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Table 5 Report of Metrichor What’s In My Pot Bacteria k24 for SQK-MAP005 v1.27 (WIMP) from the first 1000 reads of three single samples and the first 3000 reads of the mixture sample

From: Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing

Sample Reported by Metrichor Sequence type Level Accuracy
     species/strain
K. pneumoniae (ATCC BAA-2146, ST11) K. pneumoniae - Species \(\checkmark /\)
K. quasipneumoniae (ATCC 700603, ST489) K. pneumoniae subsp. pneumoniae - Sub-species \(\checkmark /\)
  K. pneumoniae 342 ST146 Strain
  K. pneumoniae JM45 ST11 Strain
  K. pneumoniae CG43 ST86 Strain
  K. oxytoca - Species ×/
  K. variicola At-22 - Strain
K. pneumoniae (ATCC 13883, ST3) K. pneumoniae subsp. pneumoniae 1084 ST1084 Strain
  K. pneumoniae CG43 ST86 Strain
  K. pneumoniae subsp. rhinoscleromatis SB3432 ST67 Strain
  E. coli O103:H2 str. 12009 ST17 Strain ×/ ×
Mixture sample E. coli UMN026 ST597 Strain
75 % E. coli (ATCC 25922, ST73) E. coli ETEC H10407 ST48 Strain
  S. aureus subsp. aureus HO 5096 0412 ST22 Strain
25 % S. aureus (ATCC 25923, ST243) S. aureus subsp. aureus MRSA252 ST36 Strain
  S. aureus subsp. aureus T0131 ST239 Strain
  Yersinia pestis - Species ×/
  1. The last column indicates if the detection is correct (\(\checkmark \)) or incorrect (×) at species/strain levels. The Metrichor was able to identify the species (with some false positives) but not the strains in our samples
  2. *K. quasipneumoniae ATCC 700603 strain was recently re-classified from K. pneumoniae as K. quasipneumoniae [49] but has not been updated in most major databases