A Case of Fungemia with Co-isolation of Candida parapsilosis and Trichosporon asahii Confirmed by MALDI-TOF MS and D2 rRNA Sequencing

Fungi are a major cause of human infections with diverse clinical manifestations. The incidence of fungal infections has increased over time, particularly in patients who have risk factors such as neutropenia, immune suppression, an intravascular catheter, parenteral nutrition, a prosthetic device, and prior broad spectrum antibiotic therapy. Here, we present an unusual case of co-infection by 2 distinct fungi, Candida parapsilosis and Trichosporon asahii, isolated from a patient who did not have any known risk factors initially, except active pulmonary tuberculosis. Despite the negative conversion of sputum acid-fast bacilli (AFB) culture test after treatment, clinical symptoms were refractory to therapy. The patient developed symptoms suggesting septic shock, and 2 distinct colonies were isolated from a blood specimen, which were identified as C. parapsilosis and T. asahii by MALDI-TOF and rRNA sequencing. Fever and hypotension were relieved after anti-fungal agent injection, and pulmonary lesions identified by imaging also improved.

Considering Revision the Criteria for Patients under Investigations for MERS-CoV Infections: Diarrhea or Not

No abstract available.

Sudden Deaths of Neonates Receiving Intravenous Infusion of Lipid Emulsion Contaminated with Citrobacter freundii

At an intensive care unit, four neonates died consecutively within 80 minutes. Citrobacter freundii was isolated from blood samples of the 4 patients. It was also cultured from the leftover SMOFlipid that had been infused intravenously into the patients. In this in vitro study, we evaluated the bacterial growth kinetics and change in size of fat globules in SMOFlipid contaminated with C. freundii. Following the growth of bacteria, pH of SMOFlipid decreased to < 6, and the number of fat globules larger than 5 µm increased. Pulmonary fat embolism is proposed as a possible cause of the sudden deaths as well as fulminant sepsis.

Annual Report on the External Quality Assessment Scheme for Clinical Microbiology in Korea (2015)

Annual proficiency surveys were conducted in March, June, and September in 2015 by the Clinical Microbiology Subcommittee of the Korean Association of External Quality Assessment Service. The program covers the sections of bacteriology, advanced bacteriology and mycology, mycobacteriology, and parasitology. Each trial was composed of three sets of different combinations of five bacteria and yeasts. These sets were distributed among laboratories for Gram staining, culture, identification, and antimicrobial susceptibility tests. Five slides with fixed sputum smears were provided as part of each trial for acid-fast bacilli detection. The survey material distribution was section-based. Two survey materials were provided in each trial, while five specimens for mycobacterial culture and identification, five specimens for anti-tuberculosis susceptibility testing and two Mycobacterium tuberculosis strains for rapid detection of rifampin and isoniazid resistance were distributed in the March and June trials. Five virtual microscopy files for stool parasite examination were availed by registered participants in the June trial. Out of the 334 enrolled laboratories, 328 (98.2%), 328 (98.2%), and 329 (98.5%) submitted responses in trials I, II, and III, respectively. Identification of bacteria, namely, Escherichia coli, Klebsiella pneumoniae, Enterococcus faecalis, Pseudomonas aeruginosa, Streptococcus pneumoniae, and Vibrio fluvialis by more than 95% of participants was acceptable. Surveillance cultures for vancomycin-resistant enterococci and carbapenem-resistant Enterobacteriaceae were determined accurately by 75.8%–85.3% and 93.1% of the respondents, respectively. Species-level identification of Candida krusei, Candida lusitanae, and Candida guilliermondii was still low at 79.8%, 55.7%, and 42.7%, respectively. Disk diffusion method revealed an unacceptably high false-positive rate of resistance to glycopeptides in E. faecalis and to trimethoprim-sulfamethoxazole in S. pneumoniae. Advanced bacteriology trials revealed unsatisfactory results for species-level identification of moulds. Mycobacterial culture, identification and susceptibility testing, and molecular detection of rifampin and isoniazid resistance were performed exceedingly well by participants. Hymenolepsis diminuta could not be identified by participants, with a correct answer rate of only 46.5% and ‘no parasite seen’ answer rate of only 31.8% for negative specimens. Species-level identification of Candida and moulds was challenging for clinical microbiology laboratories. Disk diffusion method was found to be problematic in testing the susceptibility of microorganisms to glycopeptides and trimethoprim-sulfamethoxazole. Improvement is required in result interpretation of negative specimens in parasitology.

