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Chapter 21 : The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials

Authors: Val Fernández Lanza1, Ana P. Tedim4, José Luís Martínez7, Fernando Baquero9, Teresa M. Coque12
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Affiliations: 1: Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; 2: Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (HRYC-CSIC), Madrid, Spain; 3: Centro de Investigación en Red en Epidemiología y Salud Pública (CIBER-ESP), Spain; 4: Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; 5: Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (HRYC-CSIC), Madrid, Spain; 6: Centro de Investigación en Red en Epidemiología y Salud Pública (CIBER-ESP), Spain; 7: Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (HRYC-CSIC), Madrid, Spain; 8: Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain; 9: Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; 10: Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (HRYC-CSIC), Madrid, Spain; 11: Centro de Investigación en Red en Epidemiología y Salud Pública (CIBER-ESP), Spain; 12: Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; 13: Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (HRYC-CSIC), Madrid, Spain; 14: Centro de Investigación en Red en Epidemiología y Salud Pública (CIBER-ESP), Spain
Content Type: Monograph
Publication Year: 2015

Category: Clinical Microbiology

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Abstract:

constitutes one of the dominant bacteria phyla of human and animal gut microbiota. It comprises a number of genera of outstanding relevance in health care and industry such as , , and lactic acid bacteria (LAB), a group of microorganisms that ferment carbohydrates into lactic acid and that includes the genera , , , , , , and . Furthermore, species of (, ) and have clinical interest for humans and animals ( Table 1 ).

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials
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Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
/content/10.1128/9781555818982.chap21.fig21-1
Figure 1
Protein content network (PCN) of AbR proteins found in plasmids and chromosomes of and . To determine the AbR protein catalog of Gram-positive strains (chromosomes and plasmids), a Blastp search was performed of all their proteomes against the ARG-ANNOT database (http://en.mediterranee-infection.com/article.php?laref=283&titre=arg-annot) using a cut-off of 1e-30 and 85% of identity. The presence of the Gram-positive AbR proteins identified above in all bacterial species (only complete sequences, not partial) was determined using a similar Blast search (blastp, 1e-30 E-value and 85% identity) against the NCBI GenBank database. The nodes correspond to bacterial species (circular nodes; each color indicates one genus) and AbR proteins (square nodes). Nodes were connected by an edge when a positive hit between AbR proteins and one or more strains of a given species were identified. Edges further indicate the location of the AbR genes associated with each AbR protein of the Gram-positive catalog. Solid lines represent chromosomal location, and dotted lines represent plasmid location. When an AbR gene was located in both chromosomes and plasmids, both lines were plotted.
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Figure 1

Protein content network (PCN) of AbR proteins found in plasmids and chromosomes of and . To determine the AbR protein catalog of Gram-positive strains (chromosomes and plasmids), a Blastp search was performed of all their proteomes against the ARG-ANNOT database (http://en.mediterranee-infection.com/article.php?laref=283&titre=arg-annot) using a cut-off of 1e-30 and 85% of identity. The presence of the Gram-positive AbR proteins identified above in all bacterial species (only complete sequences, not partial) was determined using a similar Blast search (blastp, 1e-30 E-value and 85% identity) against the NCBI GenBank database. The nodes correspond to bacterial species (circular nodes; each color indicates one genus) and AbR proteins (square nodes). Nodes were connected by an edge when a positive hit between AbR proteins and one or more strains of a given species were identified. Edges further indicate the location of the AbR genes associated with each AbR protein of the Gram-positive catalog. Solid lines represent chromosomal location, and dotted lines represent plasmid location. When an AbR gene was located in both chromosomes and plasmids, both lines were plotted.

