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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