High Throughput Pathogen Monitoring and Diagnostics on the Fluidigm BioMarkTM Microfluidics Platform

Modernization of the pathogen diagnostic field facilitated by application of high throughput approaches such as microfluidics quantitative PCR and high throughput sequencing is a necessary step to move to cheaper, faster, and more precise detection of infectious diseases.  We have developed and analytically validated a high throughput pathogen monitoring system based on Fluidigm’s Biomark^TM technology that can assess the presence and load of 47 pathogens at once in duplicate assays across 96 samples.  With an average limit of detection of less than 10 copies per chamber, specificity equal to that of single assay qPCR platforms, repeatability and reproducibility generally >0.95, and the ability to conduct over 36,000 qPCR reactions per day at a cost of less than 40 cents per assay, the performance of this system is hard to beat.  Moreover, the Access Array^TM system allows the rapid development of sequencing libraries based on up to 384 indexed samples amplified across 48 assays.  Our laboratory is not only conducting pathogen monitoring and diagnostics, but is merging quantitative pathogen detection with host transcriptome analyses on the same platform to identify the linkages between pathogen loads and host immune response.  This talk will outline not only the development and evaluation of the pathogen monitoring platform, but will provide specific examples of the ways in which it is currently being applied in research to address the role of pathogens and other stressors in the decreasing abundance and productivity of wild salmon.