Multidrug-resistant (MDR) Klebsiella pneumoniae clinical isolates: a zone of high heterogeneity (HHZ) as a tool for epidemiological studies.

Comparison of genome-wide, high-resolution restriction maps of Klebsiella pneumoniae clinical isolates, including an NDM-1 producer, and in silico-generated restriction maps of sequenced genomes revealed a highly heterogeneous region we designated the 'high heterogeneity zone' (HHZ). The HHZ consists of several regions, including a 'hot spot' prone to insertions and other rearrangements. The HHZ is a characteristic genomic area that can be used in the identification and tracking of outbreak-causing strains.

Systematic analysis of a conserved region of the aminoglycoside 6'-N-acetyltransferase type Ib.

Alanine-scanning mutagenesis was applied to the aminoglycoside 6'-N-acetyltransferase type Ib conserved motif B, and the effects of the substitutions were analyzed by measuring the MICs of kanamycin (KAN) and its semisynthetic derivative, amikacin (AMK). Several substitutions resulted in no major change in MICs. E167A and F171A resulted in derivatives that lost the ability to confer resistance to KAN and AMK. P155A, P157A, N159A, L160A, I163A, K168A, and G170A conferred intermediate levels of resistance. Y166A resulted in an enzyme derivative with a modified specificity; it conferred a high level of resistance to KAN but lost the ability to confer resistance to AMK. Although not as pronounced, the resistance profiles conferred by substitutions N159A and G170A were related to that conferred by Y166A. These phenotypes, taken together with previous results indicating that mutant F171L could not catalyze acetylation of AMK when the assays were carried out at 42 degrees C (D. Panaite and M. Tolmasky, Plasmid 39:123-133, 1998), suggest that some motif B amino acids play a direct or indirect role in acceptor substrate specificity. MICs of AMK and KAN for cells harboring the substitution C165A were high, suggesting that the active form of the enzyme may not be a dimer formed through a disulfide bond. Furthermore, this result indicated that the acetylation reaction occurs through a direct mechanism rather than a ping-pong mechanism that includes a transient transfer of the acetyl group to a cysteine residue. Deletion of fragments at the C terminus demonstrated that up to 10 amino acids could be deleted without a loss of activity.

Bacterial resistance to aminoglycosides and beta-lactams: the Tn1331 transposon paradigm.

Aminoglycosides (Ags) are a group of antibiotics that exert their bactericidal activity primarily by inhibition of protein synthesis. Aminoglycoside (Ag) molecules bind to the bacterial 30S ribosomal subunit rendering the ribosomes unavailable for translation, which results in cell death. Although these antibiotics are and have been very useful to treat a variety of bacterial infections, in recent years the number of Ag resistant and multiresistant isolates has seriously increased. Mechanisms of resistance to Ag include enzymatic inactivation by acetyltransferases, nucleotidyltransferases (adenylyltransferases), and phosphotransferases, ribosomal alterations, and reduced permeability. Of all Ags, amikacin (Ak) is the most resistant to the action of Ag-modifying enzymes. However, AAC(6')-I type enzymes (a group of 6'-N-acetyltransferases) can utilize Ak as substrate and confer resistance to this antibiotic in addition to other Ags. The gene aac(6')-Ib was found in various bacterial species and various research groups performed mutagenesis studies on this or related enzymes. In one case, aac(6')-Ib was identified in a transposable element, Tn1331, included in pJHCMW1, a plasmid isolated from a clinical K. pneumoniae strain. Tn1331 includes genes encoding two Ag-modifying enzymes (aac(6')-Ib and ant(3")-Ia) and two beta-lactamases (blaTEM and blaOXA-9). Characterization of other functions of the pJHCMW1 plasmid showed the presence of an RNA-regulated replication origin and a functional oriT. Stability by multimer resolution is achieved by the Tn1331 resolvase.

Characterization of the angR gene of Vibrio anguillarum: essential role in virulence.

