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Mac Aogáin M, Dicker AJ, Mertsch P, Chotirmall SH. Infection and the microbiome in bronchiectasis. Eur Respir Rev 2024; 33:240038. [PMID: 38960615 PMCID: PMC11220623 DOI: 10.1183/16000617.0038-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/02/2024] [Indexed: 07/05/2024] Open
Abstract
Bronchiectasis is marked by bronchial dilatation, recurrent infections and significant morbidity, underpinned by a complex interplay between microbial dysbiosis and immune dysregulation. The identification of distinct endophenotypes have refined our understanding of its pathogenesis, including its heterogeneous disease mechanisms that influence treatment and prognosis responses. Next-generation sequencing (NGS) has revolutionised the way we view airway microbiology, allowing insights into the "unculturable". Understanding the bronchiectasis microbiome through targeted amplicon sequencing and/or shotgun metagenomics has provided key information on the interplay of the microbiome and host immunity, a central feature of disease progression. The rapid increase in translational and clinical studies in bronchiectasis now provides scope for the application of precision medicine and a better understanding of the efficacy of interventions aimed at restoring microbial balance and/or modulating immune responses. Holistic integration of these insights is driving an evolving paradigm shift in our understanding of bronchiectasis, which includes the critical role of the microbiome and its unique interplay with clinical, inflammatory, immunological and metabolic factors. Here, we review the current state of infection and the microbiome in bronchiectasis and provide views on the future directions in this field.
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Affiliation(s)
- Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James's Hospital, Dublin, Ireland
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Alison J Dicker
- Respiratory Research Group, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Pontus Mertsch
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center (CPC), Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
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2
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Azoicai A, Lupu A, Alexoae MM, Starcea IM, Mocanu A, Lupu VV, Mitrofan EC, Nedelcu AH, Tepordei RT, Munteanu D, Mitrofan C, Salaru DL, Ioniuc I. Lung microbiome: new insights into bronchiectasis' outcome. Front Cell Infect Microbiol 2024; 14:1405399. [PMID: 38895737 PMCID: PMC11183332 DOI: 10.3389/fcimb.2024.1405399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/15/2024] [Indexed: 06/21/2024] Open
Abstract
The present treatments for bronchiectasis, which is defined by pathological dilatation of the airways, are confined to symptom relief and minimizing exacerbations. The condition is becoming more common worldwide. Since the disease's pathophysiology is not entirely well understood, developing novel treatments is critically important. The interplay of chronic infection, inflammation, and compromised mucociliary clearance, which results in structural alterations and the emergence of new infection, is most likely responsible for the progression of bronchiectasis. Other than treating bronchiectasis caused by cystic fibrosis, there are no approved treatments. Understanding the involvement of the microbiome in this disease is crucial, the microbiome is defined as the collective genetic material of all bacteria in an environment. In clinical practice, bacteria in the lungs have been studied using cultures; however, in recent years, researchers use next-generation sequencing methods, such as 16S rRNA sequencing. Although the microbiome in bronchiectasis has not been entirely investigated, what is known about it suggests that Haemophilus, Pseudomonas and Streptococcus dominate the lung bacterial ecosystems, they present significant intraindividual stability and interindividual heterogeneity. Pseudomonas and Haemophilus-dominated microbiomes have been linked to more severe diseases and frequent exacerbations, however additional research is required to fully comprehend the role of microbiome in the evolution of bronchiectasis. This review discusses recent findings on the lung microbiota and its association with bronchiectasis.
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Affiliation(s)
- Alice Azoicai
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Ancuta Lupu
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Monica Mihaela Alexoae
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Iuliana Magdalena Starcea
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Adriana Mocanu
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Vasile Valeriu Lupu
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | | | - Alin Horatiu Nedelcu
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Razvan Tudor Tepordei
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Dragos Munteanu
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Costica Mitrofan
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Delia Lidia Salaru
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Ileana Ioniuc
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
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3
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Clark JA, Curran MD, Gouliouris T, Conway Morris A, Bousfield R, Navapurkar V, Kean IRL, Daubney E, White D, Baker S, Pathan N. Rapid Detection of Antimicrobial Resistance Genes in Critically Ill Children Using a Custom TaqMan Array Card. Antibiotics (Basel) 2023; 12:1701. [PMID: 38136735 PMCID: PMC10740637 DOI: 10.3390/antibiotics12121701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Bacteria are identified in only 22% of critically ill children with respiratory infections treated with antimicrobial therapy. Once an organism is isolated, antimicrobial susceptibility results (phenotypic testing) can take another day. A rapid diagnostic test identifying antimicrobial resistance (AMR) genes could help clinicians make earlier, informed antimicrobial decisions. Here we aimed to validate a custom AMR gene TaqMan Array Card (AMR-TAC) for the first time and assess its feasibility as a screening tool in critically ill children. An AMR-TAC was developed using a combination of commercial and bespoke targets capable of detecting 23 AMR genes. This was validated using isolates with known phenotypic resistance. The card was then tested on lower respiratory tract and faecal samples obtained from mechanically ventilated children in a single-centre observational study of respiratory infection. There were 82 children with samples available, with a median age of 1.2 years. Major comorbidity was present in 29 (35%) children. A bacterial respiratory pathogen was identified in 13/82 (16%) of children, of which 4/13 (31%) had phenotypic AMR. One AMR gene was detected in 49/82 (60%), and multiple AMR genes were detected in 14/82 (17%) children. Most AMR gene detections were not associated with the identification of phenotypic AMR. AMR genes are commonly detected in samples collected from mechanically ventilated children with suspected respiratory infections. AMR-TAC may have a role as an adjunct test in selected children in whom there is a high suspicion of antimicrobial treatment failure.
