. 2014 Oct;58(10):6277–6283. doi: 10.1128/AAC.03116-14

TABLE 3.

Sequencing analysis of oprD, gyrA, and parC genes^a

Isolate no.^b	ST	IPM MIC (μg/ml)	OprD size	Amino acid polymorphisms in OprD^c	Amino acid insertions/deletions in OprD^c^,^d	CIP MIC (μg/ml)	Amino acid change in GyrA	Amino acid change in ParC
8	111	2	441^e	V127L, E185Q, P186G, V189T, E202Q, I210A, E230K, S240T, N262T, T276A, A281G, K296Q, Q301E, R310E, G312R, A315G, L347 M, S403A, Q424E	Loop L7-short	NP	ND	ND
16	111	32	441^e	V127L, E185Q, P186G, V189T, E202Q, I210A, E230K, S240T, N262T, T276A, A281G, K296Q, Q301E, R310E, G312R, A315G, L347 M, S403A, Q424E	Loop L7-short	NP	ND	ND
6	111	32	18^f	Q19STOP,^g V127L,^h E185Q,^h P186G,^h V189T,^h E202Q,^h I210A,^h E230K,^h S240T,^h N262T,^h T276A,^h A281G,^h K296Q,^h Q301E,^h R310E,^h G312R,^h A315G,^h L347M,^h S403A,^h Q424E^h	Loop L7-short^h	NP	ND	ND
33	111	32	109^f	V127L,^h E185Q,^h P186G,^h V189T,^h E202Q,^h I210A,^h E230K,^h S240T,^h N262T,^h T276A,^h A281G,^h K296Q,^h Q301E,^h R310E,^h G312R,^h A315G,^h L347M,^h S403A,^h Q424E^h	1-bp deletion at codon 108 (nt 323), stop codon 110, loop L7-short^h	NP	ND	ND
20	132	32	>443ⁱ	D43N, S57E, S59R, E202Q, I210A, E230K, S240T, N262T, A267S, A281G, K296Q, Q301E, R310G, V359L	Loop L7-short, 1-bp insertion at codon 402 (nt 1206), undetected stop codon	NP	ND	ND
25	132	32	>443ⁱ	D43N, S57E, S59R, E202Q, I210A, E230K, S240T, N262T, A267S, A281G, K296Q, Q301E, R310G, V359L	Loop L7-short, 1-bp insertion at codon 402 (nt 1206), undetected stop codon	NP	ND	ND
30	175	128	>443ⁱ	D43N, S57E, S59R, E202Q, I210A, E230K, S240T, N262T, A267S, A281G, K296Q, Q301E, R310G, V359L	Loop L7-short, 1-bp insertion at codon 402 (nt 1206), undetected stop codon	32	T83I	S87W
26	292	8	441^e	D43N, S57E, S59R, E202Q, I210A, E230K, S240T, N262T, A267S, A281G, K296Q, Q301E, R310G, V359L	Loop L7-short	NP	ND	ND
2	235 (VIM-1)	128	>443ⁱ	T103S, K115T, F170L, E185Q, P186G, V189T, R310E, A315G	1-bp insertion at codon 402 (nt 1206), undetected stop codon	NP	ND	ND
29	235	0.5	443	T103S, K115T, F170L, E185Q, P186G, V189T, R310E, A315G, G425A		NP	ND	ND
59	235	16	232^f	T103S,^h K115T,^h F170L,^h E185Q,^h P186G,^h V189T,^h R310E,^h A315G,^h G425A^h	13-bp deletion at codon 137 (nt 410–422) and 3-bp deletion at codon 142 (nt 425–427), stop codon 233	NP	ND	ND
61	235	32	64^f	W65STOP,^g T103S,^h K115T,^h F170L,^h E185Q,^h P186G,^h V189T,^h R310E,^h A315G,^h G425A^h		NP	ND	ND
64	244	32	137^f	W138STOP^g		0.125
74	308	16	—^j	T103S,^h K115T,^h F170L,^h E185Q,^h P186G,^h V189T,^h R310E,^h A315G,^h G425A^h	ISRP10 insertion inside codon 69 (nt 205)	NP	ND	ND
23	633	NP	ND	ND	ND	0.25
99	319	NP	ND	ND	ND	2	D87N
1	111	NP	ND	ND	ND	4	T83I
73	207	NP	ND	ND	ND	4	T83I
49	235	NP	ND	ND	ND	8	T83I	S87L
4	235	NP	ND	ND	ND	32	T83I	S87L
45	292	NP	ND	ND	ND	32	T83I	S87L
48	244	NP	ND	ND	ND	32	T83I	S87L
75	621	NP	ND	ND	ND	>32	T83I	S87W
84	132	NP	ND	ND	ND	>32	T83I	S87L

IPM, imipenem; CIP; ciprofloxacin; NP, not presented; ND, not determined; nt, nucleotide(s).

The isolates used in the OprD analysis are ordered according to their STs, whereas the isolates used in the GyrA/ParC analysis are ordered according to increasing ciprofloxacin MICs; isolates 30 and 64 were used in both analyses and are shown in the OprD order.

Amino acid polymorphisms represent differences of the sequences obtained in this study from that of the P. aeruginosa PAO1 strain (GenBank accession no. AE004091).

Loop L7-short indicates modification of the amino acid stretch between position 372 and position 383 from MSDNNVGYKNYG to VDSSSSYAGL caused by several nucleotide changes (35).

The size of 441 amino acids is due to loop L7-short; the original stop codon is retained.

OprD protein sizes reduced by premature stop codons generated by point mutations.

Stop codons generated by point mutations.

Theoretical polymorphisms and loop L7-short, located either behind premature stop codons and/or within frames altered by insertions/deletions.

ⁱ

The size of >443 indicates situations in which insertions at the end of the oprD gene caused frameshifts and extension of the altered frames.

—, disruption of oprD by ISRP10 caused massive changes in the sequence; therefore, the size of a putative altered protein was not calculated.