OXA-type carbapenemases

The origin of Acinetobacter baumannii TYTH-1: a comparative genomics study

There have been increasing reports of bla(OXA-23)-carrying strains of carbapenem-resistant Acinetobacter baumannii (CRAB), which has become a significant public health concern in Taiwan. To determine the origin of these CRAB strains, the prevalence of CRAB and bla(OXA-23)-carrying CRAB in a regional hospital was analysed retrospectively. The genome of A. baumannii TYTH-1 was completely sequenced and annotated. Multiple comparative genomics studies, including phylogenetic analysis, functional comparison via the Clusters of Orthologous Groups (COGs) database, and determination of variance in GC profiles in the whole genome and gene arrangements in resistance islands, were performed using 11 completely sequenced A. baumannii genomes. bla(OXA-23)-carrying CRAB isolates became dominant clones in 2007. A comparative genomics analysis revealed a common strain lineage between Taiwanese strains (TYTH-1 and TCDC-AB0715) and Chinese strains (MDR-TJ and MDR-ZJ06). Phylogenetic studies and GC profiles showed that the genome of TYTH-1 was closest to MDR-ZJ06. However, the resistance island of TYTH-1 (RI(TYTH-1)) was nearly identical to that of RI(MDT-TJ). The functional category for COGs was similar in the tested genomes. The results reveal that dissemination of bla(OXA-23)-carrying CRAB in Taiwan may have been mediated by the transfer of people between Taiwan and China during 2007. The global spread of CRAB is now a worldwide public health problem. In Taiwan, the government needs to focus more attention on the importance of identifying and tracing resistant pathogens and issuing notifications of CRAB infections.

Carbapenemases in Klebsiella pneumoniae and other Enterobacteriaceae: an evolving crisis of global dimensions

SUMMARY

The spread of Enterobacteriaceae, primarily Klebsiella pneumoniae, producing KPC, VIM, IMP, and NDM carbapenemases, is causing an unprecedented public health crisis. Carbapenemase-producing enterobacteria (CPE) infect mainly hospitalized patients but also have been spreading in long-term care facilities. Given their multidrug resistance, therapeutic options are limited and, as discussed here, should be reevaluated and optimized. Based on susceptibility data, colistin and tigecycline are commonly used to treat CPE infections. Nevertheless, a review of the literature revealed high failure rates in cases of monotherapy with these drugs, whilst monotherapy with either a carbapenem or an aminoglycoside appeared to be more effective. Combination therapies not including carbapenems were comparable to aminoglycoside and carbapenem monotherapies. Higher success rates have been achieved with carbapenem-containing combinations. Pharmacodynamic simulations and experimental infections indicate that modification of the current patterns of carbapenem use against CPE warrants further attention. Epidemiological data, though fragmentary in many countries, indicate CPE foci and transmission routes, to some extent, whilst also underlining the lack of international collaborative systems that could react promptly and effectively. Fortunately, there are sound studies showing successful containment of CPE by bundles of measures, among which the most important are active surveillance cultures, separation of carriers, and assignment of dedicated nursing staff.

Molecular and epidemiological characterization of carbapenem-resistant Acinetobacter baumannii in non-tertiary Korean hospitals

PURPOSE

The increasing prevalence and global spread of carbapenem-resistant Acinetobacter baumannii (A. baumannii) has become a serious problem. The aim of this study was to investigate molecular and epidemiological characteristics of carbapenem-resistant A. baumannii isolates collected from Korean non-tertiary hospitals.

MATERIALS AND METHODS

Thirty six non-duplicated carbapenem-resistant A. baumannii isolates were collected from 17 non-tertiary hospitals in Korea between 2004 and 2006. Isolates were typed by multilocus sequence typing and repetitive-sequence-based PCR (rep-PCR). Detection of genes encoding OXA carbapenemase and their relationship with ISAba1 was performed by PCR.

RESULTS

Two clones were prevalent among 36 isolates: ST69 (17 isolates, 47.2%) and ST92 (19 isolates, 52.8%). Rep-PCR patterns were diverse and revealed that all isolates were clustered into eight band patterns. The ISAba1-activated blaOXA-23-like and ISAba1-activated blaOXA-51-like genes were prevalent among the carbapenem- resistant A. baumannii isolates.

CONCLUSION

The class D β-lactamase genes of A. baumannii were distributed nationwide in non-tertiary Korean hospitals.

Molecular characterization of oxacillinases and genotyping of invasive Acinetobacter baumannii isolates using repetitive extragenic palindromic sequence-based polymerase chain reaction in Ankara between 2004 and 2010

BACKGROUND

Multidrug-resistant Acinetobacter baumannii (MDRAB) is an increasing problem worldwide. We aimed to determine the antibiotic susceptibility, diversity of oxacillinases, and molecular types of MDRAB.

METHODS

A total of 100 non-duplicate A. baumannii blood culture isolates were evaluated. Antimicrobial susceptibilities of the isolates were determined according to the standard Clinical and Laboratory Standards Institute (CLSI) broth microdilution method. Colistin, doripenem, and tigecycline susceptibilities were analyzed by E-test. The presence of bla(OXA-23-like), bla(OXA-24-like), bla(OXA-51-like), and bla(OXA-58-like) genes was investigated by multiplex polymerase chain reaction (PCR). Typing of A. baumannii isolates was performed using repetitive extragenic palindromic sequence-based PCR (rep-PCR; DiversiLab).

RESULTS

Most isolates were susceptible to colistin (98% susceptible) and tigecycline (94% susceptible), whereas fewer isolates were susceptible to imipenem, meropenem, and doripenem (17%, 17%, and 18% susceptible, respectively). Carbapenem resistance was associated with the presence of bla(OXA-23-like) (31% of isolates) and bla(OXA-58-like) (23% of isolates) genes. The occurrence of isolates carrying bla(OXA-58-like) genes increased between y 2004 and 2009, but decreased in 2010. In contrast, isolates with bla(OXA-23-like) genes increased during the 2008-2010 period. Out of 100 isolates, 62 were categorized into 13 major rep-PCR patterns, with the highest prevalence in pattern 1 (10 isolates), followed by patterns 2 and 3 (9 isolates each).

