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Ugedo J, Tabernero E, Altube L, Leal MV, García JA. Nontuberculous Mycobacteria Isolates in Respiratory Samples and Mycobacterial Pulmonary Disease in an Area of Northern Spain. OPEN RESPIRATORY ARCHIVES 2024; 6:100353. [PMID: 39318829 PMCID: PMC11421231 DOI: 10.1016/j.opresp.2024.100353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/16/2024] [Indexed: 09/26/2024] Open
Abstract
Introduction The epidemiology of nontuberculous mycobacteria (NTM) is not well known. In this study, we aimed to determine the incidence of NTM isolates and nontuberculous mycobacterial pulmonary disease (NTM-PD) in five closely located hospitals in an area of northern Spain and analyse differences between them. Material and methods Demographic, microbiological, clinical and radiological data were collected retrospectively from all patients with a NTM isolated from respiratory specimens at five hospitals between 2012 and 2019. Mycobacterium gordonae isolates were excluded. Once the data was collected, it was determined which patients met the NMT-PD criteria. Results 594 patients were included in the study. The mean incidence rate of NTM isolates across all five hospitals in the period studied was 4.15 per 100,000 person-year, while the rate of NTM-PD was 1.2. The annual number of isolates showed an upward trend over this period, but the same did not occur in the number of cases of NTM-PD. The species most frequently isolated were Mycobacterium avium complex (MAC) and Mycobacterium xenopi and those most frequently causing disease were MAC and Mycobacterium kansassi. There were significant differences between the five centres. Conclusions Our results are in line with similar studies in Europe in terms of NTM isolation and NTM-PD incidence and species isolated; however, we do not see the upward trend in NTM-PD rates described elsewhere. The great variability in isolation and disease rates, as well as in species isolated in geographically close areas, underlines, in our opinion, the importance of local environmental factors.
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Affiliation(s)
- Javier Ugedo
- Department of Respiratory Medicine, San Pedro University Hospital, Logroño, La Rioja, Spain
| | - Eva Tabernero
- Department of Respiratory Medicine, Cruces University Hospital, BioBizkaia Health Research Institute, Barakaldo, Bizkaia, Spain
| | - Lander Altube
- Department of Respiratory Medicine, Galdakao University Hospital, Bizkaia, Spain
| | - María Victoria Leal
- Department of Respiratory Medicine, Basurto University Hospital, Bizkaia, Spain
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Prevots DR, Marshall JE, Wagner D, Morimoto K. Global Epidemiology of Nontuberculous Mycobacterial Pulmonary Disease: A Review. Clin Chest Med 2023; 44:675-721. [PMID: 37890910 PMCID: PMC10625169 DOI: 10.1016/j.ccm.2023.08.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
Nontuberculous mycobacterial (NTM) isolation and pulmonary disease (NTM-PD) have continued to increase in most regions of the world, driven mainly by Mycobacterium avium. Single-center studies also support increasing trends as well as a persistent burden of undiagnosed NTM among persons suspected of having tuberculosis (TB), in countries with moderate-to-high TB prevalence. Cumulative exposure to water and soil presents an increased risk to susceptible hosts, and trace metals in water supply are recently recognized risk factors. Establishing standard case definitions for subnational and national surveillance systems with mandatory notification of NTM-PD are needed to allow comparisons within and across countries and regions.
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Affiliation(s)
- D Rebecca Prevots
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, Bethesda, MD 20852, USA.
