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

Next-generation sequencing (NGS) of bacterial genomes has recently becomemore accessible and is now available to the routine diagnostic microbiology laboratory. However, questions remain regarding its feasibility, particularly with respect to data analy-sis in nonspecialist centers. To test the applicability of NGS to outbreak investigations, Ion Torrent sequencing was used to in-vestigate a putative multidrug-resistant Escherichia coli outbreak in the neonatal unit of the Mercy Hospital for Women, Mel-bourne, Australia. Four suspected outbreak strains and a comparator strain were sequenced. Genome-wide single nucleotide polymorphism (SNP) analysis demonstrated that the four neonatal intensive care unit (NICU) strains were identical and easily differentiated from the comparator strain. Genome sequence data also determined that the NICU strains belonged to multilocus sequence type 131 and carried the blaCTX-M-15 extended-spectrum beta-lactamase. Comparison of the outbreak strains to all pub-licly available complete E. coli genome sequences showed that they clustered with neonatal meningitis and uropathogenic iso-lates. The turnaround time from a positive culture to the completion of sequencing (prior to data analysis) was 5 days, and the cost was approximately $300 per strain (for the reagents only). The main obstacles to a mainstream adoption of NGS technolo-gies in diagnostic microbiology laboratories are currently cost (although this is decreasing), a paucity of user-friendly and clini-cally focused bioinformatics platforms, and a lack of genomics expertise outside the research environment. Despite these hur-dles, NGS technologies provide unparalleled high-resolution genotyping in a short time frame and are likely to be widel