Isolation, characterization, and cloning of a plasmid-borne gene encoding a phosphotransferase that confers high-level amikacin resistance in enteric bacilli

Substrate specificity of radical S-adenosyl-l-methionine dehydratase AprD4 and its partner reductase AprD3 in the C3'-deoxygenation of aminoglycoside antibiotics

A radical S-adenosyl-l-methionine dehydratase AprD4 and an NADPH-dependent reductase AprD3 are responsible for the C3'-deoxygenation of pseudodisaccharide paromamine in the biosynthesis of apramycin. These enzymes are involved in the construction of the characteristic structural motif that is not modified by 3'-phosphotransferase in aminoglycoside-resistant bacterial strains. AprD4 catalyzes the C3'-dehydration of paromamine via a radical-mediated reaction mechanism to give 4'-oxolividamine, which is then reduced by AprD3 with NADPH to afford lividamine. In the present study, the substrate specificity of this unique combination of enzymes has been investigated. AprD4 was found to recognize paromamine, neamine, kanamycin C, and kanamycin B to afford 5'-deoxyadenosine as one of products during the C3'-dehydration of aminoglycosides, but not 2'-N-acetylparomamine and paromomycin. Only paromamine and kanamycin C were converted to the corresponding C3'-deoxygenated compounds by AprD4 and AprD3. AprD3 recognizes the 4'-oxolividamine moiety, including the pseudotrisaccharide kanamycin C, and seems to reject the amino group at C6' of neamine and kanamycin B. Chirally deuterium-labeled NADPH was used to identify that that AprD3 transfers the pro-S hydrogen atom of NADPH when reducing 4'-oxolividamine to give lividamine.

KPC-producing Klebsiella pneumoniae strains that harbor AAC(6')-Ib exhibit intermediate resistance to amikacin

The aminoglycoside-modifying enzyme AAC(6')-Ib is common among carbapenem-resistant Klebsiella pneumoniae (CR-Kp) strains. We investigated amikacin (AMK) activity against 20 AAC(6')-Ib-producing CR-Kp strains. MICs clustered at 16 to 32 μg/ml. By the time-kill study, AMK (1× and 4× the MIC) was bactericidal against 30% and 85% of the strains, respectively. At achievable human serum concentrations, however, the majority of strains showed regrowth, suggesting that AAC(6')-Ib confers intermediate AMK resistance. AMK and trimethoprim-sulfamethoxazole (TMP-SMX) were synergistic against 90% of the strains, indicating that the combination may overcome resistance.

Aminoglycoside modifying enzymes

Aminoglycosides have been an essential component of the armamentarium in the treatment of life-threatening infections. Unfortunately, their efficacy has been reduced by the surge and dissemination of resistance. In some cases the levels of resistance reached the point that rendered them virtually useless. Among many known mechanisms of resistance to aminoglycosides, enzymatic modification is the most prevalent in the clinical setting. Aminoglycoside modifying enzymes catalyze the modification at different -OH or -NH₂ groups of the 2-deoxystreptamine nucleus or the sugar moieties and can be nucleotidyltransferases, phosphotransferases, or acetyltransferases. The number of aminoglycoside modifying enzymes identified to date as well as the genetic environments where the coding genes are located is impressive and there is virtually no bacteria that is unable to support enzymatic resistance to aminoglycosides. Aside from the development of new aminoglycosides refractory to as many as possible modifying enzymes there are currently two main strategies being pursued to overcome the action of aminoglycoside modifying enzymes. Their successful development would extend the useful life of existing antibiotics that have proven effective in the treatment of infections. These strategies consist of the development of inhibitors of the enzymatic action or of the expression of the modifying enzymes.

Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycoside-modifying enzymes

The three classes of enzymes which inactivate aminoglycosides and lead to bacterial resistance are reviewed. DNA hybridization studies have shown that different genes can encode aminoglycoside-modifying enzymes with identical resistance profiles. Comparisons of the amino acid sequences of 49 aminoglycoside-modifying enzymes have revealed new insights into the evolution and relatedness of these proteins. A preliminary assessment of the amino acids which may be important in binding aminoglycosides was obtained from these data and from the results of mutational analysis of several of the genes encoding aminoglycoside-modifying enzymes. Recent studies have demonstrated that aminoglycoside resistance can emerge as a result of alterations in the regulation of normally quiescent cellular genes or as a result of acquiring genes which may have originated from aminoglycoside-producing organisms or from other resistant organisms. Dissemination of these genes is aided by a variety of genetic elements including integrons, transposons, and broad-host-range plasmids. As knowledge of the molecular structure of these enzymes increases, progress can be made in our understanding of how resistance to new aminoglycosides emerges.

Increased resistance to amikacin in a neonatal unit following intensive amikacin usage

Gram-negative isolates from blood and cerebrospinal fluid were monitored for 1 year before and for 1 year after the first-line aminoglycoside in a busy pediatric department was changed from gentamicin to amikacin. In the general pediatric wards, the switch to amikacin resulted in no change in resistance of nosocomial gram-negative infections to either amikacin (0% before and after) or gentamicin (23.9% [before] versus 26.5% [after]). In the neonatal unit, the switch to amikacin was followed by an outbreak of Serratia spp. that were commonly resistant to amikacin but susceptible to gentamicin. This outbreak abated spontaneously. In the year after the change in aminoglycoside usage, the resistance to amikacin of nosocomially acquired gram-negative infections increased from 7.6 to 27.7% (P less than 0.001), and the resistance to gentamicin decreased from 71.2 to 60.2% (P = 0.07). The increase in amikacin resistance of gram-negative bacilli other than Serratia spp. has persisted for more than a year after the introduction of amikacin as the sole aminoglycoside. The different effects observed in the two sections of the pediatric department may be related to the more intensive usage of aminoglycosides in the neonatal unit.

Epidemiological survey of genes encoding aminoglycoside phosphotransferases APH (3') I and APH (3') II using DNA probes

The epidemiological survey of APH (3') I and APH (3') II genes, at a time when the specific antibiotic pressure was very low, was carried out by DNA-DNA hybridization. The sample included 334 aminoglycoside resistant Gram-negative bacteria collected from patients of a General Hospital. Of these, 251 hybridized with the APH (3') I-probe and 19 with the APH (3') II-probe but only 190 strains showed high resistance levels (CIM greater than 64 micrograms/ml) for kanamycin, neomycin and paromomycin. These strains were isolated both from inpatients and outpatients with different infectious diseases. The APH (3') I-gene was dispersed among all the bacterial species and clinical specimens tested but the APH (3') II-gene was not found in Pseudomonas spp, Escherichia coli, Citrobacter freundii and Enterobacter cloacae, nor in infected catheters. Several plasmids of different sizes carrying APH (3') genes were detected among different bacteria. Plasmids along with transposable elements (the probes used in this work were developed from Tn906 and Tn5) and the high consumption of other antibiotics whose resistance is carried by these bacteria might be playing an important role in the maintenance and dispersion of APH (3') genes.

Correlation between aminoglycoside resistance profiles and DNA hybridization of clinical isolates

DNA hybridization data and aminoglycoside resistance profiles (AGRPs) were determined for 4,088 clinical isolates from three studies (United States, Belgium, and Argentina). The correlation between susceptibility profiles and hybridization results was determined with nine DNA probes. For each of the seven aminoglycoside resistance profiles which we were able to test, the data suggested at least two distinct genes could encode enzymes which lead to identical resistance profiles. Furthermore, the DNA hybridization data showed that individual strains carried up to six unique aminoglycoside resistance genes. DNA hybridization revealed interesting differences in the frequencies of these genes by organism and by country.

