PT  - JOURNAL ARTICLE
AU  - Nikolaos I. Kanellakis
AU  - Eihab O. Bedawi
AU  - John M. Wrightson
AU  - John P. Corcoran
AU  - Robert Hallifax
AU  - Rachel M. Mercer
AU  - Vineeth George
AU  - Radhika Banka
AU  - Maisha Jabeen
AU  - Rachelle Asciak
AU  - Robert F. Miller
AU  - Nick A. Maskell
AU  - Ioannis Psallidas
AU  - Timothy Hinks
AU  - Derrick Crook
AU  - Najib M. Rahman
TI  - Identification of pleural infection microbiological patterns by applying next generation sequencing and bioinformatics analysis
AID  - 10.1183/13993003.congress-2020.4673
DP  - 2020 Sep 07
TA  - European Respiratory Journal
PG  - 4673
VI  - 56
IP  - suppl 64
4099  - http://erj.ersjournals.com/content/56/suppl_64/4673.short
4100  - http://erj.ersjournals.com/content/56/suppl_64/4673.full
SO  - Eur Respir J2020 Sep 07; 56
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).