Translocation of sequences encoding antibiotic resistance from the chromosome to a receptor plasmid in Salmonella ordonez

IS26 and the IS26 family: versatile resistance gene movers and genome reorganizers

SUMMARYIn Gram-negative bacteria, the insertion sequence IS26 is highly active in disseminating antibiotic resistance genes. IS26 can recruit a gene or group of genes into the mobile gene pool and support their continued dissemination to new locations by creating pseudo-compound transposons (PCTs) that can be further mobilized by the insertion sequence (IS). IS26 can also enhance expression of adjacent potential resistance genes. IS26 encodes a DDE transposase but has unique properties. It forms cointegrates between two separate DNA molecules using two mechanisms. The well-known copy-in (replicative) route generates an additional IS copy and duplicates the target site. The recently discovered and more efficient and targeted conservative mechanism requires an IS in both participating molecules and does not generate any new sequence. The unit of movement for PCTs, known as a translocatable unit or TU, includes only one IS26. TU formed by homologous recombination between the bounding IS26s can be reincorporated via either cointegration route. However, the targeted conservative reaction is key to generation of arrays of overlapping PCTs seen in resistant pathogens. Using the copy-in route, IS26 can also act on a site in the same DNA molecule, either inverting adjacent DNA or generating an adjacent deletion plus a circular molecule carrying the DNA segment lost and an IS copy. If reincorporated, these circular molecules create a new PCT. IS26 is the best characterized IS in the IS26 family, which includes IS257/IS431, ISSau10, IS1216, IS1006, and IS1008 that are also implicated in spreading resistance genes in Gram-positive and Gram-negative pathogens.

Tetracycline-resistant coliforms in the effluent of the main sewage treatment plant in Hamilton, Ontario - do they have a common ancestral strain?

Sewage, a major source of bacterial contamination of the environment, can be an important health hazard. The presence of antibiotic-resistant bacteria in sewage can exacerbate this problem. The sources of antibiotic-resistant bacteria in sewage are, for this reason, worth identifying and addressing. The bacterial flora in the effluent of the Woodward Avenue Wastewater Treatment Plant (WAWTP) in Hamilton, Ontario, Canada, contains many antibiotic-resistant coliforms. Here we ask, are the antibiotic resistance genes in the coliforms in the effluent of WAWTP descended from a recent common ancestor strain? If so, the source could be identified and eliminated. If, on the other hand, the antibiotic resistance genes in the bacterial flora of the WAWTP have more than one origin, identification and elimination of the source(s) could be difficult. There was considerable diversity of antibiotic resistance patterns and antibiotic resistance genes among the effluent and influent coliform isolates of the WAWTP, suggesting multiple genetic ancestry. The patterns of horizontal transmissibility and sequence differences in the genes tetA and tetE among these coliform isolates also suggest that they have no one predominant ancestral strain. Using the same logic, the evidence presented here is not compatible with a single ancestral origin of the antibiotic resistance genes in the isolates described herein.

Worldwide disseminated armA aminoglycoside resistance methylase gene is borne by composite transposon Tn1548

The armA (aminoglycoside resistance methylase) gene, which confers resistance to 4,6-disubstituted deoxystreptamines and fortimicin, was initially found in Klebsiella pneumoniae BM4536 on IncL/M plasmid pIP1204 of ca. 90 kb which also encodes the extended-spectrum beta-lactamase CTX-M-3. Thirty-four enterobacteria from various countries that were likely to produce a CTX-M enzyme since they were more resistant to cefotaxime than to ceftazidime were studied. The armA gene was detected in 12 clinical isolates of Citrobacter freundii, Enterobacter cloacae, Escherichia coli, K. pneumoniae, Salmonella enterica, and Shigella flexneri, in which it was always associated with bla(CTX-M-3) on an IncL/M plasmid. Conjugation, analysis of DNA sequences, PCR mapping, and plasmid conduction experiments indicated that the armA gene was part of composite transposon Tn1548 together with genes ant3"9, sul1, and dfrXII, which are responsible for resistance to streptomycin-spectinomycin, sulfonamides, and trimethoprim, respectively. The 16.6-kb genetic element was flanked by two copies of IS6 and migrated by replicative transposition. This observation accounts for the presence of armA on self-transferable plasmids of various incompatibility groups and its worldwide dissemination. It thus appears that posttranscriptional modification of 16S rRNA confers high-level resistance to all the clinically available aminoglycosides except streptomycin in gram-negative human and animal pathogens.

Plasmid-mediated high-level resistance to aminoglycosides in Enterobacteriaceae due to 16S rRNA methylation

A self-transferable plasmid of ca. 80 kb, pIP1204, conferred multiple-antibiotic resistance to Klebsiella pneumoniae BM4536, which was isolated from a urinary tract infection. Resistance to beta-lactams was due to the bla(TEM1) and bla(CTX-M) genes, resistance to trimethroprim was due to the dhfrXII gene, resistance to sulfonamides was due to the sul1 gene, resistance to streptomycin-spectinomycin was due to the ant3"9 gene, and resistance to nearly all remaining aminoglycosides was due to the aac3-II gene and a new gene designated armA (aminoglycoside resistance methylase). The cloning of armA into a plasmid in Escherichia coli conferred to the new host high-level resistance to 4,6-disubstituted deoxystreptamines and fortimicin. The deduced sequence of ArmA displayed from 37 to 47% similarity to those of 16S rRNA m(7)G methyltransferases from various actinomycetes, which confer resistance to aminoglycoside-producing strains. However, the low guanine-plus-cytosine content of armA (30%) does not favor an actinomycete origin for the gene. It therefore appears that posttranscriptional modification of 16S rRNA can confer high-level broad-range resistance to aminoglycosides in gram-negative human pathogens.