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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Figure 2
PCN of metal-biocide (Met/Bc) proteins found in plasmids and chromosomes of and . To determine the Met/Bc protein catalog of Gram-positive strains (chromosomes and plasmids), a Blastp search was performed of all their proteomes against the BacMet database (http://bacmet.biomedicine.gu.se/) using a cut-off of 1e-30 and 85% of identity. The presence of the Gram-positive Met/Bc proteins identified above in all bacterial species (only complete sequences, not partial) was determined using a similar Blastp search (blastp, 1e-30 evalue and 85% identity) against the NCBI GenBank database. The nodes correspond to bacterial species (circular nodes) and Met/Bc proteins (triangular nodes). Nodes were connected by an edge when a positive hit between Met/Bc proteins on one or more strains of a given species was identified. Edges further indicate the location of the Met/Bc genes associated with each Met/Bc protein of the Gram-positive catalog. Solid lines represent chromosomal location, and dotted lines represent plasmid location. When a Met/Bc gene was located in both chromosomes and plasmids, both lines were plotted.
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Figure 2

PCN of metal-biocide (Met/Bc) proteins found in plasmids and chromosomes of and . To determine the Met/Bc protein catalog of Gram-positive strains (chromosomes and plasmids), a Blastp search was performed of all their proteomes against the BacMet database (http://bacmet.biomedicine.gu.se/) using a cut-off of 1e-30 and 85% of identity. The presence of the Gram-positive Met/Bc proteins identified above in all bacterial species (only complete sequences, not partial) was determined using a similar Blastp search (blastp, 1e-30 evalue and 85% identity) against the NCBI GenBank database. The nodes correspond to bacterial species (circular nodes) and Met/Bc proteins (triangular nodes). Nodes were connected by an edge when a positive hit between Met/Bc proteins on one or more strains of a given species was identified. Edges further indicate the location of the Met/Bc genes associated with each Met/Bc protein of the Gram-positive catalog. Solid lines represent chromosomal location, and dotted lines represent plasmid location. When a Met/Bc gene was located in both chromosomes and plasmids, both lines were plotted.

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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Figure 3
Plasmid homology network. The genomic homology network was performed using “All-versus-All” genomic Megablast ( ) of 1,326 fully sequenced plasmids from low G+C bacterial species ( and phyla) available at public gene databases. The nodes correspond to bacterial plasmids (circular nodes; different colors representing different genera). Two nodes are connected by an edge if they share homologous DNA.
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Figure 3

Plasmid homology network. The genomic homology network was performed using “All-versus-All” genomic Megablast ( ) of 1,326 fully sequenced plasmids from low G+C bacterial species ( and phyla) available at public gene databases. The nodes correspond to bacterial plasmids (circular nodes; different colors representing different genera). Two nodes are connected by an edge if they share homologous DNA.

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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Figure 4
PCN of AbR and Met/Bc proteins located on plasmids of and . PCN of AbR and Met proteins found in Gram-positive plasmids. We formed the PCN by representing plasmids as circular nodes, AbR as square nodes, and Met/Bc as triangular nodes, connecting two nodes (plasmid and AbR or Met/Bc) if one plasmid has this AbR or Met/Bc. The presence of the Met/Bc gene was determined by blasp of all plasmid proteins against the BacMet database. The presence of the AbR gene was determined by blasp of all plasmid proteins against the ARG-ANNOT database. The colors for the genus are the same as those in Fig. 3 .
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Figure 4

PCN of AbR and Met/Bc proteins located on plasmids of and . PCN of AbR and Met proteins found in Gram-positive plasmids. We formed the PCN by representing plasmids as circular nodes, AbR as square nodes, and Met/Bc as triangular nodes, connecting two nodes (plasmid and AbR or Met/Bc) if one plasmid has this AbR or Met/Bc. The presence of the Met/Bc gene was determined by blasp of all plasmid proteins against the BacMet database. The presence of the AbR gene was determined by blasp of all plasmid proteins against the ARG-ANNOT database. The colors for the genus are the same as those in Fig. 3 .

