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Dowdell KS, Potgieter SC, Olsen K, Lee S, Vedrin M, Caverly LJ, LiPuma JJ, Raskin L. Source-to-tap investigation of the occurrence of nontuberculous mycobacteria in a full-scale chloraminated drinking water system. Appl Environ Microbiol 2024; 90:e0060924. [PMID: 39109876 PMCID: PMC11409651 DOI: 10.1128/aem.00609-24] [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: 04/16/2024] [Accepted: 07/08/2024] [Indexed: 09/19/2024] Open
Abstract
Nontuberculous mycobacteria (NTM) in drinking water are a significant public health concern. However, an incomplete understanding of the factors that influence the occurrence of NTM in drinking water limits our ability to characterize risk and prevent infection. This study sought to evaluate the influence of season and water treatment, distribution, and stagnation on NTM in drinking water. Samples were collected source-to-tap in a full-scale, chloraminated drinking water system approximately monthly from December 2019 to November 2020. NTM were characterized using culture-dependent (plate culture with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry [MALDI-TOF MS] isolate analysis) and culture-independent methods (quantitative PCR and genome-resolved metagenomics). Sampling locations included source waters, three locations within the treatment plant, and five buildings receiving water from the distribution system. Building plumbing samples consisted of first draw, 5-min flush, and full flush cold-water samples. As the study took place during the COVID-19 pandemic, the influence of reduced water usage in three of the five buildings was also investigated. The highest NTM densities source-to-tap were found in the summer first draw building water samples (107 gene copies/L), which also had the lowest monochloramine concentrations. Flushing was found to be effective for reducing NTM and restoring disinfectant residuals, though flush times necessary to improve water quality varied by building. Clinically relevant NTM species, including Mycobacterium avium, were recovered via plate culture, with increased occurrence observed in buildings with higher water age. Four of five NTM metagenome-assembled genomes were identified to the species level and matched identified isolates.IMPORTANCENTM infections are increasing in prevalence, difficult to treat, and associated with high morbidity and mortality rates. Our lack of understanding of the factors that influence NTM occurrence in drinking water limits our ability to prevent infections, accurately characterize risk, and focus remediation efforts. In this study, we comprehensively evaluated NTM in a full-scale drinking water system, showing that various steps in treatment and distribution influence NTM presence. Stagnant building water contained the highest NTM densities source-to-tap and was associated with low disinfectant residuals. We illustrated the differences in NTM detection and characterization obtained from culture-based and culture-independent methods, highlighting the complementarity between these approaches. We demonstrated that focusing NTM mitigation efforts in building plumbing systems, which have the highest NTM densities source-to-tap, has potential for immediate positive effects. We also identified steps during treatment that increase NTM levels, which provides beneficial information for utilities seeking to reduce NTM in finished water.
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Affiliation(s)
- Katherine S. Dowdell
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Sarah C. Potgieter
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Kirk Olsen
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Soojung Lee
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthew Vedrin
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Lindsay J. Caverly
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - John J. LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
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2
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Naseem R, Howe N, Williams CJ, Pretorius S, Green K. What diagnostic tests are available for respiratory infections or pulmonary exacerbations in cystic fibrosis: A scoping literature review. Respir Investig 2024; 62:817-831. [PMID: 39024929 DOI: 10.1016/j.resinv.2024.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/02/2024] [Accepted: 07/06/2024] [Indexed: 07/20/2024]
Abstract
A scoping review methodological framework formed the basis of this review. A search of two electronic databases captured relevant literature published from 2013. 1184 articles were screened, 200 of which met inclusion criteria. Included studies were categorised as tests for either respiratory infections OR pulmonary exacerbations. Data were extracted to ascertain test type, sample type, and indication of use for each test type. For infection, culture is the most common testing method, particularly for bacterial infections, whereas PCR is utilised more for the diagnosis of viral infections. Spirometry tests, indicating lung function, facilitate respiratory infection diagnoses. There is no clear definition of what an exacerbation is in persons with CF. A clinical checklist with risk criteria can determine if a patient is experiencing an exacerbation event, however the diagnosis is clinician-led and will vary between individuals. Fuchs criteria are one of the most frequently used tests to assess signs and symptoms of exacerbation in persons with CF. This scoping review highlights the development of home monitoring tests to facilitate earlier and easier diagnoses, and the identification of novel biomarkers for indication of infections/exacerbations as areas of current research and development. Research is particularly prevalent regarding exhaled breath condensate and volatile organic compounds as an alternative sampling/biomarker respectively for infection diagnosis. Whilst there are a wide range of tests available for diagnosing respiratory infections and/or exacerbations, these are typically used clinically in combination to ensure a rapid, accurate diagnosis which will ultimately benefit both the patient and clinician.
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Affiliation(s)
- Raasti Naseem
- NIHR Newcastle HealthTech Research Centre in Diagnostic and Technology Evaluation, Fourth floor William Leech Building, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Nicola Howe
- NIHR Newcastle HealthTech Research Centre in Diagnostic and Technology Evaluation, Fourth floor William Leech Building, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom.
| | - Cameron J Williams
- NIHR Newcastle HealthTech Research Centre in Diagnostic and Technology Evaluation, Fourth floor William Leech Building, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Sara Pretorius
- NIHR Newcastle HealthTech Research Centre in Diagnostic and Technology Evaluation, Fourth floor William Leech Building, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Kile Green
- NIHR Newcastle HealthTech Research Centre in Diagnostic and Technology Evaluation, Fourth floor William Leech Building, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
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3
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Opperman CJ, Singh S, Goosen W, Cox H, Warren R, Esmail A. Incorporating direct molecular diagnostics in management algorithms for nontuberculous mycobacteria: Is it high time? IJID REGIONS 2024; 10:140-145. [PMID: 38304760 PMCID: PMC10831244 DOI: 10.1016/j.ijregi.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 02/03/2024]
Abstract
Nontuberculous mycobacteria (NTM) are a group of acid-fast mycobacteria other than Mycobacterium tuberculosis complex (MTBC) that cause pulmonary disease that is similar to the disease caused by MTBC. International guidelines for the diagnosis of pulmonary NTM disease are rigid and have remained unchanged for nearly 2 decades. In this opinion piece, we provide a new perspective on the traditional criteria by suggesting a diagnostic algorithm that incorporates direct molecular identification of NTM performed on raw sputum specimens (using Sanger or targeted deep sequencing approaches, among others) paired with traditional culture methods. Our approach ensures a more rapid diagnosis of pulmonary NTM disease, thus, facilitating timeous clinical diagnosis, and prompt treatment initiation, where indicated, and leverages recent advances in novel molecular techniques into routine NTM identification practice.
