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 meningiti...
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2019-06-01
|
| Series: | BMC Infectious Diseases |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12879-019-4132-y |
| _version_ | 1818408975635316736 |
|---|---|
| author | Xi-xi Zhang Ling-yun Guo Lin-lin Liu Ao Shen Wen-ya Feng Wen-hua Huang Hui-li Hu Bing Hu Xin Guo Tian-ming Chen He-ying Chen Yong-qiang Jiang Gang Liu |
| author_facet | Xi-xi Zhang Ling-yun Guo Lin-lin Liu Ao Shen Wen-ya Feng Wen-hua Huang Hui-li Hu Bing Hu Xin Guo Tian-ming Chen He-ying Chen Yong-qiang Jiang Gang Liu |
| author_sort | Xi-xi Zhang |
| collection | DOAJ |
| description | 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. 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. |
| first_indexed | 2024-12-14T09:52:16Z |
| format | Article |
| id | doaj.art-54b9f7718db7477c8d03bd8c056c894b |
| institution | Directory Open Access Journal |
| issn | 1471-2334 |
| language | English |
| last_indexed | 2024-12-14T09:52:16Z |
| publishDate | 2019-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Infectious Diseases |
| spelling | doaj.art-54b9f7718db7477c8d03bd8c056c894b2022-12-21T23:07:30ZengBMCBMC Infectious Diseases1471-23342019-06-011911810.1186/s12879-019-4132-yThe diagnostic value of metagenomic next-generation sequencing for identifying Streptococcus pneumoniae in paediatric bacterial meningitisXi-xi Zhang0Ling-yun Guo1Lin-lin Liu2Ao Shen3Wen-ya Feng4Wen-hua Huang5Hui-li Hu6Bing Hu7Xin Guo8Tian-ming Chen9He-ying Chen10Yong-qiang Jiang11Gang Liu12Key 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 HealthKey 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 HealthKey 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 HealthTianjin Medical Laboratory, BGI-TianjinKey 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 HealthState Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical ScienceKey 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 HealthKey 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 HealthKey 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 HealthKey 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 HealthKey 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 HealthState Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical ScienceKey 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 HealthAbstract 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.http://link.springer.com/article/10.1186/s12879-019-4132-yMetagenomic next-generation sequencing (mNGS)SensitivitySpecificityStreptococcus pneumoniaMeningitisChildren |
| spellingShingle | Xi-xi Zhang Ling-yun Guo Lin-lin Liu Ao Shen Wen-ya Feng Wen-hua Huang Hui-li Hu Bing Hu Xin Guo Tian-ming Chen He-ying Chen Yong-qiang Jiang Gang Liu The diagnostic value of metagenomic next-generation sequencing for identifying Streptococcus pneumoniae in paediatric bacterial meningitis BMC Infectious Diseases Metagenomic next-generation sequencing (mNGS) Sensitivity Specificity Streptococcus pneumonia Meningitis Children |
| title | The diagnostic value of metagenomic next-generation sequencing for identifying Streptococcus pneumoniae in paediatric bacterial meningitis |
| title_full | The diagnostic value of metagenomic next-generation sequencing for identifying Streptococcus pneumoniae in paediatric bacterial meningitis |
| title_fullStr | The diagnostic value of metagenomic next-generation sequencing for identifying Streptococcus pneumoniae in paediatric bacterial meningitis |
| title_full_unstemmed | The diagnostic value of metagenomic next-generation sequencing for identifying Streptococcus pneumoniae in paediatric bacterial meningitis |
| title_short | The diagnostic value of metagenomic next-generation sequencing for identifying Streptococcus pneumoniae in paediatric bacterial meningitis |
| title_sort | diagnostic value of metagenomic next generation sequencing for identifying streptococcus pneumoniae in paediatric bacterial meningitis |
| topic | Metagenomic next-generation sequencing (mNGS) Sensitivity Specificity Streptococcus pneumonia Meningitis Children |
| url | http://link.springer.com/article/10.1186/s12879-019-4132-y |
| work_keys_str_mv | AT xixizhang thediagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT lingyunguo thediagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT linlinliu thediagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT aoshen thediagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT wenyafeng thediagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT wenhuahuang thediagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT huilihu thediagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT binghu thediagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT xinguo thediagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT tianmingchen thediagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT heyingchen thediagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT yongqiangjiang thediagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT gangliu thediagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT xixizhang diagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT lingyunguo diagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT linlinliu diagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT aoshen diagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT wenyafeng diagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT wenhuahuang diagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT huilihu diagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT binghu diagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT xinguo diagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT tianmingchen diagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT heyingchen diagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT yongqiangjiang diagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis AT gangliu diagnosticvalueofmetagenomicnextgenerationsequencingforidentifyingstreptococcuspneumoniaeinpaediatricbacterialmeningitis |