CONCLUSIONS

Carbapenem-resistant invasive A. baumannii isolates carrying the bla(OXA-23-like) gene became more prevalent and replaced isolates carrying the bla(OXA-58-like) carbapenemase gene through the 7 y. Rep-PCR genotyping of these strains confirmed that ongoing MDRAB resulted from a long-term persistence and mixture of several clusters.

OXA-162, a novel variant of OXA-48 displays extended hydrolytic activity towards imipenem, meropenem and doripenem

CONTEXT

Isolation and characterization of OXA-162, a novel variant of OXA-48.

OBJECTIVES

Klebsiella pneumoniae isolate with decreased susceptibility to carbapenems was recovered from a Turkish patient. This study aimed at characterizing the carbapenem resistance determinants of this isolate.

MATERIALS AND METHODS

Antibiotic susceptibility tests, analytic isoelectric focusing (IEF), cloning and sequencing were performed. Cloned β-lactamase was purified by means of preparative gel electrophoresis and the kinetic constants were determined under initial rate conditions.

RESULTS

The identified bla(OXA-162) gene was located on a ca. 45-kb plasmid carrying a transposon consisted of two IS1999-2 elements. OXA-162 differed from OXA-48 by a single amino acid substitution (Thr213Ala) which increased the catalytic efficiency (k(cat)/K(M)) of OXA-162 towards imipenem and meropenem. Also this substitution caused a gain of hydrolysis ability towards doripenem. Analysis of OXA-162 model implied that the amino acid change might generate an extension in the opening of the substrate entry site and might cause extended hydrolytic activity towards imipenem, meropenem and doripenem.

DISCUSSION AND CONCLUSION

OXA-162, a derivative of OXA-48 has enhanced catalytic properties.

Genetic characteristics of one highly multi-drug-resistant strain of Klebsiella ozaenae

One highly multi-drug-resistant, mucus-producing and foul-smelling strain of Klebsiella ozaenae was isolated from a patient in the ICU of a Chinese tertiary hospital. MICs of several clinical antimicrobials against the strain were obtained using the Vitek-2 Compact System with AST-GN13 cards and resistance genes were evaluated by PCR and gene sequencing. The strain was resistant to most of the β-lactams and quinolones tested and carried several antibiotic resistance genes, including bla(KPC-2), bla(TEM-98), bla(CTX-M-3), bla(SHV-26) and qnrS. To our knowledge, this is the first report of β-lactam and quinolone resistance genes co-existing in a K. ozaenae strain in China.

Purification and characterization of OXA-23 from Acinetobacter baumannii

Although the existence of bla(OXA-23) is reported in various parts of the world, the product of bla(OXA-23) gene, OXA-23, has not been purified and its kinetic properties are not known. In this study, OXA-23 of Acinetobacter baumannii isolated from Kocaeli University intensive care unit was characterized after purification using recombinant methods. Preliminary results showed that conventional protein purification methods were not effective for purification of OXA-23. Therefore, OXA-23 was fused to maltose-binding protein of Escherichia coli, the fused protein was expressed and purified to homogeneity. Kinetic properties of the pure protein were then studied with substrates e.g., imipenem, meropenem, cefepime, ceftazidime, ampicilline, piperacillin, penicillin G, and nitrocefin. Also clavulanic acid, tazobactam, and sulbactam concentrations that inhibit 50% of OXA-23 enzyme activity were calculated. Modelling of OXA-23 revealed its ionic surface structure, conformation in the fused form and its topology allowing us to make predictions for OXA-23 substrate specificity.

The threat of carbapenem-resistant Enterobacteriaceae in Lebanon: an update on the regional and local epidemiology

Bacterial resistance to antimicrobial agents is increasing. Complex resistant mechanisms have resulted in a wide spectrum of species and strains with multidrug-resistant patterns. In addition to the production of extended-spectrum-β-lactamases (ESBLs), Gram-negative rods have acquired the capacity to hydrolyze carbapenem antibiotics by means of carbapenemases. The enzyme that has gained the most publicity recently is the New Delhi metallo-β-lactamase (NDM-1). This enzyme and others are now spreading from their homeland on the Indian subcontinent to other continents, primarily via medical tourists. This spread contributes to be a global threat in an era when no potent antibiotics are expected to be developed. Patients coming from countries where antimicrobial use is not restricted, such as Iraq, may harbor similar organisms. Reports from the Middle East and Arabian countries describing the occurrence of carbapenem-resistant Enterobacteriaceae are rare. In this communication, an update on the epidemiology, prevalence and mechanisms of carbapenem-resistant Enterobacteriaceae in Lebanon and the surrounding region will be addressed in addition to the detection methods and required infection control practices.

Site-saturation mutagenesis of position V117 in OXA-1 β-lactamase: effect of side chain polarity on enzyme carboxylation and substrate turnover

Class D β-lactamases pose an emerging threat to the efficacy of β-lactam therapy for bacterial infections. Class D enzymes differ mechanistically from other β-lactamases by the presence of an active-site N-carboxylated lysine that serves as a general base to activate the serine nucleophile for attack. We have used site-saturation mutagenesis at position V117 in the class D β-lactamase OXA-1 to investigate how alterations in the environment around N-carboxylated K70 affect the ability of that modified residue to carry out its normal function. Minimum inhibitory concentration analysis of the 20 position 117 variants demonstrates a clear pattern of charge and polarity effects on the level of ampicillin resistance imparted on Escherichia coli (E. coli). Substitutions that introduce a negative charge (D, E) at position 117 reduce resistance to near background levels, while the positively charged K and R residues maintain the highest resistance levels of all mutants. Treatment of the acidic variants with the fluorescent penicillin BOCILLIN FL followed by SDS-PAGE shows that they are active for acylation by substrate but deacylation-deficient. We used a novel fluorescence anisotropy assay to show that the specific charge and hydrogen-bonding potential of the residue at position 117 affect CO(2) binding to K70, which in turn correlates to deacylation activity. These conclusions are discussed in light of the mechanisms proposed for both class D β-lactamases and BlaR β-lactam sensor proteins and suggest a reason for the preponderance of asparagine at the V117-homologous position in the sensors.