| | - Julia E Marshall
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, Bethesda, MD 20852, USA
| | - Dirk Wagner
- Division of Infectious Diseases, Department of Internal Medicine II, Medical Center- University of Freiburg, Faculty of Medicine, Hugstetter Street. 55, Freiburg b106, Germany
| | - Kozo Morimoto
- Division of Clinical Research, Fukujuji Hospital, Japan Anti-Tuberculosis Association (JATA), 3-1-24, Matsuyama, Kiyose, Tokyo, Japan
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Ku JH, Henkle E, Carlson KF, Marino M, Brode SK, Marras TK, Winthrop KL. Evaluation of Mycobacterium Avium Complex Pulmonary Disease Treatment Completion and Adherence to ATS/IDSA Guidelines. Clin Infect Dis 2023; 76:e1408-e1415. [PMID: 35607719 DOI: 10.1093/cid/ciac394] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/06/2022] [Accepted: 05/17/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Nontuberculous mycobacteria are environmental organisms that cause infections leading to chronic, debilitating pulmonary disease, among which Mycobacterium avium complex (MAC) is the most common species. METHODS We described patterns of macrolide-based multidrug antibiotic therapies for MAC pulmonary disease (MAC-PD) in US Medicare beneficiaries with bronchiectasis between January 2006 and December 2014. MAC therapy was defined as a multidrug regimen containing a macrolide plus ≥1 other drug targeting MAC-PD (rifamycin, ethambutol, fluoroquinolone, or amikacin) prescribed concomitantly for >28 days. RESULTS We identified 9189 new MAC therapy users, with a mean age (standard deviation) of 74 (6 years) at the start of therapy; 75% female and 87% non-Hispanic white. A guideline-based regimen (a macrolide, ethambutol, and rifamycin, with or without amikacin) was prescribed for 51% of new MAC therapy users at treatment start, of whom 41% were continuing guideline-based therapy at 6 months, and only 18% at 12 months. Of all new MAC therapy users, by 18 months only 11% were still receiving MAC treatment, 55% had discontinued therapy, and 34% were censored owing to death or the end of the study period. CONCLUSIONS Overall, nearly half of new MAC therapy users were prescribed a non-guideline-recommended macrolide-based therapy, including regimens commonly associated with promoting macrolide resistance. Treatment discontinuation was common, and once discontinued, only a few beneficiaries resumed therapy at a later time. Our study adds important data to the current literature on treatment patterns for MAC-PD among older US populations. Future research should examine treatment patterns using more contemporary data sources.
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Affiliation(s)
- Jennifer H Ku
- Oregon Health & Science University - Portland State University School of Public Health, Portland, Oregon, USA.,Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
| | - Emily Henkle
- Oregon Health & Science University - Portland State University School of Public Health, Portland, Oregon, USA
| | - Kathleen F Carlson
- Oregon Health & Science University - Portland State University School of Public Health, Portland, Oregon, USA.,Center to Improve Veteran Involvement in Care, Veterans Affairs Portland Healthcare System, Portland, Oregon, USA
| | - Miguel Marino
- Oregon Health & Science University - Portland State University School of Public Health, Portland, Oregon, USA
| | - Sarah K Brode
- Department of Medicine, University Health Network and University of Toronto, Toronto, Ontario, Canada.,Department of Respiratory Medicine, West Park Healthcare Centre, Toronto, Ontario, Canada
| | - Theodore K Marras
- Department of Medicine, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Kevin L Winthrop
- Oregon Health & Science University - Portland State University School of Public Health, Portland, Oregon, USA
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Jarchow-MacDonald A, Smith M, Seagar AL, Russell CD, Claxton P, Laurenson IF, Moncayo-Nieto OL. Changing Incidence and Characteristics of Nontuberculous Mycobacterial Infections in Scotland and Comparison With Mycobacterium tuberculosis Complex Incidence (2011 to 2019). Open Forum Infect Dis 2022; 10:ofac665. [PMID: 36726549 PMCID: PMC9879710 DOI: 10.1093/ofid/ofac665] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Background An increase in infections with nontuberculous mycobacteria (NTM) has been noted globally, and their incidence has overtaken that of Mycobacterium tuberculosis complex (MTBc) in many countries. Using data from a national reference laboratory, we aimed to determine if this trend could be observed in Scotland. Methods We undertook a retrospective review of all NTM isolates received by the Scottish Mycobacteria Reference Laboratory (SMRL) over 9 years from 2011 to 2019 inclusive. Clinical episodes were defined as per 2017 British Thoracic Society and 2020 American Thoracic Society/European Respiratory Society/European Society of Clinical Microbiology and Infectious Diseases/Infectious Diseases Society of America NTM guidelines. These rates were compared with Scottish tuberculosis rates over the same period. Results Of 8552 NTM isolates from 4586 patients in 2011 to 2019, 7739 (90.5%) were considered clinically relevant. These represented 2409 episodes of NTM infection, with M. avium, M. intracellulare, and M. abscessus complex being most common. A total of 1953 (81.1%) were pulmonary NTM infection episodes from 1470 patients and 456 extrapulmonary episodes from 370 patients. We estimated a rise in incidence from 3.4 to 6.5 per 100 000 person-years (2011-2019 inclusive), with an increase in NTM incidence over MTBc incidence in Scotland by 2017. Conclusions The incidence of NTM infection in Scotland has overtaken MTBc incidence. NTM infection leads to a costly health care burden, possibly as much as UK£1.47 million (US$ and €1.73 million) annually. We recommend standardization of isolate referral with clinical surveillance and implementation of agreed standards of care delivered through multidisciplinary teams. This would improve diagnosis and patient management as well as assessment of diagnostics and novel treatments through clinical trials.