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Affiliation(s)
- Christoffel Johannes Opperman
- National Health Laboratory Service, Green Point TB Laboratory, Cape Town, South Africa
- SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Sarishna Singh
- National Health Laboratory Service, Green Point TB Laboratory, Cape Town, South Africa
- SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Wynand Goosen
- SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Helen Cox
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine and Wellcome Centre for Infectious Disease Research, University of Cape Town, Cape Town, South Africa
| | - Rob Warren
- SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Aliasgar Esmail
- UCT Lung Institute, Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town, & Groote Schuur Hospital
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4
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Thornton CS, Carmody LA, Kalikin LM, Opron K, Caverly LJ, LiPuma JJ. Airway bacterial community composition in persons with advanced cystic fibrosis lung disease. J Cyst Fibros 2023; 22:623-629. [PMID: 36628831 DOI: 10.1016/j.jcf.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023]
Abstract
BACKGROUND The progression of lung disease in people with cystic fibrosis (pwCF) has been associated with a decrease in the diversity of airway bacterial communities. How often low diversity communities occur in advanced CF lung disease and how they may be associated with clinical outcomes is not clear, however. METHODS We sequenced a region of the bacterial 16S ribosomal RNA gene to characterize bacterial communities in sputum from 190 pwCF with advanced lung disease (FEV1≤40% predicted), with particular attention to the prevalence and relative abundance of dominant genera. We evaluated relationships between community diversity and clinical outcomes. RESULTS Although most of the 190 pwCF with advanced lung disease had airway bacterial communities characterized by low diversity with a dominant genus, a considerable minority (40%) did not. The absence of a dominant genus, presence of methicillin-susceptible Staphylococcus aureus, and greater bacterial richness positively correlated with lung function. Higher relative abundance of the dominant genus and greater antimicrobial use negatively correlated with lung function. PwCF with a low diversity community and dominant genus had reduced lung transplant-free survival compared to those without (median survival of 1.6 vs 2.9 years). CONCLUSIONS A considerable proportion of pwCF with advanced lung disease do not have airway bacterial communities characterized by low diversity and a dominant genus and these individuals had better survival. An understanding of the antecedents of low diversity airway communities- and the impact these may have on lung disease trajectory - may provide avenues for improved management strategies.
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Affiliation(s)
- Christina S Thornton
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Lisa A Carmody
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Linda M Kalikin
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kristopher Opron
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lindsay J Caverly
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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5
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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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Kim BG, Kang N, Kim SY, Kim DH, Kim H, Kwon OJ, Huh HJ, Lee NY, Jhun BW. The lung microbiota in nontuberculous mycobacterial pulmonary disease. PLoS One 2023; 18:e0285143. [PMID: 37235629 DOI: 10.1371/journal.pone.0285143] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/14/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND The role of bacterial microbiota in the pathogenesis of nontuberculous mycobacterial pulmonary disease (NTM-PD) is unclear. We aimed to compare the bacterial microbiome of disease-invaded lesions and non-invaded lung tissue from NTM-PD patients. METHODS We analyzed lung tissues from 23 NTM-PD patients who underwent surgical lung resection. Lung tissues were collected in pairs from each patient, with one sample from a disease-involved site and the other from a non-involved site. Lung tissue microbiome libraries were constructed using 16S rRNA gene sequences (V3-V4 regions). RESULTS Sixteen (70%) patients had Mycobacterium avium complex (MAC)-PD, and the remaining seven (30%) had Mycobacterium abscessus-PD. Compared to non-involved sites, involved sites showed greater species richness (ACE, Chao1, and Jackknife analyses, all p = 0.001); greater diversity on the Shannon index (p = 0.007); and genus-level differences (Jensen-Shannon, PERMANOVA p = 0.001). Analysis of taxonomic biomarkers using linear discriminant analysis (LDA) effect sizes (LEfSe) demonstrated that several genera, including Limnohabitans, Rahnella, Lachnospira, Flavobacterium, Megamonas, Gaiella, Subdoligranulum, Rheinheimera, Dorea, Collinsella, and Phascolarctobacterium, had significantly greater abundance in involved sites (LDA >3.00, p <0.05, and q <0.05). In contrast, Acinetobacter had significantly greater abundance at non-involved sites (LDA = 4.27, p<0.001, and q = 0.002). Several genera were differentially distributed between lung tissues from MAC-PD (n = 16) and M. abscessus-PD (n = 7), and between nodular bronchiectatic form (n = 12) and fibrocavitary form (n = 11) patients. However, there was no genus with a significant q-value. CONCLUSIONS We identified differential microbial distributions between disease-invaded and normal lung tissues from NTM-PD patients, and microbial diversity was significantly higher in disease-invaded tissues. TRIAL REGISTRATION Clinical Trial registration number: NCT00970801.
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Affiliation(s)
- Bo-Guen Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Noeul Kang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Dae Hun Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hojoong Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - O Jung Kwon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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7
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Burke A, Thomson RM, Wainwright CE, Bell SC. Nontuberculous Mycobacteria in Cystic Fibrosis in the Era of Cystic Fibrosis Transmembrane Regulator Modulators. Semin Respir Crit Care Med 2023; 44:287-296. [PMID: 36649736 DOI: 10.1055/s-0042-1759883] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nontuberculous mycobacteria (NTM) are a group of mycobacteria which represent opportunistic pathogens that are of increasing concern in people with cystic fibrosis (pwCF). The acquisition has been traditionally though to be from environmental sources, though recent work has suggested clustered clonal infections do occur and transmission potential demonstrated among pwCF attending CF specialist centers. Guidelines for the screening, diagnosis, and identification of NTM and management of pwCF have been published. The emergence of CF-specific therapies, in particular cystic fibrosis transmembrane regulator (CFTR) modulator drugs, have led to significant improvement in the health and well-being of pwCF and may lead to challenges in sampling the lower respiratory tract including to screen for NTM. This review highlights the epidemiology, modes of acquisition, screening and diagnosis, therapeutic approaches in the context of improved clinical status for pwCF, and the clinical application of CFTR modulator therapies.
