TABLE 2.

Summarized assay accuracy results for validation samples and retrieved reference sequences.

Sample ID	Reference species	Alignment based assays				k-mer based assays
		Taxonomic identification	Bacterial typing		Marker detection	Taxonomic identification	Bacterial typing		Marker detection
		16S rRNA identification	MLST	rMLST/Species	AMR gene detection (val/ref)	Kraken 2	MLST	rMLST/Species	AMR gene detection (total val/ref)
ID244	A. baumannii	A. baumannii	ST1	rST8954/ A. baumannii	178/191	A. baumannii	ST1	rST8954/ A. baumannii	179/191
ID245	P. aeruginosa	P. aeruginosa	ST155	rST20748/ P. aeruginosa	86/86	P. aeruginosa	ST155	rST20748/ P. aeruginosa	86/86
ID246	K. pneumoniae	K. pneumoniae	ST489	rST19205/ K. quasipneumoniae	345/357	K. quasipneumoniae	ST489	rST19205/ K. quasipneumoniae	346/357
ID247	S. aureus	S. aureus	ST130	rSTnew/ S. aureus	115/116	S. aureus	ST130	rSTnew/S. aureus	115/116
ID248	E. coli	E. coli	ST33	rST2194/ E. coli	332/333	E. coli	ST33	rST2194/ E. coli	331/333
ID249	E. faecium	E. faecium	ST17	rST18445/E. faecium	17/19	E. faecium	ST17	rST18445/E. faecium	17/19
ID250	E. cloacae	E. cloacae	ST278	rST71024/ E. hormaechei	265/301	E. hormaechei	ST278	rST71024/ E. hormaechei	266/301
Average Accuracy (%)		100%	100%	100%	99.76%	100%	100%	100%	99.76%

For taxonomic identification respectively bacterial typing, alignment as well as k-mer based assays revealed 100% accuracy determined by the agreement between validation and reference sequences. AMR gene detection revealed an average accuracy of 99.1 and 99.9% for alignment based respectively kmer based assays. rSTnew = a novel rMLST for ID247 was identified due to a new combination of alleles (val/ref) = number of correctly identified AMR markers in the validation sequence/total number of AMR markers detected in the reference sequence. Bold species names indicate assay results that differed from the reference genome species classification.