Genetic structure associated with blaOXA-18, encoding a clavulanic acid-inhibited extended-spectrum oxacillinase

Molecular and Functional Characterization of a Novel Plasmid-Borne bla NDM-Like Gene, bla AFM-1, in a Clinical Strain of Aeromonas hydrophila

Purpose

An increasing frequency of antibiotic resistance has been observed in both clinical and environmental Aeromonas hydrophila isolates in recent years. However, there are still very few in-depth studies regarding the role of plasmids in the antibiotic resistance of A. hydrophila. Hence, we investigated the molecular and functional characterization of a multidrug-resistant plasmid encoding an NDM-like metallo-β-lactamase, AFM-1, in the clinical A. hydrophila isolate SS332.

Methods

The minimum inhibitory concentrations (MICs) of 24 antibiotics against A. hydrophila SS332 were measured by the agar dilution method. The genome of A. hydrophila SS332 was sequenced with PacBio and Illumina platforms. Six plasmid-borne antimicrobial resistance genes were chosen for cloning, including bla_AFM-1, bla_OXA-1, msr(E), mph(E), aac(6ʹ)-Ib10, and aph(3ʹ)-Ia. Phylogenetic analysis, amino acid sequence alignment, and comparative genomic analysis were performed to elucidate the active site requirements and genetic context of the bla_AFM-1 gene.

Results

A. hydrophila SS332 showed high levels of resistance to 15 antibiotics, especially those with MIC levels at or above 1024 μg/mL, including ampicillin, cefazolin, ceftriaxone, aztreonam, spectinomycin, and roxithromycin. Six plasmid-borne resistance genes from A. hydrophila were verified to be functional in E. coli DH5α. AFM-1 shared 86% amino acid identity with NDM-1 and showed resistance to ampicillin, cefazolin, cefoxitin, and ceftazidime. In addition, the bla_AFM-1 gene was associated with three different novel ISCR19-like elements, designated ISCR19-1, ISCR19-2 and ∆ISCR19-3, which may be involved in the acquisition and mobilization of the bla_AFM-1 gene.

Conclusion

Our investigation showed that plasmid-borne resistance genes can contribute to antibiotic resistance in A. hydrophila SS332. A novel bla_NDM-like gene, bla_AFM-1, was verified to be functional and associated with novel ISCR19-like elements. This fact indicated the risk of spread of bla_AFM-1 genes and ISCR19-like elements.

OXA β-lactamases

The OXA β-lactamases were among the earliest β-lactamases detected; however, these molecular class D β-lactamases were originally relatively rare and always plasmid mediated. They had a substrate profile limited to the penicillins, but some became able to confer resistance to cephalosporins. From the 1980s onwards, isolates of Acinetobacter baumannii that were resistant to the carbapenems emerged, manifested by plasmid-encoded β-lactamases (OXA-23, OXA-40, and OXA-58) categorized as OXA enzymes because of their sequence similarity to earlier OXA β-lactamases. It was soon found that every A. baumannii strain possessed a chromosomally encoded OXA β-lactamase (OXA-51-like), some of which could confer resistance to carbapenems when the genetic environment around the gene promoted its expression. Similarly, Acinetobacter species closely related to A. baumannii also possessed their own chromosomally encoded OXA β-lactamases; some could be transferred to A. baumannii, and they formed the basis of transferable carbapenem resistance in this species. In some cases, the carbapenem-resistant OXA β-lactamases (OXA-48) have migrated into the Enterobacteriaceae and are becoming a significant cause of carbapenem resistance. The emergence of OXA enzymes that can confer resistance to carbapenems, particularly in A. baumannii, has transformed these β-lactamases from a minor hindrance into a major problem set to demote the clinical efficacy of the carbapenems.

