Highly multiplexed targeted sequencing strategy for infectious disease surveillance

BMC Biotechnology

Research

Flor Pineiro¹  Anastasia Magoulopoulou¹  Iván Hernández-Neuta¹  Mats Nilsson¹  Jan Gorm Lisby²  Mats Gulberg³ 

[1] Department of Biochemistry and Biophysics, Faculty of Science, Stockholm University, Svante Arrhenius väg 16C, 104 05, Stockholm, Sweden;Science for Life Laboratory (SciLifeLab), Tomtebodavägen 23, 171 65, Solna, Sweden;Department of Clinical Microbiology, Amager and Hvidovre Hospital, University of Copenhagen, Kettegaard Alle 30, 2650, Hvidovre, Denmark;Q-linea AB, Dag Hammarskjölds Väg 52A, 752 37, Uppsala, Sweden;

关键词: Molecular inversion probes (MIPs);    Next generation sequencing (NGS);    Infectious diseases;    Diagnostics;    Disease surveillance;    Pathogen detection;   

DOI  :  10.1186/s12896-023-00804-7

 received in 2023-03-13, accepted in 2023-08-17,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundGlobal 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).ResultsOur 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.ConclusionsOverall, 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.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

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