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Bernard C, Liu Y, Larrouy-Maumus G, Guilhot C, Cam K, Chalut C. Altered serine metabolism promotes drug tolerance in Mycobacterium abscessus via a WhiB7-mediated adaptive stress response. Antimicrob Agents Chemother 2024:e0145623. [PMID: 38651855 DOI: 10.1128/aac.01456-23] [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: 11/07/2023] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
Abstract
Mycobacterium abscessus is an emerging opportunistic pathogen responsible for chronic lung diseases, especially in patients with cystic fibrosis. Treatment failure of M. abscessus infections is primarily associated with intrinsic or acquired antibiotic resistance. However, there is growing evidence that antibiotic tolerance, i.e., the ability of bacteria to transiently survive exposure to bactericidal antibiotics through physiological adaptations, contributes to the relapse of chronic infections and the emergence of acquired drug resistance. Yet, our understanding of the molecular mechanisms that underlie antibiotic tolerance in M. abscessus remains limited. In the present work, a mutant with increased cross-tolerance to the first- and second-line antibiotics cefoxitin and moxifloxacin, respectively, has been isolated by experimental evolution. This mutant harbors a mutation in serB2, a gene involved in L-serine biosynthesis. Metabolic changes caused by this mutation alter the intracellular redox balance to a more reduced state that induces overexpression of the transcriptional regulator WhiB7 during the stationary phase, promoting tolerance through activation of a WhiB7-dependant adaptive stress response. These findings suggest that alteration of amino acid metabolism and, more generally, conditions that trigger whiB7 overexpression, makes M. abscessus more tolerant to antibiotic treatment.
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Affiliation(s)
- Célia Bernard
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Yi Liu
- Faculty of Natural Sciences, Department of Life Sciences, Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
| | - Gérald Larrouy-Maumus
- Faculty of Natural Sciences, Department of Life Sciences, Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
| | - Christophe Guilhot
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Kaymeuang Cam
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Christian Chalut
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
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Wiesel V, Aviram M, Mei-Zahav M, Dotan M, Prais D, Cohen-Cymberknoh M, Gur M, Bar-Yoseph R, Livnat G, Goldbart A, Hazan G, Hazan I, Golan-Tripto I. Eradication of Nontuberculous Mycobacteria in People with Cystic Fibrosis Treated with Elexacaftor/Tezacaftor/Ivacaftor: A Multicenter Cohort Study. J Cyst Fibros 2024; 23:41-49. [PMID: 37173154 DOI: 10.1016/j.jcf.2023.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND The prevalence of nontuberculous mycobacteria (NTM) infections is rising in people with cystic fibrosis (pwCF). NTM infection, especially infection with Mycobacterium abscessus complex (MABC), is commonly associated with severe lung deterioration. The current treatment modalities, including multiple intravenous antibiotics, frequently fail to achieve airway eradication. Although treatment with elexacaftor/tezacaftor/ivacaftor (ETI) has been shown to modulate the lung microbiome, data regarding its role in eradicating NTM in pwCF is lacking. Our aim was to evaluate the impact of ETI on the rate of NTM eradication in pwCF. METHODS This retrospective multicenter cohort study included pwCF from five CF centers in Israel. PwCF aged older than 6 who had at least one positive NTM airway culture in the past two years and were treated with ETI for at least one year were included. The annual NTM and bacterial isolations, pulmonary function tests, and body mass index were analyzed before and after ETI treatment. RESULTS Fifteen pwCF were included (median age 20.9 years, 73.3% females, 80% pancreatic insufficient). In nine patients (66%) NTM isolations were eradicated following treatment with ETI. Seven of them had MABC. The median time between the first NTM isolation and treatment with ETI was 2.71 years (0.27-10.35 years). Eradication of NTM was associated with improved pulmonary function tests (p<0.05). CONCLUSIONS For the first time, we report successful eradication of NTM, including MABC, following treatment with ETI in pwCF. Additional studies are needed to assess whether treatment with ETI can result in the long-term eradication of NTM.
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Affiliation(s)
- Vered Wiesel
- Medical School for International Health, Ben Gurion University, Beer Sheva, Israel; Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Micha Aviram
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Pediatric Pulmonary Unit, Soroka University Medical Center, Beer Sheva, Israel
| | - Meir Mei-Zahav
- Kathy and Lee Graub Cystic Fibrosis Center, Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Miri Dotan
- Kathy and Lee Graub Cystic Fibrosis Center, Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dario Prais
- Kathy and Lee Graub Cystic Fibrosis Center, Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Malena Cohen-Cymberknoh
- Pediatric Pulmonary Unit and Cystic Fibrosis Center, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Michal Gur
- Pediatric Pulmonary Institute and CF Center, Rappaport Children's Hospital, Rambam Health Care Campus, Haifa, Israel; Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ronen Bar-Yoseph
- Pediatric Pulmonary Institute and CF Center, Rappaport Children's Hospital, Rambam Health Care Campus, Haifa, Israel; Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Galit Livnat
- Pediatric Pulmonology Unit and CF center, Carmel Medical Center, Haifa, Israel
| | - Aviv Goldbart
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Pediatric Pulmonary Unit, Soroka University Medical Center, Beer Sheva, Israel
| | - Guy Hazan
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Pediatric Pulmonary Unit, Soroka University Medical Center, Beer Sheva, Israel
| | - Itai Hazan
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Clinical Research Center, Soroka University Medical Center and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Inbal Golan-Tripto
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Pediatric Pulmonary Unit, Soroka University Medical Center, Beer Sheva, Israel.
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3
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Martiniano SL, Caceres SM, Poch K, Rysavy NM, Lovell VK, Armantrout E, Jones M, Anthony M, Keck A, Nichols DP, Vandalfsen JM, Sagel SD, Wagner B, Xie J, Weaver K, Heltshe SL, Daley CL, Davidson RM, Nick JA. Prospective evaluation of nontuberculous mycobacteria disease in cystic fibrosis: The design of the PREDICT study. J Cyst Fibros 2024; 23:50-57. [PMID: 37666709 PMCID: PMC10907544 DOI: 10.1016/j.jcf.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/07/2023] [Accepted: 08/25/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND Nontuberculous mycobacteria (NTM) are an important cause of airway infections in people with cystic fibrosis (pwCF). Isolation of NTM from respiratory specimens of pwCF do not mandate treatment in the absence of clinical and radiologic features of NTM pulmonary disease (NTM-PD), as some pwCF clear the infection without treatment and others do not appear to progress to NTM-PD despite persistent infection. An evidence-based protocol to standardize diagnosis of NTM-PD is needed to systematically identify pwCF who may benefit from treatment. METHODS In this multicenter observational study, eligible pwCF who are 6 years of age and older and who have had a recent positive NTM culture are systematically evaluated for NTM-PD. Participants are identified based on positive NTM culture results obtained during routine clinical care and following enrollment are evaluated for NTM-PD and CF-related comorbidities. Participants are followed in PREDICT until they meet NTM-PD diagnostic criteria and are ready to initiate NTM treatment, or until study termination. Active participants who have not met these criteria are re-consented every 5 years to enable long-term participation. RESULTS The primary endpoint will summarize the proportion of participants who meet the NTM-PD diagnosis definition. The time from enrollment to NTM-PD diagnosis will be derived from Kaplan-Meier estimates. CONCLUSION A prospective protocol to identify NTM-PD in pwCF will test if this standardized approach defines a cohort with signs and symptoms associated with NTM-PD, to assist with clinical decision making and to build a framework for future therapeutic trials. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02073409.
