Table 1. Plasmids identified in this study.

RFLP type	VanA modular profile	Size	No. isolates	Tn1546	PFGE type	City	Year
RFLP_1	Rep17.2::Rel6	60	1	A	ST190_H98	Coimbra	1998
RFLP_2	Rep17.2::Rel6	80	1	A	ST18_H92	Coimbra	2000
RFLP_8 c	Rep17.2::Rel6	120	1	PP2b	ST18_H70	Coimbra	2001
RFLP_9 c	Rep17.2::Rel6	60	1	PP2b	ST18_H70	Viseu	NI
RFLP_10 c	Rep17.2::Rel6	60	3	PP2b	ST18_H70, H93	Coimbra, Viseu	2002
RFLP_11	Rep17.2::Rel6	60	1	PP27	ST18_H87	Coimbra	2002
RFLP_3 b	Rep17.2::Rel6	95	3	PP4	ST18_H108	Coimbra	1998–2000-NI
RFLP_4 b	Rep17.2::Rel6	85	2	PP4	ST670_H90; ST18_H81	Coimbra	1997–2001
RFLP_7	Rep17.2::Rel6	50	1	PP5	NI	Viseu	2008
RFLP_6 b	Rep17.2::Rel6	80	1	PP5	ST18_H70	Coimbra	NI
RFLP_5 b	Rep17.2::Rel6	90	12	PP3, PP4, PP5, PP24	ST18_H78, H72, H94, H123, H129	Coimbra, Porto, Matosinhos	2001–2007
RFLP_5.2b	Rep17.2::Rel6	90	2	PP5	ST280_ H100	Porto, Viseu	2002–2003
RFLP_5.3b	Rep17.2::Rel6	90	1	PP5	ST125_H126	Matosinhos	2007
RFLP_5.3’b	Rep17.2::Rep2:: Rel6	85	2	PP5	ST132_H103	Coimbra	2002–2003
RFLP_5.2’b	Rep17.2::Rep2:: Rel6	90	1	PP4	ST132_H132	Coimbra	2001
RFLP_5.4’b	Rep17.2::Rep2:: Rel6	90	1	PP5	ST280_ H71	Viseu	2003
RFLP_5.5b	Rep17.2::Rep2:: Rel6	75	1	PP5	ST18_H125	Matosinhos	2007
RFLP_6.4	Rep17.2::Rep2:: Rel6	85	1	PP5	ST366_H99	Coimbra	2000
RFLP_20	Rep17.2::Rep2:: Rel6	30	1	A	ST656_H130	Vila Real	2008
RFLP_12 a	Rep17.2::Rep2:: Rel6	40	1	PP10	ST18_H83	Coimbra	1996
RFLP_13 b	Rep17.2:: Rel6::TAInc18 a	60	1	PP5	ST280_ H71	Oporto	2002
RFLP_18	Rep17.2:: Rep1:: Rel6:: TAInc18	50	1	PP13	ST132_H86	Oporto	2001
RFLP_16	Rep17.2:: Rep1:: Rep2:: Rel6::TAInc18	50	1	PP13	ST18_H78	Oporto	2001
RFLP_17	Rep17.2:: Rep1:: Rep2:: Rel6::TAInc18	110	1	PP13	ST132_H88	Oporto	2001
RFLP_19	Rep17.2:: Rep1:: Rep2:: Rel6::TAInc18	60	3	PP13, PP20, PP23	ST132_H119	Oporto	2002
RFLP_19	Rep17.2:: Rep1:: Rep2:: Rel6::TAInc18	60	2	PP17, PP20	ST368_SWH	Oporto	2001
RFLP_19.1	Rep17.2:: Rep1:: Rep2:: Rel6::TAInc18	60	1	X	ST369_RP	Oporto	2003
RFLP_21	Rep17.2:: Rep2:: Rel6:: TApRUM	65	1	PP15	ST719_H96	Oporto	2001
RFLP_22	Rep17.2:: Rep2:: Rel6:: TApRUM	30	1	PP16	ST132_SWC	Oporto	2002
RFPL_27d	Rep9: Rep2: Rep1:: Rel5::TApAD1	75–85	4	PP2a, PP4	ST6_HB, ST55_HG, ST159_HN	Coimbra	1996–2002
RFPL_27.3d	Rep9: Rep2: Rep1:: Rel5::TApAD1	85	2	PP4	ST6_HB, ST159_HN	Viseu	2001–2002
RFPL_27.1d	Rep9: Rep1:: Rel5:: TApAD1	75	1	PP4	ST6_HB	Oporto	2001
RFPL_27d	Rep9: Rep2: Rep1:: Rel5	85	1	PP9	ST132_H106	Coimbra	2000
RFPL_28.5	Rep9: Rep2	100	1	PP16	ST80_SWM	Oporto	2002
RFPL_28	Rep9: Rep2: Rel5:: TApAD1	100	2	PP15, PP16	ST6_HB	Oporto	2001–2002
RFLP_29	Rep9: Rep2: Rel5	100	1	A	ST6_HB	Swine	2007
RFLP_30	Rep9: Rel9	100	1	A	ST30_HK	Oporto	2001
RFLP_24	Rep2	110	1	PP4	ST80_H80	Coimbra	1997
RFLP_14	Rep2	40	1	PP16	ST132_SWC	Oporto	2002
RFLP_15	Rep1:: Rep2	30	2	PP16	ST18_SWA, ST132_SWC	Oporto	2001
RFLP_23	Rel6	85	1	PP9	ST16_H74	Coimbra	2000
RFLP_26	Rep20:: Rel6	150	1	D	ST5_SA	Oporto	2002
RFLP_25	–	120	1	PP5	ST391_H124	Covilhã	2007

Abbreviations: RFLP, restriction fragment length polymorphism; ST, sequence type; NI, not identified.

^aPlasmid type RFLP_12 (Rep_{17.2/pRUM-like} + Rep_2/pRE25/pEF1 + Rel_6/pEF1) contains a partial sequence of the replication gene of the RCR plasmid pEFNP1 (GenBank accession number AB038522), suggesting the integration of this RCR plasmid on the mobile element carrying Tn1546 involving truncation of the rep_{14/pRI1/pEFNP1}.

^bPlasmid types RFLP_3, _4, _5, _6 and _13 (Rep_{17.2/pRUM-like} + Rel_6/pEF1 and eventually containing Rep_1/pIP501, Rep_2/pRE25/pEF1 or TAI_nc18) shared common bands and were identified in the same or different clonal backgrounds in different cities for extended periods of time.

^cPlasmids types RFLP 8, _9 and _10 also shared a variable number of common bands.

^dPlasmids showing patterns related to RFLP_27 (75–85 kb; rep_9/pAD1 + rel_5/pAD1 + rep_1/pIP501 + par _pAD1 and/or rep_2/pRE25/pEF1) initially recovered from the widespread ST6-CC2 Efs clone in Coimbra in 1996 and other Efs (ST55 and ST159) and Efm clones contained similar ISEf1-Tn1546 variants (PP-2a, PP-4, PP-9). Other highly related mosaic Inc18-pAD1-related plasmids carrying IS1216-Tn1546 were recovered from ST6 VREfs and ST80 VREfm isolates (type ˝II_Efs ˝, rep_9/pAD1 +rel_5/pAD1 + par _pAD1 + rep_2/pRE25/pEF1 versus type ˝II_Efm ˝, rep_9/pAD1 + rep_2/pRE25/pEF1).