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ABSTRACT: The bacteriology of pleural infection using next generation sequencing: The Oxford Pleural Infection Metagenomics Studies (TORPIDS)

PROVIDER: PRJNA665994 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12731000_1.fastq.gz	Fastqsanger.gz
	SRR12731000_2.fastq.gz	Fastqsanger.gz
	SRR12731100_1.fastq.gz	Fastqsanger.gz
	SRR12731100_2.fastq.gz	Fastqsanger.gz
	SRR12731200_1.fastq.gz	Fastqsanger.gz

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Project description:Pleural infection is a severe and complicated disease with increasing incidence worldwide and is characterised by substantial associated morbidity and mortality.1,2 Although it is accepted that the disease is heterogeneous, and there is a validated clinical prediction score (RAPID)3,4, the biological endotypes of pleural infection remain elusive and pleural fluid specific criteria to assess the intrapleural response are not available. A better understanding of pleural infection subtypes could lead to improved treatment strategies and clinical outcomes. All patients with pleural infection follow the same clinical journey which focusses on hospital admission, pleural fluid drainage and administration of antibiotics however, their recovery progress and clinical outcomes differ significantly.1,2 A subgroup of patients exhibits ineffective or failed intrapleural fibrinolysis leading to the development of fibrous septations which further complicates treatment. Consequently, approximately 30% of patients do not respond to treatment and require invasive treatments including surgical drainage. Tandem mass spectrometry is a high-throughput proteomics assay which is a reliable, unbiased, and hypothesis-free analytical method for investigating the underlying biology of disease using clinical specimens.5 The pleural fluid proteome faithfully reflects the intrapleural environment and could be utilised to identify disease key mediators, biomarkers, and treatment targets. For instance, pleural fluid pH, glucose and lactate dehydrogenase are used as clinical biochemistry markers for diagnosing patients with pleural infection.1 Our study (The Oxford Pleural Infection Endotyping Study, TORPIDS 2) applied mass spectrometry to pleural fluid specimens (n=80) from the PILOT trial.4 Our primary aims were to discover endotypes in pleural infection, characterise the intrapleural immune response and investigate the association between patient endotypes and high-precision bacterial patterns. We assessed the association between pleural infection endotypes and important clinical outcomes (1-year survival and need for surgery)

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