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Affiliation(s)
- Andrew Burke
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia.,Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Rachel M Thomson
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia.,Gallipoli Medical Research Foundation, Greenslopes Private Hospital, Greenslopes, Queensland, Australia
| | - Claire E Wainwright
- Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, South Brisbane, Australia.,Children's Health Research Centre, Faculty of Medicine, The University of Queensland, South Brisbane, Australia
| | - Scott C Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia.,Children's Health Research Centre, Faculty of Medicine, The University of Queensland, South Brisbane, Australia.,Translational Research Institute, Woolloongabba, Australia
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8
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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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Dziedzinska R, Okunkova J, Kralik P, Svobodova J, Mala M, Slana I. Identification of and discrimination between the Mycobacterium abscessus complex and Mycobacterium avium complex directly from sputum using quadruplex real-time PCR. J Med Microbiol 2022; 71. [PMID: 36748608 DOI: 10.1099/jmm.0.001611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Introduction. Cystic fibrosis (CF) is a serious disease with multisystemic clinical signs that is easily and frequently complicated by bacterial infection. Recently, the prevalence of nontuberculous mycobacteria as secondary contaminants of CF has increased, with the Mycobacterium avium complex (MAC) and Mycobacterium abscessus complex (MABSC) being the most frequently identified. The MABSC includes subspecies of significant clinical importance, mainly due to their resistance to antibiotics.Gap statement. Sensitive method for early detection and differentiation of MABSC members and MAC complex for use in routine clinical laboratories is lacking. A method based on direct DNA isolation from sputum, using standard equipment in clinical laboratories and allowing uncovering of possible sample inhibition (false negative results) would be required. The availability of such a method would allow accurate and accelerated time detection of MABSC members and their timely and targeted treatment.Aim. To develop a real time multiplex assay for rapid and sensitive identification and discrimination of MABSC members and MAC complex.Methodology. The method of DNA isolation directly from the sputum of patients followed by quadruplex real-time quantitative PCR (qPCR) detection was developed and optimised. The sensitivity and limit of detection (LOD) of the qPCR was determined using human sputum samples artificially spiked with a known amount of M. abscessus subsp. massiliense (MAM).Results. The method can distinguish between MAC and MABSC members and, at the same time, to differentiate between M. abscessus subsp. abscessus/subsp. bolletii (MAAb/MAB) and MAM. The system was verified using 61 culture isolates and sputum samples from CF and non-CF patients showing 29.5 % MAAb/MAB, 14.7 % MAM and 26.2 % MAC. The LOD was determined to be 1 490 MAM cells in the sputum sample with the efficiency of DNA isolation being 95.4 %. Verification of the qPCR results with sequencing showed 100 % homology.Conclusions. The developed quadruplex qPCR assay, which is preceded by DNA extraction directly from patients' sputum without the need for culturing, significantly improves and speeds up the entire process of diagnosing CF patients and is therefore particularly suitable for use in routine laboratories.
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Affiliation(s)
- Radka Dziedzinska
- Laboratory of Neurobiology and Pathological Physiology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia
| | - Jana Okunkova
- Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Czechia
| | - Petr Kralik
- Laboratory of Neurobiology and Pathological Physiology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia
| | | | - Miriam Mala
- Department of Pediatric Infectious Diseases, Centre of Cystic Fibrosis, University Hospital Brno, Brno, Czechia.,Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Iva Slana
- Department of Animal Origin Food & Gastronomic Sciences, University of Veterinary Sciences Brno, Brno, Czechia
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10
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Sharma P, Silva C, Pfreundschuh S, Ye H, Sampath H. Metabolic protection by the dietary flavonoid 7,8-dihydroxyflavone requires an intact gut microbiome. Front Nutr 2022; 9:987956. [PMID: 36061902 PMCID: PMC9428675 DOI: 10.3389/fnut.2022.987956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 07/29/2022] [Indexed: 11/18/2022] Open
Abstract
Background 7,8-dihydroxyflavone (DHF) is a naturally occurring flavonoid found in Godmania, Tridax, and Primula species that confers protection against high-fat diet (HFD) induced metabolic pathologies selectively in female mice. We have previously reported that this metabolic protection is associated with early and stable remodeling of the intestinal microbiome, evident in female but not male DHF-supplemented mice. Early changes in the gut microbiome in female DHF-fed mice were highly predictive of subsequent metabolic protection, suggesting a causative association between the gut microbiome and the metabolic effects of DHF. Objective To investigate a causal association between the gut microbiome and the metabolic effects of DHF using a model of antibiotic-induced gut microbiome ablation. Materials and methods Age-matched male and female C57Bl6/J mice were given ad libitum access to HFD and drinking water containing vehicle or DHF for 12 weeks. For antibiotic (Abx) treatment, female mice were given drinking water containing a cocktail of antibiotics for 2 weeks prior to HFD feeding and throughout the feeding period. Metabolic phenotyping consisted of longitudinal assessments of body weights, body composition, food, and water intake, as well as measurement of energy expenditure, glucose tolerance, and plasma and hepatic lipids. Protein markers mediating the cellular effects of DHF were assessed in brown adipose tissue (BAT) and skeletal muscle. Results Metabolic protection conferred by DHF in female HFD-fed mice was only apparent in the presence of an intact gut microbiome. Abx-treated mice were not protected from HFD-induced obesity by DHF administration. Further, tissue activation of the tropomyosin-related kinase receptor B (TrkB) receptor, which has been attributed to the biological activity of DHF, was lost upon gut microbiome ablation, indicating a requirement for microbial “activation” of DHF for its systemic effects. In addition, we report for the first time that DHF supplementation significantly activates TrkB in BAT of female, but not male, mice uncovering a novel target tissue of DHF. DHF supplementation also increased uncoupling protein 1 (UCP1) and AMP-activated protein kinase (AMPK) protein in BAT, consistent with protection from diet-induced obesity. Conclusion These results establish for the first time a requirement for the gut microbiome in mediating the metabolic effects of DHF in female mice and uncover a novel target tissue that may mediate these sexually-dimorphic protective effects.
