Ion Torrent Personal Genome Machine Sequencing for Genomic Typing of Neisseria meningitidis for Rapid Determination of Multiple Layers of Typing Information

TLDR: The feasibility and accuracy of Ion Torrent Personal Genome Machine (PGM) sequencing for genomic typing of meningococci was explored and the amount of typing information could be substantially increased by the combined use of genome sequencing and BIGSdb compared to conventional methods.

Abstract: Neisseria meningitidis causes invasive meningococcal disease in infants, toddlers and adolescents worldwide. DNA sequence based typing has become the standard for molecular epidemiology of the organism including multilocus sequence typing, analysis of genetic determinants of antibiotic resistance, and sequence typing of vaccine antigens. However, PCR of multiple targets and consecutive Sanger sequencing provides logistic constraints to reference laboratories. Taking advantage of the recent development of benchtop next generation sequencers (NGS) and of BIGSdb, a database accommodating and analyzing genome sequence data, we therefore explored the feasibility and accuracy of Ion Torrent Personal Genome Machine™ (PGM™) sequencing for genomic typing of meningococci. Three strains from a previous meningococcus B community outbreak were selected to compare conventional typing results with data generated by semiconductor chip based sequencing. In addition, sequencing of the meningococcal type strain MC58 provided information about the general performance of the technology. The PGM™ technology generated sequence information for almost all target genes addressed. The results were 100% concordant with conventional typing results with no further editing necessary. In addition, the amount of typing information, i.e. nucleotides and target genes analyzed, could be substantially increased by the combined use of genome sequencing and BIGSdb compared to conventional methods. In a near future, affordable and fast benchtop-NGS machines like the PGM™ might enable reference laboratories to switch to genomic typing on a routine basis. This will reduce workload and rapidly provide information for laboratory surveillance, outbreak investigation, assessment of vaccine preventability and antibiotic resistance gene monitoring.