Serotype Distribution and Antimicrobial Susceptibilities of Invasive Streptococcus pneumoniae Isolates from Adults in Korea from 1997 to 2012

In Republic of Korea, a 7-valent pneumococcal conjugated vaccine (PCV7) was licensed for use in infants in 2003, and 13-valent PCV (PCV13) replaced it since 2010. We investigated trends in serotype distribution and antibiotic susceptibility of pneumococcal isolates from adult patients with invasive pneumococcal diseases (IPD). Invasive pneumococcal isolates from adult patients of ≥ 16 years of age were collected from 1997 to 2012. Serotypes of the isolates were determined by the Quellung reaction. Distribution of serotypes was analyzed according to the vaccine types. Antibiotic susceptibility was tested by using E-test strips. A total of 272 invasive pneumococcal isolates were included. The most common serotypes were serotype 19F (8.5%, 23/272), and serotype 3 (8.1%, 22/272), and 24.6% (67/272) of the isolates were of non-vaccine serotypes. Of the 272 isolates, 2.6% (7/272) were penicillin MICs of ≥ 4 µg/mL. The proportion of the PCV13 serotypes decreased from 63.3% (50/79) in 1997-2003 to 48.6% (17/35) in 2011-2012, whereas that of non-vaccine serotypes was 26.6% (21/79) and 25.7% (9/35), respectively, for the same periods. The proportion of the PCV13 serotypes showed a decreasing trend among adult patients with IPD over the study period.

Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens

Rapid and accurate identification of an influenza outbreak is essential for patient care and treatment. We describe a next-generation sequencing (NGS)-based, unbiased deep sequencing method in clinical specimens to investigate an influenza outbreak. Nasopharyngeal swabs from patients were collected for molecular epidemiological analysis. Total RNA was sequenced by using the NGS technology as paired-end 250 bp reads. Total of 7 to 12 million reads were obtained. After mapping to the human reference genome, we analyzed the 3-4% of reads that originated from a non-human source. A BLAST search of the contigs reconstructed de novo revealed high sequence similarity with that of the pandemic H1N1 virus. In the phylogenetic analysis, the HA gene of our samples clustered closely with that of A/Senegal/VR785/2010(H1N1), A/Wisconsin/11/2013(H1N1), and A/Korea/01/2009(H1N1), and the NA gene of our samples clustered closely with A/Wisconsin/11/2013(H1N1). This study suggests that NGS-based unbiased sequencing can be effectively applied to investigate molecular characteristics of nosocomial influenza outbreak by using clinical specimens such as nasopharyngeal swabs.

Analysis of the Vaginal Microbiome by Next-Generation Sequencing and Evaluation of its Performance as a Clinical Diagnostic Tool in Vaginitis

BACKGROUND: Next-generation sequencing (NGS) can detect many more microorganisms of a microbiome than traditional methods. This study aimed to analyze the vaginal microbiomes of Korean women by using NGS that included bacteria and other microorganisms. The NGS results were compared with the results of other assays, and NGS was evaluated for its feasibility for predicting vaginitis. METHODS: In total, 89 vaginal swab specimens were collected. Microscopic examinations of Gram staining and microbiological cultures were conducted on 67 specimens. NGS was performed with GS junior system on all of the vaginal specimens for the 16S rRNA, internal transcribed spacer (ITS), and Tvk genes to detect bacteria, fungi, and Trichomonas vaginalis. In addition, DNA probe assays of the Candida spp., Gardnerella vaginalis, and Trichomonas vaginalis were performed. Various predictors of diversity that were obtained from the NGS data were analyzed to predict vaginitis. RESULTS: ITS sequences were obtained in most of the specimens (56.2%). The compositions of the intermediate and vaginitis Nugent score groups were similar to each other but differed from the composition of the normal score group. The fraction of the Lactobacillus spp. showed the highest area under the curve value (0.8559) in ROC curve analysis. The NGS and DNA probe assay results showed good agreement (range, 86.2-89.7%). CONCLUSIONS: Fungi as well as bacteria should be considered for the investigation of vaginal microbiome. The intermediate and vaginitis Nugent score groups were indistinguishable in NGS. NGS is a promising diagnostic tool of the vaginal microbiome and vaginitis, although some problems need to be resolved.

