Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting
Abstract Aim The aim of the present study is to compare the performance of 16S rRNA Nanopore sequencing and conventional culture in detecting infectious pathogens in patients with suspected meningitis in a resource-limited setting without extensive bioinformatics expertise. Methods DNA was isolated...
| Main Authors: | , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2022-09-01
|
| Series: | Annals of Clinical Microbiology and Antimicrobials |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12941-022-00530-6 |
| _version_ | 1798002993096818688 |
|---|---|
| author | Srinivas Reddy Pallerla Do Van Dong Le Thi Kieu Linh Trinh Van Son Dao Thanh Quyen Phan Quoc Hoan Ngo Tat Trung Nguyen Trong The Jule Rüter Sébastien Boutin Dennis Nurjadi Bui Tien Sy Peter G. Kremsner Christian G. Meyer Le Huu Song Thirumalaisamy P. Velavan |
| author_facet | Srinivas Reddy Pallerla Do Van Dong Le Thi Kieu Linh Trinh Van Son Dao Thanh Quyen Phan Quoc Hoan Ngo Tat Trung Nguyen Trong The Jule Rüter Sébastien Boutin Dennis Nurjadi Bui Tien Sy Peter G. Kremsner Christian G. Meyer Le Huu Song Thirumalaisamy P. Velavan |
| author_sort | Srinivas Reddy Pallerla |
| collection | DOAJ |
| description | Abstract Aim The aim of the present study is to compare the performance of 16S rRNA Nanopore sequencing and conventional culture in detecting infectious pathogens in patients with suspected meningitis in a resource-limited setting without extensive bioinformatics expertise. Methods DNA was isolated from the cerebrospinal fluid (CSF) of 30 patients with suspected bacterial meningitis. The isolated DNA was subjected to 16S sequencing using MinION™. The data were analysed in real time via the EPI2ME cloud platform. The Nanopore sequencing was done in parallel to routine microbiological diagnostics. Results Nanopore sequencing detected bacterial pathogens to species level in 13 of 30 (43%) samples. CSF culture showed 40% (12/30) positivity. In 21 of 30 patients (70%) with suspected bacterial meningitis, both methods yielded concordant results. About nine of 30 samples showed discordant results, of these five were false positive and four were false negative. In five of the culture negative results, nanopore sequencing was able to detect pathogen genome, due to the higher sensitivity of the molecular diagnostics. In two other samples, the CSF culture revealed Cryptococcus neoformans and Streptococcus pneumoniae, which were not detected by Nanopore sequencing. Overall, using both the cultures and 16S Nanopore sequencing, positivity rate increased from 40% (12/30) to 57% (17/30). Conclusion Next-generation sequencing could detect pathogens within six hours and could become an important tool for both pathogen screening and surveillance in low- and middle-income countries (LMICs) that do not have direct access to extensive bioinformatics expertise. |
| first_indexed | 2024-04-11T12:01:12Z |
| format | Article |
| id | doaj.art-c8233bc704bb4eefa5fbf1c8e469bdb6 |
| institution | Directory Open Access Journal |
| issn | 1476-0711 |
| language | English |
| last_indexed | 2024-04-11T12:01:12Z |
| publishDate | 2022-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Annals of Clinical Microbiology and Antimicrobials |
| spelling | doaj.art-c8233bc704bb4eefa5fbf1c8e469bdb62022-12-22T04:24:51ZengBMCAnnals of Clinical Microbiology and Antimicrobials1476-07112022-09-012111810.1186/s12941-022-00530-6Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited settingSrinivas Reddy Pallerla0Do Van Dong1Le Thi Kieu Linh2Trinh Van Son3Dao Thanh Quyen4Phan Quoc Hoan5Ngo Tat Trung6Nguyen Trong The7Jule Rüter8Sébastien Boutin9Dennis Nurjadi10Bui Tien Sy11Peter G. Kremsner12Christian G. Meyer13Le Huu Song14Thirumalaisamy P. Velavan15Institute of Tropical Medicine, Universitätsklinikum TübingenVietnamese-German Center for Medical Research, VG-CAREInstitute of Tropical Medicine, Universitätsklinikum TübingenVietnamese-German Center for Medical Research, VG-CAREVietnamese-German Center for Medical Research, VG-CAREVietnamese-German Center for Medical Research, VG-CAREVietnamese-German Center for Medical Research, VG-CAREVietnamese-German Center for Medical Research, VG-CAREInstitute of Tropical Medicine, Universitätsklinikum TübingenDepartment of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University HospitalDepartment of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University HospitalVietnamese-German Center for Medical Research, VG-CAREInstitute of Tropical Medicine, Universitätsklinikum TübingenInstitute of Tropical Medicine, Universitätsklinikum TübingenVietnamese-German Center for Medical Research, VG-CAREInstitute of Tropical Medicine, Universitätsklinikum TübingenAbstract