Extended-spectrum beta-lactamases in Klebsiella pneumoniae bloodstream isolates from seven countries: dominance and widespread prevalence of SHV- and CTX-M-type beta-lactamases

Antibiotic susceptibility profiles and first report of TEM extended-spectrum β-lactamase in Pseudomonas fluorescens from coastal waters of the Kaštela Bay, Croatia

The aim of this study was to investigate the antibiotic susceptibility profiles and the presence of extended-spectrum-β-lactamases (ESBLs) in Pseudomonas fluorescens isolates from coastal waters of the Kaštela Bay, Croatia. Twenty-two water samples were collected during 2009. Isolates were tested for susceptibilities to 13 antibiotics by Etest. ESBL production was confirmed by double-disk synergy test carried out on Mueller-Hinton agar plates containing efflux pump inhibitor Phe-Arg-β-naphthylamide dihydrochloride. PCR and DNA sequencing analysis were used to identify ESBL-encoding genes. The transferability of cephalosporin resistance was tested by conjugation experiments. Genetic relatedness of ESBL-producing isolates was determined by random amplified polymorphic DNA (RAPD) analysis. Out of 185 P. fluorescens isolates recovered, 70 (37.8%) demonstrated multiresistance phenotype with highest rates of resistance to tetracycline (61.6%), aztreonam (31.9%), meropenem (17.3%), ceftazidime (15.1%) and cefotaxime (12.4%). Ten (5.4%) isolates were identified as ESBL producers. All isolates carried chromosomally located bla (TEM-116) gene. RAPD analysis identified four different genotypes. Here, we demonstrated a baseline profiles of antimicrobial resistance of P. fluorescens from coastal waters of the Kaštela Bay, Croatia. To our knowledge, this is the first report of the presence of TEM-type ESBL in P. fluorescens, indicating this bacterium as a reservoir of antibiotic resistance genes with clinical relevance.

Synthesis and characterization of the antibacterial potential of ZnO nanoparticles against extended-spectrum β-lactamases-producing Escherichia coli and Klebsiella pneumoniae isolated from a tertiary care hospital of North India

The reemergence of infectious diseases and the continuous development of multidrug resistance among a variety of disease-causing bacteria in clinical setting pose a serious threat to public health worldwide. Extended-spectrum β-lactamases (ESBLs) that mediate resistance to third-generation cephalosporin are now observed all over the world in all species of Enterobacteriaceae, especially Escherichia coli and Klebsiella pneumoniae. In this work, ZnO nanoparticles (NPs) were synthesized by the sol-gel method and characterized by powder X-ray diffraction, scanning electron microscopy (SEM) and atomic force microscopy (AFM). The image of synthesized ZnO NPs appeared spherical in SEM with a diameter of ≈19 nm and as hexagonal crystal in AFM. Clinical isolates were assessed for ESBL production and shown to be sensitive to ZnO NPs by different methods such as minimal inhibitory concentration (MIC) and minimal bactericidal concentration, time-dependent growth inhibition assay, well diffusion agar methods and estimation of colony forming units (CFU) of bacteria. The lowest MIC value for E. coli and K. pneumoniae was found to be 500 μg/ml. The results showed that ZnO NPs at 1,000 μg/ml completely inhibit the bacterial growth. The antibacterial effect of ZnO nanoparticles was gradual, but time- and concentration-dependent. The maximum inhibition zone at100 μg/ml for E. coli and K. pneumoniae was 22 and 20 mm, respectively. With the increasing ZnO NP loading, there is significant reduction in the numbers of CFU. At the concentration of 1,000 μg/ml, the decline in per cent survival of E. coli and K. pneumoniae was found to be 99.3% and 98.6%, respectively.

Multiparametric determination of genes and their point mutations for identification of beta-lactamases

More than half of all currently used antibiotics belong to the beta-lactam group, but their clinical effectiveness is severely limited by antibiotic resistance of microorganisms that are the causative agents of infectious diseases. Several mechanisms for the resistance of Enterobacteriaceae have been established, but the main one is the enzymatic hydrolysis of the antibiotic by specific enzymes called beta-lactamases. Beta-lactamases represent a large group of genetically and functionally different enzymes of which extended-spectrum beta-lactamases (ESBLs) pose the greatest threat. Due to the plasmid localization of the encoded genes, the distribution of these enzymes among the pathogens increases every year. Among ESBLs the most widespread and clinically relevant are class A ESBLs of TEM, SHV, and CTX-M types. TEM and SHV type ESBLs are derived from penicillinases TEM-1, TEM-2, and SHV-1 and are characterized by several single amino acid substitutions. The extended spectrum of substrate specificity for CTX-M beta-lactamases is also associated with the emergence of single mutations in the coding genes. The present review describes various molecular-biological methods used to identify determinants of antibiotic resistance. Particular attention is given to the method of hybridization analysis on microarrays, which allows simultaneous multiparametric determination of many genes and point mutations in them. A separate chapter deals with the use of hybridization analysis on microarrays for genotyping of the major clinically significant ESBLs. Specificity of mutation detection by means of hybridization analysis with different detection techniques is compared.

Accuracy of carbapenem nonsusceptibility for identification of KPC-possessing Enterobacteriaceae by use of the revised CLSI breakpoints

Using the updated 2010 CLSI carbapenem breakpoints for the Enterobacteriaceae, nonsusceptibility to ertapenem and imipenem predicted the presence of bla(KPC) poorly, especially among Escherichia coli and Enterobacter species. In regions where KPC-producing bacteria are endemic, testing for nonsusceptibility to meropenem may provide improved accuracy in identifying these isolates.

Characteristics of infections caused by extended-spectrum β-lactamase-producing Escherichia coli from community hospitals in South Africa

A study was designed to characterize 22 nonrepeat extended-spectrum β-lactamase (ESBL)-producing Escherichia coli clinical isolates recovered from specimens originating from doctor's consultation rooms and several private and a state hospital in the Cape Town metropolitan area during 2008-2009. Characterization was done by using isoelectric focusing, PCR, sequencing of bla(CTX-M), bla(TEM), bla(SHV), and bla(OXA) as well as PCR for plasmid-mediated quinolone resistance determinants, ST131, phylogenetic groups, and plasmid replicon typing. Genetic relatedness was determined with pulsed-field gel electrophoresis using XbaI and multilocus sequencing typing. The majority of patients (17/22 [77%]) presented with urinary tract infections (UTIs) originating from the hospital setting. Thirteen (59%) of the isolates produced CTX-M-15, 7 produced CTX-M-14, and 1 isolate each produced CTX-M-3 and SHV-2, respectively. Sixteen (73%) isolates were nonsusceptible to ciprofloxacin and 8 (36%) were positive for aac(6')-Ib-cr. Overall, 10/22 (45%) of ESBL producers belonged to clonal complex ST131 that produced CTX-M-15 or CTX-M-14. Molecular characteristics of ST131 showed that this clone belonged to phylogenetic group B2. Our study illustrated that clonal complex ST131 isolates producing CTX-M-15 and CTX-M-14 had emerged as an important cause of UTIs due to ESBL-producing E. coli in the Cape Town area. This is the first report to identify ST131 in ESBL-producing E. coli from Southern Africa.

