Ruis C, Weimann A, Tonkin-Hill G, Pandurangan AP, Matuszewska M, Murray GGR, Lévesque RC, Blundell TL, Floto RA, Parkhill J. Mutational spectra are associated with bacterial niche. Nat Commun 2023; 14:7091. [PMID: 37925514 PMCID: PMC10625568 DOI: 10.1038/s41467-023-42916-w] [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: 08/03/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
As observed in cancers, individual mutagens and defects in DNA repair create distinctive mutational signatures that combine to form context-specific spectra within cells. We reasoned that similar processes must occur in bacterial lineages, potentially allowing decomposition analysis to detect both disruption of DNA repair processes and exposure to niche-specific mutagens. Here we reconstruct mutational spectra for 84 clades from 31 diverse bacterial species and find distinct mutational patterns. We extract signatures driven by specific DNA repair defects using hypermutator lineages, and further deconvolute the spectra into multiple signatures operating within different clades. We show that these signatures are explained by both bacterial phylogeny and replication niche. By comparing mutational spectra of clades from different environmental and biological locations, we identify niche-associated mutational signatures, and then employ these signatures to infer the predominant replication niches for several clades where this was previously obscure. Our results show that mutational spectra may be associated with sites of bacterial replication when mutagen exposures differ, and can be used in these cases to infer transmission routes for established and emergent human bacterial pathogens.
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Affiliation(s)
- Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Aaron Weimann
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gemma G R Murray
- Parasites and Microbes Programme, Wellcome Sanger Institute; Wellcome Genome Campus, Cambridge, UK
| | - Roger C Lévesque
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec City, Québec, Canada
| | - Tom L Blundell
- Department of Biochemistry, Sanger Building, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK.
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK.
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
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5
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Carneiro S, Pinto M, Silva S, Santos A, Rodrigues I, Santos D, Duarte S, Vieira L, Gomes JP, Macedo R. Genome-Scale Characterization of Mycobacterium abscessus Complex Isolates from Portugal. Int J Mol Sci 2023; 24:15402. [PMID: 37895081 PMCID: PMC10606986 DOI: 10.3390/ijms242015402] [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] [Received: 09/27/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
The Mycobacterium abscessus complex (MABC) is an emerging, difficult to treat, multidrug-resistant nontuberculous mycobacteria responsible for a wide spectrum of infections and associated with an increasing number of cases worldwide. Dominant circulating clones (DCCs) of MABC have been genetically identified as groups of strains associated with higher prevalence, higher levels of antimicrobial resistance, and worse clinical outcomes. To date, little is known about the genomic characteristics of MABC species circulating in Portugal. Here, we examined the genetic diversity and antimicrobial resistance profiles of 30 MABC strains isolated between 2014 and 2022 in Portugal. The genetic diversity of circulating MABC strains was assessed through a gene-by-gene approach (wgMLST), allowing their subspecies differentiation and the classification of isolates into DCCs. Antimicrobial resistance profiles were defined using phenotypic, molecular, and genomic approaches. The majority of isolates were resistant to at least two antimicrobials, although a poor correlation between phenotype and genotype data was observed. Portuguese genomes were highly diverse, and data suggest the existence of MABC lineages with potential international circulation or cross-border transmission. This study highlights the genetic diversity and antimicrobial resistance profile of circulating MABC isolates in Portugal while representing the first step towards the implementation of a genomic-based surveillance system for MABC at the Portuguese NIH.
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Affiliation(s)
- Sofia Carneiro
- National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (S.C.); (A.S.)
- Department of Life Science, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (M.P.); (J.P.G.)
| | - Sónia Silva
- National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (S.C.); (A.S.)
| | - Andrea Santos
- National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (S.C.); (A.S.)
| | - Irene Rodrigues
- National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (S.C.); (A.S.)
| | - Daniela Santos
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (D.S.); (S.D.)
| | - Sílvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (D.S.); (S.D.)
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (D.S.); (S.D.)
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (M.P.); (J.P.G.)
- Veterinary and Animal Research Centre (CECAV), Faculty of Veterinary Medicine, Lusófona University, 376 Campo Grande, 1749-024 Lisbon, Portugal
| | - Rita Macedo
- National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (S.C.); (A.S.)
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6
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Bar-Oz M, Martini MC, Alonso MN, Meir M, Lore NI, Miotto P, Riva C, Angala SK, Xiao J, Masiello CS, Misiakou MA, Sun H, Moy JK, Jackson M, Johansen HK, Cirillo DM, Shell SS, Barkan D. The small non-coding RNA B11 regulates multiple facets of Mycobacterium abscessus virulence. PLoS Pathog 2023; 19:e1011575. [PMID: 37603560 PMCID: PMC10470900 DOI: 10.1371/journal.ppat.1011575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 08/31/2023] [Accepted: 07/24/2023] [Indexed: 08/23/2023] Open
Abstract
Mycobacterium abscessus causes severe disease in patients with cystic fibrosis. Little is known in M. abscessus about the roles of small regulatory RNAs (sRNA) in gene regulation. We show that the sRNA B11 controls gene expression and virulence-associated phenotypes in this pathogen. B11 deletion from the smooth strain ATCC_19977 produced a rough strain, increased pro-inflammatory signaling and virulence in multiple infection models, and increased resistance to antibiotics. Examination of clinical isolate cohorts identified isolates with B11 mutations or reduced expression. We used RNAseq and proteomics to investigate the effects of B11 on gene expression and test the impact of mutations found in clinical isolates. Over 200 genes were differentially expressed in the deletion mutant. Strains with the clinical B11 mutations showed expression trends similar to the deletion mutant, suggesting partial loss of function. Among genes upregulated in the B11 mutant, there was a strong enrichment for genes with B11-complementary sequences in their predicted ribosome binding sites (RBS), consistent with B11 functioning as a negative regulator that represses translation via base-pairing to RBSs. Comparing the proteomes similarly revealed that upregulated proteins were strongly enriched for B11-complementary sequences. Intriguingly, genes upregulated in the absence of B11 included components of the ESX-4 secretion system, critical for M. abscessus virulence. Many of these genes had B11-complementary sequences at their RBSs, which we show is sufficient to mediate repression by B11 through direct binding. Altogether, our data show that B11 acts as a direct negative regulator and mediates (likely indirect) positive regulation with pleiotropic effects on gene expression and clinically important phenotypes in M. abscessus. The presence of hypomorphic B11 mutations in clinical strains is consistent with the idea that lower B11 activity may be advantageous for M. abscessus in some clinical contexts. This is the first report on an sRNA role in M. abscessus.
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Affiliation(s)
- Michal Bar-Oz
- Koret School of Veterinary Medicine, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maria Carla Martini
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Maria Natalia Alonso
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | | | | | - Paolo Miotto
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Camilla Riva
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Shiva K Angala
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Junpei Xiao
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Catherine S Masiello
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Maria-Anna Misiakou
- Center for Genomic Medicine, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Huaming Sun
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Justin K Moy
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | | | | | - Scarlet S Shell
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Daniel Barkan
- Koret School of Veterinary Medicine, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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7
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Bolden N, Mell JC, Logan JB, Planet PJ. Phylogenomics of nontuberculous mycobacteria respiratory infections in people with cystic fibrosis. Paediatr Respir Rev 2023; 46:63-70. [PMID: 36828670 PMCID: PMC10659050 DOI: 10.1016/j.prrv.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
Nontuberculous mycobacteria (NTM) can cause severe pulmonary disease in people with cystic fibrosis (pwCF). These infections present unique challenges for diagnosis and treatment, prompting a recent interest in understanding NTM transmission and pathogenesis during chronic infection. Major gaps remain in our knowledge regarding basic pathogenesis, immune evasion strategies, population dynamics, recombination potential, and the evolutionary implications of host and antibiotic pressures of long-term NTM infections in pwCF. Phylogenomic techniques have emerged as an important tool for tracking global patterns of transmission and are beginning to be used to ask fundamental biological questions about adaptation to the host during pathogenesis. In this review, we discuss the burden of NTM lung disease (NTM-LD), highlight the use of phylogenomics in NTM research, and address the clinical implications associated with these studies.
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Affiliation(s)
- Nicholas Bolden
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| | - Joshua Chang Mell
- Center for Genomic Sciences, Drexel University College of Medicine, Philadelphia, PA, United States; Department of Microbiology & Immunology, Drexel University, Philadelphia, PA, United States.
| | - Jennifer Bouso Logan
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pulmonary Medicine and Cystic Fibrosis Center, Lehigh Valley Reilly Children's Hospital, PA, United States.
| | - Paul J Planet
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Comparative Genomics, American Museum of Natural History, New York, NY, United States.
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8
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Commins N, Sullivan MR, McGowen K, Koch EM, Rubin EJ, Farhat M. Mutation rates and adaptive variation among the clinically dominant clusters of Mycobacterium abscessus. Proc Natl Acad Sci U S A 2023; 120:e2302033120. [PMID: 37216535 PMCID: PMC10235944 DOI: 10.1073/pnas.2302033120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
Mycobacterium abscessus (Mab) is a multidrug-resistant pathogen increasingly responsible for severe pulmonary infections. Analysis of whole-genome sequences (WGS) of Mab demonstrates dense genetic clustering of clinical isolates collected from disparate geographic locations. This has been interpreted as supporting patient-to-patient transmission, but epidemiological studies have contradicted this interpretation. Here, we present evidence for a slowing of the Mab molecular clock rate coincident with the emergence of phylogenetic clusters. We performed phylogenetic inference using publicly available WGS from 483 Mab patient isolates. We implement a subsampling approach in combination with coalescent analysis to estimate the molecular clock rate along the long internal branches of the tree, indicating a faster long-term molecular clock rate compared to branches within phylogenetic clusters. We used ancestry simulation to predict the effects of clock rate variation on phylogenetic clustering and found that the degree of clustering in the observed phylogeny is more easily explained by a clock rate slowdown than by transmission. We also find that phylogenetic clusters are enriched in mutations affecting DNA repair machinery and report that clustered isolates have lower spontaneous mutation rates in vitro. We propose that Mab adaptation to the host environment through variation in DNA repair genes affects the organism's mutation rate and that this manifests as phylogenetic clustering. These results challenge the model that phylogenetic clustering in Mab is explained by person-to-person transmission and inform our understanding of transmission inference in emerging, facultative pathogens.
