Performance evaluation of a new matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, ASTA MicroIDSys system, in bacterial identification against clinical isolates of anaerobic bacteria.

INTRODUCTION: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been introduced for bacterial identification. The ASTA MicroIDSys system (ASTA, Suwon, Korea) is a new MALDI-TOF MS system developed for species identification of microorganisms. We evaluated the performance of MicroIDSys against clinical isolates of anaerobic bacteria. MATERIAL AND METHODS: A total of 370 non-duplicated clinical isolates of anaerobic bacteria were tested in this study. Bacterial identification with MicroIDSys was performed with a direct smear method, and measured spectra were analyzed using respective software. The results of MicroIDSys were compared with the results of Bruker Biotyper and 16S rRNA sequencing. RESULTS: The overall agreement rates for the 370 clinical isolates (34 genera and 99 species) were 95.4% (353/370) at the genus level and 91.6% (n = 340) at the species level. Only 17 isolates were incorrectly identified at the genus level: five misidentifications and 12 unidentifications. The MicroIDSys system exhibited excellent performance in the identification of clinically relevant bacterial species. Most of the Bacteroides isolates (98.0%, 99/101) and all of the Clostridium difficile (100%, n = 11), Clostridium perfringens (100%, n = 10), Finegoldia magna (100%, n = 11), and Parvimonas micra (100%, n = 10) isolates were correctly identified at the species level. CONCLUSION: The MicroIDSys system proved useful in the identification of anaerobic bacteria, especially clinically relevant species. This system could be of use in clinical microbiology laboratories as a primary tool for identifying anaerobic bacteria.

Biochemical characterization of the TEM-107 extended-spectrum ß-lactamase in a Klebsiella pneumoniae isolate from South Korea.

The TEM-107 extended-spectrum ß-lactamase detected in a Klebsiella pneumoniae clinical isolate had a Gly238Ser substitution compared to the TEM-43 ß-lactamase. The MIC of ceftazidime was higher (64 µg/ml) than that of cefotaxime (2 µg/ml) for the isolate. Clavulanic acid reduced the MIC of ceftazidime 64-fold.

Comparative in vitro activities of torezolid (DA-7157) against clinical isolates of aerobic and anaerobic bacteria in South Korea.

Resistance of Gram-positive pathogens to first-line antimicrobial agents has been increasing in many parts of the world. We compared the in vitro activities of torezolid with those of other antimicrobial agents, including linezolid, against clinical isolates of major aerobic and anaerobic bacteria. Torezolid had an MIC(90) of ≤0.5 µg/ml for the Gram-positive bacterial isolates tested and was more potent than either linezolid or vancomycin.

Modification and evaluation of the Triton Hodge test for screening carbapenemase-producing Enterobacteriaceae.

Detection of carbapenemase-producing Enterobacteriaceae (CPE) has become critical for appropriate antimicrobial therapy and for controlling the spread of infection. We evaluated Triton Hodge test (THT) for screening CPE. A spreader can be used to apply more constant volume of Triton on whole surface of Mueller-Hinton agar (MHA), or alternatively, a 10-µL inoculating loop can be used to apply a 20% Triton solution lineally. The THT procedure can be simplified by eliminating the 1/10 dilution step of indicator bacteria from the McFarland 0.5 turbidity suspension. The presence of Triton in the MHA plates significantly increased the enhanced growth size of not only Enterobacteriaceae producing NDM-1-like enzymes but also those producing the most prevalent KPC-2-like enzyme, resulting in 100% sensitivity of the test.

Reduced imipenem susceptibility in Klebsiella pneumoniae clinical isolates with plasmid-mediated CMY-2 and DHA-1 beta-lactamases co-mediated by porin loss.