Expression of OXA-type and SFO-1 β-lactamases induces changes in peptidoglycan composition and affects bacterial fitness

β-Lactamases and penicillin-binding proteins (PBPs) have evolved from a common ancestor. β-Lactamases are enzymes that degrade β-lactam antibiotics, whereas PBPs are involved in the synthesis and processing of peptidoglycan, which forms an elastic network in the bacterial cell wall. This study analyzed the interaction between β-lactamases and peptidoglycan and the impact on fitness and biofilm production. A representative set of all classes of β-lactamases was cloned in the expression vector pBGS18 under the control of the CTX-M promoter and expressed in Escherichia coli MG1655. The peptidoglycan composition of all clones was evaluated, and quantitative changes were found in E. coli strains expressing OXA-24, OXA-10-like, and SFO-1 (with its upstream regulator AmpR) β-lactamases; the level of cross-linked muropeptides decreased, and their average length increased. These changes were associated with a statistically significant fitness cost, which was demonstrated in both in vitro and in vivo experiments. The observed changes in peptidoglycan may be explained by the presence of residual DD-endopeptidase activity in these β-lactamases, which may result in hydrolysis of the peptide cross bridge. The biological cost associated with these changes provides important data regarding the interaction between β-lactamases and the metabolism of peptidoglycan and may provide an explanation for the epidemiology of these β-lactamases in Enterobacteriaceae.

Epidemiological expansion, structural studies, and clinical challenges of new β-lactamases from gram-negative bacteria

β-Lactamase evolution presents to the infectious disease community a major challenge in the treatment of infections caused by multidrug-resistant gram-negative bacteria. Because over 1,000 of these naturally occurring β-lactamases exist, attempts to correlate structure and function have become daunting. Although new enzymes in the extended-spectrum β-lactamase (ESBL) families are frequently identified, the older CTX-M-14 and CTX-M-15 enzymes have become the most prevalent ESBLs in global surveillance. Carbapenemases with either serine-based or zinc-facilitated hydrolysis mechanisms are posing some of the most critical problems. Most geographical regions now report KPC serine carbapenemases and the metallo-β-lactamases VIM, IMP, and NDM-1, even though NDM-1 was only recently identified. The rapid emergence of these newer enzymes, with multiple β-lactamases appearing in a single organism, makes the design of new β-lactamase inactivators or β-lactamase-stable β-lactams all the more difficult. Combination therapy will likely be required to counteract the continuing evolution of these insidious enzymes in multidrug-resistant pathogens.

OXA beta-lactamase-mediated carbapenem resistance in Acinetobacter baumannii

OBJECTIVES

Acinetobacter baumannii is a significant pathogen in health care settings. In recent years, an increase in carbapenem resistance among A. baumannii due to Ambler class B metallo-beta-lactamases or class D OXA carbapenamases has been reported. In this study we detected the presence of OXA carbapenamases and coproduction of metallo-beta-lactamases (blaVIM and blaIMP ) by phenotypic and genotypic methods in carbapenem resistant clinical isolates of Acinetobacter baumannii.

MATERIALS AND METHODS

A total of 116 consecutive, non-duplicate carbapenem resistant A. baumannii isolated from various clinical specimens were included in the study. The modified Hodge test and inhibitor potentiated disk diffusion tests were done for the screening of carbapenamase and metallo-beta-lactamase production, respectively. Polymerase chain reaction (PCR) was performed for the detection of OXA (blaOXA 23 like, blaOXA 24 like, blaOXA-51 like and blaOXA-58 like genes) and metallo-beta-lactamases (blaVIM and blaIMP ) genes. Gene sequencing was performed for representative isolates.

RESULTS

Among 116 A. baumannii, OXA genes were detected in 106 isolates. BlaOXA 51 like (n = 99) and blaOXA -23 like (n = 95) were the most common and they coexisted in 89 isolates. blaOXA-24 like gene was detected in two isolates of which one also carried blaOXA-51 like and blaOXA-58 like genes. The modified Hodge test was positive in 113 isolates. The metallo-beta-lactamase screening test was positive in 92 isolates. blavim was detected in 54 isolates of which 1 also carried the blaIMP gene.

CONCLUSIONS

blaOXA-23 like and bla OXA 51 like genes are the most common types of OXA carbapenamases while the blaVIM type is the most common type of metallo-beta-lactamase contributing to carbapenem resistance in clinical isolates of A. baumannii. The coproduction of OXA and metallo-beta-lactamases is not an uncommon phenomenon in A. baumannii.

Outbreak of imipenem-resistant Acinetobacter calcoaceticus-Acinetobacter baumannii complex harboring different carbapenemase gene-associated genetic structures in an intensive care unit

BACKGROUND AND PURPOSE

To investigate the clinical and molecular epidemiology of the imipenem-resistant Acinetobacter calcoaceticus-Acinetobacter baumannii (IRAcb) complex during an outbreak in an intensive care unit (ICU).

METHODS

Forty-six clinical and 11 environmental isolates of the IRAcb complex were collected from the ICU of Taipei Veterans General Hospital, Taiwan between December 2003 and March 2004. These isolates were genotyped using pulsed-field gel electrophoresis (PFGE). Carbapenemase genes and their associated genetic structures were analyzed using PCR. Clinical data obtained from the patients were also reviewed and analyzed.

RESULTS

The isolates were identified at the genomic species level as A. baumannii (42 clinical and five environmental isolates) and Acinetobacter genomic species 13TU (four clinical and six environmental isolates). Both species were comprised of two pulsotypes, but those of A. baumannii were closely related (83% similar). IS1008-ΔISAba3-bla(OXA-58-like) and ISAba1-bla(OXA-51-like) were identified in 22 and 21 clinical isolates of A. baumannii, respectively (one isolate contained both). The ISAba3-bracketed bla(OXA-58-like) gene was detected in all isolates of Acinetobacter genomic species 13TU. Patient transfers between different sections of the ICU were important factors that contributed to the spread of the two pulsotypes of A. baumannii. However, among the A. baumannii isolates identified, only those carrying IS1008-ΔISAba3-bla(OXA-58-like) could be found in the environment, indicating an additional route of transmission. The prior use of carbapenem or cefepime was associated with the subsequent infection with A. baumannii carrying the ISAba1-bla(OXA-51-like) gene, while prior piperacillin/tazobactam use was associated with the subsequent infection with A. baumannii carrying the IS1008-ΔISAba3-bla(OXA-58-like) gene.