Prevalence and genetic characteristics of TEM, SHV, and CTX-M in clinical Klebsiella pneumoniae isolates from Saudi Arabia

The prevalence and genetic basis of extended-spectrum beta-lactamases (ESBLs) in Klebsiella pneumoniae remains unclear in Saudi Arabia. Therefore, this study was devoted to determine the prevalence and characterize ESBL-producing K. pneumoniae in Al-Qassim area, Saudi Arabia. A total of 430 isolates of K. pneumoniae isolated from clinical samples were collected over 6 months from January to June 2008. These isolates were screened for the presence of ESBLs by double-disk synergy test and re-evaluated by E-test ESBL method. Minimum inhibitory concentrations of 15 antibiotics against ESBL-positive strains were determined by E-test strips. The β-lactamases involved were characterized by polymerase chain reaction assays and DNA sequencing. Conjugation experiments were done and ISEcp1 elements were tested among CTX-M positive isolates. The prevalence of ESBL was 25.6% (110/430) and all ESBL-positive isolates were sensitive to imipenem and tigecycline; however, the resistance rate to gentamicin, amikacin, and ciprofloxacin was 87.3%, 10%, and 9.1%, respectively. Of these, 89.1% produced SHV, 70.9% produced TEM, and 36.4% were CTX-M-producing strains. The prevalence of ESBL SHV SHV-12 and SHV-5 was of 60% and 18.2%, respectively, and various non-ESBL SHV, including SHV-1 (5.5%), -11 (3.6%), and -85 (1.8%), was detected. However, the prevalence of CTX-M-15 and CTX-M-14 was 34.5% and 1.8%, respectively. ISEcp1 element was detected in 60% of bla(CTX-M-15) genes. All bla(CTX-M) genes were transferable; however, most of bla(SHV-12) and bla(SHV-5) were not transferable. TEM-type ESBLs were not detected in any of the isolates. This is the first description of CTX-M-14, SHV-5, SHV-11, and SHV-85 in Saudi Arabia. We have documented the dominance of K. pneumoniae SHV-12 and highlighted the emergence of CTX-M-15 in Saudi Arabia.

Phylogenetic groups among Klebsiella pneumoniae isolates from Brazil: relationship with antimicrobial resistance and origin

The objectives of this study were to determine the distribution of phylogenetic groups among Klebsiella pneumoniae isolates from Recife, Brazil and to assess the relationship between the groups and the isolation sites and resistance profile. Ninety four isolates of K. pneumoniae from hospital or community infections and from normal microbiota were analyzed by gyrA PCR-RFLP, antibiotic susceptibility, and adonitol fermentation. The results revealed the distinction of three phylogenetic groups, as it has also been reported in Europe, showing that these clusters are highly conserved within K. pneumoniae. Group KpI was dominantly represented by hospital and community isolates while groups KpII and KpIII displayed mainly normal microbiota isolates. The resistance to third generation cephalosporins, aztreonam, imipenem, amoxicillin/clavulanic acid, and streptomycin was only observed in KpI. The percentage of resistance was higher in KpI, followed by KpII and KpIII. The differences in the distribution of K. pneumoniae phylogenetic groups observed in this study suggest distinctive clinical and epidemiological characteristics among the three groups, which is important to understand the epidemiology of infections caused by this organism. This is the first study in Brazil on K. pneumoniae isolates from normal microbiota and community infections regarding the distribution of phylogenetic groups based on the gyrA gene.

High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis

Background

The Enterobacteriaceae comprise a large number of clinically relevant species with several individual subspecies. Overlapping virulence-associated gene pools and the high overall genome plasticity often interferes with correct enterobacterial strain typing and risk assessment. Array technology offers a fast, reproducible and standardisable means for bacterial typing and thus provides many advantages for bacterial diagnostics, risk assessment and surveillance. The development of highly discriminative broad-range microbial diagnostic microarrays remains a challenge, because of marked genome plasticity of many bacterial pathogens.

Results

We developed a DNA microarray for strain typing and detection of major antimicrobial resistance genes of clinically relevant enterobacteria. For this purpose, we applied a global genome-wide probe selection strategy on 32 available complete enterobacterial genomes combined with a regression model for pathogen classification. The discriminative power of the probe set was further tested in silico on 15 additional complete enterobacterial genome sequences. DNA microarrays based on the selected probes were used to type 92 clinical enterobacterial isolates. Phenotypic tests confirmed the array-based typing results and corroborate that the selected probes allowed correct typing and prediction of major antibiotic resistances of clinically relevant Enterobacteriaceae, including the subspecies level, e.g. the reliable distinction of different E. coli pathotypes.

Conclusions

Our results demonstrate that the global probe selection approach based on longest common factor statistics as well as the design of a DNA microarray with a restricted set of discriminative probes enables robust discrimination of different enterobacterial variants and represents a proof of concept that can be adopted for diagnostics of a wide range of microbial pathogens. Our approach circumvents misclassifications arising from the application of virulence markers, which are highly affected by horizontal gene transfer. Moreover, a broad range of pathogens have been covered by an efficient probe set size enabling the design of high-throughput diagnostics.

SHV Lactamase Engineering Database: a reconciliation tool for SHV β-lactamases in public databases

Background

SHV β-lactamases confer resistance to a broad range of antibiotics by accumulating mutations. The number of SHV variants is steadily increasing. 117 SHV variants have been assigned in the SHV mutation table (http://www.lahey.org/Studies/). Besides, information about SHV β-lactamases can be found in the rapidly growing NCBI protein database. The SHV β-Lactamase Engineering Database (SHVED) has been developed to collect the SHV β-lactamase sequences from the NCBI protein database and the SHV mutation table. It serves as a tool for the detection and reconciliation of inconsistencies, and for the identification of new SHV variants and amino acid substitutions.

