Table 2 Plasmid content of OXA-48-producing Escherichia coli isolates and location of resistance and virulence genes.

From: Whole genome sequencing, molecular typing and in vivo virulence of OXA-48-producing Escherichia coli isolates including ST131 H30-Rx, H22 and H41 subclones

Isolate

Plasmids Chromosome

Size (bp)

Contigs

Relaxase proteina,e

Replication roteina,e

Inc group (pMLST)b,e

Resistance genesc,e

Virulence genesd,e

Ec-HUCA 1

pEc-HUCA 1_1

131330

26

MOBF12

RepFII, RepFIB

IncF (F29:A-:B10)

bla TEM-1b, mph(A), tet(B)

senB, finO, traT

pEc-HUCA 1_2

61395

6

MOBP131

IncFII_RepA_superfamily (pfam02387)

IncL/M

bla OXA-48

nd

pEc-HUCA 1_3

40230

6

MOBF11

Rep3_superfamily (pfam01051)

IncN (ST9)

nd

nd

pEc-HUCA 1_4

34530

4

MOBP3

Rep3_superfamily (pfam01051)

IncX1

nd

nd

ICE_Ec-HUCA 1

201132 f

1

MOBH2

nd

nd

nd

nd

Chr_Ec-HUCA 1

4903773

62

na

na

na

gyrA-S83L

gad, fimABCDEFGHI, ibeBC, iha, pic, sfaX, usp, matB, betA, irp2, sitC, fyuA/psn

Ec-HUCA 2

pEc-HUCA 2_1 + 2

347908

346

MOBF12

RepFII (x3), RepFIB

IncF (F2/51/40:A:B1)

bla TEM-1b, bla OXA-30, bla CTX-M-15, aadA1, strB, aph(3’)-Ia, mph(A), sul1, dfrA5, tet(A)

iroN, mchF, ompT, sitC, cba, hlyF, iroBCDE, iss, iucABCD, iutA, etsABC, finO, traT, cvaC

pEc-HUCA 2_3

61304

6

MOBP131

IncFII_RepA_superfamily (pfam02387)

IncL/M

bla OXA-48

nd

pEc-HUCA 2_4

6187

1*

MOBQ12

Replicase (pfam03090) + priCT1 (pfam 08708)

nd

nd

celB

pEc-HUCA 2_5

3003

1*

MOBP51

RNAI-II replication system

ColE-like

nd

nd

Chr_Ec-HUCA 2

4741812

134

na

na

na

nd

gad, lpfA, fimABCDEFGHI, ibeBC, matB, betA, irp2, fyuA/psn, iss

Ec-HUCA 3

pEc-HUCA 3_1

111201

1*

no-MOB

nd

nd

nd

nd

pEc-HUCA 3_2

61879

6

MOBP131

IncFII_RepA_superfamily (pfam02387)

IncL/M

bla OXA-48

nd

Chr_Ec-HUCA 3

4747878

64

na

na

na

ampC2, ampH

gad, pic, fimABCDEFGHI, ibeABC, sfaX, usp, matB, betA, irp2, sitC, fyuA/psn, vat, papBCDFHJK

Ec-HUCA 4

pEc-HUCA 4_1 + 2

253046

24

MOBF12 + MOBP12

RepFII, RepFIB, IncFII_RepA_superfamily (pfam02387)

IncF (F2:A-:B1) + IncI1 (ST48)

bla TEM-1c, cmlA1, tet(A), sul3

iroN, mchF, ompT, sitC, hlyF, iroBCDE, iss, iucABCD, iutA, etsABC, finO, traT, cvaC

pEc-HUCA 4_3

62423

5

MOBP131

IncFII_RepA_superfamily (pfam02387)

IncL/M

bla OXA-48

nd

pEc-HUCA 4_4

33543

1*

MOBP3

Rep3_superfamily (pfam01051)

IncX4

nd

nd

pEc-HUCA 4_5

6544

1

MOBP51

RNAI-II replication system

ColE-like

nd

nd

pEc-HUCA 4_6

4502

1

MOBP51

RNAI-II replication system

ColE-like

nd

nd

pEc-HUCA 4_7

1546

1*

no-MOB

RepA_HTH36_pfam13730

nd

nd

nd

Chr_Ec-HUCA 4

4996329

48

na

na

na

gyrA-S83L

gad, mchF, iss, cnf1, pic, fimABCDEFGHI, ibeABC, iha, sfaX, usp, matB, betA, irp2, fyuA/psn, papBCDFHJK, hlyABCD

Ec-HUCA 5

pEc-HUCA 5_1

5251

1*

MOBP51

RNAI-II replication system

ColE-like

nd

nd

 

Chr_Ec-HUCA 5

5187005

184

na

na

na

bla OXA-48, bla CTX-M-15, gyrA-S83L + D87N; parC-S80I + E84V; parE-I529L, folA-W30R

gad, cnf1, pic, fimABCDEFGHI, ibeBC, iha, usp, matB, betA, irp2, sitC, fyuA/psn, sat, papBCDFGHJK, cnf1, hlyABCD, iss, iucABCD, iutA

Ec-HUCA 6

pEc-HUCA 6_1

45832

14

MOBF11

Rep3_superfamily (pfam01051)

IncN (ST7)

qnrS1, dfrA14

 

pEc-HUCA 6_2

5251

1*

MOBP51

RNAI-II replication system

ColE-like

nd

nd

Chr_Ec-HUCA 6

5218580

123

na

na

na

bla OXA-48, bla CTX-M-15, gyrA-S83L + D87N; parC-S80I + E84V; parE-I529L

gad, cnf1, pic, fimABCDEFGHI, ibeBC, iha, usp, matB, betA, irp2, sitC, fyuA/psn, sat, papBCDEFGHJK, cnf1, hlyABCD, iss, iucABCD, iutA

Ec-HUCA 7

pEc-HUCA 7_1

48671

14

MOBF11

Rep3_superfamily (pfam01051)

IncN (ST7)

bla CTX-M-15, qnrS1, dfrA14

nd

pEc-HUCA 7_2

5251

1*

MOBP51

RNAI-II replication system

ColE-like

nd

nd

Chr_EcHUCA 7

5186594

125

na

na

na

bla OXA-48, gyrA-S83L + D87N; parC-S80I + E84V; parE-I529L

gad, cnf1, pic, fimABCDEFGHI, ibeBC, iha, usp, matB, betA, irp2, sitC, fyuA/psn, sat, papBCDEFGHJK, cnf1, hlyABCD, iss, iucABCD, iutA

  1. aRelaxase and replication proteins were identified by the use of homemade databases51. bIncompatibility groups were determined according to the PBRT scheme8 and pMLST subtypes according to the allele scheme in http://pubmlst.org/plasmid/. cAntimicrobial resistance genes were detected using the ARG-ANNOT48 and ResFinder49 databases. dVirulence genes were detected according to VirulenceFinder50 and homemade databases. ena, not applicable; nd, not detected. fLength of the ICE (integrative and conjugative element)-containing contig. *Closed plasmids.
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