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

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

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	×/

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
^*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

ISSN: 2047-217X