CONCLUSION

A. baumannii isolates carrying different carbapenemase genes and their associated genetic structures might be transmitted or selected in different ways.

Clonal spread of multidrug-resistant Acinetobacter baumannii in eastern Taiwan

BACKGROUND AND PURPOSE

This study was conducted to investigate the molecular epidemiology and antimicrobial susceptibility of multidrug-resistant (MDR) Acinetobacter baumannii to three types of antibiotics.

METHODS

One hundred and thirty-four specimens of MDR A baumannii were collected from three branches (Taipei, Dalin, and Hualien branches) of Buddhist Tzu Chi Hospital, which are located in northern, southern, and eastern Taiwan, during 2007. Genotyping was performed by pulsed-field gel electrophoresis. Antibiotic susceptibilities to colistin, rifampicin, and tigecycline were determined. The synergistic effects of rifampin and colistin were also evaluated.

RESULTS

Antibiotic susceptibility testing showed that 10.4%, 47.8% and 45.5% of the MDR A baumannii isolates are resistant to colistin, rifampicin, and tigecycline, respectively. A majority of the rifampicin-resistant isolates (62.7%) were found in the Haulien branch, whereas 62.2% of tigecycline-resistant isolates were found in the Taipei branch. The combination of colistin and rifampicin had a synergistic effect on all of the isolates. Genotyping by pulsed-field gel electrophoresis identified 17, 23, and 11 pulsotypes in the Taipei, Dalin, and Haulien branches, respectively. Furthermore, 74.5% of isolates in the Haulien branch were identified as one of three pulsotypes. Among 37 rifampicin-resistant and 22 tigecycline-resistant MDR A baumannii isolates found in the Haulien branch, 51.3% (19/37) and 50% (11/22) of the isolates belonged to the same clone, respectively.

CONCLUSION

This study confirms the high prevalence of resistance to rifampicin and tigecycline in MDR A baumannii in the three hospitals that were studied, and the high proportion of identical strains that exist in eastern Taiwan.

Tn2008 is a major vehicle carrying bla(OXA-23) in Acinetobacter baumannii from China

bla(OXA-23) and bla(OXA-66) were detected in 49 Acinetobacter baumannii isolates. These isolates were assigned to 7 subtypes by enterobacterial repetitive intergenic consensus polymerase chain reaction and 7 representative isolates were of ST92 or ST75. In most cases, the ISAba1-bla(OXA-23)-ATPaseΔ structure was identical to Tn2008. The 16-bp sequence at the left end of Tn2008 resembled the inverted repeat of ISAba1, suggesting that ISAba1 might have utilized an alternative boundary to mobilize bla(OXA-23).

The Class D beta-lactamase family: residues governing the maintenance and diversity of function

Class D β-lactamases, a major source of bacterial resistance to β-lactam antibiotic therapies, represent a distinct subset of the β-lactamase superfamily. They share a serine hydrolase mechanism with Classes A/C vs. Class B. Further understanding of their sequence-structure-function relationships would benefit efforts to design a new generation of antibiotics as well as to predict evolutionary mechanisms in response to such therapies. Here we describe analyses based on our high-resolution multiple sequence alignment and phylogenetic tree of ∼80 Class D β-lactamases that leverage several 3D structures of these enzymes. We observe several sequence clusters on the phylogenetic tree, some that are species specific while others include several species from α-, β- and γ-proteobacteria. Residues characteristic of a specific cluster were identified and shown to be located just outside the active site, possibly modulating the function of the catalytic residues to facilitate reactions with specific types of β-lactams. Most significant was the discovery of a likely disulfide bond in a large group composed of α-, β- and γ-proteobacteria that would contribute to enzyme stability and hence bacterial viability under antibiotic assault. A network of co-evolving residues was identified which suggested the importance of maintaining a surface for binding a highly conserved Phe69.

Hydrolytic mechanism of OXA-58 enzyme, a carbapenem-hydrolyzing class D β-lactamase from Acinetobacter baumannii

Carbapenem-hydrolyzing class D β-lactamases (CHDLs) represent an emerging antibiotic resistance mechanism encountered among the most opportunistic Gram-negative bacterial pathogens. We report here the substrate kinetics and mechanistic characterization of a prominent CHDL, the OXA-58 enzyme, from Acinetobacter baumannii. OXA-58 uses a carbamylated lysine to activate the nucleophilic serine used for β-lactam hydrolysis. The deacylating water molecule approaches the acyl-enzyme species, anchored at this serine (Ser-83), from the α-face. Our data show that OXA-58 retains the catalytic machinery found in class D β-lactamases, of which OXA-10 is representative. Comparison of the homology model of OXA-58 and the recently solved crystal structures of OXA-24 and OXA-48 with the OXA-10 crystal structure suggests that these CHDLs have evolved the ability to hydrolyze imipenem, an important carbapenem in clinical use, by subtle structural changes in the active site. These changes may contribute to tighter binding of imipenem to the active site and removal of steric hindrances from the path of the deacylating water molecule.

Molecular characterisation of multiple drug-resistant Acinetobacter baumannii isolates in southern Taiwan