Export of the siderophore enterobactin in Escherichia coli: involvement of a 43 kDa membrane exporter

The enterobactin system for iron transport in Escherichia coli is well characterized with the exception of the mechanism of enterobactin secretion to the extracellular environment. Escherichia coli membrane protein P43, encoded by ybdA in the chromosomal region of genes involved in enterobactin synthesis, shows strong homology to the 12-transmembrane segment major facilitator superfamily of export pumps. A P43-null mutation was created and siderophore nutrition assays, performed with a panel of E. coli strains expressing one or more outer membrane receptors for enterobactin-related compounds, demonstrated that the P43 mutant was unable to secrete enterobactin efficiently. Products released from the mutant strain were identified with thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC), revealing that the P43 mutant secretes little, if any, enterobactin, but elevated levels of enterobactin breakdown products 2,3- dihydroxybenzoylserine (DHBS) monomer, dimer, and trimer. These data establish that P43 is a critical component of the E. coli enterobactin secretion machinery and provides a rationale for the designation of the previous genetic locus ybdA as entS to reflect its relevant biological function.

Comparative molecular analysis of erythromycin-resistance determinants in staphylococcal isolates of poultry and human origin

The ermA, ermB, ermC and msrA/msrB genes were detected in multidrug-resistant Staphylococcus spp. strains by PCR. Among 25 human clinical staphylococcal isolates the ermA, ermB, ermC and the msrA/msrB genes were detected in 88, 72, 4 and 100% of the strains, respectively. Among 24 poultry isolates the ermA, ermB, ermC and the msrA/msrB genes were detected in 100, 16.6, 50 and 12.5% of the strains, respectively. The ermA gene was found exclusively on the chromosome, whereas the ermC gene was found on 2.4-4.2 kb plasmids. Restriction fragment length polymorphism (RFLP) analysis of the ermA gene with Eco RI revealed five patterns (25.0, 21.0, 10.5, 6.2 and 4. 8 kb) for the clinical strains and two (8.0 and 6.2 kb) for the poultry strains. The 6.2 kb RFLP pattern, in both the poultry and human clinical isolates, indicates a common lineage for the ermA gene.

Transfer of erythromycin resistance from poultry to human clinical strains of Staphylococcus aureus

The transfer of ermA and ermC genes, the two most common resistance determinants of erythromycin resistance, was studied with Luria-Bertani broth in the absence of additional Ca(2+) or Mg(2+) ions. Fifteen human and five poultry isolates of Staphylococcus aureus, which were resistant to erythromycin but carried different genetic markers for erythromycin resistance, were used for conjugation. Since both the donors (Amp(s)-Tet(r)) and recipients (Amp(r)-Tet(s)) were resistant to erythromycin, the transconjugants were initially picked up as ampicillin- and tetracycline-resistant colonies. The resistance transfer mechanisms of the chromosomally located erythromycin rRNA methylase gene ermA and the plasmid-borne ermC gene were monitored by a multiplex PCR and gene-specific internal probing assay. Four groups of transconjugants, based upon the transfer of the ermA and/or ermC gene, were distinguished from each other by the use of this method. Selective antibiotic screening revealed only one type of transconjugant that was resistant to ampicillin and tetracycline. A high frequency of transfer (4.5 x 10(-3)) was observed in all of the 23 transconjugants obtained, and the direction of tetracycline and erythromycin resistance marker transfer was determined to be from poultry to clinical isolates. The transfers of the ermA and ermC genes were via transposition and transformation, respectively.

Emergence of clinical isolates of Escherichia coli producing TEM-1 derivatives or an OXA-1 beta-lactamase conferring resistance to beta-lactamase inhibitors

Sixteen Escherichia coli clinical isolates which were resistant to ampicillin and amoxicillin-clavulanate but susceptible to cephalothin were studied. Eight strains showed the presence of a beta-lactamase which comigrates with reference OXA-1 enzyme. The eight other strains produced different TEM-1 derivatives which had in common a higher Km for penicillins and a higher 50% inhibitory concentration for the beta-lactamase inhibitors. By oligotyping and sequencing of PCR products, it was shown that Ser (AGC) (TEM-30; also called TRI-1) in three strains and Cys (TGC) (TEM-31; also called TRI-2) in one strain were substituted for Arg-241 (CGC), that Leu (CTG) (TEM-33) and Val (GTG) (TEM-34) in one strain each were substituted for Met-67 (ATG), and that in other mutants the two latter substitutions occurred together with the substitution of Asp (GAT) (TEM-35 and TEM-36) for Asn-272 (AAT). Therefore, different sets of amino acid substitutions of TEM-1 can be found in clinical isolates and lead to resistance to beta-lactamase inhibitors.

Characterization of transposon Tn1528, which confers amikacin resistance by synthesis of aminoglycoside 3'-O-phosphotransferase type VI

Providencia stuartii BM2667, which was isolated from an abdominal abscess, was resistant to amikacin by synthesis of aminoglycoside 3'-O-phosphotransferase type VI. The corresponding gene, aph(3')-VIa, was carried by a 30-kb self-transferable plasmid of incompatibility group IncN. The resistance gene was cloned into pUC18, and the recombinant plasmid, pAT246, was transformed into Escherichia coli DH1 (recA) harboring pOX38Gm. The resulting clones were mixed with E. coli HB101 (recA), and transconjugants were used to transfer pAT246 by plasmid conduction to E. coli K802N (rec+). Analysis of plasmid DNAs from the transconjugants of K802N by agarose gel electrophoresis and Southern hybridization indicated the presence of a transposon, designated Tn1528, in various sites of pOX38Gm. This 5.2-kb composite element consisted of aph(3')-VIa flanked by two direct copies of IS15-delta and transposed at a frequency of 4 x 10(-5). It therefore appears that IS15-delta, an insertion sequence widely spread in gram-negative bacteria, is likely responsible for dissemination to members of the family Enterobacteriaceae of aph(3')-VIa, a gene previously confined to Acinetobacter spp.