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Affiliation(s)
- Anna Jarchow-MacDonald
- Correspondence: Anna A. Jarchow-MacDonald, MD, MSc, DTMH, Scottish Mycobacteria Reference Laboratory, NHS Lothian Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK (). Dr. Olga-Lucia Moncayo-Nieto, MD, FRCPath, PhD, Scottish Mycobacteria Reference Laboratory, NHS Lothian Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK ()
| | - Michael Smith
- Scottish Mycobacteria Reference Laboratory, NHS Lothian Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Amie-Louise Seagar
- Scottish Mycobacteria Reference Laboratory, NHS Lothian Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Clark D Russell
- Queen's Medical Research Institute, University of Edinburgh Centre for Inflammation Research, Edinburgh, United Kingdom
| | - Pauline Claxton
- Scottish Mycobacteria Reference Laboratory, NHS Lothian Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Ian F Laurenson
- Scottish Mycobacteria Reference Laboratory, NHS Lothian Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
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Kilinç G, Walburg KV, Franken KLMC, Valkenburg ML, Aubry A, Haks MC, Saris A, Ottenhoff THM. Development of Human Cell-Based In Vitro Infection Models to Determine the Intracellular Survival of Mycobacterium avium. Front Cell Infect Microbiol 2022; 12:872361. [PMID: 35811670 PMCID: PMC9263196 DOI: 10.3389/fcimb.2022.872361] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/24/2022] [Indexed: 11/21/2022] Open
Abstract
The Mycobacterium avium (Mav) complex accounts for more than 80% of all pulmonary diseases caused by non-tuberculous mycobacteria (NTM) infections, which have an alarming increase in prevalence and vary in different regions, currently reaching 0.3–9.8 per 100,000 individuals. Poor clinical outcomes, as a result of increasing microbial drug resistance and low treatment adherence due to drug-toxicities, emphasize the need for more effective treatments. Identification of more effective treatments, however, appears to be difficult, which may be due to the intracellular life of NTM and concomitant altered drug sensitivity that is not taken into account using traditional drug susceptibility testing screenings. We therefore developed human cell-based in vitro Mav infection models using the human MelJuSo cell line as well as primary human macrophages and a fluorescently labeled Mav strain. By testing a range of multiplicity of infection (MOI) and using flow cytometry and colony-forming unit (CFU) analysis, we found that an MOI of 10 was the most suitable for Mav infection in primary human macrophages, whereas an MOI of 50 was required to achieve similar results in MelJuSo cells. Moreover, by monitoring intracellular bacterial loads over time, the macrophages were shown to be capable of controlling the infection, while MelJuSo cells failed to do so. When comparing the MGIT system with the classical CFU counting assay to determine intracellular bacterial loads, MGIT appeared as a less labor-intensive, more precise, and more objective alternative. Next, using our macrophage Mav infection models, the drug efficacy of the first-line drug rifampicin and the more recently discovered bedaquiline on intracellular bacteria was compared to the activity on extracellular bacteria. The efficacy of the antibiotics inhibiting bacterial growth was significantly lower against intracellular bacteria compared to extracellular bacteria. This finding emphasizes the crucial role of the host cell during infection and drug susceptibility and highlights the usefulness of the models. Taken together, the human cell-based Mav infection models are reliable tools to determine the intracellular loads of Mav, which will enable researchers to investigate host–pathogen interactions and to evaluate the efficacy of (host-directed) therapeutic strategies against Mav.
