Amplification of resistance genes in Haemophilus influenzae plasmids

Tandem multiplication of the IS26-flanked amplicon with the bla(SHV-5) gene within plasmid p1658/97

The IncF plasmid p1658/97 (c. 125 kb) from Escherichia coli isolates recovered during a clonal outbreak in a hospital in Warsaw, Poland, in 1997 contains the extended-spectrum β-lactamase (ESBL) gene bla(SHV-5), originated from the Klebsiella pneumoniae chromosome. A region containing the bla(SHV-5) gene is flanked by two IS26 copies and its copy number multiplies spontaneously within p1658/97 and RecA-deficient E. coli strains. Here, we demonstrate that the amplified IS26-bla(SHV-5) units were arranged in tandems, containing up to more than 10 units, which could raise ceftazidime MICs for host strains from 4 μg mL(-1) to more than 128 μg mL(-1). Successive deletions within p1658/97, located outside the amplifiable module and encompassing even as little as c. 15% of the plasmid, blocked the amplification. Moreover, the complementing re-introduction of the deleted fragments in trans did not restore the process. Similarly, insertions of a 1-kb DNA fragment into the amplicon inhibited its self-multiplication ability. The module was able to transmit into another IS26-containing plasmid by recombination. The results prompted us to speculate that local DNA structure, especially favorable in p1658/97, might have been responsible for the IS26-bla(SHV-5) multiplication ability.

Bacterial gene amplification: implications for the evolution of antibiotic resistance

Recent data suggest that, in response to the presence of antibiotics, gene duplication and amplification (GDA) constitutes an important adaptive mechanism in bacteria. For example, resistance to sulphonamide, trimethoprim and beta-lactams can be conferred by increased gene dosage through GDA of antibiotic hydrolytic enzymes, target enzymes or efflux pumps. Furthermore, most types of antibiotic resistance mechanism are deleterious in the absence of antibiotics, and these fitness costs can be ameliorated by increased gene dosage of limiting functions. In this Review, we highlight the dynamic properties of gene amplifications and describe how they can facilitate adaptive evolution in response to toxic drugs.

Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance

Tetracyclines were discovered in the 1940s and exhibited activity against a wide range of microorganisms including gram-positive and gram-negative bacteria, chlamydiae, mycoplasmas, rickettsiae, and protozoan parasites. They are inexpensive antibiotics, which have been used extensively in the prophlylaxis and therapy of human and animal infections and also at subtherapeutic levels in animal feed as growth promoters. The first tetracycline-resistant bacterium, Shigella dysenteriae, was isolated in 1953. Tetracycline resistance now occurs in an increasing number of pathogenic, opportunistic, and commensal bacteria. The presence of tetracycline-resistant pathogens limits the use of these agents in treatment of disease. Tetracycline resistance is often due to the acquisition of new genes, which code for energy-dependent efflux of tetracyclines or for a protein that protects bacterial ribosomes from the action of tetracyclines. Many of these genes are associated with mobile plasmids or transposons and can be distinguished from each other using molecular methods including DNA-DNA hybridization with oligonucleotide probes and DNA sequencing. A limited number of bacteria acquire resistance by mutations, which alter the permeability of the outer membrane porins and/or lipopolysaccharides in the outer membrane, change the regulation of innate efflux systems, or alter the 16S rRNA. New tetracycline derivatives are being examined, although their role in treatment is not clear. Changing the use of tetracyclines in human and animal health as well as in food production is needed if we are to continue to use this class of broad-spectrum antimicrobials through the present century.

Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance

Tetracyclines were discovered in the 1940s and exhibited activity against a wide range of microorganisms including gram-positive and gram-negative bacteria, chlamydiae, mycoplasmas, rickettsiae, and protozoan parasites. They are inexpensive antibiotics, which have been used extensively in the prophlylaxis and therapy of human and animal infections and also at subtherapeutic levels in animal feed as growth promoters. The first tetracycline-resistant bacterium, Shigella dysenteriae, was isolated in 1953. Tetracycline resistance now occurs in an increasing number of pathogenic, opportunistic, and commensal bacteria. The presence of tetracycline-resistant pathogens limits the use of these agents in treatment of disease. Tetracycline resistance is often due to the acquisition of new genes, which code for energy-dependent efflux of tetracyclines or for a protein that protects bacterial ribosomes from the action of tetracyclines. Many of these genes are associated with mobile plasmids or transposons and can be distinguished from each other using molecular methods including DNA-DNA hybridization with oligonucleotide probes and DNA sequencing. A limited number of bacteria acquire resistance by mutations, which alter the permeability of the outer membrane porins and/or lipopolysaccharides in the outer membrane, change the regulation of innate efflux systems, or alter the 16S rRNA. New tetracycline derivatives are being examined, although their role in treatment is not clear. Changing the use of tetracyclines in human and animal health as well as in food production is needed if we are to continue to use this class of broad-spectrum antimicrobials through the present century.