External Quality Assessment of MERS-CoV Molecular Diagnostics During the 2015 Korean Outbreak

BACKGROUND: The largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection outside Middle East Asia in 2015 has necessitated the rapid expansion of laboratories that conduct MERS-CoV molecular testing in Korea, together with external quality assessment (EQA) to evaluate the assays used. METHODS: The EQA program consisted of two phases; self-validation and blind assessment. For the first EQA phase, in vitro transcribed upstream region of the envelope gene (upE) and the open reading frame (ORF)1a RNAs were used at a concentration of 1,000 copies/microL. The test panel for the second EQA phase consisted of RNA extracts from three samples, which were obtained from two MERS-CoV positive patients and one MERS-CoV negative patient. RESULTS: The first EQA phase results for 46 participants showed a linear relationship between the threshold cycle (CT) values of RNA materials and the logarithmic concentrations for both upE and ORF1a gene targets (R2=0.73 and 0.75, respectively). The mean CT value for each concentration was different depending on which commercial kit was used for the assay. Among the three commonly used kits, PowerChek MERS Real-Time PCR kit (KogeneBiotech, Korea) showed the lowest CT values at all concentrations of upE and most concentrations of ORF1a. The second EQA phase results for 47 participants were 100% correct for all tested samples. CONCLUSIONS: This EQA survey demonstrates that the MERS-CoV molecular testing performed in Korea during the 2015 outbreak is of robust capability. However, careful establishment and validation of a cut-off value are recommended to ensure good analytical sensitivity.

Comparison of Nasopharyngeal Aspirates and Nasopharyngeal Flocked Swabs for Respiratory Virus Detection / 대한임상미생물학회지

BACKGROUND: Nasopharyngeal aspirate (NPA) is known as the best specimen for accurate diagnosis of viral respiratory infections in pediatric patients, but the procedure is very annoying. Recently introduced flocked swabs have been reported to be easy to obtain a good quality specimen and comfortable to patients. The purpose of this study was to compare the sensitivities between NPA and nasopharyngeal flocked swabs (NPFS) for detection of respiratory viruses in children. METHODS: For this study, 111 hospitalized children with acute respiratory tract infections were recruited. NPA and NPFS were performed in parallel from each patient. NPFS were always collected after NPA. Specimens were tested for six common respiratory viruses in triplicate using indirect immunofluorescence (IIF), viral cultures, and multiplex reverse transcription PCR (RT-PCR). RESULTS: The proportion of specimens inadequate for IIF was higher in NPA (23.4%) than NPFS (5.4%). According to the consensus positive, the positive rates of NPFS were higher than those of NPA when using IIF (45.7% and 30.6%, P=0.048) and culture (38.7% and 27.9%, P=0.004). However, the false-positive rates of NPFS were higher than those of NPA when using IIF (12.4% and 1.2%, P=0.004). The positive rates of NPFS and those of NPA were not different in multiplex RT-PCR (67.6% and 55.9%, P=0.055). CONCLUSION: The higher sensitivity of IIF for NPFS specimens and of culture for respiratory viruses and the similar sensitivities in multiplex PCR could make them an alternative to NPA samples, especially in physician clinics or emergency rooms.

Neonatal invasive Streptococcus gallolyticus subsp. pasteurianus infection with delayed central nervous system complications / 소아과

Group D streptococci are known to cause newborn septicemia and meningitis, but the Streptococcus bovis group strains rarely cause serious neonatal infections in Korea. Central nervous system (CNS) complications of neonatal S. bovis group infection have rarely been reported. In adults, S. bovis group strains cause bacteremia and endocarditis, and are associated with gastrointestinal malignancy. However, only a few studies have reported meningitis and septicemia in infants. Here, we describe a case of bacteremia and meningitis due to Streptococcus gallolyticus subsp. pasteurianus with a delayed CNS complication in an infant. A 28-day-old male infant was admitted to the hospital with a 1-day history of fever. Cultures of blood, cerebrospinal fluid, and urine showed the presence of S. bovis group strain-S. gallolyticus subsp. pasteurianus. He was discharged after 21 days of intravenous ampicillin and cefotaxime administration. Two weeks later, he was readmitted with a fever and short episodes of tonic-clonic movements. Brain magnetic resonance imaging showed marked bilateral frontal subdural effusion. He was discharged after 31 days of antibiotic therapy, and no neurological sequelae were observed at the 9-month follow-up. In conclusion, we present a rare case of neonatal S. gallolyticus subsp. pasteurianus infection causing urinary tract infection, septicemia, meningitis, and delayed CNS complications. This case emphasizes the need for physicians to be aware of S. bovis infection in infants.