The ability to utilize the iron bound by high-affinity iron-binding proteins in the vertebrate host is an important virulence factor for the marine fish pathogen Vibrio anguillarum. Virulence in septicemic infections is due to the presence of a highly efficient plasmid-encoded iron transport system. AngR, a 110-kDa protein component of this system, appears to play a role in both regulation of the expression of the iron transport genes fatDCBA and the production of the siderophore anguibactin. Therefore, study of the expression of the angR gene and the properties of its product, the AngR protein, may contribute to the understanding of the mechanisms of virulence of this pathogen. In this work, we present genetic and molecular evidence from transposition mutagenesis experiments and RNA analysis that angR, which maps immediately downstream of the fatA gene, is part of a polycistronic transcript that also includes the iron transport genes fatDCBA and angT, a gene located downstream of angR which showed domain homology to certain thioesterases involved in nonribosomal peptide synthesis of siderophores and antibiotics. In order to dissect the specific domains of AngR associated with regulation of iron transport gene expression, anguibactin production, and virulence, we also generated a panel of site-directed angR mutants, as well as deletion derivatives. Both virulence and anguibactin production were dramatically affected by each one of the angR modifications. In contrast to the need for an intact AngR molecule for anguibactin production and virulence, the regulation of iron transport gene expression does not require the entire AngR molecule, since truncation of the carboxy terminus carrying the nonribosomal peptide synthetase cores, as well as the site-directed mutations, resulted in derivatives that retained their ability to regulate gene expression which was only abolished after truncation of amino-terminal sequences containing helix-turn-helix and leucine zipper motifs and a specialized heterocyclization and condensation domain found in certain nonribosomal peptide synthetases. The evidence, while not rigorously eliminating the possibility that a separate regulatory polypeptide exists and is encoded somewhere within the 5'-end region of the angR gene, strongly supports the idea that AngR is a bifunctional protein and that it plays an essential role in the virulence mechanisms of V. anguillarum. We also show in this study that the angT gene, found downstream of angR, intervenes in the mechanism of anguibactin production but is not essential for virulence or iron transport gene expression.

Effects of F171 mutations in the 6'-N-acetyltransferase type Ib [AAC(6')-Ib] enzyme on susceptibility to aminoglycosides.

Substitutions at position F171 of 6'-N-acetyltransferase type Ib cause variable loss of aminoglycoside resistance, indicating that this residue plays an important role in the structure and/or function of the enzyme.

Bacterial plasmids: replication of extrachromosomal genetic elements encoding resistance to antimicrobial compounds.

Plasmids are self-replicating extrachromosomal DNA molecules found in Gram-negative and Gram-positive bacteria as well as in some yeast and other fungi. Although most of them are covalently closed circular double-stranded DNA molecules, recently linear plasmids have been isolated from different bacteria. In general, plasmids are not essential for the survival of bacteria, but they may nevertheless encode a wide variety of genetic determinants, which permit their bacterial hosts to survive better in an adverse environment or to compete better with other microorganisms occupying the same ecological niche. The medical importance of plasmids that encode for antibiotic resistance, as well as specific virulence traits has been well documented and demonstrated the important role these bacterial genetic elements play in nature. Although they encode specific molecules required for initiation of their replication, plasmids rely on host-encoded factors for their replication. Plasmid replication initiates in a predetermined cis-site called ori and can proceed either by a rolling circle or a theta replication mechanism. Some of the plasmid-encoded elements required for their replication, such antisense RNA molecules and DNA repeated sequences located close to ori, determine plasmid attributes like copy number and incompatibility.

Characterization of OXA-9, a beta-lactamase encoded by the multiresistance transposon Tn1331.

