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Chapter 24 : Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: The Paradigm

Authors: Maria S. Ramirez1, German M. Traglia3, David L. Lin4, Tung Tran5, Marcelo E. Tolmasky6
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Affiliations: 1: Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA; 2: Institute of Microbiology and Medical Parasitology, National Scientific and Technical Research Council (CONICET), University of Buenos Aires, Buenos Aires, Argentina; 3: Institute of Microbiology and Medical Parasitology, National Scientific and Technical Research Council (CONICET), University of Buenos Aires, Buenos Aires, Argentina; 4: Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA; 5: Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA; 6: Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA
Content Type: Monograph
Publication Year: 2015

Category: Clinical Microbiology

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Abstract:

The study of plasmids and their biology has had a decisive impact on the advance of molecular genetics, contributing numerous fundamental discoveries beyond the field of plasmid biology ( ). Interestingly, the study of plasmids was already well under way before the structure of DNA was known, with the experiments that led to the discovery of conjugation and recombination in bacteria using as a system the plasmid F, known at that time as the “F factor” ( ). The continuation of these studies showed that bacterial plasmids are responsible for many of the particular properties of bacteria that are of medical, industrial, and agricultural interest. Their fundamental role in shaping the characteristics of the host bacteria and their ability to propagate led some authors to propose the somewhat controversial idea that they should be considered independent organisms ( ). The role of plasmids in antibiotic resistance was first recognized in Japan when strains that were susceptible or multiresistant were isolated from the same patient during a single epidemic of dysentery. This fact suggested that susceptible strains were becoming multiresistant, not through successive mutational steps, but rather by acquisition of the necessary genetic determinants in a single step. Watanabe and Fukasawa reported that this process was due to transfer of a plasmid (at that time called the resistance transfer factor, RTF, or R-factor) that harbored the resistance genes ( ). Later it became clear that plasmids were carriers of not only antibiotic resistance genes but also genes or groups of genes that specify properties that are essential or contribute to the virulence of the host bacteria ( ). Studies during the following few decades revealed in some detail numerous biological characteristics of plasmids, as well as the high diversity of existing plasmids and their association with other genetic mobile elements.

Citation: Ramirez M, Traglia G, Lin D, Tran T, Tolmasky M. 2015. Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: The Paradigm, p 459-474. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0016-2013
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Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: The Klebsiella pneumoniae Paradigm
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Citation: Ramirez M, Traglia G, Lin D, Tran T, Tolmasky M. 2015. Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: The Paradigm, p 459-474. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0016-2013
/content/10.1128/9781555818982.chap24.fig24-1
Figure 1
Small plasmids. General genetic organization of small ColE1-type plasmids from and other . Alignment of the nucleotide sequences of the replication regions of ColE1-type plasmids using CLUSTAL W ( ). Alignment of the nucleotide sequences of Xer site-specific recombination sites of ColE1-type plasmids using CLUSTAL W. The ARG box, XerC, and XerD binding sites are shown in color, and the central regions are boxed. Blue capital letters indicate the most important conserved nucleotides in the ARG box. The downward pointing arrowhead shows the conserved T nucleotide that is substituted by a C in several Xer site-specific recombination sites ( ).
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Figure 1

Small plasmids. General genetic organization of small ColE1-type plasmids from and other . Alignment of the nucleotide sequences of the replication regions of ColE1-type plasmids using CLUSTAL W ( ). Alignment of the nucleotide sequences of Xer site-specific recombination sites of ColE1-type plasmids using CLUSTAL W. The ARG box, XerC, and XerD binding sites are shown in color, and the central regions are boxed. Blue capital letters indicate the most important conserved nucleotides in the ARG box. The downward pointing arrowhead shows the conserved T nucleotide that is substituted by a C in several Xer site-specific recombination sites ( ).