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Affiliation(s)
- Stacey L Martiniano
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Silvia M Caceres
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Katie Poch
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Noel M Rysavy
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Valerie K Lovell
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Emily Armantrout
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Marion Jones
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Margaret Anthony
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Allison Keck
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - David P Nichols
- Cystic Fibrosis Foundation Therapeutics Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Jill M Vandalfsen
- Cystic Fibrosis Foundation Therapeutics Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Scott D Sagel
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Brandie Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health University of Colorado Anschutz Medical Campus Aurora Colorado, USA
| | - Jing Xie
- Cystic Fibrosis Foundation Therapeutics Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Katie Weaver
- Cystic Fibrosis Foundation Therapeutics Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Sonya L Heltshe
- Cystic Fibrosis Foundation Therapeutics Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Charles L Daley
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Rebecca M Davidson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Gramegna A, Misuraca S, Lombardi A, Premuda C, Barone I, Ori M, Amati F, Retucci M, Nazzari E, Alicandro G, Ferrarese M, Codecasa L, Bandera A, Aliberti S, Daccò V, Blasi F. Treatable traits and challenges in the clinical management of non-tuberculous mycobacteria lung disease in people with cystic fibrosis. Respir Res 2023; 24:316. [PMID: 38104098 PMCID: PMC10725605 DOI: 10.1186/s12931-023-02612-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023] Open
Abstract
INTRODUCTION Over the last ten years an increasing prevalence and incidence of non-tuberculous mycobacteria (NTM) has been reported among patients with cystic fibrosis (CF) Viviani (J Cyst Fibros, 15(5):619-623, 2016). NTM pulmonary disease has been associated with negative clinical outcomes and often requires pharmacological treatment. Although specific guidelines help clinicians in the process of diagnosis and clinical management, the focus on the multidimensional assessment of concomitant problems is still scarce. MAIN BODY This review aims to identify the treatable traits of NTM pulmonary disease in people with CF and discuss the importance of a multidisciplinary approach in order to detect and manage all the clinical and behavioral aspects of the disease. The multidisciplinary complexity of NTM pulmonary disease in CF requires careful management of respiratory and extra-respiratory, including control of comorbidities, drug interactions and behavioral factors as adherence to therapies. CONCLUSIONS The treatable trait strategy can help to optimize clinical management through systematic assessment of all the aspects of the disease, providing a holistic treatment for such a multi-systemic and complex condition.
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Affiliation(s)
- Andrea Gramegna
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy.
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy.
| | - Sofia Misuraca
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Andrea Lombardi
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
- Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Chiara Premuda
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Ivan Barone
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Margherita Ori
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Francesco Amati
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072, Milan, Italy
- Respiratory Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089, Milan, Italy
| | - Mariangela Retucci
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
- Healthcare Professions Department, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Erica Nazzari
- Cystic Fibrosis Center, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milan, Italy
| | - Gianfranco Alicandro
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Maurizio Ferrarese
- Regional TB Reference Centre, Villa Marelli Institute, Niguarda Hospital, Milan, Italy
| | - Luigi Codecasa
- Regional TB Reference Centre, Villa Marelli Institute, Niguarda Hospital, Milan, Italy
| | - Alessandra Bandera
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
- Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Aliberti
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072, Milan, Italy
- Respiratory Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089, Milan, Italy
| | - Valeria Daccò
- Cystic Fibrosis Center, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milan, Italy
| | - Francesco Blasi
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
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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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6
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Nick JA, Malcolm KC, Hisert KB, Wheeler EA, Rysavy NM, Poch K, Caceres S, Lovell VK, Armantrout E, Saavedra MT, Calhoun K, Chatterjee D, Aboellail I, De P, Martiniano SL, Jia F, Davidson RM. Culture independent markers of nontuberculous mycobacterial (NTM) lung infection and disease in the cystic fibrosis airway. Tuberculosis (Edinb) 2023; 138:102276. [PMID: 36417800 PMCID: PMC10965158 DOI: 10.1016/j.tube.2022.102276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
Nontuberculous mycobacteria (NTM) are opportunistic pathogens that affect a relatively small but significant portion of the people with cystic fibrosis (CF), and may cause increased morbidity and mortality in this population. Cultures from the airway are the only test currently in clinical use for detecting NTM. Culture techniques used in clinical laboratories are insensitive and poorly suited for population screening or to follow progression of disease or treatment response. The lack of sensitive and quantitative markers of NTM in the airway impedes patient care and clinical trial design, and has limited our understanding of patterns of acquisition, latency and pathogenesis of disease. Culture-independent markers of NTM infection have the potential to overcome many of the limitations of standard NTM cultures, especially the very slow growth, inability to quantitate bacterial burden, and low sensitivity due to required decontamination procedures. A range of markers have been identified in sputum, saliva, breath, blood, urine, as well as radiographic studies. Proposed markers to detect presence of NTM or transition to NTM disease include bacterial cell wall products and DNA, as well as markers of host immune response such as immunoglobulins and the gene expression of circulating leukocytes. In all cases the sensitivity of culture-independent markers is greater than standard cultures; however, most do not discriminate between various NTM species. Thus, each marker may be best suited for a specific clinical application, or combined with other markers and traditional cultures to improve diagnosis and monitoring of treatment response.