Annual Report on External Quality Assessment Scheme for Clinical Microbiology in Korea (2014)

Annual proficiency surveys were performed in March, June and September 2014 by clinical microbiology division of The Korean Association of Quality Assurance for Clinical Laboratory. Parasitology part has been newly incorporated in this survey. For each trial, three sets which were composed of different combinations of five bacteria and yeast were distributed for gram stain, culture, identification, and antimicrobial susceptibility tests of general bacteriology and five fixed sputum smear on slides were distributed for acid fast bacilli stain. Two advanced bacteriology survey materials for culture and identification of anaerobic bacteria and mold were distributed to the voluntary participants in every trial and five mycobacterial culture and identification specimens, five anti-tuberculosis susceptibility testing specimens, and two Mycobacterium tuberculosis strains for rapid detection of rifampin and isoniazid resistance were distributed to the voluntary participants in March and June trials. Five virtual microscopic slides for stool parasite examination were open for the registered participants in June trial. A total of 340 laboratories were enrolled and 330 (97.0%), 331 (97.4%), and 331 (97.4%) returned the results on trial I, II, and III, respectively. For bacterial identification, the percent acceptable identification of Burkholderia cepacia, Klebsiella pneumoniae, Streptococcus pyogenes, Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumoniae, Streptococcus agalactiae, Plesiomonas shigelloides, and Enterococcus faecalis were greater than 95%. Group C and group D Salmonella species challenged as the different sets of M1422 resulted in the acceptable rate lower than 95% because nine participants reported the identification of different sets. Surveillance cultures for methicillin-resistant S. aureus and vancomycin-resistant enterococci were correctly determined by 89.6% and 69.0% of the respondents, respectively. Correct identification to species level of Candida albicans, Candida auris, Candida glabrata, and Candida parapsilosis were 86.1%, 1.6%, 48.1%, and 83.8%. Vancomycin disk diffusion test in S. aureus, missing oxacillin screen or penicillin susceptibility test in S. pneumoniae and lack of reliable methods of quinolone resistance detection in Salmonella species caused unacceptable results in antimicrobial susceptibility testing. Advanced bacteriology trials revealed low performance in species identification of mold. Mycobacterial culture, identification and susceptibility test performance was kept in excellence. The performance of identification of stool parasites was acceptable >90% for detection of helminth eggs and amebic cysts but 28.6% false positive responses resulted from negative specimens. In conclusion, species-level identification of fungi of both candida species and mold were challenging to clinical microbiology laboratories. Vancomycin disk diffusion method for S. aureus and lack of proper penicillin susceptibility test for S. pneumoniae were still common cause of inaccurate results. Virtual microscopic survey has been successfully introduced in parasitology.

First Korean Case of Cedecea lapagei Pneumonia in a Patient With Chronic Obstructive Pulmonary Disease

No abstract available.

MALDI-TOF MS: Its Application in the Clinical Laboratory and a Paradigm Shift in Clinical Microbiology

In the past decade, clinical microbiology underwent revolutionary changes in methods used to identify microorganisms, a transition from slow and traditional microbial identification algorithms to rapid molecular methods and mass spectrometry (MS). Earlier, MS was clinically used as a highly complex method that was adapted for protein-centered analysis of samples in chemistry laboratories. Recently, a paradigm-shift happened when matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS was implemented to be used in microbiology laboratories for rapid and robust methods for accurate microbial identification. Two instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases even genetic sequence-based identification practices. This review summarizes the current role of MALDI-TOF MS in clinical research, in diagnostic clinical microbiology laboratories, and serves as an introduction to MALDI-TOF MS, highlighting research associated with sample preparation, algorithms, interpretations, and limitations. Currently available MALDI-TOF MS instruments as well as software platforms that support the use of MALDI-TOF with direct specimens have been discussed in this review. Finally, clinical laboratories are consistently striving to extend the potential of these new methods, often in partnership with developmental scientists, resulting in novel technologies, such as MALDI-TOF MS, which could shape and define the diagnostic landscape for years to come.