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Affiliation(s)
- Priyanka Sharma
- Department of Nutritional Sciences, Rutgers University, New Brunswick, NJ, United States
- Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ, United States
- Center for Microbiome, Nutrition, and Health, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ, United States
| | - Camila Silva
- Department of Biotechnology, Rutgers University, New Brunswick, NJ, United States
| | - Sarah Pfreundschuh
- Department of Nutritional Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Hong Ye
- Department of Nutritional Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Harini Sampath
- Department of Nutritional Sciences, Rutgers University, New Brunswick, NJ, United States
- Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ, United States
- Center for Microbiome, Nutrition, and Health, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ, United States
- *Correspondence: Harini Sampath,
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11
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Abstract
Nontuberculous mycobacterial (NTM) pulmonary infections in people with cystic fibrosis (CF) are associated with significant morbidity and mortality and are increasing in prevalence. Host risk factors for NTM infection in CF are largely unknown. We hypothesize that the airway microbiota represents a host risk factor for NTM infection. In this study, 69 sputum samples were collected from 59 people with CF; 42 samples from 32 subjects with NTM infection (14 samples collected before incident NTM infection and 28 samples collected following incident NTM infection) were compared to 27 samples from 27 subjects without NTM infection. Sputum samples were analyzed with 16S rRNA gene sequencing and metabolomics. A supervised classification and correlation analysis framework (sparse partial least-squares discriminant analysis [sPLS-DA]) was used to identify correlations between the microbial and metabolomic profiles of the NTM cases compared to the NTM-negative controls. Several metabolites significantly differed in the NTM cases compared to controls, including decreased levels of tryptophan-associated and branched-chain amino acid metabolites, while compounds involved in phospholipid metabolism displayed increased levels. When the metabolome and microbiome data were integrated by sPLS-DA, the models and component ordinations showed separation between the NTM and control samples. While this study could not determine if the observed differences in sputum metabolites between the cohorts reflect metabolic changes that occurred as a result of the NTM infection or metabolic features that contributed to NTM acquisition, it is hypothesis generating for future work to investigate host and bacterial community factors that may contribute to NTM infection risk in CF. IMPORTANCE Host risk factors for nontuberculous mycobacterial (NTM) infection in people with cystic fibrosis (CF) are largely unclear. The goal of this study was to help identify potential host and bacterial community risk factors for NTM infection in people with CF, using microbiome and metabolome data from CF sputum samples. The data obtained in this study identified several metabolic profile differences in sputum associated with NTM infection in CF, including 2-methylcitrate/homocitrate and selected ceramides. These findings represent potential risk factors and therapeutic targets for preventing and/or treating NTM infections in people with CF.
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12
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Iwasaki K, Matsuzawa Y, Wakabayashi H, Shioya M, Hayakawa S, Tatsuno I. Lower airway microbiota in patients with clinically suspected Mycobacterium avium complex lung disease. Heliyon 2021; 7:e07283. [PMID: 34179537 PMCID: PMC8214089 DOI: 10.1016/j.heliyon.2021.e07283] [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: 01/05/2021] [Revised: 03/29/2021] [Accepted: 06/08/2021] [Indexed: 11/05/2022] Open
Abstract
The relationship between the lower airway microbiota in humans and respiratory illness has gained attention recently. However, the relationship between nontuberculous mycobacterial lung disease (NTM-LD) and the lower airway microbiota is not fully understood yet. We conducted a study to characterize the lower airway microbiota in Mycobacterium avium complex lung disease (MAC-LD), a representative subclass of the NTM-LD. The subject sample included 25 patients clinically suspected of having mild MAC disease whose condition could not be diagnosed using sputum culture. Upon testing MAC antibodies (anti-glycopeptidolipid (GPL)-core IgA antibodies), mycobacterial culture of bronchoalveolar lavage fluid (BALF), and performing BALF 16S rRNA gene sequencing, we divided the subjects into two groups of patients: those in whom MAC was detected in BALF mycobacterial culture (MAC-LD group) and in whom MAC was not detected in BALF mycobacterial culture (non-MAC-LD group), which was then comparatively examined. BALF mycobacterial culture showed that 9 out of 25 patients were positive for NTM; the detected Mycobacterium was MAC in all. No patients were positive for acid-fast bacteria other than MAC. Eighteen patients were positive for MAC antibodies (anti-glycopeptidolipid (GPL)-core IgA antibodies), including nine patients positive for mycobacterial culture. On BALF 16S rRNA gene sequencing, six patients were positive for the genus Mycobacterium and were culture-positive. Among the 16 patients in the non-MAC-LD group, the genus Pseudomonas was detected by 16S rRNA gene sequencing in 7 patients, 4 among whom were positive for MAC antibodies (anti-GPL-core IgA antibodies). Conversely, the genus Pseudomonas was not detected among the nine patients in the MAC-LD group. Other than the genus Pseudomonas, there was no clear difference in the composition of and no significant difference in the diversity of the bacterial flora between the MAC-LD and non-MAC-LD groups. However, we found that the genus Pseudomonas and MAC tended to exist exclusively.
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Affiliation(s)
- Kotaro Iwasaki
- Department of Internal Medicine, Toho University Sakura Medical Center, Japan.,Department of Diabetes, Endocrinology and Metabolism, Toho University Graduate School of Medicine, Japan
| | - Yasuo Matsuzawa
- Department of Internal Medicine, Toho University Sakura Medical Center, Japan
| | - Hiroki Wakabayashi
- Department of Internal Medicine, Toho University Sakura Medical Center, Japan
| | - Moe Shioya
- Department of Internal Medicine, Toho University Sakura Medical Center, Japan
| | - Sho Hayakawa
- Department of Internal Medicine, Toho University Sakura Medical Center, Japan
| | - Ichiro Tatsuno
- Department of Internal Medicine, Toho University Sakura Medical Center, Japan
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13
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Thornton CS, Mellett M, Jarand J, Barss L, Field SK, Fisher DA. The respiratory microbiome and nontuberculous mycobacteria: an emerging concern in human health. Eur Respir Rev 2021; 30:30/160/200299. [PMID: 34039671 DOI: 10.1183/16000617.0299-2020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/09/2021] [Indexed: 12/24/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) are diverse microbial species encompassing commensals and pathogens with the ability to cause pulmonary disease in both immunocompetent and immunocompromised individuals. In contrast to Mycobacterium tuberculosis, which has seen a reduction in disease rates in developed countries, the incidence and prevalence of NTM disease is increasing. NTM are difficult to treat with standard antimicrobial regimens and may contain both virulence and antibiotic-resistance genes with potential for pathogenicity. With the advent of molecular techniques, it has been elucidated that these organisms do not reside in isolation and are rather part of a complex milieu of microorganisms within the host lung microbiome. Over the last decade, studies have highlighted the impact of the microbiome on host immunity, metabolism and cell-cell communication. This recognition of a broader community raises the possibility that the microbiome may disrupt the balance between infection and disease. Additionally, NTM disease progression and antimicrobial therapy may affect the healthy steady state of the host and function of the microbiome, contributing to further dysbiosis and clinical deterioration. There have been limited studies assessing how NTM may influence the relationship between microbiome and host. In this review, we highlight available studies about NTM and the microbiome, postulate on virulence mechanisms by which these microorganisms communicate and discuss implications for treatment.