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Affiliation(s)
- Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
| | - Kenneth C Malcolm
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Katherine B Hisert
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Emily A Wheeler
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Noel M Rysavy
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Katie Poch
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Silvia Caceres
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Valerie K Lovell
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Emily Armantrout
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Milene T Saavedra
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Kara Calhoun
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Delphi Chatterjee
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Ibrahim Aboellail
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Prithwiraj De
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Stacey L Martiniano
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Fan Jia
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Rebecca M Davidson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206, USA
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7
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Narayanaswamy VP, Townsend SM, Loughran AJ, Wiesmann W, Baker S. Polycationic Glycopolymer Demonstrates Activity Against Persisters and Biofilms of Non-tuberculosis Mycobacteria Cystic Fibrosis Clinical Isolates in vitro. Front Microbiol 2022; 13:821820. [PMID: 35265060 PMCID: PMC8900536 DOI: 10.3389/fmicb.2022.821820] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/31/2022] [Indexed: 01/15/2023] Open
Abstract
Non-tuberculosis Mycobacterium (NTM) is a group of opportunistic pathogens associated with pulmonary infections that are difficult to diagnose and treat. Standard treatment typically consists of prolonged combination antibiotic therapy. Antibiotic resistance and the role of biofilms in pathogen communities, such as NTM persister cells, is an important unmet challenge that leads to increased toxicity, frequent relapse, poor clinical management, and an extended treatment period. Infection recurrence and relapse are not uncommon among individuals with cystic fibrosis (CF) or chronic obstructive pulmonary disease (COPD), where thick mucus supports bacterial biofilm production and impairs mucociliary clearance. The study evaluates a membrane-active cationic glycopolymer [poly (acetyl, arginyl) glucosamine (PAAG)] being developed to support the safe and effective treatment of NTM biofilm infections. PAAG shows antibacterial activity against a wide range of pathogenic bacteria at concentrations non-toxic to human epithelial cells. Time-kill curves demonstrated PAAG's rapid bactericidal potential at concentrations as low as 1X MIC against all NTM strains tested and compared to the standard of care. PAAG treatment prevents persister formation and eradicates antibiotic-induced persister cells in planktonic NTM cultures below the limit of detection (10 colony-forming unit (CFU)/ml). Further, PAAG showed the ability to penetrate and disperse NTM biofilms formed by both rapidly and slowly growing strains, significantly reducing the biofilm biomass (p < 0.0001) compared to the untreated NTM biofilms. Microscopical examination confirmed PAAG's ability to disrupt and disperse mycobacterial biofilms. A single PAAG treatment resulted in up to a 25-fold reduction in live-labeled NTM and a 78% reduction in biofilm thickness. Similar to other polycationic molecules, PAAG's bactericidal and antibiofilm activities employ rapid permeabilization of the outer membrane of the NTM strains, and subsequently, reduce the membrane potential even at concentrations as low as 50 μg/ml (p < 0.001). The outcomes of these in vitro analyses suggest the importance of this polycationic glycopolymer, PAAG, as a potential therapeutic agent for opportunistic NTM infections.
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Affiliation(s)
| | | | | | | | - Shenda Baker
- Synedgen, Inc., Claremont, CA, United States
- Synspira Therapeutics, Inc., Framingham, MA, United States
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8
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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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9
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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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10
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Waters VJ, Kidd TJ, Canton R, Ekkelenkamp MB, Johansen HK, LiPuma JJ, Bell SC, Elborn JS, Flume PA, VanDevanter DR, Gilligan P. Reconciling Antimicrobial Susceptibility Testing and Clinical Response in Antimicrobial Treatment of Chronic Cystic Fibrosis Lung Infections. Clin Infect Dis 2020; 69:1812-1816. [PMID: 31056660 DOI: 10.1093/cid/ciz364] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/29/2019] [Indexed: 01/28/2023] Open
Abstract
Median cystic fibrosis (CF) survival has increased dramatically over time due to several factors, including greater availability and use of antimicrobial therapies. During the progression of CF lung disease, however, the emergence of multidrug antimicrobial resistance can limit treatment effectiveness, threatening patient longevity. Current planktonic-based antimicrobial susceptibility testing lacks the ability to predict clinical response to antimicrobial treatment of chronic CF lung infections. There are numerous reasons for these limitations including bacterial phenotypic and genotypic diversity, polymicrobial interactions, and impaired antibiotic efficacy within the CF lung environment. The parallels to other chronic diseases such as non-CF bronchiectasis are discussed as well as research priorities for moving forward.
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Affiliation(s)
- Valerie J Waters
- Division of Infectious Diseases, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Canada
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Rafael Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Miquel B Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor
| | - Scott C Bell
- Department of Thoracic Medicine, Prince Charles Hospital and QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - J Stuart Elborn
- Imperial College Hospital, Queen's University Belfast, Northern Ireland
| | - Patrick A Flume
- Departments of Medicine and Pediatrics, Medical University of South Carolina, Charleston
| | - Donald R VanDevanter
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Peter Gilligan
- Department of Pathology-Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill
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11
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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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12
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Wheelock CE, Strandvik B. Abnormal n-6 fatty acid metabolism in cystic fibrosis contributes to pulmonary symptoms. Prostaglandins Leukot Essent Fatty Acids 2020; 160:102156. [PMID: 32750662 DOI: 10.1016/j.plefa.2020.102156] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 01/09/2023]
Abstract
Cystic fibrosis (CF) is a recessively inherited fatal disease that is the subject of extensive research and ongoing development of therapeutics targeting the defective protein, cystic fibrosis transmembrane conductance regulator (CFTR). Despite progress, the link between CFTR and clinical symptoms is incomplete. The severe CF phenotypes are associated with a deficiency of linoleic acid, which is the precursor of arachidonic acid. The release of arachidonic acid from membranes via phospholipase A2 is the rate-limiting step for eicosanoid synthesis and is increased in CF, which contributes to the observed inflammation. A potential deficiency of docosahexaenoic acid may lead to decreased levels of specialized pro-resolving mediators. This pathophysiology may contribute to an early and sterile inflammation, mucus production, and to bacterial colonization, which further increases inflammation and potentiates the clinical symptoms. Advances in lipid technology will assist in elucidating the role of lipid metabolism in CF, and stimulate therapeutic modulations of inflammation.
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Affiliation(s)
- Craig E Wheelock
- Division of Physiological Chemistry 2, Dept of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Birgitta Strandvik
- Dept of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.
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13
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Meoli A, Deolmi M, Iannarella R, Esposito S. Non-Tuberculous Mycobacterial Diseases in Children. Pathogens 2020; 9:pathogens9070553. [PMID: 32660053 PMCID: PMC7400539 DOI: 10.3390/pathogens9070553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/19/2020] [Accepted: 07/07/2020] [Indexed: 01/19/2023] Open
Abstract
Non-tuberculous mycobacteria (NTMs) are ubiquitous and opportunistic emerging bacteria with the potential to colonize and eventually infect either immunocompromised or immunocompetent individuals. In the last three decades, the prevalence of disease caused by NTMs has increased in several countries. The increased prevalence of NTM infection can be explained by an ageing population with rising comorbidities, HIV infection, the common use of immunosuppressive drugs, and improved diagnostic methods. The aim of this review is to demonstrate the clinical relevance of NTMs in children, describing their features and manifestations, diagnostic tools, and therapeutic approaches. We collected data from the literature about NTM infections in young patients over the past five years (2014–2019) using the keywords “non-tuberculous”, “mycobacteria”, “paediatric”, “NTM”, “cystic fibrosis”, and “children”. Recent literature points out that NTMs are ubiquitous, with several species including both those that are pathogens for humans and those that are not. This means that, if a mycobacterium is isolated from a patient’s specimen, we have to distinguish between a simple colonization and an NTM-related disease. The start of treatment depends on many factors that are necessary to consider, such as clinical and imaging features, patient comorbidity and immunocompetence, drug adverse effects, and compliance with a very long therapy that can last many months. Due to the increasing prevalence and clinical relevance of NTMs, guidelines for their optimal management, especially in the presence of chronic underlying disease, are urgently needed.
