Abstract
Identification of the offending organism and appropriate antimicrobial therapy are crucial for treating empyema. Diagnosis of empyema is largely obscured by the conventional bacterial cultivation and PCR process that has relatively low sensitivity, leading to limited understanding of the etiopathogenesis, microbiology, and role of antibiotics in the pleural cavity. To expand our understanding of its pathophysiology, we have carried out a metagenomic snapshot of the pleural effusion from 45 empyema patients by Illumina sequencing platform to assess its taxonomic, and antibiotic resistome structure. Our results showed that the variation of microbiota in the pleural effusion is generally stratified, not continuous. There are two distinct microbiome clusters observed in the forty-five samples: HA-SA type and LA-SA type. The categorization is mostly driven by species composition: HA-SA type is marked by Staphylococcus aureus as the core species, with other enriched 6 bacteria and 3 fungi, forming a low diversity and highly stable microbial community; whereas the LA-SA type has a more diverse microbial community with a distinct set of bacterial species that are assumed to be the oral origin. The microbial community does not shape the dominant antibiotic resistance classes which were common in the two types, while the increase of microbial diversity was correlated with the increase in antibiotic resistance genes. The existence of well-balanced microbial symbiotic states might respond differently to pathogen colonization and drug intake. This study provides a deeper understanding of the pathobiology of pleural empyema and suggests that potential resistance genes may hinder the antimicrobial therapy of empyema.
Highlights
Empyema is defined as the presence of germs and/or macroscopic pus in the pleural cavity, which is a serious infection with high rates of morbidity and mortality (Asai et al, 2017)
Our study reveals the potential risks of treatment failure of pleural empyema due to the high abundance of antibiotic-resistance genes (ARGs) in the microbial community and provides data for better understanding of the pathophysiological mechanism in empyema
The microbiome and resistome of pleural effusion collected from 45 empyema infection patients were explored based on Next-generation sequencing (NGS) metagenomic analysis
Summary
Empyema is defined as the presence of germs and/or macroscopic pus in the pleural cavity, which is a serious infection with high rates of morbidity and mortality (Asai et al, 2017). Previous analysis of pleural effusion microbiome of empyema patients was mainly based on bacterial cultivation (Lasken and McLean, 2014), PCR and Multiplex bacterial PCR (Blaschke et al, 2011; Franchetti et al, 2020). Next-generation sequencing (NGS)-based metagenomic approach has been employed to examine the population structures and functions of the microbiome in human and environmental samples, which provides biomarkers and risk assessment information, such as antibiotic-resistant bacteria and antibiotic-resistance genes (ARGs) (Cote et al, 2016). We collected pleural effusion (PE) samples from 45 empyema patients and applied NGS metagenomic analysis to characterize the microbial community and antibiotic resistome. Our study reveals the potential risks of treatment failure of pleural empyema due to the high abundance of ARGs in the microbial community and provides data for better understanding of the pathophysiological mechanism in empyema
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