Streamlining diagnosis of bloodstream infections with high-throughput microfluidic isolation and aptamer-based...

Bloodstream infections have high morbidity and mortality rates. Currently, the gold standard for diagnosing bloodstream infections involves re-culturing bacteria from positive culture bottles for mass spectrometry and drug resistance analysis. However, this process incurs a delay of at least a day, which can lead to a 7.6 % increase in the hourly mortality rate. Therefore, accelerating the identification of bacterial species and determining drug resistance is critical. Here, we present a new high-throughput Dean flow fractionation (DFF^HT) spiral chip to efficiently sort pathogenic bacteria from positive blood culture bottles, achieving an efficiency >80 %. Pathogens enriched in DFF^HT devices are directly identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), followed by the determination of drug-resistance by aptamer fluorescence, thereby eliminating the need for plate recultivation. Three high probability drug-resistant bacteria (carbapenem-resistant Acinetobacter baumannii [CRAB], carbapenem-resistant Pseudomonas aeruginosa [CRPA], and methicillin-resistant Staphylococcus aureus [MRSA]) were successfully identified directly from positive blood culture bottles. This combination of DFF^HT microfluidic bacterial isolation and aptamer-based detection of drug resistance can be completed within 1 h with a 2 mL sample from a positive blood bottle, which is helpful for doctors choosing the right antibiotic in time to treat the patient effectively.