A Case of Whole Genome Analysis of SARSCoV-2 Using Oxford Nanopore MinION System / 대한임상미생물학회지

The application of whole genome sequencing on SARS-CoV-2 viral genome is essential for our understanding of the molecular epidemiology and spread of viruses in the community. The portable whole genome sequencer MinION (Oxford Nanopore Technologies, ONT, UK) could be feasibly used in a clinical microbiology laboratory without the need of vast resources or stringent operating conditions. We used the MinION sequencer to analyze the viral genome sequence of one SARS-CoV-2 strain. In June 2020, nasopharyngeal specimen from one patient was subjected to whole-genome analysis using the nCoV-2019 sequencing protocol v2 of ARTIC using the MinION sequencer. The ONT MinKNOW software, RAMPART tool, and Genome Workbench were used. We identified 11 nucleotide variants using the Wuhan-Hu-1 isolate (NC_045512.2) as the reference sequence. There were six nucleotide variants (T265I, F924, Y3884L, P4715L, L5462, and Q6804L) in the ORF1ab region, one variant (D614G) in the S gene, one variant (Q57H) in ORF3a, one variant (P302) in the N gene, and two variants in each the 5′-UTR and 3′-UTR. In this prolonged coronavirus disease 2019 (COVID-19) pandemic season, the MinION system that operates an amplicon-based whole-genome sequencing protocol could be a rapid and reliable sequencer without the need of cumbersome viral cultivation.

Nasal Colonization of Serine Protease esp Positive Staphylococcus epidermidis Affecting Staphylococcus aureus Colonization / 대한임상미생물학회지

Background@#Staphylococcus aureus is a common colonizer of the nasal vestibule and is found in approximately 20%–30% of healthy adults, while Staphylococcus epidermidis appears to be the most frequent colonizer in all regions of the upper respiratory tract. Esp, aserine protease of S. epidermidis, was reported to inhibit S.aureus colonization. This study was performed to examine the nasal colonization of S. aureus and S. epidermidis and the presence of esp determinants. @*Methods@#Nasal swab specimens from 54 patients were cultured on blood agar plates (BAP) and selective media for S. aureus (S. aureus ID, bioMerieux, France) for the isolation of S.aureus and S. epidermidis. After 48 hours of incubation of with BAP, three or four colonies suspected of being coagulase-negative staphylococci (CNS) were identified by MALDI-TOF MS (Bruker, Germany). Polymerase chain reaction (PCR) for esp was performed on all CNS isolates identified as S. epidermidis. @*Results@#Forty-three S. epidermidis strains were isolated from 18 (33.3%) of the 54 patients.Nine (50.0%) of the 18 patients carried S. aureus, while the other nine did not. Of the 36 S. epidermidis non-carriers, 13 (36.1%) were colonized by S. aureus. All S. epidermidis strains were confirmed by PCR to have esp determinants. @*Conclusion@#S. epidermidis colonization did not affect S. aureus colonization in the nasal cavity. All S. epidermidis strains harbored the esp gene. We could not find any differences in the nasal colonization rates of S. aureus according to the presence of esp-positive S. epidermidis. Further research on the characterization of S. epidermidis in Korea is needed to understand the association between S. epidermidis and S. aureus colonization.

Nasal Colonization of Serine Protease esp Positive Staphylococcus epidermidis Affecting Staphylococcus aureus Colonization / 대한임상미생물학회지