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Affiliation(s)
- Nicoletta Commins
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
| | - Mark R. Sullivan
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA02115
| | - Kerry McGowen
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA02115
| | - Evan M. Koch
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
| | - Eric J. Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA02115
- Department of Microbiology, Harvard Medical School, Boston, MA02115
| | - Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA02114
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9
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Burke A, Thomson RM, Wainwright CE, Bell SC. Nontuberculous Mycobacteria in Cystic Fibrosis in the Era of Cystic Fibrosis Transmembrane Regulator Modulators. Semin Respir Crit Care Med 2023; 44:287-296. [PMID: 36649736 DOI: 10.1055/s-0042-1759883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nontuberculous mycobacteria (NTM) are a group of mycobacteria which represent opportunistic pathogens that are of increasing concern in people with cystic fibrosis (pwCF). The acquisition has been traditionally though to be from environmental sources, though recent work has suggested clustered clonal infections do occur and transmission potential demonstrated among pwCF attending CF specialist centers. Guidelines for the screening, diagnosis, and identification of NTM and management of pwCF have been published. The emergence of CF-specific therapies, in particular cystic fibrosis transmembrane regulator (CFTR) modulator drugs, have led to significant improvement in the health and well-being of pwCF and may lead to challenges in sampling the lower respiratory tract including to screen for NTM. This review highlights the epidemiology, modes of acquisition, screening and diagnosis, therapeutic approaches in the context of improved clinical status for pwCF, and the clinical application of CFTR modulator therapies.
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Affiliation(s)
- Andrew Burke
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia.,Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Rachel M Thomson
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia.,Gallipoli Medical Research Foundation, Greenslopes Private Hospital, Greenslopes, Queensland, Australia
| | - Claire E Wainwright
- Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, South Brisbane, Australia.,Children's Health Research Centre, Faculty of Medicine, The University of Queensland, South Brisbane, Australia
| | - Scott C Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia.,Children's Health Research Centre, Faculty of Medicine, The University of Queensland, South Brisbane, Australia.,Translational Research Institute, Woolloongabba, Australia
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10
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Daley CL, Hasan N. Transmission of Mycobacterium avium complex in healthcare settings: from environment, person to person, or both? Eur Respir J 2023; 61:61/4/2300308. [PMID: 37080577 DOI: 10.1183/13993003.00308-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/04/2023] [Indexed: 04/22/2023]
Affiliation(s)
- Charles L Daley
- Department of Medicine, National Jewish Health, Denver, CO, USA
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nabeeh Hasan
- Department of Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
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11
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Nguyen TT, He C, Carter R, Ballard EL, Smith K, Groth R, Jaatinen E, Kidd TJ, Thomson RM, Tay G, Johnson GR, Bell SC, Knibbs LD. Quantifying the effectiveness of ultraviolet-C light at inactivating airborne Mycobacterium abscessus. J Hosp Infect 2023; 132:133-139. [PMID: 36309203 DOI: 10.1016/j.jhin.2022.10.008] [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: 07/25/2022] [Revised: 09/26/2022] [Accepted: 10/06/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Mycobacterium abscessus (MABS) group are environmental organisms that can cause infection in people with cystic fibrosis (CF) and other suppurative lung diseases. There is potential for person-to-person airborne transmission of MABS among people with CF attending the same care centre. Ultraviolet light (band C, UV-C) is used for Mycobacterium tuberculosis control indoors; however, no studies have assessed UV-C for airborne MABS. AIM To determine whether a range of UV-C doses increased the inactivation of airborne MABS, compared with no-UVC conditions. METHODS MABS was generated by a vibrating mesh nebulizer located within a 400 L rotating drum sampler, and then exposed to an array of 265 nm UV-C light-emitting diodes (LED). A six-stage Andersen Cascade Impactor was used to collect aerosols. Standard microbiological protocols were used for enumerating MABS, and these quantified the effectiveness of UV-C doses (in triplicate). UV-C effectiveness was estimated using the difference between inactivation with and without UV-C. FINDINGS Sixteen tests were performed, with UV-C doses ranging from 276 to 1104 μW s/cm2. Mean (±SD) UV-C effectiveness ranged from 47.1% (±13.4) to 83.6% (±3.3). UV-C led to significantly greater inactivation of MABS (all P-values ≤0.045) than natural decay at all doses assessed. Using an indoor model of the hospital environment, it was estimated that UV-C doses in the range studied here could be safely delivered in clinical settings where patients and staff are present. CONCLUSION This study provides empirical in-vitro evidence that nebulized MABS are susceptible to UV-C inactivation.
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Affiliation(s)
- T T Nguyen
- Faculty of Medicine, School of Public Health, University of Queensland, Brisbane, QLD, Australia.
| | - C He
- International Laboratory for Air Quality & Health, School of Earth and Atmospheric Sciences, Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - R Carter
- Centre for Children's Health Research, Brisbane, QLD, Australia
| | - E L Ballard
- QIMR Berghofer Institute of Medical Research, Brisbane, QLD 4006, Australia
| | - K Smith
- Centre for Children's Health Research, Brisbane, QLD, Australia
| | - R Groth
- International Laboratory for Air Quality & Health, School of Earth and Atmospheric Sciences, Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - E Jaatinen
- School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - T J Kidd
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia; Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - R M Thomson
- The Prince Charles Hospital, Brisbane, QLD, Australia; Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia; Gallipoli Medical Research Foundation, Greenslopes Private Hospital, Brisbane, QLD, Australia
| | - G Tay
- The Prince Charles Hospital, Brisbane, QLD, Australia
| | - G R Johnson
- International Laboratory for Air Quality & Health, School of Earth and Atmospheric Sciences, Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - S C Bell
- Centre for Children's Health Research, Brisbane, QLD, Australia; The Prince Charles Hospital, Brisbane, QLD, Australia; Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia; Translational Research Institute, Brisbane, QLD, Australia
| | - L D Knibbs
- Public Health Unit, Sydney Local Health District, Camperdown, NSW, Australia; Faculty of Medicine and Health, School of Public Health, University of Sydney, NSW, Australia
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12
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Lorè NI, Saliu F, Spitaleri A, Schäfle D, Nicola F, Cirillo DM, Sander P. The aminoglycoside-modifying enzyme Eis2 represents a new potential in vivo target for reducing antimicrobial drug resistance in Mycobacterium abscessus complex. Eur Respir J 2022; 60:2201541. [PMID: 36265879 DOI: 10.1183/13993003.01541-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/12/2022] [Indexed: 12/14/2022]
Affiliation(s)
- Nicola Ivan Lorè
- Emerging Bacterial Pathogens Unit, DITID-IRCCS Ospedale San Raffaele, Milan, Italy
| | - Fabio Saliu
- Emerging Bacterial Pathogens Unit, DITID-IRCCS Ospedale San Raffaele, Milan, Italy
| | - Andrea Spitaleri
- Emerging Bacterial Pathogens Unit, DITID-IRCCS Ospedale San Raffaele, Milan, Italy
| | - Daniel Schäfle
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Francesca Nicola
- Emerging Bacterial Pathogens Unit, DITID-IRCCS Ospedale San Raffaele, Milan, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, DITID-IRCCS Ospedale San Raffaele, Milan, Italy
- P. Sander and D.M. Cirillo have contributed equally to this article as co-last authors and supervised the work
| | - Peter Sander
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- National Center for Mycobacteria, Zurich, Switzerland
- P. Sander and D.M. Cirillo have contributed equally to this article as co-last authors and supervised the work
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13
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Abstract
Nontuberculous mycobacteria (NTM) are important pathogens, with a longitudinal prevalence of up to 20% within the cystic fibrosis (CF) population. Diagnosis of NTM pulmonary disease in people with CF (pwCF) is challenging, as a majority have NTM infection that is transient or indolent, without evidence of clinical consequence. In addition, the radiographic and clinical manifestations of chronic coinfections with typical CF pathogens can overlap those of NTM, making diagnosis difficult. Comprehensive care of pwCF must be optimized to assess the true clinical impact of NTM and to improve response to treatment. Treatment requires prolonged, multidrug therapy that varies depending on NTM species, resistance pattern, and extent of disease. With a widespread use of highly effective modulator therapy (HEMT), clinical signs and symptoms of NTM disease may be less apparent, and sensitivity of sputum cultures further reduced. The development of a disease-specific approach to the diagnosis and treatment of NTM infection in pwCF is a research priority, as a lifelong strategy is needed for this high-risk population.
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14
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Waglechner N, Tullis E, Stephenson AL, Waters V, McIntosh F, Ma J, Jamieson FB, Behr MA, Batt J, Lee RS. Genomic epidemiology of Mycobacterium abscessus in a Canadian cystic fibrosis centre. Sci Rep 2022; 12:16116. [PMID: 36167715 PMCID: PMC9514693 DOI: 10.1038/s41598-022-19666-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/01/2022] [Indexed: 11/09/2022] Open
Abstract
The Mycobacterium abscessus complex causes significant morbidity and mortality among patients with Cystic Fibrosis (CF). It has been hypothesized that these organisms are transmitted from patient to patient based on genomics. However, few studies incorporate epidemiologic data to confirm this hypothesis. We longitudinally sampled 27 CF and 7 non-CF patients attending a metropolitan hospital in Ontario, Canada from 2013 to 2018. Whole genome sequencing along with epidemiological data was used to evaluate the likelihood of transmission. Overall, the genetic diversity of M. abscessus was large, with a median pairwise distance (IQR) of 1,279 (143-134) SNVs between all Ontario M. abscessus isolates and 2,908 (21-3,204) single nucleotide variants (SNVs) between M. massiliense isolates. This reflects the global diversity of this pathogen, with Ontario isolates widely dispersed throughout global phylogenetic trees of each subspecies. Using a maximum distance of 25 SNVs as a threshold to identify possible transmission, we identified 23 (of 276 total) pairs of closely-related isolates. However, transmission was probable for only one pair based on both genomic and epidemiological data. This suggests that person-to-person transmission of M. abscessus among CF patients is indeed rare and reinforces the critical importance of epidemiological data for inferences of transmission.
