Table 5 Characterization of E. coli isolates grouped on profil III in terms of phenotypic resistance and its genotypic basis, phylogenetic groups, and clonal relatedness.

From: Molecular mechanisms impact on fluoroquinolone resistance among E.coli from enteric carriage monitoring before prostate biopsy and earliest description of qnrB81

Strains	Qs-FQs resistance phenotypes NAL NXN OFX CIP	Qs- FQs MICs (mg/L)			ATB resistance profiles		QRDRs mutations			PMQRs gene	Phylogenetic group	ST131 clone	PFGE pulsotype/subtype
Strains	Qs-FQs resistance phenotypes NAL NXN OFX CIP	NAL S ≤ 16 R > 16	OFX S ≤ 0.25 R > 0.5	C.I.P. S ≤ 0.25 R > 0.5	ß-lactams	Aminoglycosides	Other	gyrA	parC	PMQRs gene	Phylogenetic group	ST131 clone	PFGE pulsotype/subtype
1 QRDRs ( 1 gyrA mutation + PMQR )
E.coli (16)	R R RR	256<	1	1	AMP, TIC, PIP	-	-	S83L	PS	qnrS1	B2	-	-
E.coli (17)	R RR R	256<	1	1	-	-	-	S83Y	PS	qnrS15	Clade I or II	-	-
2 QRDRs ( 2 gyrA mutations)
E.coli (18 )	RRRR	256 <	32	32	AMP, TIC, PIP	-	-	S83L + D87N	ND	-	B2	+	Pulsotype III
E.coli (19)	RRRR	256<	8	8	AMP, TIC, PIP	-	-	S83L + D87N	ND	-	B2	-	Subtype IIId
2QRDRs (1 gyrA mutation + 1 parC mutation)
E.coli (20)	RRRR	256<	2	1	AMP, TIC, PIP	-	SXT	S83L	S80I	-	B2	+	-
E.coli (21)	RRRR	256<	1	1	-	-	-	S83L	S80I	-	B2	-	-
E.coli (22)	RRRR	256<	2	1	AMP, TIC , PIP	-	SXT	S83W	S80I	-	B2	+	-
E.coli (23)	RRRR	256<	4	4	AMP, AMC, TIC, TCC, PIP	-	SXT	S83L	S80I	-	Clade I or II	-	Pulsotype VIII
E. coli (24)	RRRR	256<	4	4	-	-	CHL, SXT	S83L	S80I	-	Unknown	-	-
E. coli (25)	RRRR	256<	4	4	AMP, AMC, TIC, TCC, PIP, TZP, CN, MEC, CXM	-	CHL	D87N	S80I	-	Unknown	-	Pulsotype IX
2 QRDRs (2 gyrA mutation ) + 1 PMQR gene
E. coli (26)	RRRR	256<	64	32	-	-	-	S83L + D87N	-	qnrB	B2	+	Subtype IIIb
E.coli (27)	RRRR	256<	8	8	AMP, TIC, PIP, AMC, CN, CXM, CTX, CAZ, CEF, ATM	TOB	SXT	S83L + D87N	-	aac(6)-Ib-cr	B2	-	Subtype IIIc
E. coli (28)	RRRR	256<	64	32	-	-	-	S83L + D87N	-	qnrS1	B2	+	-
3QRDRs (2 gyrA mutations + 1 parC mutation)
E.coli (29)	RRRR	256<	64	64	AMP, TIC, PIP, CN, MEC, CXM, CTX, CEF, ATM	-	SXT	S83L + D87N	S80I	-	Clade I or II	-	-
E. coli (30)	RRRR	256<	32	16	-	-	SXT	S83L + D87N	E84K	-	F	-	-
E.coli (31)	RRRR	256<	32	16	AMP, TIC, PIP	-	CHL, SXT	S83L + D87N	S80I	-	Unknown	-	-
E. coli (32)	RRRR	256<	32	32	AMP, TIC, PIP	-	SXT	S83L + D87N	S80I	-	Unknown	-	-
E. coli (33)	RRRR	256<	16	16	AMP, TIC, PIP	-	SXT	S83L + D87N	S80I	-	Unknown	-	-
E.coli (34)	RRRR	256<	16	16	AMP, AMC, TIC, TCC, PIP, TZP, MEC	-	SXT	S83L + D87N	S80I	-	B2	+	-