Background@#Staphylococcus aureus is a common colonizer of the nasal vestibule and is found in approximately 20%–30% of healthy adults, while Staphylococcus epidermidis appears to be the most frequent colonizer in all regions of the upper respiratory tract. Esp, aserine protease of S. epidermidis, was reported to inhibit S.aureus colonization. This study was performed to examine the nasal colonization of S. aureus and S. epidermidis and the presence of esp determinants. @*Methods@#Nasal swab specimens from 54 patients were cultured on blood agar plates (BAP) and selective media for S. aureus (S. aureus ID, bioMerieux, France) for the isolation of S.aureus and S. epidermidis. After 48 hours of incubation of with BAP, three or four colonies suspected of being coagulase-negative staphylococci (CNS) were identified by MALDI-TOF MS (Bruker, Germany). Polymerase chain reaction (PCR) for esp was performed on all CNS isolates identified as S. epidermidis. @*Results@#Forty-three S. epidermidis strains were isolated from 18 (33.3%) of the 54 patients.Nine (50.0%) of the 18 patients carried S. aureus, while the other nine did not. Of the 36 S. epidermidis non-carriers, 13 (36.1%) were colonized by S. aureus. All S. epidermidis strains were confirmed by PCR to have esp determinants. @*Conclusion@#S. epidermidis colonization did not affect S. aureus colonization in the nasal cavity. All S. epidermidis strains harbored the esp gene. We could not find any differences in the nasal colonization rates of S. aureus according to the presence of esp-positive S. epidermidis. Further research on the characterization of S. epidermidis in Korea is needed to understand the association between S. epidermidis and S. aureus colonization.

Positivity of Carbapenemase-producing Enterobacteriaceae in Patients Following Exposure within Long-term Care Facilities in Seoul, Korea

Background@#Carbapenemase-producing Enterobacteriaceae (CPE) are emerging as a worldwide threat. Long-term care facilities (LTCFs) are considered a reservoir for CPE and play a central role in transmission to acute care hospitals. We investigated the CPE positivity in patients exposed to CPE in LTCFs. Furthermore, we analyzed the CPE positivity rates in the environment exposed to CPE. @*Methods@#We collected rectal swab specimens from patients residing in LTCFs who were exposed to CPE. Environmental sampling was performed by infection control practitioners from sites classified as patient private space, common space in the patient room, common space other than patient rooms, and nursing station. Each sample was cultured on a Chrom KlebsiellaF pneumoniae carbapenemase (KPC) agar for CPE screening. The positive isolates were subjected to a polymerase chain reaction to identify the presence of bla KPC , bla VIM , bla IMP , bla OXA-48 , and bla NDM and determine CPE genotype. @*Results@#From 65 index cases, a total of 24 hospitals and 481 patients were enrolled; 414 patients who had resided in the same patient room as a patient with confirmed CPE and 67 patients who were newly admitted to that patient room. A total of 117 (24.3%) patients were positive for CPE among which 93 (22.5%, 93/414) were already admitted patients and 24 (35.8%, 24/67) were newly admitted patients. A total of 163 CPEs were detected and K. pneumoniae (n = 104, 63.8%) was the most common bacteria followed by Escherichia coli (n = 43, 26.4%) and Citrobacter koseri (n = 11, 6.7%). Environmental sampling was performed in 24 hospitals and 604 sites. A total of 12 sites (2.0%) were positive for CPE and sink in the nursing station (n = 6, 4.2%) was the most contaminated space. @*Conclusion@#CPE colonization rates in patients exposed to CPE in LTCFs were higher than those found in acute care hospitals. Proper infection control measures for detecting and reducing CPE colonization in patients residing in LTCFs are required. Newly admitted patients could also be carriers; therefore, infection control for newly admitted patients also needs to be thorough.

Seroprevalence of Anti-SARS-CoV-2 Antibodies among Outpatients in Southwestern Seoul, Korea

Serosurveillance studies reveal the actual disease burden and herd immunity level in the population. In Seoul, Korea, a cross-sectional investigation showed 0.07% anti-severe acute respiratory syndrome coronavirus-2 antibody seropositivity among 1,500 outpatients of the university hospitals. Low seroprevalence reflects well-implemented social distancing.Serosurveillance should be repeated as the pandemic progresses.