We investigated the resistance mechanisms and clonality among 42 imipenem-non-susceptible Klebsiella pneumoniae isolated at a tertiary care hospital in Korea. Two isolates had bla(VIM-2) alleles, whereas bla(CMY-2)- and bla(DHA-1)-like alleles were detected in 24 and 16 isolates, respectively, with these enzymes confirmed by sequencing for representative isolates. Transfer of bla(CMY-2) and bla(DHA-1) was achieved by conjugation. Addition of 300 mg/L 3-aminophenylboronic acid (APB) reduced the minimum inhibitory concentration for 90% of the organisms (MIC(90)) of imipenem and meropenem eight- and four-fold, respectively, for the bla(CMY-2)- and bla(DHA-1)-positive isolates, confirming the role of these enzymes in resistance. SDS-PAGE of outer membrane proteins for representative isolates showed lack or greatly diminished expression of OmpK35 and OmpK36 porins. Pulsed-field gel electrophoresis of XbaI-restricted genomic DNA revealed two closely related clusters among 23 bla(CMY-2)-positive isolates, whereas those with bla(DHA-1) were more heterogeneous. In conclusion, reduced imipenem susceptibility among K. pneumoniae at this Korean hospital was largely co-mediated by production of plasmid-mediated AmpC beta-lactamases along with lack or greatly diminished expression of OmpK35 and OmpK36 porins.

The first detection of CTX-M-14 extended-spectrum beta-lactamase among diverse beta-lactamase-producing Proteus mirabilis clinical isolates.

CTX-M-14- and -2-like extended-spectrum beta-lactamases were detected in 5 and 1 Proteus mirabilis isolates, respectively, among 92 non-duplicate strains tested from December 2002 to September 2003. This is the first report of the CTX-M-14 enzyme in P. mirabilis to the best of our knowledge and suggests that the CTX-M-type enzyme is gradually spreading to this species. bla(TEM), bla(SHV-1), and/or bla(OXA-10) alleles were also detected in 35 ampicillin-resistant isolates tested.

Dissemination of 16S rRNA methylase-mediated highly amikacin-resistant isolates of Klebsiella pneumoniae and Acinetobacter baumannii in Korea.

Novel 16S rRNA methylase-mediated high-level resistance to amikacin and arbekacin has been reported recently in clinical isolates of Gram-negative bacilli only from several countries. We tested amikacin- or arbekacin-nonsusceptible Gram-negative bacilli isolated in 2003 and 2005 at a tertiary-care hospital in Korea by polymerase chain reaction to detect 16S rRNA methylase genes. armA alleles were detected in 14 isolates of Klebsiella pneumoniae, 10 other species of Enterobacteriaceae, and 16 Acinetobacter baumannii, whereas the rmtB allele was detected in 1 K. pneumoniae isolate. The resistance 1st detected in 2003 persisted in 2005. 16S rRNA methylase-producing isolates were highly resistant to arbekacin and amikacin, and were mostly coresistant to levofloxacin. Most K. pneumoniae isolates also produced extended-spectrum beta-lactamases and plasmid-mediated AmpC beta-lactamases, and most A. baumannii isolates were nonsusceptible to carbapenems.

Prevalence of inducible clindamycin resistance in staphylococcal isolates at a Korean tertiary care hospital.

Clindamycin resistance in Staphylococcus species can be either constitutive or inducible. Inducible resistance cannot be detected by the conventional antimicrobial susceptibility test. In this study, we determined the prevalence of inducible clindamycin resistance in staphylococcal isolates at a Korean tertiary care hospital. Between February and September 2004, 1,519 isolates of Staphylococcus aureus and 1,043 isolates of coagulase-negative staphylococci (CNS) were tested for inducible resistance by the D-zone test. Overall, 17% of MRSA, 84% of MSSA, 37% of MRCNS, and 70% of MSCNS were susceptible to clindamycin. Of the erythromycin non-susceptible, clindamycin-susceptible isolates, 32% of MRSA, 35% of MSSA, 90% of MRCNS, and 94% of MSCNS had inducible clindamycin resistance. Inducible clindamycin resistance in staphylococci was highly prevalent in Korea. This study indicates importance of the D-zone test in detecting inducible clindamycin resistance in staphylococci to aid in the optimal treatment of patients.

Plasmid-mediated, inducible AmpC beta-lactamase (DHA-1)-producing Enterobacteriaceae at a Korean hospital: wide dissemination in Klebsiella pneumoniae and Klebsiella oxytoca and emergence in Proteus mirabilis.