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Affiliation(s)
- Nicholas Waglechner
- Dalla Lana School of Public Health, University of Toronto, 155 College St., Toronto, ON, M5T 3M7, Canada.
| | - Elizabeth Tullis
- Adult Cystic Fibrosis Program, Division of Respirology, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Anne L Stephenson
- Adult Cystic Fibrosis Program, Division of Respirology, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Valerie Waters
- Department of Pediatrics, Division of Infectious Diseases, Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
| | - Fiona McIntosh
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,McGill International TB Centre, McGill University, Montreal, QC, Canada
| | - Jennifer Ma
- Public Health Ontario, Public Health Ontario Laboratories, 661 University Avenue, Suite 1701, Toronto, ON, M5G 1V2, Canada
| | - Frances B Jamieson
- Public Health Ontario, Public Health Ontario Laboratories, 661 University Avenue, Suite 1701, Toronto, ON, M5G 1V2, Canada
| | - Marcel A Behr
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,McGill International TB Centre, McGill University, Montreal, QC, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Jane Batt
- Keenan Research Center for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada.,Tuberculosis Program, St. Michael's Hospital Unity Health Toronto, Toronto, ON, M5B 1WB, Canada
| | - Robyn S Lee
- Dalla Lana School of Public Health, University of Toronto, 155 College St., Toronto, ON, M5T 3M7, Canada. .,McGill International TB Centre, McGill University, Montreal, QC, Canada. .,Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, MA, USA.
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15
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Wetzstein N, Diricks M, Kohl TA, Wichelhaus TA, Andres S, Paulowski L, Schwarz C, Lewin A, Kehrmann J, Kahl BC, Dichtl K, Hügel C, Eickmeier O, Smaczny C, Schmidt A, Zimmermann S, Nährlich L, Hafkemeyer S, Niemann S, Maurer FP, Hogardt M. Molecular Epidemiology of Mycobacterium abscessus Isolates Recovered from German Cystic Fibrosis Patients. Microbiol Spectr 2022; 10:e0171422. [PMID: 35938728 PMCID: PMC9431180 DOI: 10.1128/spectrum.01714-22] [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: 05/14/2022] [Accepted: 07/17/2022] [Indexed: 11/20/2022] Open
Abstract
Infections due to Mycobacterium abscessus are a major cause of mortality and morbidity in cystic fibrosis (CF) patients. Furthermore, M. abscessus has been suspected to be involved in person-to-person transmissions. In 2016, dominant global clonal complexes (DCCs) that occur worldwide among CF patients have been described. To elucidate the epidemiological situation of M. abscessus among CF patients in Germany and to put these data into a global context, we performed whole-genome sequencing of a set of 154 M. abscessus isolates from 123 German patients treated in 14 CF centers. We used MTBseq pipeline to identify clusters of closely related isolates and correlate those with global findings. Genotypic drug susceptibility for macrolides and aminoglycosides was assessed by characterization of the erm(41), rrl, and rrs genes. By this approach, we could identify representatives of all major DCCs (Absc 1, Absc 2, and Mass 1) in our cohort. Intrapersonal isolates showed higher genetic relatedness than interpersonal isolates (median 3 SNPs versus 16 SNPs; P < 0.001). We further identified four clusters with German patients from same centers clustering with less than 25 SNPs distance (range 3 to 18 SNPs) but did not find any hint for in-hospital person-to-person transmission. This is the largest study investigating phylogenetic relations of M. abscessus isolates in Germany. We identified representatives of all reported DCCs but evidence for nosocomial transmission remained inconclusive. Thus, the occurrence of genetically closely related isolates of M. abscessus has to be interpreted with care, as a direct interhuman transmission cannot be directly deduced. IMPORTANCE Mycobacterium abscessus is a major respiratory pathogen in cystic fibrosis (CF) patients. Recently it has been shown that dominant global clonal complexes (DCCs) have spread worldwide among CF patients. This study investigated the epidemiological situation of M. abscessus among CF patients in Germany by performing whole-genome sequencing (WGS) of a set of 154 M. abscessus from 123 German patients treated in 14 CF centers. This is the largest study investigating the phylogenetic relationship of M. abscessus CF isolates in Germany.
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Affiliation(s)
- Nils Wetzstein
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Margo Diricks
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Thomas A. Kohl
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Thomas A. Wichelhaus
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Sönke Andres
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Laura Paulowski
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Carsten Schwarz
- Division of Cystic Fibrosis, Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
- 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
| | - Karl Dichtl
- Max von Pettenkofer Institut, Institute of Medical Microbiology and Hygiene, Medizinische Fakultät, Ludwig-Maximilians-Universität, Munich, Germany
| | - Christian Hügel
- Department of Respiratory Medicine and Allergology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- Christiane Herzog CF Center, Medical Clinic, Department of Respiratory Medicine and Allergology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Olaf Eickmeier
- Division for Allergy, Pneumology and Cystic Fibrosis, Department for Children and Adolescence, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Christina Smaczny
- Department of Respiratory Medicine and Allergology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- Christiane Herzog CF Center, Medical Clinic, Department of Respiratory Medicine and Allergology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Annika Schmidt
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Insitute 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
| | - Lutz Nährlich
- Department of Pediatrics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Sylvia Hafkemeyer
- Mukoviszidose Institut, gemeinnützige Gesellschaft für Forschung und Therapieentwicklung mbH, Bonn, Germany
| | - Stefan Niemann
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Florian P. Maurer
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- Institute of Medical Microbiology, Virology and Hospital Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Hogardt
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- German National Consiliary Laboratory on Cystic Fibrosis Bacteriology, Frankfurt am Main, Germany
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16
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Delineating Mycobacterium abscessus population structure and transmission employing high-resolution core genome multilocus sequence typing. Nat Commun 2022; 13:4936. [PMID: 35999208 PMCID: PMC9399081 DOI: 10.1038/s41467-022-32122-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/19/2022] [Indexed: 11/08/2022] Open
Abstract
Mycobacterium abscessus is an emerging multidrug-resistant non-tuberculous mycobacterium that causes a wide spectrum of infections and has caused several local outbreaks worldwide. To facilitate standardized prospective molecular surveillance, we established a novel core genome multilocus sequence typing (cgMLST) scheme. Whole genome sequencing data of 1991 isolates were employed to validate the scheme, re-analyze global population structure and set genetic distance thresholds for cluster detection and taxonomic identification. We confirmed and amended the nomenclature of the main dominant circulating clones and found that these also correlate well with traditional 7-loci MLST. Dominant circulating clones could be linked to a corresponding reference genome with less than 250 alleles while 99% of pairwise comparisons between epidemiologically linked isolates were below 25 alleles and 90% below 10 alleles. These thresholds can be used to guide further epidemiological investigations. Overall, the scheme will help to unravel the apparent global spread of certain clonal complexes and as yet undiscovered transmission routes.
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17
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A Novel Leucyl-tRNA Synthetase Inhibitor, MRX-6038, Expresses Anti-Mycobacterium abscessus Activity In Vitro and In Vivo. Antimicrob Agents Chemother 2022; 66:e0060122. [PMID: 35969055 PMCID: PMC9487484 DOI: 10.1128/aac.00601-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Therapeutic options for Mycobacterium abscessus infections are extremely limited, and new drugs are needed. The anti-M. abscessus activity of MRX-6038, a new leucyl-tRNA synthetase inhibitor, was evaluated in vitro and in vivo. Antimicrobial susceptibility testing was performed on 12 nontuberculosis mycobacteria (NTM) reference strains and 227 clinical NTM isolates. A minimum bactericidal concentration assay was conducted to distinguish the bactericidal versus bacteriostatic activity of MRX-6038. The synergy between MRX-6038 and 12 clinically important antibiotics was determined using a checkerboard assay. The activity of MRX-6038 against M. abscessus residing inside macrophages was also evaluated. Finally, the potency of MRX-6038 in vivo was determined in a neutropenic mouse model that mimicked a pulmonary M. abscessus infection. MRX-6038 exhibited high anti-M. abscessus activity against extracellular M. abscessus in culture, with a MIC50 of 0.063 mg/L and a MIC90 of 0.125 mg/L. Fifty percent of the activity was bactericidal, and fifty percent was bacteriostatic. A synergy between MRX-6038 and clarithromycin or azithromycin was found in 25% of strains. No antagonism was evident between MRX-6038 and 12 antibiotics commonly used to treat NTM infections. MRX-6038 also exhibited activity against intracellular NTM, which caused a significant reduction in the bacterial load in the lungs of M. abscessus-infected neutropenic mice. In conclusion, MRX-6038 was active against M. abscessusin vitro and in vivo, and it represents a potential candidate for incorporation into strategies by which M. abscessus infections are treated.
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18
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Sur S, Patra T, Karmakar M, Banerjee A. Mycobacterium abscessus: insights from a bioinformatic perspective. Crit Rev Microbiol 2022:1-16. [PMID: 35696783 DOI: 10.1080/1040841x.2022.2082268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Mycobacterium abscessus is a nontuberculous mycobacterium, associated with broncho-pulmonary infections in individuals suffering from cystic fibrosis, bronchiectasis, and pulmonary diseases. The risk factors for transmission include biofilms, contaminated water resources, fomites, and infected individuals. M. abscessus is extensively resistant to antibiotics. To date, there is no vaccine and combination antibiotic therapy is followed. However, drug toxicities, low cure rates, and high cost of treatment make it imperfect. Over the last 20 years, bioinformatic studies on M. abscessus have advanced our understanding of the pathogen. This review integrates knowledge from the analysis of genomes, microbiomes, genomic variations, phylogeny, proteome, transcriptome, secretome, antibiotic resistance, and vaccine design to further our understanding. The utility of genome-based studies in comprehending disease progression, surveillance, tracing transmission routes, and epidemiological outbreaks on a global scale has been highlighted. Furthermore, this review underlined the importance of using computational methodologies for pinpointing factors responsible for pathogen survival and resistance. We reiterate the significance of interdisciplinary research to fight M. abscessus. In a nutshell, the outcome of computational studies can go a long way in creating novel therapeutic avenues to control M. abscessus mediated pulmonary infections.
