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

Farnaes, Lauge; Wilke, Julianne; Loker, Kathleen Ryan; Bradley, John S.; Cannavino, Christopher; Hong, David K.; Pong, Alice; Foley, Joseph M.; Coufal, Nicole G.

doi:10.1016/j.diagmicrobio.2018.12.016

Cited by 62 publications

(54 citation statements)

References 20 publications

(19 reference statements)

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“…In patients whose final clinical diagnosis was viral pneumonia, the BALF mNGS detected more sequences than blood in our study, which was consistent with previous studies that showed a higher level of CMV DNA detected in BALF compared with the blood using real-time PCR [25,26]. Pathogen DNA in blood may also reflect the pulmonary infection because high blood flow in the lung may lead to increased pathogen DNA shedding [18]. In the 16 patients whose diagnoses were confirmed by culture, mNGS detected additional microbes including Enterococcus faecium, Pneumocystis jirovecii, Acinetobacter baumannii, Streptococcus pneumoniae, Candida glabrata, Klebsiella pneumoniae, Haemophilus influenzae, Candida parapsilosis, and Aspergillus fumigatus.…”

Section: Discussionsupporting

confidence: 91%

“…Studies have shown that blood culture should not be recommended even in severe pulmonary infections due to its extremely low yield [15,16]. Contrary to this, molecular diagnostic methods such as polymerase chain reaction (PCR) and mNGS have been proven feasible in blood samples to detect pathogens in pulmonary infections [17,18]. As an evolutional diagnostic tool, the positive rate of BALF and blood mNGS in pulmonary infections is still unknown.…”

Section: Introductionmentioning

confidence: 99%

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Blood and Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Pneumonia

Ding

Cheng

et al. 2020

Canadian Journal of Infectious Diseases and Medical Microbiolog

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Background. Metagenomic next-generation sequencing (mNGS) has made a revolution in the mode of pathogen identification. We decided to explore the diagnostic value of blood and bronchoalveolar lavage fluid (BALF) as mNGS samples in pneumonia. Methods. We retrospectively reviewed 467 mNGS results and assessed the diagnostic performance of paired blood and BALF mNGS in 39 patients with pneumonia. Results. For bacteria and fungi, 16 patients had culture-confirmed pathogen diagnosis, while 13 patients were culture-negative. BALF mNGS was more sensitive than blood mNGS (81.3% vs. 25.0%, p=0.003), and the specificity in BALF and blood mNGS was not statistically significant different (76.9% vs. 84.6%, p=0.317). For 10 patients without culture test, treatments were changed in 2 patients. For viruses, Epstein-Barr virus was positive in blood mNGS in 9 patients. Human adenovirus was detected in both BALF and blood mNGS in 3 patients. Conclusion. Our study suggests that BALF mNGS is more sensitive than blood mNGS in detecting bacteria and fungi, but blood also has advantages to identify the pathogens of pneumonia, especially for some viruses.

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Section: Discussionsupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Blood and Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Pneumonia

Ding

Cheng

et al. 2020

Canadian Journal of Infectious Diseases and Medical Microbiolog

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“…Only 6/36 (17%) studies reported use of a positive control, including using a mixture of 7 representative organisms and a single Corynebacterium glutamicum ATCC 13032 positive control. 6,16,18,30,42,49 Sequencing technologies Illumina sequencing was used exclusively in 50% (18/36) studies ( Supplementary Table S3).…”

Section: Methodology: Controlsmentioning

confidence: 99%

“…The most commonly used method include a parametric approach based on an assumed distribution for contaminating reads informed by numbers of reads in the control and other samples (n=6). [16][17][18]24,30,40 Some studies (n=5) took an empirical approach to setting these absolute thresholds based on sequencing known negative and positive samples 3,6,39,42,49 while, other studies developed composite measures to determine contamination using factors such as absolute and percentage reads, DNA quantity and relative importance of bacteria among others (n=5). [27][28][29]38,50 Seven studies primarily identified contamination manually from known literature or if reported to be a contaminant previously in the local laboratory.…”

