Rapid identification, capsular typing and molecular characterization of Streptococcus pneumoniae by using whole genome nanopore sequencing

Table 1 MinION and Sanger workflow times comparison

Steps	MinION workflow	Sanger workflow
Sample preparation	Strains cultured overnight and harvested the following day
DNA extraction	2 h	40 min
Preparation for sequencing	1 h	8h15min
Sequencing	5 min-3 h*	6 h
Data analysis	1 h	2 h
Total	4 h5 min-7 h	16 h45min

Clarifications for Sanger workflow: a) “Preparation for sequencing” step includes four different steps which make it more laborious [amplification (3h30min), 1st purification (1 h15min), sequence reaction (3 h) and 2nd purification (30 min)]; b) “Sequencing” step only includes the seven housekeeping genes: aroE, gdh, gki, recP, spi, xpt and ddl
^*Five minutes are enough for identification at species level and at least 3 h are required to obtain whole genome data. However, we always initiated a standard 18 h sequencing procedure
Abbreviations: NA not available, WGS whole-genome sequencing

ISSN: 1471-2180