scholarly journals 329. Performance of Next Generation Sequencing in Isolating a Pathogen in Pediatric Osteoarticular Infections

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S236-S237
Author(s):  
Nanda Ramchandar ◽  
Jessica Burns ◽  
Andrew Pennock ◽  
Christopher R Cannavino ◽  
Lauge Farnaes
Keyword(s):  
Next Generation Sequencing ◽  
Septic Arthritis ◽  
Standard Care ◽  
Pediatric Population ◽  
Single Site ◽  
Acute Osteomyelitis ◽  
Next Generation ◽  
Pathogenic Organism ◽  
Osteoarticular Infections ◽  
Generation Sequencing

Abstract Background Osteoarticular infections are often encountered in the pediatric population. Therapy is guided by isolation of a putative organism, however, operative cultures are often negative. Next generation sequencing (NGS) allows for more sensitive sampling of body compartments generally considered sterile. We sought to evaluate the utility of NGS in comparison to culture in detecting a pathogenic organism in acute osteomyelitis and septic arthritis in children. Methods This was a single-site study to evaluate the utility of NGS in comparison to culture in detecting a pathogenic organism in acute osteomyelitis and septic arthritis in children. Eligible patients were all patients with osteomyelitis or septic arthritis admitted to Rady Children’s Hospital from July 2019 through July 2020. We excluded any patients with bone or joint surgery within 30 days prior to admission. Operative samples were chosen at the surgeon’s discretion (joint aspirate, synovium, or bone) based on operative findings. We compared NGS testing to standard care culture from the same site. Results We enrolled 41 subjects. NGS of the operative samples identified a pathogen in 26 (63.4%) patients versus 18 (43.9%) by culture. Operative culture missed the diagnosis in 10 cases, though PCR identified the organism in 6 of those cases (5 were cases in which Kingella kingae was identified). In 4 subjects, NGS identified a putative organism where standard care testing (either PCR or culture) was negative. NGS was falsely positive in 1 subject and falsely negative for one other subject. Sensitivity was 96.3% (CI 95%, 81.0–99.9%) and Specificity was 92.9% (CI 95%, 66.1–99.8) for NGS versus 64.3% (CI 95%, 44.1–81.4) and 84.6% (CI 95%, 54.6–99.9%) for culture respectively. Conclusion In this single site prospective study of pediatric osteoarticular infections, we demonstrate improved sensitivity and specificity of NGS testing when compared to standard culture. Disclosures All Authors: No reported disclosures

scholarly journals Use of Metagenomic Next-Generation Sequencing to Identify Pathogens in Pediatric Osteoarticular Infections

2021 ◽  
Author(s):  
Nanda Ramchandar ◽  
Jessica Burns ◽  
Nicole G Coufal ◽  
Andrew Pennock ◽  
Benjamin Briggs ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Septic Arthritis ◽  
Usual Care ◽  
Pathogen Detection ◽  
Single Site ◽  
Diagnostic Utility ◽  
Next Generation ◽  
Osteoarticular Infections ◽  
Operative Findings ◽  
Generation Sequencing

Abstract Background Osteoarticular infections (OAI) are frequently encountered in children. Treatment may be guided by isolation of a pathogen; however, operative cultures are often negative. Metagenomic next-generation sequencing (mNGS) allows for broad and sensitive pathogen detection that is culture-independent. We sought to evaluate the diagnostic utility of mNGS in comparison to culture and usual care testing to detect pathogens in acute osteomyelitis and/or septic arthritis in children. Methods This was a single-site study to evaluate the use of mNGS in comparison to culture to detect pathogens in acute pediatric osteomyelitis and/or septic arthritis. Subjects admitted to a tertiary children’s hospital with suspected OAI were eligible for enrollment. We excluded subjects with bone or joint surgery within 30 days of admission or with chronic osteomyelitis. Operative samples were obtained at the surgeon’s discretion per standard care (fluid or tissue) and based on imagining and operative findings. We compared mNGS to culture and usual care testing (culture and PCR) from the same site. Results We recruited 42 subjects over the enrollment period. mNGS of the operative samples identified a pathogen in 26 subjects compared to 19 subjects in whom culture identified a pathogen. In four subjects, mNGS identified a pathogen where combined usual care testing (culture and PCR) was negative. Positive predictive agreement and negative predictive agreement both were 93.0% for mNGS. Conclusion In this single site prospective study of pediatric OAI, we demonstrated the diagnostic utility of mNGS testing in comparison to culture and usual care (culture and PCR) from operative specimens.

scholarly journals Somatic Variation as an Incidental Finding in the Pediatric Next Generation Sequencing Era

2021 ◽  
pp. mcs.a006135
Author(s):  
Marilena Melas ◽  
Mariam T Mathew ◽  
Mari Mori ◽  
Vijayakumar Jayaraman ◽  
Sarah A Wilson ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
De Novo ◽  
Tissue Sample ◽  
Incidental Finding ◽  
Pediatric Population ◽  
Genomic Analysis ◽  
Juvenile Myelomonocytic Leukemia ◽  
Next Generation ◽  
Somatic Variation ◽  
Generation Sequencing