Comparison of Three Methods with CHROMagar for Surveillance Culture of Carbapenem-Resistant Acinetobacter baumannii / 대한임상미생물학회지

Background@#Carbapenem-resistant Acinetobacter baumannii (CRAB) has emerged as an important nosocomial pathogen.The purpose of this study was to determine the effective methods for performing surveillance cultures of CRAB. @*Methods@#Nasal and rectal swabs were obtained concurrently from hospitalized intensive care unit patients colonized with CRAB. All the samples were inoculated in CHROMagar Acinetobacter medium with CR102 (CHROMagar), MacConkey agar medium supplemented with 5 µg/mL imipenem (MCA-IPM), and triptic soy broth medium supplemented with 5 µg/ mL imipenem (TSB-IPM). CRAB detection rates for each sample were compared. @*Results@#The CRAB detection rate in either one of the nasal or rectal swabs from the 37 patients tested were 89.2% (33/37) with the use of CHROMagar, 78.4% (29/37) with the use of MCA-IMP, and 86.5% (32/37) with the use of TSB-IMP. @*Conclusion@#We determined that concurrent use of both nasal and rectal swabs and CHROMagar could be an effective method for CRAB surveillance cultures.

Rapid Identification of OXA-48-like, KPC, NDM, and VIM Carbapenemase-Producing Enterobacteriaceae From Culture: Evaluation of the RESIST-4 O.K.N.V. Multiplex Lateral Flow Assay

There is an urgent need for accurate and rapid diagnostic assays capable of identifying carbapenemase-producing Enterobacteriaceae (CPE). We assessed the performance of the RESIST-4 O.K.N.V. (OKNV) assay (Coris BioConcept, Gembloux, Belgium) for the identification of oxacillinase (OXA)-48-like-, Klebsiella pneumoniae carbapenemase (KPC)-, New Delhi metallo-β-lactamase (NDM)-, and Verona integron-encoded metallo-β-lactamase (VIM)-producing Enterobacteriaceae grown on sheep blood agar (SBA) and the CHROMagar KPC medium. Sixty-five carbapenem-resistant Enterobacteriaceae (CRE) isolates with characterized carbapenemase content were used to evaluate the OKNV assay. The assay correctly identified all 30 isolates that produced one of the four targeted carbapenemase families. Additionally, it correctly identified 15 isolates that co-produced KPC and NDM, VIM and NDM or OXA-48-like and NDM, but failed to identify an NDM-1 and OXA-232 co-producing Klebsiella pneumoniae isolate. All 16 non-carbapenemase-producing CRE and four CPE isolates exhibited negative results, and no cross-reaction was observed. Overall, the sensitivity and specificity of the assay were 97.8% and 100%, respectively. The OKNV assay is an accurate and rapid assay for identifying OXA-48-like, KPC, NDM, and VIM carbapenemases produced by Enterobacteriaceae isolates cultured on both SBA and the CHROMagar KPC media in the clinical microbiology laboratory.

Serotype Distribution and Antimicrobial Resistance of Invasive and Noninvasive Streptococcus pneumoniae Isolates in Korea between 2014 and 2016

BACKGROUND: Several factors contribute to differences in Streptococcus pneumoniae serotype distribution. We investigated the serotype distribution and antimicrobial resistance of S. pneumoniae isolated between 2014 and 2016 in Korea. METHODS: We collected a total of 1,855 S. pneumoniae isolates from 44 hospitals between May 2014 and May 2016, and analyzed the serotypes by sequential multiplex PCR. We investigated the distribution of each serotype by patient age, source of the clinical specimen, and antimicrobial resistance pattern. RESULTS: The most common serotypes were 11A (10.1%), followed by 19A (8.8%), 3 (8.5%), 34 (8.1%), 23A (7.3%), and 35B (6.2%). The major invasive serotypes were 3 (12.6%), 19A (7.8%), 34 (7.8%), 10A (6.8%), and 11A (6.8%). Serotypes 10A, 15B, 19A, and 12F were more common in patients ≤5 years old, while serotype 3 was more common in patients ≥65 years old compared with the other age groups. The coverage rates of pneumococcal conjugate vaccine (PCV)7, PCV10, PCV13, and pneumococcal polysaccharide vaccine 23 were 11.8%, 12.12%, 33.3%, and 53.6%, respectively. Of the 1,855 isolates, 857 (46.2%) were multi-drug resistant (MDR), with serotypes 11A and 19A predominant among the MDR strains. The resistance rates against penicillin, cefotaxime, and levofloxacin were 22.8%, 12.5%, and 9.4%, respectively. CONCLUSIONS: There were significant changes in the major S. pneumoniae serotypes in the community. Non-PCV13 serotypes increased in patients ≤5 years old following the introduction of national immunization programs with the 10- and 13-polyvalent vaccines.

