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Epidemiology and Surveillance

In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

Alessandra Carattoli, Ea Zankari, Aurora García-Fernández, Mette Voldby Larsen, Ole Lund, Laura Villa, Frank Møller Aarestrup, Henrik Hasman
Alessandra Carattoli
Department of Infectious, Parasitic and Immuno-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
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Ea Zankari
Danish Technical University, National Food Institute, Division for Epidemiology and Microbial Genomics, Lyngby, Denmark
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Aurora García-Fernández
Department of Infectious, Parasitic and Immuno-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
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Mette Voldby Larsen
Danish Technical University, Center for Biological Sequence Analysis, Department of Systems Biology, Lyngby, Denmark
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Ole Lund
Danish Technical University, Center for Biological Sequence Analysis, Department of Systems Biology, Lyngby, Denmark
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Laura Villa
Department of Infectious, Parasitic and Immuno-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
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Frank Møller Aarestrup
Danish Technical University, National Food Institute, Division for Epidemiology and Microbial Genomics, Lyngby, Denmark
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Henrik Hasman
Danish Technical University, National Food Institute, Division for Epidemiology and Microbial Genomics, Lyngby, Denmark
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DOI: 10.1128/AAC.02412-14
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    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).

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  • TABLE 1

    List of probes detecting previously characterized replicons

    ProbeaPositionLocus targetedReference
    A/C2_1_JN15780459363–58947repA2
    B/O/K/Z_2_GU2566416440–6281RNAI2
    B/O/K/Z_4_413–561RNAI26
    FIA_1_AP00191848305–48692repFIA2
    FIA(HI1)_1_HI1_AF250878157744–157357repFIA27
    FIB_1_AP00191837699–37018repFIB2
    FIB(Kpn3)_1_Kpn3_JN23370476861–77420repFIB19
    FIB(KpQIL)_1_pKpQIL_JN23370585120–85859repFIB19
    FIB(Mar)_1_pNDM-Mar_JN42033629199–29637repFIB5
    FIB(S)_1__FN43203114696–14054repFIB4
    FIC_1_AP0019183421–3660repFIC2
    FII_1_AY45801689119–88859RNAI-FII2
    FII(K)_1__CP0006485614–5761RNAI-FII4
    FII(S)_1_CP00085826564–26303RNAI-FII4
    FII(Yp)_1_Yersinia_CP000670114633–114862RNAI-FII4
    FII(Y)_1_ps_CP00104920297–20071RNAI-FII4
    HI1A_1_AF25087840122–39702repHIA27
    HI1A(CIT)_1_pNDM-CIT_JX182975220487–220906repHIA8
    HI1B(R27)_1_R27_AF25087854421–54960repHIB8
    HI2_1_BX664015209836–209510repHI22
    HI2A_1_BX664015211–840repHIA28
    HI1B_1_pNDM-MAR_JN420336126037–126606repHIB5
    HI1B(CIT)_1_pNDM-CIT_JX182975203748–203211repHIB8
    I1_1_Alpha_AP005147198–339RNAI-I12
    L/M_1_AF55041554207–54947repA2
    N_1_AY04627631781–32294repA2
    N2_1_JF78554914890–15366repA29
    P_1_alpha_L2775812765–12232Control of repA2
    R_1_DQ44957819367–19617repA6
    T_1_AP004237423–1172repA2
    U_1_DQ40110351–615repA2
    W_1_EF63350725644–25886repA2
    X1_1_EU37091335767–36140repA30
    X2_1_JQ2693359035–8662repA2
    X3_1_JN2478526440–6067repA9
    X3(pEC14)_1_pEC14_JN9358997–380repA9
    X4_2_FN5435046671–7382repA9
    X4_1_CP0028953–376repA9
    Y_1_K023801075–1839repA2
    • ↵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