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Affiliation(s)
- Saubashya Sur
- Postgraduate Department of Botany, Ramananda College, Bishnupur, India
| | - Tanushree Patra
- Postgraduate Department of Botany, Ramananda College, Bishnupur, India
| | - Mistu Karmakar
- Postgraduate Department of Botany, Ramananda College, Bishnupur, India
| | - Anindita Banerjee
- Postgraduate Department of Botany, Ramananda College, Bishnupur, India
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19
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Olivier KN, Prevots DR. HALTing Nontuberculous Mycobacteria in Cystic Fibrosis Centers: Is There Something in the Water? Am J Respir Crit Care Med 2022; 205:982-983. [PMID: 35275803 PMCID: PMC9851476 DOI: 10.1164/rccm.202202-0337ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Kenneth N. Olivier
- Division of Intramural ResearchNational Heart, Lung, and Blood InstituteBethesda, Maryland
| | - D. Rebecca Prevots
- Division of Intramural ResearchNational Institute of Allergy and Infectious DiseasesBethesda, Maryland
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20
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Gross JE, Caceres S, Poch K, Hasan NA, Jia F, Epperson LE, Lipner E, Vang C, Honda JR, Strand M, Calado Nogueira de Moura V, Daley CL, Strong M, Davidson RM, Nick JA. Investigating Nontuberculous Mycobacteria Transmission at the Colorado Adult Cystic Fibrosis Program. Am J Respir Crit Care Med 2022; 205:1064-1074. [PMID: 35085056 PMCID: PMC9851486 DOI: 10.1164/rccm.202108-1911oc] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Rationale: Healthcare-associated transmission of nontuberculous mycobacteria (NTM) among people with cystic fibrosis (pwCF) has been investigated at CF centers worldwide, with conflicting conclusions. We investigated transmission at the Colorado Adult CF Program. Objectives: To systematically investigate healthcare-associated transmission and/or acquisition of NTM to determine similarity among respiratory and environmental isolates, and to compare home residence watershed mapping among pwCF having genetically similar NTM isolates. Methods: Whole-genome sequencing of NTM isolates from 80 pwCF was conducted to identify genetically similar isolate clusters (⩽30 SNP differences). Epidemiology, comparison of respiratory and environmental isolates, and home residence watershed mapping were analyzed. Measurements and Main Results: Whole-genome sequencing analysis revealed 11 clusters of NTM [6 Mycobacterium abscessus subspecies (ssp.) abscessus, 1 M. abscessus ssp. massiliense, 2 Mycobacterium avium, and 2 Mycobacterium intracellulare] among pwCF. Epidemiologic investigation demonstrated opportunities for healthcare-associated transmission in two M. abscessus and two M. avium clusters. Respiratory and healthcare environmental isolate comparisons revealed no genetic similarity. Individuals comprising one M. abscessus cluster, with no plausible healthcare-associated transmission, resided in the same watershed. Conclusions: This study suggests healthcare-associated transmission of M. abscessus is rare and includes a report of potential healthcare-associated transmission of M. avium among pwCF. One M. abscessus cluster possibly had common acquisition arising from residing in the same watershed. The presence of genetically similar isolates is insufficient to demonstrate healthcare-associated NTM transmission. Standardizing epidemiologic investigation, combined with environmental sampling and watershed analysis, will improve understanding of the frequency and nature of healthcare-associated NTM transmission among pwCF.
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Affiliation(s)
| | | | | | | | - Fan Jia
- Center for Genes, Environment and Health
| | | | | | | | | | | | | | - Charles L. Daley
- Division of Mycobacterial and Respiratory Infections, National Jewish Health, Denver, Colorado
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21
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Molecular Epidemiological Characteristics of Mycobacterium abscessus Complex Derived from Non-Cystic Fibrosis Patients in Japan and Taiwan. Microbiol Spectr 2022; 10:e0057122. [PMID: 35446117 PMCID: PMC9248903 DOI: 10.1128/spectrum.00571-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mycobacterium abscessus complex (MABC) is a group of emerging, highly antimicrobial-resistant non-tuberculous mycobacteria. Specific MABC clones are spreading globally in patients with cystic fibrosis (CF); however, associated genomic epidemiology is lacking in East Asia, with very few patients with CF. Here, we investigated MABC populations derived from non-CF patients in Japan and Taiwan. Analysis of whole-genome sequencing data of 220 MABC isolates revealed that 112, 105, and 3 were M. abscessus subsp. abscessus (ABS), M. abscessus subsp. massiliense (MAS), and M. abscessus subsp. bolletii (BOL), respectively. Moreover, >50% of ABS and >70% of MAS were related to four predominant clones in the region. Known mutations conferring macrolide resistance were rare (1.4%) and were not enriched in the predominant clones. Conversely, the macrolide-susceptible erm(41) T28C mutation was significantly enriched in one predominant ABS clone. The most predominant ABS clone was genetically related to the previously described dominant circulating clone (DCC)1 in patients with CF, whereas no isolates were related to DCC2; isolates related to DCC3 were not necessarily predominant in our sample set. We found that the erm(41) T28C mutants spread globally, and some of them reacquired the functional erm(41) gene through both point mutation and recombination. This study revealed predominant MABC clones in Japan and Taiwan and their relationship with the globally superadding clones in the patient community with CF. Our study provides insights into the genetic characteristics of globally dominant and area-specific strains isolated from patients with or without CF and differences between globally spread and regionally specific strains. IMPORTANCE Members of Mycobacterium abscessus complex (MABC) are frequently isolated from patients. Studies have reported that predominant clones of MABC (known as dominant circulating clones; DCCs) are distributed worldwide and transmitted from humans to humans in patients with cystic fibrosis (CF). However, associated genomic epidemiology has not yet been conducted in East Asia, including Japan and Taiwan, where there are only a few patients with CF. Using whole-genome sequencing data derived from non-CF patients in Japan and Taiwan, we revealed prevalent clones and the incidence of macrolide resistance-associated mutations in the MABC population in this region. We also clarified the associations between these predominant clones and DCCs in the global CF patient community. Our results would assist further studies in elucidating the genetic characteristics of strains isolated from patients with or without CF, the differences between globally spread and regionally specific strains, and the adaptive evolution of MABC within the host.
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22
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Healthcare-associated links in transmission of nontuberculous mycobacteria among people with cystic fibrosis (HALT NTM) study: Rationale and study design. PLoS One 2021; 16:e0261628. [PMID: 34929010 PMCID: PMC8687591 DOI: 10.1371/journal.pone.0261628] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/06/2021] [Indexed: 11/24/2022] Open
Abstract
Background Healthcare-associated transmission of nontuberculous mycobacteria (NTM) among people with cystic fibrosis (pwCF) has been reported and is of increasing concern. No standardized epidemiologic investigation tool has been published for healthcare-associated NTM outbreak investigations. This report describes the design of an ongoing observational study to standardize the approach to NTM outbreak investigation among pwCF. Methods This is a parallel multi-site study of pwCF within a single Center who have respiratory NTM isolates identified as being highly-similar. Participants have a history of positive airway cultures for NTM, receive care within a single Center, and have been identified as part of a possible outbreak based on genomic analysis of NTM isolates. Participants are enrolled in the study over a 3-year period. Primary endpoints are identification of a shared healthcare-associated encounter(s) among patients in a Center and identification of environmental isolates that are genetically highly-similar to respiratory isolates recovered from pwCF. Secondary endpoints include characterization of potential transmission modes and settings, as well as incidence and prevalence of healthcare-associated environmental NTM species/subspecies by geographical region. Discussion We hypothesize that genetically highly-similar strains of NTM among pwCF cared for at the same Center may arise from healthcare sources including patient-to-patient transmission and/or acquisition from environmental sources. This novel study design will establish a standardized, evidence-based epidemiologic investigation tool for healthcare-associated NTM outbreak investigation within CF Care Centers, will broaden the scope of independent outbreak investigations and demonstrate the frequency and nature of healthcare-associated NTM transmission in CF Care Centers nationwide. Furthermore, it will provide valuable insights into modeling risk factors associated with healthcare-associated NTM transmission and better inform future infection prevention and control guidelines. This study will systematically characterize clinically-relevant NTM isolates of CF healthcare environmental dust and water biofilms and set the stage to describe the most common environmental sources within the healthcare setting harboring clinically-relevant NTM isolates. Trial registration ClinicalTrials.gov NCT04024423. Date of registry July 18, 2019.
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23
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Davidson RM, Hasan NA, Epperson LE, Benoit JB, Kammlade SM, Levin AR, Calado de Moura V, Hunkins J, Weakly N, Beagle S, Sagel SD, Martiniano SL, Salfinger M, Daley CL, Nick JA, Strong M. Population Genomics of Mycobacterium abscessus from U.S. Cystic Fibrosis Care Centers. Ann Am Thorac Soc 2021; 18:1960-1969. [PMID: 33856965 PMCID: PMC8641822 DOI: 10.1513/annalsats.202009-1214oc] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 04/14/2021] [Indexed: 12/25/2022] Open
Abstract
Rationale:Mycobacterium abscessus is a significant threat to individuals with cystic fibrosis (CF) because of innate drug resistance and potential transmission between patients. Recent studies described global dominant circulating clones of M. abscessus, but detailed genomic surveys have not yet been described for the United States. Objectives: We examined the genetic diversity of respiratory M. abscessus isolates from U.S. patients with CF and evaluated the potential for transmission events within CF Care Centers. Methods: Whole-genome sequencing was performed on 558 M. abscessus isolates from 266 patients with CF attending 48 CF Care Centers in 28 U.S. states as part of a nationwide surveillance program. U.S. isolates were also compared with 64 isolate genomes from 13 previous studies to evaluate the prevalence of recently described dominant circulating clones. Results: More than half of study patients with CF and M. abscessus had isolates within four dominant clones; two clones of M. abscessus subspecies (subsp.) abscessus (MAB) and two clones of M. abscessus subsp. massiliense (MMAS). Acquired drug resistance mutations for aminoglycosides and macrolides were rare in the isolate population, and they were not significantly enriched in dominant clones compared with unclustered isolates. For a subset of 55 patients, there was no relationship between dominant clones and diagnosis of active lung disease (P = 1.0). Twenty-nine clusters of genetically similar MAB isolates and eight clusters of genetically similar MMAS isolates were identified. Overall, 28 of 204 (14%) patients with MAB and 15 of 64 (23%) patients with MMAS had genetically isolates similar to those of at least one other patient at the same CF Care Center. Genetically similar isolates were also found between 60 of 204 (29%) patients with MAB and 19 of 64 (30%) patients with MMAS from different geographic locations. Conclusions: Our study reveals the predominant genotypes of M. abscessus and frequency of shared strains between patients in U.S. CF Care Centers. Integrated epidemiological and environmental studies would help to explain the widespread presence of dominant clones in the United States, including the potential for broad distribution in the environment. Single site studies using systematic, evidence-based approaches will be needed to establish the contributions of health care-associated transmission versus shared environmental exposures.