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14
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De P, Amin AG, Graham B, Martiniano SL, Caceres SM, Poch KR, Jones MC, Saavedra MT, Malcolm KC, Nick JA, Chatterjee D. Urine lipoarabinomannan as a marker for low-risk of NTM infection in the CF airway. J Cyst Fibros 2020; 19:801-807. [PMID: 32624408 DOI: 10.1016/j.jcf.2020.06.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 01/21/2023]
Abstract
BACKGROUND Individuals with Cystic fibrosis (CF) are the most vulnerable population for pulmonary infection with nontuberculous mycobacteria (NTM). Screening, diagnosis, and assessment of treatment response currently depend on traditional culture techniques, but sputum analysis for NTM in CF is challenging, and associated with a low sensitivity. The cell wall lipoarabinomannan (LAM), a lipoglycan found in all mycobacterial species, and has been validated as a biomarker in urine for active Mycobacterium tuberculosis infection. METHODS Urine from a CF cohort (n = 44) well-characterized for NTM infection status by airway cultures was analyzed for LAM by gas chromatography/mass spectrometry. All subjects with positive sputum cultures for NTM had varying amounts of LAM in their urine. No LAM was detected in subjects who never had a positive culture (14/45). One individual initially classified as NTM sputum negative subsequently developed NTM disease 657 days after the initial urine LAM testing. Repeat urine LAM testing turned positive, correlating to her positive NTM status. Subjects infected with subspecies of M. abscessus had greater LAM quantities than those infected with M. avium complex (MAC). There was no correlation with disease activity or treatment status and LAM quantity. A TB Capture ELISA using anti-LAM antibodies demonstrated very poor sensitivity in identifying individuals with positive NTM sputum cultures. CONCLUSION These findings support the conclusion that urine LAM related to NTM infection may be a useful screening test to determine patients at low risk for having a positive NTM sputum culture, as part of a lifetime screening strategy in the CF population.
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Affiliation(s)
- Prithwiraj De
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, United States
| | - Anita G Amin
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, United States
| | - Barbara Graham
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, United States
| | - Stacey L Martiniano
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Silvia M Caceres
- Department of Medicine, National Jewish Health, Denver, Colorado, United States
| | - Katie R Poch
- Department of Medicine, National Jewish Health, Denver, Colorado, United States
| | - Marion C Jones
- Department of Medicine, National Jewish Health, Denver, Colorado, United States
| | - Milene T Saavedra
- Department of Medicine, National Jewish Health, Denver, Colorado, United States
| | - Kenneth C Malcolm
- Department of Medicine, National Jewish Health, Denver, Colorado, United States
| | - Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, Colorado, United States.
| | - Delphi Chatterjee
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, United States.
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15
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Non-tuberculous mycobacterial infections-A neglected and emerging problem. Int J Infect Dis 2020; 92S:S46-S50. [PMID: 32114200 DOI: 10.1016/j.ijid.2020.02.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/12/2020] [Accepted: 02/12/2020] [Indexed: 11/22/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are ubiquitous dwellers of environmental niches and are an established cause of natural and nosocomial infections. The incidence of NTM infections is rising owing to a growing population of immunocompromised and vulnerable individuals, complex medical and surgical procedures, as well as increased awareness and diagnostic capabilities. The prevalence of different NTM varies between continents, regions, and countries. The true global burden of pulmonary and extrapulmonary disease is unknown and estimates are subject to under and/or over-estimation. Diagnosis requires confirmation by isolation of NTM along with clinical and radiological criteria, which may be suboptimal at all levels. Susceptibility testing is complex and clinical breakpoints are not available for many of the drugs. Frequently, NTM infections are not considered until late in the course of disease. Improved and rapid detection of tuberculosis cases in high-burden countries has, however, also brought NTM infections into the limelight, and has identified a need for research efforts towards rapid diagnostic tests and the identification of biomarkers to monitor the treatment response in patients with NTM infections.
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16
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Nontuberculous Mycobacterium. Respir Med 2020. [DOI: 10.1007/978-3-030-42382-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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17
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Prevention of transmission of Mycobacterium abscessus among patients with cystic fibrosis. Curr Opin Pulm Med 2019; 25:646-653. [DOI: 10.1097/mcp.0000000000000621] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Revisiting John Snow to Meet the Challenge of Nontuberculous Mycobacterial Lung Disease. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16214250. [PMID: 31683836 PMCID: PMC6862550 DOI: 10.3390/ijerph16214250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 01/09/2023]
Abstract
Nontuberculous mycobacteria (NTM) are ubiquitous components of the soil and surface water microbiome. Disparities by sex, age, and geography demonstrate that both host and environmental factors are key determinants of NTM disease in populations, which predominates in the form of chronic pulmonary disease. As the incidence of NTM pulmonary disease rises across the United States, it becomes increasingly evident that addressing this emerging human health issue requires a bold, multi-disciplinary research framework that incorporates host risk factors for NTM pulmonary disease alongside the determinants of NTM residence in the environment. Such a framework should include the assessment of environmental characteristics promoting NTM growth in soil and surface water, detailed evaluations of water distribution systems, direct sampling of water sources for NTM contamination and species diversity, and studies of host and bacterial factors involved in NTM pathogenesis. This comprehensive approach can identify intervention points to interrupt the transmission of pathogenic NTM species from the environment to the susceptible host and to reduce NTM pulmonary disease incidence.
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19
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Bouso JM, Planet PJ. Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing. BMC Genomics 2019; 20:793. [PMID: 31666009 PMCID: PMC6822416 DOI: 10.1186/s12864-019-6134-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/23/2019] [Indexed: 12/15/2022] Open
Abstract
Background Nontuberculous mycobacteria (NTM) are a major cause of pulmonary and systemic disease in at-risk populations. Gaps in knowledge about transmission patterns, evolution, and pathogenicity during infection have prompted a recent surge in genomic NTM research. Increased availability and affordability of whole genome sequencing (WGS) techniques provide new opportunities to sequence and construct complete bacterial genomes faster and at a lower cost. However, extracting large quantities of pure genomic DNA is particularly challenging with NTM due to its slow growth and recalcitrant cell wall. Here we report a DNA extraction protocol that is optimized for long-read WGS of NTM, yielding large quantities of highly pure DNA with no additional clean-up steps. Results Our DNA extraction method was compared to 6 other methods with variations in timing of mechanical disruption and enzymatic digestion of the cell wall, quantity of matrix material, and reagents used in extraction and precipitation. We tested our optimized method on 38 clinical isolates from the M. avium and M. abscessus complexes, which yielded optimal quality and quantity measurements for Oxford Nanopore Technologies sequencing. We also present the efficient completion of circularized M. avium subspecies hominissuis genomes using our extraction technique and the long-read sequencing MinION platform, including the identification of a novel plasmid. Conclusions Our optimized extraction protocol and assembly pipeline was both sufficient and efficient for genome closure. We expect that our finely-tuned extraction method will prove to be a valuable tool in long-read sequencing and completion of mycobacterial genomes going forward. Utilization of comprehensive, long-read based approaches will advance the understanding evolution and pathogenicity of NTM infections.