Description

The SHVED contains 200 protein entries with distinct sequences and 20 crystal structures. 83 protein sequences are included in the both the SHV mutation table and the NCBI protein database, while 35 and 82 protein sequences are only in the SHV mutation table and the NCBI protein database, respectively. Of these 82 sequences, 41 originate from microbial sources, and 22 of them are full-length sequences that harbour a mutation profile which has not been classified yet in the SHV mutation table. 27 protein entries from the NCBI protein database were found to have an inconsistency in SHV name identification. These inconsistencies were reconciled using information from the SHV mutation table and stored in the SHVED.

The SHVED is accessible at http://www.LacED.uni-stuttgart.de/classA/SHVED/. It provides sequences, structures, and a multisequence alignment of SHV β-lactamases with the corrected annotation. Amino acid substitutions at each position are also provided. The SHVED is updated monthly and supplies all data for download.

Conclusions

The SHV β-Lactamase Engineering Database (SHVED) contains information about SHV variants with reconciled annotation. It serves as a tool for detection of inconsistencies in the NCBI protein database, helps to identify new mutations resulting in new SHV variants, and thus supports the investigation of sequence-function relationships of SHV β-lactamases.

Evaluation of updated interpretative criteria for categorizing Klebsiella pneumoniae with reduced carbapenem susceptibility

We studied the accuracy of various susceptibility testing methods, including the 2009, 2010, and updated 2010 CLSI recommendations, to identify Klebsiella pneumoniae isolates with reduced susceptibility to carbapenems associated with different mechanisms of resistance. Forty-three wild-type (WT) strains, 42 extended-spectrum β-lactamase (ESBL) producers, 18 ESBL producers with outer membrane porin protein loss (ESBL/Omp strains), and 42 blaKPC-possessing K. pneumoniae (KPC-Kp) isolates were evaluated. Imipenem (IPM), meropenem (MEM), ertapenem (ERT), and doripenem (DOR) were tested by broth microdilution (BMD), Etest, and disk diffusion (DD), and the modified Hodge test (MHT) was performed using IPM and MEM disks. Results were interpreted according to original as well as recently updated interpretative criteria. MHT was positive for all 42 KPC-Kp isolates and 10 of 18 ESBL/Omp strains and therefore had poor specificity in differentiating between KPC-Kp and ESBL/Omp isolates. Based on the updated CLSI standards, phenotypic susceptibility testing by BMD and DD differentiated most carbapenem-susceptible from carbapenem-nonsusceptible K. pneumoniae isolates without the need for MHT, while the Etest method characterized many KPC-Kp isolates as susceptible, and breakpoints may need to be lowered for this method. However, both the original and updated CLSI criteria do not adequately differentiate between isolates in the KPC-Kp group, which are unlikely to respond to carbapenem therapy, and those in the ESBL/Omp group, which are likely to respond to carbapenem therapy if MICs are within pharmacokinetic/pharmacodynamic targets. Further studies are required to determine if there is a clinical need to differentiate between KPC-Kp and ESBL/Omp groups.

Clinical and molecular epidemiology of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae in a long-term study from Japan

The detection rates of extended-spectrum β-lactamase (ESBL)-producing bacteria in Japan are very low (∼5%) compared with those obtained worldwide. Further, the current trend of these bacteria in Japan is not known, and few studies with longitudinal observations have been reported. To obtain epidemiologic data on ESBL-producing bacteria, their genotypic features, and their antibiotic resistance patterns in Japan, we analyzed bacterial isolates from hospitalized patients at our institution over the 7-year period from 2003 to 2009. Of 2,304 isolates, 202 (8.8%) were found to be ESBL producers, including Escherichia coli, Klebsiella pneumonia, and Proteus mirabilis. The detection rates of the ESBL-producing isolates gradually increased and reached 17.1% and 10.5% for the E. coli and K. pneumoniae strains, respectively, in 2009. Genotyping analysis showed that ∼90% of the ESBL-producing isolates carried the CTX-M genotype, in which the CTX-M-9 group was predominant, although the CTX-M-2 group is considered to be the main genotype in Japan; further, many of the strains produced multiple β-lactamases. The detection rates of ESBL-producing bacteria may tend to be high within a limited region in Japan. A countrywide survey is required to understand the trend for ESBL-producing bacteria at the national level. In addition, our findings suggest that the genotypes of the detected ESBL producers are similar to those exhibiting a successful nosocomial spread worldwide.

Evaluation of a commercial microarray system for detection of SHV-, TEM-, CTX-M-, and KPC-type beta-lactamase genes in Gram-negative isolates

We evaluated the ability of a commercial microarray system (Check KPC/ESBL; Check-Points Health BV) to detect clinically important class A beta-lactamase genes. A total of 106 Gram-negative strains were tested. The following sensitivity and specificity results were recorded, respectively: for bla(SHV), 98.8% and 100%; for bla(TEM), 100% and 96.4%; and for bla(CTX-M) and bla(KPC), 100% and 100%.

First detection of CTX-M and SHV extended-spectrum beta-lactamases in Escherichia coli urinary tract isolates from dogs and cats in the United States

One hundred fifty canine and feline Escherichia coli isolates associated with urinary tract infections were screened for the presence of extended-spectrum beta-lactamase (ESBL) genes. Out of 60 isolates suspected to be ESBL positive based on antimicrobial susceptibility testing, 11 ESBLs were identified, including one SHV-12 gene, one CTX-M-14 gene, and nine CTX-M-15 genes. This study provides the first report of CTX-M- and SHV-type ESBLs in dogs and cats in the United States.

Carriage of genes for various extended-spectrum beta-lactamases: a novel resistance strategy of Klebsiella pneumoniae in Poland

Among 110 randomly sampled strains from a collection of 247 extended-spectrum beta-lactamase (ESBL)-producing clinical isolates of Klebsiella pneumoniae collected from hospitalised children in three paediatric hospitals in Poland, 64 strains (58.2%) with multiple ESBLs were found, including five non-clonal strains (4.5%) harbouring bla genes for ESBLs of three families (CTX-M, SHV and TEM). This is the first report of the emergence of triple ESBL-producing K. pneumoniae in Poland. In addition, K. pneumoniae strains harbouring bla genes for TEM-130 and TEM-132 ESBLs were detected in Poland for the first time. Epidemiological analysis of the multiple ESBL-producing K. pneumoniae isolates by pulsed-field gel electrophoresis (PFGE) revealed a relatively high genetic diversity between isolates producing the same combination of enzymes. Clonally related strains were uncommon.