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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Figure 5
Plasmids from spp. The presence of an orange border in the RIP family indicates that the corresponding RIP is truncated. PriCT_1; *One of these plasmids (GenBank accession number NC_013381) has a truncated rep_pKH21 (rep_1) gene, and no other known RIPs were identified. **Two of these plasmids (GenBank accession number NC_016054 and NC_019144) appear to have two copies of the MOB gene. One of these plasmids (GenBank accession number NC_008354) has two copies of the gene. One plasmid (GenBank accession number NC_001393) has a truncated copy of the gene. One plasmid (GenBank accession number NC_010419) has a truncated copy of the gene. The plasmid (GenBank accession number NC_005076) appears to have two copies of the MOB gene. One plasmid (GenBank accession number NC_018959) has a truncated copy of the gene. Two plasmids (GenBank accession numbers NC_007931 and NC_016942) have two copies of the and genes. This plasmid (GenBank accession number NC_013320) appears to have two copies of the MOB gene. This plasmid (GenBank accession number NC_005004) has a truncated copy of the gene. Three plasmids (GenBank accession numbers NC_013321, NC_019007, and NC_018976) have a truncated copy of the gene. Eleven of these plasmids have a truncated copy of the gene (GenBank accession numbers NC_020531, NC_020538, NC_013337, NC_020534, NC_020565, NC_020567, NC_020530, NC_020539, NC_017352, NC_013323, and NC_022610). One plasmid (GenBank accession number NC_013334) has a truncated copy of the gene. This plasmid (GenBank accession number NC_020237) appears to have two copies of the MOB gene. This plasmid (GenBank accession number NC_022598) appears to have two copies of the MOB gene. Abbreviations: MRIP, Multi-RIP; S, spp; Sar, ; Sa, ; Sc, ; Se, ; Sha, ; Shy, ; Sle, ; Slu, ; Sp, ; Ssa, ; Ssc, ; Ssi, ; Sw, .
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Figure 5

Plasmids from spp. The presence of an orange border in the RIP family indicates that the corresponding RIP is truncated. PriCT_1; *One of these plasmids (GenBank accession number NC_013381) has a truncated rep_pKH21 (rep_1) gene, and no other known RIPs were identified. **Two of these plasmids (GenBank accession number NC_016054 and NC_019144) appear to have two copies of the MOB gene. One of these plasmids (GenBank accession number NC_008354) has two copies of the gene. One plasmid (GenBank accession number NC_001393) has a truncated copy of the gene. One plasmid (GenBank accession number NC_010419) has a truncated copy of the gene. The plasmid (GenBank accession number NC_005076) appears to have two copies of the MOB gene. One plasmid (GenBank accession number NC_018959) has a truncated copy of the gene. Two plasmids (GenBank accession numbers NC_007931 and NC_016942) have two copies of the and genes. This plasmid (GenBank accession number NC_013320) appears to have two copies of the MOB gene. This plasmid (GenBank accession number NC_005004) has a truncated copy of the gene. Three plasmids (GenBank accession numbers NC_013321, NC_019007, and NC_018976) have a truncated copy of the gene. Eleven of these plasmids have a truncated copy of the gene (GenBank accession numbers NC_020531, NC_020538, NC_013337, NC_020534, NC_020565, NC_020567, NC_020530, NC_020539, NC_017352, NC_013323, and NC_022610). One plasmid (GenBank accession number NC_013334) has a truncated copy of the gene. This plasmid (GenBank accession number NC_020237) appears to have two copies of the MOB gene. This plasmid (GenBank accession number NC_022598) appears to have two copies of the MOB gene. Abbreviations: MRIP, Multi-RIP; S, spp; Sar, ; Sa, ; Sc, ; Se, ; Sha, ; Shy, ; Sle, ; Slu, ; Sp, ; Ssa, ; Ssc, ; Ssi, ; Sw, .

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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Figure 6
Hierarchical clustering dendrogram of plasmids from enterococci. The matrix distance used for building the UPGMA dendrogram is based on the Raup-Crick distance of the orthologous protein profile of each plasmid. For each plasmid, a presence/absence protein profile was made using cut-off values of 80% identity and 80% coverage. Protein clustering was made by using CD-HIT ( ). Different background colors are used to emphasize branches of related plasmids and are the same as those defined in Fig. 5 . Names to the left of the dendrogram indicate the RIP family. Background colors were used to point out plasmid groups frequently involved in mobility of AbR genes and pheromone-responsive plasmids. Circles indicate RIPs identified in each plasmid according to data shown in Fig. 7 .
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Figure 6

Hierarchical clustering dendrogram of plasmids from enterococci. The matrix distance used for building the UPGMA dendrogram is based on the Raup-Crick distance of the orthologous protein profile of each plasmid. For each plasmid, a presence/absence protein profile was made using cut-off values of 80% identity and 80% coverage. Protein clustering was made by using CD-HIT ( ). Different background colors are used to emphasize branches of related plasmids and are the same as those defined in Fig. 5 . Names to the left of the dendrogram indicate the RIP family. Background colors were used to point out plasmid groups frequently involved in mobility of AbR genes and pheromone-responsive plasmids. Circles indicate RIPs identified in each plasmid according to data shown in Fig. 7 .

