DOI: 10.1128/AAC.02412-14
Article Figures & Data
Figures
- FIG 1
Numbers of fully sequenced plasmids (y axis) classified into incompatibility groups occurring in the different bacterial species of the Enterobacteriaceae family. The collection of 335 large plasmids (>20 kb) (listed in Table S1 in the supplemental material) downloaded from the GenBank database was classified into Inc groups by BLASTn (using the criterion of >95% nucleotide identity) using reference replicon sequences (Table 1) and the novel probes in the PlasmidFinder database (Table 2).
Tables
- TABLE 1
List of probes detecting previously characterized replicons
Probea Position Locus targeted Reference A/C2_1_JN157804 59363–58947 repA 2 B/O/K/Z_2_GU256641 6440–6281 RNAI 2 B/O/K/Z_4_ 413–561 RNAI 26 FIA_1_AP001918 48305–48692 repFIA 2 FIA(HI1)_1_HI1_AF250878 157744–157357 repFIA 27 FIB_1_AP001918 37699–37018 repFIB 2 FIB(Kpn3)_1_Kpn3_JN233704 76861–77420 repFIB 19 FIB(KpQIL)_1_pKpQIL_JN233705 85120–85859 repFIB 19 FIB(Mar)_1_pNDM-Mar_JN420336 29199–29637 repFIB 5 FIB(S)_1__FN432031 14696–14054 repFIB 4 FIC_1_AP001918 3421–3660 repFIC 2 FII_1_AY458016 89119–88859 RNAI-FII 2 FII(K)_1__CP000648 5614–5761 RNAI-FII 4 FII(S)_1_CP000858 26564–26303 RNAI-FII 4 FII(Yp)_1_Yersinia_CP000670 114633–114862 RNAI-FII 4 FII(Y)_1_ps_CP001049 20297–20071 RNAI-FII 4 HI1A_1_AF250878 40122–39702 repHIA 27 HI1A(CIT)_1_pNDM-CIT_JX182975 220487–220906 repHIA 8 HI1B(R27)_1_R27_AF250878 54421–54960 repHIB 8 HI2_1_BX664015 209836–209510 repHI2 2 HI2A_1_BX664015 211–840 repHIA 28 HI1B_1_pNDM-MAR_JN420336 126037–126606 repHIB 5 HI1B(CIT)_1_pNDM-CIT_JX182975 203748–203211 repHIB 8 I1_1_Alpha_AP005147 198–339 RNAI-I1 2 L/M_1_AF550415 54207–54947 repA 2 N_1_AY046276 31781–32294 repA 2 N2_1_JF785549 14890–15366 repA 29 P_1_alpha_L27758 12765–12232 Control of repA 2 R_1_DQ449578 19367–19617 repA 6 T_1_AP004237 423–1172 repA 2 U_1_DQ401103 51–615 repA 2 W_1_EF633507 25644–25886 repA 2 X1_1_EU370913 35767–36140 repA 30 X2_1_JQ269335 9035–8662 repA 2 X3_1_JN247852 6440–6067 repA 9 X3(pEC14)_1_pEC14_JN935899 7–380 repA 9 X4_2_FN543504 6671–7382 repA 9 X4_1_CP002895 3–376 repA 9 Y_1_K02380 1075–1839 repA 2 ↵a The number following the final underscore is the GenBank accession number of the sequence.
- TABLE 2
List of probes detecting novel replicons in large plasmids
Probea Position Locus targeted Source A/C_1__FJ705807 684–1100 repA This study B/O/K/Z_1_CU928147 119424–119574 RNAI This study B/O/K/Z_3_GQ259888 24642–24793 RNAI This study FII(p14)_1_p14_JQ418538 34250–33989 repFII This study FII(p96A)_1_p96A_JQ418521 42799–43332 repFII This study FII(pCoo)_1_pCoo_CR942285 27847–27586 repFII This study FII(pCRY)_1_pCRY_NC_005814 739–1331 repFII This study FII(pCTU2)_1_pCTU2_FN543095 8327–8903 repFII This study FII(pECLA)_1_pECLA_CP001919 3–749 repFII This study FII(Phn7A8)_JN232517 412–671 repFII This study FII(pENTA)_1_pENTA_CP003027 84306–84865 repFII This study FII(pMET)_1_pMET1_EU383016 690–1266 repFII This study FII(pRSB107)_1_pRSB107_AJ851089 21949–21689 repFII This study FII(pSE11)_1_pSE11_AP009242 75349–75085 repFII This study FII(pseudo)_1_pseudo_NC_011759 76101–76490 repFII This study FII(pYVa12790)_1_pYVa12790_AY150843 121–794 repFII This study FII(SARC14)_1_SARC14_JQ418540 36938–37382 repFII This study FII(Serratia)_1_Serratia_NC_009829 40691–40968 repFII This study FII(29)_ pCE10A_CP003035 1393–1135 repFII This study FII(pSFO)_AF401292 3516–3773 repFII This study FII(pKP91)_CP000966 89831–90060 repFII This study FIB(pHCM2)_1_pHCM2_AL513384 104938–105812 repFIB This study FIB(pB171)_1_pB171_AB024946 250–892 repFIB This study FIB(pCTU1)_1_pCTU1_FN543094 2655–3347 repFIB This study FIB(pCTU3)_1_pCTU3_FN543096 142054–142620 repFIB This study FIB(pECLA)_1_pECLA_CP001919 211–771 repFIB This study FIB(pENTAS01)_1_pENTAS01_CP003027 141679–142239 repFIB This study FIB(pENTE01)_1_pENTE01_CP000654 142054–142620 repFIB This study FIB(pKPHS1)_1_pKPHS1_CP003223 201–761 repFIB This study FIB(pLF82)_1_pLF82_CU638872 211–771 repFIB This study I2_1_Delta_AP002527 207–522 repR This study L/M(pOXA-48)_1_JN626286 55802–56462 repA This study L/M(pMU407)_1_pMU407_U27345 22–760 repA This study N3_EF219134 29016–29492 repA This study P(Beta)_1_Beta_U67194 15582–16163 repA This study X1_2_CP003417 24754–25101 repA This study X1_3_CP001123 36953–37325 repA This study X1_4_JN935898 844–1220 repA This study X5_1_NC_015054 34413–34786 repA This study X6_1_AM942760 1–374 repA This study p0111_AP010962 54482–53598 repA This study ICC168_FN543504 6671–7382 repA This study pADAP_1_AF135182 113796–114335 repA This study pENTAS02_1_CP003028 25220–24242 repA This study pESA2_CP000784 2497–3246 repA This study pIP31758_1_CP000718 639–1556 repA This study pIP31758_1_CP000719 150807–151715 repA This study pIP32953_1_BX936400 262–1188 repA This study pSL483_1_CP001137 23947–22953 repA This study pXuzhou21_1_CP001927 71–791 repA This study pYE854_1_AM905950 77347–78325 repA This study pEC4115_1__NC_011351 93–798 repA This study pJARS36_1__NC_015068 179–712 repA This study pSM22_1__NC_015972 17401–18023 repA This study ↵a The number following the final underscore is the GenBank accession number of the sequence.