The aim of the study was to investigate the phenotypic and genetic characteristics of recently emerging cefoxitin-resistant and induction-positive isolates of Escherichia coli, Klebsiella species, and Proteus mirabilis. Strains of Enterobacteriaceae were isolated at a Korean tertiary care hospital between June and December 2002. Induction was tested using cefoxitin and aztreonam disks, the blaDHA allele was detected by PCR, and pulsed-field gel electrophoresis (PFGE) patterns were also analyzed. Among the cefoxitin-resistant isolates, 2.7% of E. coli, 21.1% of Klebsiella pneumoniae, 32.0% of Klebsiella oxytoca, and 8.3% of P. mirabilis isolates showed induction, and were blaDHA-1 allele positive. To the best of our knowledge, this is the first report of blaDHA-1 in P. mirabilis. The MICs of ceftazidime, cefotaxime, and aztreonam increased significantly by higher inoculum, suggesting that their clinical usefulness is limited. Presence of multiple PFGE patterns and identical patterns in some isolates suggest that the widely disseminated blaDHA-1 in Klebsiella species was because of both horizontal and clonal spread.

A new integron carrying VIM-2 metallo-beta-lactamase gene cassette in a Serratia marcescens isolate.

Serratia marcescens is an important nosocomial pathogen which is often resistant to multiple antimicrobial agents. An imipenem-resistant S. marcescens isolate from a urine specimen was found to carry a bla(VIM-2) gene cassette on a class 1 integron. This finding indicates that bla(VIM-2) is presently spreading even to Serratia spp. in Korea, which could compromise the usefulness of carbapenem in the treatment of multi-resistant Gram-negative bacilli infections. Clinical laboratory should be able to detect the VIM-2-producing isolates with even low carbapenem MIC.

Further modification of the Hodge test to screen AmpC beta-lactamase (CMY-1)-producing strains of Escherichia coli and Klebsiella pneumoniae.

Cefoxitin-resistant Escherichia coli and Klebsiella pneumoniae are widespread in Korea. Significant proportions of them are considered to be CMY-1 producers. For effective screening of CMY-1 producers, the Hodge test was modified by using a cefoxitin disk and the performance was evaluated. The sensitivity and specifity of the test were 100% and 94.9%, respectively. The test was easier to perform than the three-dimensional extract test. This modified test should be suitable for screening CMY-1-producing strains of E. coli and K. pneumoniae.

CTX-M-55-type extended-spectrum ß-lactamase-producing Shigella sonnei isolated from a Korean patient who had travelled to China.

We report a case of CTX-M-55-type extended-spectrum ß-lactamase (ESBL)-producing Shigella sonnei infection in a 27-year-old Korean woman who had traveled to China. The patient was admitted to the hospital due to abdominal pain, watery diarrhea, and fever (39.3℃). S. sonnei was isolated from her stool specimens, and the pathogen was found to be resistant to cefotaxime due to CTX-M-55-type ESBL. Insertion sequence (IS)Ecp1 was found upstream of the blaCTX-M-55 gene. The blaCTX-M-55 gene was transferred from the S. sonnei isolate to an Escherichia coli J53 recipient by conjugation. Pulsed-field gel electrophoresis and Southern blotting revealed that the blaCTX-M-55 gene was located on a plasmid of approximately 130 kb.

Clonal change of blaSIM-1-carrying Acinetobacter spp. from 2003 to 2008 in the hospital where it was initially discovered.