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Affiliation(s)
| | | | | | | | | | - Adrah R. Levin
- Department of Medicine, National Jewish Health, Denver, Colorado
| | | | | | | | | | - Scott D. Sagel
- Department of Pediatrics, Children’s Hospital Colorado–School of Medicine, University of Colorado, Aurora, Colorado; and
| | - Stacey L. Martiniano
- Department of Pediatrics, Children’s Hospital Colorado–School of Medicine, University of Colorado, Aurora, Colorado; and
| | - Max Salfinger
- College of Public Health and
- Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Charles L. Daley
- Department of Medicine, National Jewish Health, Denver, Colorado
- Department of Medicine, School of Medicine, University of Colorado, Aurora, Colorado
| | - Jerry A. Nick
- Department of Medicine, National Jewish Health, Denver, Colorado
- Department of Medicine, School of Medicine, University of Colorado, Aurora, Colorado
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24
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Nick JA, Daley CL, Lenhart-Pendergrass PM, Davidson RM. Nontuberculous mycobacteria in cystic fibrosis. Curr Opin Pulm Med 2021; 27:586-592. [PMID: 34431787 DOI: 10.1097/mcp.0000000000000816] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PURPOSE OF REVIEW Nontuberculous mycobacteria (NTM) are challenging infections among people with cystic fibrosis (pwCF) as the source, modes of transmission, and best practices for diagnosis and treatment are not known. Investigators have defined aspects of NTM infection that are unique to the CF population, as well as features shared with other conditions at risk. This review describes recent advances in our understanding of NTM infection among pwCF. RECENT FINDINGS The presence of dominant circulating clones of Mycobacterium abscessus within the CF community worldwide continue to be described, as well as pathogen phenotypes that could evoke greater environmental fitness and infectivity. The risk of direct or indirect transmission between pwCF remains an active focus of investigation, with divergent findings and conclusions reached in a site-specific fashion. Derived largely from studies in non-CF populations, new clinical guidelines are now available. A wide variety of agents are in preclinical development or early phase trials with promising findings, and new therapeutic targets have been identified as our understanding of the complex biology of NTM continues to expand. SUMMARY Significant challenges remain in the fight against NTM, however, recent advances in our understanding of the genetics, epidemiology and pathophysiology of pulmonary NTM infection in pwCF are leading efforts to improve clinical care.
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Affiliation(s)
- Jerry A Nick
- Department of Medicine, National Jewish Health, Denver
- University of Colorado Denver, School of Medicine
| | - Charles L Daley
- Department of Medicine, National Jewish Health, Denver
- University of Colorado Denver, School of Medicine
| | | | - Rebecca M Davidson
- Center for Genes, Environment and Health and Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA
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25
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Genomic Analysis of a Hospital-Associated Outbreak of Mycobacterium abscessus: Implications on Transmission. J Clin Microbiol 2021; 60:e0154721. [PMID: 34705540 DOI: 10.1128/jcm.01547-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whole genome sequencing (WGS) has recently been used to investigate acquisition of Mycobacterium abscessus (MABC). Investigators have reached conflicting conclusions about the meaning of genetic distances for interpretation of person-to-person transmission. Existing genomic studies were limited by a lack of WGS from environmental MABC isolates. In this study, we retrospectively analyzed the core and accessory genomes of 26 M. abscessus subsp. abscessus (MAA) isolates collected over seven years. Clinical isolates (n=22) were obtained from a large hospital-associated outbreak of MAA, the outbreak hospital before or after the outbreak, a neighboring hospital, and two outside laboratories. Environmental MAA isolates (n=4) were obtained from outbreak hospital water outlets. Phylogenomic analysis of study isolates revealed three clades with pairwise genetic distances ranging from 0-135 single nucleotide polymorphisms (SNPs). Compared to a reference environmental outbreak isolate, all seven clinical outbreak isolates and the remaining three environmental isolates had highly similar core and accessory genomes, differing by up to 7 SNPs and a median of 1.6% accessory genes, respectively. Although genomic comparisons of 15 non-outbreak clinical isolates revealed greater heterogeneity, five (33%) isolates had fewer than 20 SNPs compared to the reference environmental isolate, including two unrelated outside laboratory isolates with less than 4% accessory genome variation. Detailed genomic comparisons confirmed environmental acquisition of outbreak isolates of MAA. SNP distances alone, however, did not clearly differentiate the mechanism of acquisition of outbreak versus non-outbreak isolates. We conclude that successful investigation of MAA clusters requires molecular and epidemiologic components, ideally complemented by environmental sampling.
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26
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Dohál M, Porvazník I, Solovič I, Mokrý J. Whole Genome Sequencing in the Management of Non-Tuberculous Mycobacterial Infections. Microorganisms 2021; 9:microorganisms9112237. [PMID: 34835363 PMCID: PMC8621650 DOI: 10.3390/microorganisms9112237] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
Infections caused by non-tuberculous mycobacteria (NTM) have been a public health problem in recent decades and contribute significantly to the clinical and economic burden globally. The diagnosis of infections is difficult and time-consuming and, in addition, the conventional diagnostics tests do not have sufficient discrimination power in species identification due to cross-reactions and not fully specific probes. However, technological advances have been made and the whole genome sequencing (WGS) method has been shown to be an essential part of routine diagnostics in clinical mycobacteriology laboratories. The use of this technology has contributed to the characterization of new species of mycobacteria, as well as the identification of gene mutations encoding resistance and virulence factors. Sequencing data also allowed to track global outbreaks of nosocomial NTM infections caused by M. abscessus complex and M. chimaera. To highlight the utility of WGS, we summarize recent scientific studies on WGS as a tool suitable for the management of NTM-induced infections in clinical practice.
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Affiliation(s)
- Matúš Dohál
- Biomedical Center Martin, Department of Pharmacology, Jessenius Faculty of Medicine, Comenius University, 036 01 Martin, Slovakia;
- Correspondence: ; Tel.: +42-19-0252-4199
| | - Igor Porvazník
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, 059 81 Vyšné Hágy, Slovakia; (I.P.); (I.S.)
- Faculty of Health, Catholic University, 034 01 Ružomberok, Slovakia
| | - Ivan Solovič
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, 059 81 Vyšné Hágy, Slovakia; (I.P.); (I.S.)
- Faculty of Health, Catholic University, 034 01 Ružomberok, Slovakia
| | - Juraj Mokrý
- Biomedical Center Martin, Department of Pharmacology, Jessenius Faculty of Medicine, Comenius University, 036 01 Martin, Slovakia;
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Gardini G, Ori M, Codecasa LR, Matteelli A. Pulmonary nontuberculous mycobacterial infections and environmental factors: A review of the literature. Respir Med 2021; 189:106660. [PMID: 34715617 DOI: 10.1016/j.rmed.2021.106660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 09/19/2021] [Accepted: 10/11/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Pulmonary nontuberculous mycobacterial (pNTM) infection is mainly acquired through the inhalation of bioaerosols. Nevertheless, behavioural restrictions are rarely given by clinicians to susceptible populations, in part because the available guidelines for pNTM management emphasize more diagnosis and treatment than prevention. Aim of this review is to clarify if pNTM prevention should routinely include recommendations about risk reducing behaviors. METHODS We used PubMed as biomedical database. We limited our search to the publication period 2000 to 2020 with selected keyword combinations including "nontuberculous mycobacteria", "water", "soil", and "exposure". Titles and abstract of selected articles were systematically screened. Articles were included in the analysis if they were published under free access through the digital library of the University of Brescia (Italy), and provided full text either in English, French, German or Italian. Articles were excluded if the topic was beyond the aim of our study. Finally, we selected 20 articles. RESULTS Studies disagree in identifying the type of aerosol posing the highest risk for the development of pNTM infection. In the retrieved publications the colonization of household niches has been associated with a higher risk of pNTM disease, such as in the exposure to shower aerosols. Considering the non-household settings, the exposure to aerosols in indoor swimming and the higher soil exposure (>2 h/week) seem to correlate with a higher risk to develop pNTM disease. According to our findings, randomized behavioural intervention studies are missing. CONCLUSIONS Stringent scientific evidence is missing to formulate recommendations on behavioural risk reduction for pNTM.
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Affiliation(s)
- Giulia Gardini
- University of Brescia, Division of Tropical and Infectious Diseases, Spedali Civili Hospital, Brescia, Italy.
| | - Margherita Ori
- Division of Pneumology, Fondazione IRCCS Ca Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - Luigi Ruffo Codecasa
- Regional TB Reference Centre, Istituto Villa Marelli, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy.
| | - Alberto Matteelli
- University of Brescia, Division of Tropical and Infectious Diseases, Spedali Civili Hospital, Brescia, Italy.
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28
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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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29
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Ruis C, Bryant JM, Bell SC, Thomson R, Davidson RM, Hasan NA, van Ingen J, Strong M, Floto RA, Parkhill J. Dissemination of Mycobacterium abscessus via global transmission networks. Nat Microbiol 2021; 6:1279-1288. [PMID: 34545208 PMCID: PMC8478660 DOI: 10.1038/s41564-021-00963-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/18/2021] [Indexed: 02/07/2023]
Abstract
Mycobacterium abscessus, a multidrug-resistant nontuberculous mycobacterium, has emerged as a major pathogen affecting people with cystic fibrosis (CF). Although originally thought to be acquired independently from the environment, most individuals are infected with one of several dominant circulating clones (DCCs), indicating the presence of global transmission networks of M. abscessus. How and when these clones emerged and spread globally is unclear. Here, we use evolutionary analyses of isolates from individuals both with and without CF to reconstruct the population history, spatiotemporal spread and recent transmission networks of the DCCs. We demonstrate synchronous expansion of six unrelated DCCs in the 1960s, a period associated with major changes in CF care and survival. Each of these clones has spread globally as a result of rare intercontinental transmission events. We show that the DCCs, but not environmentally acquired isolates, exhibit a specific smoking-associated mutational signature and that current transmission networks include individuals both with and without CF. We therefore propose that the DCCs initially emerged in non-CF populations but were then amplified and spread through the CF community. While individuals with CF are probably the most permissive host, non-CF individuals continue to play a key role in transmission networks and may facilitate long-distance transmission.
