Next Generation Sequencing Outperforms Cultivation-Based Methods for Detection of Bacterial Genera in Bile After...

Area of Science:

• Hepatology
• Microbiology
• Transplantation Medicine

Background:

• Bacterial cholangitis is a frequent complication post-liver transplantation (LTX), particularly with ischemic biliary lesions or anastomotic strictures.
• Current diagnostics rely on standard microbiological cultivation (SMC) of bile, which has limitations in detecting all relevant bacteria.
• Antibiotic treatment decisions are based on SMC, potentially leading to suboptimal therapy due to incomplete microbial identification.

Purpose of the Study:

• To evaluate the diagnostic value of next-generation sequencing (NGS) as an adjunct to SMC.
• To compare the bacterial detection capabilities of NGS versus SMC in bile samples from liver transplant recipients.
• To assess the potential of NGS in improving the accuracy of diagnosing bacterial cholangitis.

Main Methods:

• A total of 242 stored bile samples from patients post-LTX were analyzed using NGS targeting the 16S rRNA gene.
• SMC was performed on 135 (56%) fresh bile samples as part of routine clinical care.
• Results from NGS were compared with findings from SMC to determine differences in bacterial genus detection.

Main Results:

• NGS detected significantly more bacterial genera in bile samples than SMC (P = 5.42 × 10⁻⁷⁴).
• SMC demonstrated insufficient discovery of bacterial genera compared to NGS, missing numerous genera identified by sequencing.
• NGS showed higher sensitivity, even in patients who had received antibiotics prior to endoscopic retrograde cholangiography (ERC).

Conclusions:

• NGS is more sensitive than SMC for detecting bacteria in bile samples from liver transplant patients.
• Clinical parameters did not improve the discovery rates of SMC, highlighting its limitations.
• A combined approach utilizing both NGS and SMC is recommended for enhanced diagnostics and more targeted antibiotic treatments.