Genomic surveillance of multidrug-resistant organisms based on long-read sequencing

Area of Science:

• Genomics
• Microbiology
• Public Health

Background:

• Multidrug-resistant organisms (MDRO) present a global public health challenge.
• Effective surveillance and infection prevention require molecular characterization of MDRO.
• Long-read sequencing offers a promising alternative to short-read sequencing for MDRO analysis.

Purpose of the Study:

• To evaluate the utility of long-read sequencing for molecular characterization of MDRO.
• To assess its accuracy for surveillance and transmission studies.
• To determine its applicability in resource-constrained settings.

Main Methods:

• Automated DNA extraction from 356 MDRO isolates.
• Whole-genome sequencing (WGS) using both long-read (Nanopore) and short-read (Illumina) technologies.
• Assembly and analysis of long-read WGS data for typing (MLST, wgMLST, iMLVA) and resistance gene identification.

Main Results:

• Long-read sequencing achieved >95% concordance in wgMLST profiles with short-read data for most species.
• High sensitivity and specificity (92-100%/99-100%) for antimicrobial resistance gene detection.
• Successful analysis of a methicillin-resistant Staphylococcus aureus (MRSA) outbreak using long-read data.

Conclusions:

• Long-read sequencing is accurate and suitable for MDRO typing and outbreak analysis in genomic surveillance.
• Further optimization is needed for Pseudomonas aeruginosa analysis.
• Low implementation costs and rapid library preparation make it ideal for resource-limited settings.