Application of the Whole Genome-Based Bacterial Identification System, TrueBac ID, Using Clinical Isolates That Were Not Identified With Three Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Systems

BACKGROUND: Next-generation sequencing is increasingly used for taxonomic identification of pathogenic bacterial isolates. We evaluated the performance of a newly introduced whole genome-based bacterial identification system, TrueBac ID (ChunLab Inc., Seoul, Korea), using clinical isolates that were not identified by three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems and 16S rRNA gene sequencing. METHODS: Thirty-six bacterial isolates were selected from a university-affiliated hospital and a commercial clinical laboratory. Species was identified by three MALDI-TOF MS systems: Bruker Biotyper MS (Bruker Daltonics, Billerica, MA, USA), VITEK MS (bioMérieux, Marcy l'Étoile, France), and ASTA MicroIDSys (ASTA Inc., Suwon, Korea). Whole genome sequencing was conducted using the Illumina MiSeq system (Illumina, San Diego, CA, USA), and genome-based identification was performed using the TrueBac ID cloud system (www.truebacid.com). RESULTS: TrueBac ID assigned 94% (34/36) of the isolates to known (N=25) or novel (N=4) species, genomospecies (N=3), or species group (N=2). The remaining two were identified at the genus level. CONCLUSIONS: TrueBac ID successfully identified the majority of isolates that MALDI-TOF MS failed to identify. Genome-based identification can be a useful tool in clinical laboratories, with its superior accuracy and database-driven operations.ope

Antimicrobial Resistance of Clinically Important Bacteria Isolated from 12 Hospitals in Korea in 2005 and 2006

Background: Emergence and spread of antimicrobial resistant bacteria make it difficult to treat infections. A rapid increase in antimicrobial-resistant bacteria has become a serious problem in many countries including Korea, and it is important to perform a nationwide study of antimicrobial resistance to obtain some basic data that will help solve these problems. The aim of this study was to determine the nationwide prevalence of resistance among frequently isolated bacterial pathogens in 2005 and 2006 in Korea. Methods: We collected routine susceptibility data for medically important bacterial pathogens from 12 university and general hospital laboratories in Korea from April to September in 2005 and from January to June in 2006. Collected data was analyzed by patient group. Results: The proportions of methicillin-resistant Staphylococcus aureus (MRSA) were 65% in 2005 and 72% in 2006, respectively. The resistance rates of Enterococcus faecium to vancomycin were 29% in 2005 and 24% in 2006. The non-susceptible rates of Streptococcus pneumoniae to penicillin were 68% in 2005 and 74% in 2006. The resistant rates of Escherichia coli and Klebsiella pneumoniae to the 3rd generation cephalosporin were 10∼12% and 25∼39%, respectively, in 2005 and 11∼15% and 30∼34% in 2006. In Citrobacter freundii, Enterobacter cloacae and Serratia marcescens, the resistance rates to 3rd generation cephalosporin were 23∼31%, 32∼34%, and 17∼27%, respectively, in 2005 and 21∼37%, 37∼43%, and 13∼31% in 2006. The resistance rates to imipenem and meropenem were 21% and 18%, respectively, in Pseudomonas aeruginosa and 18% and 25% in Acinetobacter baumannii in 2005; 29% and 20% in P. aeruginosa and 18% and 23% in A. baumannii in 2006. Cotrimoxazole and levofloxacin resistance rates of Stenotrophomonas maltophilia were 5% and 13%, respectively, in 2005 and 3% and 7% in 2006. There were no isolates resistant to 3rd generation cephalosporin and fluoroquinolone among non-typhoidal Salmonella in 2005. Conclusion: Antimicrobial resistance of medically important bacteria is still a serious problem in Korea. To manage the problem, a continuous nationwide surveillance and diversified investigation and effort have become more important.ope

The Efficiency of Plasma Exchange for Renal Allograft Recipients with HLA Antibody before Transplantation