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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Figure 7
Plasmids from spp. The presence of an orange border in the RIP family indicates that the corresponding RIP is truncated. Rep_2; *One of these plasmids (GenBank accession number NC_015849) has a truncated rep_AUS0004_p2 (Rep_1) gene, and no other known replication initiator proteins were found. **This plasmid (GenBank accession number NC_017962) has two copies of Tn; in one of them the gene is not truncated; this plasmid also appears to have two copies of the MOB gene. These two plasmids (GenBank accession numbers NC_008768 and NC_008821) have a truncated copy of the gene. Abbreviations: MRIP, multi-RIP; Efm, ; Efc, ; Emu, ; Edu, ; Ehi, .
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Figure 7

Plasmids from spp. The presence of an orange border in the RIP family indicates that the corresponding RIP is truncated. Rep_2; *One of these plasmids (GenBank accession number NC_015849) has a truncated rep_AUS0004_p2 (Rep_1) gene, and no other known replication initiator proteins were found. **This plasmid (GenBank accession number NC_017962) has two copies of Tn; in one of them the gene is not truncated; this plasmid also appears to have two copies of the MOB gene. These two plasmids (GenBank accession numbers NC_008768 and NC_008821) have a truncated copy of the gene. Abbreviations: MRIP, multi-RIP; Efm, ; Efc, ; Emu, ; Edu, ; Ehi, .

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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Figure 8
Plasmids from spp. Rep_trans; This plasmid (GenBank accession number NC_015219) has two similar replication genes belonging to the Rep_3 family. This plasmid (GenBank accession number NC_006979) has two similar replication genes belonging to the PriCT_1 family. Abbreviations: MRIP, Multi-RIP; Sag, ; Sdy, ; Sga, ; Siu, ; Sin, ; Sma, ; Smu, ; Spa, ; Spn, ; Sps, ; Spy, ; Ssu, ; Sth,
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Figure 8

Plasmids from spp. Rep_trans; This plasmid (GenBank accession number NC_015219) has two similar replication genes belonging to the Rep_3 family. This plasmid (GenBank accession number NC_006979) has two similar replication genes belonging to the PriCT_1 family. Abbreviations: MRIP, Multi-RIP; Sag, ; Sdy, ; Sga, ; Siu, ; Sin, ; Sma, ; Smu, ; Spa, ; Spn, ; Sps, ; Spy, ; Ssu, ; Sth,

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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Figure 9
Plasmids from spp. rep_3. One plasmid (GenBank NC_013767) has two copies of the gene, one of which is truncated. One plasmid (GenBank NC_018888) has a truncated copy of the gene. This plasmid (GenBank NC_022045) has two copies of the operon. Abbreviations: MRIP, multi-RIP; Lm, ; Lg, ; Li,
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Figure 9

Plasmids from spp. rep_3. One plasmid (GenBank NC_013767) has two copies of the gene, one of which is truncated. One plasmid (GenBank NC_018888) has a truncated copy of the gene. This plasmid (GenBank NC_022045) has two copies of the operon. Abbreviations: MRIP, multi-RIP; Lm, ; Lg, ; Li,

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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Figure 10
Plasmids from LAB. Rep_1. Rep_trans. PriCT_1. *This plasmid (GenBank accession number NC_010540) has two copies of the gene. **One of these plasmids (GenBank accession number NC_010603) has a truncated copy of the gene. One of these plasmids (GenBank accession number NC_014133) appears to have three copies of the MOB gene. One of these plasmids (GenBank accession number NC_022123) appears to have two copies of the MOB gene. Abbreviations: MRip, multi-RIP; Lb, spp; Lca, ; Lam, ; Lbr, ; Lbu, ; Lca, ; Lfe ; Lpa, ; Lpl, ; Lre, ; Lsa, Lga, ; Lla, ; Lcm, ; Lci, ; Lki, ; Lme,
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Figure 10