    ProbeaPositionLocus targetedSource
    A/C_1__FJ705807684–1100repAThis study
    B/O/K/Z_1_CU928147119424–119574RNAIThis study
    B/O/K/Z_3_GQ25988824642–24793RNAIThis study
    FII(p14)_1_p14_JQ41853834250–33989repFIIThis study
    FII(p96A)_1_p96A_JQ41852142799–43332repFIIThis study
    FII(pCoo)_1_pCoo_CR94228527847–27586repFIIThis study
    FII(pCRY)_1_pCRY_NC_005814739–1331repFIIThis study
    FII(pCTU2)_1_pCTU2_FN5430958327–8903repFIIThis study
    FII(pECLA)_1_pECLA_CP0019193–749repFIIThis study
    FII(Phn7A8)_JN232517412–671repFIIThis study
    FII(pENTA)_1_pENTA_CP00302784306–84865repFIIThis study
    FII(pMET)_1_pMET1_EU383016690–1266repFIIThis study
    FII(pRSB107)_1_pRSB107_AJ85108921949–21689repFIIThis study
    FII(pSE11)_1_pSE11_AP00924275349–75085repFIIThis study
    FII(pseudo)_1_pseudo_NC_01175976101–76490repFIIThis study
    FII(pYVa12790)_1_pYVa12790_AY150843121–794repFIIThis study
    FII(SARC14)_1_SARC14_JQ41854036938–37382repFIIThis study
    FII(Serratia)_1_Serratia_NC_00982940691–40968repFIIThis study
    FII(29)_ pCE10A_CP0030351393–1135repFIIThis study
    FII(pSFO)_AF4012923516–3773repFIIThis study
    FII(pKP91)_CP00096689831–90060repFIIThis study
    FIB(pHCM2)_1_pHCM2_AL513384104938–105812repFIBThis study
    FIB(pB171)_1_pB171_AB024946250–892repFIBThis study
    FIB(pCTU1)_1_pCTU1_FN5430942655–3347repFIBThis study
    FIB(pCTU3)_1_pCTU3_FN543096142054–142620repFIBThis study
    FIB(pECLA)_1_pECLA_CP001919211–771repFIBThis study
    FIB(pENTAS01)_1_pENTAS01_CP003027141679–142239repFIBThis study
    FIB(pENTE01)_1_pENTE01_CP000654142054–142620repFIBThis study
    FIB(pKPHS1)_1_pKPHS1_CP003223201–761repFIBThis study
    FIB(pLF82)_1_pLF82_CU638872211–771repFIBThis study
    I2_1_Delta_AP002527207–522repRThis study
    L/M(pOXA-48)_1_JN62628655802–56462repAThis study
    L/M(pMU407)_1_pMU407_U2734522–760repAThis study
    N3_EF21913429016–29492repAThis study
    P(Beta)_1_Beta_U6719415582–16163repAThis study
    X1_2_CP00341724754–25101repAThis study
    X1_3_CP00112336953–37325repAThis study
    X1_4_JN935898844–1220repAThis study
    X5_1_NC_01505434413–34786repAThis study
    X6_1_AM9427601–374repAThis study
    p0111_AP01096254482–53598repAThis study
    ICC168_FN5435046671–7382repAThis study
    pADAP_1_AF135182113796–114335repAThis study
    pENTAS02_1_CP00302825220–24242repAThis study
    pESA2_CP0007842497–3246repAThis study
    pIP31758_1_CP000718639–1556repAThis study
    pIP31758_1_CP000719150807–151715repAThis study
    pIP32953_1_BX936400262–1188repAThis study
    pSL483_1_CP00113723947–22953repAThis study
    pXuzhou21_1_CP00192771–791repAThis study
    pYE854_1_AM90595077347–78325repAThis study
    pEC4115_1__NC_01135193–798repAThis study
    pJARS36_1__NC_015068179–712repAThis study
    pSM22_1__NC_01597217401–18023repAThis study
    • ↵a The number following the final underscore is the GenBank accession number of the sequence.

  • TABLE 3

    List of probes detecting small plasmids

    ProbeaPositionLocus targetedbSource
    Col156_NC_0097811552–1705repAThis study
    Col3M_JX5140652453–2609Intergenic regionThis study
    Col8282_DQ9953523349–3555repAThis study
    Col(BS512)_1_NC_0106561096–1328repAThis study
    ColE10_1_AY167049159–177Intergenic regionThis study
    Col(IMGS31)_1_NC_011406700–897ORF2This study
    Col(IRGK)_1_AY5430712041–2224ORF2This study
    ColKP3_JN2058006541–6820repAThis study
    Col(KPHS6)_1_NC_016841326–503repAThis study
    Col(MG828)_1_NC_008486967–1228repAThis study
    Col(MGD2)_NC_0037891235–1370repAThis study
    Col(MP18)_1_NC_013652266–458repAThis study
    Col(pVC)_JX133088799–991repAThis study
    Col(pWES)_1_DQ26876410151–10328repAThis study
    ColRNAI_DQ2980195738–5867RNAIThis study
    Col(SD853)_1_NC_0153921363–1556repAThis study
    Col(VCM04)_1_HM231165776–952repAThis study
    Col(YC)_1_NC_0021445043–5195repAThis study
    Col(Ye4449)_1_FJ6964052409–2602mobCThis study
    Col(YF27601)_1_JF9376551–175RNAIThis study
    Q1_1_HE6547262181–2630repAThis study
    Q2_1_NC_0143564547–4996repAThis study
    P(6)_1__JF7855501477–2282repAThis study
    • ↵a The number following the final underscore is the GenBank accession number of the sequence.

    • ↵b ORF, open reading frame.

  • TABLE 4

    Distribution of replicons identified among 49 whole-genome-sequenced Salmonella Typhimurium isolates by using the PlasmidFinder Web server

    RepliconaIsolate(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)
    Q1S3 (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)
    I1S13 (100), S25 (99.3), S31 (99.3)
    FIA(HI1)S25 (100), S36 (100), S38 (100)
    HI1AS25 (99.8), S36 (99.8), S38 (99.8)
    HI1B(R27)S25 (100), S36 (100), S38 (100)
    X1S1 (98.9), S28 (98.7)
    X4S28 (100), S37 (99.7)
    COL(156)S39 (94.8), S40 (94.8), S49* (95.1)
    F1AS49 (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)
    HI2S39 (100)
    HI2AS39 (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.

Additional Files

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    Files in this Data Supplement:

    • Supplemental file 1 -

      Table of plasmids analyzed in this study to generate the PlasmidFinder database.

      PDF, 297K

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In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
Alessandra Carattoli, Ea Zankari, Aurora García-Fernández, Mette Voldby Larsen, Ole Lund, Laura Villa, Frank Møller Aarestrup, Henrik Hasman
Antimicrobial Agents and Chemotherapy Jun 2014, 58 (7) 3895-3903; DOI: 10.1128/AAC.02412-14

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In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
Alessandra Carattoli, Ea Zankari, Aurora García-Fernández, Mette Voldby Larsen, Ole Lund, Laura Villa, Frank Møller Aarestrup, Henrik Hasman
Antimicrobial Agents and Chemotherapy Jun 2014, 58 (7) 3895-3903; DOI: 10.1128/AAC.02412-14
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