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

Table 5 Predicted genotypic AST results from the 1928 platform and the in-house pipeline compared to phenotypic AST

Antibiotic (n)^a	Phenotypic AST (n)	Predicted genotypic AST from 1928 (n) and INH (n)				Discordant across methods (n [%])	Very major errors (n)		Major errors (n)
Antibiotic (n)^a	Phenotypic AST (n)	RR	SS	RS	SR	Discordant across methods (n [%])	1928	INH	1928	INH
Ciprofloxacin (70)	R (4)	0	0	4	0	5 (7.1)	0	4	1	0
Ciprofloxacin (70)	S (66)	0	65	1	0	5 (7.1)	0	4	1	0
Clindamycin (212)	R (3)	0	3	0	0	3 (1.4)	3	3	0	0
Clindamycin (212)	S (209)	0	209	0	0	3 (1.4)	3	3	0	0
Erythromycin (215)	R (3)	2	1	0	0	1 (0.47)	1	1	0	0
Erythromycin (215)	S (212)	0	212	0	0	1 (0.47)	1	1	0	0
Rifampicin (5)	R (0)	0	0	0	0	0 (0)	0	0	0	0
Rifampicin (5)	S (5)	0	5	0	0	0 (0)	0	0	0	0
Isoxazolyl penicillin (244)	R (3)	3	0	0	0	1 (0.41)	0	0	1	1
Isoxazolyl penicillin (244)	S (241)	1	240	0	0	1 (0.41)	0	0	1	1
Trimethoprim (26)	R (1)	1	0	0	0	0 (0)	0	0	0	0
Trimethoprim (26)	S (25)	0	25	0	0	0 (0)	0	0	0	0
Tetracycline (1)	R (1)	1	0	0	0	0 (0)	0	0	0	0
Tetracycline (1)	S (0)	0	0	0	0	0 (0)	0	0	0	0
Vancomycin (27)	R (0)	0	0	0	0	0 (0)	0	0	0	0
Vancomycin (27)	S (27)	0	27	0	0	0 (0)	0	0	0	0
Fusidic acid (206)	R (10)	3	4	3	0	7 (3.4)	4	7	0	0
Fusidic acid (206)	S (196)	0	196	0	0	7 (3.4)	4	7	0	0
Total n^b = 1006	S (981) R (25)	10/11	979/987	8	0	n^c = 17 (1.7)	n^d = 8	n^e = 15	n^f = 2	n^g = 1
Error rate %							0.8	1.5	0.2	0.1

The bioinformatic results are presented as 1928 platform/in-house pipeline (INH), where R/R is resistant/resistant, S/S is susceptible/susceptible, R/S is resistant/ susceptible, and S/R is susceptible/resistant
^aNumber of isolates tested with a specific antibiotic disc by disc diffusion. ^bTotal number of cases tested by disc diffusion. ^cNumber of discordant result implying both of the bioinformatic workflows. ^dtotal very major error for 1928. ^eTotal very major error for INH. ^fTotal major error for 1928. ^gTotal major error for 1928, R-resistant; phenotypic AST R is retrieved from the EUCAST assay, genotypic AST R was conferred by the presence of resistance markers or genes, S-susceptible; phenotypic AST S was retrieved from the EUCAST assay, genotypic S was conferred by the absence of resistance markers and genes. INH-in-house pipeline using Resfinder. Very major error: resistant phenotype predicted as a susceptible genotype. Major error: susceptible phenotype predicted as resistant genotype. Bold 100% agreement with both bioinformatic tools

ISSN: 1471-2334