RT Journal Article
SR Electronic
T1 Identification of pleural infection microbiological patterns by applying next generation sequencing and bioinformatics analysis
JF European Respiratory Journal
JO Eur Respir J
FD European Respiratory Society
SP 4673
DO 10.1183/13993003.congress-2020.4673
VO 56
IS suppl 64
A1 Nikolaos I. Kanellakis
A1 Eihab O. Bedawi
A1 John M. Wrightson
A1 John P. Corcoran
A1 Robert Hallifax
A1 Rachel M. Mercer
A1 Vineeth George
A1 Radhika Banka
A1 Maisha Jabeen
A1 Rachelle Asciak
A1 Robert F. Miller
A1 Nick A. Maskell
A1 Ioannis Psallidas
A1 Timothy Hinks
A1 Derrick Crook
A1 Najib M. Rahman
YR 2020
UL http://erj.ersjournals.com/content/56/suppl_64/4673.abstract
AB Background: Pleural infection (PI) is a common and complex disease which can be life threatening for immunocompromised and elderly populations. Prior antibiotic use and special bacterial nutritional requirements hamper the accuracy of bacterial identification using current clinical culture-based techniques. Consequently, PI microbiology remains unclear. Next generation sequencing (NGS) has the potential to improve identification of the total bacterial population of a complex sample.Aim: To discover and characterise the microbial patterns of PI using NGS and bioinformatics techniques.Methods: Pleural fluid samples from the “Pleural Infection Longitudinal Outcome Study” (PILOT, ISRCTN50236700, n=243) underwent bacterial DNA extraction followed by 16S rRNA NGS using Illumina MiSeq. Data were analysed with DADA2 and Phyloseq R packages.Results: Analysis showed diverse microbiological patterns for PI as 391 different pathogens were identified up to the genus level. 131 (54%) samples had one pathogen with relative abundance over 50% and 89 (36%) samples had at least three pathogens with relative abundance over 10%, suggesting a polymicrobial infection. Streptococcus pneumoniae was detected in 40 (16%) and Staphylococcus aureus in 20 (8%) samples.Discussion: We established a methodology to extract bacterial DNA from patients with PI and used it as a template to apply NGS. 16S rRNA gene NGS provides a robust method to investigate the bacteriological patterns in pleural fluid of patients with PI.Funding: National Institute for Health Research, Oxford Biomedical Research CentreFootnotesCite this article as: European Respiratory Journal 2020; 56: Suppl. 64, 4673.This abstract was presented at the 2020 ERS International Congress, in session “Respiratory viruses in the "pre COVID-19" era”.This is an ERS International Congress abstract. No full-text version is available. Further material to accompany this abstract may be available at www.ers-education.org (ERS member access only).