Tracking Antimicrobial Resistant Organisms Timely: a workflow validation study for successive core-genome SNP-based...

Area of Science:

• Microbiology
• Genomics
• Infectious Diseases

Background:

• Effective hospital infection prevention and control (IPC) relies on timely data regarding antimicrobial-resistant (AMR) organism transmission.
• Methicillin-resistant Staphylococcus aureus (MRSA) poses a significant nosocomial threat, necessitating rapid detection methods.

Purpose of the Study:

• To develop and evaluate a successive core-genome SNP (cgSNP)-based phylogenetic analysis workflow, named TAROT, utilizing Oxford Nanopore Technologies (ONT) sequencing.
• To compare the performance of the TAROT workflow with traditional Illumina sequencing for MRSA transmission analysis.

Main Methods:

• Developed the 'Tracking Antimicrobial Resistant Organisms Timely' (TAROT) workflow for successive phylogenetic analysis using ONT data.
• Sequenced 34 MRSA strains using both ONT (MinION) and Illumina (MiSeq) platforms.
• Performed successive cgSNP-based phylogenetic analysis on ONT data (TAROT-ONT) and batched analysis on Illumina data.

Main Results:

• TAROT-ONT generated phylogenetic trees rapidly, with bioinformatic analysis per strain taking 5-42 minutes.
• Highly suspected MRSA transmission pairs were identified using TAROT-ONT, with results showing high concordance to Illumina sequencing.
• Assembly-based analysis successfully identified AMR genes, AMR mutations, and virulence genes with high agreement between sequencing platforms.

Conclusions:

• The TAROT-ONT workflow facilitates effective IPC interventions for MRSA nosocomial transmissions.
• Timely feedback through successive phylogenetic analyses based on cgSNPs aids in controlling hospital-acquired infections.
• This approach offers a rapid and reliable method for tracking AMR organism spread in healthcare settings.