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Affiliation(s)
- Christina S Thornton
- Division of Respirology, University of Calgary, Calgary, Canada .,Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Joint first authors
| | - Madeline Mellett
- Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Joint first authors
| | - Julie Jarand
- Division of Respirology, University of Calgary, Calgary, Canada.,Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,TB Services, University of Calgary, Calgary, Canada
| | - Leila Barss
- Division of Respirology, University of Calgary, Calgary, Canada.,Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,TB Services, University of Calgary, Calgary, Canada
| | - Stephen K Field
- Division of Respirology, University of Calgary, Calgary, Canada.,Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,TB Services, University of Calgary, Calgary, Canada
| | - Dina A Fisher
- Division of Respirology, University of Calgary, Calgary, Canada.,Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,TB Services, University of Calgary, Calgary, Canada.,Dept of Community Health Sciences, University of Calgary, Calgary, Canada
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14
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Bordin A, Pandey S, Coulter C, Syrmis M, Pardo C, Hackett H, Bell SC, Wainwright CE, Nimmo GR, Jennison AV, Clark JE, Whiley DM. Rapid macrolide and amikacin resistance testing for Mycobacterium abscessus in people with cystic fibrosis. J Med Microbiol 2021; 70. [PMID: 33909552 DOI: 10.1099/jmm.0.001349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Introduction. Mycobacterium abscessus complex (MABSC) is an environmental organism and opportunistic pathogen. MABSC pulmonary infections in people with cystic fibrosis are of growing clinical concern. Resistance data guide the use of macrolides and amikacin in MABSC pulmonary disease treatment. MABSC can acquire resistance against macrolides or amikacin via 23S or 16S rRNA gene mutations, respectively.Gap Statement. Current culture-based methods for MABSC detection and antibiotic resistance characterization are typically prolonged, limiting their utility to directly inform treatment or clinical trials. Culture-independent molecular methods may help address this limitation.Aim. To develop real-time PCR assays for characterization of key 23S or 16S rRNA gene mutations associated with constitutive resistance in MABSC.Methodology. We designed two real-time PCR assays to detect the key 23S and 16S rRNA gene mutations. The highly conserved nature of rRNA genes was a major design challenge. To reduce potential cross-reactivity, primers included non-template bases and targeted single-nucleotide polymorphisms unique to MABSC. We applied these assays, as well as a previously developed real-time PCR assay for MABSC detection, to 968 respiratory samples from people with cystic fibrosis. The results from the molecular methods were compared to those for gold standard culture methods and 23S and 16S rRNA gene sequencing.Results.The real-time PCR MABSC detection assay provided a sensitivity of 83.8 % and a specificity of 97.8 % compared to culture. The results from the real-time PCR resistance detection assays were mostly concordant (>77.4 %) with cultured isolate sequencing. The real-time PCR resistance detection assays identified several samples harbouring both resistant and susceptible MABSC, while culture-dependent methods only identified susceptible MABSC in these samples.Conclusion. Using the molecular methods described here, results for health care providers or researchers could be available days or weeks earlier than is currently possible via culture-based antibiotic susceptibility testing.
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Affiliation(s)
- Amanda Bordin
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Sushil Pandey
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Christopher Coulter
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Melanie Syrmis
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia.,The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Carolyn Pardo
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Hazel Hackett
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Scott C Bell
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,The Prince Charles Hospital, Department of Thoracic Medicine, Brisbane, Queensland, Australia
| | - Claire E Wainwright
- Respiratory and Sleep Medicine Department, Queensland Children's Hospital, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Graeme R Nimmo
- Central Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Amy V Jennison
- Forensic and Scientific Services, Queensland Health, Brisbane, Queensland, Australia
| | - Julia E Clark
- Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - David M Whiley
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia.,Central Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
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15
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Caverly LJ, Zimbric M, Azar M, Opron K, LiPuma JJ. Cystic fibrosis airway microbiota associated with outcomes of nontuberculous mycobacterial infection. ERJ Open Res 2021; 7:00578-2020. [PMID: 33898611 PMCID: PMC8053818 DOI: 10.1183/23120541.00578-2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/29/2021] [Indexed: 01/03/2023] Open
Abstract
Rationale Pulmonary infections with nontuberculous mycobacteria (NTM) are increasingly prevalent in people with cystic fibrosis (CF). Clinical outcomes following NTM acquisition are highly variable, ranging from transient self-resolving infection to NTM pulmonary disease associated with significant morbidity. Relationships between airway microbiota and variability of NTM outcomes in CF are unclear. Objective To identify features of CF airway microbiota associated with outcomes of NTM infection. Methods 188 sputum samples, obtained from 24 subjects with CF, each with three or more samples collected from 3.5 years prior to, and up to 6 months following incident NTM infection, were selected from a sample repository. Sputum DNA underwent bacterial 16S rRNA gene sequencing. Airway microbiota were compared based on the primary outcome, a diagnosis of NTM pulmonary disease, using Wilcoxon rank-sum testing, autoregressive integrated moving average modelling and network analyses. Measurements and main results Subjects with and without NTM pulmonary disease were similar in clinical characteristics, including age and lung function at the time of incident NTM infection. Time-series analyses of sputum samples prior to incident NTM infection identified positive correlations between Pseudomonas, Streptococcus, Veillonella, Prevotella and Rothia with diagnosis of NTM pulmonary disease and with persistent NTM infection. Network analyses identified differences in clustering of taxa between subjects with and without NTM pulmonary disease, and between subjects with persistent versus transient NTM infection. Conclusions CF airway microbiota prior to incident NTM infection are associated with subsequent outcomes, including diagnosis of NTM pulmonary disease, and persistence of NTM infection. Associations between airway microbiota and NTM outcomes represent targets for validation as predictive markers and for future therapies.