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Affiliation(s)
- John A. Clark
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
| | - Martin D. Curran
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge CB2 0QQ, UK;
| | - Theodore Gouliouris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge CB2 0QQ, UK;
| | - Andrew Conway Morris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge CB2 2QQ, UK
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Rachel Bousfield
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge CB2 0QQ, UK;
| | - Vilas Navapurkar
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
| | - Iain R. L. Kean
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
| | - Esther Daubney
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
| | - Deborah White
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK;
| | - Nazima Pathan
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
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4
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O’Connor L, Heyderman R. The challenges of defining the human nasopharyngeal resistome. Trends Microbiol 2023:S0966-842X(23)00056-2. [DOI: 10.1016/j.tim.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 04/03/2023]
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5
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Ghosh A, Saha S. Meta-analysis of sputum microbiome studies identifies airway disease-specific taxonomic and functional signatures. J Med Microbiol 2022; 72. [PMID: 36748565 DOI: 10.1099/jmm.0.001617] [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: 12/23/2022] Open
Abstract
Introduction. Studying taxonomic and functional signatures of respiratory microbiomes provide a better understanding of airway diseases.Gap Statement. Several human airway metagenomics studies have identified taxonomic and functional features restricted to a single disease condition and the findings are not comparable across airway diseases due to use of different samples, NGS platforms, and bioinformatics databases and tools.Aim. To study the microbial taxonomic and functional components of sputum microbiome across airway diseases and healthy smokers.Methodology. Here, 57 whole metagenome shotgun sequencing (WMSS) runs coming from the sputum of five airway diseases: asthma, bronchiectasis, chronic obstructive pulmonary diseases (COPD), cystic fibrosis (CF), tuberculosis (TB), and healthy smokers as the control were reanalysed using a common WMSS analysis pipeline.Results. Shannon's index (alpha diversity) of the healthy smoker group was the highest among all. The beta diversity showed that the sputum microbiome is distinct in major airway diseases such as asthma, COPD and cystic fibrosis. The microbial composition based on differential analysis showed that there are specific markers for each airway disease like Acinetobacter bereziniae as a marker for COPD and Achromobacter xylosoxidans as a marker of cystic fibrosis. Pathways and metabolites identified from the sputum microbiome of these five diseases and healthy smokers also show specific markers. 'ppGpp biosynthesis' and 'purine ribonucleosides degradation' pathways were identified as differential markers for bronchiectasis and COPD. In this meta-analysis, besides bacteria kingdom, Aspergillus fumigatus was detected in asthma and COPD, and Roseolovirus human betaherpesvirus 7 was detected in COPD. Our analysis showed that the majority of the gene families specific to the drug-resistant associated genes were detected from opportunistic pathogens across all the groups.Conclusion. In summary, the specific species in the sputum of airway diseases along with the microbial features like specific gene families, pathways, and metabolites were identified which can be explored for better diagnosis and therapy.
