Highly multiplexed targeted sequencing strategy for infectious disease surveillance
Abstract Background Global efforts to characterize diseases of poverty are hampered by lack of affordable and comprehensive detection platforms, resulting in suboptimal allocation of health care resources and inefficient disease control. Next generation sequencing (NGS) can provide accurate data and...
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| Format: | Article |
| Language: | English |
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BMC
2023-08-01
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| Series: | BMC Biotechnology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12896-023-00804-7 |
| _version_ | 1797452195145187328 |
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| author | Iván Hernández-Neuta Anastasia Magoulopoulou Flor Pineiro Jan Gorm Lisby Mats Gulberg Mats Nilsson |
| author_facet | Iván Hernández-Neuta Anastasia Magoulopoulou Flor Pineiro Jan Gorm Lisby Mats Gulberg Mats Nilsson |
| author_sort | Iván Hernández-Neuta |
| collection | DOAJ |
| description | Abstract Background Global efforts to characterize diseases of poverty are hampered by lack of affordable and comprehensive detection platforms, resulting in suboptimal allocation of health care resources and inefficient disease control. Next generation sequencing (NGS) can provide accurate data and high throughput. However, shotgun and metagenome-based NGS approaches are limited by low concentrations of microbial DNA in clinical samples, requirements for tailored sample and library preparations plus extensive bioinformatics analysis. Here, we adapted molecular inversion probes (MIPs) as a cost-effective target enrichment approach to characterize microbial infections from blood samples using short-read sequencing. We designed a probe panel targeting 2 bacterial genera, 21 bacterial and 6 fungi species and 7 antimicrobial resistance markers (AMRs). Results Our approach proved to be highly specific to detect down to 1 in a 1000 pathogen DNA targets contained in host DNA. Additionally, we were able to accurately survey pathogens and AMRs in 20 out of 24 samples previously profiled with routine blood culture for sepsis. Conclusions Overall, our targeted assay identifies microbial pathogens and AMRs with high specificity at high throughput, without the need for extensive sample preparation or bioinformatics analysis, simplifying its application for characterization and surveillance of infectious diseases in medium- to low- resource settings. |
| first_indexed | 2024-03-09T15:05:17Z |
| format | Article |
| id | doaj.art-c070396d5198491c9314f8098d8638a0 |
| institution | Directory Open Access Journal |
| issn | 1472-6750 |
| language | English |
| last_indexed | 2024-03-09T15:05:17Z |
| publishDate | 2023-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biotechnology |
| spelling | doaj.art-c070396d5198491c9314f8098d8638a02023-11-26T13:43:52ZengBMCBMC Biotechnology1472-67502023-08-0123111010.1186/s12896-023-00804-7Highly multiplexed targeted sequencing strategy for infectious disease surveillanceIván Hernández-Neuta0Anastasia Magoulopoulou1Flor Pineiro2Jan Gorm Lisby3Mats Gulberg4Mats Nilsson5Department of Biochemistry and Biophysics, Faculty of Science, Stockholm UniversityDepartment of Biochemistry and Biophysics, Faculty of Science, Stockholm UniversityDepartment of Biochemistry and Biophysics, Faculty of Science, Stockholm UniversityDepartment of Clinical Microbiology, Amager and Hvidovre Hospital, University of CopenhagenQ-linea ABDepartment of Biochemistry and Biophysics, Faculty of Science, Stockholm UniversityAbstract Background Global efforts to characterize diseases of poverty are hampered by lack of affordable and comprehensive detection platforms, resulting in suboptimal allocation of health care resources and inefficient disease control. Next generation sequencing (NGS) can provide accurate data and high throughput. However, shotgun and metagenome-based NGS approaches are limited by low concentrations of microbial DNA in clinical samples, requirements for tailored sample and library preparations plus extensive bioinformatics analysis. Here, we adapted molecular inversion probes (MIPs) as a cost-effective target enrichment approach to characterize microbial infections from blood samples using short-read sequencing. We designed a probe panel targeting 2 bacterial genera, 21 bacterial and 6 fungi species and 7 antimicrobial resistance markers (AMRs). Results Our approach proved to be highly specific to detect down to 1 in a 1000 pathogen DNA targets contained in host DNA. Additionally, we were able to accurately survey pathogens and AMRs in 20 out of 24 samples previously profiled with routine blood culture for sepsis. Conclusions Overall, our targeted assay identifies microbial pathogens and AMRs with high specificity at high throughput, without the need for extensive sample preparation or bioinformatics analysis, simplifying its application for characterization and surveillance of infectious diseases in medium- to low- resource settings.https://doi.org/10.1186/s12896-023-00804-7Molecular inversion probes (MIPs)Next generation sequencing (NGS)Infectious diseasesDiagnosticsDisease surveillancePathogen detection |
| spellingShingle | Iván Hernández-Neuta Anastasia Magoulopoulou Flor Pineiro Jan Gorm Lisby Mats Gulberg Mats Nilsson Highly multiplexed targeted sequencing strategy for infectious disease surveillance BMC Biotechnology Molecular inversion probes (MIPs) Next generation sequencing (NGS) Infectious diseases Diagnostics Disease surveillance Pathogen detection |
| title | Highly multiplexed targeted sequencing strategy for infectious disease surveillance |
| title_full | Highly multiplexed targeted sequencing strategy for infectious disease surveillance |
| title_fullStr | Highly multiplexed targeted sequencing strategy for infectious disease surveillance |
| title_full_unstemmed | Highly multiplexed targeted sequencing strategy for infectious disease surveillance |
| title_short | Highly multiplexed targeted sequencing strategy for infectious disease surveillance |
| title_sort | highly multiplexed targeted sequencing strategy for infectious disease surveillance |
| topic | Molecular inversion probes (MIPs) Next generation sequencing (NGS) Infectious diseases Diagnostics Disease surveillance Pathogen detection |
| url | https://doi.org/10.1186/s12896-023-00804-7 |
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