Nanopore 16S-Full Length and ITS Sequencing for Microbiota Identification in Intra-Abdominal Infections

Area of Science:

• Microbiology
• Genomics
• Infectious Diseases

Background:

• Intra-abdominal infections (IAIs) pose significant clinical challenges, potentially leading to severe outcomes if not treated promptly.
• Conventional culture-based methods for pathogen identification in IAIs have limitations, including long turnaround times (TATs) and difficulty detecting polymicrobial or anaerobic infections.

Purpose of the Study:

• To evaluate the utility of Oxford Nanopore Technology (ONT) sequencing for rapid and comprehensive microbiota analysis in patients with IAIs.
• To compare ONT sequencing with traditional culture-based methods for pathogen detection in IAIs.

Main Methods:

• Implementation of ONT sequencing for microbiota analysis in 16 patients with IAIs at Taichung Veterans General Hospital.
• DNA extraction, followed by full-length 16S rRNA and ITS region amplification and ONT sequencing of patient specimens.

Main Results:

• ONT sequencing identified a diverse range of bacteria and fungi in IAIs, with read counts varying widely.
• Polymicrobial and anaerobe-enriched communities were prevalent in lower gastrointestinal tract infections, while upper GI perforations showed distinct microbial profiles.
• Sequencing results were concordant with culture findings for common pathogens like *Escherichia coli* and *Candida albicans*, and uniquely identified anaerobic or low-abundance taxa.

Conclusions:

• ONT sequencing provides results within 24 hours, significantly reducing TAT compared to traditional methods.
• The technology successfully detected pathogens in culture-negative cases, highlighting its advantage in complex IAIs.
• ONT sequencing is a valuable tool for expeditious and comprehensive diagnosis of IAIs, improving patient management.