Gene amplification and genomic plasticity in prokaryotes

Gene amplification is a common feature of the genome of prokaryotic organisms. In this review, we analyze different instances of gene amplification in a variety of prokaryotes, including their mechanisms of generation and biological role. Growing evidence supports the concept that gene amplification be considered not as a mutation but rather as a dynamic genomic state related to the adaptation of bacterial populations to changing environmental conditions or biological interactions. In this context, the potentially amplifiable DNA regions impose a defined dynamic structure on the genome. If such structure has indeed been selected during evolution, it is a particularly challenging hypothesis.

Nucleotide sequences of genes encoding the type II chloramphenicol acetyltransferases of Escherichia coli and Haemophilus influenzae, which are sensitive to inhibition by thiol-reactive reagents

Sensitivity of enzymes to inhibition by thiol-reactive reagents is often presented as evidence for the possible involvement of cysteine residues in substrate binding and catalysis or to highlight possible important differences in structure and mechanism between closely related enzymes. The primary phenotypic distinction between the enterobacterial type II chloramphenicol acetyltransferase (CATII; typified by the enzyme encoded by the incW transmissible plasmid pSa) and the CATI and CATIII variants is the greatly enhanced susceptibility of CATII to inactivation by thiol-specific modifying reagents. Determination of the nucleotide sequence of the gene, catII, present on pSa and that of a related determinant, catIIH, isolated from Haemophilus influenzae indicates that sensitivity to such reagents cannot be due to the presence of additional reactive cysteine residues in CATII. Comparative analysis of the inactivation of CATII and CATIII by 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB), 4,4'-dithiodipyridine (DTDP) and methyl methanethiosulphonate (MMTS) suggests that (i) inactivation occurs as a result of chemical modification of the same residue (Cys-31) in each enzyme, (ii) reagents that inactivate via a pseudo-first-order process (DTNB and DTDP) appear to bind with a greater affinity to CATII, and (iii) the intrinsic reactivity of Cys-31 in CATII greatly exceeds that of the corresponding residue in CATIII. The results lead to the conclusion that a striking difference in chemical reactivity of a unique and conserved thiol group between closely related enzyme variants may not be easily explained even when a high-resolution tertiary structure is available for one of them. Plausible explanations include more favourable access of reagents to Cys-31 in CATII or an enhanced reactivity of its thiol group imposed by the side chains of residues that are not in immediate contact with it.

Amplification of DNA at a prophage attachment site in Haemophilus influenzae

The Escherichia coli plasmids pBR322 and pBR327 can be taken up by Haemophilus influenzae but do not replicate in this organism; however, integration of pBR into the H. influenzae chromosome was achieved by ligation to a fragment of the Haemophilus phage S2 that carried a phage attachment site (attP). Once these sequences were integrated, they could serve as sites of recombination and amplification for homologous (pBR or phage) DNA. Amplification appeared to occur in one of two prophage sites (attB) present in the H. influenzae chromosome. The extent of amplification was different in different cells and reflected the ability of these sequences to undergo rearrangement leading to the formation of a DNA ladder. The ladder was obtained by treatment of DNA with restriction enzymes that cut outside of the inserted DNA, i.e., did not cut in the repeat sequence, and represented different numbers of repeat elements. Reversed-field gel electrophoresis was instrumental in resolving amplified structures. Inasmuch as single-cell isolates gave rise to the same ladder structure, it was assumed that amplification was under regulatory control and that it reproduced the same equilibrium of repeat structures. Transformation of E. coli with the amplified H. influenzae DNA resulted in precise excision and replication of the original monomeric plasmids. This excision was independent of the recA and recBC genes.