Transmission of a Klebsiella pneumoniae clone harbouring genes for CTX-M-15-like and SHV-112 enzymes in a neonatal intensive care unit of a Kuwaiti hospital

The spread of antibiotic-resistant bacteria has become a large problem in most countries including Kuwait. This antibiotic resistance is usually due to the production of extended-spectrum beta-lactamase (ESBL) enzymes such as SHV, TEM and CTX-M. This study reports the emergence and spread of an ESBL-producing Klebsiella pneumoniae clone in a neonatal intensive care unit (NICU) in a Kuwaiti hospital. Eight ESBL-producing K. pneumoniae isolates were from blood cultures of seven neonates, and two were from the fingers of two healthcare workers in a NICU in Al Jahra Hospital, Kuwait. All isolates were obtained in February-March 2006, except for one, which was obtained in August 2005. Identification of the bacteria was based on traditional bacteriological and biochemical tests using the Vitek system. Antibiotic susceptibility was tested by the disc diffusion method using 16 different antibiotics. ESBLs were detected using disc approximation and double-disc synergy methods and confirmed as ESBLs using Etest. PCR and DNA sequencing were performed to determine the genotypes and mutations in the beta-lactamase genes (blaTEM, blaSHV and blaCTX-M). Genetic relatedness was determined by PFGE. All isolates were confirmed to have ESBLs by the Vitek system, disc approximation test, double-disc diffusion test and Etest, being resistant to cefotaxime, ceftazidime, cefepime, gentamicin, tobramycin and ciprofloxacin but susceptible to tetracycline and trimethoprim-sulfamethoxazole. Molecular studies showed the isolates to have TEM-1 beta-lactamase, a CTX-M-15-like ESBL and the newly discovered SHV-112 ESBL. PFGE showed that all isolates had identical banding patterns. The results indicate that a single clone of ESBL-producing K. pneumoniae caused bloodstream infections among babies in a NICU of a Kuwaiti hospital, and may have emerged at least 5 years ago. This clone was also present on the hands of healthcare workers, suggesting that they may have been involved in its transmission. Further studies are recommended to determine whether this clone is also spreading in other Kuwaiti hospitals.

Inhibitor resistance in the KPC-2 beta-lactamase, a preeminent property of this class A beta-lactamase

As resistance determinants, KPC beta-lactamases demonstrate a wide substrate spectrum that includes carbapenems, oxyimino-cephalosporins, and cephamycins. In addition, clinical strains harboring KPC-type beta-lactamases are often identified as resistant to standard beta-lactam-beta-lactamase inhibitor combinations in susceptibility testing. The KPC-2 carbapenemase presents a significant clinical challenge, as the mechanistic bases for KPC-2-associated phenotypes remain elusive. Here, we demonstrate resistance by KPC-2 to beta-lactamase inhibitors by determining that clavulanic acid, sulbactam, and tazobactam are hydrolyzed by KPC-2 with partition ratios (kcat/kinact ratios, where kinact is the rate constant of enzyme inactivation) of 2,500, 1,000, and 500, respectively. Methylidene penems that contain an sp2-hybridized C3 carboxylate and a bicyclic R1 side chain (dihydropyrazolo[1,5-c][1,3]thiazole [penem 1] and dihydropyrazolo[5,1-c][1,4]thiazine [penem 2]) are potent inhibitors: Km of penem 1, 0.06+/-0.01 microM, and Km of penem 2, 0.006+/-0.001 microM. We also demonstrate that penems 1 and 2 are mechanism-based inactivators, having partition ratios (kcat/kinact ratios) of 250 and 50, respectively. To understand the mechanism of inhibition by these penems, we generated molecular representations of both inhibitors in the active site of KPC-2. These models (i) suggest that penem 1 and penem 2 interact differently with active site residues, with the carbonyl of penem 2 being positioned outside the oxyanion hole and in a less favorable position for hydrolysis than that of penem 1, and (ii) support the kinetic observations that penem 2 is the better inhibitor (kinact/Km=6.5+/-0.6 microM(-1) s(-1)). We conclude that KPC-2 is unique among class A beta-lactamases in being able to readily hydrolyze clavulanic acid, sulbactam, and tazobactam. In contrast, penem-type beta-lactamase inhibitors, by exhibiting unique active site chemistry, may serve as an important scaffold for future development and offer an attractive alternative to our current beta-lactamase inhibitors.

Extended-spectrum beta-lactamases among Enterobacteriaceae isolated in a public hospital in Brazil

Extended-spectrum beta-lactamases (ESBL) in enterobacteria are recognized worldwide as a great hospital problem. In this study, 127 ESBL-producing Enterobacteriaceae isolated in one year from inpatients and outpatients at a public teaching hospital at São Paulo, Brazil, were submitted to analysis by PCR with specific primers for bla SHV, bla TEM and bla CTX-M genes. From the 127 isolates, 96 (75.6%) Klebsiella pneumoniae, 12 (9.3%) Escherichia coli, 8 (6.2%) Morganella morganii, 3 (2.3%) Proteus mirabilis, 2 (1.6%) Klebsiella oxytoca, 2 (1.6%) Providencia rettgeri, 2 (1.6%) Providencia stuartti, 1 (0.8%) Enterobacter aerogenes and 1 (0.8%) Enterobacter cloacae were identified as ESBL producers. Bla SHV, bla TEM and bla CTX-M were detected in 63%, 17.3% and 33.9% strains, respectively. Pulsed field gel eletrophoresis genotyping of K. pneumoniae revealed four main molecular patterns and 29 unrelated profiles. PCR results showed a high variety of ESBL groups among strains, in nine different species. The results suggest the spread of resistance genes among genetically different strains of ESBL-producing K. pneumoniae in some hospital wards, and also that some strongly related strains were identified in different hospital wards, suggesting clonal spread in the institutional environment.

[CTX-M-15-producing Klebsiella pneumoniae: a change in the epidemiology of ESBL]

Klebsiella pneumoniae is frequently involved in nosocomial outbreaks worldwide. High level of resistance is common for these bacteria leading to reduce antibiotic treatments and prolonged hospital stay for patients. Resistance determinants are often located on plasmids. During the 1980-1990s, ESBL encoding genes belonged to the TEM and SHV type. From the early 2000s, a new trend was observed with ESBL of the CTX-M type being increasingly described in K. pneumoniae, and more particularly CTX-M-15.