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Affiliation(s)
- Lindsay J Caverly
- Dept of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Madsen Zimbric
- Dept of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michelle Azar
- Dept of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kristopher Opron
- Dept of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John J LiPuma
- Dept of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
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16
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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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17
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Philips RC, Hoyer PE, White SM, Tinkey KT, Loeffelholz M, Andersen CR, Wilkerson MG, Gibson BR, Kelly BC. Cutaneous nontuberculous mycobacteria infections: A retrospective case series of 78 patients from the Texas Gulf Coast region. J Am Acad Dermatol 2019; 81:730-739. [PMID: 31002850 DOI: 10.1016/j.jaad.2019.04.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND The incidence of cutaneous nontuberculous mycobacteria (NTM) infections is increasing. These infections are a diagnostic and therapeutic challenge. OBJECTIVE We investigated the clinical features, diagnosis, and management of cutaneous NTM infections. METHODS A retrospective case series studied 78 patients from a Gulf Coast tertiary referral center diagnosed with cutaneous NTM infection by culture or stain of a skin biopsy specimen. RESULTS A history of trauma, procedure, or environmental exposure was common. The mean time between the initial evaluation and diagnosis was 12 weeks. Only 15% of acid-fast bacillus-positive cultures had a positive acid-fast bacillus smear, and only 43% of those accompanied by skin biopsy specimen had a positive Fite stain. Immunosuppressed patients were more likely to have a positive Fite stain. Treatment included surgery and multiple antibiotics. Immunosuppressed patients and Mycobacterium abscessus group infections were more likely to have persistent disease. LIMITATIONS M chelonae and M abscessus isolates were indistinguishable and therefore were reported together. Five cases were not confirmed by culture. CONCLUSIONS Even with clinical suspicion, the diagnosis of NTM infection can be difficult. Results of acid-fast bacillus smears and special stains are frequently negative. Antibiotic resistance is common. Multidrug treatment is often required, and surgical therapy may be needed.
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Affiliation(s)
- Rebecca C Philips
- Department of Dermatology, University of Texas Medical Branch, Galveston, Texas.
| | - Paige E Hoyer
- Department of Dermatology, University of Texas Medical Branch, Galveston, Texas
| | - Skyler M White
- Department of Dermatology, University of Texas Medical Branch, Galveston, Texas
| | - Katherine T Tinkey
- School of Medicine, University of Texas Medical Branch, Galveston, Texas
| | - Michael Loeffelholz
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| | - Clark R Andersen
- Office of Biostatistics, Department of Preventive Medicine and Community Health, University of Texas Medical Branch, Galveston, Texas
| | - Michael G Wilkerson
- Department of Dermatology, University of Texas Medical Branch, Galveston, Texas
| | - Bernard R Gibson
- Department of Dermatology, University of Texas Medical Branch, Galveston, Texas
| | - Brent C Kelly
- Department of Dermatology, University of Texas Medical Branch, Galveston, Texas
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18
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Dowdell K, Haig SJ, Caverly LJ, Shen Y, LiPuma JJ, Raskin L. Nontuberculous mycobacteria in drinking water systems - the challenges of characterization and risk mitigation. Curr Opin Biotechnol 2019; 57:127-136. [PMID: 31003169 DOI: 10.1016/j.copbio.2019.03.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 12/18/2022]
Abstract
Nontuberculous mycobacteria (NTM) pulmonary infections are a growing concern worldwide, with a disproportionate incidence in persons with pre-existing health conditions. NTM have frequently been found in municipally-treated drinking water and building plumbing, leading to the hypothesis that an important source of NTM exposure is drinking water. The identification and quantification of NTM in environmental samples are complicated by genetic variability among NTM species, making it challenging to determine if clinically relevant NTM are present. Additionally, their unique cellular features and lifestyles make NTM and their nucleic acids difficult to recover. This review highlights a recent work focused on quantification and characterization of NTM and on understanding the influence of source water, treatment plants, distribution systems, and building plumbing on the abundance of NTM in drinking water.
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Affiliation(s)
- Katherine Dowdell
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Sarah-Jane Haig
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA; Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lindsay J Caverly
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Yun Shen
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA.
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19
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Dickson RP. Kudzu and sleeper cells: the varied ecology of respiratory infections. Eur Respir J 2018; 52:52/4/1801607. [PMID: 30361265 DOI: 10.1183/13993003.01607-2018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Dept of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA .,Michigan Center for Integrative Research in Critical Care, Ann Arbor, MI, USA
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20
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Sulaiman I, Wu BG, Li Y, Scott AS, Malecha P, Scaglione B, Wang J, Basavaraj A, Chung S, Bantis K, Carpenito J, Clemente JC, Shen N, Bessich J, Rafeq S, Michaud G, Donington J, Naidoo C, Theron G, Schattner G, Garofano S, Condos R, Kamelhar D, Addrizzo-Harris D, Segal LN. Evaluation of the airway microbiome in nontuberculous mycobacteria disease. Eur Respir J 2018; 52:13993003.00810-2018. [PMID: 30093571 DOI: 10.1183/13993003.00810-2018] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/29/2018] [Indexed: 01/15/2023]
Abstract
Aspiration is associated with nontuberculous mycobacterial (NTM) pulmonary disease and airway dysbiosis is associated with increased inflammation. We examined whether NTM disease was associated with a distinct airway microbiota and immune profile.297 oral wash and induced sputum samples were collected from 106 participants with respiratory symptoms and imaging abnormalities compatible with NTM. Lower airway samples were obtained in 20 participants undergoing bronchoscopy. 16S rRNA gene and nested mycobacteriome sequencing approaches characterised microbiota composition. In addition, inflammatory profiles of lower airway samples were examined.The prevalence of NTM+ cultures was 58%. Few changes were noted in microbiota characteristics or composition in oral wash and sputum samples among groups. Among NTM+ samples, 27% of the lower airway samples were enriched with Mycobacterium A mycobacteriome approach identified Mycobacterium in a greater percentage of samples, including some nonpathogenic strains. In NTM+ lower airway samples, taxa identified as oral commensals were associated with increased inflammatory biomarkers.The 16S rRNA gene sequencing approach is not sensitive in identifying NTM among airway samples that are culture-positive. However, associations between lower airway inflammation and microbiota signatures suggest a potential role for these microbes in the inflammatory process in NTM disease.