The enzyme OXA-9, an oxacillinase-carbenicillinase, is encoded by the blaOXA-9 gene which was originally found within the structure of Tn1331, a multiresistance transposon first isolated from a clinical Klebsiella pneumoniae strain. Studies to characterize OXA-9 demonstrated that it has a pI of 6.9 and the optimal pH for enzyme activity was between 7.7 and 8.2. When total soluble extracts were preincubated at 37 degrees C and at 42 degrees C, enzyme activity decayed to approximately 56% of the original value after 6 hrs. at 37 degrees C and to 50% after 30 min. at 42 degrees C. Enzymatic activity of OXA-9 was inhibited in the presence of p-chloromercuribenzoate, cloxacillin and clavulanic acid, but not by 200 mM sodium chloride. The inhibition by p-chloromercuribenzoate may indicate the presence of a cysteine residue playing a role in the catalytic activity of the enzyme. The OXA-9 enzyme was released by osmotic shock of E. coli cells harboring a recombinant clone including the blaOXA-9 gene indicating that it is located in the periplasmic space of the cells. The OXA-9 enzyme was purified from soluble protein extracts of E. coli cells carrying a recombinant clone including the blaOXA-9 by ion exchange chromatography.

Characterization of mutants of the 6'-N-acetyltransferase encoded by the multiresistance transposon Tn1331: effect of Phen171-to-Leu171 and Tyr80-to-Cys80 substitutions.

The Klebsiella pneumoniae plasmid pJHCMW1 harbors a copy of Tn1331, a multiresistance transposon that includes the aac(6')-Ib gene which encodes a 6'-N-aminoglycoside acetyltransferase. This gene was mutagenized using the mutator Escherichia coli XL1-Red. Two plasmids with a single nucleotide mutation in aac(6')-Ib were selected for further analysis: pDP1 and pDP6. Plasmid pDP1 codes for a mutant enzyme, AAC(6')-IbDP1, that has the Phe171 replaced by a Leu residue. This mutant derivative showed a lower specific activity than the wild-type enzyme when either kanamycin (Km) or its semisynthetic derivative amikacin (Ak) were used as substrates in enzymatic assays performed at 30 degrees C. Furthermore, AAC(6')-IbDP1 showed a change of specificity of substrate when incubated at 42 degrees C. While its acetylating activity for Km was higher at this temperature than at 30 degrees C, it had its ability to utilize Ak as substrate for acetylation considerably reduced. Accordingly, minimal inhibitory concentration assays showed that E. coli(pDP1) was resistant to Ak at 37 degrees C but susceptible at 42 degrees C. The same assays showed that E. coli(pDP1) was highly resistant to Km at either 37 degrees C or 42 degrees C. A high level of resistance to Ak was observed for E. coli(pJHCMW1) which harbors the wild-type AAC(6')-Ib at either 37 or 42 degrees C. Extension of the analyses to other aminoglycosides showed that the enzymatic activity of AAC(6')-IbDP1 as well as the E. coli(pDP1) MICs for netilmicin dropped at 42 degrees C as was the case for Ak. These results could indicate that at 42 degrees C the mutant adopts a conformation that makes it unable to efficiently acetylate aminoglycoside molecules substituted in the C-1amino group of the deoxystreptamine moiety. Plasmid pDP6 encodes the mutant AAC(6')-IbDP6 which has the Tyr80 substituted by a Cys residue. E. coli(pDP6) exhibited reduced MICs for Ak, Km, tobramycin, and netilmicin. Analysis of the acetylating activity of AAC(6')-IbDP6 showed only marginal levels of activity when either Ak, Km, tobramycin, or netilmicin were used as substrates.

Characterization of the replication and mobilization regions of the multiresistance Klebsiella pneumoniae plasmid pJHCMW1.

A 2.4-kb EcoRI fragment including the replication and origin of transfer regions of the Klebsiella pneumoniae multiresistance plasmid pJHCMW1 has been cloned and sequenced. The isolated replication region was sufficient for stable maintenance of the plasmid and shares homology with RNA-regulated replicons. Homology was highest with the replication region of the plasmid p15A. Incompatibility experiments, however, determined that pJHCMW1 is compatible with pACYC177, a plasmid harboring the p15A replicon. Differences in their RNA I nucleotide sequences may account for their compatibility. A mobilization origin was also found in the 2.4-kb EcoRI pJHCMW1 DNA fragment analyzed. Conjugation experiments showed that although non-self-transmissible, the recombinant clone including the 2.4-kb EcoRI pJHCMW1 fragment could be mobilized in the presence of the helper plasmid pRK2073.