Performance of HemosIL ReadiPlasTin, a Liquid Reagent for Prothrombin Time Measurement

BACKGROUND: Prothrombin time (PT) measurement is an important test for screening blood coagulation disorders and monitoring anticoagulant therapy. In this study, we evaluated the analytical performance of HemosIL ReadiPlasTin (Instrumentation Laboratory, USA), a liquid reagent for PT measurement. METHODS: The precision of HemosIL ReadiPlasTin was evaluated according to the Clinical and Laboratory Standards Institute (CLSI) EP5-A3 guidelines. Further, comparison with HemosIL RecombiPlasTin 2G (Instrumentation Laboratory, USA) was made according to the CLSI EP9-A3 guidelines. The reference intervals were established according to the CLSI C28-A3 guidelines. RESULTS: The coefficient of variation values for repeatability and total imprecision at two levels of control materials were lower than 1.1% and 3.4%, respectively. The performance of HemosIL ReadiPlasTin was comparable to that of HemosIL RecombiPlasTin 2G, with a high correlation (r=0.996). The reference interval for normal subjects was 10.4–13.3 seconds. CONCLUSIONS: HemosIL ReadiPlasTin showed an acceptable degree of imprecision and its performance showed high correlation with that of a conventional reagent. Therefore, it is expected to be useful for PT measurement in clinical laboratories.

Evaluation of the Real-Q RV Detection Kit for the Identification of Viruses That Result in Respiratory Infections

Viral respiratory infections are one of the most common infections worldwide. It is important to detect the virus early and precisely. In this study, we evaluated the limit of detection (LoD) and usefulness of the Real-Q RV Detection kit (BioSewoom, Seoul, Korea). We measured the LoD of the Real-Q RV Detection kit using 10 strains of standard viruses. We then compared the detection results by the Allplex Respiratory Panel Assay kit (Seegene, Seoul, Korea) using 123 clinical specimens. The discrepant results were confirmed by sequencing. Among the 10 standard viruses, the LoD of human rhinovirus (HRV) was the lowest and that of parainfluenza virus 2 and 3 was relatively high as detected by Real-Q RV Detection kit. Agreements of the two kits ranged from 95.9% to 100%. Three specimens detected negative by the Allplex Respiratory Panel kit were detected as adenovirus (AdV) by the Real-Q RV Detection kit and were confirmed by sequencing. Similarly, a specimen detected negative by the Allplex Respiratory Panel kit was detected as HRV by the Real-Q RV Detection kit and was confirmed by sequencing. A specimen detected as human enterovirus by the Allplex Respiratory Panel kit was detected as HRV by the Real-Q RV Detection kit and was confirmed by sequencing. Real-Q RV Detection kit showed good diagnostic performance and can be useful for detecting major viruses that cause respiratory infections.