Flavobacterium ceti From Blood Samples of a Korean Patient With Alcoholic Liver Cirrhosis

No abstract available.

First Korean Case of Mycobacterium arupense Tenosynovitis

No abstract available.

Capnocytophaga sputigena Bacteremia in a Patient with Chronic Lymphocytic Leukemia

No abstract available.

First Korean Case of Helcococcus kunzii Bacteremia in a Patient with Diabetes

No abstract available.

Annual Report on External Quality Assessment Scheme in Clinical Microbiology in Korea (2013) / 임상검사와정도관리

Annual external quality assessment was performed three times for clinical microbiology division of The Korean Association of Quality Assurance for Clinical Laboratory. For each trial, three sets composed of different combinations of four bacteria and one yeast were distributed for culture, identification, and antimicrobial susceptibility tests. A total of 340 laboratories were enrolled and 330 (97.0%), 331(97.4%), and 331(97.4%) returned the results on trial I, II, and III, respectively. For bacterial identification, the correct identification of gram-negative bacilli, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus capitis, Streptococcus agalactiae, Listeria monocytogenes, and Candida species was greater than 95%. However, correct identification of Staphylococcus lugdunensis, Corynebacterium striatum, Vibrio vulnificus, Aeromonas hydrophila, Cryptococcus neoformans, and Malassezia pachydermatis was relatively less accurate, with values of 95.4%, 89.9%, 50.7%, 91.3%, 93.6%, and 93.9%, respectively. Surveillance cultures for vancomycin-resistant enterococci and methicillin-resistant S. aureus were correctly determined by 95.4% and 93.9% of the respondents, respectively. False carbapenem-resistance due to AmpC beta-lactamase, disk diffusion testing for vancomycin in Staphylococcus species, oxacillin and penicillin susceptibility testing in S. lugdunensis and false imipenem-resistance in Proteus species were common sources of inaccurate results. The accuracy of species identification for Corynebacterium species and Vibrio species requires improvement. Consistent problems occurred with antimicrobial susceptibility testing of vancomycin for Staphylococcus species using the disk diffusion method.

Annual Report on External Quality Assessment Scheme in Clinical Microbiology in Korea (2013) / 임상검사와정도관리

Annual external quality assessment was performed three times for clinical microbiology division of The Korean Association of Quality Assurance for Clinical Laboratory. For each trial, three sets composed of different combinations of four bacteria and one yeast were distributed for culture, identification, and antimicrobial susceptibility tests. A total of 340 laboratories were enrolled and 330 (97.0%), 331(97.4%), and 331(97.4%) returned the results on trial I, II, and III, respectively. For bacterial identification, the correct identification of gram-negative bacilli, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus capitis, Streptococcus agalactiae, Listeria monocytogenes, and Candida species was greater than 95%. However, correct identification of Staphylococcus lugdunensis, Corynebacterium striatum, Vibrio vulnificus, Aeromonas hydrophila, Cryptococcus neoformans, and Malassezia pachydermatis was relatively less accurate, with values of 95.4%, 89.9%, 50.7%, 91.3%, 93.6%, and 93.9%, respectively. Surveillance cultures for vancomycin-resistant enterococci and methicillin-resistant S. aureus were correctly determined by 95.4% and 93.9% of the respondents, respectively. False carbapenem-resistance due to AmpC beta-lactamase, disk diffusion testing for vancomycin in Staphylococcus species, oxacillin and penicillin susceptibility testing in S. lugdunensis and false imipenem-resistance in Proteus species were common sources of inaccurate results. The accuracy of species identification for Corynebacterium species and Vibrio species requires improvement. Consistent problems occurred with antimicrobial susceptibility testing of vancomycin for Staphylococcus species using the disk diffusion method.

The First Case of Eggerthella lenta Bacteremia in Korea

No abstract available.