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Vasiljevs S, Witney AA, Baines DL. The presence of cystic fibrosis-related diabetes modifies the sputum microbiome in cystic fibrosis disease. Am J Physiol Lung Cell Mol Physiol 2024; 326:L125-L134. [PMID: 38084404 DOI: 10.1152/ajplung.00219.2023] [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: 07/17/2023] [Revised: 10/30/2023] [Accepted: 11/23/2023] [Indexed: 01/24/2024] Open
Abstract
Cystic fibrosis-related diabetes (CFRD) affects 40%-50% of adults with CF and is associated with a decline in respiratory health. The microbial flora of the lung is known to change with the development of CF disease, but how CFRD affects the microbiome has not been described. We analyzed the microbiome in sputa from 14 people with CF, 14 with CFRD, and two who were classed as pre-CFRD by extracting DNA and amplifying the variable V3-V4 region of the microbial 16S ribosomal RNA gene by PCR. Sequences were analyzed and sources were identified to genus level. We found that the α-diversity of the microbiome using Shannon's diversity index was increased in CFRD compared with CF. Bray Curtis dissimilarity analysis showed that there was separation of the microbiomes in CF and CFRD sputa. The most abundant phyla identified in the sputum samples were Firmicutes and Proteobacteria, Actinobacteriota and Bacteroidota, and the ratio of Firmicutes/Bacteroidota was reduced in CFRD compared with CF. Pseudomonas, Azhorizophilus, Porphyromonas, and Actinobacillus were more abundant in CFRD compared with CF, whereas Staphylococcus was less abundant. The relative abundance of these genera did not correlate with age; some correlated with a decline in FEV1/FVC but all correlated with hemoglobin A1C (HbA1c) indicating that development of CFRD mediates further changes to the respiratory microbiome in CF.NEW & NOTEWORTHY Cystic fibrosis-related diabetes (CFRD) is associated with a decline in respiratory health. We show for the first time that there was a change in the sputum microbiome of people with CFRD compared with CF that correlated with markers of raised blood glucose.
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Affiliation(s)
- Stanislavs Vasiljevs
- Institute for Infection and Immunity, St George's, University of London, London, United Kingdom
| | - Adam A Witney
- Institute for Infection and Immunity, St George's, University of London, London, United Kingdom
| | - Deborah L Baines
- Institute for Infection and Immunity, St George's, University of London, London, United Kingdom
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Somayaji R, Thornton CS, Acosta N, Smith K, Clark J, Fatovich L, Thakrar MV, Parkins MD. Evaluating Sinus Microbiology by Transplant Status in Persons With Cystic Fibrosis: A Matched Cohort Study. OTO Open 2024; 8:e101. [PMID: 38317784 PMCID: PMC10840018 DOI: 10.1002/oto2.101] [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: 08/29/2023] [Revised: 10/31/2023] [Accepted: 12/02/2023] [Indexed: 02/07/2024] Open
Abstract
Objective Sinus disease is prevalent in persons with cystic fibrosis (PwCF) and may be a reservoir of airway infection in postlung transplant (pTx) patients. The microbial composition of cystic fibrosis sinuses and its associations with chronic rhinosinusitis (CRS) is relatively unexplored. We aimed to examine the sinus and lower airway microbiome and their associations with CRS in PwCF and pTxPwCF. Study Design Prospective single-centre study. Setting A total of 31 sex and age (±2 years) matched PwCF and pTxPwCF. Methods Demographic and clinical data along with sinus swabs and sputum were collected. CRS was assessed using Sinonasal Outcome Test-22 (SNOT-22) (patient reported outcome) and Lund-McKay (computed tomography sinus) scores. Samples underwent MiSeq Illumina sequencing of the universal 16S ribosomal RNA gene. Results A total of 31 PwCF (15 pTxPwCF) were included. Aggregate airways microbiome composition was dominated by Pseudomonas (46%), Haemophilus (14%), Staphylococcus (11%), Streptococcus (10%), and Fusobacterium (6%). α-diversity was significantly lower in post-Tx samples across both sputum and sinus samples (P = .005). β-diversity was significantly different between sputum (P = .004), but not sinus (P = .75) samples by transplant status. While there was a trend in higher β-diversity associated with lower SNOT-22 score at time of first visit, this did not reach significance (P = .05). Conclusion Sinus and airway microbiomes differed in PwCF and pTxPwCF, but the prevalent organisms remained consistent. Elucidating the relationship of the microbiome with clinical status to better understand when to intervene accordingly is needed to optimize sinus disease management in PwCF.