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Affiliation(s)
- Jennifer M Bouso
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul J Planet
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
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20
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Dedrick RM, Guerrero-Bustamante CA, Garlena RA, Russell DA, Ford K, Harris K, Gilmour KC, Soothill J, Jacobs-Sera D, Schooley RT, Hatfull GF, Spencer H. Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus. Nat Med 2019; 25:730-733. [PMID: 31068712 PMCID: PMC6557439 DOI: 10.1038/s41591-019-0437-z] [Citation(s) in RCA: 775] [Impact Index Per Article: 155.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/27/2019] [Indexed: 12/17/2022]
Abstract
A 15-year-old patient with cystic fibrosis with a disseminated Mycobacterium abscessus infection was treated with a three-phage cocktail following bilateral lung transplantation. Effective lytic phage derivatives that efficiently kill the infectious M. abscessus strain were developed by genome engineering and forward genetics. Intravenous phage treatment was well tolerated and associated with objective clinical improvement, including sternal wound closure, improved liver function, and substantial resolution of infected skin nodules.
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Affiliation(s)
- Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | | | | | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert T Schooley
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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21
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Danelishvili L, Rojony R, Carson KL, Palmer AL, Rose SJ, Bermudez LE. Mycobacterium avium subsp. hominissuis effector MAVA5_06970 promotes rapid apoptosis in secondary-infected macrophages during cell-to-cell spread. Virulence 2019; 9:1287-1300. [PMID: 30134761 PMCID: PMC6177253 DOI: 10.1080/21505594.2018.1504559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Mycobacterium avium subsp. hominissuis is an opportunistic intracellular pathogen associated with disease in patients either immunosuppression or chronic lung pathology. Once in the host, M. avium preferentially infects and replicates within the phagocytic cells. The host driven macrophage apoptosis appears to be an essential aspect of innate immunity during bacterial infection; however, the existing evidence suggests that M. avium has evolved adaptive approaches to trigger the phagocyte apoptosis, exit apoptotic cells or via ingestion of infected apoptotic bodies subsequently infect neighboring macrophages. By evaluating 4,000 transposon mutants of M. avium in THP-1 cells, we identified clones that can trigger a new form of early host cell apoptosis, which is only observed upon entry into the “secondary-infected” macrophages. Inactivation of MAVA5_06970 gene lead to significant attenuation in intracellular growth within macrophages and mice, and impaired M. avium to induce rapid apoptosis in the “secondary-infected” cells as measured by Annexin V-FITC detection assay. Complementation of MAVA5_06970 gene corrected the attenuation as well as apoptotic phenotypes. The MAVA5_06970 gene encodes for a secreted protein. Using the pull-down assay and then confirmed with the yeast two-hybrid screen, we found that MAVA5_06970 effector interacts with the Secreted Phosphoprotein 1, the cytokine also known as Osteopontin. This interaction enhances the THP-1 cell apoptosis and, consequently, restricts the production of interleukin-12 that likely may limit the activation of the type I immunity pathway in vivo. This work identified a key virulence effector of M. avium that contributes to the cell-to-cell spread of the pathogen.
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Affiliation(s)
- Lia Danelishvili
- a Department of Biomedical Sciences, College of Veterinary Medicine , Oregon State University , Corvallis , OR , USA
| | - Rajoana Rojony
- a Department of Biomedical Sciences, College of Veterinary Medicine , Oregon State University , Corvallis , OR , USA
| | - Kylee L Carson
- a Department of Biomedical Sciences, College of Veterinary Medicine , Oregon State University , Corvallis , OR , USA
| | - Amy L Palmer
- a Department of Biomedical Sciences, College of Veterinary Medicine , Oregon State University , Corvallis , OR , USA
| | - Sasha J Rose
- a Department of Biomedical Sciences, College of Veterinary Medicine , Oregon State University , Corvallis , OR , USA
| | - Luiz E Bermudez
- a Department of Biomedical Sciences, College of Veterinary Medicine , Oregon State University , Corvallis , OR , USA.,b Department of Microbiology, College of Science , Oregon State University , Corvallis , OR , USA
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Pandey R, Chen L, Manca C, Jenkins S, Glaser L, Vinnard C, Stone G, Lee J, Mathema B, Nuermberger EL, Bonomo RA, Kreiswirth BN. Dual β-Lactam Combinations Highly Active against Mycobacterium abscessus Complex In Vitro. mBio 2019; 10:e02895-18. [PMID: 30755518 PMCID: PMC6372805 DOI: 10.1128/mbio.02895-18] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 01/07/2019] [Indexed: 01/25/2023] Open
Abstract
As a consequence of a growing population of immunocompromised individuals, including transplant recipients and cystic fibrosis patients, there has been a dramatic increase in chronic infections caused by Mycobacterium abscessus complex (MABC) strains that are usually recalcitrant to effective antibiotic therapy. The recent rise of macrolide resistance in MABC has further complicated this clinical dilemma, dramatizing the need for novel agents. The repurposing of current antibiotics is one rapid path from discovery to patient care. In this study, we have discovered that dual β-lactams, and specifically the combination of ceftazidime with either ceftaroline or imipenem, are synergistic and have clinically relevant activities, with MIC50s of 0.25 (ceftaroline with 100 µg/ml ceftazidime) and 0.5 µg/ml (imipenem with 100 µg/ml ceftazidime) against clinical MABC isolates. Similar synergy was observed in time-kill studies against the M. abscessus ATCC 19977 strain using clinically achievable concentrations of either imipenem (4 µg/ml) or ceftaroline (2 µg/ml), as the addition of ceftazidime at concentrations of ≥50 µg/ml showed a persistent bactericidal effect over 5 days. Treatment of THP-1 human macrophages infected with three different M. abscessus clinical isolates supported the in vitro findings, as the combination of 100 µg/ml ceftazidime and 0.125 µg/ml ceftaroline or 100 µg/ml ceftazidime and 0.25 µg/ml imipenem dramatically reduced the CFU counts to near baseline levels of infection. This study's finding that there is synergy between certain β-lactam combinations against M. abscessus infection provides optimism toward identifying an optimum dual β-lactam treatment regimen.IMPORTANCE The emergence of chronic MABC infections among immunocompromised populations and their inherent and acquired resistance to effective antibiotic therapy have created clinical challenges in advancing patients for transplant surgery and treating those with disease. There is an urgent need for new treatment regimens, and the repurposing of existing antibiotics provides a rapid strategy to advance a laboratory finding to patient care. Our recent discoveries that dual β-lactams, specifically the combination of ceftazidime with ceftaroline or ceftazidime with imipenem, have significant in vitro MIC values and kill curve activities and are effective against infected THP-1 human macrophages provide optimism for a dual β-lactam treatment strategy against MABC infections. The unexpected synergistic activities reported in this study create a new path of discovery to repurpose the large family of β-lactam drugs.