The purpose of this study was to develop a multiplex polymerase chain reaction (mt-PCR) assay for synchronous detection of carbapenem resistance genes and/or pandrug resistance genes in clinical isolates of multidrug-resistant Acinetobacter baumannii (MDR-AB) and to investigate the association between the genetic make-up and a drug-resistant pattern. In total, 213 MDR-AB isolates were collected. All clinical isolates underwent antimicrobial susceptibility testing and were analysed for the presence of oxacillinase genes (bla(OXA-23), bla(OXA-24), bla(OXA-51)-like and bla(OXA-58)), class A and C β-lactamase genes (bla(TEM-1) and bla(AmpC), respectively), and an integron-associated antibiotic resistance gene (int1) by an in-house-designed mt-PCR assay. Of the 213 isolates, 73.87% harboured both bla(TEM-1) and bla(AmpC) and 83.92% carried at least three oxacillinase genes. Moreover, 64.82% of the isolates were significant in that they had two β-lactamase genes and three oxacillinase genes (P<0.001), indicating the complexity of the genetic make-up of carbapenem-resistant A. baumannii. The bla(OXA-51)-like allele was detected in the majority of these A. baumannii isolates (97.49%), whereas bla(OXA-23) was rarely prevalent in these isolates. In multivariate logistic regression, the presence of bla(OXA-23) and bla(TEM-1) had a statistically significant association with imipenem resistance [bla(OXA-23), P=0.004, odds ratio (OR)=10.52, 95% confidence interval (CI) 2.12-52.17; bla(TEM-1), P=0.005, OR=6.14, 95% CI 1.74-21.62]. These results suggest that detecting bla(OXA-23) and bla(TEM-1) genes could be used to predict imipenem resistance in MDR-AB isolates. A mt-PCR for detecting carbapenem resistance genes and pandrug resistance genes of A. baumannii isolates was developed to provide an assay to quickly screen for potential imipenem-resistant A. baumannii in the clinic.

OXA-198, an acquired carbapenem-hydrolyzing class D beta-lactamase from Pseudomonas aeruginosa

A carbapenem-resistant Pseudomonas aeruginosa strain (PA41437) susceptible to expanded-spectrum cephalosporins was recovered from several consecutive lower-respiratory-tract specimens of a patient who developed a ventilator-associated pneumonia while hospitalized in an intensive care unit. Cloning experiments identified OXA-198, a new class D β-lactamase which was weakly related (less than 45% amino acid identity) to other class D β-lactamases. Expression in Escherichia coli TOP10 and in P. aeruginosa PAO1 led to transformants that were resistant to ticarcillin and showed reduced susceptibility to carbapenems and cefepime. The bla(OXA-198) gene was harbored by a class 1 integron carried by a ca. 46-kb nontypeable plasmid. This study describes a novel class D β-lactamase involved in carbapenem resistance in P. aeruginosa.

Prevalence of OXA-type carbapenemase genes and genetic heterogeneity in clinical isolates of Acinetobacter spp. from Mangalore, India

The prevalence of OXA-type carbapenemase genes, ISAba1 insertion sequence, carbapenem resistance, biofilm forming ability and genetic heterogeneity in clinical isolates of Acinetobacter spp. from hospitals in Mangalore, South India was studied. Based on the presence of the bla(OXA-51) -like gene, the 62 isolates of Acinetobacter spp. were identified as 48 A. baumannii and 14 other Acinetobacter spp. The prevalence of bla(OXA-23) -like, bla(OXA-24) -like and bla(OXA-58) -like genes in A. baumannii was 47.9%, 22.9% and 4.2%, while in other Acinetobacter spp. it was 28.5%, 64.3% and 35.7% respectively. Several A. baumannii isolates (16/48) harbored the insertion sequence ISAba1 in the upstream region of the bla(OXA-23) -like gene. Resistance to meropenem was seen in 39.6% and 14.2% of A. baumannii and other Acinetobacter spp. isolates, respectively. The ability to form biofilm was observed to be higher among A. baumannii in comparison to other Acinetobacter spp. The present study shows that bla(OXA-23) -like genes are more common in A. baumannii,whereas bla(OXA-24) -like genes are common to other Acinetobacter spp. The study revealed genetic heterogeneity among the isolates, indicating multiple sources in the hospitals.

Multidrug resistant acinetobacter

Emergence and spread of Acinetobacter species, resistant to most of the available antimicrobial agents, is an area of great concern. It is now being frequently associated with healthcare associated infections. Literature was searched at PUBMED, Google Scholar, and Cochrane Library, using the terms ‘Acinetobacter Resistance, multidrug resistant (MDR), Antimicrobial Therapy, Outbreak, Colistin, Tigecycline, AmpC enzymes, and carbapenemases in various combinations. The terms such as MDR, Extensively Drug Resistant (XDR), and Pan Drug Resistant (PDR) have been used in published literature with varied definitions, leading to confusion in the correlation of data from various studies. In this review various mechanisms of resistance in the Acinetobacter species have been discussed. The review also probes upon the current therapeutic options, including combination therapies available to treat infections due to resistant Acinetobacter species in adults as well as children. There is an urgent need to enforce infection control measures and antimicrobial stewardship programs to prevent the further spread of these resistant Acinetobacter species and to delay the emergence of increased resistance in the bacteria.

Rapid control of a hospital-wide outbreak caused by extensively drug-resistant OXA-72-producing Acinetobacter baumannii

Extensively drug-resistant Acinetobacter baumannii (XDRAb) emerges as an important pathogen of health care-associated infections and outbreaks worldwide. During January and February 2006, there was a hospital-wide outbreak of XDRAb at a medical center in Taiwan. Without limiting the usage of carbapenems or the closure of any ward, this outbreak was effectively controlled. We investigated the molecular epidemiology and reported the infection control experiences. XDRAb is defined as A baumannii that is resistant to multiple antibiotics but susceptible to tigecycline and polymyxin B. During the outbreak, the clinical and environmental XDRAb isolates were collected and studied by antimicrobial susceptibility testing, pulsed-field gel electrophoresis, and polymerase chain reaction for Verona integron-encoded metallo-beta-lactamases, imipenemases, and oxacillinases (OXA). Our measures to control the outbreak included private room isolation of patients until there were three successive negative cultures, reinforcement of contact precautions, daily environmental cleansing with room-dedicated cleaning tools and sodium hypochlorite, and careful auditing of adherence. During the outbreak, 32 clinical XDRAb isolates came from 13 patients who were hospitalized in four intensive care units and three wards. Most (7 of 13, 53.8%) cases were associated with a surgical intensive care unit. The results from pulsed-field gel electrophoresis study indicated that all isolates were of one genotype. All 32 isolates harbored ISAba1-bla(OxA-51-like) and bla(OxA-72) genes. After this outbreak till August 2010, further incidences of XDRAb were sporadic cases of XDRAb with different clones and did not reach the level of outbreak. To our knowledge, this is the first reported hospital-wide outbreak caused by OXA-72 carbapenemase-producing A baumannii in the Asia-Pacific region, with successful and sustained control. Although the source or vehicle of the outbreak was not identified, our results suggest that a hospital-wide outbreak can be successfully managed with strict infection control measures, and that the limitation of the use of carbapenems and closure of wards may not be necessary.