Nosocomial spread of an amikacin resistance gene on both a mobilized, nonconjugative plasmid and a conjugative plasmid

Resistance to amikacin among members of the family Enterobacteriaceae at a hospital in Venezuela rose from 2% in 1979 to 5% in 1984 and 10% in 1985 as amikacin usage rose 20-fold to exceed gentamicin usage. Resistance to gentamicin remained at 25 to 27%. We examined the plasmids from 21 isolates obtained in 1984 and 1985. Nine of eleven in 1984 and three of ten in 1985 carried aacA and sul on a 3.8-kb BamHI fragment of pBWH300, a 10.4-kb nonconjugative plasmid that had been mobilized into strains of six species by at least two different coresident conjugative plasmids. Six 1985 isolates of two species carried these genes on a similar BamHI fragment of the 104-kb conjugative plasmid pBWH303. One isolate in 1984 and one in 1985 carried the 69-kb conjugative plasmid pBWH301, which had aacA as the promoter-proximal gene of an operon that also encompassed the cat and aadB resistance genes. Another conjugative plasmid, pBWH302, was found in a single isolate. It carried a different aacA allele on the functional transposon Tn654, which appeared to be closely related to Tn1331, a transposon previously isolated in Argentina and Chile. Increased selection may thus have led to dissemination of an endemic aacA allele on two endemic plasmids, one spread by mobilization, with occasional intrusion of additional aacA alleles from outside.

Cloning, sequencing, and use as a molecular probe of a gene encoding an aminoglycoside 6'-N-acetyltransferase of broad substrate profile

A gene coding for an aminoglycoside 6'-N-acetyltransferase that was able to modify amikacin was cloned from a plasmid isolated from a clinical strain of Enterobacter cloacae. Sequencing of a 955-bp segment which mediates the modifying activity revealed a single open reading frame of 432 nucleotides that predicted a polypeptide of 144 amino acid residues with a molecular weight of 16,021. Putative ribosomal binding sites and -10 and -35 sequences were located at the 5' end of the gene. The size of the polypeptide was confirmed through minicell analysis of the expression products of plasmids containing the sequence. The use of the gene as a molecular probe revealed its specificity toward strains harboring genes coding for related enzymes. This probe is therefore useful for epidemiological studies.

Appearance of amikacin and tobramycin resistance due to 4'-aminoglycoside nucleotidyltransferase [ANT(4')-II] in gram-negative pathogens

Following the use of amikacin as the principal aminoglycoside at a Denver hospital, amikacin resistance appeared first in Pseudomonas aeruginosa and then in Escherichia coli, Klebsiella pneumoniae, and other enteric organisms from debilitated and compromised patients who had spent time in intensive care units and who had been treated with multiple antibiotics, usually including amikacin. In a P. aeruginosa isolate, resistance to amikacin and tobramycin was transferable by the IncP-2 plasmid pMG77, while in E. coli and K. pneumoniae resistance was carried by the transmissible plasmids pMG220, pMG221, and pMG222 belonging to the IncM group. Isolates and transconjugants produced an enzyme with adenyltransferase activity with substrates having a 4'-hydroxyl group, such as amikacin, kanamycin, neomycin, Sch 21768, isepamicin (Sch 21420), or tobramycin, but not with aminoglycosides lacking this target, such as dibekacin, netilmicin, sisomicin, or gentamicin C components. Genes encoding the 4'-aminoglycoside nucleotidyltransferase [ANT(4')] activity were cloned from pMG77, pMG221, and pMG222. A DNA probe prepared from the ANT(4') found in P. aeruginosa hybridized with the ANT(4') determinant found in E. coli. A probe for the ANT(4') from Staphylococcal spp., which differs in its modification of substrates, like dibekacin, that have a 4"- but not a 4'-hydroxyl group, failed to hybridize with the gram-negative ANT(4') determinant, which consequently has been termed ANT(4')-II.

Dissemination of amikacin resistance gene aphA6 in Acinetobacter spp

The distribution of the aphA6 gene, encoding a 3'-aminoglycoside phosphotransferase type VI, was studied by dot blot hybridization with 115 amikacin-resistant Acinetobacter strains from various geographical areas. Nucleotide sequences related to aphA6 were found in 109 strains belonging to seven species. As inferred from results of Southern hybridization, dissemination of amikacin resistance in Acinetobacter spp. is due to a gene rather than a strain or plasmid epidemic.