Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory

Area of Science:

• Microbiology
• Genomics
• Infectious Disease Epidemiology

Background:

• Next-generation sequencing (NGS) is increasingly accessible for diagnostic microbiology labs.
• Feasibility and data analysis for NGS in non-specialist settings remain a concern.
• Outbreak investigations require high-resolution genotyping methods.

Purpose of the Study:

• To evaluate the applicability of NGS for investigating a multidrug-resistant Escherichia coli outbreak.
• To assess the feasibility, cost, and turnaround time of NGS in a routine diagnostic setting.
• To determine the genomic characteristics and evolutionary context of the outbreak strains.

Main Methods:

• Ion Torrent sequencing was used to analyze four suspected outbreak strains and one comparator strain of Escherichia coli.
• Genome-wide single nucleotide polymorphism (SNP) analysis was performed.
• Multilocus sequence typing (MLST) and identification of antimicrobial resistance genes were conducted.

Main Results:

• The four suspected outbreak strains were genetically identical and distinct from the comparator strain.
• The outbreak strains belonged to multilocus sequence type 131 and harbored the bla(CTX-M-15) gene, conferring extended-spectrum beta-lactamase resistance.
• Sequencing data revealed clustering with neonatal meningitis and uropathogenic E. coli isolates in public databases.
• Turnaround time was 5 days, with reagent costs around $300 per strain.

Conclusions:

• NGS provides high-resolution genotyping for bacterial outbreak investigations, surpassing traditional methods.
• Barriers to NGS adoption include cost, bioinformatics platform usability, and expertise.
• NGS is poised for widespread implementation in diagnostic microbiology for epidemiology and resistance characterization.