Rapid Whole Genome Characterization of High-Risk Pathogens Using Long-Read Sequencing to Identify Potential...

Area of Science:

• Microbiology
• Genomics
• Infectious Disease Epidemiology

Background:

• Whole genome sequencing (WGS) is crucial for identifying healthcare-associated infection (HAI) pathogen transmission.
• Current short-read Illumina WGS methods are labor- and time-intensive, hindering timely infection prevention and control (IPC).
• Advancements in long-read Oxford Nanopore Technologies (ONT) offer potential for faster, more accessible WGS.

Purpose of the Study:

• To develop and validate a low-resource utilization approach using ONT sequencing for accurate WGS-based comparisons of HAI pathogens.
• To enable WGS analysis within a timeframe suitable for effective IPC interventions.

Main Methods:

• Prospective WGS of antimicrobial-resistant pathogens using the ONT MinION sequencer and Dorado basecalling.
• Assessment of potential transmission using Ridom SeqSphere+ and MINTyper for core genome analysis.
• Comparison of ONT pipeline accuracy against Illumina-based WGS data.

Main Results:

• A single operator processed 242 bacterial isolates from 216 patients over six months.
• The ONT pipeline achieved a Q score of 60, comparable to Illumina, with low coverage (40X).
• Mean turnaround time from DNA extraction to genetic analysis was 2 days, identifying five transmission clusters.

Conclusions:

• A stand-alone ONT pipeline rapidly and accurately detects potentially transmitted HAI pathogens, correlating with epidemiological data.
• This low-resource method can enhance the efficiency of HAI transmission detection and prevention strategies.