Characterization of the chromosomal aac(6')-Ii gene specific for Enterococcus faecium

Chromosomal gene aac(6')-Ii of Enterococcus faecium CIP 54-32, encoding a 6'-N-aminoglycoside acetyltransferase was characterized. The gene was identified as a coding sequence of 549 bp corresponding to a protein with a calculated mass of 20,666 Da. Analysis of the sequence of the deduced protein suggested that it was the second member of a subfamily of AAC(6')-I enzymes. Insertional inactivation of aac(6')-Ii led to aminoglycoside susceptibility of CIP 54-32, suggesting that this gene plays a role in resistance to AAC(6')-I substrates. The gene was detected by DNA hybridization in all 26 strains of E. faecium tested but not in 44 other enterococci of 13 species. These data suggest that the aac(6')-Ii gene is species specific and may be used to identify E. faecium.

Characterization of the aac(6')-Ib gene encoding an aminoglycoside 6'-N-acetyltransferase in Pseudomonas aeruginosa BM2656

Pseudomonas aeruginosa BM2656 was resistant to tobramycin and susceptible to gentamicin and amikacin by disk diffusion testing. This unusual resistance was not transferable by conjugation to Escherichia coli or P. aeruginosa PAO38, and plasmid DNA was not detected in this strain. A 0.9-kb fragment harboring the tobramycin resistance gene was cloned from BM2656 into pUC18, generating pAT129. Analysis for aminoglycoside-modifying activity in extracts of BM2656 and E. coli harboring pAT129 indicated that tobramycin resistance was due to synthesis of an aminoglycoside 6'-N-acetyltransferase type I [AAC(6')-I] enzyme which modified amikacin and tobramycin. Although amikacin was acetylated, the bactericidal synergism of this aminoglycoside with ceftazidime against BM2656 was minimally affected. The sequence of the DNA fragment was determined. It contained an aac (6')-Ib-like gene and was located downstream from a conserved region related to Tn21. The translated sequence of this aac(6')-Ib gene possessed 99.2% identity with the putative products of the aac(6')-Ib gene cassettes from Serratia marcescens and Klebsiella pneumoniae and 69% identity with the putative aacA(6')-II gene product from P. aeruginosa. We conclude that an aac(6')-Ib gene has spread to the chromosome of P. aeruginosa, probably by transposition.

Nucleotide sequence of class D tetracycline resistance genes from Salmonella ordonez

Plasmid pIP173, isolated from Salmonella ordonez strain BM2000, confers resistance to tetracycline and a number of other antibiotics. We determined the nucleotide sequence of the pIP173 tetR repressor and tetA resistance genes. The pIP173 tetR gene is essentially identical to the class D tetR gene from plasmid RA1. The pIP173 tet genes are flanked by directly repeated copies of the insertion sequence IS26. Interestingly, the 3' end of the tetR gene, encoding the C-terminal 16 amino acids of the TetR protein, extends into the flanking IS26 sequence. The relationships between the class A, B, C, and D TetA sequences parallel the relationships between the corresponding TetR sequences; class D is more closely related to class B than to either class A or C. Overall, the four TetA sequences show 38% identity and 57% similarity.

Overproduction of 3'-aminoglycoside phosphotransferase type I confers resistance to tobramycin in Escherichia coli

Escherichia coli HM69, isolated from urine, was resistant to high levels of kanamycin (MIC, > 1,000 micrograms/ml) and a low level of tobramycin (MIC, 8 micrograms/ml). Phosphocellulose paper-binding assays and molecular cloning indicated that resistance to both aminoglycosides was due to synthesis of a 3'-aminoglycoside phosphotransferase type I, an enzyme that phosphorylates kanamycin but not tobramycin. The structural gene for the enzyme was borne by an 80-kb conjugative plasmid, pIP1518, and was nearly identical to aphA1 of Tn903. Incubation of extracts of resistant cells with tobramycin or kanamycin led to a decrease (> 80%) of antibiotic activity as determined by a microbiological assay. Heat treatment showed that loss of activity was reversible and dependent upon the native enzyme. In the presence of ATP, only inactivation of kanamycin was reversible. These results suggest that resistance to low levels of tobramycin was due to formation of a complex between the enzyme and the antibiotic.

In vitro activities of 15 oral beta-lactams against Klebsiella pneumoniae harboring new extended-spectrum beta-lactamases

The activities of 15 oral beta-lactams against Klebsiella pneumoniae harboring new extended-spectrum beta-lactamases were studied. All compounds were affected by these enzymes, especially by the SHV derivatives. Except for ceftibuten, the compounds with the greatest intrinsic activity were more affected by the presence of these enzymes than were older compounds with moderate intrinsic activity.

Physical map and properties of a 90-MDa plasmid of Azospirillum brasilense Sp7

Homology was previously detected between the DNA restriction fragments containing Rhizobium meliloti nodulation genes and the 90-MDa plasmid, p90, of Azospirillum brasilense Sp7. Two DNA loci from Sp7 genome that complement mutations in the exopolysaccharide synthesis genes, exoB and exoC, of R. meliloti were also shown to be present on the plasmid. A more detailed characterization of the plasmid was undertaken to establish its physical map and to localize the nod homologies and other specific regions. Six loci were mapped, the region homologous to the nodulation genes, nodPQ, of R. meliloti, the exoB and exoC mutation-correcting loci, a locus for Ap resistance, a bla homology region different from the Ap resistance locus, and a region necessary for the maintenance of p90 as an independent replicon. Mobilization into Agrobacterium tumefaciens of p90-Tn5-Mob was obtained at a frequency of 10(-4), with the plasmid helper pJB3JI. Self-transfer of p90 was not demonstrated. Fragments of p90 hybridized with a plasmid of 90 MDa present in most A. brasilense and some A. lipoferum strains, suggesting a plasmid family in Azospirillum.

