Diagnosis of Sepsis with Cell-free DNA by Next-Generation Sequencing Technology in ICU Patients

Long, Yun; Zhang, Yinxin; Gong, Yanping; Sun, Ruixia; Su, Longxiang; Lin, Xin; Shen, Ao; Zhou, Jiali; Caiji, Zhuoma; Wang, Xinying; Li, Dongfang; Wu, Honglong; Tan, Hongdong

doi:10.1016/j.arcmed.2016.08.004

Cited by 184 publications

(151 citation statements)

References 20 publications

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“…Procedures including clinical specimen collection, sample preservation, transportation and the experimental procedures, may cause pollution and lead to contaminate the specimen mixed with so called “background” microbial gene sequence, which may affect the NGS data analysis [15,19,20] , resulting in false positive results and hinder the doctors. Similar to previous reports, we found that the most common background bacterium was Propionibacterium acnes in our study (data not shown here) [14] .…”

Section: Discussionsupporting

confidence: 92%

“…Brown JR et al recommend NGS should be considered as a front-line diagnostic test in chronic and recurring encephalitis. And the results in our study consistent with a study of NGS which conducted in patients with sepsis, and detectability were significantly increased from 12.82% to 30.77% [14] . It indicates that an NGS-based approach has great potential to detect causative pathogens of infectious diseases.…”

Section: Discussionsupporting

confidence: 91%

“…As can be seen from our study, 95.35% of the NGS sequencing data were compared to the human genome, whereas less than <1 % to the pathogen genome. Previous studies referred to the application of NGS in clinical pathogen detection showed similar situation in both bacterial and/or virus infections [14] . In addition, this method clearly shows the advantages of recognizing multi-pathogens infection.…”

Section: Discussionmentioning

confidence: 93%

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Next-Generation Sequencing Could be a Promising Diagnostic Approach for Pathogen Detection: Pathogenic Analysis of Pediatric Bacterial Meningitis by Next-Generation Sequencing Technology Directly from Cerebrospinal Fluid Specimens

Guo

Liu

et al. 2018

Preprint

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BackgroundBacterial meningitis remains one of the major challenges in infectious diseases, leading to sequel in many cases. A prompt diagnosis of the causative microorganism is critical to significantly improve outcome of bacterial meningitis. Although various targeted tests for cerebrospinal fluid (CSF) samples are available, it is a big problem for the identification of etiology of bacterial meningitis.MethodsHere we describe the use of unbiased sequence analyses by next-generation sequencing (NGS) technology for the identification of infectious microorganisms from CSF samples of pediatric bacterial meningitis patients in the Department of Infectious Diseases from Beijing Children’s Hospital.ResultsIn total, we had 99 bacterial meningitis patients in our study, 55 (55.6%) of these were etiologically confirmed by clinical microbiology methods. Combined with NGS, 68 cases (68.7%) were etiologically confirmed. The main pathogens identified in this study were Streptococcus pneumoniae (n=29), group B streptococcus (n=15), Staphylococcus aureus (n=7), Escherichia coli (n=7). In addition, two cases with cytomegalovirus infection and one with Taenia saginata asiatica were confirmed by NGS.ConclusionsNGS could be a promising alternative diagnostic approach for critically ill patients suffering from bacterial meningitis in pediatric population.SummaryWe conducted the study for the identification of microorganisms by next-generation sequencing directly from CSF samples of pediatric bacterial meningitis patients. And the study showed that NGS could be a promising alternative diagnostic approach for bacterial meningitis in pediatric population.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 93%

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Next-Generation Sequencing Could be a Promising Diagnostic Approach for Pathogen Detection: Pathogenic Analysis of Pediatric Bacterial Meningitis by Next-Generation Sequencing Technology Directly from Cerebrospinal Fluid Specimens

Guo

Liu

et al. 2018

Preprint

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“…DNA sequencing of cell-free plasma (De Vlaminck et al, 2015;Long et al, 2016;Hong et al, 2018) allows for detection of pathogen DNA derived from both bloodstream infections and deeper body sites, including cases where there has been antibiotic pretreatment prior to cultures and in those with fastidious, difficult-to-culture organisms (Abril et al, 2016). This case series reflects an institutional experience applying…”

Section: Introductionmentioning

confidence: 98%

Community-acquired pneumonia in children: cell-free plasma sequencing for diagnosis and management

Farnaes

Wilke

Loker

et al. 2019

Diagnostic Microbiology and Infectious Disease

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“…Recently, it has been suggested that pathogens can be accurately detected directly from the cell‐free plasma DNA of sepsis patients without culture . However, when the genomic DNA is extracted from the infected blood sample, both bacterial and human genomic DNAs are co‐extracted.…”

Section: Discussionmentioning

confidence: 99%

Multiplex identification of sepsis‐causing Gram‐negative pathogens from the plasma of infected blood

et al. 2017

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Early and accurate detection of bacterial pathogens in the blood is the most crucial step for sepsis management. Gram-negative bacteria are the most common organisms causing severe sepsis and responsible for high morbidity and mortality. We aimed to develop a method for rapid multiplex identification of clinically important Gram-negative pathogens and also validated whether our system can identify Gram-negative pathogens with the cell-free plasm DNA from infected blood. We designed five MLPA probe sets targeting the genes specific to major Gram-negative pathogens (uidA and lacY for E. coli, ompA for A. baumannii, phoE for K. pneumoniae, and ecfX for P. aeruginosa) and one set targeting the CTX-M group 1 to identify the ESBL producing Gram-negative pathogens. All six target-specific peaks were clearly separated without any non-specific peaks in a multiplex reaction condition. The minimum detection limit was 100 fg of pathogen DNA. When we tested 28 Gram-negative clinical isolates, all of them were successfully identified without any non-specific peaks. To evaluate the clinical applicability, we tested seven blood samples from febrile patients. Three blood culture positive cases showed E. coli specific peaks, while no peak was detected in the other four culture negative samples. This technology can be useful for detection of major sepsis-causing, drug-resistant Gram-negative pathogens and also the major ESBL producing Gram-negatives from the blood of sepsis patients in a clinical setting. This system can help early initiation of effective antimicrobial treatment against Gram-negative pathogens for sepsis patients, which is very crucial for better treatment outcomes.

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Diagnosis of Sepsis with Cell-free DNA by Next-Generation Sequencing Technology in ICU Patients

Cited by 184 publications

References 20 publications

Next-Generation Sequencing Could be a Promising Diagnostic Approach for Pathogen Detection: Pathogenic Analysis of Pediatric Bacterial Meningitis by Next-Generation Sequencing Technology Directly from Cerebrospinal Fluid Specimens

Next-Generation Sequencing Could be a Promising Diagnostic Approach for Pathogen Detection: Pathogenic Analysis of Pediatric Bacterial Meningitis by Next-Generation Sequencing Technology Directly from Cerebrospinal Fluid Specimens

Community-acquired pneumonia in children: cell-free plasma sequencing for diagnosis and management

Multiplex identification of sepsis‐causing Gram‐negative pathogens from the plasma of infected blood

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