Utility of Metagenomic Next-Generation Sequencing for Etiological Diagnosis of Patients with Sepsis in Intensive Care Units

Chien, Jung-Yien; Yu, Chong-Jen; Hsueh, Po-Ren

doi:10.1128/spectrum.00746-22

Cited by 21 publications

(15 citation statements)

References 46 publications

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“…11.11%), and the proportions of 1-3 and 4-6 pathogens detected were 72.22% and 11.11%, respectively. It was reported that the positive rate of mNGS test in blood samples of adult patients with sepsis was 62.0% ( Chien et al., 2022 ), while a higher positive rate (83.33%) of children with sepsis was observed in this study. However, no mNGS related studies of pleural or peritoneal effusions have been reported so far.…”

Section: Discussioncontrasting

confidence: 50%

“…To improve the pathogen positive rate and pathogen diagnosis accuracy, clinicians can collect samples from multiple suspected infected sites for mNGS pathogen screening ( Chien et al., 2022 ). As one of the most common sample types, blood has the easiest access for mNGS testing and is the most important sample type for joint analysis in this study.…”

Section: Discussionmentioning

confidence: 99%

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

Liu

Wang²,

Li³

et al. 2023

Front. Cell. Infect. Microbiol.

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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.

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Section: Discussioncontrasting

confidence: 50%

Section: Discussionmentioning

confidence: 99%

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

Liu

Wang²,

Li³

et al. 2023

Front. Cell. Infect. Microbiol.

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“…The antibiotic treatments affect the pathogens in bloodstream infection, making it tough to achieve the clinical examination. By detecting the blood samples of patients with sepsis in intensive care units, the usage of mNGS considerably improved the number of fungi ( p = 0.012) compared to conventional culture [ 79 ]. Moreover, using ITS sequencing for allogeneic hematopoietic cell transplantation (alloHCT), researchers found that the load of C. albicans was significantly high in some blood samples [ 80 ].…”

Section: Ngs and Fungal Infection In Different Organsmentioning

confidence: 99%

Next-Generation Sequencing Applications for the Study of Fungal Pathogens

Jiang

Chen

et al. 2022

Microorganisms

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Next-generation sequencing (NGS) has become a widely used technology in biological research. NGS applications for clinical pathogen detection have become vital technologies. It is increasingly common to perform fast, accurate, and specific detection of clinical specimens using NGS. Pathogenic fungi with high virulence and drug resistance cause life-threatening clinical infections. NGS has had a significant biotechnological impact on detecting bacteria and viruses but is not equally applicable to fungi. There is a particularly urgent clinical need to use NGS to help identify fungi causing infections and prevent negative impacts. This review summarizes current research on NGS applications for fungi and offers a visual method of fungal detection. With the development of NGS and solutions for overcoming sequencing limitations, we suggest clinicians test specimens as soon as possible when encountering infections of unknown cause, suspected infections in vital organs, or rapidly progressive disease.

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“…These patients are at higher risk for infections by opportunistic pathogens and thus may particularly benefit from early, reliable identification of the causative pathogen. NGS can identify a wide variety of pathogens (bacteria, fungi and viruses) within a single sample, including pathogens that are difficult to cultivate or are slow-growing such as atypical mycobacteria, which are rarely examined [6]. However, 7 patients are a very small number and larger multicenter cohorts are needed to make valid statements.…”

Section: Discussionmentioning

confidence: 99%

Next Generation Sequencing of Free Microbial DNA for Rapid Identification of Pathogens in Critically Ill Children with Systemic Inflammatory Response Syndrome (SIRS)

Goretzki¹,

Schäfer²,

Dogan³

et al. 2022

Front. Biosci. (Landmark Ed)

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Background: Infections, major surgeries, and hyperinflammatory syndromes are known to trigger Systemic Inflammatory Response Syndrome (SIRS). Discrimination between infectious and noninfectious inflammation often poses a challenge in chronically ill patients with multiple comorbidities. These patients are routinely treated with a variety of anti-infective medications before a pathogen is identified. With the goal of improving pathogen detection rates and interventions, we evaluated Next Generation Sequencing (NGS) as a highly sensitive and fast means of detecting free microbial DNA in a small amount of serum samples from children with ongoing SIRS. Methods: We describe seven complex pediatric patients of SIRS or prolonged fever (>38.5 °C) >72 hours in which serum samples analyzed by NGS had a major impact on therapy. One patient was analyzed twice. Results: In eight NGS there were six positive results (two bacterial, three viral, one fungal) which were subsequently confirmed by microbiological culture or polymerase chain reaction (PCR) in five of the six NGS. In five of the eight performed NGS, results led to a change of therapy: antibiotic therapy was discontinued in two, escalated in one, an initiated in another; in one an antiviral was administered. Conclusions: NGS may become a valuable addition to infectious disease diagnostics in cases of pediatric SIRS. However, NGS has not yet been validated as a diagnostic method in pediatric as a diagnostic method in pediatric patients and results should therefore be interpreted with caution. Multi-center NGS evaluation studies are currently being planned.

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Utility of Metagenomic Next-Generation Sequencing for Etiological Diagnosis of Patients with Sepsis in Intensive Care Units

Abstract: Delays in effective antimicrobial therapy have resulted in decreased survival rates among patients with sepsis. However, current culture-based diagnostic methods have low sensitivity because of concurrent antibiotic exposure and fastidious and atypical causative organisms.

Cited by 21 publications

References 46 publications

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

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

Next-Generation Sequencing Applications for the Study of Fungal Pathogens

Next Generation Sequencing of Free Microbial DNA for Rapid Identification of Pathogens in Critically Ill Children with Systemic Inflammatory Response Syndrome (SIRS)

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