TEM-4, a new plasmid-mediated beta-lactamase that hydrolyzes broad-spectrum cephalosporins in a clinical isolate of Escherichia coli

A clinical isolate of Escherichia coli, strain CB-134, recovered in 1986 from an abdominal abscess, exhibited resistance to penams, oxyimino-beta-lactams including broad-spectrum cephalosporins (cefotaxime, ceftriaxone, ceftazidime), and aztreonam but remained susceptible to cephamycins (cefoxitin, cefotetan) and to moxalactam and imipenem. Clavulanate (2 micrograms/ml) restored the susceptibility of the strain to broad-spectrum cephalosporins and aztreonam. A beta-lactamase with an isoelectric point (pI) of 5.9 was detected in strain CB-134, and the corresponding gene was transferred by conjugation to E. coli together with the associated aminoglycoside resistance determinant [AAC(3)-II] and tetracycline, trimethoprim, and sulfonamide resistance. The beta-lactamase efficiently hydrolyzed cefotaxime and ceftriaxone but only moderately hydrolyzed ceftazidime and was inhibited by clavulanate and sulbactam (1 microM) and by anti-TEM-1 and anti-TEM-2 sera. This extended-spectrum beta-lactamase, conferring resistance to cefotaxime, ceftriaxone, ceftazidime, and aztreonam, was comparable to CTX-1 (TEM-3) but differed from it by pI. Agarose gel electrophoresis of the plasmid DNA indicated that this new enzyme was coded by pUD16, a plasmid of 220 kilobases which belongs to the Inc6 incompatibility group. Hybridization with an intragenic probe for TEM-1 revealed that this beta-lactamase derives from TEM-type beta-lactamases and hence it was named TEM-4.

SHV-5, a novel SHV-type beta-lactamase that hydrolyzes broad-spectrum cephalosporins and monobactams

SHV-5 (pI 8.2), a novel broad-spectrum beta-lactamase encoded by a ca. 150-kilobase plasmid, was found in Klebsiella pneumoniae 160. SHV-5 beta-lactamase caused decreased susceptibility to most penicillins, cephalosporins, and monobactams, except imipenem and compounds which have a C6 or C7 alpha-methoxy substituent. beta-Lactamase inhibitors (clavulanic acid, sulbactam, and tazobactam) inhibited its activity and showed a synergistic effect when associated with different hydrolyzable beta-lactam compounds. Hybridization studies suggested that this enzyme may be related to, or derived from, the SHV enzyme. Increased MICs of cephamycins and temocillin associated with a decreased synergistic effect of the inhibitors on K. pneumoniae 160 might be linked to a decrease in two outer membrane proteins.

Substitution of serine for arginine in position 162 of TEM-type beta-lactamases extends the substrate profile of mutant enzymes, TEM-7 and TEM-101, to ceftazidime and aztreonam

TEM-7 is a novel broad-spectrum beta-lactamase (Bla), selected in vivo, with a resistance profile similar to that of TEM-1 and TEM-2, but extended to ceftazidime (Caz) and aztreonam. Nucleotide sequencing revealed that the TEM-7 gene is almost identical with that of TEM-2. There was 1 bp change which would result in the substitution of Ser (TEM-7) for Arg (TEM-2) in amino acid (aa) position 162 (i.e., aa position 139 of the mature enzyme). This substitution, also found in TEM-101, a spontaneous in vitro derivative of TEM-1 selected on Caz, was assumed to be responsible for the extension of the substrate profile. The assumption was verified by exchange of a DNA fragment, carrying the mutation of the TEM-7-coding gene, with the homologous fragment of the TEM-1-coding gene in pBR322. In the three-dimensional model of class-A Bla [Joris et al., Biochem. J. 250 (1988) 313-324], aa 139 is located at the rim of the groove which contains the active center and adjacent to the evolutionarily conserved BoxV. It is speculated that extra free hydroxyl groups in this area may participate in the stabilization of otherwise non-substrate compounds.

IS257 from Staphylococcus aureus: member of an insertion sequence superfamily prevalent among gram-positive and gram-negative bacteria

The nucleotide sequences for the IS257 family of insertion sequences from Staphylococcus aureus were compared with those of the ISS1 family from Streptococcus lactis and the IS15 family which is widespread amongst Gram-negative bacteria. These elements have a striking degree of similarity in both their putative transposase polypeptide sequences and their nucleotide sequences (40 to 64% between pairs), including 12 out of 14 bp conservation in their terminal inverted repeats. The evolutionary distance between the IS15 family and the IS257 and ISS1 families of Gram-positive origin is approximately twice that between the IS257 and ISS1 families. Analysis of base substitutions in the three sequences has provided insights into the effect of selection for the G + C content of immigrant genes to conform to that of their hosts, and into the evolution of biases in overall amino acid composition of cellular proteins in prokaryotes and eukaryotes. The IS257, ISS1, IS15 families form a superfamily of insertion sequences that has been involved in the spread of a number of antimicrobial resistance determinants in Gram-positive and Gram-negative pathogens.

Trimethoprim resistance transposon Tn4003 from Staphylococcus aureus encodes genes for a dihydrofolate reductase and thymidylate synthetase flanked by three copies of IS257

Trimethoprim resistance mediated by the Staphylococcus aureus multi-resistance plasmid pSK1 is encoded by a structure with characteristics of a composite transposon which we have designated Tn4003. Nucleotide sequence analysis of Tn4003 revealed it to be 4717 bp in length and to contain three copies of the insertion element IS257 (789-790 bp), the outside two of which are flanked by directly repeated 8-bp target sequences. IS257 has imperfect terminal inverted repeats of 27-28 bp and encodes for a putative transposase with two potential alpha-helix-turn-alpha-helix DNA recognition motifs. IS257 shares sequence similarities with members of the IS15 family of insertion sequences from Gram-negative bacteria and with ISS1 from Streptococcus lactis. The central region of the transposon contains the dfrA gene that specifies the S1 dihydrofolate reductase (DHFR) responsible for trimethoprim resistance. The S1 enzyme shows sequence homology with type I and V trimethoprim-resistant DHFRs from Gram-negative bacteria and with chromosomally encoded DHFRs from Gram-positive and Gram-negative bacteria. 5' to dfrA is a thymidylate synthetase gene, designated thyE.

