The diagnostic value of metagenomic next-generation sequencing for identifying Streptococcus pneumoniae in paediatric bacterial meningitis

Abstract

Background There is currently no research on the diagnostic value of metagenomic next-generation sequencing (mNGS) for a single pathogens in CSF. The aim of this study was to analyse the value of mNGS for identifying Streptococcus pneumoniae ( S. pneumoniae ) in paediatric bacterial meningitis. Methods Bacterial meningitis (BM) cases from October 23, 2014, to December 31, 2016, and December 1, 2017, to July 31, 2018 at Beijing Children’s Hospital were reviewed. Clinical features and pathogens were analysed. Results We diagnosed 135 patients with BM in this study. A total of 43 S. pneumoniae were identified by combination methods. 26/135 (19.3%) patients had positive results in S. pneumoniae by blood and/or cerebrospinal fluid (CSF) culture. Alere BinaxNow® Streptococcus pneumoniae Antigen test was positive in 35/135(25.9%) cases. 32/135 (23.7%) S. pneumoniae were identified by mNGS. Six CSF samples were identified as S. pneumoniae only by mNGS technology. Taking culture as the gold standard, the sensitivity and specificity of mNGS for diagnosing S. pneumoniae meningitis were 73.1 and 88.1%, respectively. The positive predictive value (PPV) and negative predictive value (NPV) of diagnosing S. pneumoniae meningitis by mNGS were 59.4 and 93.2%, respectively. When comparison between mNGS and combined tests (culture and Alere BinaxNow® Streptococcus pneumoniae Antigen test), the sensitivity and specificity of mNGS for S. pneumoniae identification were 70.3 and 93.9%, the PPV and NPV in the identification of S. pneumoniae by mNGS were 81.4 and 89.3%, respectively. The difference in number of unique reads of S. pneumoniae in from CSF sample (< 14 days onset) and CSF sample (> 14 days from onset) was statistically significant (170.5 VS. 13, P = 0.019). The difference in the collected time of CSF for culture and mNGS was statistically significant (4 days VS. 14 days, P < 0.001). Conclusions mNGS has high sensitivity and specificity for S. pneumoniae identification. The pathogen load (number of unique reads) of S. pneumonia is related to the CSF collection time. mNGS was less affected than culture by the use of antibiotics before CSF collection.

Metagenomics for neurological infections — expanding our imagination

“…A second important consideration is the patient's exposure to antimicrobials before the sample was obtained. Although pathogen specific PCR and mNGS can detect residual microbial nucleic acid even after antibiotics have decreased the yield of culture 14,43,44 , a negative mNGS result needs to be interpreted with caution in this context. Finally, if a patient's infection is compartmentalized (for example, brain abscess) or if the suspected pathogen is typically diagnosed by serology because of a low abundance or absence in the CSF (such as Borrelia burgdorferi (Lyme disease) or Treponema pallidum (syphilis)), a negative CSF mNGS result should be interpreted with caution 14 .…”

Rapid sequencing‐based diagnosis of infectious bacterial species from meningitis patients in Zambia

“…Studies for sequencing-based diagnosis of meningitis are ongoing all over the world. [27][28][29] However, the sequencing methods and bioinformatics pipelines used for the diagnosis are different in different studies. This is because sequencing technology, as well as bioinformatics technology including genome databases, has progressed quickly, making it difficult to establish standards.…”

“…Studies for sequencing‐based diagnosis of meningitis are ongoing all over the world . However, the sequencing methods and bioinformatics pipelines used for the diagnosis are different in different studies.…”

Case Report: Comparison of Plasma Metagenomics to Bacterial PCR in a Case of Prosthetic Valve Endocarditis

“…mNGS consists of agnostic DNA, RNA, or total nucleic acid sequencing followed by bioinformatic classification of sequence reads against databases of known organisms. Applications of this approach have ranged from the detection of occult pathogens during fulminant infection ( 3 ), chronic disease monitoring in at-risk populations like Cystic Fibrosis patients ( 8 ) and diagnosis of infection following antibiotic exposure ( 10 ).…”

“…Nevertheless, only a few clinical mNGS assays are currently available from commercial or academic providers ( 3 , 11 ), and their clinical utility remains uncertain ( 5 ). Recent studies examining the performance characteristics of mNGS for pathogen detection have estimated clinical sensitivity above 70% ( 1 , 10 ) and specificity approaching 99% ( 1 , 12 ). Nevertheless, other large, longitudinal studies of mNGS have demonstrated positivity rates at 32% ( 6 ), 49% ( 13 ), or 61% ( 4 ).…”