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Affiliation(s)
- Ranjani Somayaji
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
- Department of Medicine, Cumming School of Medicine, Alberta Health ServicesUniversity of CalgaryCalgaryCanada
- Snyder Institute for Chronic DiseasesUniversity of CalgaryCalgaryCanada
- Department of Community Health Sciences, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
| | - Christina S. Thornton
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
- Department of Medicine, Cumming School of Medicine, Alberta Health ServicesUniversity of CalgaryCalgaryCanada
- Snyder Institute for Chronic DiseasesUniversity of CalgaryCalgaryCanada
| | - Nicola Acosta
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
| | - Kristine Smith
- Department of Otolaryngology–Head and Neck surgeryUniversity of UtahSalt Lake CityUtahUSA
| | - Jessica Clark
- Department of Surgery, Otolaryngology–Head and Neck Surgery, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
| | - Linda Fatovich
- Department of Medicine, Cumming School of Medicine, Alberta Health ServicesUniversity of CalgaryCalgaryCanada
| | - Mitesh V. Thakrar
- Department of Medicine, Cumming School of Medicine, Alberta Health ServicesUniversity of CalgaryCalgaryCanada
| | - Michael D. Parkins
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
- Department of Medicine, Cumming School of Medicine, Alberta Health ServicesUniversity of CalgaryCalgaryCanada
- Snyder Institute for Chronic DiseasesUniversity of CalgaryCalgaryCanada
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Wagner BD, Zemanick ET, Sagel SD, Robertson CE, Stevens MJ, Mayer-Hamblett N, Retsch-Bogart G, Ramsey BW, Harris JK. Limited effects of azithromycin on the oropharyngeal microbiome in children with CF and early pseudomonas infection. BMC Microbiol 2023; 23:312. [PMID: 37891457 PMCID: PMC10612347 DOI: 10.1186/s12866-023-03073-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Tobramycin inhalation solution (TIS) and chronic azithromycin (AZ) have known clinical benefits for children with CF, likely due to antimicrobial and anti-inflammatory activity. The effects of chronic AZ in combination with TIS on the airway microbiome have not been extensively investigated. Oropharyngeal swab samples were collected in the OPTIMIZE multicenter, randomized, placebo-controlled trial examining the addition of AZ to TIS in 198 children with CF and early P. aeruginosa infection. Bacterial small subunit rRNA gene community profiles were determined. The effects of TIS and AZ were assessed on oropharyngeal microbial diversity and composition to uncover whether effects on the bacterial community may be a mechanism of action related to the observed changes in clinical outcomes. RESULTS Substantial changes in bacterial communities (total bacterial load, diversity and relative abundance of specific taxa) were observed by week 3 of TIS treatment for both the AZ and placebo groups. On average, these shifts were due to changes in non-traditional CF taxa that were not sustained at the later study visits (weeks 13 and 26). Bacterial community measures did not differ between the AZ and placebo groups. CONCLUSIONS This study provides further evidence that the mechanism for AZ's effect on clinical outcomes is not due solely to action on airway microbial composition.
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Affiliation(s)
- Brandie D Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA.