The AngR protein and the siderophore anguibactin positively regulate the expression of iron-transport genes in Vibrio anguillarum.

Vibrio anguillarum virulence is associated with the presence of a plasmid-mediated iron-uptake system expressed under iron-limiting conditions, which consists of the siderophore anguibactin and specific iron-transport proteins. This system is maximally expressed under iron-limiting conditions and requires the AngR protein that acts as a positive regulator of anguibactin biosynthesis and also possess an EntE-like enzymatic function that may play a role in anguibactin biosynthesis. In this work, we demonstrate that in addition to possessing these functions related to anguibactin production, AngR also positively regulated transcription of the iron-transport genes fatA and fatB. We also show that transcription of angR is repressed by Fur under iron-rich conditions. In addition, we present evidence that anguibactin itself enhanced transcription of the iron-transport genes fatA and fatB, independently of AngR and the trans-acting factor (TAF) product(s). The presence of either AngR (together with the TAF product(s)) or anguibactin alone led to a partial level of expression of the iron-transport genes fatA and fatB, while full expression is achieved when AngR, the TAF products and anguibactin are all present.

Characterization and regulation of the expression of FatB, an iron transport protein encoded by the pJM1 virulence plasmid.

The pJM1-encoded genes fatDCBA are essential for iron acquisition via the siderophore anguibactin. Sequence analysis indicated that the open reading frame corresponding to the fatB gene possesses domains that are characteristic of periplasmic proteins that bind the ferric siderophore. In this work, a monospecific antiserum against an oligopeptide containing the last 27 amino acids of the carboxy-terminal region from this open reading frame was used to demonstrate that fatB encodes a 35 kDa protein that is essential for iron transport. By using this antibody we were able to demonstrate that expression of the fatB gene is negatively regulated by the Fur protein at high iron concentrations. Conversely, its expression was positively regulated by the combined action of the AngR protein and products of the TAF region. FatB, the product of the fatB gene, is isolated with the membrane fraction. In accordance with these findings is the fact that the first 23 amino acid residues of this protein have the properties of a lipoprotein signal sequence. The lipoprotein nature of FatB is supported by the fact that treatment of Vibrio anguillarum cells with globomycin, an inhibitor of the lipoprotein signal peptidase, results in the accumulation of a 38 kDa proFatB precursor protein.

Iron transport genes of the pJM1-mediated iron uptake system of Vibrio anguillarum are included in a transposonlike structure.

The pJM1 genes encoding the proteins involved in iron transport in the anguibactin iron uptake system were found to be flanked by insertion sequences in a composite transposonlike structure. These Vibrio anguillarum insertion sequences, ISV-A1 and ISV-A2, are related to IS903, IS102, and the ISVs found in Vibrio parahaemoliticus, Vibrio mimicus, and non-O1 Vibrio cholerae flanking various tdh (thermostable direct hemolysin) genes. The inverted repeats at the ends of ISV-A1 and ISV-A2 have no more than three mismatches when compared to the inverted repeats of the other ISVs or IS903 and IS102. ISV-A1 and ISV-A2 are flanked by 9-bp direct repeats, which is the number of bases that are duplicated upon IS903 or IS102 transposition. The similarities found between the V. anguillarum ISVs and the other ISVs as well as IS903 and IS102 suggest that they derive from a common ancestral insertion sequence. At the end of ISV-A1 there is a -35 sequence region followed by a -10 sequence found in the pJM1 sequence immediately outside the ISV. This promoter region is followed by an open reading frame with the potential to encode a polypeptide of 26,985 Da whose function is still unknown. The functionality of this promoter has been demonstrated and expression analysis showed that the promoter is regulated by the iron concentration of the media.

A histidine decarboxylase gene encoded by the Vibrio anguillarum plasmid pJM1 is essential for virulence: histamine is a precursor in the biosynthesis of anguibactin.