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Affiliation(s)
- Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Yonghua Li
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Adrienne S Scott
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Patrick Malecha
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Benjamin Scaglione
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Jing Wang
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Ashwin Basavaraj
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Samuel Chung
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Katrina Bantis
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Joseph Carpenito
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Jose C Clemente
- Dept of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nan Shen
- Dept of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jamie Bessich
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Samaan Rafeq
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Gaetene Michaud
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Jessica Donington
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Charissa Naidoo
- Medicine and Health Sciences, Stellenbosch University, DST/NRF of Excellence for Biomedical Tuberculosis Research and SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics Tygerberg, Cape Town, South Africa
| | - Grant Theron
- Medicine and Health Sciences, Stellenbosch University, DST/NRF of Excellence for Biomedical Tuberculosis Research and SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics Tygerberg, Cape Town, South Africa
| | - Gail Schattner
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Suzette Garofano
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Rany Condos
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - David Kamelhar
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Doreen Addrizzo-Harris
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA.,Dept of Medicine, New York University School of Medicine, New York, NY, USA
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21
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Flume PA, Chalmers JD, Olivier KN. Advances in bronchiectasis: endotyping, genetics, microbiome, and disease heterogeneity. Lancet 2018; 392:880-890. [PMID: 30215383 PMCID: PMC6173801 DOI: 10.1016/s0140-6736(18)31767-7] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/16/2018] [Accepted: 07/25/2018] [Indexed: 12/29/2022]
Abstract
Bronchiectasis is characterised by pathological dilation of the airways. More specifically, the radiographic demonstration of airway enlargement is the common feature of a heterogeneous set of conditions and clinical presentations. No approved therapies exist for the condition other than for bronchiectasis caused by cystic fibrosis. The heterogeneity of bronchiectasis is a major challenge in clinical practice and the main reason for difficulty in achieving endpoints in clinical trials. Recent observations of the past 2 years have improved the understanding of physicians regarding bronchiectasis, and have indicated that it might be more effective to classify patients in a different way. Patients could be categorised according to a heterogeneous group of endotypes (defined by a distinct functional or pathobiological mechanism) or by clinical phenotypes (defined by relevant and common features of the disease). In doing so, more specific therapies needed to effectively treat patients might finally be developed. Here, we describe some of the recent advances in endotyping, genetics, and disease heterogeneity of bronchiectasis including observations related to the microbiome.
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Affiliation(s)
- Patrick A. Flume
- Departments of Medicine and Pediatrics, Medical University
of South Carolina, Charleston, SC, USA.
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22
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Acharya KR, Dhand NK, Whittington RJ, Plain KM. Culture-Independent Identification of Mycobacterium avium Subspecies paratuberculosis in Ovine Tissues: Comparison with Bacterial Culture and Histopathological Lesions. Front Vet Sci 2017; 4:232. [PMID: 29312970 PMCID: PMC5744039 DOI: 10.3389/fvets.2017.00232] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/13/2017] [Indexed: 12/11/2022] Open
Abstract
Johne’s disease is a chronic debilitating enteropathy of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Current abattoir surveillance programs detect disease via examination of gross lesions and confirmation by histopathological and/or tissue culture, which is time-consuming and has relatively low sensitivity. This study aimed to investigate whether a high-throughput quantitative PCR (qPCR) test is a viable alternative for tissue testing. Intestine and mesenteric lymph nodes were sourced from sheep experimentally infected with MAP and the DNA extracted using a protocol developed for tissues, comprised enzymatic digestion of the tissue homogenate, chemical and mechanical lysis, and magnetic bead-based DNA purification. The extracted DNA was tested by adapting a previously validated qPCR for fecal samples, and the results were compared with culture and histopathology results of the corresponding tissues. The MAP tissue qPCR confirmed infection in the majority of sheep with gross lesions on postmortem (37/38). Likewise, almost all tissue culture (61/64) or histopathology (52/58) positives were detected with good to moderate agreement (Cohen’s kappa statistic) and no significant difference to the reference tests (McNemar’s Chi-square test). Higher MAP DNA quantities corresponded to animals with more severe histopathology (odds ratio: 1.82; 95% confidence interval: 1.60, 2.07). Culture-independent strain typing on tissue DNA was successfully performed. This MAP tissue qPCR method had a sensitivity equivalent to the reference tests and is thus a viable replacement for gross- and histopathological examination of tissue samples in abattoirs. In addition, the test could be validated for testing tissue samples intended for human consumption.
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Affiliation(s)
- Kamal R Acharya
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, Australia
| | - Navneet K Dhand
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, Australia
| | - Richard J Whittington
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, Australia.,School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Karren M Plain
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, Australia
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23
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Zemanick ET, Wagner BD, Robertson CE, Ahrens RC, Chmiel JF, Clancy JP, Gibson RL, Harris WT, Kurland G, Laguna TA, McColley SA, McCoy K, Retsch-Bogart G, Sobush KT, Zeitlin PL, Stevens MJ, Accurso FJ, Sagel SD, Harris JK. Airway microbiota across age and disease spectrum in cystic fibrosis. Eur Respir J 2017; 50:50/5/1700832. [PMID: 29146601 DOI: 10.1183/13993003.00832-2017] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 08/10/2017] [Indexed: 01/20/2023]
Abstract
Our objectives were to characterise the microbiota in cystic fibrosis (CF) bronchoalveolar lavage fluid (BALF), and determine its relationship to inflammation and disease status.BALF from paediatric and adult CF patients and paediatric disease controls undergoing clinically indicated bronchoscopy was analysed for total bacterial load and for microbiota by 16S rDNA sequencing.We examined 191 BALF samples (146 CF and 45 disease controls) from 13 CF centres. In CF patients aged <2 years, nontraditional taxa (e.gStreptococcus, Prevotella and Veillonella) constituted ∼50% of the microbiota, whereas in CF patients aged ≥6 years, traditional CF taxa (e.gPseudomonas, Staphylococcus and Stenotrophomonas) predominated. Sequencing detected a dominant taxon not traditionally associated with CF (e.gStreptococcus or Prevotella) in 20% of CF BALF and identified bacteria in 24% of culture-negative BALF. Microbial diversity and relative abundance of Streptococcus, Prevotella and Veillonella were inversely associated with airway inflammation. Microbiota communities were distinct in CF compared with disease controls, but did not differ based on pulmonary exacerbation status in CF.The CF microbiota detected in BALF differs with age. In CF patients aged <2 years, Streptococcus predominates, whereas classic CF pathogens predominate in most older children and adults.
