Genetic and enzymatic properties of metallo-beta-lactamase VIM-5 from a clinical isolate of Enterobacter cloacae

The biogenesis of β-lactamase enzymes

The discovery of penicillin by Alexander Fleming marked a new era for modern medicine, allowing not only the treatment of infectious diseases, but also the safe performance of life-saving interventions, like surgery and chemotherapy. Unfortunately, resistance against penicillin, as well as more complex β-lactam antibiotics, has rapidly emerged since the introduction of these drugs in the clinic, and is largely driven by a single type of extra-cytoplasmic proteins, hydrolytic enzymes called β-lactamases. While the structures, biochemistry and epidemiology of these resistance determinants have been extensively characterized, their biogenesis, a complex process including multiple steps and involving several fundamental biochemical pathways, is rarely discussed. In this review, we provide a comprehensive overview of the journey of β-lactamases, from the moment they exit the ribosomal channel until they reach their final cellular destination as folded and active enzymes.

Occurrence of intI1-associated VIM-5 carbapenemase and co-existence of all four classes of β-lactamase in carbapenem-resistant clinical Pseudomonas aeruginosa DMC-27b

OBJECTIVES

Emergence of carbapenem-resistant Pseudomonas aeruginosa is limiting current treatment options. Carbapenemases and their association with integrons can cause rapid dissemination of resistance traits. We report here the co-existence and chromosomal inheritance of all four classes of β-lactamase and the presence of a unique class 1 integron (intI1) harbouring blaVIM-5 within a single isolate of P. aeruginosa, DMC-27b.

METHODS

DMC-27b, isolated from urine, was characterized for carbapenem resistance both phenotypically and genotypically. The orientation of gene cassette structures of class 1 integrons was determined using referenced and designed overlapping primers and complete genome sequence (CGS) data. The antimicrobial resistance profile, porin protein mutations and the presence of active efflux activity were studied from the CGS.

RESULTS

P. aeruginosa DMC-27b was resistant to a total of 20 antibiotics, with imipenem and meropenem MIC90s of >512 mg/L. The isolate harboured all four classes of β-lactamase: VEB-1 (class A), VIM-5 (class B), PDC-35 (class C) and OXA-2 and OXA-50 (both class D). Chromosomal harbouring of blaVIM-5 was associated with the intI1 gene cassette as the sole gene, a unique cassette so far reported. A total of 11 mutations, among them some mutations causing extra folds and changes in binding sites, in porin protein OprD might also affect its functionality regarding the transportation of antibiotics.

CONCLUSIONS

This is one of the earliest reports of its kind on the co-existence of all four β-lactamase classes in P. aeruginosa DMC-27b. Acquisition of multiple resistance determinants is paving the way for the development of MDR. This superbug is a model for rapid dissemination of resistance traits both horizontally and vertically.

Detection of the carbapenemase gene blaVIM-5 in members of the Pseudomonas putida group isolated from polluted Nigerian wetlands

There are increasing concerns about possible dissemination of clinically relevant antibiotic resistance genes, including genes encoding for carbapenemases in the environment. However, little is known about environmental distribution of antibiotic resistance in Africa. In this study, four polluted urban wetlands in Nigeria were investigated as potential reservoirs of carbapenem-resistant bacteria (CRB). CRB were isolated from the wetlands, characterized by Blue-Carba test, MIC determinations and whole genome sequencing (WGS). Nine of 65 bacterial isolates identified as members of the Pseudomonas putida group (P. plecoglossicida and P. guariconensis, respectively) harboured the metallo-beta-lactamase gene bla_VIM-5. WGS revealed the bla_VIM-5 in three novel Tn402-like class 1 integron structures containing the cassette arrays aadB|bla_VIM-5|bla_PSE-1, aadB|bla_VIM-5|aadB|bla_PSE-1, and bla_VIM-5|aadB|tnpA|bla_PSE-1|smr2|tnpA, respectively. Strains carrying the aadB|bla_VIM-5|bla_PSE-1 cassette also carried an identical integron without bla_VIM-5. In addition_, the strains harboured another Tn402-like class 1 integron carrying bcr2, several multidrug resistance efflux pumps, and at least one of ampC, aph(3”)-lb, aph(6)-ld, tetB, tetC, tetG, floR, and macAB. This is the first report of a carbapenemase gene in bacteria from environmental sources in Nigeria and the first report of bla_VIM-5 in environmental bacteria isolates. This result underscores the role of the Nigerian environment as reservoir of bacteria carrying clinically relevant antibiotic resistance genes.

Comparison of Verona Integron-Borne Metallo-β-Lactamase (VIM) Variants Reveals Differences in Stability and Inhibition Profiles

Metallo-β-lactamases (MBLs) are of increasing clinical significance; the development of clinically useful MBL inhibitors is challenged by the rapid evolution of variant MBLs. The Verona integron-borne metallo-β-lactamase (VIM) enzymes are among the most widely distributed MBLs, with >40 VIM variants having been reported. We report on the crystallographic analysis of VIM-5 and comparison of biochemical and biophysical properties of VIM-1, VIM-2, VIM-4, VIM-5, and VIM-38. Recombinant VIM variants were produced and purified, and their secondary structure and thermal stabilities were investigated by circular dichroism analyses. Steady-state kinetic analyses with a representative panel of β-lactam substrates were carried out to compare the catalytic efficiencies of the VIM variants. Furthermore, a set of metalloenzyme inhibitors were screened to compare their effects on the different VIM variants. The results reveal only small variations in the kinetic parameters of the VIM variants but substantial differences in their thermal stabilities and inhibition profiles. Overall, these results support the proposal that protein stability may be a factor in MBL evolution and highlight the importance of screening MBL variants during inhibitor development programs.