Acquired Class D β-Lactamases

The Class D β-lactamases have emerged as a prominent resistance mechanism against β-lactam antibiotics that previously had efficacy against infections caused by pathogenic bacteria, especially by Acinetobacter baumannii and the Enterobacteriaceae. The phenotypic and structural characteristics of these enzymes correlate to activities that are classified either as a narrow spectrum, an extended spectrum, or a carbapenemase spectrum. We focus on Class D β-lactamases that are carried on plasmids and, thus, present particular clinical concern. Following a historical perspective, the susceptibility and kinetics patterns of the important plasmid-encoded Class D β-lactamases and the mechanisms for mobilization of the chromosomal Class D β-lactamases are discussed.

New Delhi metallo-β-lactamase-producing Acinetobacter baumannii: a novel paradigm for spreading antibiotic resistance genes

The impact of carbapenemase production among clinically significant Gram-negative rods is becoming a major medical issue. To date, Acinetobacter baumannii has been considered as a final recipient of carbapenemase genes (imipenemase, Verona metallo-β-lactamase, Guiana extended-spectrum β-lactamase and Klebsiella pneumonia carbapenemase types) from Enterobacteriaceae and Pseudomonas aeruginosa. However, recent findings regarding the spread of the blaNDM carbapenemase genes revealed that A. baumannii likely acts as a source of emerging antibiotic resistance genes. The analysis of genetic structure surrounding the blaNDM-1 gene revealed that the genetic structure (Tn125) responsible for its dissemination most probably originates from Acinetobacter. Moreover, analysis of the blaNDM-1 gene itself demonstrated that it might be constructed in Acinetobacter through a recombination event with another resistance gene found in A. baumannii (aphA6). This novel paradigm highlights a novel and unexpected role played by A. baumannii.

KPC-2-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan

OBJECTIVES

Two plasmids carrying bla(KPC-2) isolated from carbapenem-resistant Escherichia coli (CR-EC) and carbapenem-resistant Klebsiella pneumoniae (CR-KP), respectively, were completely sequenced. The CR-KP strain was selected from an outbreak in 2012, and the CR-EC strain was the first blaKPC-2-carrying E. coli identified in the same carbapenem resistance monitoring programme in Taiwan.

METHODS

Antimicrobial susceptibility tests, multilocus sequence typing (MLST) and the conjugal transfer of plasmids were performed. Complete sequencing of the plasmids was performed using a shotgun approach.

RESULTS

The CR-EC and CR-KP strains in this study were determined to be ST410 and ST11, respectively, by MLST. From CR-EC, we identified a 145 kb conjugative plasmid that carries bla(KPC-2), bla(CMY-2), bla(CTX-M-3) and bla(TEM-1). The plasmid is a chimera composed of three regions related to IncI, IncN and RepFIC replicons. From CR-KP, we identified an 86.5 kb plasmid, pKPC-LK30, which carries bla(KPC-2) and bla(SHV-11). The plasmid is very similar to two bla(KPC-2)-carrying IncFII(K) plasmids, but lacks one of the replication origins and cannot conjugate.

CONCLUSIONS

The differences in cross-species transferability of the two plasmids can be explained by genetic differences between their backbones and could have resulted in the confined bla(KPC-2)-carrying CR-KP outbreak in Taiwan. Plasmid pKPC-LKEc is the first bla(KPC-2)-carrying plasmid identified from CR-EC in Taiwan. With relatively high transferability it should be closely monitored.

FIM-1, a new acquired metallo-β-lactamase from a Pseudomonas aeruginosa clinical isolate from Italy