SIM-1 metallo-ß-lactamase was first discovered from carbapenem-resistant Acinetobacter spp. isolated in a Korean University Hospital in 2003, and was recently reported to have been discovered in A. baylyi isolated in nearby China. The aims of this study were to reveal clonal changes in bla(SIM-1)-harboring Acinetobacter isolates collected from 2003 to 2008 in the same Korean hospital, where they were first discovered to gain further insight into the relation between bla(SIM-1)-harboring plasmids and Acinetobacter spp. Among 1,761 nonduplicated imipenem-resistant Acinetobacter spp. isolates, 29 isolates were identified as bla(SIM-1) carriers. They were categorized into nine types according to pulsed-field gel electrophoresis findings. While most bla(SIM-1)-carrying isolates from 2003 to 2005 belonged to A. pittii, those from 2006 to 2007 were mostly isolates of A. nosocomialis. Most of the bla(SIM-1) genes were carried on ca. 280-kb plasmids and were only discovered in non-baumannii Acinetobacter spp. Integrons carrying the bla(SIM-1) gene were identical in structure in all species. These findings suggest that the plasmids were transferable, but not promiscuous. Further surveillance should be continued to detect and control further spread of the bla(SIM-1) gene, as the appearance of the bla(SIM-1) gene in different Acinetobacter spp. in different countries has already begun.

Gene cloning and characterization of MdeA, a novel multidrug efflux pump in Streptococcus mutans.

Multidrug resistance, especially multidrug efflux mechanisms that extrude structurally unrelated cytotoxic compounds from the cell by multidrug transporters, is a serious problem and one of the main reasons for the failure of therapeutic treatment of infections by pathogenic microorganisms as well as of cancer cells. Streptococcus mutans is considered one of the primary causative agents of dental caries and periodontal disease, which comprise the most common oral diseases. A fragment of chromosomal DNA from S. mutans KCTC3065 was cloned using Escherichia coli KAM32 as host cells lacking major multidrug efflux pumps. Although E. coli KAM32 cells were very sensitive to many antimicrobial agents, the transformed cells harboring a recombinant plasmid became resistant to several structurally unrelated antimicrobial agents such as tetracycline, kanamycin, rhodamin 6G, ampicillin, acriflavine, ethidium bromide, and tetraphenylphosphonium chloride. This suggested that the cloned DNA fragment carries a gene encoding a multidrug efflux pump. Among 49 of the multidrug-resistant transformants, we report the functional gene cloning and characterization of the function of one multidrug efflux pump, namely MdeA from S. mutans, which was expressed in E. coli KAM32. Judging from the structural and biochemical properties, we concluded that MdeA is the first cloned and characterized multidrug efflux pump using the proton motive force as the energy for efflux drugs.

Molecular mechanisms of carbapenem resistance in Enterobacter cloacae clinical isolates from Korea and clinical outcome.

We investigated the molecular mechanisms of carbapenem resistance in clinical isolates of Enterobacter cloacae and their clinical characteristics. Nonreplicable E. cloacae isolates were recovered from six cancer patients and one patient with liver cirrhosis at a tertiary-care hospital in Korea between 2002 and 2009. Two patients who were considered to have a true infection caused by these microorganisms have died. All isolates produced AmpC ß-lactamases, including ACT-1, ACT-2, MIR-3 and DHA-1, and CTX-M- or SHV-type extended-spectrum ß-lactamase. Two isolates produced plasmid-borne VIM-2 carbapenemase. All probes specific for bla(AmpC) genes hybridized with I-CeuI chromosomal fragments were also recognized by a probe specific for 16S rDNA, suggesting a chromosomal location. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that a major outer membrane protein, OmpF, was absent in all isolates. PFGE of XbaI-digested DNA were considered to be unrelated. The results of our study suggest that the chromosomal AmpC ß-lactamase with impermeability in E. cloacae clinical isolates implicated in reduced carbapenem susceptibility. Although carbapenem-resistant E. cloacae isolates were isolated in a few patients in our study, the clinical outcomes were grave. Therefore, the patients colonized or infected by carbapenem-resistant E. cloacae isolates should gain attention of antibiotic therapy.

Comparison of the genetic structures surrounding qnrA1 in Korean Enterobacter cloacae and Chinese Escherichia coli strains isolated in the early 2000s: evidence for qnrA mobilization via Inc HI2 type plasmid.

The flanking genetic structure of qnrA1 in Korean Enterobacter loacae was identical to that of the Chinese Escherichia coli strain, the first qnrA1-carrying strain reported in Asia. Analysis of restriction enzyme sites and Southern blot hybridization results showed that qnrA1 was transferred between E. cloacae and E. coli via Inc HI2 type plasmid.

