TABLE 4.

Comparison of AMR in E. coli isolates according to phenotypic and genotypic testing

Antimicrobial	Characteristics of isolate					Agreement between resistance phenotype and genotype (n = 151)e
	NPa	Gene(s) carried	NGb	P+/G−c	P−/G+d	OR	95% CI	P	κ
Ampicillin	69	Any	60	10	1	534	54-5280	<0.0001	0.85
		blaTEM	60		1	534	54-5280	<0.0001
Chloramphenicol	48	Any	0	48	0
Kanamycin	34	Any	21	14	1	55	16-182	<0.0001	0.67
		aph(3′)-1a	16		0	32	9.4-108	<0.0001
		aph(3′)-IIa	3		0
		aac(3)-IV	2		1
Streptomycin	82	Any	79	20	17	10	5.3-20	<0.0001	0.51
		aadA1	35		10	2.5	1.2-5.3	0.01
		aadA6	1		0
		strA-strB	51		7	11	5.3-22	<0.0001
Sulfamethoxazole	111	Any	69	42	8	3.3	2.6-16	<0.0001	0.33
		sul1	22		1	9.7	1.2-78	0.03
		sul2	27		1	13	1.2-142	0.03
		sul3	40		6	2.7	0.9-8.0	0.06
Tetracycline	125	Any	124	5	4	95	29-312	<0.0001	0.77
		tetA	52		3	3.5	1.2-10	0.03
		tetB	81		1	17	4.6-61	<0.0001
Tetracycline		tetC	2		1	0.4	0.1-3.4
Trimethoprim-sulfamethoxazole	24	Any	14	14	4	23	4.6-116	<0.0001	0.46
		dhfrI	7		3	8.3	1.6-44	0.01
		dhfrXIII	6		1	35	2.0-619	0.01
		dhfrXV	1		0

^aN_P, number of E. coli isolates expressing phenotypic resistance to the indicated antimicrobial agent.

^bN_G, number of E. coli isolates carrying the indicated resistance gene.

^cP+/G−, number of phenotypically resistant E. coli isolates (P+) with no resistance gene (G−) for the drug identified.

^dP−/G+, number of phenotypically susceptible E. coli isolates (P−) with a resistance gene (G+) for the drug identified.

^eAssociation between drug phenotypes and resistance genes and phenotype-genotype intertest agreement. n, number of isolates.