Use of the Oxford Nanopore MinION sequencer for rapid MLST genotyping of streptococcus pneumoniae
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Molecular epidemiological surveillance of Streptococcus pneumoniae (S. pneumoniae) is essential to characterize the serotypes and clones causing invasive pneumococcal disease, an important health problem. Multilocus sequence typing (MLST) consist of characterizing S. pneumoniae clones by means of DNA sequencing of 7 highly conserved housekeeping genes (aroE, gdh, gki, recP, spi, xpt, and ddl) and their allelic variations.
Conventional MLST methodology, based on Sanger DNA sequencing,has been the preferred method for clonal characterization of S. pneumoniae but it is cost and time consuming. MinION, a third-generation sequencer,is being used as a rapid tool for easy strains identification and molecular characterization by using whole genome sequencing(WGS) based process.