The methodologic approach used in next-generation sequencing (NGS) affords a high depth of coverage in genomic analysis. Inherent in the nature of genomic testing, there exists potential for identifying genomic findings that are incidental or secondary to the indication for clinical testing, with the frequency dependent on the breadth of analysis and the tissue sample under study. The interpretation and management of clinically meaningful incidental genomic findings is a pressing issue particularly in the pediatric population. Our study describes a 16-month old male who presented with Dandy-Walker malformation, metopic craniosynostosis and developmental delay. Clinical exome sequencing (ES) trio analysis revealed the presence of two variants in the proband. The first was a de novo variant in the PPP2R1A gene (c.773G>A, p.Arg258His), which is associated with autosomal dominant (AD) intellectual disability, accounting for the proband's clinical phenotype. The second was a recurrent hotspot variant in the CBL gene (c.1111T>C, p.Tyr371His), which was present at a variant allele fraction of 11%, consistent with somatic variation in the peripheral blood sample. Germline pathogenic variants in CBL are associated with AD Noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia (JMML). Molecular analyses using a different tissue source, buccal epithelial cells, suggest that the CBL alteration may represent a clonal population of cells restricted to leukocytes. This report highlights the laboratory methodologic and interpretative processes and clinical considerations in the setting of acquired variation detected during clinical ES in a pediatric patient.

scholarly journals 342. Clinical Utility of a Next Generation Sequencing Test for Pathogen Detection in Pediatric Central Nervous System Infections

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S241-S241
Author(s):  
Nanda Ramchandar ◽  
Jennifer Foley ◽  
Claudia Enriquez ◽  
Stephanie Osborne ◽  
Antonio Arrieta ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Next Generation Sequencing ◽  
Standard Care ◽  
Cns Infection ◽  
Next Generation ◽  
Diagnostic Modality ◽  
Cns Infections ◽  
Pcr Multiplex ◽  
Generation Sequencing

Abstract Background Pediatric central nervous system (CNS) infections are potentially life-threatening and may incur significant morbidity. Identifying a pathogen is important, both in terms of guiding therapeutic management, but also in characterizing prognosis. However, standard care testing by culture, serology, and PCR is often unable to identify a pathogen. We examined use of next generation sequencing (NGS) of cerebrospinal fluid (CSF) in detecting an organism in children with CNS infections. Methods We prospectively enrolled children with CSF pleocytosis and suspected CNS infection admitted to 3 tertiary pediatric hospitals. After standard care testing had been performed, the remaining CSF was submitted for analysis by NGS. Results We enrolled 70 subjects over a 12-month recruitment period. A putative organism was isolated from CSF in 24 (34.3%) subjects by any diagnostic modality. NGS of the CSF samples identified a pathogen in 20 (28.6%) subjects. False positive results by NGS were identified in 2 patients. There were no cases in which NGS alone identified a pathogen. In 4 cases, a putative organism was recovered by standard care testing of the CSF, but not by CSF NGS. CSF culture recovered a putative organism in 12 cases (12.1%). A CSF PCR multiplex panel was utilized for 51 subjects. An organism was detected in 15 of these (29.4%). Using a reference composite of standard care testing, we determined the sensitivity and specificity of CSF NGS to be 83.3% (95% CI, 62.6–95.3%) and 91.3% (95% CI, 79.2–97.6%) respectively. Conclusion Sequencing of CSF has the potential to rapidly and comprehensively identify infection with a single test. Further studies are needed to determine the optimal use of NGS for diagnosis of CNS infections. Disclosures All Authors: No reported disclosures

scholarly journals 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

2018 ◽  
Author(s):  
Ling-yun Guo ◽  
Yong-jun Li ◽  
Lin-lin Liu ◽  
Hong-long Wu ◽  
Jia-li Zhou ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Next Generation Sequencing ◽  
Bacterial Meningitis ◽  
Infectious Diseases ◽  
Pediatric Population ◽  
Diagnostic Approach ◽  
Next Generation ◽  
Promising Alternative ◽  
Causative Microorganism ◽  
Generation Sequencing

AbstractBackgroundBacterial 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.

scholarly journals Pathogenic Detection by Metagenomic Next-Generation Sequencing in Osteoarticular Infections

2020 ◽  
Vol 10 ◽  
Author(s):  
Zi-da Huang ◽  
Zi-jie Zhang ◽  
Bin Yang ◽  
Wen-bo Li ◽  
Chong-jing Zhang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Osteoarticular Infections ◽  
Generation Sequencing

scholarly journals Direct Diagnosis of Echovirus 12 Meningitis Using Metagenomic Next Generation Sequencing

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 610
Author(s):  
Madjid Morsli ◽  
Christine Zandotti ◽  
Aurelie Morand ◽  
Philippe Colson ◽  
Michel Drancourt
Keyword(s):  
Cerebrospinal Fluid ◽  
Case Report ◽  
Next Generation Sequencing ◽  
Point Of Care ◽  
Pediatric Population ◽  
Next Generation ◽  
Viral Genotype ◽  
Acute Meningitis ◽  
Current Point ◽  
Generation Sequencing

The current point-of-care diagnosis of enterovirus meningitis does not identify the viral genotype, which is prognostic. In this case report, more than 81% of an Echovirus 12 genome were detected and identified by metagenomic next-generation sequencing, directly from the cerebrospinal fluid collected in a 6-month-old child with meningeal syndrome and meningitis: introducing Echovirus 12 as an etiological agent of acute meningitis in the pediatric population.

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