Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria

Abstract

Bacteria have existed on Earth for three billion years or so and have become adept at protecting themselves against toxic chemicals. Antibiotics have been in clinical use for a little more than 6 decades. That antibiotic resistance is now a major clinical problem all over the world attests to the success and speed of bacterial adaptation. Mechanisms of antibiotic resistance in bacteria are varied and include target protection, target substitution, antibiotic detoxification and block of intracellular antibiotic accumulation. Acquisition of genes needed to elaborate the various mechanisms is greatly aided by a variety of promiscuous gene transfer systems, such as bacterial conjugative plasmids, transposable elements and integron systems, that move genes from one DNA system to another and from one bacterial cell to another, not necessarily one related to the gene donor. Bacterial plasmids serve as the scaffold on which are assembled arrays of antibiotic resistance genes, by transposition (transposable elements and ISCR mediated transposition) and site-specific recombination mechanisms (integron gene cassettes).The evidence suggests that antibiotic resistance genes in human bacterial pathogens originate from a multitude of bacterial sources, indicating that the genomes of all bacteria can be considered as a single global gene pool into which most, if not all, bacteria can dip for genes necessary for survival. In terms of antibiotic resistance, plasmids serve a central role, as the vehicles for resistance gene capture and their subsequent dissemination. These various aspects of bacterial resistance to antibiotics will be explored in this presentation.

Figure 1

An electron microscope picture of a small bacterial plasmid.

Figure 2

A diagrammatic representation of the composite resistance transposon Tn5 that confers resistance to kanamycin, bleomycin and streptomycin. O, I, outside and inside boundaries of the terminal inverted IS50 elements accommodating the short terminal inverted repeats (IRs) that define IS50L (left-hand copy of IS50) and IS50R (right-hand copy of IS50) and that are essential for transposition of both IS50 and Tn5; km, kanamycin resistance gene; bl, bleomycin resistance gene; sm, streptomycin resistance gene; tnp, gene encoding the IS50 transposase; inh, gene encoding an inhibitor of the IS50 transposase; bp, base pairs (for further information see Reznikoff, 2002).

Figure 3

A diagrammatic representation of the composite resistance transposon Tn10 that confers resistance to tetracyclines. Tn10 displays terminal inverted repeats of IS10; IS10L, left-hand copy of IS10, a non-functional copy of IS10 due to multiple mutations in the transposase gene; IS10R, right-hand copy of IS10 that encodes a functional transposase and an antisense RNA molecule used for downregulated expression of the transposase gene; IR, short inverted repeat sequences found at the extremities of IS10, which are essential for transposition of both IS50 and Tn10; tetA, gene encoding the tetracycline resistance efflux pump; tetC,D, genes co-regulated with tetA; tetR, gene encoding a transcriptional repressor necessary for inducible expression, by tetracycline, of tetracycline efflux pump TetA; bp, base pairs (for further information see Haniford, 2002).

Figure 4

A diagrammatic representation of the complex resistance transposon Tn3 that confers resistance to ampicillin and some other β-lactam antibiotics. IR, the short inverted repeated sequences found at the extremities of the transposon, which are essential for Tn3 transposition; tnpA, gene encoding element's transposase; tnpR, gene encoding a site-specific recombinase that resolves the transposition cointegrate structure generated by transposition; bla_TEM-1, gene encoding the TEM-1 β-lactamase; bp, base pairs; kb, kilobase.

Figure 5

A diagrammatic representation of the complex resistance transposon Tn21 that confers resistance to streptomycin, spectinomycin, sulphonamides and mercuric ions. merTPCAD, genes encoding resistance to mercuric ions and some organo-mercurial compounds; merR, gene encoding the transcriptional repressor of the inducible mer operon; sul1, gene encoding resistance to sulphonamides; aadA1, gene encoding resistance to streptomycin and spectinomycin; int, integrase gene; attI, integron gene cassette insertion site; tnpA, gene encoding the Tn21 transposase; tnpR, gene encoding a site-specific recombinase responsible for resolution of the transposition cointegrate structure generated by transposition; p_int, int promoter; p_c, promoter for integron gene cassettes and sul1.

Figure 6

A diagrammatic representation of the elements of a class 1 resistance integron. 5′-CS, 5′ constant sequence; 3′-CS, 3′ constant sequence; int, integrase gene; attI, integron gene cassette integration site; attC, gene cassette insertion sequence (also called a 59 base element); qacEΔ, truncated version of the quaternary ammonium compound resistance gene qacE; sul1, gene encoding resistance to sulphonamides; orf5,6, possible genes (open reading frames) of unknown function(for further information see Hall, 1997).

Figure 7

Cartoon of gene cassette capture by a bacterial integron.

Figure 8

Some examples of resistance gene arrays in class 1 bacterial integrons. int1, class 1 integrase gene; qac, gene encoding resistance to quaternary ammonium compounds; attI, integron gene cassette insertion site; attC, gene cassette insertion sequence; qacEΔ1, truncated version of qacE; sul1, gene conferring resistance to sulphonamides; orf (open reading frame), possible gene of unknown function; bla_VIM, gene encoding a VIM metallo-β-lactamase; bla_IMP, gene encoding an IMP metallo-β-lactamase; aacA, aadA, aph, genes encoding resistance to aminoglycosides; cat, gene encoding resistance to chloramphenicol.

Figure 9

Examples of complex class 1 bacterial resistance integrons displaying copies of ISCR1 and duplications of 3′-CS. The broken line indicates the 5′-CS and variable regions of the class 1 integron components of the complex integrons; DHA-1, FOX-1, CMY-1,8, MOX-1, genes encoding β-lactamases that confer resistance to third generation cephalosporins, probably recruited from the chromosomes of the bacterial species indicated; for other abbreviations see legend to previous figure.

Figure 10

A phylogenetic tree of ISCR elements. Based on a CLUSTAL alignment with the PAM 250 matrix prepared using Lasergene DNAstar software (for further information see Toleman et al., 2006a).

Figure 11

Mobilization of a class 1 integron by ISCR1. ISCR1 is shown in (a) delineated by its terminal sequences terIS-1 and oriIS. It is proposed that a copy of ISCR1 is transposed into a site close to the 3′-CS end of a class 1 integron. A deletion then removed part of the 3′-CS (including orf5,6) to generate the distinctive 3′-CS-ISCR1 arrangement seen in complex class 1 integrons.

Figure 12

Model of ISCR1-mediated generation of a complex class 1 integron. See text for an explanation of the steps involved in generation of complex class 1 integrons.