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Identification of Microbiome Etiology Associated With Drug Resistance in Pleural Empyema.

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.

SUBMITTER: Chen Z

PROVIDER: S-EPMC8008065 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundPrevious studies of decortication for empyema demonstrated that patient characteristics are associated with mortality, but the relationship of infectious pathogen to outcome has not been described. Our objective was to analyze the association of microbiology and antibiotic resistance with postoperative mortality after decortication for empyema. We hypothesized that bacterial pathogens, antibiotic resistance, and patient characteristics would all contribute to perioperative morbidity and mortality.MethodsPatients undergoing pulmonary decortication for empyema from January 1, 2010 to October 1, 2017 were reviewed retrospectively. Cases were matched with microbiology cultures. Outcomes of interest were a composite of death, tracheostomy, initial ventilator support greater than 48 hours, or unexpected intensive care unit readmission. Antibiotic resistance was categorized as present or absent, and the number of antibiotics with resistance was counted for each patient. We describe the relationship of patient characteristics, antibiotic resistance, and microbiology to mortality.ResultsDuring the study period, 185 patients underwent decortication, 118 of whom had a diagnosis of primary empyema (63.8%). Positive culture results were present in 79 of 185 patients (43%). The most common isolate was Streptococcus, which was present in 29 of 79 (37%), followed by Staphylococcus in 19 of 79 (24%). Of 79 patients, 11 had fungal infections (13.9%). In addition, 16 of 79 patients had polymicrobial empyema (20%). Of 185 patients, 30 experienced the composite adverse outcome (16.2%). In multivariable regression, the composite adverse outcome was associated with emphysema, Candida in pleural culture, and antibiotic resistance count.ConclusionsPerioperative mortality and morbidity after decortication for empyema is considerable. In this cohort, infections with increasing antibiotic resistance are associated with morbidity and mortality among patients with empyema.

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Identification of Microbiome Etiology Associated With Drug Resistance in Pleural Empyema.

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