Citation: Ramirez M, Traglia G, Lin D, Tran T, Tolmasky M. 2015. Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: The Paradigm, p 459-474. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0016-2013
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Figure 2
Comparison of pFPTB1 and pJHCMW1. The black lines, which represent regions of homology (coordinates 473 to 3361 in pJHCMW1), are drawn to scale. The Tn-like transposons, Tn and Tn/DeltaTn, as well as the dots indicating and the Xer target sites, are shown at the correct locations but are not drawn to scale. The replication regions (REP) share 97% homology. The numbers indicate the coordinates in the GenBank database (pJHCMW1, accession number AF479774; pFPTB1, accession number AJ634602). The location of the similar but not identical Xer site-specific recombination sites ( ) is indicated.
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Figure 2

Comparison of pFPTB1 and pJHCMW1. The black lines, which represent regions of homology (coordinates 473 to 3361 in pJHCMW1), are drawn to scale. The Tn-like transposons, Tn and Tn/DeltaTn, as well as the dots indicating and the Xer target sites, are shown at the correct locations but are not drawn to scale. The replication regions (REP) share 97% homology. The numbers indicate the coordinates in the GenBank database (pJHCMW1, accession number AF479774; pFPTB1, accession number AJ634602). The location of the similar but not identical Xer site-specific recombination sites ( ) is indicated.

Citation: Ramirez M, Traglia G, Lin D, Tran T, Tolmasky M. 2015. Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: The Paradigm, p 459-474. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0016-2013
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Figure 3
Effect of changes in osmolarity of the culture medium on Xer site-specific recombination at . Schematic representation of the possible chain of events that lead to a higher efficiency of Xer site-specific recombination at the plasmid pJHCMW1 site . A decrease in the NaCl concentration in the growth medium (L broth containing 0.5% NaCl added to no NaCl added) is correlated with an increase in supercoiling density, which facilitates interaction of ArgR with the substandard ARG box leading to a more efficient formation of a productive synaptic complex and Holliday junction ( ). Molecular models of the interwrapped synaptic complex are available in references . The two strands are shown only in the core recombination site (red and green lines); blue lines represent the accessory sequences.
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Figure 3

Effect of changes in osmolarity of the culture medium on Xer site-specific recombination at . Schematic representation of the possible chain of events that lead to a higher efficiency of Xer site-specific recombination at the plasmid pJHCMW1 site . A decrease in the NaCl concentration in the growth medium (L broth containing 0.5% NaCl added to no NaCl added) is correlated with an increase in supercoiling density, which facilitates interaction of ArgR with the substandard ARG box leading to a more efficient formation of a productive synaptic complex and Holliday junction ( ). Molecular models of the interwrapped synaptic complex are available in references . The two strands are shown only in the core recombination site (red and green lines); blue lines represent the accessory sequences.

Citation: Ramirez M, Traglia G, Lin D, Tran T, Tolmasky M. 2015. Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: The Paradigm, p 459-474. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0016-2013
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Figure 4
Genetic maps comparing the pIP843 and the pE66An. The shadowed areas show regions of homology (6681/6701 identities and six gaps in the region with 99% homology). The ColE1-type replication region is schematically shown on top of the pIP843 map. The semicircle in pE66An represents the region encompassing nucleotides 6697 to 79713.
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Image of Figure 4
Figure 4

Genetic maps comparing the pIP843 and the pE66An. The shadowed areas show regions of homology (6681/6701 identities and six gaps in the region with 99% homology). The ColE1-type replication region is schematically shown on top of the pIP843 map. The semicircle in pE66An represents the region encompassing nucleotides 6697 to 79713.

Citation: Ramirez M, Traglia G, Lin D, Tran T, Tolmasky M. 2015. Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: The Paradigm, p 459-474. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0016-2013
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Figure 5
Multiple alignment of pLVPK, pK2044, and pKCTC2242. The nucleotide sequences of pLVPK (accession number AY378100.1) ( ), pK2044 (accession number AP006726.1) ( ), and pKCTC2242 (accession number CP002911.1) ( ) were compared using the MAUVE aligner version 2.3.1 ( ). Different colors represent local LCBs. Inside each block there is a similarity profile of the sequence; the height corresponds to the average level of conservation. Completely white areas are not aligned and probably contain sequences specific to the particular molecule. In pKCTC2242 the LCBs drawn below the black line are inverted with respect to their homologs in pLVPK and pK2044. Some genes or clusters present in these blocks are identified by name. The gene has been reported as “truncated” ( ). The truncation is a consequence of an extra T in the sequence that could also be a sequencing error. The genes are sufficient for the tellurite resistance phenotype (Te). The cluster is also responsible for the phage inhibition (Phi) and colicin resistance (PacB) phenotypes ( ). Copper (), silver (), lead (), and tellurite () resistance related genes; IUS, iron uptake system.
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Figure 5