Evaluation of a New Multiplex Real-Time PCR Assay for Detecting Gastroenteritis-Causing Viruses in Stool Samples

BACKGROUND: Diarrhea has been the second leading cause of death among children under the age of five, and the rapid and accurate pathogen diagnosis in patients with diarrhea is crucial for reducing morbidity and mortality. A newly developed one-step multiplex real-time PCR assay, the Allplex GI-Virus Assay, was evaluated for its ability to detect six diarrhea-causing viruses (rotavirus, norovirus genogroup I (GI) and genogroup II (GII), enteric adenovirus, astrovirus, and sapovirus) in stool samples. METHODS: The performance of the Allplex assay was compared with those of another multiplex PCR assay (Seeplex Diarrhea-V Ace Detection) and genotyping by sequencing, using 446 stool samples from patients with acute gastroenteritis. RESULTS: The overall agreement rates between the results of the Allplex and Seeplex assays were 98.7% for rotavirus, 99.1% for norovirus GI, 93.3% for norovirus GII, 98.0% for adenovirus, and 99.6% for astrovirus. The overall agreement rates between the Allplex assay and genotyping were 99.1% for rotavirus, 99.1% for norovirus GI, 98.7% for norovirus GII, 89.7% for adenovirus, 98.2% for astrovirus, and 99.8% for sapovirus. In addition, eight rotavirus genotypes, three norovirus GI genotypes, four norovirus GII genotypes, eight adenovirus genotypes, two astrovirus genotypes, and two sapovirus genotypes were detected. CONCLUSIONS: The Allplex assay showed high agreement with Seeplex and genotyping results, and was able to additionally detect sapoviruses. The Allplex assay could be useful in identifying viral gastrointestinal infections in patients with acute gastroenteritis symptoms.

Comparison of the Luminex xTAG Respiratory Viral Panel Fast v2 Assay With Anyplex II RV16 Detection Kit and AdvanSure RV Real-Time RT-PCR Assay for the Detection of Respiratory Viruses

BACKGROUND: The accurate and rapid identification of the causative viruses is important for the timely diagnosis and management of respiratory infections. Multiplex molecular diagnostic techniques have been widely adopted to detect respiratory viruses. We compared the results of a newly upgraded, multiplex, molecular bead-based respiratory viral panel (RVP) assay with the results of Anyplex II RV16 detection kit and AdvanSure RV real-time RT-PCR assay. METHODS: We tested 254 respiratory specimens and cultured viral strains using the Luminex xTAG RVP Fast v2 assay (Luminex Molecular Diagnostics, Canada) and Anyplex II RV16 detection kit and compared the results. Specimens showing discordant results between the two assays were tested with a AdvanSure RV real-time RT-PCR assay. RESULTS: Of the 254 respiratory specimens, there was total agreement in the results between the xTAG RVP Fast v2 assay and the other real-time PCR assay in 94.1–100% of the specimens. The agreement levels were relatively low (94.1–97.6%) for specimens of adenovirus, coronavirus NL63, and parainfluenza type 3. In comparison to the other assay, the xTAG RVP Fast v2 assay detected a higher number of parainfluenza type 3 (4 cases) and metapneumovirus (9 cases). CONCLUSIONS: The xTAG RVP Fast v2 assay showed comparable capabilities compared with the other assays; it will be useful for identifying respiratory viral infections in patients with respiratory symptoms. Clinicians should be aware of the characteristics of the assays they use, since different assays show different detectability for each virus.

Evaluation of Diagnostic Performance of RAPIDEC CARBA NP Test for Carbapenemase-Producing Enterobacteriaceae / 대한임상미생물학회지