- Children's Hospital Colorado, Aurora, CO, USA.
| | - Edith T Zemanick
- Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - Scott D Sagel
- Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | | | - Mark J Stevens
- Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - Nicole Mayer-Hamblett
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Seattle Children's Hospital, Seattle, WA, USA
| | | | - Bonnie W Ramsey
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Seattle Children's Hospital, Seattle, WA, USA
| | - J Kirk Harris
- Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Aurora, CO, USA
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Hong G, Daniel SG, Lee JJ, Bittinger K, Glaser L, Mattei LM, Dorgan DJ, Hadjiliadis D, Kawut SM, Collman RG. Distinct community structures of the fungal microbiome and respiratory health in adults with cystic fibrosis. J Cyst Fibros 2023; 22:636-643. [PMID: 36822979 PMCID: PMC10440372 DOI: 10.1016/j.jcf.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/05/2023] [Accepted: 02/06/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND The respiratory tract fungal microbiome in cystic fibrosis (CF) has been understudied despite increasing recognition of fungal pathogens in CF lung disease. We sought to better understand the fungal communities in adults with CF, and to define relationships between fungal profiles and clinical characteristics. METHODS We enrolled 66 adults with CF and collected expectorated sputum, spirometry, Cystic Fibrosis Questionnaire-revised, and clinical data. Fungi were molecularly profiled by sequencing of the internal transcribed spacer (ITS) region. Total fungal abundance was measured by quantitative PCR. Relative abundance and qPCR-corrected abundances were determined. Selective fungus culture identified cultivable fungi. Alpha diversity and beta diversity were measured and relationships with clinical parameters were interrogated. RESULTS Median age was 29 years and median FEV1 percent predicted 58%. Members of the Candida genus were the most frequent dominant taxa in CF sputum. Apiotrichum, Trichosporon, Saccharomyces cerevisiae, and Scedosporium were present in high relative abundance in few samples; whereas, Aspergillus species were detected at low levels. Higher FEV1% predicted and CFTR modulator use were associated with greater alpha-diversity. Chronic azithromycin use was associated with lower alpha-diversity. Patients with acute pulmonary had distinct fungal community composition compared to clinically stable subjects. Differing yeast species were mainly responsible for the community differences. CONCLUSION The respiratory tract fungal microbiome in adults with CF is associated with lung function, pulmonary exacerbation status, macrolide use, and CFTR modulator use. Future work to better understand fungal diversity in the CF airway and its impact on lung health is necessary.
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Affiliation(s)
- Gina Hong
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of.
| | - Scott G Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Jung-Jin Lee
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Laurel Glaser
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Lisa M Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Daniel J Dorgan
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
| | - Denis Hadjiliadis
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
| | - Steven M Kawut
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
| | - Ronald G Collman
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
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Caparrós-Martín JA, Saladie M, Agudelo-Romero SP, Reen FJ, Ware RS, Sly PD, Stick SM, O'Gara F. Detection of bile acids in bronchoalveolar lavage fluid defines the inflammatory and microbial landscape of the lower airways in infants with cystic fibrosis. MICROBIOME 2023; 11:132. [PMID: 37312128 DOI: 10.1186/s40168-023-01543-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 04/05/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND Cystic Fibrosis (CF) is a genetic condition characterized by neutrophilic inflammation and recurrent infection of the airways. How these processes are initiated and perpetuated in CF remains largely unknown. We have demonstrated a link between the intestinal microbiota-related metabolites bile acids (BA) and inflammation in the bronchoalveolar lavage fluid (BALF) from children with stable CF lung disease. To establish if BA indicate early pathological processes in CF lung disease, we combined targeted mass spectrometry and amplicon sequencing-based microbial characterization of 121 BALF specimens collected from 12-month old infants with CF enrolled in the COMBAT-CF study, a multicentre randomized placebo-controlled clinical trial comparing azithromycin versus placebo. We evaluated whether detection of BA in BALF is associated with the establishment of the inflammatory and microbial landscape of early CF lung disease, and whether azithromycin, a motilin agonist that has been demonstrated to reduce aspiration of gastric contents, alters the odds of detecting BA in BALF. We also explored how different prophylactic antibiotics regimens impact the early life BALF microbiota. RESULTS Detection of BA in BALF was strongly associated with biomarkers of airway inflammation, more exacerbation episodes during the first year of life, increased use of oral antibiotics with prolonged treatment periods, a higher degree of structural lung damage, and distinct microbial profiles. Treatment with azithromycin, a motilin agonist, which has been reported to reduce aspiration of gastric contents, did not reduce the odds of detecting BA in BALF. Culture and molecular methods showed that azithromycin does not alter bacterial load or diversity in BALF. Conversely, penicillin-type prophylaxis reduced the odds of detecting BAs in BALF, which was associated with elevated levels of circulating biomarkers of cholestasis. We also observed that environmental factors such as penicillin-type prophylaxis or BAs detection were linked to distinct early microbial communities of the CF airways, which were associated with different inflammatory landscapes but not with structural lung damage. CONCLUSIONS Detection of BA in BALF portend early pathological events in CF lung disease. Benefits early in life associated with azithromycin are not linked to its antimicrobial properties. Video Abstract.
