Laboratory and Clinical Evaluation of DNA Microarray for the Detection of Carbapenemase Genes in Gram-Negative Bacteria from Hospitalized Patients

Table 4

Microarray results on various clinical samples harboring carbapenemase genes.

Species		P. aeruginosa	A. baumann	E. coli	K. pneumoniae	S. marcescens	S. maltophilia	Flavobacterium meningosepticum	R. mannitolilytica	Achromobacter xylosoxidans	Burkholderia cepacia	Klebsiella oxytoca	Enterobacter cloacae	E. aerogenes	Total
No. of; samples		263	42	36	55	5	4	3	1	1	1	2	2	1	416
No. with gene	PCR	193	15	7	38	0	2	3	0	1	1	0	0	0	260
	Array	190	15	7	37	0	2	3	0	1	1	0	0	0	256
	% Concordance of results	98.4	100	100	97.4	100	100	100	100	100	100	100	100	100	98.5
No. with gene	PCR	19	2	0	5	0	1	0	0	0	0	0	0	0	27
	Array	19	2	0	5	0	1	0	0	0	0	0	0	0	27
	% Concordance of results	100	100	100	100	100	100	100	100	100	100	100	100	100	100
No. with gene	PCR	8	31	1	0	0	1	0	0	0	0	0	0	0	41
	Array	8	30	1	0	0	1	0	0	0	0	0	0	0	40
	% Concordance of results	100	96.8	100	100	100	100	100	100	100	100	100	100	100	97.6
No. with gene	PCR	20	1	1	1	0	0	0	0	0	0	0	0	0	23
	Array	19	1	1	1	0	0	0	0	0	0	0	0	0	22
	% Concordance of results	95	100	100	100	100	100	100	100	100	100	100	100	100	95.7
No. with gene	PCR	84	40	5	7	0	2	1	0	1	0	0	0	0	140
	Array	82	39	5	7	0	2	1	0	1	0	0	0	0	137
	% Concordance of results	97.6	100	100	100	100	100	100	100	100	100	100	100	100	97.9
No. with gene	PCR	4	1	0	0	0	0	0	0	0	0	0	0	0	5
	Array	4	1	0	0	0	0	0	0	0	0	0	0	0	5
	% Concordance of results	100	100	100	100	100	100	100	100	100	100	100	100	100	100
No. with gene	PCR	3	0	0	0	0	0	0	0	0	0	0	0	0	3
	Array	3	0	0	0	0	0	0	0	0	0	0	0	0	3
	% Concordance of results	100	100	100	100	100	100	100	100	100	100	100	100	100	100
No. with gene	PCR	4	1	0	0	0	0	0	1	0	0	0	0	0	6
	Array	4	1	0	0	0	0	0	1	0	0	0	0	0	6
	% Concordance of results	100	100	100	100	100	100	100	100	100	100	100	100	100	100
Total no. of strains that agree/total no. of strains		257/263	38/40	36/36	54/55	5/5	4/4	3/3	1/1	1/1	1/1	2/2	2/2	1/1	407/416
% agreement for all strains		97.7	95	100	98.2	100	100	100	100	100	100	100	100	100	97.8

All tested samples include sputum, urine, and cultured isolates; the specific clinical information and test results of each sample are shown in the Supplementary Table.
Results obtained with classical PCR/sequencing.
Microarray results were obtained using carbapenemase-array designed in this study.
A sensitivity of 98.5%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 97.5% for KPC detection.
A sensitivity of 100%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 100%f or NDM-1 detection.
A sensitivity of 97.6%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 99.7% for OXA-23 detection.
A sensitivity of 95.7%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 99.7% for OXA-48 detection.
A sensitivity of 97.9%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 98.9% for OXA-51 detection.
A sensitivity of 100%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 100% for IMP detection.
A sensitivity of 100%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 100% for VIM detection.
A sensitivity of 100%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 100% for DIM detection.