The value of next-generation metagenomic sequencing in pathogen detection of pleural effusions and ascites from children with sepsis

Abstract

ObjectiveTo investigate the diagnostic value of metagenomic next-generation sequencing (mNGS) using pleural effusion and ascites from children with sepsis.MethodsIn this study, children with sepsis or severe sepsis and appeared pleural or peritoneal effusions were enrolled, of whom the pleural effusions or ascites and blood samples were conducted pathogen detection using both conventional and mNGS methods. The samples were divided into pathogen-consistent and pathogen-inconsistent groups based on the consistency of mNGS results from different sample types, and into exudate and transudate groups based on their pleural effusion and ascites properties. The pathogen positive rates, pathogen spectrum, consistency between different sample types, and clinical diagnosis consistency were compared between mNGS and conventional pathogen tests.ResultsA total of 42 pleural effusions or ascites and 50 other type samples were collected from 32 children. The pathogen positive rate of the mNGS test was significantly higher than that of traditional methods (78.57% vs. 14.29%, P < 0.001) in pleural effusion and ascites samples, with a consistent rate of 66.67% between the two methods. Nearly 78.79% (26/33) of mNGS positive results of the pleural effusions and ascites samples were consistent with clinical evaluation, and 81.82% (27/33) of these positive samples reported 1-3 pathogens. The pathogen-consistent group outperformed the pathogen-inconsistent group in terms of consistency with respect to clinical evaluation (88.46% vs. 57.14%, P = 0.093), while there was no significant difference between the exudate and transudate groups (66.67% vs. 50.00%, P = 0.483).ConclusionCompared to conventional methods, mNGS has great advantages in pathogen detection of pleural effusion and ascites samples. Moreover, consistent results of mNGS tests with different sample types provide more reference values in clinical diagnosis.

Nanopore sequencing of infectious fluid is a promising supplement for gold-standard culture in real-world clinical scenario

“…As for clinically relevant bacteria, the top 3 frequently detected species were Klebsiella pneumoniae , E. coli and Staphylococcus aureus , from sterile body sites, while Mycobacterium tuberculosis , E. coli and Pseudomonas aeruginosa , from microbial-colonized sites. These species were in line with the results of several previous studies that investigated pathogens detected from plasma ( Eichenberger et al., 2022 ), SCE ( Liu et al., 2023 ), abscess ( Zhao et al., 2021 ) and respiratory tract ( Jin et al., 2022 ). Among the above species, there was a high concordance in detection of E. coli , P. aeruginosa and S. aureus between NST and culture.…”

Evaluating the feasibility, sensitivity, and specificity of next-generation molecular methods for pleural infection diagnosis

“…Furthermore, metagenomics and bacterial metataxonomics unveiled greater microbial heterogeneity than could be detected by conventional culture. Similar to recent work 16,19 , we observed that polymicrobial bacterial infection was also occasionally associated with fungal coinfection (albeit in very low abundance) using metagenomics, confirming the challenging nature of diagnosing and treating complex polymicrobial pleural infections across microbial domains. Streptococcal and staphylococcal phages were also seen in five cases of pleural infection, with their host species not always detected, suggesting possible lytic activity towards their host within the pleural space, or incidental phage transit from other body sites 30 .…”

“…Clinical decision-making in suspected pleural infection is challenging due to low culture positivity rates 5–8 , resulting in frequent diagnostic uncertainty and antimicrobial overuse. Recent work 7,8,15,16,19 has highlighted potential advantages of molecular methods for diagnosing and determining the aetiology of pleural infection. Our pilot feasibility study adds to this growing body of work, being one of the first studies to apply shotgun metagenomics on pleural infections, and the first to prospectively collect and profile consecutive pleural fluid specimens.…”

“…This collective work has revealed a pleural microbiome that is often polymicrobial and characterized by a diverse range of classical pathogens and bystander microbes 7,8,[15][16][17][18][19][20][21] . Earlier investigations implemented bacterial metataxonomics to profile the bacterial microbiome 7,8,15,21 ; however, three recent studies have implemented metagenomics to more comprehensively profile pleural microbiota 16,19,20 . However, the authors only reported taxonomic findings to the genus level, limiting in-depth understanding of microbiome composition and diversity 16 .…”

“…reported on a single case study of viral pleurisy caused by Epstein-Barr virus, which was successfully treated with acyclovir 20 . Finally, Liu et al 2023 examined microbiomes of pleural and ascitic fluid in 92 specimens retrieved from 32 Chinese children, identifying Klebsiella pneumoniae as the dominant pathogen (n=17), followed by Escherichia coli (n=9), and Acinetobacter baumannii (n=7); yeasts (n=6) and several viruses (n=33) were also identified 19 . In all three studies, metagenomics yielded a higher pathogen positive rate than conventional culture 16,19,20 .…”