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Affiliation(s)
- Jose A Caparrós-Martín
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia
- Curtin Health Innovation Research Institute (CHIRI), Curtin University, Perth, WA, Australia
| | - Montserrat Saladie
- Curtin Health Innovation Research Institute (CHIRI), Curtin University, Perth, WA, Australia
- Present Address: Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira I Virgili-EURECAT, Reus, Spain
| | - S Patricia Agudelo-Romero
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - F Jerry Reen
- School of Microbiology, University College Cork, Cork, Ireland
- Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland
| | - Robert S Ware
- Menzies Health Institute Queensland, Griffith University, Brisbane, Australia
| | - Peter D Sly
- Children's Health and Environment Program, Child Health Research Centre, The University of Queensland, Brisbane, Australia
| | - Stephen M Stick
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
- Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, WA, Australia
| | - Fergal O'Gara
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia.
- Curtin Health Innovation Research Institute (CHIRI), Curtin University, Perth, WA, Australia.
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, T12 K8AF, Ireland.
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6
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Thornton CS, Parkins MD. Microbial Epidemiology of the Cystic Fibrosis Airways: Past, Present, and Future. Semin Respir Crit Care Med 2023; 44:269-286. [PMID: 36623820 DOI: 10.1055/s-0042-1758732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Progressive obstructive lung disease secondary to chronic airway infection, coupled with impaired host immunity, is the leading cause of morbidity and mortality in cystic fibrosis (CF). Classical pathogens found in the airways of persons with CF (pwCF) include Pseudomonas aeruginosa, Staphylococcus aureus, the Burkholderia cepacia complex, Achromobacter species, and Haemophilus influenzae. While traditional respiratory-tract surveillance culturing has focused on this limited range of pathogens, the use of both comprehensive culture and culture-independent molecular approaches have demonstrated complex highly personalized microbial communities. Loss of bacterial community diversity and richness, counteracted with relative increases in dominant taxa by traditional CF pathogens such as Burkholderia or Pseudomonas, have long been considered the hallmark of disease progression. Acquisition of these classic pathogens is viewed as a harbinger of advanced disease and postulated to be driven in part by recurrent and frequent antibiotic exposure driven by frequent acute pulmonary exacerbations. Recently, CF transmembrane conductance regulator (CFTR) modulators, small molecules designed to potentiate or restore diminished protein levels/function, have been successfully developed and have profoundly influenced disease course. Despite the multitude of clinical benefits, structural lung damage and consequent chronic airway infection persist in pwCF. In this article, we review the microbial epidemiology of pwCF, focus on our evolving understanding of these infections in the era of modulators, and identify future challenges in infection surveillance and clinical management.