A block of urovirulence genes encoding multiple fimbriae and hemolysin in Escherichia coli O4:K12:H-

Cosmid gene libraries were constructed from a uropathogenic isolate of Escherichia coli O4:K12:H- that secretes alpha-hemolysin and produces the F14, F12-rel, F1C, and F13 fimbrial antigens. A series of overlapping clones was generated, and individual cosmid clones were found to express various combinations of fimbriae and hemolysin, suggesting that the genes for these potential virulence factors are closely linked. By using Southern hybridization analysis and restriction endonuclease mapping, it was demonstrated that the cosmid clones carried a nested set of overlapping, cloned, genomic DNA fragments. A comparison of the phenotypic properties of individual cosmid clones and subclones allowed the order of the gene clusters encoding these factors to be deduced. The cloning also revealed the presence of a fifth fimbria that had P-adhesin specificity.

Dissemination of the novel plasmid-mediated beta-lactamase CTX-1, which confers resistance to broad-spectrum cephalosporins, and its inhibition by beta-lactamase inhibitors

The novel beta-lactamase CTX-1 (pI 6.3) encoded on a transferable 84-kilobase plasmid was found in six different bacterial species. It was responsible for a significant decrease in susceptibility towards most penicillins and cephalosporins, except imipenem, temocillin, and cephalosporins which have a 7-alpha-methoxy substituent. Synergy between either ampicillin, piperacillin, cefotaxime, ceftazidime, or aztreonam and three beta-lactamase inhibitors (clavulanic acid, sulbactam, and YTR 830) was generally found for different strains harboring CTX-1. This enzyme may be related to or derived from the TEM enzyme, since an intragenic probe of the TEM-1 gene hybridized with a fragment of the plasmid carrying CTX-1.

Primary structure of an aminoglycoside 6'-N-acetyltransferase AAC(6')-4, fused in vivo with the signal peptide of the Tn3-encoded beta-lactamase

The gene aacA4 encoding an aminoglycoside 6'-N-acetyltransferase, AAC(6')-4, was cloned from a natural multiresistance plasmid, and its nucleotide sequence was determined. The gene was 600 base pairs (bp) long, and the AAC(6')-4 had a calculated molecular size of 22.4 kilodaltons and an isoelectric point of 5.35. The sequence of the 17 N-terminal amino acids was determined from the purified enzyme. The AAC(6')-4 gene was part of a resistance gene cluster, and its expression was under the control of the regulatory sequences of the beta-lactamase encoded by Tn3. The five N-terminal amino acids were identical to those of the signal peptide of the Tn3-encoded beta-lactamase, and the entire 5' region of aacA4, as far as it was sequenced (354 bp, including the promoter and the ribosome-binding site sequences), was identical to that of the beta-lactamase gene. This led us to presume an in vivo fusion between the beta-lactamase and the acetyltransferase genes. The latter was followed, in a polycistronic arrangement, by an aminoglycoside 3",9-adenylyltransferase gene, aadA, with an intergenic region of 68 bp. At a distance of ca. 1.3 kilobases in the 3' direction, we found remnants of a second Tn3-like element specifying an active beta-lactamase. At their 5' extremities, the two incomplete copies of Tn3, which were in tandem orientation, were interrupted within the resolvase gene. We speculate that Tn3-related sequences have played a role in the process of selection and dissemination of the AAC(6')-4 gene, which specifies resistance to amikacin and related aminoglycosides.

Distribution of erythromycin esterase and rRNA methylase genes in members of the family Enterobacteriaceae highly resistant to erythromycin

The distribution of nucleotide sequences related to ereA, ereB, and ermAM was studied by colony hybridization in 112 strains of members of the family Enterobacteriaceae that are highly resistant to erythromycin. The ereA and ereB genes encoding erythromycin esterases type I and II, respectively, were detected in strains inactivating the 14-membered macrolides erythromycin and oleandomycin. Because all 52 strains resisting these antibiotics by inactivation were detected by ereA (n = 23), ereB (n = 23), or both probes (n = 6), only two classes of genes accounted for this resistance phenotype. The ermAM gene encoding a streptococcal rRNA methylase was detected in 21 strains of Escherichia coli and two strains of Klebsiella spp. Determination of the MICs of macrolide, lincosamide, and streptogramin (MLS) antibiotics demonstrated a correlation between hybridization with ermAM and the so-called MLS resistance phenotype. The presence of 11 strains coresistant to MLS antibiotics that did not hybridize to the ermAM probe suggests that, as in gram-positive organisms, MLS resistance in members of the family Enterobacteriaceae involves more than one class of rRNA methylase. Numerous strains (n = 18) were found to produce both an erythromycin esterase type II and an rRNA methylase. Physical linkage between ereB and ermAM may be responsible for the codissemination of the genes. Despite their exogenous origin, ereB and ermAM are already disseminated in various genera of the Enterobacteriaceae.

Tn1545: a conjugative shuttle transposon

Tn1545, from Streptococcus pneumoniae BM4200, confers resistance to kanamycin (aphA-3), erythromycin (ermAM) and tetracycline (tetM). The 25.3 kb element is self-transferable to various Gram-positive bacterial genera where it transposes. Tn1545 was cloned in its entirety in the recombination deficient Escherichia coli HB101 where it was unstable. The three resistance genes aphA-3, ermAM and tetM were expressed but were not transferable to other E. coli cells. Tn1545 transposed from the hybrid plasmid to multiple sites of the chromosome of its new host. The element re-transposed, at a frequency of 5 X 10(-9), from the chromosome to various sites of a conjugative plasmid where it could be lost by apparently clean excision. The element transformed and transposed to the chromosome of Bacillus subtilis. The properties of the conjugative shuttle transposon Tn1545 may account for the recent emergence of genes from Gram-positive bacteria in Gram-negative organisms.

