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Highly multiplexed targeted sequencing strategy for infectious disease surveillance. | LitMetric

Highly multiplexed targeted sequencing strategy for infectious disease surveillance.

BMC Biotechnol

Department of Biochemistry and Biophysics, Faculty of Science, Stockholm University, Svante Arrhenius väg 16C, Stockholm, 104 05, Sweden.

Published: August 2023

AI Article Synopsis

  • Global efforts to detect diseases of poverty face challenges due to expensive detection methods and low levels of microbial DNA in samples, leading to inefficient healthcare use.
  • This study adapted molecular inversion probes (MIPs) for a cost-effective way to enrich and analyze microbial infections from blood samples, targeting various bacteria and fungi as well as antimicrobial resistance markers.
  • The method demonstrated high specificity and accuracy, identifying pathogens in most samples without complex preparations or data analysis, making it suitable for health settings with limited resources.

Article 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.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10463907PMC
http://dx.doi.org/10.1186/s12896-023-00804-7DOI Listing

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