We have identified and sequenced an hdc gene in the Vibrio anguillarum plasmid pJM1 which encodes a histidine decarboxylase enzyme and is an essential component for the biosynthesis of anguibactin. The open reading frame corresponds to a protein of 386 amino acids with a calculated molecular mass of 44,259.69 Da. The amino acid sequence has extensive homology with the pyridoxal-P-dependent histidine decarboxylases of Morganella morganii, Klebsiella planticola, and Enterobacter aerogenes. Tn3-HoHo1 transposition mutagenesis of the hdc gene present in a recombinant clone carrying the entire pJM1 iron uptake region produced two derivatives, one with the lacZ gene in the same orientation as the direction of hdc transcription and the other with the lacZ gene in the opposite orientation. A. V. anguillarum strain harbouring one of the mutated derivatives was unable to grow under iron-limiting conditions and did not produce anguibactin. Therefore, the hdc gene must play a role in the biosynthetic pathway of this siderophore and consequently in conferring the high virulence phenotype to this bacterium. The role of histidine decarboxylase in biosynthesis of anguibactin was confirmed by the fact that growth under iron starvation was restored by addition of histamine to the medium. The presence of anguibactin was also demonstrated in supernatants from cultures of the hdc mutant strains grown under iron starvation with the addition of histamine, further confirming that histamine is a precursor in the biosynthesis of the siderophore.(ABSTRACT TRUNCATED AT 250 WORDS)

Structural and functional analyses of mutant Fur proteins with impaired regulatory function.

Vibrio anguillarum Fur mutants, 775met9 and 775met11, were characterized. V. anguillarum 775met9 had a change of D to G at position 104 located in the carboxy terminus resulting in impaired Fur activity. Computer analysis predicts perturbation of an alpha-helix in the carboxy terminus which may interfere with Fur protein conformation. Strain 775met11 had a change in the start codon resulting in no protein synthesis. The mutants are unstable, and reversion to the wild type occurs frequently.

Chromosome-mediated 2,3-dihydroxybenzoic acid is a precursor in the biosynthesis of the plasmid-mediated siderophore anguibactin in Vibrio anguillarum.

We have isolated a recombinant clone harboring the chromosomal aroC gene, encoding chorismate synthase, from Vibrio anguillarum 775 by complementation of the Escherichia coli aroC mutant AB2849 which was transfected with a cosmid gene bank of the plasmidless V. anguillarum H775-3. The nucleotide sequence was determined, and an open reading frame that corresponds to a protein of 372 amino acids was found. The calculated mass of 40,417 Da was correlated with the size of the V. anguillarum aroC product detected in vitro. The homology of the V. anguillarum aroC gene to the aroC genes of E. coli and Salmonella typhi is 68% at the nucleotide level and 78% at the protein level. The expression of the aroC transcript is not regulated by iron, as determined by Northern (RNA) blot hybridization analysis. After insertion of an antibiotic resistance gene cassette within the cloned aroC gene, an aroC mutant of V. anguillarum was generated by allelic exchange. This mutant is deficient in the production of 2,3-dihydroxybenzoic acid (2,3-DHBA). Our bioassay and complementation experiments with this mutant demonstrate that the chromosome-mediated 2,3-DHBA is a precursor of the pJM1 plasmid-mediated siderophore anguibactin.

Characterization of the Vibrio anguillarum fur gene: role in regulation of expression of the FatA outer membrane protein and catechols.

The chromosomally encoded Vibrio anguillarum fur gene was characterized. The amino acid sequence of the Fur protein showed a very high degree of homology with those of V. cholerae and V. vulnificus. The degree of homology was lower, although still high, with the Escherichia coli and Yersinia pestis Fur amino acid sequences, while the lowest degree of homology was found with the Pseudomonas aeruginosa Fur protein. The C-terminal portion of Fur is the least conserved region among these Fur proteins. Within this portion, two regions spanning amino acids 105 to 121 and 132 to the end are the least conserved. A certain degree of variation is also present in the N termini spanning amino acids 28 to 46. Regulation of expression of the V. anguillarum fur gene by iron was not detected by immunoblot analysis. Mutations in the cloned fur gene were generated either by site-directed mutagenesis (the Lys-77 was changed to a Gly to generate the derivative FurG77) or by insertion of a DNA fragment harboring the aph gene in the same position. FurG77 was impaired in its ability to regulate a reporter gene with the Fur box in its promoter, while the insertion mutant was completely inactive. V. anguillarum fur mutants were obtained by isolating manganese-resistant derivatives. In one of these mutants, which encoded a Fur protein with an apparent lower molecular weight, the regulation of the production of catechols and synthesis of the outer membrane protein FatA were partially lost. In the case of another mutant, no protein was detected by anti-Fur serum. This derivative showed a total lack of regulation of biosynthesis of catechols and FatA protein by iron.