Acquired metallo-β-lactamases (MBLs) are resistance determinants of increasing clinical importance in Gram-negative bacterial pathogens, which confer a broad-spectrum β-lactam resistance, including carbapenems. Several such enzymes have been described since the 1990s. In the present study, a novel acquired MBL, named FIM-1, was identified and characterized. The bla(FIM-1) gene was cloned from a multidrug-resistant Pseudomonas aeruginosa clinical isolate (FI-14/157) cultured from a patient with a vascular graft infection in Florence, Italy. The isolate belonged in the sequence type 235 epidemic clonal lineage. The FIM-1 enzyme is a member of subclass B1 and, among acquired MBLs, exhibited the highest similarity (ca. 40% amino acid identity) with NDM-type enzymes. In P. aeruginosa FI-14/157, the bla(FIM-1) gene was apparently inserted into the chromosome and associated with ISCR19-like elements that were likely involved in the capture and mobilization of this MBL gene. Transfer experiments of the bla(FIM-1) gene to an Escherichia coli strain or another P. aeruginosa strain by conjugation or electrotransformation were not successful. The FIM-1 protein was produced in E. coli and purified by two chromatography steps. Analysis of the kinetic parameters, carried out with the purified enzyme, revealed that FIM-1 has a broad substrate specificity, with a preference for penicillins (except the 6α-methoxy derivative temocillin) and carbapenems. Aztreonam was not hydrolyzed. Detection of this novel type of acquired MBL in a P. aeruginosa clinical isolate underscores the increasing diversity of such enzymes that can be encountered in the clinical setting.

[Detection of extended spectrum β-lactamase OXA-141 in Pseudomonas aeruginosa strains isolated from patients with cystic fibrosis]

INTRODUCTION

The aims of this research were to study the presence of extended spectrum β-lactamases (ESBL) to investigate the location of the genes encoding these enzymes, and determine the clonal relationship of strains of ceftazidime-resistant Pseudomonas aeruginosa isolated from Mexican patients with cystic fibrosis.

METHODS

We determined the resistance profile to 11 antibiotics (CLSI) and phenotypic ESBL detection following a disk diffusion method adapted for P. aeruginosa. Characterization of ESBL genes and integrons was performed by polymerase chain reaction (PCR) and DNA sequencing, while analysis of the clonal relationship was performed by pulsed field gel electrophoresis (PFGE).

RESULTS

Of the 148 strains studied, 22 were resistant to ceftazidime, and analysis by PCR and sequencing revealed the presence of the gene bla(OXA-141) in 7 strains, 6 of which were resistant and one, susceptible to ceftazidime. In addition, bla(GES) was detected in 11 strains. intI2 and intI3 genes were not detected by PCR, but in the 6 ceftazidime-resistant strains, the bla(OXA-141) gene was determined in a class 1 integron. Analysis of the clonal relationship of isolates showed that the majority of patients were infected during the study period with P. aeruginosa strains that exhibit different patterns, especially in individuals without a familial relationship.

CONCLUSIONS

This report demonstrates the existence of the bla(OXA-141) gene associated with a class 1 integron in several strains of P. aeruginosa, as well as bla(GES) genes, and their location and variants are being studied by our research group. This, combined with the diversity of strains able to infect several susceptible individuals, suggests the risk of spread of P. aeruginosa-strain ESBL producers among Mexican populations with cystic fibrosis.

Tn125-related acquisition of blaNDM-like genes in Acinetobacter baumannii

A multidrug-resistant Acinetobacter baumannii isolate recovered from a patient hospitalized in Switzerland after a transfer from Serbia produced the NDM-1 carbapenemase. The bla(NDM-1) gene was part of a chromosomally located Tn125 composite transposon bracketed by two copies of the same insertion sequence, ISAba125. This transposon was also associated with the acquisition and expression of the bla(NDM-2) gene in an A. baumannii isolate in Germany. Tn125 appears to be the main vehicle for dissemination of bla(NDM) genes in that species.

Molecular characterization of blaNDM-1 in an Acinetobacter baumannii strain isolated in Germany in 2007

OBJECTIVES

To investigate the genetic environment of the metallo-β-lactamase gene bla(NDM-1) in an Acinetobacter baumannii isolated in 2007 in a German hospital.