Aim The aim of the present study is to compare the performance of 16S rRNA Nanopore sequencing and conventional culture in detecting infectious pathogens in patients with suspected meningitis in a resource-limited setting without extensive bioinformatics expertise. Methods DNA was isolated from the cerebrospinal fluid (CSF) of 30 patients with suspected bacterial meningitis. The isolated DNA was subjected to 16S sequencing using MinION™. The data were analysed in real time via the EPI2ME cloud platform. The Nanopore sequencing was done in parallel to routine microbiological diagnostics. Results Nanopore sequencing detected bacterial pathogens to species level in 13 of 30 (43%) samples. CSF culture showed 40% (12/30) positivity. In 21 of 30 patients (70%) with suspected bacterial meningitis, both methods yielded concordant results. About nine of 30 samples showed discordant results, of these five were false positive and four were false negative. In five of the culture negative results, nanopore sequencing was able to detect pathogen genome, due to the higher sensitivity of the molecular diagnostics. In two other samples, the CSF culture revealed Cryptococcus neoformans and Streptococcus pneumoniae, which were not detected by Nanopore sequencing. Overall, using both the cultures and 16S Nanopore sequencing, positivity rate increased from 40% (12/30) to 57% (17/30). Conclusion Next-generation sequencing could detect pathogens within six hours and could become an important tool for both pathogen screening and surveillance in low- and middle-income countries (LMICs) that do not have direct access to extensive bioinformatics expertise.https://doi.org/10.1186/s12941-022-00530-6NanoporeBacterial meningitisVietnam16S rRNANext-generation sequencingDiagnosis and pathogen genome |
| spellingShingle | Srinivas Reddy Pallerla Do Van Dong Le Thi Kieu Linh Trinh Van Son Dao Thanh Quyen Phan Quoc Hoan Ngo Tat Trung Nguyen Trong The Jule Rüter Sébastien Boutin Dennis Nurjadi Bui Tien Sy Peter G. Kremsner Christian G. Meyer Le Huu Song Thirumalaisamy P. Velavan Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting Annals of Clinical Microbiology and Antimicrobials Nanopore Bacterial meningitis Vietnam 16S rRNA Next-generation sequencing Diagnosis and pathogen genome |
| title | Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting |
| title_full | Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting |
| title_fullStr | Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting |
| title_full_unstemmed | Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting |
| title_short | Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting |
| title_sort | diagnosis of pathogens causing bacterial meningitis using nanopore sequencing in a resource limited setting |
| topic | Nanopore Bacterial meningitis Vietnam 16S rRNA Next-generation sequencing Diagnosis and pathogen genome |
| url | https://doi.org/10.1186/s12941-022-00530-6 |
| work_keys_str_mv | AT srinivasreddypallerla diagnosisofpathogenscausingbacterialmeningitisusingnanoporesequencinginaresourcelimitedsetting AT dovandong diagnosisofpathogenscausingbacterialmeningitisusingnanoporesequencinginaresourcelimitedsetting AT lethikieulinh diagnosisofpathogenscausingbacterialmeningitisusingnanoporesequencinginaresourcelimitedsetting AT trinhvanson diagnosisofpathogenscausingbacterialmeningitisusingnanoporesequencinginaresourcelimitedsetting AT daothanhquyen diagnosisofpathogenscausingbacterialmeningitisusingnanoporesequencinginaresourcelimitedsetting AT phanquochoan diagnosisofpathogenscausingbacterialmeningitisusingnanoporesequencinginaresourcelimitedsetting AT ngotattrung diagnosisofpathogenscausingbacterialmeningitisusingnanoporesequencinginaresourcelimitedsetting AT nguyentrongthe diagnosisofpathogenscausingbacterialmeningitisusingnanoporesequencinginaresourcelimitedsetting AT juleruter diagnosisofpathogenscausingbacterialmeningitisusingnanoporesequencinginaresourcelimitedsetting AT sebastienboutin diagnosisofpathogenscausingbacterialmeningitisusingnanoporesequencinginaresourcelimitedsetting AT dennisnurjadi diagnosisofpathogenscausingbacterialmeningitisusingnanoporesequencinginaresourcelimitedsetting AT buitiensy diagnosisofpathogenscausingbacterialmeningitisusingnanoporesequencinginaresourcelimitedsetting AT petergkremsner diagnosisofpathogenscausingbacterialmeningitisusingnanoporesequencinginaresourcelimitedsetting AT christiangmeyer diagnosisofpathogenscausingbacterialmeningitisusingnanoporesequencinginaresourcelimitedsetting AT lehuusong diagnosisofpathogenscausingbacterialmeningitisusingnanoporesequencinginaresourcelimitedsetting AT thirumalaisamypvelavan diagnosisofpathogenscausingbacterialmeningitisusingnanoporesequencinginaresourcelimitedsetting |