Multiple alignment of pLVPK, pK2044, and pKCTC2242. The nucleotide sequences of pLVPK (accession number AY378100.1) ( ), pK2044 (accession number AP006726.1) ( ), and pKCTC2242 (accession number CP002911.1) ( ) were compared using the MAUVE aligner version 2.3.1 ( ). Different colors represent local LCBs. Inside each block there is a similarity profile of the sequence; the height corresponds to the average level of conservation. Completely white areas are not aligned and probably contain sequences specific to the particular molecule. In pKCTC2242 the LCBs drawn below the black line are inverted with respect to their homologs in pLVPK and pK2044. Some genes or clusters present in these blocks are identified by name. The gene has been reported as “truncated” ( ). The truncation is a consequence of an extra T in the sequence that could also be a sequencing error. The genes are sufficient for the tellurite resistance phenotype (Te). The cluster is also responsible for the phage inhibition (Phi) and colicin resistance (PacB) phenotypes ( ). Copper (), silver (), lead (), and tellurite () resistance related genes; IUS, iron uptake system.

Citation: Ramirez M, Traglia G, Lin D, Tran T, Tolmasky M. 2015. Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: The Paradigm, p 459-474. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0016-2013
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Figure 6
Multiple alignment of pNDM-MAR, pTR3/4, pNDM-HN380, pNDM-KN, and pNDM10469. The nucleotide sequences of pNDM-MAR (accession number JN420336) ( ), pTR3/4 (accession number JQ349086) ( ), pNDM-HN380 (accession number JX104760) ( ), pNDM-KN (accession number JN157804) ( ), and pNDM10469 (accession number JN861072) were compared using the MAUVE aligner version 2.3.1 ( ). The gene is represented in red; genes MBL and are represented in light blue and light brown, respectively. Plasmids pTR3 and pTR4, originally thought to be similar but not identical were later proved to be identical and were renamed pTR3/4 ( ). The comparison of the complete nucleotide sequence is shown with LCBs represented in blocks of different colors. Zoom-in of the region including the gene.
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Figure 6

Multiple alignment of pNDM-MAR, pTR3/4, pNDM-HN380, pNDM-KN, and pNDM10469. The nucleotide sequences of pNDM-MAR (accession number JN420336) ( ), pTR3/4 (accession number JQ349086) ( ), pNDM-HN380 (accession number JX104760) ( ), pNDM-KN (accession number JN157804) ( ), and pNDM10469 (accession number JN861072) were compared using the MAUVE aligner version 2.3.1 ( ). The gene is represented in red; genes MBL and are represented in light blue and light brown, respectively. Plasmids pTR3 and pTR4, originally thought to be similar but not identical were later proved to be identical and were renamed pTR3/4 ( ). The comparison of the complete nucleotide sequence is shown with LCBs represented in blocks of different colors. Zoom-in of the region including the gene.

Citation: Ramirez M, Traglia G, Lin D, Tran T, Tolmasky M. 2015. Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: The Paradigm, p 459-474. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0016-2013
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Figure 7
Genetic map of the Tn: :Tn region in the plasmid pBK15692.
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Figure 7

Genetic map of the Tn: :Tn region in the plasmid pBK15692.

Citation: Ramirez M, Traglia G, Lin D, Tran T, Tolmasky M. 2015. Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: The Paradigm, p 459-474. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0016-2013
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Tables

Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: The Klebsiella pneumoniae Paradigm
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Citation: Ramirez M, Traglia G, Lin D, Tran T, Tolmasky M. 2015. Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: The Paradigm, p 459-474. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0016-2013
/content/10.1128/9781555818982.chap24.tab24-1
TABLE 1
Completely sequenced ColE1-type plasmids of
Generic image for table
TABLE 1

Completely sequenced ColE1-type plasmids of

Citation: Ramirez M, Traglia G, Lin D, Tran T, Tolmasky M. 2015. Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: The Paradigm, p 459-474. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0016-2013

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