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Affiliation(s)
- Gül Kilinç
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Kimberley V. Walburg
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Kees L. M. C. Franken
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Merel L. Valkenburg
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Alexandra Aubry
- Sorbonne Université, INSERM, Centre d’Immunologie et des Maladies Infectieuses, U1135, AP-HP, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Mariëlle C. Haks
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Anno Saris
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
- *Correspondence: Anno Saris, ; orcid.org/0000-0003-0493-9501
| | - Tom H. M. Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
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Neff SL, Hampton TH, Puerner C, Cengher L, Doing G, Lee AJ, Koeppen K, Cheung AL, Hogan DA, Cramer RA, Stanton BA. CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies. Sci Data 2022; 9:343. [PMID: 35710652 PMCID: PMC9203545 DOI: 10.1038/s41597-022-01431-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/25/2022] [Indexed: 01/13/2023] Open
Abstract
Researchers studying cystic fibrosis (CF) pathogens have produced numerous RNA-seq datasets which are available in the gene expression omnibus (GEO). Although these studies are publicly available, substantial computational expertise and manual effort are required to compare similar studies, visualize gene expression patterns within studies, and use published data to generate new experimental hypotheses. Furthermore, it is difficult to filter available studies by domain-relevant attributes such as strain, treatment, or media, or for a researcher to assess how a specific gene responds to various experimental conditions across studies. To reduce these barriers to data re-analysis, we have developed an R Shiny application called CF-Seq, which works with a compendium of 128 studies and 1,322 individual samples from 13 clinically relevant CF pathogens. The application allows users to filter studies by experimental factors and to view complex differential gene expression analyses at the click of a button. Here we present a series of use cases that demonstrate the application is a useful and efficient tool for new hypothesis generation. (CF-Seq: http://scangeo.dartmouth.edu/CFSeq/ ).
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Affiliation(s)
- Samuel L Neff
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | | | - Charles Puerner
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Liviu Cengher
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Georgia Doing
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | | | - Katja Koeppen
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | | | - Deborah A Hogan
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Robert A Cramer
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Bruce A Stanton
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.
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7
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Chai J, Han X, Mei Q, Liu T, Walline JH, Xu J, Liu Y, Zhu H. Clinical Characteristics and Mortality of Non-tuberculous Mycobacterial Infection in Immunocompromised vs. Immunocompetent Hosts. Front Med (Lausanne) 2022; 9:884446. [PMID: 35665363 PMCID: PMC9159854 DOI: 10.3389/fmed.2022.884446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Immunosuppression and host vulnerability play a key role in non-tuberculous mycobacteria (NTM) pathogenesis. The objective of this study was to compare the clinical characteristics and mortality of NTM infections in immunocompromised and immunocompetent patients. We used a retrospective dataset obtained from our large, tertiary, urban, teaching hospital which is the medical records of hospitalized patients with NTM infections between January 1, 2013 to December 31, 2020. The information including clinical manifestations, imaging, and NTM etiological data were obtained from the hospital's clinical data system. A total of 480 patients with NTM infections completed species identification. 118 hospitalized NTM patients who met ATS/IDSA NTM diagnostic criteria and had complete medical records were included in the study. The average age was 49.4 years, 57 (48.3%) were female, and 64 (54.2%) were immunosuppressed hosts. In our study, the most common species in order of frequency were: M. intracellulare, M. abscessus, M. avium, and M. kansasii among NTM patients. The most common comorbidity was history of previous tuberculosis (30.5%). Besides malignancy, the most common immunodeficiencies were adult-onset immunodeficiency induced by anti-interferon-gamma autoantibody, SLE, and vasculitis. The immunocompromised patients with NTM had more clinical symptoms, comorbidities and lower lymphocyte counts compared to immunocompetent patients. The mortality we observed in immunocompromised patients of NTM disease was significantly higher than that of immunocompetent patients (HR 3.537, 95% CI 1.526–8.362). Immunosuppressed NTM patients with lower B and CD4+ T lymphocyte counts may more frequently present with disseminated NTM infections, clinical exacerbations, and higher mortality than immunocompetent patients.
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Affiliation(s)
- Jingjing Chai
- Emergency Department, State Key Laboratory for Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xu Han
- Emergency Department, State Key Laboratory for Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qimin Mei
- Emergency Department, State Key Laboratory for Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Tao Liu
- Department of Pulmonary and Critical Care Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Joseph Harold Walline
- Accident and Emergency Medicine Academic Unit, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, China
| | - Jia Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yecheng Liu
- Emergency Department, State Key Laboratory for Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Huadong Zhu
- Emergency Department, State Key Laboratory for Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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