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Affiliation(s)
- Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Josephine M Bryant
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Scott C Bell
- Children's Health Research Institute, The University of Queensland, Brisbane, Australia
- Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia
| | - Rachel Thomson
- Gallipoli Medical Research Institute, The University of Queensland, Brisbane, Australia
| | - Rebecca M Davidson
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Nabeeh A Hasan
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Jakko van Ingen
- Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Michael Strong
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - R Andres Floto
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK.
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK.
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK.
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
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30
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Lipworth S, Hough N, Weston N, Muller-Pebody B, Phin N, Myers R, Chapman S, Flight W, Alexander E, Smith EG, Robinson E, Peto TEA, Crook DW, Walker AS, Hopkins S, Eyre DW, Walker TM. Epidemiology of Mycobacterium abscessus in England: an observational study. THE LANCET. MICROBE 2021; 2:e498-e507. [PMID: 34632432 PMCID: PMC8481905 DOI: 10.1016/s2666-5247(21)00128-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Mycobacterium abscessus has emerged as a significant clinical concern following reports that it is readily transmissible in health-care settings between patients with cystic fibrosis. We linked routinely collected whole-genome sequencing and health-care usage data with the aim of investigating the extent to which such transmission explains acquisition in patients with and without cystic fibrosis in England. METHODS In this retrospective observational study, we analysed consecutive M abscessus whole-genome sequencing data from England (beginning of February, 2015, to Nov 14, 2019) to identify genomically similar isolates. Linkage to a national health-care usage database was used to investigate possible contacts between patients. Multivariable regression analysis was done to investigate factors associated with acquisition of a genomically clustered strain (genomic distance <25 single nucleotide polymorphisms [SNPs]). FINDINGS 2297 isolates from 906 patients underwent whole-genome sequencing as part of the routine Public Health England diagnostic service. Of 14 genomic clusters containing isolates from ten or more patients, all but one contained patients with cystic fibrosis and patients without cystic fibrosis. Patients with cystic fibrosis were equally likely to have clustered isolates (258 [60%] of 431 patients) as those without cystic fibrosis (322 [63%] of 513 patients; p=0·38). High-density phylogenetic clusters were randomly distributed over a wide geographical area. Most isolates with a closest genetic neighbour consistent with potential transmission had no identifiable relevant epidemiological contacts. Having a clustered isolate was independently associated with increasing age (adjusted odds ratio 1·14 per 10 years, 95% CI 1·04-1·26), but not time spent as an hospital inpatient or outpatient. We identified two sibling pairs with cystic fibrosis with genetically highly divergent isolates and one pair with closely related isolates, and 25 uninfected presumed household contacts with cystic fibrosis. INTERPRETATION Previously identified widely disseminated dominant clones of M abscessus are not restricted to patients with cystic fibrosis and occur in other chronic respiratory diseases. Although our analysis showed a small number of cases where person-to-person transmission could not be excluded, it did not support this being a major mechanism for M abscessus dissemination at a national level in England. Overall, these data should reassure patients and clinicians that the risk of acquisition from other patients in health-care settings is relatively low and motivate future research efforts to focus on identifying routes of acquisition outside of the cystic fibrosis health-care-associated niche. FUNDING The National Institute for Health Research, Health Data Research UK, The Wellcome Trust, The Medical Research Council, and Public Health England.
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Affiliation(s)
- Samuel Lipworth
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford University Hospitals NHS Foundation Trust, Oxford, UK,Correspondence to: Dr Samuel Lipworth, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Natasha Hough
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Natasha Weston
- National Mycobacterial Reference Service-Central and North, Public Health England, Public Health Laboratory, Birmingham, UK
| | - Berit Muller-Pebody
- Tuberculosis, Acute Respiratory, Gastrointestinal, Emerging and Zoonotic Infections and Travel Migrant Health Division, National Infection Service, Public Health England, London, UK
| | - Nick Phin
- Tuberculosis, Acute Respiratory, Gastrointestinal, Emerging and Zoonotic Infections and Travel Migrant Health Division, National Infection Service, Public Health England, London, UK
| | - Richard Myers
- Tuberculosis, Acute Respiratory, Gastrointestinal, Emerging and Zoonotic Infections and Travel Migrant Health Division, National Infection Service, Public Health England, London, UK
| | - Stephen Chapman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - William Flight
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Eliza Alexander
- National Mycobacterial Reference Service-South, Public Health England, London, UK
| | - E Grace Smith
- National Mycobacterial Reference Service-Central and North, Public Health England, Public Health Laboratory, Birmingham, UK
| | - Esther Robinson
- National Mycobacterial Reference Service-Central and North, Public Health England, Public Health Laboratory, Birmingham, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford University Hospitals NHS Foundation Trust, Oxford, UK,NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford University Hospitals NHS Foundation Trust, Oxford, UK,NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Susan Hopkins
- Tuberculosis, Acute Respiratory, Gastrointestinal, Emerging and Zoonotic Infections and Travel Migrant Health Division, National Infection Service, Public Health England, London, UK
| | - David W Eyre
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK,Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Timothy M Walker
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK,Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
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Lewin A, Kamal E, Semmler T, Winter K, Kaiser S, Schäfer H, Mao L, Eschenhagen P, Grehn C, Bender J, Schwarz C. Genetic diversification of persistent Mycobacterium abscessus within cystic fibrosis patients. Virulence 2021; 12:2415-2429. [PMID: 34546836 PMCID: PMC8526041 DOI: 10.1080/21505594.2021.1959808] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mycobacterium (M.) abscessus infections in Cystic Fibrosis (CF) patients cause a deterioration of lung function. Treatment of these multidrug-resistant pathogens is associated with severe side-effects, while frequently unsuccessful. Insight on M. abscessus genomic evolvement during chronic lung infection would be beneficial for improving treatment strategies. A longitudinal study enrolling 42 CF patients was performed at a CF center in Berlin, Germany, to elaborate phylogeny and genomic diversification of in-patient M. abscessus. Eleven of the 42 CF patients were infected with M. abscessus. Five of these 11 patients were infected with global human-transmissible M. abscessus cluster strains. Phylogenetic analysis of 88 genomes from isolates of the 11 patients excluded occurrence of M. abscessus transmission among members of the study group. Genome sequencing and variant analysis of 30 isolates from 11 serial respiratory samples collected over 4.5 years from a chronically infected patient demonstrated accumulation of gene mutations. In total, 53 genes exhibiting non-synonymous variations were identified. Enrichment analysis emphasized genes involved in synthesis of glycopeptidolipids, genes from the embABC (arabinosyltransferase) operon, betA (glucose-methanol-choline oxidoreductase) and choD (cholesterol oxidase). Genetic diversity evolved in a variety of virulence- and resistance-associated genes. The strategy of M. abscessus populations in chronic lung infection is not clonal expansion of dominant variants, but to sustain simultaneously a wide range of genetic variants facilitating adaptation of the population to changing living conditions in the lung. Genomic diversification during chronic infection requires increased attention when new control strategies against M. abscessus infections are explored.
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Affiliation(s)
- Astrid Lewin
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Elisabeth Kamal
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Unit NG 1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Katja Winter
- Unit MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
| | - Sandra Kaiser
- Unit MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
| | - Hubert Schäfer
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Lei Mao
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany.,Unit 31 Infectious Disease Data Science Unit, Robert Koch Institute, Berlin, Germany
| | - Patience Eschenhagen
- Klinikum Westbrandenburg, Campus Potsdam, Cystic Fibrosis Section, Potsdam, Germany.,Pediatric Respiratory Medicine, Immunology and Intensive Care Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Claudia Grehn
- Department of Pediatrics, Division of Pulmonology, Immunology and Intensive Care Medicine, Division of Cystic Fibrosis, Charité - Universitätsmedizin, Berlin, Germany
| | - Jennifer Bender
- Unit 13 Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany.,ECDC Fellowship Programme, Public Health Microbiology Path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Carsten Schwarz
- Klinikum Westbrandenburg, Campus Potsdam, Cystic Fibrosis Section, Potsdam, Germany.,Pediatric Respiratory Medicine, Immunology and Intensive Care Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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Davidson RM, Benoit JB, Kammlade SM, Hasan NA, Epperson LE, Smith T, Vasireddy S, Brown-Elliott BA, Nick JA, Olivier KN, Zelazny AM, Daley CL, Strong M, Wallace RJ. Genomic characterization of sporadic isolates of the dominant clone of Mycobacterium abscessus subspecies massiliense. Sci Rep 2021; 11:15336. [PMID: 34321532 PMCID: PMC8319421 DOI: 10.1038/s41598-021-94789-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022] Open
Abstract
Recent studies have characterized a dominant clone (Clone 1) of Mycobacterium abscessus subspecies massiliense (M. massiliense) associated with high prevalence in cystic fibrosis (CF) patients, pulmonary outbreaks in the United States (US) and United Kingdom (UK), and a Brazilian epidemic of skin infections. The prevalence of Clone 1 in non-CF patients in the US and the relationship of sporadic US isolates to outbreak clones are not known. We surveyed a reference US Mycobacteria Laboratory and a US biorepository of CF-associated Mycobacteria isolates for Clone 1. We then compared genomic variation and antimicrobial resistance (AMR) mutations between sporadic non-CF, CF, and outbreak Clone 1 isolates. Among reference lab samples, 57/147 (39%) of patients with M. massiliense had Clone 1, including pulmonary and extrapulmonary infections, compared to 11/64 (17%) in the CF isolate biorepository. Core and pan genome analyses revealed that outbreak isolates had similar numbers of single nucleotide polymorphisms (SNPs) and accessory genes as sporadic US Clone 1 isolates. However, pulmonary outbreak isolates were more likely to have AMR mutations compared to sporadic isolates. Clone 1 isolates are present among non-CF and CF patients across the US, but additional studies will be needed to resolve potential routes of transmission and spread.
