An invisible threat? Aspergillus positive cultures and co-infecting bacteria in airway samples

Hughes, D.; Rosenthal, Mark; Cuthbertson, Leah; Ramadan, Newara; Felton, Imogen; Simmonds, Nicholas J.; Loebinger, Michael R.; Price, Henry; Armstrong‐James, Darius; Elborn, J.S.; Cookson, William; Moffatt, Miriam F.; Davies, Jane C.

doi:10.1016/j.jcf.2022.07.009

Cited by 2 publications

(3 citation statements)

References 38 publications

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“…In a clinical context, pathogen infection status in CF is based on culture-based presence-absence data alone and does not incorporate measures of pathogen abundance [ 4 ]. Moreover, culture has recently been found to significantly underestimate lung pathogen detection and chronic infection status in CF [ 3 , 43 , 44 ]. Here we found that bacterial taxa chronically infecting a patient were both persistent and common, whereas intermittent taxa were typically infrequent and rare.…”

Section: Discussionmentioning

confidence: 99%

“…Combined, this study further illustrates the inadequacy of traditional ‘one microbe, one disease’ models of lung microbiology and infection pathogenesis. While culture has been useful for clinical microbiological surveillance, it has repeatedly been shown to be both limited and biased in CF, e.g., [ 3 , 43 , 44 ]. Given the unquestionable polymicrobial nature of CF lung infection, it is sensible to recommend using molecular approaches that can define all microbial species within a patient’s lung infection microbiota.…”

Section: Discussionmentioning

confidence: 99%

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Ecological patterns and processes of temporal turnover within lung infection microbiota

Gavillet,

Hatfield,

Jones

et al. 2024

Microbiome

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Background Chronic infection and consequent airway inflammation are the leading causes of morbidity and early mortality for people living with cystic fibrosis (CF). However, lower airway infections across a range of chronic respiratory diseases, including in CF, do not follow classical ‘one microbe, one disease’ concepts of infection pathogenesis. Instead, they are comprised of diverse and temporally dynamic lung infection microbiota. Consequently, temporal dynamics need to be considered when attempting to associate lung microbiota with changes in disease status. Set within an island biogeography framework, we aimed to determine the ecological patterns and processes of temporal turnover within the lung microbiota of 30 paediatric and adult CF patients prospectively sampled over a 3-year period. Moreover, we aimed to ascertain the contributions of constituent chronic and intermittent colonizers on turnover within the wider microbiota. Results The lung microbiota within individual patients was partitioned into constituent chronic and intermittent colonizing groups using the Leeds criteria and visualised with persistence-abundance relationships. This revealed bacteria chronically infecting a patient were both persistent and common through time, whereas intermittently infecting taxa were infrequent and rare; respectively representing the resident and transient portions of the wider microbiota. It also indicated that the extent of chronic colonization was far greater than could be appreciated with microbiological culture alone. Using species-time relationships to measure temporal turnover and Vellend’s rationalized ecological processes demonstrated turnover in the resident chronic infecting groups was conserved and underpinned principally by the deterministic process of homogenizing dispersal. Conversely, intermittent colonizing groups, representing newly arrived immigrants and transient species, drove turnover in the wider microbiota and were predominately underpinned by the stochastic process of drift. For adult patients, homogenizing dispersal and drift were found to be significantly associated with lung function. Where a greater frequency of homogenizing dispersal was observed with worsening lung function and conversely drift increased with better lung function. Conclusions Our work provides a novel ecological framework for understanding the temporal dynamics of polymicrobial infection in CF that has translational potential to guide and improve therapeutic targeting of lung microbiota in CF and across a range of chronic airway diseases.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Ecological patterns and processes of temporal turnover within lung infection microbiota

Gavillet,

Hatfield,

Jones

et al. 2024

Microbiome

View full text Add to dashboard Cite

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“…A recent study carried out by Hughes et al . established that using culture-based methodologies, the known CF pathogens, Pseudomonas aeruginosa and Aspergillus fumigatus are rarely cultured from the same sample (32). Despite this, our culture independent techniques clearly show the common presence of both Pseudomonas aeruginosa and Aspergillus fumigatus reads in the samples.…”

Section: Discussionmentioning

confidence: 99%

Cross-kingdom analysis of microbial communities in Cystic Fibrosis and Bronchiectasis

Cuthbertson

Ish-Horowicz

Felton

et al. 2022

Preprint

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Background: Cystic fibrosis (CF) and non-CF bronchiectasis (BX) are lung diseases characterised by severe chronic infections. Fungal and bacterial components of infection are both recognized. Recent molecular investigation of sputum from patients with CF and BX has revealed a complex mycobiome. However, little is known about how fungal and bacterial organisms interact or whether the interactions impact on disease outcomes. Methods: Quantitative PCR and next generation sequencing of ITS2 and 16S rRNA gene was carried out on 107 patients with CF and BX and defined clinical fungal infection status. Fungal and bacterial communities were explored using supervised and unsupervised machine learning to understand associations between fungal and bacterial communities and their relationship to disease. Results: Fungal and bacterial communities both had significantly higher biomass and lower diversity in CF compared to BX patients. Random forest modelling demonstrated that the fungal and bacterial communities were distinct between CF and BX patients. Within the CF group, bacterial communities contained no predictive signal for fungal disease status. Neither bacterial nor fungal community composition were predictive of the presence of CF pulmonary exacerbation (CFPE). Intra-kingdom correlations were far stronger than those between the two kingdoms. Dirichlet mixture components analysis identified two distinct clusters of bacteria related to the relative abundance of Pseudomonas. Fungal community composition contained no predictive signal for bacterial clusters. Conclusions: Clear changes in diversity were observed between patients with different clinical disease status. Although our results demonstrate that bacterial community composition differs in the presence of fungal disease, no direct relationship between bacterial and fungal OTUs was found.

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An invisible threat? Aspergillus positive cultures and co-infecting bacteria in airway samples

Cited by 2 publications

References 38 publications

Ecological patterns and processes of temporal turnover within lung infection microbiota

Ecological patterns and processes of temporal turnover within lung infection microbiota

Cross-kingdom analysis of microbial communities in Cystic Fibrosis and Bronchiectasis

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