Detection of CTX-M-type extended-spectrum beta-lactamase (ESBLs) by testing with MicroScan overnight and ESBL confirmation panels

CTX-M extended-spectrum beta-lactamases (ESBLs) have emerged as the most common type of ESBL globally, their incidence easily surpassing those of SHV and TEM ESBLs in most locales. This study compared the performance of two MicroScan dried panels with CLSI reference broth microdilution and disk diffusion methods on a collection of genetically characterized ESBL-producing isolates. These included 64 Enterobacteriaceae isolates that produced CTX-M8, -14, -15, or -16 according to PCR and sequencing of the bla gene, 17 isolates that produced a SHV or TEM ESBL, and 19 that produced both CTX-M and SHV ESBLs. Each isolate was tested by a frozen reference microdilution panel, the MicroScan ESbetaL plus confirmation panel, and a routine dried panel containing streamlined ESBL confirmation dilutions (MicroScan Neg MIC panel type 32) that included cefotaxime and ceftazidime tested alone or with a fixed concentration of 4 microg/ml of clavulanate. Each isolate was also tested by the standard CLSI double-disk confirmation tests. The disk diffusion method detected all ESBL-producing isolates, the frozen reference panel detected 90% of isolates (10 out of 100 could not be analyzed because of off-scale MICs that exceeded the clavulanate combination concentrations in the panel), the ESbetaL plus panel detected 98% (1 missed and 1 off scale), and the streamlined ESBL panel detected 95% (5 off scale). Very high MICs for a few strains that produced SHV or both CTX-M and SHV ESBLs precluded noting the required three twofold-dilution differences with clavulanate needed to confirm an ESBL primarily in the reference panel and the Neg type 32 panel.

Antibiotic resistance: the perfect storm

The worldwide epidemic of antibiotic resistance is in danger of ending the golden age of antibiotic therapy. Resistance impacts on all areas of medicine, and is making successful empirical therapy much more difficult to achieve. Antibiotic choices are often severely restricted, and the pipeline of new antibiotics is almost dry. Resistance cannot be prevented, but its development and spread can be slowed. One of the tools at our disposal is maximising diversity in our prescribing. The advent of tigecycline, the first in a new class of intravenous antibiotics, is important in this context, giving us a further monotherapy option for severe infections. Another strategy is seriously to curtail the large amount of unnecessary antibiotic use in many areas of life, not only medical practice. The various aspects of this strategy are briefly reviewed.

Incidence, risk factors, and outcomes of Klebsiella pneumoniae bacteremia

BACKGROUND

Although Klebsiella pneumoniae is the second most common cause of Gram-negative bloodstream infections, its epidemiology has not been defined in a nonselected population. We sought to describe the incidence of, risk factors for, and outcomes associated with K. pneumoniae bacteremia.

METHODS

Population-based surveillance for K. pneumoniae bacteremia was conducted in the Calgary Health Region (population 1.2 million) from 2000 to 2007.

RESULTS

A total of 640 episodes of K. pneumoniae bacteremia were identified for an overall annual population incidence of 7.1 per 100,000; 174 (27%) were nosocomial, 276 (43%) were healthcare-associated community onset, and 190 (30%) were community acquired. Elderly patients and men were at highest risk for K. pneumoniae bacteremia. Dialysis, solid-organ transplantation, chronic liver disease, and cancer were the most important risk factors for acquiring K. pneumoniae bacteremia. Rates of resistance to trimethoprim/sulfamethoxazole increased significantly during 2000 to 2007. The case fatality rate was 20%, and the annual population mortality rate was 1.3 per 100,000. Increasing age, nosocomial acquisition, non-urinary and non-biliary focus of infection, and several comorbid illnesses were independently associated with an increased risk of death.

CONCLUSION

This is the first population-based study to document the major burden of illness associated with K. pneumoniae bacteremia and identifies groups at increased risk of acquiring and dying of these infections.

The Lactamase Engineering Database: a critical survey of TEM sequences in public databases

BACKGROUND

TEM beta-lactamases are the main cause for resistance against beta-lactam antibiotics. Sequence information about TEM beta-lactamases is mainly found in the NCBI peptide database and TEM mutation table at http://www.lahey.org/Studies/temtable.asp. While the TEM mutation table is manually curated by experts in the lactamase field, who guarantee reliable and consistent information, the rapidly growing sequence and annotation information from the NCBI peptide database is sometimes inconsistent. Therefore, the Lactamase Engineering Database has been developed to collect the TEM beta-lactamase sequences from the NCBI peptide database and the TEM mutation table, systematically compare sequence information and naming, identify inconsistencies, and thus provide a versatile tool for reconciliation of data and for an investigation of the sequence-function relationship.

DESCRIPTION

The LacED currently provides 2399 sequence entries and 37 structure entries. Sequence information on 150 different TEM beta-lactamases was derived from the TEM mutation table which provides a unique number to each protein classified as TEM beta-lactamase. 293 TEM-like proteins were found in the NCBI protein database, but only 113 TEM beta-lactamase were common to both data sets. The 180 TEM beta-lactamases from the NCBI protein database which have not yet been assigned to a TEM number fall in three classes: (1) 89 proteins from microbial organisms and 35 proteins from cloning or expression vectors had a new mutation profile; (2) 55 proteins had inconsistent annotation in terms of TEM assignment or reported mutation profile; (3) 39 proteins are fragments. The LacED is web accessible at http://www.LacED.uni-stuttgart.de and contains multisequence alignments, structure information and reconciled annotation of TEM beta-lactamases. The LacED is weekly updated and supplies all data for download.

CONCLUSION

The Lactamase Engineering Database enables a systematic analysis of TEM beta-lactamase sequence and annotation data from different data sources, and thus provides a valuable tool to identify inconsistencies in sequences from the NCBI peptide database, to detect TEM beta-lactamases with a novel mutation profile, and to identify new amino acid positions at which mutations can occur.

Prevalence and molecular characterization of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae in Riyadh, Saudi Arabia

BACKGROUND AND OBJECTIVES

Reports on extended-spectrum beta-lactamases (ESBL) production by Enterobacteriaceae, and especially in Klebsiella pneumoniae, are few in Saudi Arabia. Therefore, we determined the prevalence of ESBL in K pneumoniae from Riyadh and characterized the predominant beta-lactamase gene in these isolates.

METHODS

A total of 400 K pneumoniae samples were isolated from two hospitals in Riyadh during 2007 and screened for production of ESBL using ESBL-E-strips and combined disk methods. PCR assay was used to detect bla(TEM), bla(SHV), and bla(CTX-M) genes.