BACKGROUND: Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae are resistant to most β-lactam antibiotics except carbapenems. In recent years, infrequently isolated Enterobacteriaceae that produce carbapenemase pose a serious threat in the selection of appropriate therapeutic antibiotics. The rapid detection method of carbapenemase-producing Enterobacteriaceae (CPE) is necessary to prevent the spread of CPE into healthcare facilities. METHODS: One hundred clinical Enterobacteriaceae isolates (Klebsiella pneumoniae 40, Escherichia coli 40, others 20) showing susceptibility to carbapenems and positivity in the CLSI ESBL phenotypic test from November 2015 to March 2016 and 59 stocked Enterobacteriaceae isolates harboring resistance genes producing carbapenemase (K. pneumoniae 56, Enterobacter cloacae 2, E. coli 1; types of CPE: KPC 36, GES 12, NDM 6, VIM 2, OXA 2, IMP 1) were subjected to the RAPIDEC CARBA NP test (bioMérieux, France) and CPE phenotypic test using the modified Hodge test (MHT) and carbapenemase inhibition test. RESULTS: All of the 100 Enterobacteriaceae isolates with carbapenem susceptibility and ESBL positivity were negative on the RAPIDEC CARBA NP test and CPE phenotypic test. Of 59 stock CPE isolates, 53 and 42 showed positive results to the RAPIDEC CARBA NP test and MHT, respectively. The sensitivity and specificity of the RAPIDEC CARBA NP test for detecting CPE were 89.8% and 100%, respectively. CONCLUSION: The RAPIDEC CARBA NP test is simple and produces a result within 3 hr. In conclusion, the test is a useful screen for detecting CPE because it shows high sensitivity and specificity for CPE detection.

Disk Carbapenemase Test for the Rapid Detection of KPC-, NDM-, and Other Metallo-β-Lactamase-Producing Gram-Negative Bacilli

BACKGROUND: Rapid detection of carbapenemase-producing gram-negative bacilli (GNB) is required for optimal treatment of infected patients. We developed and assessed a new disk carbapenemase test (DCT). METHODS: Paper disks containing 0.3 mg of imipenem and bromothymol blue indicator were developed, and the performance of the DCT were evaluated by using 742 strains of GNB with or without carbapenemases. RESULTS: The paper disks were simple to prepare, and the dried disks were stable at -20℃ and at 4℃. The DCT detected 212 of 215 strains (98.6% sensitivity with 95% confidence interval [CI] 96.0-99.5%) of GNB with known class A (KPC and Sme) and class B (NDM, IMP, VIM, and SIM) carbapenemases within 60 min, but failed to detect GES-5 carbapenemase. The DCT also detected all two Escherichia coli isolates with OXA-48, but failed to detect GNB with OXA-232, and other OXA carbapenemases. The DCT showed 100% specificity (95% CI, 99.2-100%) in the test of 448 imipenem-nonsusceptible, but carbapenemase genes not tested, clinical isolates of GNB. CONCLUSIONS: The DCT is simple and can be easily performed, even in small laboratories, for the rapid detection of GNB with KPC, NDM and the majority of IMP, VIM, and SIM carbapenemases.

In Vitro Synergistic Effects of Antimicrobial Combinations on Extensively Drug-Resistant Pseudomonas aeruginosa and Acinetobacter baumannii Isolates

BACKGROUND: Extensively drug-resistant (XDR) Pseudomonas aeruginosa and Acinetobacter baumannii are a threat to hospitalized patients. We evaluated the effects of antimicrobial combinations on XDR P. aeruginosa and A. baumannii isolates. METHODS: P. aeruginosa and A. baumannii isolates, which were resistant to all antibiotics except colistin (CL), were collected from eight hospitals in Korea. Genes encoding metallo-beta-lactamases (MBLs) and OXA carbapenemases were detected by PCR in eight P. aeruginosa and 30 A. baumannii isolates. In vitro synergy of antimicrobial combinations was tested by using the checkerboard method. RESULTS: Minimum inhibitory concentrations of beta-lactams, aminoglycosides, and fluoroquinolones were very high, while that of CL was low for majority of XDR P. aeruginosa and A. baumannii isolates. Antimicrobial combinations including Imipenem (IPM)-CL, ceftazidime (CAZ)-CL, and rifampin (RIF)-CL exerted only additive/indifferent effects on majority of XDR P. aeruginosa isolates. Proportions of XDR A. baumannii isolates that showed synergistic and additive/indifferent inhibition after treatment with antimicrobial combinations used are as follows: IPM-ampicillin-sulbactam (AMS), 17% and 80% isolates, respectively; IPM-rifampin (RIF), 13% and 81% isolates, respectively; IPM-CL, 13% and 87% isolates, respectively; and RIF-COL, 20% and 73% isolates, respectively. Significant proportion (19%) of XDR P. aeruginosa isolates produced MBLs, and majority (82%) of A. baumannii isolates produced either MBLs or OXA-23. CONCLUSIONS: Our results suggest that combinations of IPM-AMS, IPM-RIF, IPM-CL, and RIF-CL are more useful than individual drugs for treating 13-20% of XDR A. baumannii infections.

