MinION: Rapid culture-independent metagenomic bacterial pathogen identification during breast-implant salvage procedures
Mathew T. Epps, MS, MD, DABS, Taylor K. Pels, BA, Mark Brzezienski, MS, MS, FACS.
University of Tennessee College of Medicine Chattanooga, Chattanooga, TN, USA.
Background: Implant-associated infections continue to complicate reconstructive breast surgery. Traditional culture-based studies, requiring multiple days for completion, delay targeted anti-microbial treatment. Next-generation Sequencing (NGS) allows for rapid non-discretionary whole-genome DNA sequencing through nanopore technology. The MinION™ is a USB-powered palm-sized NGS nanopore device. Though NGS nanopore sample preparation protocols are in their infancy, this device has promise in bacterial species and antimicrobial-resistance identification. In this study, the MinION™ is utilized to rapidly identify infectious pathogens during implant-based breast reconstruction (IBR) salvage techniques.
Methods: Peri-prosthetic fluid collections were aspirated prior to implant-salvage procedures. Study aspirates (n=3) underwent both traditional bacterial culture and metagenomic analysis. Bacterial DNA (16S) was purified and amplified from a 1cc specimen aliquot, then sequenced using the MinION™ (10-30min sequencing). A standard E. coli lambda-virus was the control. Real-time analysis was performed using ONT’s Epi2ME software (CARD database) and compared to culture findings.
Results: Sequence data from the study set (n=3) accurately matched culture results and identified bacterial species with gene allele alignment to antibiotic-resistance genes included in the ARMA(CARD)-database across multiple taxons. Additionally, NGS sequencing revealed polyclonal infections not identified during routine culture.
Conclusions: This study demonstrates the potential to identify infectious pathogens during IBR salvage procedures in near real-time using the MinION™, in comparison to protracted traditional culture techniques, though refinements in specimen preparation protocols are essential. NGS technologies may revolutionize the speed and accuracy of pathogen diagnosis, improve antimicrobial stewardship, and additionally may perhaps be a tool for the surveillance of a BIA-ALCL genetic footprint. 
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