Constitutive expression of tetracycline resistance mediated by a Tn10-like element in Haemophilus parainfluenzae results from a mutation in the repressor gene

The Tn10-like constitutively expressed tetracycline resistance determinant from a Haemophilus parainfluenzae strain was cloned in Escherichia coli. Toxicity resulting from expression on multicopy plasmids necessitated its being cloned on a low-copy plasmid vector or in cells containing the Tn10-encoded repressor. Constitutive expression of tetracycline resistance was found to result from the synthesis of a truncated inactive repressor molecule. Instead of the 23-kilodalton repressor found in other Tn10-containing strains, this determinant encoded a 14.5-kilodalton molecule. The DNA sequence of the 700-base-pair region spanning the repressor gene and promoter-operator regions of the Haemophilus determinant was identical to that of the same region of Tn10, except for the absence of a single T X A base pair in the repressor gene. This deletion leads to premature termination of the protein. Antisera to the repressor suggested that the repressor was also absent in a second independently isolated H. parainfluenzae strain bearing a Tn10-like constitutive tetracycline resistance determinant.

Recombination sites in plasmid drug resistance gene amplification

The resistance plasmid NR1 derivative pRR330 consists of a neomycin-kanamycin resistance gene (neo-kan) flanked by directly repeated sequences of both insertion element IS1 DNA (768 base pairs) and 840 base pairs of DNA which are a part of the chloramphenicol acetyltransferase (cam) gene. Most Escherichia coli cell populations that were cultured in high neomycin concentrations carried plasmids whose neo-kan gene amplification was mediated either by IS1 DNA or by cam DNA as homologous recombination sites. This suggests that the final amplified cell populations were the descendants of a single cell.

Drug resistance gene amplification of plasmid NR1 derivatives with various amounts of resistance determinant DNA

Drug resistance gene amplification of derivatives of plasmid NR1 having various amounts of resistance (r) determinant DNA was examined with two types of NR1 derivatives. The first was an NR1 derivative that carried two tandem copies of the r determinant component which was isolated as an intermediate in the amplification process. The plating efficiency of host cells and restriction endonuclease analysis of the plasmid DNA indicate that plasmids with two tandem copies of the r determinant undergo spontaneous amplification to a more highly amplified state at a frequency 150-fold higher than that of wild-type NR1. The second class of derivatives consisted of plasmids in which different regions of the r determinant component had been deleted. The relationship between spontaneous amplification frequency and r determinant size was examined with these plasmids. Plating efficiency of host cells indicated that plasmids with a smaller r determinant undergo spontaneous amplification at a lower frequency than do plasmids with a larger r determinant. These results suggest that there is an ordered sequence of events in the amplification of the r determinant of NR1.

Transposon Tn10-like tetracycline resistance determinants in Haemophilus parainfluenzae

Tetracycline resistance (Tcr) determinants from three different strains of Haemophilus parainfluenzae expressed 10-fold higher levels of resistance when mated into Escherichia coli. No plasmid was found in any of the E. coli recipients, even in matings in which a plasmid was identified in the donor Haemophilus sp. The Tcr determinant from Haemophilus sp. caused instability of resident plasmids in the recipient E. coli: all plasmids were lost within 30 generations in antibiotic-free media. However, by serial subculture in antibiotics, stable resident plasmids were obtained which carried the Tcr determinant from Haemophilus sp. and were transferable by conjugation and transformation among E. coli strains. All Haemophilus determinants hybridized with a probe for the Tcr determinant on Tn10, which bears inducible Tcr. However, Haemophilus determinants were constitutively resistant to tetracycline in the Haemophilus donors and in the E. coli recipients. This constitutive expression was recessive to wild-type Tn10 in the same cell, indicating that the constitutive phenotype resulted from the absence of an active repressor. Restrictive enzyme analysis of various E. coli plasmid derivatives bearing a Tcr determinant from Haemophilus sp. demonstrated that the inserted DNA was of similar size (8.95 to 9.35 kilobases), close to that of Tn10. Heteroduplex analysis and DNA:DNA hybridization confirmed that the Tcr determinant from Haemophilus sp. had greater than 90% homology with the Tn10 determinant, including the DNA sequence for the repressor.

Circularized copies of amplifiable resistance genes from Haemophilus influenzae plasmids

Tandem repeat amplification of resistance determinants in Haemophilus influenzae plasmids is associated with the occurrence of separate circular DNA molecules. They were demonstrated to represent mono- and multimeric forms of the amplifiable segments of the plasmids which comprise the respective resistance transposons and an additional region designated as an amplification sequence. The latter region mediates the recombinational events involved in amplification. The DNA circles apparently lack the ability to replicate autonomously but most probably provide an effective means for the translocation of resistance genes from one plasmid to another.