Prevalence and Molecular Characteristics of Carbapenemase-Producing Enterobacteriaceae From Five Hospitals in Korea

BACKGROUND: The emergence of carbapenemase-producing Enterobacteriaceae (CPE) represents a major clinical problem because these bacteria are resistant to most antibiotics. CPE remain relatively uncommon in Korea. We report the prevalence, clinical characteristics, and molecular epidemiology of CPE isolates collected from five university hospitals in Korea. METHODS: Between January and December 2015, 393 non-duplicated isolates that were nonsusceptible to ertapenem were analyzed. Production of carbapenemase, extended-spectrum β-lactamase, and AmpC β-lactamase was determined by genotypic tests. Antimicrobial susceptibility profiles were determined by using an Etest. Clonality of Klebsiella pneumoniae carbapenemase (KPC)-2-producing and oxacillinase (OXA)-232-producing Klebsiella pneumoniae isolates was determined by pulsed-field gel electrophoresis (PFGE). RESULTS: Of the 393 isolates tested, 79 (20.1%) were CPE. Of these 79 isolates, 47 (59.5%) harbored the bla(OXA-232) gene while the remaining isolates carried genes bla(KPC-2) (n=27), bla(IMP-1) (n=4), and bla(NDM-1) (n=1). Among the 24 KPC-2 K. pneumoniae isolates from hospital B, 100% were resistant to carbapenems, 8% to colistin, and 0% to tigecycline. Among the 45 OXA-232 K. pneumoniae at hospital C, 95% were resistant to ertapenem, 68% to imipenem, 95% to meropenem, 10% to colistin, and 24% to tigecycline. PFGE analysis revealed a unique pattern for KPC-2 K. pneumoniae and identified 30 isolates belonging to the dominant pulsotypes (PT)1 and PT2 among 41 OXA-232 K. pneumoniae isolates. CONCLUSIONS: CPE strains are present in Korea, with the majority of K. pneumoniae isolates producing OXA-232 and KPC-2. The prevalence and predominant genotypes of CPE show hospital-specific differences.

Detection of Rotavirus from the Inner Surfaces of Domestic Refrigerators

BACKGROUND: Rotavirus is the leading cause of acute viral gastroenteritis, particularly in children, and is transmitted through the fecal-to-oral route by contaminated food or the environment. This study examined the contamination of the inner surfaces of domestic refrigerators with pathogens causing gastroenteritis. METHODS: Swab specimens from shelf surfaces of freezers and refrigerators were collected from 10 domestic refrigerators. Multiplex PCR for bacterial and viral pathogens causing acute gastroenteritis was performed. The VP7 and VP4 genes of rotavirus were amplified and then analyzed by DNA sequencing. RESULTS: Rotavirus was detected in five domestic refrigerators in the same apartment complex. All rotavirus samples showed the G1 genotype and the same DNA sequences. No pathogens causing acute gastroenteritis were identified in the other five domestic refrigerators. CONCLUSIONS: The inner surfaces of domestic refrigerators can be contaminated with pathogens causing acute gastroenteritis, such as rotavirus. Attention should be given to the hygiene of refrigerators. To estimate the contamination or hygienic status for food storage, testing for viral pathogens combined with ordinary bacterial cultures may be necessary.