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Affiliation(s)
- Abhirupa Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata - 700091, India
| | - Sudipto Saha
- Division of Bioinformatics, Bose Institute, Kolkata - 700091, India
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Pailhoriès H, Herrmann JL, Velo-Suarez L, Lamoureux C, Beauruelle C, Burgel PR, Héry-Arnaud G. Antibiotic resistance in chronic respiratory diseases: from susceptibility testing to the resistome. Eur Respir Rev 2022; 31:31/164/210259. [PMID: 35613743 DOI: 10.1183/16000617.0259-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/02/2022] [Indexed: 12/28/2022] Open
Abstract
The development of resistome analysis, i.e. the comprehensive analysis of antibiotic-resistance genes (ARGs), is enabling a better understanding of the mechanisms of antibiotic-resistance emergence. The respiratory microbiome is a dynamic and interactive network of bacteria, with a set of ARGs that could influence the response to antibiotics. Viruses such as bacteriophages, potential carriers of ARGs, may also form part of this respiratory resistome. Chronic respiratory diseases (CRDs) such as cystic fibrosis, severe asthma, chronic obstructive pulmonary disease and bronchiectasis, managed with long-term antibiotic therapies, lead to multidrug resistance. Antibiotic susceptibility testing provides a partial view of the bacterial response to antibiotics in the complex lung environment. Assessing the ARG network would allow personalised, targeted therapeutic strategies and suitable antibiotic stewardship in CRDs, depending on individual resistome and microbiome signatures. This review summarises the influence of pulmonary antibiotic protocols on the respiratory microbiome, detailing the variable consequences according to antibiotic class and duration of treatment. The different resistome-profiling methods are explained to clarify their respective place in antibiotic-resistance analysis in the lungs. Finally, this review details current knowledge on the respiratory resistome related to therapeutic strategies and provides insight into the application of resistome analysis to counter the emergence of multidrug-resistant respiratory pathogens.
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Affiliation(s)
- Hélène Pailhoriès
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU Angers, Angers, France.,HIFIH Laboratory UPRES EA3859, SFR ICAT 4208, Angers University, Angers, France
| | - Jean-Louis Herrmann
- Université Paris-Saclay, UVSQ, INSERM, Infection and Inflammation, Montigny-le-Bretonneux, France.,AP-HP, Groupe Hospitalo-Universitaire Paris-Saclay, Hôpital Raymond Poincaré, Garches, France
| | - Lourdes Velo-Suarez
- Brest Center for Microbiota Analysis (CBAM), Brest University Hospital, Brest, France
| | - Claudie Lamoureux
- Dept of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Université de Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
| | - Clémence Beauruelle
- Dept of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Université de Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
| | - Pierre-Régis Burgel
- Respiratory Medicine and National Cystic Fibrosis Reference Center, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Institut Cochin, INSERM U1016, Paris, France
| | - Geneviève Héry-Arnaud
- Brest Center for Microbiota Analysis (CBAM), Brest University Hospital, Brest, France .,Dept of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Université de Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
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7
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8
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Zeineldin M, A Elolimy A, Barakat R. Meta-analysis of bovine respiratory microbiota: link between respiratory microbiota and bovine respiratory health. FEMS Microbiol Ecol 2021; 96:5861316. [PMID: 32573684 DOI: 10.1093/femsec/fiaa127] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/19/2020] [Indexed: 12/17/2022] Open
Abstract
Bovine respiratory microbiota plays a significant role in bovine respiratory health. We conducted a meta-analysis using publicly available 16S rRNA gene datasets from the respiratory tract to characterize respiratory microbiota in feedlot cattle. Our aims were to determine the factors that influence microbiota development and to assess the differences in microbiota composition and diversity between healthy calves and those that developed bovine respiratory disease (BRD). Our results showed that the overall composition and diversity of respiratory microbiota in cattle were significantly affected by study design, 16S rRNA hypervariable region sequenced, health status, time since arrival to the feedlot, sampling sites in the respiratory tract and antibiotic treatment. Assessment of diversity indices showed a statistically significant difference between the BRD-affected cattle and healthy control calves. Using multivariate network analysis and Spearman's correlation analyses, we further distinguished the taxa that were commonly associated with BRD when the day of arrival to the feedlot was added to the model. The probability of being identified as BRD was significantly correlated with days 7, 12 and 14 following the calf's arrival to the feedlot. These findings could help in proposing strategies to further evaluate the link between respiratory microbiota and bovine respiratory health.