Strains	Quinolone resistance phenotypes and FQs NAL NXN OFX CIP	Qs - FQs MICS (mg/L)			ATB resistance profiles		QRDRs mutations			PMQR gene	Phylogenetic group	ST131 clone	PFGE pulsotype/subtype
Strains	Quinolone resistance phenotypes and FQs NAL NXN OFX CIP	NAL S ≤ 16 R > 16	OFX S ≤ 0.25 R > 0.5	C.I.P. S ≤ 0.25 R > 0.5	ß-lactams	Aminoglycosides	Other	gyrA	parC	PMQR gene	Phylogenetic group	ST131 clone	PFGE pulsotype/subtype
3 QRDRs ( 2 gyrA mutations + 1 parC mutation )
E.coli (35)	RRRR	256<	16	16	AMP, TIC, CBT, PIP	-	CHL, SXT	S83L + D87N	S80I	-	B2	+	-
E. coli (36)	RRRR	256<	32	32	AMP, TIC, PIP	-	SXT	S83L + D87N	S80I	-	Clade I or II	-	-
E.coli (37)	RRRR	256<	16	16	AMP, AMC, TIC, TCC, PIP, MEC	-	SXT	S83L + D87N	S80I	-	B2	+	-
E.coli (38)	RRRR	256<	64	64	AMP, TIC, PIP, CN, CXM	-	SXT	S83L + D87N	S80I	-	Clade I or II	-	-
E.coli (39)	RRRR	256<	64	64	AMP, TIC, PIP	GM, NET, TOB	CHL	S83L + D87N	S80I	-	B2	+	-
E. coli (40)	RRRR	256<	64	64	AMP, AMC, TIC, TCC, PIP, CN, CXM, CFM, CTX, CAZ, CEF, ATM	-	SXT	S83L + D87N	S80I	-	Clade I or II	-	Subtype VIIa
E.coli (41)	RRRR	256<	64	64	AMP, AMC, TIC, TCC, PIP	GM, TOB	SXT	S83L + D87N	S80I	-	Clade I or II	-	Pulsotype VII
E.coli (42)	RRRR	256<	32	32	AMP, TIC, PIP	-	SXT	S83L + D87N	S80I	-	B2	+	-
E.coli (43)	RRRR	256<	16	16	-	-	-	S83L + D87N	S80I		B2	+	Subtype IIa
E.coli (44)	RRRR	256<	32	16	AMP, TIC, PIP	-	CHL, SXT	S83L + D87N	S80I		B2	+	Subtype IIb
E.coli (45)	RRRR	256<	32	32	AMP, TIC, PIP	-	CHL, SXT	S83L + D87N	S80I		Clade I or II	-	Subtype IIc
E.coli (46)	RRRR	256<	32	32	AMP, TIC, PIP	-	CHL, SXT	S83L + D87N	S80I		Clade I or II	-	IId subtype
E.coli (47)	RRRR	256<	32	16	AMP, AMC, TIC, TCC, PIP	-	CHL, SXT	S83L + D87N	S80I		Clade I or II	-	Subtype VIIIa
E.coli (48)	RRRR	256<	32	16	AMP, TIC, PIP	GM, TOB	CHL, SXT	S83L + D87N	S80I		Unknown	-	-
E.coli (49)	RRRR	256<	16	8	AMP, AMC, TIC, TCC, PIP	GM, NET, TOB	CHL, SXT	S83L + D87N	S80I		B2	+	-
E.coli (50)	RRRR	256<	8	8	AMP, ICT, PIP	-	CHL, SXT	S83L + D87N	S80I		B2	+	-
E. coli (51)	R RRR	256<	16	8	AMP, AMC, TIC, TCC, PIP		- CHL	S83L + D87N	S80I		-B2	+
E.coli (52)	RRRR	256<	32	32	AMP, AMC, TIC, TCC, PIP	-	SXT	S83L + D87N	S80I	-	B2	+	-
E.coli (53)	RRRR	256<	64	64	AMP, AMC, TIC, TCC, PIP	GM, NET, TOB	CHL	S83L + D87N	S80I	-	B2	+	-
E.coli (54)	RRRR	256<	64	32	AMP, AMC, TIC, TCC, PIP	GM, NET, TOB	CHL	S83L + D87N	S80I	-	Clade I or II	-	-
E. coli (55)	RRRR	256<	32	32	AMP, TIC, PIP	-	-	S83L + D87N	S80I	-	Clade I or II	-	-
E.coli (56)	RRRR	256<	32	32	AMP, TIC, PIP, MEC	-	-	S83L + D87N	S80I	-	B2	+	-
E. coli (57)	RRRR	256<	32	32	AMP, ICT, PIP	GM, TOB	CHL, SXT	S83L + D87N	S80I	-	B2	+	-
E. coli (58)	RRRR	256<	32	32	AMP, AMC, TIC, PIP	-	-	S83L + D87N	S80I	-	Clade I or II	-	-
E.coli (59)	RRRR	256<	32	32	-	-	-	S83L + D87N	S80I	-	Clade I or II	-	-
E.coli (60)	RRRR	256<	32	32	-	-	-	S83L + D87N	S80I	-	B2	+	-
E.coli (61)	RRRR	256<	32	16	AMP, TIC, PIP	-	-	S83L + D87N	S80I	-	Clade I or II	-	-
E.coli (62)	RRRR	256<	32	32	AMP, TIC, PIP, CN, MEC, CXM	-	-	S83L + D87N	S80I	-	Clade I or II	-	Subtype IXa
E.coli (63)	RRRR	256<	8	8	AMP, TIC, PIP, MEC	-	SXT	S83L + D87N	S80I	-	B2	+	Xa subtype

