Real-time Plasmid Transmission Detection Pipeline

Overview

Journal Microbiol Spectr

Specialty Microbiology

Date 2024 Oct 29

PMID 39470278

Authors

Natalie Scherff

Jorg Rothganger

Thomas Weniger

Alexander Mellmann

Dag Harmsen

Affiliations

Soon will be listed here.

Abstract

Importance: Plasmid-mediated spread of antimicrobial resistance is a major challenge for clinical microbiology, and monitoring of potential plasmid transmissions is essential to combat further dissemination. Whole-genome sequencing is often used to surveil nosocomial transmissions but usually limited to the detection of clonal transmissions (based on chromosomal markers). Recent advances in long-read sequencing technologies enable full reconstruction of plasmids and the detection of very similar plasmids, but so far, easy-to-use bioinformatic tools for this purpose have been missing. Here, we present an evaluation of an innovative real-time plasmid transmission detection pipeline. It is integrated into the GUI-based SeqSphere software, which already offers core-genome multi-locus sequence typing-based pathogen outbreak detection. It requires very limited bioinformatics knowledge, and its database, automated analyses, and alert system make it well suited for prospective clinical application.

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