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Affiliation(s)
- Christina S Thornton
- Department of Medicine, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Michael D Parkins
- Department of Medicine, Cumming School of Medicine, University of Calgary, Alberta, Canada.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Alberta, Canada
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Abotsi RE, Dube FS, Rehman AM, Claassen-Weitz S, Xia Y, Simms V, Mwaikono KS, Gardner-Lubbe S, McHugh G, Ngwira LG, Kwambana-Adams B, Heyderman RS, Odland JØ, Ferrand RA, Nicol MP. Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease. MICROBIOME 2023; 11:29. [PMID: 36803868 PMCID: PMC9940396 DOI: 10.1186/s40168-023-01460-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Long-term azithromycin (AZM) treatment reduces the frequency of acute respiratory exacerbation in children and adolescents with HIV-associated chronic lung disease (HCLD). However, the impact of this treatment on the respiratory bacteriome is unknown. METHOD African children with HCLD (defined as forced expiratory volume in 1 s z-score (FEV1z) less than - 1.0 with no reversibility) were enrolled in a placebo-controlled trial of once-weekly AZM given for 48-weeks (BREATHE trial). Sputum samples were collected at baseline, 48 weeks (end of treatment) and 72 weeks (6 months post-intervention in participants who reached this timepoint before trial conclusion). Sputum bacterial load and bacteriome profiles were determined using 16S rRNA gene qPCR and V4 region amplicon sequencing, respectively. The primary outcomes were within-participant and within-arm (AZM vs placebo) changes in the sputum bacteriome measured across baseline, 48 weeks and 72 weeks. Associations between clinical or socio-demographic factors and bacteriome profiles were also assessed using linear regression. RESULTS In total, 347 participants (median age: 15.3 years, interquartile range [12.7-17.7]) were enrolled and randomised to AZM (173) or placebo (174). After 48 weeks, participants in the AZM arm had reduced sputum bacterial load vs placebo arm (16S rRNA copies/µl in log10, mean difference and 95% confidence interval [CI] of AZM vs placebo - 0.54 [- 0.71; - 0.36]). Shannon alpha diversity remained stable in the AZM arm but declined in the placebo arm between baseline and 48 weeks (3.03 vs. 2.80, p = 0.04, Wilcoxon paired test). Bacterial community structure changed in the AZM arm at 48 weeks compared with baseline (PERMANOVA test p = 0.003) but resolved at 72 weeks. The relative abundances of genera previously associated with HCLD decreased in the AZM arm at 48 weeks compared with baseline, including Haemophilus (17.9% vs. 25.8%, p < 0.05, ANCOM ω = 32) and Moraxella (1% vs. 1.9%, p < 0.05, ANCOM ω = 47). This reduction was sustained at 72 weeks relative to baseline. Lung function (FEV1z) was negatively associated with bacterial load (coefficient, [CI]: - 0.09 [- 0.16; - 0.02]) and positively associated with Shannon diversity (0.19 [0.12; 0.27]). The relative abundance of Neisseria (coefficient, [standard error]: (2.85, [0.7], q = 0.01), and Haemophilus (- 6.1, [1.2], q < 0.001) were positively and negatively associated with FEV1z, respectively. An increase in the relative abundance of Streptococcus from baseline to 48 weeks was associated with improvement in FEV1z (3.2 [1.11], q = 0.01) whilst an increase in Moraxella was associated with decline in FEV1z (-2.74 [0.74], q = 0.002). CONCLUSIONS AZM treatment preserved sputum bacterial diversity and reduced the relative abundances of the HCLD-associated genera Haemophilus and Moraxella. These bacteriological effects were associated with improvement in lung function and may account for reduced respiratory exacerbations associated with AZM treatment of children with HCLD. Video Abstract.
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Affiliation(s)
- Regina E Abotsi
- Department of Molecular and Cell Biology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Felix S Dube
- Department of Molecular and Cell Biology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Andrea M Rehman
- International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
| | - Shantelle Claassen-Weitz
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yao Xia
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Victoria Simms
- International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
- Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Kilaza S Mwaikono
- Computational Biology Group and H3ABioNet, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Department of Science and Laboratory Technology, Dar es Salaam Institute of Technology, Dar es Salaam, Tanzania
| | - Sugnet Gardner-Lubbe
- Department of Statistics and Actuarial Science, Stellenbosch University, Stellenbosch, South Africa
| | - Grace McHugh
- Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Lucky G Ngwira
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Robert S Heyderman
- NIHR Global Health Research Unit on Mucosal Pathogens, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Jon Ø Odland
- Department of Community Medicine, University of Tromsø, Tromsø, Norway
- International Research Laboratory for Reproductive Ecotoxicology (IL RET), The National Research University Higher School of Economics, Moscow, Russia
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Rashida A Ferrand
- Biomedical Research and Training Institute, Harare, Zimbabwe
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Mark P Nicol
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia.