Background: Therapeutic plasma exchange (TPE) is used to remove antibodies from the blood stream, thereby preventing them from attacking their targets. We evaluated the strategies to increase the efficiency of TPE for renal allograft recipients with HLA antibody. Methods: A total of 11 patients were evaluated from January 2002 to April 2004. All the patients had been diagnosed with end stage renal disease (ESRD) and then they were scheduled for renal transplantation from a living unrelated donor or a living related donor. TPE was performed for all lymphocyte cross-matching (LCM) positive recipients before renal transplantation. One to three sessions of TPE were performed in 8 patients and four to seven sessions of TPE were performed in 3 patients (mean: 2.81 times). We used normal saline and 4% albumin as a replacement solution. Results: Eleven patients, after the patients' LCM positive serum converted to negative, received the renal transplantation. Of the 11 recipients, only 1 recipient suffered from chronic rejection. Ten recipients maintained normal renal function. Among the 11 recipients, 4 recipients were diagnosed with posttransplantation diabetes mellitus. 3 recipients had a past history of graft failure via acute or chronic rejection. Even these 3 recipients experienced successful renal allograft through pre-transplantation TPE. Also, all the recipients were followed up until June, 2005. Conclusion: For ESRD patients with positive LCM, pre-transplantation TPE dramatically decreases the incidence of acute or chronic rejections by converting positive LCM into negative LCM.ope

국내 분리 Bacteroides fragilis군의 8년간 내성률 변화(1997-2004)

BACKGROUND: Bacteroides fragilis group organisms are the most frequently isolated anaerobes in human infections. Increasing resistance to various antimicrobial agents is a significant problem in choosing appropriate antimicrobial agents to treat anaerobic infections. Periodic monitoring of the regional resistance trends of B. fragilis group isolates is needed. METHODS: A total of 466 nonduplicate clinical isolates of B. fragilis group organisms (276 B. fragilis, 106 Bacteroides thetaiotaomicron, and 84 other B. fragilis group organisms) were collected during the 8-yr period from 1997 to 2004 in a Korean university hospital. Minimum inhibitory concentrations to various antimicrobial agents were determined by the CLSI agar dilution method. RESULTS: Eight isolates were resistant to imipenem. Additionally, the resistance rates to cefotetan were decreased in B. thetaiotaomicron, while those for clindamycin were significantly increased compared to the rates found in previous studies. Depending on species, resistance rates were 1-4% for imipenem, 1-6% for piperacillin-tazobactam, 4-11% for cefoxitin, 33-49% for piperacillin, 14-60% for cefotetan, and 51-76% for clindamycin. No isolates were resistant to chloramphenicol or metronidazole. CONCLUSIONS: Piperacillin-tazobactam, cefoxitin, imipenem, chloramphenicol, and metronidazole are still active against B. fragilis group isolates, while clindamycin no longer has a value as an empirical therapeutic agent in Korea. Furthermore, this study identified the first imipenem-resistant B. fragilis group isolates in Koreaope

A Case of Necrotizing Fasciitis Due to Streptococcus agalactiae, Arcanobacterium haemolyticum, and Finegoldia magna in a Dog-bitten Patient with Diabetes

We report a case of necrotizing fasciitis involving Streptococcus agalactiae, Arcanobacterium haemolyticum, and Finegoldia magna in a 36-yr-old female diabetic patient, which started after a minor dog bite to the toe of the patient. This case suggested that a trivial infection after a minor dog bite in an immunocompromised patient such as diabetes patient could result in a significant complication such as necrotizing fasciitis. The life-threatening infection was cured by timely above-the-knee amputation, as well as penicillin G and clindamycin therapy.ope

Detection of mecA in Strains with Oxacillin and Cefoxitin Disk Tests for Detection of Methicillin-resistant Staphylococcus

Background :Cinical and Laboratory Standards Institute (CLSI) recommends the use of cefoxitin disks instead of long-used oxacillin disks for screening methicillin-resistant isolates of staphylococci. The frequency of discrepant results and accuracy of the tests were evaluated by detecting mecA gene. Method :A total of 3,123 Stapylococci isolates from patients in Severance Hospital were tested during September 2005 to August 2006 by the CLSI-recommended test using both cefoxitin and oxacillin disks. The mecA gene was detected by PCR and the oxacillin minimum inhibitory concentration (MIC) was determined by using agar dilution method for the isolates with discrepant tests. Result :Among 1,915 S. aureus islolates tested, one isolate was resistant to oxacillin disk but susceptible to cefoxitin disk; the isolate did not have mecA gene. Another isolate susceptible to oxacillin but resistant to cefoxitin had mecA gene. Among 1,208 coagulase-negative staphylococcal isolates, 15 isolates were resistant to oxacillin disk but susceptible to cefoxitin disk; the isolates did not have mecA genes. Two isolates susceptible to oxacillin disk but resistant to cefoxitin disk had mecA genes. Among the 16 Staphylococcus isolates that did not have mecA gene, 15 isolates had the oxacillin MICs of 2 g/mL and were considered as methicillin-susceptible, while 1 isolate with the MIC of 4 g/mL was considered as methicillin-resistant. Conclusion :Overall, 1.9% of staphylococcal isolates showed discrepant results when the screening tests were performed by using oxacillin and cefoxitin disks. None of the isolates resistant to oxacillin disk but susceptible to cefoxitin disk had mecA gene. In conclusion, the cefoxitin disk test is more reliable than oxacillin disk test in screening methicillin-resistant staphylococcal isolates.ope