Plasmids from LAB. Rep_1. Rep_trans. PriCT_1. *This plasmid (GenBank accession number NC_010540) has two copies of the gene. **One of these plasmids (GenBank accession number NC_010603) has a truncated copy of the gene. One of these plasmids (GenBank accession number NC_014133) appears to have three copies of the MOB gene. One of these plasmids (GenBank accession number NC_022123) appears to have two copies of the MOB gene. Abbreviations: MRip, multi-RIP; Lb, spp; Lca, ; Lam, ; Lbr, ; Lbu, ; Lca, ; Lfe ; Lpa, ; Lpl, ; Lre, ; Lsa, Lga, ; Lla, ; Lcm, ; Lci, ; Lki, ; Lme,

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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Figure 11
Similarity of -like sequences encoding RIPs of the Rep_1 family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_1 family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different backgrounds colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 .
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10.1128/9781555818982/fig21-11.gif
Image of Figure 11
Figure 11

Similarity of -like sequences encoding RIPs of the Rep_1 family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_1 family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different backgrounds colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 .

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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/content/10.1128/9781555818982.chap21.fig21-12
Figure 12
Similarity of -like sequences encoding RIPs of the Rep_trans family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_trans family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different backgrounds colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 . *Truncated gene. **Similar to and . Abbreviations: ND, not determined.
10.1128/9781555818982/fig21-12_thmb.gif
10.1128/9781555818982/fig21-12.gif
Image of Figure 12
Figure 12

Similarity of -like sequences encoding RIPs of the Rep_trans family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_trans family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different backgrounds colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 . *Truncated gene. **Similar to and . Abbreviations: ND, not determined.

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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/content/10.1128/9781555818982.chap21.fig21-13
Figure 13
Similarity of -like sequences encoding RIPs of the Rep_2 family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_2 family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 .
10.1128/9781555818982/fig21-13_thmb.gif
10.1128/9781555818982/fig21-13.gif
Image of Figure 13
Figure 13

Similarity of -like sequences encoding RIPs of the Rep_2 family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_2 family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 .

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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/content/10.1128/9781555818982.chap21.fig21-14
Figure 14
Similarity of -like sequences encoding RIPs of the Rep_L family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_L family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 .
10.1128/9781555818982/fig21-14_thmb.gif
10.1128/9781555818982/fig21-14.gif
Image of Figure 14
Figure 14

Similarity of -like sequences encoding RIPs of the Rep_L family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_L family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 .

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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/content/10.1128/9781555818982.chap21.fig21-15
Figure 15
Similarity of -like sequences encoding RIPs of the Rep_3 family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_3 family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 . Abbreviations: ND, not determined.
10.1128/9781555818982/fig21-15_thmb.gif
10.1128/9781555818982/fig21-15.gif
Image of Figure 15
Figure 15

Similarity of -like sequences encoding RIPs of the Rep_3 family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_3 family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 . Abbreviations: ND, not determined.

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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Figure 16
Similarity of -like sequences encoding RIPs with the PriCT_1 domain. A neighbor-joining tree of gene sequences coding for RIPs with PriCT_1 domains was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 . Abbreviations: ND, not determined.
10.1128/9781555818982/fig21-16_thmb.gif
10.1128/9781555818982/fig21-16.gif
Image of Figure 16
Figure 16

Similarity of -like sequences encoding RIPs with the PriCT_1 domain. A neighbor-joining tree of gene sequences coding for RIPs with PriCT_1 domains was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 . Abbreviations: ND, not determined.

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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Figure 17
Similarity of -like sequences encoding RIPs of the RepA_N family. A neighbor-joining tree of gene sequences coding for replication initiator proteins of the RepA_N family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 . *Truncated gene. Similar to and . Abbreviations: ND, not determined.
10.1128/9781555818982/fig21-17_thmb.gif
10.1128/9781555818982/fig21-17.gif
Image of Figure 17
Figure 17

Similarity of -like sequences encoding RIPs of the RepA_N family. A neighbor-joining tree of gene sequences coding for replication initiator proteins of the RepA_N family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 . *Truncated gene. Similar to and . Abbreviations: ND, not determined.

Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of : Impact on the Emergence and the Spread of Resistance to Antimicrobials, p 381-419. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0039-2014
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