Table 1 Presence and absence data.

Antibiotic	G+/P+	G−/P+	G+/P−	G−/P−	Sensitivity^a	Specificity^b
Ampicillin	164	8	27	539	0.86	0.99
Ceftazidime	7	1	10	724	0.41	>0.99
Chloramphenicol	12	3	46	677	0.21	>0.99
Ciprofloxacin	5	11	44	678	0.10^c	0.98
Kanamycin	0	4	0	734	n.a.^d	>0.99
Streptomycin	165	23	55	489	0.75	0.96
Sulfamethoxazole	186	34	23	495	0.89	0.94
Tetracycline	237	42	19	440	0.93	0.91
Trimethoprim	153	35	11	539	0.93	0.94
Amp + Str + Sul + Tet + Tri^e	905	142	135	2502	0.87	0.95
Amp + Sul + Tet + Tri^f	740	119	80	2013	0.90	0.94

Comparison of the presence (+) or absence (−) of antimicrobial-resistance genotypes (G) and phenotypes (P), and associated estimates of diagnostic sensitivity and specificity of the phenotype results relative to the presence of a corresponding antimicrobial-resistance gene
^aDiagnostic sensitivity is the proportion of isolates that were antibiotic resistant based on a breakpoint assay and that had a corresponding antimicrobial-resistance gene based on whole-genome sequencing (i.e., correctly identifies a true positive)
^bDiagnostic specificity is the proportion of isolates that were antimicrobial-susceptible based on a breakpoint assay and that had no corresponding antimicrobial-resistance gene based on whole-genome sequencing (i.e., correctly identifies a true negative)
^cDiagnostic sensitivity for ciprofloxacin resistance is very low even when considering the limited sample size. This is likely due to resistance being conveyed by chromosomal mutations in contrast to the presence of specific resistance genes that would normally be identified using ResFinder⁴⁹ software
^dNot applicable due to zero value n the G+/P+cell
^ePooled analysis for ampicillin, streptomycin, sulfamethoxazole, tetracycline and trimethoprim tests
^fPooled analysis for ampicillin, sulfamethoxazole, tetracycline, and trimethoprim tests

Quick links

Search