RESULTS

Phenotypic characterization identified a high ESBL rate of 55% of K pneumoniae isolates. ESBL producing K pneumoniae were PCR positive for SHV, TEM and CTX-M beta-lactamase genes with prevalences 97.3%, 84.1% and 34.1%, respectively. Within the CTX-M family, two groups of enzymes, CTX-M-1 and CTXM- 9-like genes were found with prevalences of 60% and 40%, respectively.

CONCLUSIONS

This study confirms the high rate of ESBL in K pneumoniae clinical isolates in hospitals in Riyadh. This study demonstrates the worldwide spread of bla(CTX-M) genes. This first report of the presence of the bla(CTX-M) gene in clincial isolates in Saudi Arabia is evidence of the continuing worldwide spread of this gene.

Emergence of carbapenem-non-susceptible extended-spectrum β-lactamase-producing Klebsiella pneumoniae isolates at the university hospital of Tübingen, Germany

The spread of Gram-negative bacteria with plasmid-borne extended-spectrum β-lactamases (ESBLs) has become a worldwide problem. This study analysed a total of 366 ESBL-producing Enterobacteriaceae strains isolated from non-selected patient specimens at the university hospital of Tübingen in the period January 2003 to December 2007. Although the overall ESBL rate was comparatively low (1.6 %), the percentages of ESBL-producing Enterobacter spp. and Escherichia coli increased from 0.8 and 0.5 %, respectively, in 2003 to 4.6 and 3.8 % in 2007. In particular, the emergence was observed of one carbapenem-resistant ESBL-producing E. coli isolate and five carbapenem-non-susceptible ESBL-positive Klebsiella pneumoniae isolates, in two of which carbapenem resistance development was documented in vivo under a meropenem-containing antibiotic regime. The possible underlying mechanism for this carbapenem resistance in three of the K. pneumoniae isolates was loss of the Klebsiella porin channel protein OmpK36 as shown by PCR analysis. The remaining two K. pneumoniae isolates exhibited increased expression of a tripartite AcrAB–TolC efflux pump as demonstrated by SDS-PAGE and mass spectrometry analysis of bacterial outer-membrane extracts, which, in addition to other unknown mechanisms, may contribute towards increasing the carbapenem MIC values further. Carbapenem-non-susceptible ESBL isolates may pose a new problem in the future due to possible outbreak situations and limited antibiotic treatment options. Therefore, a systematic exploration of intestinal colonization with ESBL isolates should be reconsidered, at least for haemato-oncological departments from where four of the five carbapenem-non-susceptible ESBL isolates originated.

Performance of the Phoenix bacterial identification system compared with disc diffusion methods for identifying extended-spectrum beta-lactamase, AmpC and KPC producers

Phenotypic identification of AmpC, KPC and extended-spectrum beta-lactamases (ESBLs) among members of the Enterobacteriaceae remains challenging. This study compared the Phoenix Automated Microbiology System (BD Diagnostics) with the Clinical and Laboratory Standards Institute confirmatory method to identify ESBL production among 200 Escherichia coli and Klebsiella pneumoniae clinical isolates. The Phoenix system misclassified nearly half of the isolates as ESBL-positive, requiring manual testing for confirmation. Inclusion of aztreonam +/- clavulanic acid (CA) and cefpodoxime +/- CA in the testing algorithm increased the ESBL detection rate by 6 %. Boronic acid-based screening identified 24 isolates as AmpC(+), but in a subset of genotypically characterized isolates, appeared to have a high false-positivity rate. PCR screening revealed eight KPC(+) isolates, all of which tested as ESBL(+) or ESBL(+) AmpC(+) by phenotypic methods, but half were reported as carbapenem-susceptible by the Phoenix system. Overall, these results indicate that laboratories should use the Phoenix ESBL results only as an initial screen followed by confirmation with an alternative method.

Contribution of OmpK36 to carbapenem susceptibility in KPC-producing Klebsiella pneumoniae

Isolates of Klebsiella pneumoniae harbouring the carbapenemase KPC may have carbapenem MICs that remain in the susceptible range, and may therefore go unrecognized. To understand the mechanisms contributing to the variability in carbapenem MICs, 20 clinical isolates, all belonging to either of two clonal groups of KPC-possessing K. pneumoniae endemic to New York City, were examined. Expression of genes encoding KPC, the porins OmpK35 and OmpK36, and the efflux pump AcrAB was examined by real-time RT-PCR. Outer-membrane profiles of selected KPC-producing isolates were examined by SDS-PAGE, and proteins were identified by matrix-assisted laser desorption/ionization mass spectrometry. The identification of SHV and TEM beta-lactamases and the genomic sequences of ompK35 and ompK36 were determined by PCR and DNA sequencing, respectively. For one clonal group, carbapenem MICs increased with decreasing expression of ompK36. A second clonal group also had carbapenem MICs that correlated with ompK36 expression. However, all of the isolates in this latter group continued to produce OmpK36, suggesting that porin configuration may affect entry of carbapenems. For isolates that had the greatest expression of ompK36, carbapenem MICs tended to be lower when determined by the broth microdilution technique, and scattered colonies were seen around the Etest zones of inhibition. All of the KPC-producing isolates were highly resistant to ertapenem, regardless of ompK36 expression. In conclusion, isolates of KPC-possessing K. pneumoniae that express ompK36 tend to have lower MICs to carbapenems and therefore may be more difficult to detect by clinical laboratories. Regardless of ompK36 expression, all of the KPC producers were consistently resistant to ertapenem.

Characterization of the plasmid-borne quinolone resistance gene qnrB19 in Salmonella enterica serovar Typhimurium

A qnrB19 gene variant, carried by an IncL/M-like plasmid, was detected in a multidrug Salmonella enterica serovar Typhimurium human strain with reduced susceptibility to ciprofloxacin. The genetic environment around the gene was fully sequenced (20 kb). A large gene cluster, containing the aph, qnrB19, and blaSHV-12-like resistance genes, is inserted inside a Tn3 transposon.

Detection of SHV beta-lactamases in Gram-negative bacilli using fluorescein-labeled antibodies

BACKGROUND

beta-lactam resistance in Gram-negative bacteria is a significant clinical problem in the community, long-term care facilities, and hospitals. In these organisms, beta-lactam resistance most commonly results from the production of beta-lactamases. In Gram-negative bacilli, TEM-, SHV-, and CTX-M-type beta-lactamases predominate. Therefore, new and accurate detection methods for these beta-lactamase producing isolates are needed.