Evolution of β-lactams resistance in Gram-negative bacteria in Tunisia

Antimicrobial resistance is a major health problem worldwide, but marked variations in the resistance profiles of bacterial pathogens are found between countries and in different patient settings. In Tunisia, the strikingly high prevalence of resistance of bacteria to penicillins and cephalorosporins drugs including fourth generation in clinical isolates of Gram negative bacteria has been reported. During 30 years, the emerging problem of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae isolates is substantial, and some unique enzymes have been found. Recently, evidence that Gram-negative bacteria are resistant to nearly all available antimicrobial agents, including carbapenems, have emerged.

Detection of OXA-type carbapenemases and integrons among carbapenem-resistant Acinetobactor baumannii in a teaching hospital in China

The increasing trend of carbapenem-resistance (CR) and multi-drug resistance (MDR) in A. baumannii worldwide has limited the therapeutic effectiveness of antibiotic therapy. The study was conducted to determine the prevalence of carbapenemases and integrons among the isolates of imipenem-resistant A. baumannii (IRAB). A total of 71 non-repetitive imipenem- resistant A. baumannii isolates were collected and tested for susceptibility to 17 antimicrobials. The modified Hodge test and EDTA-disc synergy test were performed for the screening of carbapenemases and metallo-β -lactamases (MBLs) production, respectively. Isolates were then subjected to multiplex-PCR targeting genes encoding for OXA-type carbapenemase, MBLs and integrases. Random amplified polymorphic DNA (RAPD) genotyping was performed to assess genetic relatedness. All isolates exhibited multi-drug resistant phenotype. Colistin was the most active antimicrobial agent tested. Seventy-one isolates (100%) demonstrated positive in the modified Hodge test. Thirty-nine isolates showed positive in the EDTA-disc synergy test, however, no MBL genes were detected. All strains possessed a bla(OXA-51) -like gene. The co-exis-tence of bla(OXA-51) -like/bla(OXA-23) -like/intI1, bla(OXA-51) -like/bla(OXA-23) -like, bla(OXA-51) -like/bla(OXA-24) -like was detected in 91.6% (n = 65), 5.6% (n = 4), 2.8% (n = 2), respectively. Analysis of the genetic con-text of bla(OXA-23) showed the presence of ISAba1 upstream of bla(OXA-23) . No ISAba1 was detected upstream of bla(OXA-51) . Two different gene cassettes were found in these strains, and a high prevalence of aacA4, aadA1 and catB8 genes was observed. RAPD of 71 isolates showed 7 genotypes. The strains were mainly recovered from patients in intensive care unit, neurosurgery and department of respiratory disease. These findings show that multi-drug resistance in A. baumannii is a common problem. This study also shows a high distribution of bla(OXA-23) -like and intI1 genes in imipenem-resistant A. baumannii isolates. The clonal spread played an important role in the increase of OXA-23 producing IRABs in the hospital environment.

Emerging carbapenemases: a global perspective

The celestial rise in antibiotic resistance among Gram-negative bacteria has challenged both the scientific and pharmaceutical sectors. The hallmark of this general increase is the unbridled dissemination of carbapenem resistance genes, namely KPC, OXA and metallo-β-lactamase variants. In particular, the media attention given to the NDM-1 metallo-β-lactamase has highlighted the global consequences of human behaviour on spreading antibiotic resistance.

Emergence and dissemination of blaOXA-23-carrying imipenem-resistant Acinetobacter sp in a regional hospital in Taiwan

BACKGROUND

The distribution and characterization of OXA-type carbapenemases in Acinetobacter sp in Taiwan has less been reported. The aim of the study was to investigate the molecular epidemiology and OXA-type carbapenemase genes in a regional hospital in Taiwan.

METHODS

Imipenem-resistant Acinetobacter sp were collected between 2005 and 2007 in a regional hospital. Genotyping was performed by pulsed-field gel electrophoresis. OXA-type carbapenemase genes were determined by multiplex polymerase chain reaction (PCR) and gene sequencing.

RESULTS

A total of 136 isolates were collected. Fifty-six pulsotypes were identified. None of the pulsotypes established predominance throughout the 3-year period. Multiplex PCR of blaOXA genes showed that 99% (135/136) of the Acinetobacter sp possessed blaOXA51-like genes. The coexistences of blaOXA51-like/blaOXA-23-like and blaOXA51-like/blaOXA-24-like were detected in 19% (26/136) and 1% (2/136) of the isolates, respectively. Among blaOXA-23-like gene-carrying isolates, two isolates (Pulsotypes 18 and 20) were found in 2006 and the remainder (n=24), including Pulsotypes 27 (n=18), 29 (n=1), 52 (n=3), and 53 (n=2), were found in 2007. Sequencing performed on the 26 representative isolates confirmed the presence of the blaOXA-23 carbapenemase gene. Analysis of the genetic content of blaOXA-23 showed that these genes were presumably chromosomal and associated with the upstream-located insertion sequence ISAba1.

CONCLUSIONS

The emergence and imminent widespread of blaOXA-23-carrying imipenem-resistant Acinetobacter sp appeared in Taiwan during the period from 2006 to 2007.

Structures of the class D carbapenemase OXA-24 from Acinetobacter baumannii in complex with doripenem

The emergence of class D β-lactamases with carbapenemase activity presents an enormous challenge to health practitioners, particularly with regard to the treatment of infections caused by Gram-negative pathogens such as Acinetobacter baumannii. Unfortunately, class D β-lactamases with carbapenemase activity are resistant to β-lactamase inhibitors. To better understand the details of the how these enzymes bind and hydrolyze carbapenems, we have determined the structures of two deacylation-deficient variants (K84D and V130D) of the class D carbapenemase OXA-24 with doripenem bound as a covalent acyl-enzyme intermediate. Doripenem adopts essentially the same configuration in both OXA-24 variant structures, but varies significantly when compared to the non-carbapenemase class D member OXA-1/doripenem complex. The alcohol of the 6α hydroxyethyl moiety is directed away from the general base carboxy-K84, with implications for activation of the deacylating water. The tunnel formed by the Y112/M223 bridge in the apo form of OXA-24 is largely unchanged by the binding of doripenem. The presence of this bridge, however, causes the distal pyrrolidine/sulfonamide group to bind in a drastically different conformation compared to doripenem bound to OXA-1. The resulting difference in the position of the side-chain bridge sulfur of doripenem is consistent with the hypothesis that the tautomeric state of the pyrroline ring contributes to the different carbapenem hydrolysis rates of OXA-1 and OXA-24. These findings represent a snapshot of a key step in the catalytic mechanism of an important class D enzyme, and might be useful for the design of novel inhibitors.