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Jean-Pierre F, Hampton TH, Schultz D, Hogan DA, Groleau MC, Déziel E, O'Toole GA. Community composition shapes microbial-specific phenotypes in a cystic fibrosis polymicrobial model system. eLife 2023; 12:81604. [PMID: 36661299 PMCID: PMC9897730 DOI: 10.7554/elife.81604] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 01/19/2023] [Indexed: 01/21/2023] Open
Abstract
Interspecies interactions can drive the emergence of unexpected microbial phenotypes that are not observed when studying monocultures. The cystic fibrosis (CF) lung consists of a complex environment where microbes, living as polymicrobial biofilm-like communities, are associated with negative clinical outcomes for persons with CF (pwCF). However, the current lack of in vitro models integrating the microbial diversity observed in the CF airway hampers our understanding of why polymicrobial communities are recalcitrant to therapy in this disease. Here, integrating computational approaches informed by clinical data, we built a mixed community of clinical relevance to the CF lung composed of Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sanguinis, and Prevotella melaninogenica. We developed and validated this model biofilm community with multiple isolates of these four genera. When challenged with tobramycin, a front-line antimicrobial used to treat pwCF, the microorganisms in the polymicrobial community show altered sensitivity to this antibiotic compared to monospecies biofilms. We observed that wild-type P. aeruginosa is sensitized to tobramycin in a mixed community versus monoculture, and this observation holds across a range of community relative abundances. We also report that LasR loss-of-function, a variant frequently detected in the CF airway, drives tolerance of P. aeruginosa to tobramycin specifically in the mixed community. Our data suggest that the molecular basis of this community-specific recalcitrance to tobramycin for the P. aeruginosa lasR mutant is increased production of phenazines. Our work supports the importance of studying a clinically relevant model of polymicrobial biofilms to understand community-specific traits relevant to infections.
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Affiliation(s)
- Fabrice Jean-Pierre
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
| | - Marie-Christine Groleau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche ScientifiqueLavalCanada
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche ScientifiqueLavalCanada
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
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Ishimoto H, Sakamoto N, Hara A, Kido T, Yamaguchi H, Yamamoto K, Obase Y, Ishimatsu Y, Mukae H. Interstitial Pneumonia with HLA-B54 Antigen that Responded Well to Erythromycin. Intern Med 2022; 61:3559-3562. [PMID: 35466169 PMCID: PMC9790779 DOI: 10.2169/internalmedicine.9304-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A 65-year-old Japanese man with interstitial pneumonia demonstrated honeycomb lung with thickened walls on chest high-resolution computed tomography (HRCT) and predominance of neutrophils in the cell fraction of the bronchoalveolar lavage fluid. Although there were no centrilobular nodular or branching shadows on chest HRCT suggestive of diffuse panbronchiolitis, he exhibited sinusitis and had the human leukocyte antigen (HLA)-B54 antigen. With long-term macrolide therapy, the cough and sputum production markedly improved, wall thickening of the honeycomb lung on chest HRCT decreased, and the forced vital capacity increased. Confirming the presence of HLA-B54 antigen may help determine the indication for long-term macrolide therapy in interstitial pneumonia patients.