Contribution of two different mechanisms to erythromycin resistance in Escherichia coli

Escherichia coli BM2570 was resistant to high levels of erythromycin by two different mechanisms. The two genes conferring resistance to erythromycin in BM2570 were carried by a 150-kilobase self-transferable plasmid, pIP1527, and were cloned separately in E. coli. A single polypeptide with an Mr of 27,000 was encoded by the gene erxA and conferred high-level resistance to macrolide, lincosamide, and streptogramin B-type antibiotics by a mechanism other than drug inactivation. This resistance phenotype, not previously reported for a clinical isolate of enterobacteria, was probably due to modification of the ribosomes. The gene ereB encoded an enzyme with an Mr of 51,000 which inactivated erythromycin and oleandomycin. The two different mechanisms specified by erxA and ereB contributed in more than an additive fashion to the high level of resistance to erythromycin conferred by plasmid pIP1527 to E. coli BM2570.

Conjugative transfer of staphylococcal antibiotic resistance markers in the absence of detectable plasmid DNA

Eleven Staphylococcus aureus clinical isolates were tested for transfer of resistance markers by transduction and filter mating. The resistance markers of six of the strains could be transferred only by transduction; however, the five remaining strains transferred their resistance both by transduction and filter mating. The resistance markers that were cotransferred in filter matings (transfer of resistance to penicillin and streptogramin A was accompanied, in each case, by the transfer of one or more markers, i.e., resistance to aminoglycosides, cadmium, or tetracycline, depending on the donor) were not cotransduced. The filter mating transfers were recA independent and were observed with both Staphylococcus aureus and Staphylococcus epidermidis recipients. Experiments to elucidate the mechanism of transfer by filter mating suggested that conjugation requiring cell-to-cell contact may have been involved. These transfers occurred in the absence of detectable plasmid DNA.

Analysis of the nucleotide sequence of the ereB gene encoding the erythromycin esterase type II

We have determined the nucleotide sequence of the ereB gene of plasmid pIP1527 which confers high-level resistance to erythromycin by inactivation in Escherichia coli. The open reading frame of the ereB gene, 1257-bp, was defined by initiation and termination codons and by cloning in vitro. The corresponding protein has a calculated Mr of 48,118 in close agreement with a previous estimation, 51,000, by electrophoresis of minicell extracts in SDS-polyacrylamide gels. The structure of the modified erythromycin was determined by physico-chemical techniques including mass spectrometry, infrared spectrophotometry and 13C nuclear magnetic resonance. The data obtained indicated that like ereA (Ounissi and Courvalin, 1985) ereB encodes an erythromycin esterase. Comparison of the amino acid sequences of the two isozymes did not reveal any statistically significant homology. Analysis of the nucleotide sequence of the ereB gene suggests that this resistance determinant should be exogenous to E. coli.

Molecular epidemiology of resistance to trimethoprim in enterobacteria isolated in a Parisian hospital

Between January, 1981 and December, 1984, 419 strains of enterobacteria isolated from patients at the Hôpital Saint-Joseph were studied for (1) the level of resistance to trimethoprim (Tp) by determination of minimal inhibitory concentration (MIC), (2) transferability of this resistance by conjugation into Escherichia coli, (3) plasmid content of wild-type strains and transconjugants by agarose gel electrophoresis of crude bacterial lysates and by incompatibility grouping, and (4) type of dihydrofolate reductase (DHFR) by colony hybridization with probes specific for DHFR types I and II. Tp resistance was defined as MIC greater than or equal to 4 micrograms/ml and high-level resistance by MIC greater than or equal to 1000 micrograms/ml. Amongst the strains studied, 90% were resistant to high levels of Tp, while 10% had low-level resistance to Tp was detected in 180 strains corresponding to 185 plasmids. In the vast majority of the plasmids, resistance to Tp was associated with resistance to sulphonamide (94%), streptomycin (75-90%), ampicillin (75-90%) and chloramphenicol (65-80%). Plasmids conferring resistance to Tp were often large, most (84%) ranging in size from 90 to 175 Kb. They belonged to six different incompatibility groups and Inc6-C was the most prevalent (34 to 75%). The study of the distribution of the dfr genes by colony hybridization in 183 transconjugants and 89 strains with non-transferable Tp resistance revealed the presence of dfrI genes in most of these strains (48 and 53%, respectively). DHFR of types I and II were found in only 3% of the transconjugants, but in 15% of the strains with non-transferable resistance. DHFR of other types were found equally (15%) in strains with transferable and non-transferable resistance. The high incidence of the type I enzyme among the Tp-resistant strains probably results from the integration of transposon Tn7 into the chromosome or into a non-transferable plasmid.

Transfer of amikacin resistance by closely related plasmids in members of the family Enterobacteriaceae isolated in Chile

During a 9-month period when amikacin was the sole aminoglycoside used clinically in a hospital in Santiago, Chile, resistance to amikacin and other antibiotics was encountered in 42 strains of the family Enterobacteriaceae, including Escherichia coli, Klebsiella pneumoniae, Citrobacter freundii, Enterobacter cloacae, Serratia marcescens, and Serratia liquefaciens. Amikacin resistance was transferable by conjugation and carried by IncM plasmids ranging in size from ca. 48.4 to 58.1 kilobase pairs. The plasmids had ca. 70 to 80% of their structure in common, as judged after digestion with restriction endonucleases. The resistance was mediated by a 6' aminoglycoside acetyltransferase. We conclude that selective pressure has favored the dissemination of a wide-host-range amikacin resistance plasmid and its derivatives.

Plasmid-mediated high-level resistance to erythromycin in Escherichia coli

Escherichia coli BM2195 was found to be resistant to high levels of erythromycin. This new resistance phenotype was due to the constitutive synthesis of an erythromycin esterase which inactivates the antibiotic. The gene conferring resistance to erythromycin in this strain is carried on a 61-kilobase self-transferable plasmid, pIP1100, belonging to incompatibility group X.

Heterogeneity of genes conferring high-level resistance to erythromycin by inactivation in enterobacteria

We have constructed a probe specific for the gene ereA of plasmid pIP1100, which confers high-level resistance to erythromycin in Escherichia by production of an erythromycin esterase. The distribution of the gene ereA in enterobacteria highly resistant to erythromycin isolated from human faeces was studied by colony hybridization. The gene ereA was detected in strains of E. coli belonging to various biotypes, in Klebsiella pneumoniae, in Enterobacter agglomerans and in one strain of a "coliform". Moreover, our results indicated the existence of at least two classes of genes specifying resistance to erythromycin by inactivation of the antibiotic in enterobacteria.