Three factors that modulate the activity of class D β-lactamases and interfere with the post-translational carboxylation of Lys70

The activity of class D β-lactamases is dependent on Lys70 carboxylation in the active site. Structural, kinetic and affinity studies show that this post-translational modification can be affected by the presence of a poor substrate such as moxalactam but also by the V117T substitution. Val117 is a strictly conserved hydrophobic residue located in the active site. In addition, inhibition of class D β-lactamases by chloride ions is due to a competition between the side chain carboxylate of the modified Lys70 and chloride ions. Determination of the individual kinetic constants shows that the deacylation of the acyl-enzyme is the rate-limiting step for the wild-type OXA-10 β-lactamase.

Can we use imipenem and meropenem Vitek 2 MICs for detection of suspected KPC and other-carbapenemase producers among species of Enterobacteriaceae?

Imipenem and meropenem Vitek 2 MICs were evaluated for a panel of 104 Enterobacteriaceae for identification of carbapenemase producers. The sensitivity and specificity values for the new CLSI interpretative criteria (CLSI document M100-S20-U, 2010) were 98% and 83% for imipenem and 76% and 83% for meropenem, respectively. We propose an algorithm that is highly sensitive (98%) and specific (94%) for carbapenemase screening based on the combined use of imipenem and meropenem MICs.

Improved performance of the modified Hodge test with MacConkey agar for screening carbapenemase-producing Gram-negative bacilli

The detection of carbapenemases in Gram-negative bacilli is important for optimal patient treatment and to control spread of the resistance. The modified Hodge test can detect carbapenemase-producing Gram-negative bacilli. In this study, we compared the performance of MacConkey agar and Mueller-Hinton agar for metallo-β-lactamase (MBL) and OXA carbapenemase screening. Overall, the performance of Hodge test was better with MacConkey agar due to enhanced release of β-lactamases from the cells in the presence of bile compounds. Concomitant use of the modified Hodge test could resolve most of the problems with uncertain double-disk synergy tests in MBL detection.

Dissemination of multidrug resistant Acinetobacter baumannii in various hospitals of Antananarivo Madagascar

This study reports the dissemination of multidrug-resistant (MDR) OXA-23-producing Acinetobacter baumannii clones in hospitals in Antananarivo, Madagascar. A total of 53 carbapenem-resistant A. baumannii isolates were obtained from September 2006 to March 2009 in five hospitals. These resistant strains represent 44% of all A. baumannii isolates. The double disk synergy test was performed to screen for production of metallo-beta-lactamases. Polymerase chain reaction (PCR) and DNA sequencing were performed for the detection of bla(AmpC), bla(OXA-51),bla(OXA-23), bla(OXA-24), bla(IMP), bla(VIM). The presence of the insertion sequence ISAba1 relative to blaOXA-23 and blaOXA-51 was assessed by PCR. Isolates were typed by Rep-PCR. All the isolates were MDR and produced the OXA-23 carbapenemase, which was confirmed by sequencing. PCR analysis for AmpC and OXA-51 gave positive results for all strains studied. No isolates produced metallo-beta-lactamases. In all isolates ISAba1 laid upstream of blaOXA-23. The A. baumannii isolates were separated into two genotypes; genotype A had a higher prevalence (41 strains) than genotype B (12 strains). Genotype A was present in four hospitals, whilst genotype B had spread in two hospitals. The high frequency of MDR OXA-23-producing A. baumannii in various hospitals in Antananarivo is curious since carbapenems are not available in Madagascar, but it emphasises the need for infection control procedures and strict adherence to them to prevent the spread of these resistant organisms in Antananarivo and also the need to control the use of carbapenems in the future.

Bench-to-bedside review: The role of beta-lactamases in antibiotic-resistant Gram-negative infections

Multidrug resistance has been increasing among Gram-negative bacteria and is strongly associated with the production of both chromosomal- and plasmid-encoded β-lactamases, whose number now exceeds 890. Many of the newer enzymes exhibit broad-spectrum hydrolytic activity against most classes of β-lactams. The most important plasmid-encoded β-lactamases include (a) AmpC cephalosporinases produced in high quantities, (b) the expanding families of extended-spectrum β-lactamases such as the CTX-M enzymes that can hydrolyze the advanced-spectrum cephalosporins and monobactams, and (c) carbapenemases from multiple molecular classes that are responsible for resistance to almost all β-lactams, including the carbapenems. Important plasmid-encoded carbapenemases include (a) the KPC β-lactamases originating in Klebsiella pneumoniae isolates and now appearing worldwide in pan-resistant Gram-negative pathogens and (b) metallo-β-lactamases that are produced in organisms with other deleterious β-lactamases, causing resistance to all β-lactams except aztreonam. β-Lactamase genes encoding these enzymes are often carried on plasmids that bear additional resistance determinants for other antibiotic classes. As a result, some infections caused by Gram-negative pathogens can now be treated with only a limited number, if any, antibiotics. Because multidrug resistance in Gram-negative bacteria is observed in both nosocomial and community isolates, eradication of these resistant strains is becoming more difficult.

OXA-24 carbapenemase gene flanked by XerC/XerD-like recombination sites in different plasmids from different Acinetobacter species isolated during a nosocomial outbreak

A clinical strain of Acinetobacter calcoaceticus resistant to carbapenems was isolated from a blood culture sample from an inpatient in a hospital in Madrid (Spain) during a large outbreak of infection (affecting more than 300 inpatients), caused by a multidrug-resistant Acinetobacter baumannii clone. The carbapenem resistance in both the A. calcoaceticus and A. baumannii clones was due to a bla(OXA-24) gene harbored in different plasmids. The plasmids were fully sequenced, revealing the presence of site-specific recombination binding sites putatively involved in mobilization of the bla(OXA-24) gene. Comparison of plasmids contained in the two strains revealed possible horizontal transmission of resistance genes between the Acinetobacter species.