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Affiliation(s)
- Rebecca M Davidson
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA.
| | - Jeanne B Benoit
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Sara M Kammlade
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Nabeeh A Hasan
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - L Elaine Epperson
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Terry Smith
- Department of Microbiology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Sruthi Vasireddy
- Department of Microbiology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Barbara A Brown-Elliott
- Department of Microbiology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Kenneth N Olivier
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrian M Zelazny
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Charles L Daley
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Michael Strong
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Richard J Wallace
- Department of Microbiology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
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MAB_2355c Confers Macrolide Resistance in Mycobacterium abscessus by Ribosome Protection. Antimicrob Agents Chemother 2021; 65:e0033021. [PMID: 34097497 PMCID: PMC8373217 DOI: 10.1128/aac.00330-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Macrolide resistance is always a concern when treating Mycobacterium abscessus infections. MAB_2355c was identified previously as a possible new factor that confers the intrinsic resistance of 194 clinical M. abscessus isolates to clarithromycin. Herein, the potential mechanism by which MAB_2355c exerts macrolide resistance was explored by bioinformatics analysis, MAB_2355c cloning and protein purification, ATP hydrolysis assay, gene knockout and complementation, antibiotic sensitivity, and transcription-translation assays. MAB_2355c is a putative ATP-binding cassette F (ABC-F) family protein. Purified MAB_2355c protein exhibits ATP hydrolysis activity, which can be inhibited by ribosome-targeting antibiotics. MAB_2355c mRNA expression is upregulated more significantly after exposure to macrolides than after exposure to other ribosome-targeting antibiotics. MAB_2355c deleted strains showed increased sensitivity to macrolides, which was reduced by MAB_2355c complementation. Finally, MAB_2355c rescued the transcription and translation activities affected by macrolides in vitro. These findings suggest that MAB_2355c confers the resistance of M. abscessus to macrolides by ribosome protection, thus complementing other known resistance mechanisms.
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Doyle RM, Rubio M, Dixon G, Hartley J, Klein N, Coll P, Harris KA. Cross-transmission Is Not the Source of New Mycobacterium abscessus Infections in a Multicenter Cohort of Cystic Fibrosis Patients. Clin Infect Dis 2021; 70:1855-1864. [PMID: 31225586 PMCID: PMC7156781 DOI: 10.1093/cid/ciz526] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/18/2019] [Indexed: 12/25/2022] Open
Abstract
Background Mycobacterium abscessus is an extensively drug–resistant pathogen that causes pulmonary disease, particularly in cystic fibrosis (CF) patients. Identifying direct patient-to-patient transmission of M. abscessus is critically important in directing an infection control policy for the management of risk in CF patients. A variety of clinical labs have used molecular epidemiology to investigate transmission. However, there is still conflicting evidence as to how M. abscessus is acquired and whether cross-transmission occurs. Recently, labs have applied whole-genome sequencing (WGS) to investigate this further and, in this study, we investigated whether WGS can reliably identify cross-transmission in M. abscessus. Methods We retrospectively sequenced the whole genomes of 145 M. abscessus isolates from 62 patients, seen at 4 hospitals in 2 countries over 16 years. Results We have shown that a comparison of a fixed number of core single nucleotide variants alone cannot be used to infer cross-transmission in M. abscessus but does provide enough information to replace multiple existing molecular assays. We detected 1 episode of possible direct patient-to-patient transmission in a sibling pair. We found that patients acquired unique M. abscessus strains even after spending considerable time on the same wards with other M. abscessus–positive patients. Conclusions This novel analysis has demonstrated that the majority of patients in this study have not acquired M. abscessus through direct patient-to-patient transmission or a common reservoir. Tracking transmission using WGS will only realize its full potential with proper environmental screening, as well as patient sampling.
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Affiliation(s)
- Ronan M Doyle
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital National Health Service Foundation Trust.,National Institute for Health Research Biomedical Research Centre at Great Ormond Street Hospital for Children National Health Service Foundation Trust and University College London, United Kingdom
| | - Marc Rubio
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Garth Dixon
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital National Health Service Foundation Trust.,National Institute for Health Research Biomedical Research Centre at Great Ormond Street Hospital for Children National Health Service Foundation Trust and University College London, United Kingdom
| | - John Hartley
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital National Health Service Foundation Trust.,National Institute for Health Research Biomedical Research Centre at Great Ormond Street Hospital for Children National Health Service Foundation Trust and University College London, United Kingdom
| | - Nigel Klein
- National Institute for Health Research Biomedical Research Centre at Great Ormond Street Hospital for Children National Health Service Foundation Trust and University College London, United Kingdom.,University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Pere Coll
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Servei de Microbiologia, Fundació de Gestió de l'Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Kathryn A Harris
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital National Health Service Foundation Trust.,National Institute for Health Research Biomedical Research Centre at Great Ormond Street Hospital for Children National Health Service Foundation Trust and University College London, United Kingdom
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Antimicrobial Susceptibility and Phylogenetic Relations in a German Cohort Infected with Mycobacterium abscessus. J Clin Microbiol 2020; 58:JCM.01813-20. [PMID: 32938741 DOI: 10.1128/jcm.01813-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
Mycobacterium abscessus is a highly antibiotic-resistant opportunistic pathogen causing clinically challenging infections in patients with preexisting lung diseases or under immunosuppression. Hence, reliable antibiotic susceptibility data are required for effective treatment. Aims of this study were to investigate (i) the congruence of genotypic and phenotypic antimicrobial susceptibility testing, (ii) the relationship between resistance profile and clinical course, and (iii) the phylogenetic relations of M. abscessus in a German patient cohort. A total of 39 isolates from 29 patients infected or colonized with M. abscessus underwent genotypic and phenotypic drug susceptibility testing. Clinical data were correlated with susceptibility data. Phylogenetic analysis was performed by means of whole-genome sequencing (WGS) and single-nucleotide polymorphism (SNP) analysis. Macrolide resistance was mainly mediated by functional Erm(41) methyltransferases (T28 sequevars) in M. abscessus subsp. abscessus (n = 25) and M. abscessus subsp. bolletii (n = 2). It was significantly associated with impaired culture conversion (P = 0.02). According to the core SNP phylogeny, we identified three clusters of closely related isolates with SNP distances below 25. Representatives of all circulating global clones (Absc. 1, Absc. 2, and Mass. 1) were identified in our cohort. However, we could not determine evidence for in-hospital interhuman transmission from clinical data. In our patient cohort, we identified three M. abscessus clusters with closely related isolates and representatives of the previously described international clusters but no human-to-human in-hospital transmission. Macrolide and aminoglycoside susceptibility data are critical for therapeutic decision-making in M. abscessus infections.
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Riva C, Tortoli E, Cugnata F, Sanvito F, Esposito A, Rossi M, Colarieti A, Canu T, Cigana C, Bragonzi A, Loré NI, Miotto P, Cirillo DM. A New Model of Chronic Mycobacterium abscessus Lung Infection in Immunocompetent Mice. Int J Mol Sci 2020; 21:ijms21186590. [PMID: 32916885 PMCID: PMC7554715 DOI: 10.3390/ijms21186590] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
Pulmonary infections caused by Mycobacterium abscessus (MA) have increased over recent decades, affecting individuals with underlying pathologies such as chronic obstructive pulmonary disease, bronchiectasis and, especially, cystic fibrosis. The lack of a representative and standardized model of chronic infection in mice has limited steps forward in the field of MA pulmonary infection. To overcome this challenge, we refined the method of agar beads to establish MA chronic infection in immunocompetent mice. We evaluated bacterial count, lung pathology and markers of inflammation and we performed longitudinal studies with magnetic resonance imaging (MRI) up to three months after MA infection. In this model, MA was able to establish a persistent lung infection for up to two months and with minimal systemic spread. Lung histopathological analysis revealed granulomatous inflammation around bronchi characterized by the presence of lymphocytes, aggregates of vacuolated histiocytes and a few neutrophils, mimicking the damage observed in humans. Furthermore, MA lung lesions were successfully monitored for the first time by MRI. The availability of this murine model and the introduction of the successfully longitudinal monitoring of the murine lung lesions with MRI pave the way for further investigations on the impact of MA pathogenesis and the efficacy of novel treatments.
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Affiliation(s)
- Camilla Riva
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (C.R.); (E.T.); (M.R.); (N.I.L.); (P.M.)
| | - Enrico Tortoli
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (C.R.); (E.T.); (M.R.); (N.I.L.); (P.M.)
| | - Federica Cugnata
- Centre of Statistics for Biomedical Sciences (CUSSB), Vita-Salute San Raffaele University, 20132 Milan, Italy;
| | - Francesca Sanvito
- Pathology Unit, Department of Experimental Oncology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Antonio Esposito
- Preclinical Imaging Facility, Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (A.E.); (A.C.); (T.C.)
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Marco Rossi
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (C.R.); (E.T.); (M.R.); (N.I.L.); (P.M.)
| | - Anna Colarieti
- Preclinical Imaging Facility, Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (A.E.); (A.C.); (T.C.)
| | - Tamara Canu
- Preclinical Imaging Facility, Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (A.E.); (A.C.); (T.C.)
| | - Cristina Cigana
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (C.C.); (A.B.)
| | - Alessandra Bragonzi
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (C.C.); (A.B.)
| | - Nicola Ivan Loré
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (C.R.); (E.T.); (M.R.); (N.I.L.); (P.M.)
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (C.R.); (E.T.); (M.R.); (N.I.L.); (P.M.)
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (C.R.); (E.T.); (M.R.); (N.I.L.); (P.M.)
- Correspondence: ; Tel.: +39-02-2443-7947
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Moustafa AM, Lal A, Planet PJ. Comparative genomics in infectious disease. Curr Opin Microbiol 2020; 53:61-70. [PMID: 32248056 DOI: 10.1016/j.mib.2020.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 02/07/2023]
Abstract
With more than one million bacterial genome sequences uploaded to public databases in the last 25 years, genomics has become a powerful tool for studying bacterial biology. Here, we review recent approaches that leverage large numbers of whole genome sequences to decipher the spread and pathogenesis of bacterial infectious diseases.
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Affiliation(s)
- Ahmed M Moustafa
- Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Arnav Lal
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul J Planet
- Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA.