METHODS

Antimicrobial susceptibility testing was performed and resistance genes were characterized by PCR amplification and sequencing. Transferability of β-lactam resistance was tested by broth mating assays and transformation of plasmids. The genetic background of bla(NDM-1) was analysed by primer walking. Typing of the A. baumannii strain was performed by repetitive extragenic palindromic sequence-based PCR (rep-PCR) using the DiversiLab system.

RESULTS

The multidrug-resistant A. baumannii isolate harboured β-lactamase genes bla(NDM-1) and intrinsic bla(OXA-64), but without the insertion sequence ISAba1 often located upstream. Transfer of carbapenem resistance by conjugation and transformation failed. Hybridization of isolated plasmid DNA with bla(NDM) probes was not successful. Shotgun cloning of whole genomic DNA and sequence analyses revealed that bla(NDM-1) was located between two insertion elements of ISAba125. Furthermore, this bla(NDM-1)-containing transposon structure was integrated into a chromosomal gene encoding a putative A. baumannii major facilitator superfamily (MFS) metabolite/H+ symporter.

CONCLUSIONS

The metallo-β-lactamase gene bla(NDM-1) in this A. baumannii strain was integrated in the chromosome on a new transposon structure composed of two copies of insertion sequence ISAba125. The variability of the genetic environment of bla(NDM-1) likely facilitates the rapid dissemination of this gene within many Gram-negative bacterial species.

rmtD2, a new allele of a 16S rRNA methylase gene, has been present in Enterobacteriaceae isolates from Argentina for more than a decade

The first allele of a 16S rRNA methyltransferase gene, rmtD2, conferring very high resistance to all clinically available aminoglycosides, was detected in 7/1,064 enterobacteria collected in 2007. rmtD2 was located on a conjugative plasmid in a Tn2670-like element inside a structure similar to that of rmtD1 but probably having an independent assembly. rmtD2 has been found since 1996 to 1998 mainly in Enterobacter and Citrobacter isolates, suggesting a possible reservoir in these genera. This presumption deserves monitoring by continuous surveillance.

Acquisition of multidrug resistance transposon Tn6061 and IS6100-mediated large chromosomal inversions in Pseudomonas aeruginosa clinical isolates

Pseudomonas aeruginosa is a major human opportunistic pathogen, especially for patients in intensive care units or with cystic fibrosis. Multidrug resistance is a common feature of this species. In a previous study we detected the ant(4')-IIb gene in six multiresistant clinical isolates of P. aeruginosa, and determination of the environment of the gene led to characterization of Tn6061. This 26 586 bp element, a member of the Tn3 family of transposons, carried 10 genes conferring resistance to six drug classes. The ant(4')-IIb sequence was flanked by directly repeated copies of ISCR6 in all but one of the strains studied, consistent with ISCR6-mediated gene acquisition. Tn6061 was chromosomally located in six strains and plasmid-borne in the remaining isolate, suggesting horizontal acquisition. Duplication-insertion of IS6100, that ended Tn6061, was responsible for large chromosomal inversions. Acquisition of Tn6061 and chromosomal inversions are further examples of intricate mechanisms that contribute to the genome plasticity of P. aeruginosa.

Diversity, epidemiology, and genetics of class D beta-lactamases

Class D beta-lactamase-mediated resistance to beta-lactams has been increasingly reported during the last decade. Those enzymes also known as oxacillinases or OXAs are widely distributed among Gram negatives. Genes encoding class D beta-lactamases are known to be intrinsic in many Gram-negative rods, including Acinetobacter baumannii and Pseudomonas aeruginosa, but play a minor role in natural resistance phenotypes. The OXAs (ca. 150 variants reported so far) are characterized by an important genetic diversity and a great heterogeneity in terms of beta-lactam hydrolysis spectrum. The acquired OXAs possess either a narrow spectrum or an expanded spectrum of hydrolysis, including carbapenems in several instances. Acquired class D beta-lactamase genes are mostly associated to class 1 integron or to insertion sequences.