Distribution of blaOXA-carrying imipenem-resistant Acinetobacter spp. in 3 hospitals in Taiwan

We investigated the molecular epidemiology and OXA-type carbapenemase genes of 83 imipenem-resistant Acinetobacter spp. collected from 2 university hospitals (hospitals A and B) and a regional hospital (hospital C) during 2007 in Taiwan. Genotyping by pulsed-field gel electrophoresis identified 51 pulsotypes. None of the pulsotypes established predominance throughout the 3 hospitals. Multiplex polymerase chain reaction of blaOXA genes showed that 100% (18/18), 91%(31/34), and 100% (31/31) of the Acinetobacter spp. collected from hospital A, B, and C, respectively, possessed blaOXA-51-like genes. None of the strains carrying blaOXA-23-like and blaOXA-24-like genes were found in hospital A. The coexistences of blaOXA-51-like/blaOXA-23-like and blaOXA-51-like/blaOXA-24-like genes detected in hospitals B and C were 26% (9/34) and 12% (4/34) and 58% (18/31) and 3% (1/31), respectively. Among blaOXA-23-like gene-carrying isolates collected from hospitals, clonal spread of strains carrying the blaOXA-23 gene was detected in the regional hospital but not the other 2 university hospitals. The results suggest that interhospital dissemination of imipenem-resistant Acinetobacter spp. was not found in these hospitals. The increasing percentage of OXA-23 in OXA-type carbapenemases in Acinetobacter spp. from the regional hospitals to medical centers deserves further attention in Taiwan.

Acquired carbapenemases in Gram-negative bacterial pathogens: detection and surveillance issues

Acquired carbapenemases are emerging resistance determinants in Gram-negative pathogens, including Enterobacteriaceae, Pseudomonas aeruginosa and other Gram-negative non-fermenters. A consistent number of acquired carbapenemases have been identified during the past few years, belonging to either molecular class B (metallo-beta-lactamases) or molecular classes A and D (serine carbapenemases), and genes encoding these enzymes are associated with mobile genetic elements that allow their rapid dissemination in the clinical setting. Therefore, detection and surveillance of carbapenemase-producing organisms have become matters of major importance for the selection of appropriate therapeutic schemes and the implementation of infection control measures. As carbapenemase production cannot be simply inferred from the resistance profile, criteria must be established for which isolates should be suspected and screened for carbapenemase production, and for which tests (phenotypic and/or genotypic) should be adopted for confirmation of the resistance mechanism. Moreover, strategies should be devised for surveillance of carbapenemase producers in order to enable the implementation of effective surveillance programmes. The above issues are addressed in this article, as a follow-up to an expert meeting on acquired carbapenemases that was recently organized by the ESCMID Study Group for Antibiotic Resistance Surveillance.

Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome

BACKGROUND

Prokaryotic plasmids have a dual importance in the microbial world: first they have a great impact on the metabolic functions of the host cell, providing additional traits that can be accumulated in the cell without altering the gene content of the bacterial chromosome. Additionally and/or alternatively, from a genome perspective, plasmids can provide a basis for genomic rearrangements via homologous recombination and so they can facilitate the loss or acquisition of genes during these events, which eventually may lead to horizontal gene transfer (HGT). Given their importance for conferring adaptive traits to the host organisms, the interest in plasmid sequencing is growing and now many complete plasmid sequences are available online.

RESULTS

By using the newly developed Blast2Network bioinformatic tool, a comparative analysis was performed on the plasmid and chromosome sequence data available for bacteria belonging to the genus Acinetobacter, an ubiquitous and clinically important group of gamma-proteobacteria. Data obtained showed that, although most of the plasmids lack mobilization and transfer functions, they have probably a long history of rearrangements with other plasmids and with chromosomes. Indeed, traces of transfers between different species can be disclosed.

CONCLUSIONS

We show that, by combining plasmid and chromosome similarity, identity based, network analysis, an evolutionary scenario can be described even for highly mobile genetic elements that lack extensively shared genes. In particular we found that transposases and selective pressure for mercury resistance seem to have played a pivotal role in plasmid evolution in Acinetobacter genomes sequenced so far.

Differences in carbapenem resistance genes among Acinetobacterbaumannii, Acinetobacter genospecies 3 and Acinetobacter genospecies 13TU in Taiwan

A total of 81 clinical isolates of the three clinically important Acinetobacter spp., namely Acinetobacterbaumannii, Acinetobacter genospecies 3 and Acinetobacter genospecies 13TU, were analysed for differences in carbapenem resistance genes. Of the 81 isolates, 40 (49%) were resistant to carbapenems. Most A. baumannii isolates (47/53, 88.7%) contained the ISAba1-bla(OXA-51)-like gene and exhibited a higher minimum inhibitory concentration to imipenem than A. baumannii without the ISAba1 element. All four carbapenem-resistant A. genospecies 3 isolates contained bla(IMP-1) and an ISAba3-bla(OXA-58)-like gene. Three A. genospecies 13TU isolates contained an ISAba3-bla(OXA-58)-like and either a bla(IMP-1) or a bla(VIM-11) gene. The five bla(IMP-1)-containing strains were resistant to imipenem and were positive for metallo-beta-lactamase (MBL) activity by the Etest, and the two bla(VIM-11)-containing strains were susceptible to imipenem and were MBL-negative by Etest. Imipenem hydrolysis tests showed that the bla(IMP-1)-containing strains exhibited much higher imipenem-hydrolysing activity than the two bla(VIM-11)-containing strains. No transcripts of bla(VIM-11) or bla(OXA-58)-like genes were detected. Analysis of outer membrane proteins showed that OprD was absent in the only bla(IMP-1)-containing A. genospecies 13TU strain owing to the presence of a premature stop codon in the oprD gene. In summary, several differences were detected between the carbapenem resistance genes of clinical Acinetobacter spp. in Taiwan, and loss of OprD may be associated with imipenem resistance in A. genospecies 13TU.