RESULTS

E. coli DH10B cells producing SHV-1 beta-lactamase and a clinical isolate of K. pneumoniae producing SHV-5 beta-lactamase were rendered membrane permeable, fixed and adhered to poly-L-lysine coated slides, and stained with purified polyclonal anti-SHV antibodies that were fluorescein labeled. E. coli DH10B cells without a blaSHV gene were used as a negative control. The procedure generated a fluorescence signal from those slides containing cells expressing SHV beta-lactamase that was sufficient for direct imaging.

CONCLUSION

We developed a rapid and accurate method of visualizing the SHV family of enzymes in clinical samples containing Gram-negative bacilli using a fluorescein-labeled polyclonal antibody.

Characterization of blaKPC-containing Klebsiella pneumoniae isolates detected in different institutions in the Eastern USA

BACKGROUND

The emergence of bla(KPC)-containing Klebsiella pneumoniae (KPC-Kp) isolates is attracting significant attention. Outbreaks in the Eastern USA have created serious treatment and infection control problems. A comparative multi-institutional analysis of these strains has not yet been performed.

METHODS

We analysed 42 KPC-Kp recovered during 2006-07 from five institutions located in the Eastern USA. Antimicrobial susceptibility tests, analytical isoelectric focusing (aIEF), PCR and sequencing of bla genes, PFGE and rep-PCR were performed. Results By in vitro testing, KPC-Kp isolates were highly resistant to all non-carbapenem beta-lactams (MIC(90)s >or= 128 mg/L). Among carbapenems, MIC(50/90)s were 4/64 mg/L for imipenem and meropenem, 4/32 mg/L for doripenem and 8/128 for ertapenem. Combinations of clavulanate or tazobactam with a carbapenem or cefepime did not significantly lower the MIC values. Genetic analysis revealed that the isolates possessed the following bla genes: bla(KPC-2) (59.5%), bla(KPC-3) (40.5%), bla(TEM-1) (90.5%), bla(SHV-11) (95.2%) and bla(SHV-12) (50.0%). aIEF of crude beta-lactamase extracts from these strains supported our findings, showing beta-lactamases at pIs of 5.4, 7.6 and 8.2. The mean number of beta-lactamases was 3.5 (range 3-5). PFGE demonstrated that 32 (76.2%) isolates were clonally related (type A). Type A KPC-Kp isolates (20 bla(KPC-2) and 12 bla(KPC-3)) were detected in each of the five institutions. rep-PCR showed patterns consistent with PFGE.

CONCLUSIONS

We demonstrated the complex beta-lactamase background of KPC-Kp isolates that are emerging in multiple centres in the Eastern USA. The prevalence of a single dominant clone suggests that interstate transmission has occurred.

Pyrosequencing using the single-nucleotide polymorphism protocol for rapid determination of TEM- and SHV-type extended-spectrum beta-lactamases in clinical isolates and identification of the novel beta-lactamase genes blaSHV-48, blaSHV-105, and blaTEM-155

TEM- and SHV-type extended-spectrum beta-lactamases (ESBLs) are the most common ESBLs found in the United States and are prevalent throughout the world. Amino acid substitutions at a number of positions in TEM-1 lead to the ESBL phenotype, although substitutions at residues 104 (E to K), 164 (R to S or H), 238 (G to S), and 240 (E to K) appear to be particularly important in modifying the spectrum of activity of the enzyme. The SHV-1-derived ESBLs are a less diverse collection of enzymes; however, the majority of amino acid substitutions resulting in an ESBL mirror those seen in the TEM-1-derived enzymes. Pyrosequencing by use of the single-nucleotide polymorphism (SNP) protocol was applied to provide sequence data at positions critical for the ESBL phenotype spanning the bla(TEM) and bla(SHV) genes. Three novel beta-lactamases are described: the ESBLs TEM-155 (Q39K, R164S, E240K) and SHV-105 (I8F, R43S, G156D, G238S, E240K) and a non-ESBL, SHV-48 (V119I). The ceftazidime, ceftriaxone, and aztreonam MICs for an Escherichia coli isolate expressing bla(SHV-105) were >128, 128, and >128 microg/ml, respectively. Likewise, the ceftazidime, ceftriaxone, and aztreonam MICs for an E. coli isolate expressing bla(TEM-155) were >128, 64, and > 128 microg/ml, respectively. Pyrosequence analysis determined the true identity of the beta-lactamase on plasmid R1010 to be SHV-11 rather than SHV-1, as previously reported. Pyrosequencing is a real-time sequencing-by-synthesis approach that was applied to SNP detection for TEM- and SHV-type ESBL identification and represents a robust tool for rapid sequence determination that may have a place in the clinical setting.

Characterization and sequence analysis of extended-spectrum-{beta}-lactamase-encoding genes from Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis isolates collected during tigecycline phase 3 clinical trials

In concert with the development of novel beta-lactams and broad-spectrum cephalosporins, bacterially encoded beta-lactamases have evolved to accommodate the new agents. This study was designed to identify, at the sequence level, the genes responsible for the extended-spectrum-beta-lactamase (ESBL) phenotypes of Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis isolates collected during the global tigecycline phase 3 clinical trials. PCR assays were developed to identify and clone the bla(TEM), bla(SHV), bla(OXA), and bla(CTX) genes from clinical strains. Isolates were also screened for AmpC genes of the bla(CMY), bla(ACT), bla(FOX), and bla(DHA) families as well as the bla(KPC) genes encoding class A carbapenemases. E. coli, K. pneumoniae, and P. mirabilis isolates with ceftazidime MICs of > or =2 microg/ml were designated possible ESBL-producing pathogens and were then subjected to a confirmatory test for ESBLs by use of Etest. Of 272 unique patient isolates, 239 were confirmed by PCR and sequencing to carry the genes for at least one ESBL, with 44% of the positive isolates harboring the genes for multiple ESBLs. In agreement with current trends for ESBL distribution, bla(CTX-M)-type beta-lactamase genes were found in 83% and 71% of the ESBL-positive E. coli and K. pneumoniae isolates, respectively, whereas bla(SHV) genes were found in 41% and 28% of the ESBL-positive K. pneumoniae and E. coli isolates, respectively. Ninety-seven percent of the E. coli and K. pneumoniae isolates were tigecycline susceptible (MIC(90) = 2 microg/ml), warranting further studies to define the therapeutic utility of tigecycline against strains producing ESBLs in a clinical setting.