Proteomic analysis on acetate metabolism in Citrobacter sp. BL-4.

Mass production of glucosamine (GlcN) using microbial cells is a worthy approach to increase added values and keep safety problems in GlcN production process. Prior to set up a microbial cellular platform, this study was to assess acetate metabolism in Citrobacter sp. BL-4 (BL-4) which has produced a polyglucosamine PGB-2. The LC-MS analysis was conducted after protein separation on the 1D-PAGE to accomplish the purpose of this study. 280 proteins were totally identified and 188 proteins were separated as acetate-related proteins in BL-4. Acetate was converted to acetyl-CoA by acetyl-CoA synthetase up-regulated in the acetate medium. The glyoxylate bypass in the acetate medium was up-regulated with over-expression of isocitrate lyases and 2D-PAGE confirmed this differential expression. Using (1)H-NMR analysis, the product of isocitrate lyases, succinate, increased about 15 times in the acetate medium. During acetate metabolism proteins involved in the lipid metabolism and hexosamine biosynthesis were over-expressed in the acetate medium, while proteins involved in TCA cycle, pentose phosphate cycle and purine metabolism were down-regulated. Taken together, the results from the proteomic analysis can be applied to improve GlcN production and to develop metabolic engineering in BL-4.

Chromosomal cephalosporinase in Enterobacter hormaechei as an ancestor of ACT-1 plasmid-mediated AmpC ß-lactamase.

In this study of the diversity of AmpC ß-lactamase in clinical isolates of Enterobacter spp., a strain was found carrying the plasmid-mediated AmpC ß-lactamase ACT-1 gene on its chromosome. The strain was identified as Enterobacter hormaechei using phylogenetic analysis of 16S rRNA and hsp60 genes. In addition, the species was confirmed by DNA-DNA hybridization. The genetic environment of the bla(ACT-1) gene was characterized, including the ampR and ampG genes, using a two-step PCR. The amino acid sequences of AmpR at serine 35, arginine 86, glycine 102, aspartic acid 135 and tyrosine 264 were conserved. Measurement of the transcription level of the bla(ACT-1) gene using real-time quantitative PCR showed that it increased 1.98-fold following cefoxitin induction. These results suggest that the plasmid-mediated bla(ACT-1) gene originated from the chromosome of E. hormaechei.

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-ß-lactamase (MBL) and OXA carbapenemase screening. Overall, the performance of Hodge test was better with MacConkey agar due to enhanced release of ß-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.

Genetic diversity of chromosomal metallo-beta-lactamase genes in clinical isolates of Elizabethkingia meningoseptica from Korea.

This study was performed to characterize the chromosomal metallo-beta-lactamases (MBLs) of Elizabethkingia meningoseptica isolated from Korea and to propose a clustering method of BlaB and GOB MBLs based on their amino acid similarities. Chromosomal MBL genes were amplified by PCR from 31 clinical isolates of E. meningoseptica. These PCR products were then cloned into a vector and electrotransformed into E. coli DH5 alpha. Nucleotide sequencing was performed by the dideoxy chain termination method using PCR products or cloned DNA fragments. Antimicrobial susceptibilities were determined by the agar dilution method. PCR experiments showed that all 31 E. meningoseptica isolates contained both the blaB and the bla (GOB) genes. DNA sequence analysis revealed that E. meningoseptica isolates possessed seven types of blaB gene, including five novel variants (blaB-9 to blaB-13) and 11 types of bla (GOB) gene, including 10 novel variants (bla (GOB-8) to bla (GOB-17)). The most common combination of MBL was BlaB-12 plus GOB-17 (n=19). Minimum inhibitory concentrations of imipenem and meropenem for the electrotransformants harboring novel BlaB and GOB MBLs were two- or four-fold higher than those for the recipient E. coli DH5 alpha. BlaB and GOB MBLs were grouped in three and six clusters including fifteen novel variants, respectively, based on amino acid similarities.