TABLE 5.

Differential quantification of gene expression in clinical isolates compared to CIP 70-10

Function or gene	Description	Change (fold)a
		AYE	BM4675	BM4676
Efflux
adeA	MFP	2.84	5.42	3.94
adeB	RND	2.80	3.99	3.58
adeC	OMF	2.28	2.28	2.72
adeI	MFP	NS	NS	1.73
adeJ	RND	NS	NS	1.83
adeK	OMF	NS	NS	NS
APC 41_138	d-serine/d-alanine/glycine transport protein	2.08	NS	NS
MFS 12_508	MFS	NS	NS	1.53
RND 29_167	RND	2.10b	NS	NS
Outer membrane protein
omp25	Putative outer membrane protein	1.72	NS	NS
omp33-36	33- to 36-kDa outer membrane protein	−1.62	NS	1.84
omp34	34-kDa outer membrane protein	2.22	NS	14.36
ompA	Outer membrane protein A	−3.01	−2.32	NS
Housekeeping and metabolism
bfmS	Sensor kinase component of a two-component regulatory system (biofilm)	NS	NS	1.59
cpn60	60-kDa chaperonin	−2.00	NS	NS
csuA/B	Putative pilus subunit, biofilm operon	NS	−1.72	1.84
fusA	Translation elongation factor EF-G	NS	NS	1.68
gltA	Citrate synthase	NS	NS	1.54
ppa	Inorganic pyrophosphatase	−2.73	NS	NS
rpoC	DNA-directed RNA polymerase beta subunit	−1.97	NS	NS
Antibiotic resistance
adc	Chromosomal cephalosporinase	22.99	5.73	5.72
blaOXA-23	Class D carbapenemase	NS	NS	29.61
blaTEM-1	β-Lactamase	NS	1.61	NS
blaVEB-1	Extended-spectrum β-lactamase	3.51	NS	NS
aac(3)-Ia	Aminoglycoside adenylyltransferase	2.62	NS	NS
ant(2′′)-Ia	Aminoglycoside nucleotidyltransferase	2.51	NA	29.39
aph(3′)-VIa	Aminoglycoside phosphotransferase	NA	NS	4.04
arr-2	Rifampin ADP-ribosylating transferase	1.76	NS	NS
catI	Chloramphenicol acetyltransferase	3.79	NS	NS
cmlA	Chloramphenicol efflux pump	1.73	NS	NS
floR	Chloramphenicol efflux pump	1.66	NS	NS
sul1	Sulfonamide resistance	4.10	NS	NS
tet(B)	Tetracycline efflux pump	NS	1.87	NS
Heavy metal resistance
HMD	Heavy metal detoxification	2.50	NS	NS
merA	Mercuric ion reductase	1.79	NS	NS
merR	Mercury resistance operon regulatory protein	1.96	NS	NS
Gene mobility and island
groEL/int1	Fusion GroEL/integrase	2.71	NS	NS
intI1	Integrase	2.32	NS	NS
IS1999	Insertion sequence	5.26	NS	NS
IS6100	Insertion sequence	1.87	NS	NS
ISAba1	Insertion sequence	NS	1.83	NS
lspA	Lipoprotein signal peptidase	1.81	NS	1.56
qacEdelta1	Quaternary ammonium compound resistance protein	6.19	NS	NS
resolvase 1_318	Resolvase	2.56	NS	NS
tniA	Transposase	NS	2.99	1.59
tnpM	Transposase	1.74	2.38	NS
uspA	Universal stress protein	NS	NS	1.50

^aPositive and negative values correspond to genes with increased and decreased expression, respectively, in the clinical isolate in comparison with CIP 70-10. NS, not statistically significant. NA, not applicable.

^bStatistically significant but not confirmed by qRT-PCR.