Dominance of blaCTX-M within an Australian extended-spectrum beta-lactamase gene pool

bla(CTX-M) genes, particularly bla(CTX-M-15), are the dominant extended-spectrum beta-lactamase (ESBL) genes among clinical isolates of Escherichia coli and Klebsiella pneumoniae in Sydney, Australia, where we also found one example of bla(CTX-M-62), encoding a novel enzyme conferring ceftazidime resistance. ESBL genes were present in diverse community isolates and in a variety of associated conjugative plasmids.

Correlation of antimicrobial resistance with beta-lactamases, the OmpA-like porin, and efflux pumps in clinical isolates of Acinetobacter baumannii endemic to New York City

Acinetobacter baumannii strains resistant to all beta-lactams, aminoglycosides, and fluoroquinolones have emerged in many medical centers. Potential mechanisms contributing to antimicrobial resistance were investigated in 40 clinical isolates endemic to New York City. The isolates were examined for the presence of various beta-lactamases, aminoglycoside-modifying enzymes, and mutations in gyrA and parC. Expression of the genes encoding the beta-lactamase AmpC, the efflux systems AdeABC and AbeM, and the OmpA-like porin was also examined by real-time reverse transcription-PCR. No VIM, IMP, KPC, OXA-23-type, OXA-24-type, or OXA-58 beta-lactamases were detected, although several isolates had acquired bla(SHV-5). Most cephalosporin-resistant isolates had increased levels of expression of ampC and/or had acquired bla(SHV-5); however, isolates without these features still had reduced susceptibility to cefepime that was mediated by the AdeABC efflux system. Although most isolates with ISAba1 upstream of the bla(OXA-51)-like carbapenemase gene were resistant to meropenem, several remained susceptible to imipenem. The presence of aminoglycoside-modifying enzymes and gyrase mutations accounted for aminoglycoside and fluoroquinolone resistance, respectively. The increased expression of adeABC was not an important contributor to aminoglycoside or fluoroquinolone resistance but did correlate with reduced susceptibility to tigecycline. The expression of abeM and ompA and phenotypic changes in OmpA did not correlate with antimicrobial resistance. A. baumannii has become a well-equipped nosocomial pathogen; defining the relative contribution of these and other mechanisms of antimicrobial resistance will require further investigation.

Molecular characterization and epidemiology of extended-spectrum-beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae isolates causing health care-associated infection in Thailand, where the CTX-M family is endemic

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae have rapidly spread worldwide and pose a serious threat for health care-associated (HA) infection. We conducted molecular detection and characterization of ESBL-related bla genes, including bla(TEM), bla(SHV), bla(CTX-M), bla(VEB), bla(OXA), bla(PER), and bla(GES), among 362 isolates of ESBL-producing E. coli (n = 235) and ESBL-producing K. pneumoniae (n = 127) collected from patients who met the definition of HA infection at two major university hospitals in Thailand from December 2004 to May 2005. The prevalence of ESBL-producing E. coli and ESBL-producing K. pneumoniae, patient demographics and the susceptibilities of these bacteria to various antimicrobial agents were described. A total of 87.3% of isolates carried several bla genes. The prevalence of bla(CTX-M) was strikingly high: 99.6% for ESBL-producing E. coli (CTX-M-14, -15, -27, -40, and -55) and 99.2% for ESBL-producing K. pneumoniae (CTX-M-3, -14, -15, -27, and -55). ISEcp1 was found in the upstream region of bla(CTX-M) in most isolates. Up to 77.0% and 71.7% of ESBL-producing E. coli and ESBL-producing K. pneumoniae, respectively, carried bla(TEM); all of them encoded TEM-1. ESBL-producing K. pneumoniae carried bla(SHV) at 87.4% (SHV-1, -2a, -11, -12, -27, -71, and -75) but only at 3.8% for ESBL-producing E. coli (SHV-11 and -12). bla genes encoding VEB-1 and OXA-10 were found in both ESBL-producing E. coli (8.5% and 8.1%, respectively) and ESBL-producing K. pneumoniae (10.2% and 11.8%, respectively). None of the isolates were positive for bla(PER) and bla(GES). Pulsed-field gel electrophoresis analysis demonstrated that there was no major clonal relationship among these ESBL producers. This is the first study to report CTX-M-3, CTX-M-27, CTX-M-40, SHV-27, SHV-71, and SHV-75 in Thailand and to show that CTX-M ESBL is highly endemic in the country.

Multiplex PCR amplification assay for the detection of blaSHV, blaTEM and blaCTX-M genes in Enterobacteriaceae

Extended-spectrum beta-lactamases (ESBLs) are often mediated by (bla-)SHV, (bla)TEM and (bla)CTX-M genes in Enterobacteriaceae and other Gram-negative bacteria. Numerous molecular typing methods, including PCR-based assays, have been developed for their identification. To reduce the number of PCR amplifications needed we have developed a multiplex PCR assay which detects and discriminates between (bla-)SHV, (bla)TEM and (bla)CTX-M PCR amplicons of 747, 445 and 593 bp, respectively. This multiplex PCR assay allowed the identification of (bla-)SHV, (bla)TEM and (bla)CTX-M genes in a series of clinical isolates of Enterobacteriaceae with previously characterised ESBL phenotype. The presence of (bla)SHV, (bla)TEM and (bla)CTX-M genes was confirmed by partial DNA sequence analysis. Apparently, the universal well-established CTX-M primer pair used here to reveal plasmid-encoded (bla)CTX-M genes would also amplify the chromosomally located K-1 enzyme gene in all Klebsiella oxytoca strains included in the study.

Molecular epidemiology of clinically significant antibiotic resistance genes

Antimicrobials were first introduced into medical practice a little over 60 years ago and since that time resistant strains of bacteria have arisen in response to the selective pressure of their use. This review uses the paradigm of the evolution and spread of beta-lactamases and in particular beta-lactamases active against antimicrobials used to treat Gram-negative infections. The emergence and evolution particularly of CTX-M extended-spectrum beta-lactamases (ESBLs) is described together with the molecular mechanisms responsible for both primary mutation and horizontal gene transfer. Reference is also made to other significant antibiotic resistance genes, resistance mechanisms in Gram-negative bacteria, such as carbepenamases, and plasmid-mediated fluoroquinolone resistance. The pathogen Staphylococcus aureus is reviewed in detail as an example of a highly successful Gram-positive bacterial pathogen that has acquired and developed resistance to a wide range of antimicrobials. The role of selective pressures in the environment as well as the medical use of antimicrobials together with the interplay of various genetic mechanisms for horizontal gene transfer are considered in the concluding part of this review.