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Affiliation(s)
- R Pandey
- Public Health Research Institute Tuberculosis Center, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - L Chen
- Public Health Research Institute Tuberculosis Center, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - C Manca
- Public Health Research Institute Tuberculosis Center, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - S Jenkins
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical Center, New York, New York, USA
| | - L Glaser
- Department of Clinical Microbiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - C Vinnard
- Public Health Research Institute Tuberculosis Center, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - G Stone
- Pfizer, Groton, Connecticut, USA
| | - J Lee
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - B Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - E L Nuermberger
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - R A Bonomo
- Medical Service and GRECC, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - B N Kreiswirth
- Public Health Research Institute Tuberculosis Center, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
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Abstract
PURPOSE OF REVIEW To compile data from the past 10 years regarding the role of modifying genes in cystic fibrosis (CF). RECENT FINDINGS CF is a model disease for understanding of the action of modifying genes. Although it is a monogenic (CFTR) autosomal recessive disease, CF presents with wide phenotypic variability. In CF, variability occurs with different intensity among patients by each organ, being organ-specific, resulting from the mutual interaction of environmental and genetic factors, including CFTR mutations and various other genes, most of which are associated with inflammatory processes. In individuals, using precision medicine, gene modification studies have revealed individualized responses to drugs depending on particular CFTR mutations and modifying genes, most of which are alternative ion channels. SUMMARY Studies of modifying genes in CF allow: understanding of clinical variability among patients with the same CFTR genotype; evaluation of precision medicine; understanding of environmental and genetic effects at the organ level; understanding the involvement of genetic variants in inflammatory responses; improvements in genetic counseling; understanding the involvement of genetic variants in inflammatory responses in lung diseases, such as asthma; and understanding the individuality of the person with the disease.
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24
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Hazbón MH, Rigouts L, Schito M, Ezewudo M, Kudo T, Itoh T, Ohkuma M, Kiss K, Wu L, Ma J, Hamada M, Strong M, Salfinger M, Daley CL, Nick JA, Lee JS, Rastogi N, Couvin D, Hurtado-Ortiz R, Bizet C, Suresh A, Rodwell T, Albertini A, Lacourciere KA, Deheer-Graham A, Alexander S, Russell JE, Bradford R, Riojas MA. Mycobacterial biomaterials and resources for researchers. Pathog Dis 2018; 76:4978419. [PMID: 29846561 DOI: 10.1093/femspd/fty042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/18/2018] [Indexed: 11/12/2022] Open
Abstract
There are many resources available to mycobacterial researchers, including culture collections around the world that distribute biomaterials to the general scientific community, genomic and clinical databases, and powerful bioinformatics tools. However, many of these resources may be unknown to the research community. This review article aims to summarize and publicize many of these resources, thus strengthening the quality and reproducibility of mycobacterial research by providing the scientific community access to authenticated and quality-controlled biomaterials and a wealth of information, analytical tools and research opportunities.
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Affiliation(s)
- Manzour Hernando Hazbón
- ATCC ®, 10801 University Boulevard, Manassas, VA 20110, USA.,BEI Resources, 10801 University Boulevard, Manassas, VA 20110, USA
| | - Leen Rigouts
- BCCM/ITM Mycobacteria Collection, Institute of Tropical Medicine, Nationalestraat 155, B-2000 Antwerpen, Belgium
| | - Marco Schito
- Critical Path Institute, 1730 E River Rd, suite 200, Tucson, AZ 85718, USA
| | - Matthew Ezewudo
- Critical Path Institute, 1730 E River Rd, suite 200, Tucson, AZ 85718, USA
| | - Takuji Kudo
- RIKEN BioResource Center (RIKEN BRC) - Japan Collection of Microorganisms (JCM), 3-1-1 Koyadai, Tsukuba-shi, Ibaraki 305-0074, JAPAN
| | - Takashi Itoh
- RIKEN BioResource Center (RIKEN BRC) - Japan Collection of Microorganisms (JCM), 3-1-1 Koyadai, Tsukuba-shi, Ibaraki 305-0074, JAPAN
| | - Moriya Ohkuma
- RIKEN BioResource Center (RIKEN BRC) - Japan Collection of Microorganisms (JCM), 3-1-1 Koyadai, Tsukuba-shi, Ibaraki 305-0074, JAPAN
| | - Katalin Kiss
- ATCC®, 10801 University Boulevard, Manassas, VA 20110, USA
| | - Linhuan Wu
- WFCC-MIRCEN World Data Center for Microorganisms (WDCM), Institute of Microbiology, Chinese Academy of Sciences, NO.1-3 West Beichen Road, Chaoyang District, Beijing 100101, P. R. China
| | - Juncai Ma
- WFCC-MIRCEN World Data Center for Microorganisms (WDCM), Institute of Microbiology, Chinese Academy of Sciences, NO.1-3 West Beichen Road, Chaoyang District, Beijing 100101, P. R. China
| | - Moriyuki Hamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Michael Strong
- National Jewish Health, Center for Genes, Environment, and Health, 1400 Jackson St., Denver, CO 80206, USA
| | - Max Salfinger
- National Jewish Health, Department of Medicine, 1400 Jackson St., Denver, CO 80206, USA
| | - Charles L Daley
- National Jewish Health, Department of Medicine, 1400 Jackson St., Denver, CO 80206, USA
| | - Jerry A Nick
- National Jewish Health, Department of Medicine, 1400 Jackson St., Denver, CO 80206, USA
| | - Jung-Sook Lee
- Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil. Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Nalin Rastogi
- Institut Pasteur de la Guadeloupe, BP 484, Morne Jolivière, 97183 ABYMES Cedex, Guadeloupe, France
| | - David Couvin
- Institut Pasteur de la Guadeloupe, BP 484, Morne Jolivière, 97183 ABYMES Cedex, Guadeloupe, France
| | - Raquel Hurtado-Ortiz
- CRBIP-Biological Resource Centre, Institut Pasteur, 25 rue du Dr Roux 75015, Paris, France
| | - Chantal Bizet
- CIP-Collection of Institut Pasteur, Institut Pasteur, 25 rue du Dr Roux 75015, Paris, France
| | - Anita Suresh
- Foundation for Innovative New Diagnostics, Campus Biotech, 9 Chemin des Mines, 1202 Geneva, Switzerland
| | - Timothy Rodwell
- Foundation for Innovative New Diagnostics, Campus Biotech, 9 Chemin des Mines, 1202 Geneva, Switzerland
| | - Audrey Albertini
- Foundation for Innovative New Diagnostics, Campus Biotech, 9 Chemin des Mines, 1202 Geneva, Switzerland
| | - Karen A Lacourciere
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892, USA
| | - Ana Deheer-Graham
- Culture Collections, Public Health England, Porton Down, Salisbury SP4 0JG, UK
| | - Sarah Alexander
- Culture Collections, Public Health England, Porton Down, Salisbury SP4 0JG, UK
| | - Julie E Russell
- Culture Collections, Public Health England, Porton Down, Salisbury SP4 0JG, UK
| | - Rebecca Bradford
- ATCC ®, 10801 University Boulevard, Manassas, VA 20110, USA.,BEI Resources, 10801 University Boulevard, Manassas, VA 20110, USA
| | - Marco A Riojas
- ATCC ®, 10801 University Boulevard, Manassas, VA 20110, USA.,BEI Resources, 10801 University Boulevard, Manassas, VA 20110, USA
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25
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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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26
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Matern WM, Bader JS, Karakousis PC. Genome analysis of Mycobacterium avium subspecies hominissuis strain 109. Sci Data 2018; 5:180277. [PMID: 30512015 PMCID: PMC6278689 DOI: 10.1038/sdata.2018.277] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/10/2018] [Indexed: 01/01/2023] Open
Abstract
Infection with Mycobacterium avium is a significant cause of morbidity and its treatment requires the use of multiple antibiotics for more than 12 months. In the current work, we provide the genome sequence, gene annotations, gene ontology annotations, and protein homology data for M. avium strain 109 (MAC109), which has been used extensively in preclinical studies. The de novo assembled genome consists of a circular chromosome of length 5,188,883 bp and two circular plasmids of sizes 147,100 bp and 16,516 bp. We have named the plasmids pMAC109a and pMAC109b, respectively. Based on its genome, we confirm that MAC109 should be classified as Mycobacterium avium subsp. hominissuis. Using genome annotation software, we identified 4,841 coding sequences and annotated these with Gene Ontology (GO) terms. Additionally, we wrote software to generate a database of homologous proteins among MAC109 and eight other commonly used mycobacterial laboratory strains. The resulting database may be useful for translating genetic data between various strains of mycobacteria, and the software may be applied readily to other organisms.
