Benchmarking of two bioinformatic workflows for the analysis of whole-genome sequenced Staphylococcus aureus collected from patients with suspected sepsis

Table 1 Genes and antibiotics assessed for each analysis in the 1928 platform accessed online June-July 2019

Antibiotics addressed for predicted genotypic antibiotic susceptibility^a	Genes present in any of the SCCmec types		Typing-genes used for MLST classification	Virulence genes
Ciprofloxacin	IS1272	ccrB3	arcC	etA
Vancomycin	ccrA1	ccrB4	aroE	etB
Clindamycin	ccrA2	ccrB6	glpF	lukF-PVL
Erythromycin	ccrA3	ccrC	gmk	lukS-PVL
Isoxazolyl penicillin^b	ccrA4	mecA	pta	tsst1
Rifampicin	ccrB1	mecC	tpi
Trimethoprim	ccrB2		yqiL
Tetracycline
Fusidic acid

^aPhenotypic AST results reported in this study are limited to the set of antibiotics included in the 1928 platform
^bIsoxazolyl penicillin belongs to the β-lactam antibiotic group

ISSN: 1471-2334