Genetic basis of trimethoprim and O/129 resistance in Vibrio cholerae

Because of its important consequences on prophylaxis and therapy of cholera and on bacterial identification, we have studied the genetic basis of cross-resistance to trimethoprim and O/129 of strains of Vibrio cholerae O1 independently isolated in Africa. Two classes of bacteria were found. In the first class, the strains were also resistant to ampicillin and kanamycin and to high levels of streptomycin by synthesis of a 3"- or 6-aminoglycoside phosphotransferase. The strains hybridized weakly with a Tn7 probe and all the resistance characters were transferable en bloc to Escherichia coli. The second class included strains which, in addition to trimethoprim and O/129, were resistant to moderate levels of streptomycin and spectinomycin by production of a 3",9-aminoglycoside-aminocyclitol adenylyltransferase. The resistance characters were not self-transferable to E. coli and the host strain hybridized strongly with Tn7. It therefore appears, that both plasmids and transposons are responsible for the dissemination of resistance to trimethoprim and O/129 in Vibrio.

Plasmid-mediated aminoglycoside phosphotransferases in Haemophilus ducreyi

Three clinical isolates of Haemophilus ducreyi, representing at least two subtypes, were shown to be resistant to streptomycin and kanamycin. They also produced a beta-lactamase and chloramphenicol acetyltransferase and were resistant to tetracycline. In the three strains the resistance to both aminoglycoside antibiotics was encoded by a plasmid of ca. 4.7 kilobases which apparently did not carry ampicillin, chloramphenicol, or tetracycline resistance genes, as determined after transfer to Escherichia coli by transformation. Resistance to streptomycin and kanamycin was due to the presence of two aminoglycoside phosphotransferases (APH). The enzyme modifying kanamycin was a 3',5"-APH of type I [APH(3',5")-I], as inferred from its substrate profile and immunological cross-reactivity with the APH(3',5")-I encoded by the transposable element Tn903. However, the APH(3',5")-I gene in H. ducreyi did not appear to be carried by Tn903.

Transposition behavior of IS15 and its progenitor IS15-delta: are cointegrates exclusive end products?

We report that the major product of IS15-promoted transposition is a cointegrate. When present in the multicopy plasmid pBR322, IS15 and its progenitor IS15-delta mediate the formation of cointegrates at frequencies of 3.5 X 10(-4) and 2.9 X 10(-5), respectively. We have studied the stability of the cointegrates generated by IS15 and IS15-delta. While these structures are resolved in a rec+ host, they were stable in a rec- host. These observations suggest that neither IS15 nor IS15-delta encode a resolvase and that cointegration is an end product of their transposition process. These properties of IS15-delta and IS15 can explain the transitions from IS15-delta to IS15 and from IS15 to IS15-delta observed in vivo.

Nucleotide sequence of the gene ereA encoding the erythromycin esterase in Escherichia coli

We have cloned and determined the nucleotide sequence of the gene ereA of plasmid pIP1100 which confers high-level resistance to erythromycin (Em) in Escherichia coli. The gene was defined by initiation and termination codons and by in vitro insertion-inactivation into an open reading frame (ORF) of 1032 bp corresponding to a product with an Mr of 37 765. However, the enzyme, an Em esterase, displayed an apparent Mr of 43 000 upon electrophoresis of a minicell extract on the SDS-polyacrylamide gels. The G + C content (50.5%) of the gene ereA and the preferential codon usage in its ORF suggest that this resistance determinant should be indigenous to E. coli.

Nucleotide sequence of the transposable element IS15

We have determined the complete nucleotide sequence of the right (R) copy of the insertion sequence IS15 which flanks, in direct orientation, the composite transposon Tn1525. IS15-R, which is capable of independent transposition, is 1648 bp long and has short (14 bp) perfect inverted repeats at its termini. Analysis of the nucleotide sequence indicates that IS15-R results from the transposition, in direct orientation, of a smaller (820 bp long) IS, designated IS15-delta, into itself. This integration event is accompanied by the duplication of 8 bp in the target DNA. IS15-delta possesses two large overlapping open reading frames (ORF) located on opposite strands. Because of this particular structure, IS15 possesses four large ORFs which, due to the integration event, exhibit some differences with those of the parental IS15-delta.

Characterization of IS46, an insertion sequence found on two IncN plasmids

The IncN plasmids R46 and N3 each contain two copies of an insertion sequence which we denote IS46. This insertion sequence has single PstI and SalI restriction sites and is 0.81 kilobases long. All four copies of IS46 were capable of forming cointegrates, although the DNA between the insertion sequences, which in each case carries a tetracycline resistance gene, was not transposable in the form of a compound transposon. IS46-mediated cointegrates resolved in Rec+ but not in RecA- cells. Recombination between two copies of IS46, causing an inversion, accounts for the existence of two distinct forms of R46. IS46-mediated deletions were probably responsible for the formation of the plasmid pKM101 from R46. IS46 was not homologous to IS1 but did show homology with IS15.

The chromosomal 3',5"-aminoglycoside phosphotransferase in Streptococcus pneumoniae is closely related to its plasmid-coded homologs in Streptococcus faecalis and Staphylococcus aureus

The apparently chromosomally encoded 3',5"-aminoglycoside phosphotransferase (type III), from the high-level aminoglycoside-resistant Streptococcus pneumoniae BM4200, was compared with homologous enzymes coded for by the plasmids pJH1 and pSH2, originally isolated from Streptococcus faecalis and Staphylococcus aureus, respectively, and also found in a wild strain of S. aureus, BM4600. The enzymes appeared to be indistinguishable, and we conclude that the gene encoding 3',5"-aminoglycoside phosphotransferase (type III) can cross generic barriers within gram-positive cocci.