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Affiliation(s)
| | - Brandie D Wagner
- University of Colorado School of Medicine, Aurora, CO, USA.,Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | | | | | - James F Chmiel
- Case Western Reserve University School of Medicine, Rainbow Babies and Children's Hospital, Cleveland, OH, USA
| | - John P Clancy
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ronald L Gibson
- University of Washington, Seattle Children's Hospital, Seattle, WA, USA
| | | | | | | | - Susanna A McColley
- Ann and Robert H. Lurie Children's Hospital of Chicago and Northwestern University, Chicago, IL, USA
| | - Karen McCoy
- Nationwide Children's Hospital, Columbus, OH, USA
| | | | | | | | - Mark J Stevens
- University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Scott D Sagel
- University of Colorado School of Medicine, Aurora, CO, USA
| | - J Kirk Harris
- University of Colorado School of Medicine, Aurora, CO, USA
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24
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Sabin AP, Ferrieri P, Kline S. Mycobacterium abscessus Complex Infections in Children: A Review. Curr Infect Dis Rep 2017; 19:46. [PMID: 28983867 PMCID: PMC5821427 DOI: 10.1007/s11908-017-0597-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW Infections in children with Mycobacterium abscessus complex represent a particular challenge for clinicians. Increasing incidence of these infections worldwide has necessitated focused attention to improve both diagnostic as well as treatment modalities. Published medical literature was reviewed, with emphasis on material published in the past 5 years. RECENT FINDINGS Increasing availability of new diagnostic tools, such as matrix-assisted laser desorption ionization-time of flight mass spectrometry and custom PCRs, has provided unique insights into the subspecies within the complex and improved diagnostic certainty. Microbiological review of all recent isolates at the University of Minnesota Medical Center was also conducted, with description of the antimicrobial sensitivity patterns encountered in our center, and compared with those published from other centers in the recent literature. A discussion of conventional antimicrobial treatment regimens, alongside detailed description of the relevant antimicrobials, is derived from recent publications. Antimicrobial therapy, combined with surgical intervention in some cases, remains the mainstay of pediatric care. Ongoing questions remain regarding the transmission mechanics, immunologic vulnerabilities exploited by these organisms in the host, and the optimal antimicrobial regimens necessary to enable a reliable cure. Updated treatment guidelines based on focused clinical studies in children and accounting especially for the immunocompromised children at greatest risk are very much needed.
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Affiliation(s)
- Arick P Sabin
- Department of Medicine, Division of Infectious Diseases and International Medicine, University of Minnesota Medical School, 420 Delaware Street SE, MMC # 250, Minneapolis, MN, 55455, USA
| | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology and Department of Pediatrics, Division of Infectious Diseases, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Susan Kline
- Department of Medicine, Division of Infectious Diseases and International Medicine, University of Minnesota Medical School, 420 Delaware Street SE, MMC # 250, Minneapolis, MN, 55455, USA.
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25
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Savant AP, McColley SA. Cystic fibrosis year in review 2016. Pediatr Pulmonol 2017; 52:1092-1102. [PMID: 28608632 DOI: 10.1002/ppul.23747] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/15/2017] [Indexed: 12/26/2022]
Abstract
In this article, we highlight cystic fibrosis (CF) research and case reports published in Pediatric Pulmonology during 2016. We also include articles from a variety of journals that are thematically related to these articles, or are of special interest to clinicians.
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Affiliation(s)
- Adrienne P Savant
- Division of Pulmonary Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Illinois.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Susanna A McColley
- Division of Pulmonary Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Illinois.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Stanley Manne Children's Resear ch Institute, Chicago, Illinois
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26
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Cystic fibrosis lung environment and Pseudomonas aeruginosa infection. BMC Pulm Med 2016; 16:174. [PMID: 27919253 PMCID: PMC5139081 DOI: 10.1186/s12890-016-0339-5] [Citation(s) in RCA: 229] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/24/2016] [Indexed: 12/20/2022] Open
Abstract
Background The airways of patients with cystic fibrosis (CF) are highly complex, subject to various environmental conditions as well as a distinct microbiota. Pseudomonas aeruginosa is recognized as one of the most important pulmonary pathogens and the predominant cause of morbidity and mortality in CF. A multifarious interplay between the host, pathogens, microbiota, and the environment shapes the course of the disease. There have been several excellent reviews detailing CF pathology, Pseudomonas and the role of environment in CF but only a few reviews connect these entities with regards to influence on the overall course of the disease. A holistic understanding of contributing factors is pertinent to inform new research and therapeutics. Discussion In this article, we discuss the deterministic alterations in lung physiology as a result of CF. We also revisit the impact of those changes on the microbiota, with special emphasis on P. aeruginosa and the influence of other non-genetic factors on CF. Substantial past and current research on various genetic and non-genetic aspects of cystic fibrosis has been reviewed to assess the effect of different factors on CF pulmonary infection. A thorough review of contributing factors in CF and the alterations in lung physiology indicate that CF lung infection is multi-factorial with no isolated cause that should be solely targeted to control disease progression. A combinatorial approach may be required to ensure better disease outcomes. Conclusion CF lung infection is a complex disease and requires a broad multidisciplinary approach to improve CF disease outcomes. A holistic understanding of the underlying mechanisms and non-genetic contributing factors in CF is central to development of new and targeted therapeutic strategies.
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