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Capsular Serotyping of Streptococcus pneumoniae Using the Quellung Reaction
Published on: February 24, 2014
The diagnostic value of metagenomic next-generation sequencing for identifying Streptococcus pneumoniae in paediatric
Xi-Xi Zhang1, Ling-Yun Guo1, Lin-Lin Liu1
1Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China.
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. pneumoniaein 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.
Insights
Metagenomic next-generation sequencing (mNGS) shows high accuracy in identifying Streptococcus pneumoniae in pediatric bacterial meningitis. Pathogen load in CSF correlates with collection time, and mNGS is less impacted by prior antibiotic use than traditional culture.
Area of Science:
- Microbiology
- Infectious Diseases
- Genomics
Background:
- Limited research exists on the diagnostic utility of metagenomic next-generation sequencing (mNGS) for single pathogens in cerebrospinal fluid (CSF).
- Streptococcus pneumoniae is a significant cause of bacterial meningitis in children.
Purpose of the Study:
- To evaluate the diagnostic value of mNGS for identifying Streptococcus pneumoniae (S. pneumoniae) in pediatric bacterial meningitis cases.
Main Methods:
- Retrospective review of bacterial meningitis cases at Beijing Children's Hospital from October 2014 to July 2018.
- Analysis of clinical features and pathogens, including comparison of mNGS with culture and antigen testing.
Main Results:
- mNGS identified S. pneumoniae in 23.7% of 135 pediatric bacterial meningitis cases.
- Compared to culture, mNGS demonstrated a sensitivity of 73.1% and specificity of 88.1%.
- Higher pathogen load (unique reads) was observed in CSF collected earlier from symptom onset, and mNGS showed less inhibition by pre-collection antibiotics.
Conclusions:
- mNGS offers high sensitivity and specificity for S. pneumoniae detection in pediatric bacterial meningitis.
- CSF collection timing influences mNGS pathogen load results.
- mNGS provides a diagnostic advantage over culture when antibiotics have been administered prior to sample collection.
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