Transferable plasmid-mediated antibiotic resistance in Acinetobacter

Acinetobacter calcoaceticus strain BM2500 was resistant to ampicillin, aminoglycoside-aminocyclitols, chloramphenicol, sulfonamides, and high levels of trimethoprim. Resistance to ampicillin was due to the presence of a beta-lactamase (TEM-1) and the aminoglycoside-aminocyclitol resistance was mediated by phosphotransferase (APH(3')(5")I) and adenylyltransferase (AAD(3)(9] activities. The resistance genes were carried by a 167 kilobase plasmid, pIP1031, belonging to incompatibility group 6-C; the plasmid was self-transferable, at extremely low frequency, to Escherichia coli by conjugation. Plasmid pIP1031 DNA was analyzed by agarose gel electrophoresis following restriction endonuclease digestion, by nucleic acid hybridization, and by CsCl analytical density gradient ultracentrifugation. The results support the hypothesis that plasmid pIP1031 may have been acquired recently by strain BM2500.

An IS15 insertion generates an eight-base-pair duplication of the target DNA

In plasmid pIP1088 the transposable module IS15 is inserted at nucleotide position 1,430 of the vector plasmid pBR322. We have sequenced the termini of the IS15 element, which consists of two perfect inverted repeat sequences, 14 bp long. The sequence is 5'-GGCACTGTTGCAAA . . . TTTGCAACAGTGCC-3'. The integration event results in the duplication of 8 bp of target DNA.

Cointegrational transduction and mobilization of gentamicin resistance plasmid pWP14a is mediated by IS140

The structures of two R-plasmids pWP14a and pWP12a (Tra-, Ap, Gm; 21 kb) and of several cointegrates they form with bacteriophages P1Cm and P1-15 were analyzed. In each case, replicon fusion was mediated by the element IS140 (about 0.8 kb), one copy of which resides on both plasmids adjacent to the gentamicin resistance determinant (AAC(3)-III). pWP14a cointegrated preferentially into or near the invertible C-loop structure of the P1 genome. Cointegrational mobilization of pWP14a was observed also with several conjugative R-factors. The process of replicon fusion is independent of the host's rec+ functions. Sequences homologous to IS140 are constituents of many R-factors, including RA1, R40a, R124, R144, Rts1, N3, and pJR255. IS140 also shows homology to two other sequences, IS15 delta and Tn2680, but not to other, well studied transposable elements. The ampicillin resistance determinant of pWP14a is within a Tn3-like transposon, Tn3651.

Tn1525, a kanamycin R determinant flanked by two direct copies of IS15

We have isolated plasmid pIP112 (IncI1) from Salmonella panama and characterized by restriction endonucleases analysis and by recombinant DNA techniques a transposable element designated Tn1525. This 4.44 kilobase (kb) transposon confers resistance to kanamycin by synthesis of an aminoglycoside phosphotransferase (3') (5") type I and contains two copies of IS15 (1.5 kb) in direct orientation. The modular organisation of Tn1525 offers the possibility for intramolecular homologous recombination between the two terminal direct repeats and thus accounts for the in vivo structural lability of plasmid pIP112: instability of kanamycin resistance and tandem amplification of the kanamycin determinant. Other transposons mediating resistance to kanamycin by the same enzymatic mechanism were analysed by agarose and polyacrylamide gel electrophoresis, following digestion with restriction endonucleases, and by Southern hybridizations. These comparisons indicate that, although the structural genes for the phosphotransferases are homologous, Tn1525 differs from Tn903 and Tn2350 and is closely related but distinct from Tn6. Using the same techniques Tn1525 was detected on plasmids belonging to different incompatibility groups and originating from various species of Gram-negative clinical isolates. These results indicate that Tn1525 is representative of a new family of class I composite transposons already spread in diverse pathogenic bacterial genera.

IS15, a new insertion sequence widely spread in R plasmids of gram-negative bacteria

We have shown that the IS15 element, first detected in Salmonella ordonez and previously designated IS1522 (Labigne-Roussel et al. 1981), could transpose, with an approximate frequency of 5 X 10(-5), to various sites of different replicons in an Escherichia coli host deficient for general homologous recombination. Physical mapping with restriction endonucleases of this 1,500 base pairs (bp) transposable module indicated the presence of two, possibly contiguous, directly repeated internal sequences, at least 480 bp in size. IS15 could generate in vivo, by intramolecular recombination between the two direct repeats, IS15-delta, which is 830 bp in size. The reverse transition, IS15-delta to IS15, was not observed. The two related structural forms of IS15 were detected, by Southern hybridization, on plasmids belonging to various incompatibility groups (Inc6-C, I1, 7-M, and Y) isolated from phylogenetically remote pathogenic bacterial genera (Escherichia coli, Salmonella panama, Enterobacter cloacae, and Acinetobacter calcoaceticus). Whereas IS15 could promote its own transposition and transposition of DNA fragments it flanked, IS15-delta resulting from the 670 bp 'clean' deletion and representing the most common natural deletion derivative could only induce replicon fusion. It appears, therefore, that the two structural configurations of IS15 have evolved to play, by transposition, distinct and complementary roles in bacterial evolution.

Transposition of a tetracycline-resistance determinant (Tn1523) and cointegration events mediated by the pIP231 plasmid in Escherichia coli

A 10.8-kb transposable DNA sequence conferring resistance to tetracycline resides on the IncY Escherichia coli plasmid pIP231. This sequence, designated Tn1523, was shown to insert into different sites of the replicons of the IncY prophage P1Cm c1.100 and the IncI1 plasmid pIP112. This process is not dependent on the host recombination system recA. Genetic results indicate that Tn1523 transposition involves the formation of a cointegrate intermediate, either between pIP231 and P1Cm c1.100, or between pIP231 and pIP112. These intermediates were found to be resolved into donor and recipient plasmids, each harboring a copy of the Tn1523 transposon. A stable structure formed by fusion of the pIP231 plasmid with the pIP112 plasmid was also observed. This event occurs in the absence of the bacterial recA gene product and seems to involve a site-specific reciprocal recombination between "IS-like" elements.