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"Answers in hours": A prospective clinical study using nanopore sequencing for bile duct cultures
Jennifer A Yonkus1, Emma Whittle2, Roberto Alva-Ruiz1
1Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinic, Rochester, MN.
Background:
Surgical site infection is a major source of morbidity in patients undergoing pancreatic head resection and is often from organisms in intraoperative bile duct cultures. As such, many institutions use prolonged prophylactic antibiotics and tailor based on bile duct cultures. However, standard cultures take days, leaving many patients unnecessarily on prolonged antibiotics. Nanopore sequencing can provide data in hours and, thus, has the potential to improve antibiotic stewardship. The present study investigates the feasibility of nanopore sequencing in intraoperative bile samples.
Methods:
Patients undergoing pancreatic head resection were included. Intra-operative bile microbial profiles were determined with standard cultures and nanopore sequencing. Antibiotic recommendations were generated, and time-to-results determined for both methods. Organism yields, resistance patterns, antibiotic recommendations, and costs were compared.
Results:
Out of 42 patients, 22 (52%) had samples resulting in positive standard cultures. All positive standard cultures had microbes detected using nanopore sequencing. All 20 patients with negative standard cultures had negative nanopore sequencing. Nanopore sequencing detected more bacterial species compared to standard cultures (10.5 vs 4.4, p < 0.05) and more resistance genotypes (10.3 vs 2.7, p < 0.05). Antimicrobial recommendations based on nanopore sequencing provided coverage for standard cultures in 27 out of 44 (61%) samples, with broader coverage recommended by nanopore sequencing in 13 out of 27 (48%) of these samples. Nanopore sequencing results were faster (8 vs 98 hours) than standard cultures but had higher associated costs ($165 vs $38.49).
Conclusion:
Rapid microbial profiling with nanopore sequencing is feasible with broader organism and resistance profiling compared to standard cultures. Nanopore sequencing has perfect negative predictive value and can potentially improve antibiotic stewardship; thus, a randomized control trial is under development.
Insights
Nanopore sequencing rapidly identifies microbes in bile samples from pancreatic surgery patients, offering broader insights than standard cultures. This technology can improve antibiotic stewardship by providing faster, more comprehensive results.
Area of Science:
- Microbiology
- Genomics
- Surgical Infectious Diseases
Background:
- Surgical site infections are a significant complication following pancreatic head resection.
- Intraoperative bile cultures guide antibiotic therapy, but standard methods delay results.
- Prolonged prophylactic antibiotics are often used due to slow culture turnaround times.
Purpose of the Study:
- To investigate the feasibility of using nanopore sequencing for intraoperative bile sample analysis.
- To compare nanopore sequencing with standard cultures for microbial profiling and antibiotic recommendations.
- To assess the potential of nanopore sequencing to enhance antibiotic stewardship in pancreatic surgery.
Main Methods:
- Intraoperative bile samples from patients undergoing pancreatic head resection were analyzed.
- Microbial profiles were determined using both standard bacterial cultures and nanopore sequencing.
- Time-to-result, organism yield, resistance patterns, and antibiotic recommendations were compared.
Main Results:
- Nanopore sequencing detected more bacterial species and resistance genotypes than standard cultures.
- Results from nanopore sequencing were significantly faster (8 hours vs. 98 hours).
- Nanopore sequencing provided broader antimicrobial coverage recommendations in a majority of cases.
Conclusions:
- Rapid microbial profiling via nanopore sequencing is feasible and offers comprehensive organism and resistance data.
- Nanopore sequencing demonstrates a perfect negative predictive value, crucial for ruling out infection.
- This technology holds promise for improving antibiotic stewardship, with a randomized trial planned.