Strains	Qs-FQs resistance phenotype NAL NXN OFX CIP	Qs-FQs MICS (mg/L)			ATB resistance profiles		QRDR mutations			PMQRs gene	Phylogenetic group	Clone ST131	PFGE pulsotype/subtype
Strains	Qs-FQs resistance phenotype NAL NXN OFX CIP	NAL S≤16 R>16	OFX S≤0.25 R>0.5	C.I.P. S≤0.25 R>0.5	ß-lactams	Aminoglycosides	Other	gyrA	parC	PMQRs gene	Phylogenetic group	Clone ST131	PFGE pulsotype/subtype
3 QRDRs ( 2 mutations gyrA + 1 mutations parC) + 1 PMQR
E. coli (64)	RRRR	>256	32	16	AMP, TIC, PIP		SXT	S83L+D87N	S80I		qnrS		Unknown
4 QRDRs ( 2 mutations gyrA + 2 mutations parC )
E. coli (65)	RRRR	256<	64	64	AMP, TIC, PIP, CN, CXM, CTX	-	SXT	S83L+D87N	S80I+E84V	-	B2	+	Subtype IIIa
E.coli (66)	RRRR	256<	64	64	AMP, TIC, PIP	-	CHL	S83L+D87N	S80I+E84V	-	B2	+	-
E. coli (67)	RRRR	256<	64	64	-	-	-	S83L+D87N	S80I+E84V	-	B2	+	-
E.coli (68)	RRRR	256<	128	128	AMP, TIC, PIP	-	SXT	S83L+D87N	S80I+E84V	-	Unknown	-	-
E. coli (69)	RRRR	256<	128	128	AMP, TIC, PIP	-	CHL, SXT	S83L+D87N	S80I+E84G	-	Clade I or II	-	Pulsotype IV
E.coli (70)	RRRR	256<	64	64	AMP, TIC, PIP	-	CHL	S83L+D87N	S80I+E84V	-	B2	-	Subtype Va
E. coli (71)	RRRR	256<	64	64	AMP, TIC, PIP, CN, CXM, CTX	-	SXT	S83L+D87N	S80L+E84V	-	B2	+	Pulsotype V
E. coli (72)	RRRR	256<	64	64	AMP, TIC, PIP, CN, CXM, CTX, CAZ, CEF	-	SXT	S83L+D87N	S80I+E84V	-	B2	+	-
E.coli (73)	RRRR	256<	64	64	AMP, AMC, TIC, TCC, PIP, CN, CXM, CFM, CTX, CAZ, CEF, ATM	-	-	S83L+D87N	S80I+E84V	-	Clade I or II	-	-
Mutation not determined
E. coli (74)	RRRR	256<	32	16	AMP, TIC, PIP	-	CHL, SXT	ND	ND	-	B2	+	-
E.coli (75)	RRRR	256<	128	128	AMP, TIC, PIP	GM	SXT	ND	ND	-	Clade I or II	-	-
E. coli (76)	RRRR	256<	2	2	AMP, TIC, PIP	-	-	ND	ND	-	Clade I or II	-	Subtype IVa
E.coli (77)	RRRR	256<	32	16	-	-	-	ND	ND	-	Clade I or II	-	Subtype IVb
E. coli (78)	R RRR	256<	16	16	AMP, TIC, PIP	-	SXT	ND	ND	-	Unknown	-	-
E. coli (79)	R RRR	256<	128	128	AMP, TIC, PIP	GM, TOB	CHL	ND	ND	-	Clade I or II	-	-
E. coli (80)	R RRR	256<	32	32	-	-	CHL	ND	ND	-	Unknown	-	-

MIC: minimum inhibitory concentration; R: resistant; NAL: Nalidixic acid, NXN: Norfloxacin, OFX: ofloxacin; CIP: ciprofloxacin AMP: ampicillin; TIC: ticarcillin; PIP: piperacillin; TCC : Ticarcillin + Ac.clavulanic; TZP : Piperacillin + Tazobactam; MEK : Mecillinam; AMC: amoxicillin + clavulanic acid; CN: cephalexin; MEC: mecillinam; CXM: cefuroxime VI; CTX: cefotaxime; CAZ: ceftazidime; CEF: cefepime; ATM: aztreonam; GM: gentamicin; TOB: tobramycin; NET: Netilmicin; CHL: chloramphenicol; SXT: cotrimoxazole RPF: plasmid resistance to fluoroquinolones, QRDRs: quinolone resistance determining region, ND: not determined (illegible sequences) ; +: positive; -: Negative.

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Table 5 Characterization of E. coli isolates grouped on profil III in terms of phenotypic resistance and its genotypic basis, phylogenetic groups, and clonal relatedness.

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