Section: Assessing True Species Presence Versus Contaminationmentioning

confidence: 99%

Metagenomic sequencing as a clinical diagnostic tool for infectious diseases: a systematic review and meta-analysis

Govender

Street

Sanderson

et al. 2020

Preprint

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Metagenomics has the potential to revolutionise infectious diseases diagnostics, from rapid species and antimicrobial resistance prediction, to finding unrecognised and sometimes untreated infections. Our aim was to summarise all literature on culture-independent metagenomic sequencing to describe the accuracy of species and antimicrobial resistance prediction and, describe the challenges and progress in the field. We conducted a systematic review with meta-analysis from eligible studies retrieved from PubMed, Google Scholar and bioRxiv and, assessed risk of bias and quality using the QUADAS-2 tool. This study is registered with PROSPERO, number CRD42020163777. We identified 36 studies, 22 of which used a species-agnostic approach to identify all possible pathogens. In these studies, the overall sensitivity and specificity of pathogen species detection were 88% (95%CI 81-92%) and 86% (95%CI 70-94%) respectively. Antimicrobial resistance prediction and comparison to phenotypic results was undertaken in six studies. Categorical agreement was 83% (95%CI 68-92%), very major (prediction sensitive, phenotype resistant) and major error (prediction resistant, phenotype sensitive) rates were 9% (95%CI 2-27%) and 1% (95%CI 0-20%) respectively. We report limited use of negative controls in studies 61% (22/36) which contribute to a major challenge of discriminating true pathogens from contamination, where there is no convergence on methodology. More efficient human DNA depletion methods are required as a median of 79% (IQR 62-96) [Range 7-98] of sequences were classified as human despite laboratory depletion techniques. The median time from sample to result was 23.5 hours (7-31) [4-144], with sequencing time accounting 10 hours (4.8-16) [1-16]. The average reported consumables cost per sample ranged from $128 to $685. The science and regulatory environment are rapidly developing, and its role as a routine test or test of last resort still needs to be determined, however it is likely that clinical metagenomics will be an increasing part of the clinician′s armamentarium to diagnose infectious diseases in the near future.

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“…in preterm labor, β-thalassemia, and fetal aneuploidy [26][27][28]. Most recently, we have validated a new laboratory developed clinical diagnostic test, the Karius 1 Test, and showed that DNA sequencing of cell-free plasma can accurately detect microbial cfDNA in bloodstream infections and deep seated infections [29,30].…”

Section: Introductionmentioning

confidence: 99%

Detection of microbial cell-free DNA in maternal and umbilical cord plasma in patients with chorioamnionitis using next generation sequencing

Witt

Blair²,

Frascoli

et al. 2020

PLoS ONE

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Background Chorioamnionitis has been linked to spontaneous preterm labor and complications such as neonatal sepsis. We hypothesized that microbial cell-free (cf) DNA would be detectable in maternal plasma in patients with chorioamnionitis and could be the basis for a non-invasive method to detect fetal exposure to microorganisms. Objective The purpose of this study was to determine whether next generation sequencing could detect microbial cfDNA in maternal plasma in patients with chorioamnionitis. Study design Maternal plasma (n = 94) and umbilical cord plasma (n = 120) were collected during delivery at gestational age 28-41 weeks. cfDNA was extracted and sequenced. Umbilical cord plasma samples with evidence of contamination were excluded. The prevalence of microorganisms previously implicated in choriomanionitis, neonatal sepsis and intra-amniotic infections, as described in the literature, were examined to determine if there was enrichment of these microorganisms in this cohort. Specific microbial cfDNA associated with chorioamnionitis was first detected in umbilical cord plasma and confirmed in the matched maternal plasma samples (n = 77 matched pairs) among 14 cases of histologically confirmed

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

Cited by 62 publications

References 20 publications

Blood and Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Pneumonia

Blood and Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Pneumonia

Metagenomic sequencing as a clinical diagnostic tool for infectious diseases: a systematic review and meta-analysis

Detection of microbial cell-free DNA in maternal and umbilical cord plasma in patients with chorioamnionitis using next generation sequencing

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