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.

Rapid evolution and spread of carbapenemases among Enterobacteriaceae in Europe

Plasmid-acquired carbapenemases in Enterobacteriaceae, which were first discovered in Europe in the 1990s, are now increasingly being identified at an alarming rate. Although their hydrolysis spectrum may vary, they hydrolyse most β-lactams, including carbapenems. They are mostly of the KPC, VIM, NDM and OXA-48 types. Their prevalence in Europe as reported in 2011 varies significantly from high (Greece and Italy) to low (Nordic countries). The types of carbapenemase vary among countries, partially depending on the cultural/population exchange relationship between the European countries and the possible reservoirs of each carbapenemase. Carbapenemase producers are mainly identified among Klebsiella pneumoniae and Escherichia coli, and still mostly in hospital settings and rarely in the community. Although important nosocomial outbreaks with carbapenemase-producing Enterobacteriaceae have been extensively reported, many new cases are still related to importation from a foreign country. Rapid identification of colonized or infected patients and screening of carriers is possible, and will probably be effective for prevention of a scenario of endemicity, as now reported for extended-spectrum β-lactamase (mainly CTX-M) producers in all European countries.

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.

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.

Characterization of metallo-beta-lactamase VIM-27, an A57S mutant of VIM-1 associated with Klebsiella pneumoniae ST147

VIM-27 metallo-β-lactamase, an Ala(57) → Ser variant of VIM-1, was identified in three Klebsiella pneumoniae isolates belonging to sequence type 147. bla(VIM-27) was part of a class 1 integron carried by non-self-transferable plasmids. Kinetic parameters and MIC determinations indicated that VIM-27 hydrolyzed most β-lactams, especially imipenem and cefoxitin, less effectively than VIM-1.

Epidemiology and genetics of VIM-type metallo-β-lactamases in Gram-negative bacilli

Metallo-β-lactamases (MBLs) are a rapidly evolving group of β-lactamases, which hydrolyze most β-lactams including the carbapenems. Of the known MBLs, VIMs are one of the most common families, with 27 variants detected in at least 23 species of Gram-negative bacilli from more than 40 countries/regions. The amino acid similarities of VIM variants range from 72.9 to 99.6% with 1–72 different residues. Most of the bla VIMs are harbored by a class 1 integron, a genetic platform able to acquire and express gene cassettes. The integrons are usually embedded in transposons and, in turn, accommodated on plasmids, making them highly mobile. Integrons display considerable diversity, with at least 110 different structures associated with the gain and spread of the bla VIMs. In most instances, the bla VIMs co-exist with one or more other resistance genes. The processes for the identification of bacteria harboring bla VIMs are also discussed in this article.

Carbapenem-resistant Escherichia coli and Klebsiella pneumoniae isolates from Turkey with OXA-48-like carbapenemases and outer membrane protein loss

Treatment options are limited in infections caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, with carbapenems generally preferred. Disturbingly, however, carbapenem-resistant strains are emerging worldwide. Here we report two clinical isolates, one Escherichia coli and one Klebsiella pneumoniae, each with high-level carbapenem resistance (imipenem minimum inhibitory concentration of 32 microg/mL). They were isolated following imipenem therapy from two hospital patients who had received imipenem therapy in different regions of Turkey. Both isolates produced OXA-48-like carbapenemases, enzymes so far reported only from Turkey. Both isolates also had group 1 CTX-M-type ESBLs and had lost major outer membrane proteins. OXA-48-like carbapenemases appear to be scattered in Turkey and surveillance to determine their prevalence is warranted.

Carbapenemases: the versatile beta-lactamases

Carbapenemases are beta-lactamases with versatile hydrolytic capacities. They have the ability to hydrolyze penicillins, cephalosporins, monobactams, and carbapenems. Bacteria producing these beta-lactamases may cause serious infections in which the carbapenemase activity renders many beta-lactams ineffective. Carbapenemases are members of the molecular class A, B, and D beta-lactamases. Class A and D enzymes have a serine-based hydrolytic mechanism, while class B enzymes are metallo-beta-lactamases that contain zinc in the active site. The class A carbapenemase group includes members of the SME, IMI, NMC, GES, and KPC families. Of these, the KPC carbapenemases are the most prevalent, found mostly on plasmids in Klebsiella pneumoniae. The class D carbapenemases consist of OXA-type beta-lactamases frequently detected in Acinetobacter baumannii. The metallo-beta-lactamases belong to the IMP, VIM, SPM, GIM, and SIM families and have been detected primarily in Pseudomonas aeruginosa; however, there are increasing numbers of reports worldwide of this group of beta-lactamases in the Enterobacteriaceae. This review updates the characteristics, epidemiology, and detection of the carbapenemases found in pathogenic bacteria.