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Degiacomi G, Sammartino JC, Chiarelli LR, Riabova O, Makarov V, Pasca MR. Mycobacterium abscessus, an Emerging and Worrisome Pathogen among Cystic Fibrosis Patients. Int J Mol Sci 2019; 20:ijms20235868. [PMID: 31766758 PMCID: PMC6928860 DOI: 10.3390/ijms20235868] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/20/2019] [Accepted: 11/20/2019] [Indexed: 01/09/2023] Open
Abstract
Nontuberculous mycobacteria (NTM) have recently emerged as important pathogens among cystic fibrosis (CF) patients worldwide. Mycobacterium abscessus is becoming the most worrisome NTM in this cohort of patients and recent findings clarified why this pathogen is so prone to this disease. M. abscessus drug therapy takes up to 2 years and its failure causes an accelerated lung function decline. The M. abscessus colonization of lung alveoli begins with smooth strains producing glycopeptidolipids and biofilm, whilst in the invasive infection, "rough" mutants are responsible for the production of trehalose dimycolate, and consequently, cording formation. Human-to-human M. abscessus transmission was demonstrated among geographically separated CF patients by whole-genome sequencing of clinical isolates worldwide. Using a M. abscessus infected CF zebrafish model, it was demonstrated that CFTR (cystic fibrosis transmembrane conductance regulator) dysfunction seems to have a specific role in the immune control of M. abscessus infections only. This pathogen is also intrinsically resistant to many drugs, thanks to its physiology and to the acquisition of new mechanisms of drug resistance. Few new compounds or drug formulations active against M. abscessus are present in preclinical and clinical development, but recently alternative strategies have been investigated, such as phage therapy and the use of β-lactamase inhibitors.
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Affiliation(s)
- Giulia Degiacomi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (G.D.); (J.C.S.); (L.R.C.)
| | - José Camilla Sammartino
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (G.D.); (J.C.S.); (L.R.C.)
- IUSS—University School for Advanced Studies, 27100 Pavia, Italy
| | - Laurent Roberto Chiarelli
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (G.D.); (J.C.S.); (L.R.C.)
| | - Olga Riabova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (O.R.); (V.M.)
| | - Vadim Makarov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (O.R.); (V.M.)
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (G.D.); (J.C.S.); (L.R.C.)
- Correspondence: ; Tel.: +39-0382-985576
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Andrew EC, Connell T, Robinson P, Curtis N, Massie J, Robertson C, Harrison J, Shanthikumar S, Bryant PA, Starr M, Steer A, Ranganathan S, Gwee A. Pulmonary Mycobacterium abscessus complex in children with cystic fibrosis: A practical management guideline. J Paediatr Child Health 2019; 55:502-511. [PMID: 30884016 DOI: 10.1111/jpc.14427] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 02/05/2019] [Accepted: 02/10/2019] [Indexed: 11/28/2022]
Abstract
The treatment of Mycobacterium abscessus complex (MABSC) pulmonary infections is an emerging challenge in patients with cystic fibrosis (CF). Multidrug therapy for prolonged durations is required and carries the significant burden of drug-related toxicity, cost and selective pressure for multiresistant bacteria. International guidelines acknowledge that clinical and in vitro data to support treatment regimens are limited, particularly in children. As part of a collaboration between the infectious diseases and respiratory units at our institution, we have developed a modified treatment guideline that aims to balance the aims of MABSC eradication and slowing disease progression with minimising drug toxicity and resistance. The outcomes of this treatment approach will be monitored and reported. In this manuscript, we discuss the available evidence for treatment choices and present our treatment guideline for paediatric patients with CF and MABSC infection.
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Affiliation(s)
- Eden C Andrew
- Infectious Diseases Unit, Department of General Medicine, Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia
| | - Tom Connell
- Infectious Diseases Unit, Department of General Medicine, Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Clinical Infectious Diseases Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Phil Robinson
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Respiratory and Sleep Medicine, Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia.,Respiratory Diseases, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Nigel Curtis
- Infectious Diseases Unit, Department of General Medicine, Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Clinical Infectious Diseases Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - John Massie
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Respiratory and Sleep Medicine, Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia.,Respiratory Diseases, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Colin Robertson
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Respiratory and Sleep Medicine, Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia.,Respiratory Diseases, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Joanne Harrison
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Respiratory and Sleep Medicine, Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia.,Respiratory Diseases, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Shivanthan Shanthikumar
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Respiratory and Sleep Medicine, Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia.,Respiratory Diseases, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Penelope A Bryant
- Infectious Diseases Unit, Department of General Medicine, Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Clinical Infectious Diseases Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Mike Starr
- Infectious Diseases Unit, Department of General Medicine, Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew Steer
- Infectious Diseases Unit, Department of General Medicine, Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Group A Streptococcal Research Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Sarath Ranganathan
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Respiratory and Sleep Medicine, Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia.,Respiratory Diseases, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Amanda Gwee
- Infectious Diseases Unit, Department of General Medicine, Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Clinical Infectious Diseases Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
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40
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Common Infections Following Lung Transplantation. ESSENTIALS IN LUNG TRANSPLANTATION 2019. [PMCID: PMC7121478 DOI: 10.1007/978-3-319-90933-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The lungs are the only transplanted organ in direct contact with the ‘outside world’. Infection is a significant cause of morbidity and mortality in lung transplantation. Early accurate diagnosis and optimal management is essential to prevent short and long term complications. Bacteria, including Mycobacteria and Nocardia, viruses and fungi are common pathogens. Organisms may be present in the recipient prior to transplantation, transmitted with the donor lungs or acquired after transplantation. The degree of immunosuppression and the routine use of antimicrobial prophylaxis alters the pattern of post-transplant infections.
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Whole-Genome Sequencing for Predicting Clarithromycin Resistance in Mycobacterium abscessus. Antimicrob Agents Chemother 2018; 63:AAC.01204-18. [PMID: 30397069 DOI: 10.1128/aac.01204-18] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/25/2018] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium abscessus is emerging as an important pathogen in chronic lung diseases, with concern regarding patient-to-patient transmission. The recent introduction of routine whole-genome sequencing (WGS) as a replacement for existing reference techniques in England provides an opportunity to characterize the genetic determinants of resistance. We conducted a systematic review to catalogue all known resistance-determining mutations. This knowledge was used to construct a predictive algorithm based on mutations in the erm(41) and rrl genes which was tested on a collection of 203 sequentially acquired clinical isolates for which there were paired genotype/phenotype data. A search for novel resistance-determining mutations was conducted using a heuristic algorithm. The sensitivity of existing knowledge for predicting resistance in clarithromycin was 95% (95% confidence interval [CI], 89 to 98%), and the specificity was 66% (95% CI, 54 to 76%). The subspecies alone was a poor predictor of resistance to clarithromycin. Eight potential new resistance-conferring single nucleotide polymorphisms (SNPs) were identified. WGS demonstrated probable resistance-determining SNPs in regions that the NTM-DR line probe cannot detect. These mutations are potentially clinically important, as they all occurred in samples that were predicted to be inducibly resistant and for which a macrolide would therefore currently be indicated. We were unable to explain all resistance, raising the possibility of the involvement of other as yet unidentified genes.
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42
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Davidson RM. A Closer Look at the Genomic Variation of Geographically Diverse Mycobacterium abscessus Clones That Cause Human Infection and Disease. Front Microbiol 2018; 9:2988. [PMID: 30568642 PMCID: PMC6290055 DOI: 10.3389/fmicb.2018.02988] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/19/2018] [Indexed: 01/15/2023] Open
Abstract
Mycobacterium abscessus is a multidrug resistant bacterium that causes pulmonary and extrapulmonary disease. The reported prevalence of pulmonary M. abscessus infections appears to be increasing in the United States (US) and around the world. In the last five years, multiple studies have utilized whole genome sequencing to investigate the genetic epidemiology of two clinically relevant subspecies, M. abscessus subsp. abscessus (MAB) and M. abscessus subsp. massiliense (MMAS). Phylogenomic comparisons of clinical isolates revealed that substantial proportions of patients have MAB and MMAS isolates that belong to genetically similar clusters also known as ‘dominant clones’. Unlike the genetic lineages of Mycobacterium tuberculosis that tend to be geographically clustered, the MAB and MMAS clones have been found in clinical populations from the US, Europe, Australia and South America. Moreover, the clones have been associated with worse clinical outcomes and show increased pathogenicity in macrophage and mouse models. While some have suggested that they may have spread locally and then globally through ‘indirect transmission’ within cystic fibrosis (CF) clinics, isolates of these clones have also been associated with sporadic pulmonary infections in non-CF patients and unrelated hospital-acquired soft tissue infections. M. abscessus has long been thought to be acquired from the environment, but the prevalence, exposure risk and environmental reservoirs of the dominant clones are currently not known. This review summarizes the genomic studies of M. abscessus and synthesizes the current knowledge surrounding the geographically diverse dominant clones identified from patient samples. Furthermore, it discusses the limitations of core genome comparisons for studying these genetically similar isolates and explores the breadth of accessory genome variation that has been observed to date. The combination of both core and accessory genome variation among these isolates may be the key to elucidating the origin, spread and evolution of these frequent genotypes.
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Affiliation(s)
- Rebecca M Davidson
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States
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43
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Zweijpfenning S, Hoefsloot W, van Ingen J. Nontuberculous mycobacteria. Tuberculosis (Edinb) 2018. [DOI: 10.1183/2312508x.10022717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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44
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Research Needs on Respiratory Health in Migrant and Refugee Populations. An Official American Thoracic Society and European Respiratory Society Workshop Report. Ann Am Thorac Soc 2018; 15:1247-1255. [DOI: 10.1513/annalsats.201807-478st] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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45
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Chalmers J, Aksamit T, Carvalho A, Rendon A, Franco I. Non-tuberculous mycobacterial pulmonary infections. Pulmonology 2018. [DOI: 10.1016/j.pulmoe.2017.12.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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46
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Martiniano SL, Davidson RM, Nick JA. Nontuberculous mycobacteria in cystic fibrosis: Updates and the path forward. Pediatr Pulmonol 2017; 52:S29-S36. [PMID: 28881094 DOI: 10.1002/ppul.23825] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 08/15/2017] [Indexed: 01/03/2023]
Abstract
Nontuberculous mycobacteria (NTM) are troublesome pathogens that can cause significant pulmonary disease in patients with cystic fibrosis (CF). Diagnosis can be difficult in the setting of underlying CF and treatment regimens are burdensome on both patients and providers. Recent consensus guidelines for treatment of NTM in CF have provided a guide for the CF community, however research is lagging regarding accuracy of our diagnostic abilities and treatment efficacy. In this review, we provide new insights into the complexity of NTM from emerging whole genome sequencing data, a summary of current NTM diagnosis and treatment guidelines, highlight new treatment options, and discuss future research projects which aim to better define which patients to treat and timing and duration of treatment.
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Affiliation(s)
- Stacey L Martiniano
- Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, Colorado
| | - Rebecca M Davidson
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado
| | - Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, Colorado
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