期刊
MICROORGANISMS
卷 9, 期 8, 页码 -出版社
MDPI
DOI: 10.3390/microorganisms9081672
关键词
target enrichment; antimicrobial resistance; next generation sequencing; human pathogens; urinary tract infection; synovial fluid; infectious disease surveillance; molecular detection
类别
资金
- Vienna Business Agency [24478239]
- Austrian Research Promotion Agency (FFG) [871243, 879570]
The newly developed ARESdb AMR panel allows for comprehensive and sensitive detection of antimicrobial resistance markers. Compared to metagenomics sequencing, the capture-based workflow has higher sensitivity and lower sequencing depth requirements, with a limit of detection for specific pathogens in synovial fluid and urine samples of 1000 CFU/mL. It also enables culture-free detection of bacterial taxa and AMR markers with an average sensitivity of 99% in septic patient samples.
The increasing incidence of antimicrobial resistance (AMR) is a major global challenge. Routine techniques for molecular AMR marker detection are largely based on low-plex PCR and detect dozens to hundreds of AMR markers. To allow for comprehensive and sensitive profiling of AMR markers, we developed a capture-based next generation sequencing (NGS) workflow featuring a novel AMR marker panel based on the curated AMR database ARESdb. Our primary objective was to compare the sensitivity of target enrichment-based AMR marker detection to metagenomics sequencing. Therefore, we determined the limit of detection (LOD) in synovial fluid and urine samples across four key pathogens. We further demonstrated proof-of-concept for AMR marker profiling from septic samples using a selection of urine samples with confirmed monoinfection. The results showed that the capture-based workflow is more sensitive and requires lower sequencing depth compared with metagenomics sequencing, allowing for comprehensive AMR marker detection with an LOD of 1000 CFU/mL. Combining the ARESdb AMR panel with 16S rRNA gene sequencing allowed for the culture-free detection of bacterial taxa and AMR markers directly from septic patient samples at an average sensitivity of 99%. Summarizing, the newly developed ARESdb AMR panel may serve as a valuable tool for comprehensive and sensitive AMR marker detection.
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