Effect of iron-limiting conditions on growth of clinical isolates of Acinetobacter baumannii.

Different clinical isolates of Acinetobacter baumannii, typed by plasmid profile, were able to grow in iron-chelated medium by secreting iron-regulated siderophores. This iron-scavenging phenotype was associated with the production of iron-repressible catechol. Siderophore utilization bioassays showed the presence of 2,3-dihydroxybenzoic acid in the growth medium, and neither enterobactin nor aerobactin was detected in culture supernatants obtained under iron-deficient conditions.

A single amino acid change in AngR, a protein encoded by pJM1-like virulence plasmids, results in hyperproduction of anguibactin.

The siderophore anguibactin is produced in vivo in a diffusible form and is an important factor in the virulence of Vibrio anguillarum. The natural isolate V. anguillarum 531A is a hyperproducer of anguibactin when compared with the prototype strain V. anguillarum 775. The angR gene was found to be responsible for this difference in levels of anguibactin produced. Nucleotide sequence analysis showed that the angR531A differed in a single nucleotide from the angR775 present in the prototype plasmid pJM1. This nucleotide substitution resulted in a change in amino acid 267 from His in strain 775 to Asn in strain 531A. This amino acid is located in a region between one of the two helix-turn-helix domains and the neighboring leucine zipper. Mutations to replace His with either Leu or Gln, generated by site-directed mutagenesis, in amino acid 267 resulted in strains for which the MIC of the iron chelator ethylenediamine di(o-hydroxyphenyl) acetic acid were lower than for the proptotype 775 but higher than for iron uptake-deficient strains. In addition to its transcriptional activating function, AngR also complemented a mutation in the Escherichia coli entE gene, which encodes the enterobactin biosynthetic enzyme 2,3-dihydroxybenzoate-AMP ligase. Therefore, AngR may also function in V. anguillarum as an EntE-like enzyme for the biosynthesis of anguibactin.

Functional characterization of a replication initiator protein.

Functional domains in the RepI replication initiator protein have been identified by classical and site-directed mutagenesis techniques. Mutations conferring an increase in plasmid copy number contained alterations in a key position of a putative helix-turn-helix DNA binding motif. The mutations did not appear to affect autorepressing functions. Regions of RepI important for autorepression were localized as well. Two classes of mutations resulting in diminished autorepression functions were identified. One class was distinguished by an elevated copy number, while the other class remained at the wild-type copy number level. Analysis of the various mutations leading to changes in copy number or autorepressing functions suggest that in some cases the autorepression and initiating functions of the RepI protein are separable. Finally, analysis with deletion clones suggests that the trans-acting autorepressing functions of RepI might depend on intermolecular coupling control.

Mechanisms for negative regulation by iron of the fatA outer membrane protein gene expression in Vibrio anguillarum 775.

Synthesis of the 86-kDa FatA outer membrane protein is repressed under iron-rich conditions. Complementation of transposition mutants derived from clones containing the pJM1 iron uptake region revealed the existence of an antisense RNA, RNA alpha. This RNA is only expressed under iron-rich conditions and acts as a negative regulator of FatA synthesis, with slight but discernible decrease in the steady-state level of fatA mRNA determined by RNase protection and by Northern blot analysis. Primer extension experiments revealed that the level of several possible fatA transcripts was reduced in the presence of RNA alpha. In addition, we found that fatA mRNA expression is slightly reduced in the presence of Escherichia coli Fur. We have identified and cloned a chromosomally encoded fur-like gene in Vibrio anguillarum.