Assessment of stability and fluctuations of cultured lower airway bacterial communities in people with cystic fibrosis

Laura J Sherrard, Gisli G Einarsson, Elinor Johnston, Katherine O'Neill, Leanne McIlreavey, Stephanie J McGrath, Deirdre F Gilpin, Damian G Downey, Alastair Reid, Noel G McElvaney, Richard C Boucher, Marianne S Muhlebach, J. Stuart Elborn, Michael M Tunney

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Abstract

BACKGROUND: Routine clinical culture detects a subset of the cystic fibrosis (CF) airways microbiota based on culture-independent (molecular) methods. This study aimed to determine how extended sputum culture of viable bacteria changes over time in relation to clinical status and predicts exacerbations.

METHODS: Sputa from patients at a baseline stable and up to three subsequent time-points were analysed by extended-quantitative culture; aerobe/anaerobe densities, ecological indexes and community structure were assessed together with clinical outcomes.

RESULTS: Eighty patients were prospectively recruited. Sputa were successfully collected and cultured at 199/267 (74.5%) study visits. Eighty-two sputa from 25 patients comprised a complete sample-set for longitudinal analyses. Bacterial density, ecological indexes and clinical outcomes were unchanged in 18 patients with three sequential stable visits. Conversely, in 7 patients who had an exacerbation, total bacterial and aerobe densities differed over four study visits (P < .001) with this difference particularly apparent between the baseline visit and completion of acute antibiotic treatment where a decrease in density was observed. Bacterial communities were more similar within than between patients but stable patients had the least variation in community structure over time. Using logistic regression in a further analysis, baseline features in 37 patients without compared to 15 patients with a subsequent exacerbation showed that clinical measures rather than bacterial density or ecological indexes were independent predictors of an exacerbation.

CONCLUSIONS: Greater fluctuation in the viable bacterial community during treatment of an exacerbation than between stable visits was observed. Extended-quantitative culture did not provide prognostic information of a future exacerbation.

LanguageEnglish
JournalJournal of cystic fibrosis : official journal of the European Cystic Fibrosis Society
Early online date21 Mar 2019
DOIs
Publication statusEarly online date - 21 Mar 2019

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Cystic Fibrosis
Sputum
Biota
Microbiota
Logistic Models
Anti-Bacterial Agents
Bacteria
Therapeutics

Bibliographical note

Copyright © 2019 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Cite this

@article{09cbdc53783846feaf420e74cdc2cf91,
title = "Assessment of stability and fluctuations of cultured lower airway bacterial communities in people with cystic fibrosis",
abstract = "BACKGROUND: Routine clinical culture detects a subset of the cystic fibrosis (CF) airways microbiota based on culture-independent (molecular) methods. This study aimed to determine how extended sputum culture of viable bacteria changes over time in relation to clinical status and predicts exacerbations.METHODS: Sputa from patients at a baseline stable and up to three subsequent time-points were analysed by extended-quantitative culture; aerobe/anaerobe densities, ecological indexes and community structure were assessed together with clinical outcomes.RESULTS: Eighty patients were prospectively recruited. Sputa were successfully collected and cultured at 199/267 (74.5{\%}) study visits. Eighty-two sputa from 25 patients comprised a complete sample-set for longitudinal analyses. Bacterial density, ecological indexes and clinical outcomes were unchanged in 18 patients with three sequential stable visits. Conversely, in 7 patients who had an exacerbation, total bacterial and aerobe densities differed over four study visits (P < .001) with this difference particularly apparent between the baseline visit and completion of acute antibiotic treatment where a decrease in density was observed. Bacterial communities were more similar within than between patients but stable patients had the least variation in community structure over time. Using logistic regression in a further analysis, baseline features in 37 patients without compared to 15 patients with a subsequent exacerbation showed that clinical measures rather than bacterial density or ecological indexes were independent predictors of an exacerbation.CONCLUSIONS: Greater fluctuation in the viable bacterial community during treatment of an exacerbation than between stable visits was observed. Extended-quantitative culture did not provide prognostic information of a future exacerbation.",
author = "Sherrard, {Laura J} and Einarsson, {Gisli G} and Elinor Johnston and Katherine O'Neill and Leanne McIlreavey and McGrath, {Stephanie J} and Gilpin, {Deirdre F} and Downey, {Damian G} and Alastair Reid and McElvaney, {Noel G} and Boucher, {Richard C} and Muhlebach, {Marianne S} and Elborn, {J. Stuart} and Tunney, {Michael M}",
note = "Copyright {\circledC} 2019 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.",
year = "2019",
month = "3",
day = "21",
doi = "10.1016/j.jcf.2019.02.012",
language = "English",
journal = "Journal of Cystic Fibrosis",
issn = "1569-1993",
publisher = "Elsevier Inc.",