- TABLE 3
List of probes detecting small plasmids
Probea Position Locus targetedb Source Col156_NC_009781 1552–1705 repA This study Col3M_JX514065 2453–2609 Intergenic region This study Col8282_DQ995352 3349–3555 repA This study Col(BS512)_1_NC_010656 1096–1328 repA This study ColE10_1_AY167049 159–177 Intergenic region This study Col(IMGS31)_1_NC_011406 700–897 ORF2 This study Col(IRGK)_1_AY543071 2041–2224 ORF2 This study ColKP3_JN205800 6541–6820 repA This study Col(KPHS6)_1_NC_016841 326–503 repA This study Col(MG828)_1_NC_008486 967–1228 repA This study Col(MGD2)_NC_003789 1235–1370 repA This study Col(MP18)_1_NC_013652 266–458 repA This study Col(pVC)_JX133088 799–991 repA This study Col(pWES)_1_DQ268764 10151–10328 repA This study ColRNAI_DQ298019 5738–5867 RNAI This study Col(SD853)_1_NC_015392 1363–1556 repA This study Col(VCM04)_1_HM231165 776–952 repA This study Col(YC)_1_NC_002144 5043–5195 repA This study Col(Ye4449)_1_FJ696405 2409–2602 mobC This study Col(YF27601)_1_JF937655 1–175 RNAI This study Q1_1_HE654726 2181–2630 repA This study Q2_1_NC_014356 4547–4996 repA This study P(6)_1__JF785550 1477–2282 repA This study - TABLE 4
Distribution of replicons identified among 49 whole-genome-sequenced Salmonella Typhimurium isolates by using the PlasmidFinder Web server
Replicona Isolate(s) with replicon (% identity)b Col(RNAI) S2* (91.7), S4* (89.4), S8* (91.3), S9* (95.0), S11* (89.4), S16* (89.4), S17* (91.2), S18* (89.4), S19* (90.4), S20* (90.4), S32* (89.4), S33* (91.5), S37* (92.0), S39* (95.1), S40* (91.2), S41* (91.5), S43* (91.6), S44 (100), S45* (89.36), S47* (91.5), S50* (92.7) Q1 S3 (100), S6 (100), S8 (100), S9 (100), S12 (100), S20 (100), S21 (100), S22 (100), S24 (100), S26 (100), S27 (100), S28 (100), S29 (100), S30 (100), S34 (100), S36 (100), S38 (100), S44 (100) FIB(S) S1 (99.8), S2 (100), S4 (99.8), S11 (100), S13 (100), S16 (99.8), S32 (99.8), S33 (100), S40 (100), S41 (100), S45 (99.8), S47 (100), S50 (100) FII(S) S1 (100), S2 (100), S4 (100), S11 (100), S13 (100), S16 (199), S32 (100), S33 (100), S40 (100), S41 (100), S45 (100), S47 (100), S50 (100) Col(pVC) S11 (100), S33* (99.2), S41* (100), S47* (100), S50 (100) Col(8282) S5 (100), S6* (91.4), S22* (91.4), S30* (91.4), S38* (91.4) I1 S13 (100), S25 (99.3), S31 (99.3) FIA(HI1) S25 (100), S36 (100), S38 (100) HI1A S25 (99.8), S36 (99.8), S38 (99.8) HI1B(R27) S25 (100), S36 (100), S38 (100) X1 S1 (98.9), S28 (98.7) X4 S28 (100), S37 (99.7) COL(156) S39 (94.8), S40 (94.8), S49* (95.1) F1A S49 (100) FII(pCoo) S49 (96.2) F(AP001918) S48 (97.7) FII(pHN7A8) S48 (97.3) HI1A(CIT) S14 (100) HI1B(CIT) S14 (99.0) HI2 S39 (100) HI2A S39 (100) Col(BS512) S2* (100) ↵a Replicon types matching the probes in the PlasmidFinder database. Subvariants of replicons are given in parentheses.
↵b Isolate names are given in boldface if more than one replicon was identified on the same contig, indicating colocalization of the replicons on the same plasmid. Hits not in full length are marked with an asterisk. No replicons were identified in strains S7, S10, S15, S23, S42, and S46.
Supplemental material
Files in this Data Supplement:
- Supplemental file 1 -
Table of plasmids analyzed in this study to generate the PlasmidFinder database.
PDF, 297K
- Supplemental file 1 -