Carbapenem Inactivation Method: Accurate Detection and Easy Interpretation of Carbapenemase Production in Enterobacteriaceae and Pseudomonas spp / 대한임상미생물학회지

BACKGROUND: We evaluated the carbapenem inactivation method (CIM) compared with the modified Hodge test (MHT) for the detection of carbapenemase-producing Gram-negative bacilli. METHODS: A total of 61 isolates of carbapenemase-producing Enterobacteriaceae (CPE: 14 KPC, 7 GES-5, 8 NDM-1, 9 VIM-2, 9 IMP-1, and 14 OXA-48-like), 34 isolates of metallo-β-lactamase (MBL)-producing Pseudomonas spp. (14 VIM-2 and 20 IMP-6), and 70 carbapenem-nonsusceptible carbapenemase-negative isolates were included. The CIM and MHT were performed for all of the isolates. To perform the CIM, a meropenem disk was incubated with a suspension of the isolate to be tested and then on Mueller-Hinton agar with the Escherichia coli ATCC 29522 strains. The absence of an inhibition zone indicates presence of a carbapenemase. The presence of a clearing zone indicates lack of a carbapenemase. RESULTS: The total sensitivity and specificity of CIM (96% sensitivity and 100% specificity) in carbapenem-nonsusceptible Enterobacteriaceae and Pseudomonas spp. were better than those of the MHT (77% sensitivity and 94% specificity). The interpretation of CIM results was easy, with no or 20 mm inhibition zones indicating negative carbapenemase activity. CONCLUSION: The CIM had excellent sensitivity and specificity for detection of CPE and MBL-producing Pseudomonas spp., and a positive result was easily determined, unlike the MHT.

Emergence and Spread of OXA-48-Like Carbapenemase-Producing Enterobacteriaceae / 병원감염관리

Since 2001, ten more OXA-48 variants have been identified. Shewanella spp. has been thought to be the original host for OXA-48-like enzymes. These enzymes strongly hydrolyze penicillins and weakly hydrolyze carbapenems, with very weak activity against broad-spectrum cephalosporins. The OXA-48-like genes are always plasmid-borne and have been located in insertion sequences. OXA-48-like carbapenemases have been identified mainly from Turkey, North African countries, the Middle East, and India. Furthermore, the emergence and outbreak of OXA-48-like producers in Korea have been reported recently. Because some OXA-48-like-producing Enterobacteriaceae isolates do not exhibit resistance to broad-spectrum cephalosporins and only decreased susceptibility to carbapenems, their detection can be difficult. Adequate screening and detection methods are required to prevent and control the dissemination of OXA-48-like-producing Enterobacteriaceae.

Establishing Quality Control Ranges for Antimicrobial Susceptibility Testing of Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus: A Cornerstone to Develop Reference Strains for Korean Clinical Microbiology Laboratories

Quality control (QC) processes are being performed in the majority of clinical microbiology laboratories to ensure the performance of microbial identification and antimicrobial susceptibility testing by using ATCC strains. To obtain these ATCC strains, some inconveniences are encountered concerning the purchase cost of the strains and the shipping time required. This study was focused on constructing a database of reference strains for QC processes using domestic bacterial strains, concentrating primarily on antimicrobial susceptibility testing. Three strains (Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus) that showed legible results in preliminary testing were selected. The minimal inhibitory concentrations (MICs) and zone diameters (ZDs) of eight antimicrobials for each strain were determined according to the CLSI M23. All resulting MIC and ZD ranges included at least 95% of the data. The ZD QC ranges obtained by using the CLSI method were less than 12 mm, and the MIC QC ranges extended no more than five dilutions. This study is a preliminary attempt to construct a bank of Korean QC strains. With further studies, a positive outcome toward cost and time reduction can be anticipated.