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Affiliation(s)
- Mohamed Zeineldin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA.,Department of Animal Medicine, College of Veterinary Medicine, Benha University, Banha, Al Qalyubia, 13511, Egypt
| | - Ahmed A Elolimy
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72002, USA.,Arkansas Children's Nutrition Center, Little Rock, AR, 72002, USA.,Department of Animal Production, National Research Centre, Giza,12622, Egypt
| | - Radwa Barakat
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
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9
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Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease. Microorganisms 2020; 8:microorganisms8071003. [PMID: 32635564 PMCID: PMC7409339 DOI: 10.3390/microorganisms8071003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/23/2020] [Accepted: 07/02/2020] [Indexed: 12/14/2022] Open
Abstract
Although the cystic fibrosis (CF) lung microbiota has been characterized in several studies, little is still known about the temporal changes occurring at the whole microbiome level using untargeted metagenomic analysis. The aim of this study was to investigate the taxonomic and functional temporal dynamics of the lower airway microbiome in a cohort of CF patients. Multiple sputum samples were collected over 15 months from 22 patients with advanced lung disease regularly attending three Italian CF Centers, given a total of 79 samples. DNA extracted from samples was subjected to shotgun metagenomic sequencing allowing both strain-level taxonomic profiling and assessment of the functional metagenomic repertoire. High inter-patient taxonomic heterogeneity was found with short-term compositional changes across clinical status. Each patient exhibited distinct sputum microbial communities at the taxonomic level, and strain-specific colonization of both traditional and atypical CF pathogens. A large core set of genes, including antibiotic resistance genes, were shared across patients despite observed differences in clinical status, and consistently detected in the lung microbiome of all subjects independently from known antibiotic exposure. In conclusion, an overall stability in the microbiome-associated genes was found despite taxonomic fluctuations of the communities.
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10
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Taylor SL, Leong LEX, Mobegi FM, Choo JM, Wesselingh S, Yang IA, Upham JW, Reynolds PN, Hodge S, James AL, Jenkins C, Peters MJ, Baraket M, Marks GB, Gibson PG, Rogers GB, Simpson JL. Long-Term Azithromycin Reduces Haemophilus influenzae and Increases Antibiotic Resistance in Severe Asthma. Am J Respir Crit Care Med 2020; 200:309-317. [PMID: 30875247 DOI: 10.1164/rccm.201809-1739oc] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Rationale: The macrolide antibiotic azithromycin reduces exacerbations in adults with persistent symptomatic asthma. However, owing to the pleotropic properties of macrolides, unintended bacteriological consequences such as augmented pathogen colonization or dissemination of antibiotic-resistant organisms can occur, calling into question the long-term safety of azithromycin maintenance therapy.Objectives: To assess the effects of azithromycin on the airway microbiota, pathogen abundance, and carriage of antibiotic resistance genes.Methods: 16S rRNA sequencing and quantitative PCR were performed to assess the effect of azithromycin on sputum microbiology from participants of the AMAZES (Asthma and Macrolides: The Azithromycin Efficacy and Safety) trial: a 48-week, double-blind, placebo-controlled trial of thrice-weekly 500 mg oral azithromycin in adults with persistent uncontrolled asthma. Pooled-template shotgun metagenomic sequencing, quantitative PCR, and isolate whole-genome sequencing were performed to assess antibiotic resistance.Measurements and Main Results: Paired sputum samples were available from 61 patients (n = 34 placebo, n = 27 azithromycin). Azithromycin did not affect bacterial load (P = 0.37) but did significantly decrease Faith's phylogenetic diversity (P = 0.026) and Haemophilus influenzae load (P < 0.0001). Azithromycin did not significantly affect levels of Streptococcus pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, or Moraxella catarrhalis. Of the 89 antibiotic resistance genes detected, five macrolide resistance genes and two tetracycline resistance genes were increased significantly.Conclusions: In patients with persistent uncontrolled asthma, azithromycin reduced airway H. influenzae load compared with placebo but did not change total bacterial load. Macrolide resistance increased, reflecting previous studies. These results highlight the need for studies assessing the efficacy of nonantibiotic macrolides as a long-term therapy for patients with persistent uncontrolled asthma.
