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Table 1 Pathogens detected by nanopore sequencing and culture, stratified by four methods

From: Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens

Sample Pathogen SD_SSD SD_ADS HD_SSD HD_ADS Culture
P4 S. pneumoniae 4/2.0 ka 180.9 k/792.7 Mb 16/16.0 k 915 k/792.7 M 39/43.6 k 950.5 k/792.7 M 65/71.4 k 1484 k/792.7 M Negative
P6 S. pneumoniae 20/14.1 k 48.7 k/74 M 38/27.5 k 137.8 k/74 M 503/470.2 k 63.1 k/74 M 557/504.1 k 80.2 k/74 M Negative
P7 S. pneumoniae 1/331 40.8 k/168 M 4/1.7 k 152.6 k/168 M 363/308.0 k 159.5 k/168 M 531/439.8 k 261 k/168 M S. dysgalactiae
H. parainfluenzae 0/0 7/15.0 k 333/323.8 k 538/535.2 k
S. dysgalactiae 1/4.0 k 8/10.1 k 1269/1.3 M 2102/2.1 M
P8 T. whipplei 13/20.9 k 35.6 k/195.7 M 28/96.8 k 72 k/195.7 M 15,951/21.5 M 162 K/195.7 M 26,929/36.1 M 276.5 K/195.7 M Negative
  1. aNumber of reads / Number of bases for the pathogen
  2. bTotal number of reads / Total number of bases for the sample