Identification of Bacterial and Fungal Isolates by Sequence Analysis of 16S rRNA and Internal Transcribed Spacer

BACKGROUND: Accurate and rapid identification of pathogens is one of the most important tasks of the clinical microbiology laboratory, and, in cases of rare pathogens, the identification is difficult and time-consuming upon the use of conventional methods alone. Herein, we will report our molecular work involving the identification of bacteria and fungi. METHODS: Sixty bacterial isolates had been collected from November 2004 to May 2007, and 15 fungal isolates had been collected from September 2005 to May 2007. Species identifications were performed using sequence analyses of the 16S rRNA region of bacteria and the internal transcribed spacer (ITS) region of fungi. The data were compared with those of GenBank (http://www.ncbi.nlm.nih.gov/) or EMBL (http://www.ebi.ac.uk/embl/). RESULTS: Sixty bacterial isolates included: 23 isolates with genus information (group 1), 17 isolates (group 2) that were too fastidious for genus or species identification, 16 isolates (group 3) with results from identification kits having low confidence, and 4 isolates (group 4) with odd antibiograms according to the species. In 58 of 60 isolates, identification of the genus or species could be obtained using molecular genetic methods. Thirty-eight isolates (63%) and 20 (33%) of 58 isolates could be identified at the species and genus levels, repectively. Among the total of 15 fungal isolates, 11 (73%) and 4 (27%) isolates were identified at the species and genus levels, respectively. CONCLUSION: 16S rRNA and ITS sequencing analyses are very useful for identifying the species or genus of a pathogenic microorganism in the clinical microbiology laboratoryope

Evaluation of Rapid Assay (Toc A/B Quik Chek) for the Detection of Clostridium difficile Toxins A and B

Background: Toxin immunoassay is widely used for rapid diagnosis of Clostridium difficile-associated diarrhea. The aim of this study was to evaluate the performance of Tox A/B Quik Chek test (TECHLAB, Blacksburg, VA, USA) compared to toxigenic culture. Methods: From September 2006 to August 2007, 959 stools were examined by Tox A/B Quik Chek test and toxigenic culture (C. difficile culture plus tcdB PCR using colonies obtained from culture). Results: Compared to the results of toxigenic culture, the sensitivity and specificity of Tox A/B Quik Chek test were 47.5% and 97.5%, respectively. Conclusion: The sensitivity of Tox A/B Quik Chek test was not high, but the specificity was high. Although Tox A/B Quik Chek test alone is not sufficient to diagnose Clostridium difficile-associated diarrhea, it may aid rapid diagnosis, early treatment and prevention of nosocomial spread of the infection, if supplemented by C. difficile culture or tissue culture cytotoxin assay.ope

In vitro activities of CG400549, a novel FabI inhibitor, against recently isolated clinical staphylococcal strains in Korea

The in vitro activities of CG400549, a novel FabI inhibitor, were compared to those of linezolid and commonly used antimicrobials against recent bacterial isolates. CG400549 had an MIC(90) of 0.5 microg/ml for Staphylococcus aureus strains and was more potent than either linezolid or vancomycin.ope

Two Cases of Vibrio fluvialis Bacteremia in Patients UndergoingCancer Chemotherapy

Vibrio fluvialis is a haplophilic gram-negative bacterium normally found in coastal water and seafood and causes gastroenteritis. There have been a few reports on V. fluvialis gastroenteritis in Korea, but no previous report of isolation from blood. We isolated V. fluvialis from the blood of two patients undergoing cancer chemotherapy.ope