Title : Answers in hours – a prospective clinical study for rapid detection of pathogens and antibacterial resistance in surgical patients using oxford nanopore sequencing
Abstract:
Surgical site infections (SSI) are a major source of morbidity in patients undergoing pancreatic head resection. Infections are often caused by organisms detected in the bile duct, resulting in many institutions using prolonged prophylactic antibiotics that are later optimized based on bile cultures. Standard cultures, however, can take days to complete, leaving many patients on prolonged courses of antibiotics that may be either unnecessary or suboptimal. We evaluated the use of Oxford Nanopore (ONT) sequencing to rapidly detect microbial species and antibacterial resistance genes present in intraoperative bile aspirates.
Patients undergoing pancreatic head resection for any clinical indication at Mayo Clinic Rochester were recruited from April 2020 – October 2020. Patients received standard care and were monitored for 90 days postoperatively. Intraoperative bile microbial profiles were determined using standard cultures and an optimized ONT sequencing pipeline. Antibiotic recommendations were made using culture and ONT results, and average time-to-results was determined for both methods. Microbial species, antibiotic resistance, antibiotic recommendations, and time-to-result were compared to determine the clinical value of using ONT sequencing to characterize biliary microbes.
In total, 42 patients were recruited, this included 9 patients undergoing total pancreatectomy and 33 patients undergoing pancreaticoduodenectomy. Bile cultures were positive for 55% (n = 23) of patients, of which 4 developed a SSI. ONT sequencing had perfect predictive power for bile culture positivity and generated no false positives. Culture of all samples yielded polymicrobial findings, with typical biliary microbes, including Enterococcus spp., Streptococcus spp., Klebsiella spp., Enterobacter spp., and Candida spp. detected. Comparison of ONT to culture results revealed that the ONT protocol detected 75% of cultured bacterial species, 76% of cultured fungal species and predicted 81% of antibiotic resistance. Additionally, ONT sequencing improved species identification, increased detection of anaerobic species, and identified significant differences in biliary microbial populations between male and female patients. Comparison of antimicrobial recommendations based on culture and ONT results found correlative recommendations were made for 32% of patients. More critically, in 39% of patients, ONT-based recommendations would have resulted in administration of more narrow-spectrum antibiotics when compared to recommendations based off standard culture results. The average result turnaround time was significantly lower for ONT sequencing (8 - 14 hours) compared to the time taken for finalize standard culture results (98 hours).
Rapid identification of microbial species and antimicrobial resistance is achievable using ONT sequencing. Following demonstration that it is clinically safe to use ONT sequencing to guide antimicrobial therapy, ONT sequencing has the potential to improve antibiotic stewardship.
Audience Take Away:
- This research demonstrates the successful use of Oxford Nanopore Technology to rapidly characterize intraoperative biliary microbes and predict antibiotic resistance within hours. The protocol that we have developed is applicable to any clinical sample type and can be applied to a wide range of infectious diseases.
- The audience will benefit from learning about a new method of rapidly identifying and characterizing infectious disease. Use of this technique in the clinical setting could significantly reduce diagnostic time for infectious disease, leading to decreased use of broad-spectrum antibiotics and improved antibiotic stewardship.