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Affiliation(s)
- Hiroshi Ishimoto
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Japan
| | - Noriho Sakamoto
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Japan
| | - Atsuko Hara
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Japan
| | - Takashi Kido
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Japan
| | - Hiroyuki Yamaguchi
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Japan
| | - Kazuko Yamamoto
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Japan
| | - Yasushi Obase
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Japan
| | - Yuji Ishimatsu
- Department of Nursing, Nagasaki University Graduate School of Biomedical Sciences, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Japan
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Kussek P, Mesa D, Vasconcelos TM, Rodrigues LS, Krul D, Ibanez H, Faoro H, Palmeiro JK, Dalla Costa LM. Lower airway microbiota and decreasing lung function in young Brazilian cystic fibrosis patients with pulmonary Staphylococcus and Pseudomonas infection. PLoS One 2022; 17:e0273453. [PMID: 36006942 PMCID: PMC9409528 DOI: 10.1371/journal.pone.0273453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 08/08/2022] [Indexed: 11/30/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator gene that leads to respiratory complications and mortality. Studies have shown shifts in the respiratory microbiota during disease progression in individuals with CF. In addition, CF patients experience short cycles of acute intermittent aggravations of symptoms called pulmonary exacerbations, which may be characterized by a decrease in lung function and weight loss. The resident microbiota become imbalanced, promoting biofilm formation, and reducing the effectiveness of therapy. The aim of this study was to monitor patients aged 8–23 years with CF to evaluate their lower respiratory microbiota using 16S rRNA sequencing. The most predominant pathogens observed in microbiota, Staphylococcus (Staph) and Pseudomonas (Pseud) were correlated with clinical variables, and the in vitro capacity of biofilm formation for these pathogens was tested. A group of 34 patients was followed up for 84 days, and 306 sputum samples were collected and sequenced. Clustering of microbiota by predominant pathogen showed that children with more Staph had reduced forced expiratory volume in one second (FEV1) and forced vital capacity (FVC) compared to children with Pseud. Furthermore, the patients’ clinical condition was consistent with the results of pulmonary function. More patients with pulmonary exacerbation were observed in the Staph group than in the Pseud group, as confirmed by lower body mass index and pulmonary function. Additionally, prediction of bacterial functional profiles identified genes encoding key enzymes involved in virulence pathways in the Pseud group. Importantly, this study is the first Brazilian study to assess the lower respiratory microbiota in a significant group of young CF patients. In this sense, the data collected for this study on the microbiota of children in Brazil with CF provide a valuable contribution to the knowledge in the field.
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Affiliation(s)
- Paulo Kussek
- Hospital Pequeno Príncipe, Curitiba, Paraná, Brazil
| | - Dany Mesa
- Big Data Center, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, Brazil
- * E-mail: (LMDC); (DM)
| | | | | | - Damaris Krul
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, Brazil
| | - Humberto Ibanez
- Big Data Center, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, Brazil
| | | | - Jussara Kasuko Palmeiro
- Departamento de Análises Clínicas, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
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Assessment of Long-Term Macrolide Exposure on the Oropharyngeal Microbiome and Macrolide Resistance in Healthy Adults and Consequences for Onward Transmission of Resistance. Antimicrob Agents Chemother 2022; 66:e0224621. [PMID: 35293783 DOI: 10.1128/aac.02246-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
While the use of long-term macrolide therapy to prevent exacerbations in chronic respiratory diseases is widespread, its impact on the oropharyngeal microbiota and macrolide resistance, and the potential for onward transmission of resistance to close contacts are poorly understood. We determined the effects of long-term exposure to azithromycin or erythromycin on phenotypic and genotypic macrolide resistance within the oropharyngeal microbiome of healthy adults and their close contacts in a randomized, single-blinded, parallel-group trial of 4 weeks of twice-daily oral 400 mg erythromycin ethylsuccinate or twice-daily oral 125 mg azithromycin. Using oropharyngeal swabs collected from 20 index healthy adults and 20 paired close contacts, the oropharyngeal microbial composition and macrolide resistance in streptococci were assessed by 16S rRNA sequencing and antibiotic susceptibility testing of oropharyngeal cultures, respectively, at baseline and weeks 4 and 8 (washout). Targeted quantitative PCR of antibiotic resistance genes was performed to evaluate paired changes in resistance gene levels in index patients and close contacts and to relate the potential transmission of antibiotic resistance. Neither azithromycin nor erythromycin altered oropharyngeal microbiota characteristics significantly. Proportional macrolide resistance in oropharyngeal streptococci increased with both erythromycin and azithromycin, remaining above baseline levels for the azithromycin group at washout. Levels of resistance genes increased significantly with azithromycin[erm(B) and mef] and erythromycin (mef), returning to baseline levels at washout only for the erythromycin group. We found no evidence of onward transmission of resistance to close contacts, as indicated by the lack of concomitant changes in resistance gene levels detected in close contacts. (This study has been registered with the Australian and New Zealand Clinical Trials Registry under identifier ACTRN12617000278336.).
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