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Affiliation(s)
- William M. Matern
- Department of Biomedical Engineering and High-Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Systems Approaches to Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joel S. Bader
- Department of Biomedical Engineering and High-Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Systems Approaches to Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Petros C. Karakousis
- Center for Systems Approaches to Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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27
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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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28
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Ravnholt C, Kolpen M, Skov M, Moser C, Katzenstein TL, Pressler T, Høiby N, Qvist T. The importance of early diagnosis of Mycobacterium abscessus complex in patients with cystic fibrosis. APMIS 2018; 126:885-891. [PMID: 30456869 DOI: 10.1111/apm.12903] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/09/2018] [Indexed: 12/18/2022]
Abstract
Mycobacterium abscessus complex can cause severe lung infections and has proven to be a serious threat to patients with cystic fibrosis and a challenge for clinicians due to difficulties in timely diagnosis and complex multidrug treatment regimes. Mycobacterial culture is the gold standard for diagnosis, but in most cystic fibrosis centers it is performed less frequently than culture for other pathogens. Consensus today recommends just one annual mycobacterial culture for asymptomatic patients with cystic fibrosis, a strategy likely to lead to diagnostic delays. Postponement of diagnosis might be the deciding factor in whether an early colonization turns into chronic infection. This review highlights the latest developments in knowledge about the pathogenicity and clinical consequences of M. abscessus complex pulmonary disease, addressing the central theme of why pulmonary infection requires early identification and aggressive antibiotic treatment. The window of opportunity, before M. abscessus complex transforms from a mucosal colonizer to a chronic biofilm infection, is where microbial eradication is most likely to be successful, making early diagnosis essential for improved outcomes.
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Affiliation(s)
- Cecilie Ravnholt
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Mette Kolpen
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Marianne Skov
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Pediatrics, Rigshospitalet, Copenhagen, Denmark
| | - Claus Moser
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Terese L Katzenstein
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
| | - Tania Pressler
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
| | - Niels Høiby
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Institute of Immunology and Medical Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Tavs Qvist
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
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29
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Protective effects of a traditional herbal extract from Stellaria dichotoma var. lanceolata against Mycobacterium abscessus infections. PLoS One 2018; 13:e0207696. [PMID: 30452471 PMCID: PMC6242687 DOI: 10.1371/journal.pone.0207696] [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: 04/19/2018] [Accepted: 11/05/2018] [Indexed: 11/24/2022] Open
Abstract
Stellaria dichotoma var. lanceolata (SdLv), a member of the Caryophyllaceae, is a traditional herbal medicine that has been used to treat fever, night sweats, and malaria in East Asia. Inflammation plays an essential role in both host defense and pathogenesis during infection by diverse intracellular pathogens. Herein, we showed that an herbal extract from SdLv effectively attenuated inflammatory responses from infection of Mycobacterium abscessus (Mab), but not Toxoplasma gondii (T. gondii). In primary murine macrophages, Mab infection resulted in the rapid activation of nuclear factor (NF)-κB and mitogen-activated protein kinase (MAPK), as well as in the generation of proinflammatory cytokines, such as tumor necrosis factor α and interleukin-6, which were all significantly inhibited by pretreatment with SdLv. However, herbal extracts from Bupleurum chinense DC. (Buch) or Bupleurum falcatum L. (Bufa) did not affect M. abs-induced activation of proinflammatory responses. Importantly, we demonstrated that generation of intracellular reactive oxygen species, which are important signaling intermediaries in the activation of NF-κB and the MAPK signaling pathway, was rapidly increased in Mab-infected macrophages, and this was effectively suppressed by pretreatment with SdLv, but not Buch and Bufa. We further found that the treatment of Buch and Bufa, but not SdLv, led to the activation of NF-κB and the MAPK signaling pathway and the generation of intracellular reactive oxygen species. Moreover, oral administration of SdLv significantly reduced lethality in Mab-infected mice. Collectively, these results suggest the possible use of SdLv as an effective treatment for Mab infection.
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30
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De Groote MA, Jarvis TC, Wong C, Graham J, Hoang T, Young CL, Ribble W, Day J, Li W, Jackson M, Gonzalez-Juarrero M, Sun X, Ochsner UA. Optimization and Lead Selection of Benzothiazole Amide Analogs Toward a Novel Antimycobacterial Agent. Front Microbiol 2018; 9:2231. [PMID: 30294313 PMCID: PMC6158578 DOI: 10.3389/fmicb.2018.02231] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/31/2018] [Indexed: 12/14/2022] Open
Abstract
Mycobacteria remain an important problem worldwide, especially drug resistant human pathogens. Novel therapeutics are urgently needed to tackle both drug-resistant tuberculosis (TB) and difficult-to-treat infections with nontuberculous mycobacteria (NTM). Benzothiazole adamantyl amide had previously emerged as a high throughput screening hit against M. tuberculosis (Mtb) and was subsequently found to be active against NTM as well. For lead optimization, we applied an iterative process of design, synthesis and screening of several 100 analogs to improve antibacterial potency as well as physicochemical and pharmacological properties to ultimately achieve efficacy. Replacement of the adamantyl group with cyclohexyl derivatives, including bicyclic moieties, resulted in advanced lead compounds that showed excellent potency and a mycobacteria-specific spectrum of activity. MIC values ranged from 0.03 to 0.12 μg/mL against M. abscessus (Mabs) and other rapid- growing NTM, 1–2 μg/mL against M. avium complex (MAC), and 0.12–0.5 μg/mL against Mtb. No pre-existing resistance was found in a collection of n = 54 clinical isolates of rapid-growing NTM. Unlike many antibacterial agents commonly used to treat mycobacterial infections, benzothiazole amides demonstrated bactericidal effects against both Mtb and Mabs. Metabolic labeling provided evidence that the compounds affect the transfer of mycolic acids to their cell envelope acceptors in mycobacteria. Mapping of resistance mutations pointed to the trehalose monomycolate transporter (MmpL3) as the most likely target. In vivo efficacy and tolerability of a benzothiazole amide was demonstrated in a mouse model of chronic NTM lung infection with Mabs. Once daily dosing over 4 weeks by intrapulmonary microspray administration as 5% corn oil/saline emulsion achieved statistically significant CFU reductions compared to vehicle control and non-inferiority compared to azithromycin. The benzothiazole amides hold promise for development of a novel therapeutic agent with broad antimycobacterial activity, though further work is needed to develop drug formulations for direct intrapulmonary delivery via aerosol.