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Affiliation(s)
- Steven L Taylor
- 1South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,2South Australian Health and Medical Research Institute Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Lex E X Leong
- 1South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,2South Australian Health and Medical Research Institute Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Fredrick M Mobegi
- 1South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,2South Australian Health and Medical Research Institute Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Jocelyn M Choo
- 1South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,2South Australian Health and Medical Research Institute Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Steve Wesselingh
- 1South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,2South Australian Health and Medical Research Institute Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Ian A Yang
- 3Faculty of Medicine, The University of Queensland, St. Lucia, Queensland, Australia.,4Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia
| | - John W Upham
- 3Faculty of Medicine, The University of Queensland, St. Lucia, Queensland, Australia.,5Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Paul N Reynolds
- 6Department of Thoracic Medicine, Lung Research Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia.,7School of Medicine, The University of Adelaide, Adelaide, South Australia, Australia
| | - Sandra Hodge
- 6Department of Thoracic Medicine, Lung Research Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia.,7School of Medicine, The University of Adelaide, Adelaide, South Australia, Australia
| | - Alan L James
- 8Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,9School of Medicine and Pharmacology, University of Western Australia, Crawley, Western Australia, Australia
| | - Christine Jenkins
- 10Respiratory Trials, The George Institute for Global Health, New South Wales, Australia.,11Department of Thoracic Medicine, Concord General Hospital, New South Wales, Australia
| | - Matthew J Peters
- 11Department of Thoracic Medicine, Concord General Hospital, New South Wales, Australia.,12Australian School of Advanced Medicine, Macquarie University, New South Wales, Australia
| | - Melissa Baraket
- 13Respiratory Medicine Department and Ingham Institute, Liverpool Hospital, New South Wales, Australia.,14South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales Australia
| | - Guy B Marks
- 13Respiratory Medicine Department and Ingham Institute, Liverpool Hospital, New South Wales, Australia.,14South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales Australia.,15Woolcock Institute of Medical Research, Glebe, New South Wales, Australia; and
| | - Peter G Gibson
- 15Woolcock Institute of Medical Research, Glebe, New South Wales, Australia; and.,16Respiratory and Sleep Medicine, Priority Research Centre for Healthy Lungs, The University of Newcastle, Callaghan, New South Wales, Australia
| | - Geraint B Rogers
- 1South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,2South Australian Health and Medical Research Institute Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Jodie L Simpson
- 16Respiratory and Sleep Medicine, Priority Research Centre for Healthy Lungs, The University of Newcastle, Callaghan, New South Wales, Australia
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11
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Allemann A, Kraemer JG, Korten I, Ramsey K, Casaulta C, Wüthrich D, Ramette A, Endimiani A, Latzin P, Hilty M. Nasal Resistome Development in Infants With Cystic Fibrosis in the First Year of Life. Front Microbiol 2019; 10:212. [PMID: 30863369 PMCID: PMC6399209 DOI: 10.3389/fmicb.2019.00212] [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: 07/18/2018] [Accepted: 01/24/2019] [Indexed: 12/20/2022] Open
Abstract
Polymicrobial infections of the respiratory tract due to antibiotic resistant bacteria are a great concern in patients with cystic fibrosis (CF). We therefore aimed at establishing a functional metagenomic method to analyze the nasal resistome in infants with CF within the first year of life. We included samples from patients before antibiotic treatment, which allowed obtaining information regarding natural status of the resistome. In total, we analyzed 130 nasal swabs from 26 infants with CF and screened for β-lactams (ampicillin, amoxicillin-clavulanic acid, and cefuroxime) and other classes of antibiotic resistances (tetracycline, chloramphenicol and trimethoprim-sulfamethoxazole). For 69 swabs (53% of total), we found at least one non-susceptible phenotype. Analyses of the inserts recovered from non-susceptible clones by nanopore MinION sequencing revealed a large reservoir of resistance genes including mobile elements within the antibiotic naïve samples. Comparing the data of the resistome with the microbiota composition showed that the bacterial phyla and operational taxonomic units (OTUs) of the microbiota rather than the antibiotic treatment were associated with the majority of non-susceptible phenotypes in the resistome. Future studies will reveal if characterization of the resistome can help in clinical decision-making in patients with CF.
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Affiliation(s)
- Aurélie Allemann
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Julia G Kraemer
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Institute for Work and Health (IST), University of Lausanne and University of Geneva, Epalinges, Switzerland
| | - Insa Korten
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.,Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Kathryn Ramsey
- Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Carmen Casaulta
- Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | | | - Daniel Wüthrich
- Applied Microbiology Research Unit, Department of Biomedicine, University of Basel, Basel, Switzerland.,Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Philipp Latzin
- Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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12
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Chang AB, Grimwood K. Contemporary Concise Review 2018: Bronchiectasis. Respirology 2019; 24:382-389. [PMID: 30743310 DOI: 10.1111/resp.13502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 01/27/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Anne B Chang
- Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, Brisbane, QLD, Australia.,Centre for Children's Health Research, Queensland University of Technology, Brisbane, QLD, Australia.,Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Keith Grimwood
- School of Medicine and Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia.,Department of Infectious Diseases, Gold Coast Health, Gold Coast, QLD, Australia.,Department of Paediatrics, Gold Coast Health, Gold Coast, QLD, Australia
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13
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Aliberti S, Chalmers JD. Get together to increase awareness in bronchiectasis: a report of the 2 nd World Bronchiectasis Conference. Multidiscip Respir Med 2018; 13:28. [PMID: 30151189 PMCID: PMC6101068 DOI: 10.1186/s40248-018-0138-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Stefano Aliberti
- Department of Pathophysiology and Transplantation, University of Milan, Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy
| | - James D. Chalmers
- Tayside Respiratory Research Group, University of Dundee, Dundee, DD1 9SY UK
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