}

TY - JOUR

T1 - Assessment of stability and fluctuations of cultured lower airway bacterial communities in people with cystic fibrosis

AU - Sherrard, Laura J

AU - Einarsson, Gisli G

AU - Johnston, Elinor

AU - O'Neill, Katherine

AU - McIlreavey, Leanne

AU - McGrath, Stephanie J

AU - Gilpin, Deirdre F

AU - Downey, Damian G

AU - Reid, Alastair

AU - McElvaney, Noel G

AU - Boucher, Richard C

AU - Muhlebach, Marianne S

AU - Elborn, J. Stuart

AU - Tunney, Michael M

N1 - Copyright © 2019 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

PY - 2019/3/21

Y1 - 2019/3/21

N2 - BACKGROUND: Routine clinical culture detects a subset of the cystic fibrosis (CF) airways microbiota based on culture-independent (molecular) methods. This study aimed to determine how extended sputum culture of viable bacteria changes over time in relation to clinical status and predicts exacerbations.METHODS: Sputa from patients at a baseline stable and up to three subsequent time-points were analysed by extended-quantitative culture; aerobe/anaerobe densities, ecological indexes and community structure were assessed together with clinical outcomes.RESULTS: Eighty patients were prospectively recruited. Sputa were successfully collected and cultured at 199/267 (74.5%) study visits. Eighty-two sputa from 25 patients comprised a complete sample-set for longitudinal analyses. Bacterial density, ecological indexes and clinical outcomes were unchanged in 18 patients with three sequential stable visits. Conversely, in 7 patients who had an exacerbation, total bacterial and aerobe densities differed over four study visits (P < .001) with this difference particularly apparent between the baseline visit and completion of acute antibiotic treatment where a decrease in density was observed. Bacterial communities were more similar within than between patients but stable patients had the least variation in community structure over time. Using logistic regression in a further analysis, baseline features in 37 patients without compared to 15 patients with a subsequent exacerbation showed that clinical measures rather than bacterial density or ecological indexes were independent predictors of an exacerbation.CONCLUSIONS: Greater fluctuation in the viable bacterial community during treatment of an exacerbation than between stable visits was observed. Extended-quantitative culture did not provide prognostic information of a future exacerbation.

AB - BACKGROUND: Routine clinical culture detects a subset of the cystic fibrosis (CF) airways microbiota based on culture-independent (molecular) methods. This study aimed to determine how extended sputum culture of viable bacteria changes over time in relation to clinical status and predicts exacerbations.METHODS: Sputa from patients at a baseline stable and up to three subsequent time-points were analysed by extended-quantitative culture; aerobe/anaerobe densities, ecological indexes and community structure were assessed together with clinical outcomes.RESULTS: Eighty patients were prospectively recruited. Sputa were successfully collected and cultured at 199/267 (74.5%) study visits. Eighty-two sputa from 25 patients comprised a complete sample-set for longitudinal analyses. Bacterial density, ecological indexes and clinical outcomes were unchanged in 18 patients with three sequential stable visits. Conversely, in 7 patients who had an exacerbation, total bacterial and aerobe densities differed over four study visits (P < .001) with this difference particularly apparent between the baseline visit and completion of acute antibiotic treatment where a decrease in density was observed. Bacterial communities were more similar within than between patients but stable patients had the least variation in community structure over time. Using logistic regression in a further analysis, baseline features in 37 patients without compared to 15 patients with a subsequent exacerbation showed that clinical measures rather than bacterial density or ecological indexes were independent predictors of an exacerbation.CONCLUSIONS: Greater fluctuation in the viable bacterial community during treatment of an exacerbation than between stable visits was observed. Extended-quantitative culture did not provide prognostic information of a future exacerbation.

U2 - 10.1016/j.jcf.2019.02.012

DO - 10.1016/j.jcf.2019.02.012

M3 - Article

JO - Journal of Cystic Fibrosis

T2 - Journal of Cystic Fibrosis

JF - Journal of Cystic Fibrosis

SN - 1569-1993

ER -