Seth K. Bechis, MD, presented “Point-Counterpoint: Next Generation Sequencing vs. Standard Culture – Next Generation Sequencing” during the 30th Annual Perspectives in Urology: Point-Counterpoint, on March 10, 2023, at Humphreys Half Moon Inn, San Diego, California.
How to cite: Bechis, Seth K. “Point-Counterpoint: Next Generation Sequencing vs. Standard Culture – Next Generation Sequencing.” March 10, 2023. Accessed Oct 2026. https://grandroundsinurology.com/point-counterpoint-next-generation-sequencing-vs-standard-culture-next-generation-sequencing/
Point-Counterpoint: Next Generation Sequencing vs. Standard Culture – Next Generation Sequencing – Summary
Seth K. Bechis, MD, expresses concerns with standard urine cultures and discusses the efficacy and efficiency of next generation sequencing. Dr. Bechis first examines standard urine cultures, noting their 30%-50% diagnostic error rate. He outlines other shortcomings of standard urine cultures, including their expensive and relatively slow process, inaccurate contamination results, unclear threshold for positive tests, and additional error rates.
Dr. Bechis cites two studies in which researchers discovered inaccuracies in urine culture results for clinically suspected UTI patients and women with dysuria. He then discusses polymerase chain reaction-based (PCR-based) assays and next generation sequencing (NGS). He highlights an advantage of this combination, explaining that it can detect every organism in a sample. Dr. Bechis evaluates PCR-based assays and NGS further and explains their ability to identify both bacteria and fungi.
He supports NGS technology by introducing three examples that compare standard urine cultures to NGS. These examples address UTI patients, cystitis patients, and renal stone patients.
Dr. Bechis highlights the increased detection capabilities of NGS compared to standard urine cultures, noting that NGS can even lead to better treatment and more appropriate antibiotic use. He also explores a pilot study that compared urine cultures to NGS and found that 80%–90% of physicians would have changed their preoperative antibiotics approach based on NGS results. Dr. Bechis completes his discussion by reviewing NGS benefits, advocating for NGS implementation in practice.
This lecture is part of a Point-Counterpoint debate. Its opposing lecture is “Point-Counterpoint: Next Generation Sequencing vs. Standard Culture–Standard Culture.”
About the 30th Annual Perspectives in Urology: Point Counterpoint conference: Presented by Program Chair and Grand Rounds in Urology Editor-in-Chief E. David Crawford, MD, this conference brought together leading experts in urology, medical oncology, and radiation oncology to discuss and debate the latest topics in genitourinary cancers, primarily prostate cancer and bladder cancer. This interactive conference offered topical lectures, pro/con debates, interesting-case presentations, interactive panel discussions, and interactive audience and faculty networking.
ABOUT THE AUTHOR
Seth K. Bechis, MD, MS, is an Associate Professor of Urology at the University of California, San Diego, San Diego, California. Dr. Bechis specializes in all procedures of the prostate, including minimally invasive procedures such as Rezum water vapor therapy and UroLift, as well as robotic surgery and GreenLight Laser photoselective vaporization of the prostate. His current research focuses on improving surgical techniques and clinical outcomes in stone disease, as well as tools for stone diagnosis and opiate-sparing pathways for managing pain.
Dr. Bechis earned his Masters of Science in Biomedical Sciences and his medical degree from the University of California, San Francisco. He completed his residency at Harvard University in Boston, Massachusetts. Dr. Bechis then completed a fellowship in Laparoscopy/Robotics and Endourology at the University of California, San Francisco, San Francisco, California.
Dr. Bechis is a member of several professional medical organizations, including the American Urological Association (AUA), the Endourological Society, and the Western Section of the AUA. He has won numerous awards and honors over the years, including the Whitehill Award for Excellence in Clinical Teaching in 2019, Plenary Address for Best Abstract from the AUA in 2015, and first place in the 2014 Max K. Willscher Resident Research Award Competition. Dr. Bechis has been invited to speak nationally and internationally at conferences on topics including benign prostatic hyperplasia and stone disease. His research has been featured in peer-reviewed medical journals, including Journal of Urology, Journal of Endourology, and World Journal of Urology. Additionally, Dr. Bechis was editor of First Aid Q&A for the USMLE Step 1, Second Edition, and has authored chapters for university handbooks.