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Affiliation(s)
- Mary A De Groote
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | | | | | | | | | | | | | - Joshua Day
- Crestone, Inc., Boulder, CO, United States
| | - Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Mercedes Gonzalez-Juarrero
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
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31
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Anjan S, Morris MI. How can we improve the outcome for transplant patients with nontuberculous mycobacterial infections? Future Microbiol 2018; 13:903-914. [PMID: 29888973 DOI: 10.2217/fmb-2018-0006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) are environmental organisms that are rapidly emerging as pathogens in the transplant population. The prevalence of infection in transplant recipients remains unknown. While guidelines exist for treatment of NTM, neither the American Thoracic Society, the Infectious Diseases Society of America, nor the British Thoracic Society guidelines dictate the approach needed for transplant recipients. Here, we summarize risk factors, important diagnostic and treatment facts, and preventive measures to be taken to help improve outcomes of those infected with NTM infections.
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Affiliation(s)
- Shweta Anjan
- Department of Medicine, Jackson Memorial Hospital, Miami, FL, 33136, USA.,Department of Medicine, Division of Infectious Disease, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Michele I Morris
- Department of Medicine, Jackson Memorial Hospital, Miami, FL, 33136, USA.,Department of Medicine, Division of Infectious Disease, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
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32
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Moreno Ortega M, Quintana Gallego ME, Carrasco Hernández L, Pérez Borrego E, Delgado Pecellín I. Mycobacterium Lentiflavum in Cystic Fibrosis Subjects. A Colonizer or a True Pathogen? Arch Bronconeumol 2018; 54:639-640. [PMID: 29861072 DOI: 10.1016/j.arbres.2018.02.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 02/27/2018] [Indexed: 01/07/2023]
Affiliation(s)
- María Moreno Ortega
- Unidad de Pediatría y áreas específicas, Hospital Universitario Virgen del Rocío, Sevilla, España; Unidad de Fibrosis Quística, Hospital Universitario Virgen del Rocío, Sevilla, España.
| | - María Esther Quintana Gallego
- Unidad de Fibrosis Quística, Hospital Universitario Virgen del Rocío, Sevilla, España; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), España
| | - Laura Carrasco Hernández
- Unidad de Fibrosis Quística, Hospital Universitario Virgen del Rocío, Sevilla, España; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), España
| | - Esther Pérez Borrego
- Unidad de Pediatría y áreas específicas, Hospital Universitario Virgen del Rocío, Sevilla, España
| | - Isabel Delgado Pecellín
- Unidad de Fibrosis Quística, Hospital Universitario Virgen del Rocío, Sevilla, España; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), España
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33
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Ditchfield N, Gilchrist FJ, Davies SJ, Carroll W. Strategies to prevent kidney injury from antibiotics in people with cystic fibrosis. Hippokratia 2018. [DOI: 10.1002/14651858.cd013032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Naomi Ditchfield
- University Hospitals of the North Midlands; Department of Respiratory Paediatrics; Newcastle Road Stoke-on-Trent UK ST4 6QG
| | - Francis J Gilchrist
- Royal Stoke University Hospital; Academic Department of Child Health; Newcastle Road Stoke-on-Trent UK ST4 6QG
| | - Simon J Davies
- University Hospital of North Staffordshire; Department of Nephrology; Princes Rd Hartshill Stoke-on-Trent UK ST4 7LN
| | - Will Carroll
- University Hospitals of the North Midlands; Department of Paediatric Respiratory Medicine; Newcastle Road Stoke-on-Trent UK ST4 6QG
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34
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Desai AN, Hurtado RM. Infections and outbreaks of nontuberculous mycobacteria in hospital settings. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2018; 10:169-181. [PMID: 30662371 DOI: 10.1007/s40506-018-0165-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Purpose of review Non-tuberculous mycobacterial [NTM] infections in the hospital setting are a complex and often challenging entity. The goal of this review is to discuss diagnostic and treatment strategies for established as well as emerging nosocomial NTM infections. Recent findings NTM outbreaks have been documented in a variety of hospital settings. Contamination of medical devices or aqueous solutions is often implicated in the spread of infection. More recently, the slow grower M. chimaera has been reported in the setting of contaminated heater-cooler devices used for cardiopulmonary bypass and extracorporeal membrane oxygenation. In addition, increases in medical tourism for cosmetic surgery have led to outbreaks of rapidly growing mycobacteria. Summary Diagnosis and treatment of nosocomial NTM pose many challenges for the clinician. Surgical resection or debridement as well as combination antimycobacterial therapy are a mainstay in therapeutic management. Strict infection control and prevention practices are critical to the identification and cessation of outbreaks.
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Affiliation(s)
- Angel N Desai
- Massachusetts General Hospital, Division of Infectious Diseases, 55 Fruit Street, Boston, MA 02114 USA
| | - Rocío M Hurtado
- Massachusetts General Hospital, Division of Infectious Diseases, 55 Fruit Street, Boston, MA 02114 USA.,Harvard Medical School, 25 Shattuck St, Boston MA 02115 USA
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Pienkowska K, Wiehlmann L, Tümmler B. Airway microbial metagenomics. Microbes Infect 2017; 20:536-542. [PMID: 29287982 DOI: 10.1016/j.micinf.2017.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/08/2017] [Accepted: 12/15/2017] [Indexed: 11/17/2022]
Abstract
High-throughput untargeted metagenome sequencing provides information about the composition of the microbial communities of viruses, bacteria, archaea and unicellular eukaryotes in the habitat of interest. This review outlines the sampling, processing, sequencing and bioinformatic analysis of secretions of the respiratory tract and summarizes our current knowledge of the upper and lower human airways metagenome in health and disease.
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Affiliation(s)
- Katarzyna Pienkowska
- Clinical Research Group, Clinic for Pediatric Pneumology, Allergology, and Neonatology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Lutz Wiehlmann
- Clinical Research Group, Clinic for Pediatric Pneumology, Allergology, and Neonatology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany; Core Unit 'Genomics', Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Burkhard Tümmler
- Clinical Research Group, Clinic for Pediatric Pneumology, Allergology, and Neonatology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.
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