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Taxonomic Identification of Bacillus Species Using Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry.

Won Seon YU ; Kyeong Min LEE ; Kyu Jam HWANG

Annals of Clinical Microbiology.2016;19(4):110-120. doi:10.5145/ACM.2016.19.4.110

BACKGROUND: In this study, we compared various methods of taxonomic identification of Bacillus strains: biochemical methods, 16S rRNA gene sequencing, and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). We also developed a pathogen- isolate resource database, thus increasing the identification rate when using MALDI-TOF MS. METHODS: Thirty Bacillus strains were obtained from the NCCP (National Culture Collection for Pathogens) and were identified using the VITEK 2 system (bio-Mérieux, France), API kit (bioMérieux, France), 16S rRNA gene sequencing, and MALDI-TOF MS. The pathogenicity of Bacillus cereus was confirmed through the identification of virulent genes using a multiplex PCR, and both protein extraction for protein profiling in MALDI-TOF MS and repetitive-sequence fingerprinting were performed. RESULTS: The identification rates at the species level were 40%, 80%, and 76.3% for the VITEK 2 system (bioMérieux), 16S rRNA gene sequencing, and MALDI-TOF MS, respectively. When the major spectrum-profiling dendrogram was compared with the phylogenetic tree, which was constructed based on the 16S rRNA gene sequences and rep-PCR fingerprinting, the classifications were confirmed to be effective. CONCLUSION: Identification of Bacillus strains using MALDI-TOF MS was more effective than that using the VITEK 2 system (bioMérieux), but was similar to that using 16S rRNA gene sequencing. Continual addition to a proteome-based database can result in increased identification rates for MALDI-TOF MS.
Bacillus cereus ; Bacillus* ; Classification ; Dermatoglyphics ; Genes, rRNA ; Mass Spectrometry* ; Multiplex Polymerase Chain Reaction ; Trees ; Virulence

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Prevalence of Bacteria in the Nationwide Survey of Stool Culture Performed in 2015, Korea..

Won Hee CHOI ; Jung Hyun BYUN ; Sunjoo KIM

Annals of Clinical Microbiology.2016;19(4):105-109. doi:10.5145/ACM.2016.19.4.105

BACKGROUND: The spectrum of bacteria causing diarrhea is highly affected by geographic area, sanitation, travel, food consumption, and previous antibiotic use. A nationwide databank for stool cultures is undeveloped. The aim of our study was to investigate the current prevalence of gastroenteritis bacterial pathogens in Korea. METHODS: We requested microbiological data via questionnaire emails sent to 98 hospitals. The frequency of each pathogen was acquired from 32 institutes. Numbers of stool cultures performed ranged from 193 to 14,296 (mean 2,724, SD 3,261) in 2015. RESULTS: Among 86,744 requested stool specimens, 917 (1.06%, range 0-4.59%, 95% confidence interval 0.63-1.48%) were positive. Salmonella was most prevalent (59.0%), followed by Candida (12.4%), Campylobacter (4.8%), Staphylococcus aureus (4.0%), Vibrio (4.0%), and Pseudomonas aeruginosa (1.75). Yersinia (0.3%) and Shigella (0.2%) were rarely isolated. CONCLUSION: As the positive rate of the stool cultures is very low (1.06%), more effort and concern should be provided to enhance the isolation of pathogens. Salmonella was the most prevalent pathogen and Campylobacter and Vibrio were relatively common pathogens causing bacterial gastroenteritis in Korea.
Academies and Institutes ; Bacteria* ; Campylobacter ; Candida ; Diarrhea ; Electronic Mail ; Gastroenteritis ; Korea* ; Prevalence* ; Pseudomonas aeruginosa ; Salmonella ; Sanitation ; Shigella ; Staphylococcus aureus ; Vibrio ; Yersinia

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Nationwide Survey of Blood Culture Protocol in Clinical Microbiology Laboratories in Korea.

Young Ah KIM ; Dokyun KIM ; Dongeun YONG ; Kyungwon LEE

Annals of Clinical Microbiology.2016;19(4):97-104. doi:10.5145/ACM.2016.19.4.97

BACKGROUND: The recovery of bacteria from blood can be affected by many factors. Standardization of blood culture methods is important for reliability. Herein, we aimed to investigate blood culture protocols in Korea. METHODS: We performed a multicenter survey with a questionnaire about blood culture practices, which was sent by email to directors and clinical physicians in charge of clinical microbiology laboratories in May 2014. Total data from 18 participating hospitals were analyzed to be used as current baseline data, which is necessary to optimize blood culture protocols. RESULTS: Many laboratories included recommended blood volume, which is a major factor for bacteria recovery rate. This varied across participating laboratories. For adults, blood sampling of 10 mL was recommended by 10 laboratories and 20 mL was recommended by 5 laboratories. For children who weighed 14-36 kg and less than 14 kg, blood sampling of 10 mL (n=8) and 5 mL (n=7) was recommended, respectively. For neonates, less than 1 mL was recommended by 12 laboratories. CONCLUSION: Substantial variations in blood culture protocols were seen across participating clinical microbiology laboratories. Efforts to standardize this protocol should be undertaken.
Adult ; Bacteria ; Blood Volume ; Child ; Electronic Mail ; Humans ; Infant, Newborn ; Korea* ; Sepsis

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Molecular Typing and Resistance Profiles of Vancomycin-Intermediate Staphylococcus aureus in Korea: Results from a National Surveillance Study, 2007-2013.

Jung Wook KIM ; Gi Su KANG ; Jae Il YOO ; Hwa Su KIM ; Yeong Seon LEE ; Jae Yon YU ; Kwang Jun LEE ; Chan PARK ; Il Hwan KIM

Annals of Clinical Microbiology.2016;19(4):88-96. doi:10.5145/ACM.2016.19.4.88

BACKGROUND: To investigate the national molecular epidemiology and resistance profiles of vancomycin-intermediate Staphylococcus aureus (VISA), we analyzed the characteristics of methicillin-resistant Staphylococcus aureus (MRSA) collected from clinical samples at tertiary or general hospitals participating in a nationwide surveillance program for VISA and vancomycin-resistant Staphylococcus aureus (VRSA) in Korea during an 12-week period in each year from 2007 to 2013. METHODS: VISA was defined by agar dilution, broth dilution and E-test methods with vancomycin minimum inhibitory concentrations of >2 μg/mL. All VISA isolates were characterized by multilocus sequence typing, staphylococcal cassette chromosome mec typing, spa typing, accessory gene regulator typing, Diversilab analysis, and antibiogram analysis. RESULTS: Of 109,345 MRSA isolates, 87,354 were screened and 426 isolates were identified as positive on brain heart infusion agar containing 4 μg/mL vancomycin (BHI-V4). Of 426 isolates, 76 isolates were identified as VISA. No VRSA isolates were detected among the isolates. Overall, a total of 6 genotypes were identified among VISA strains and the predominant clones were ST5-II-t2460, ST72-IV-t324, and ST239-III-t037 (44.7%, 15.8%, and 10.5%, respectively). Of note, ST72-IV-t324 clones are known to be a typical community-associated MRSA. ST239-III-t037 strains were more resistant to trimethoprim-sulfamethoxazole than any other type of strain. ST72-IV-t324 strains were susceptible to all of the antimicrobial agents tested except erythromycin and daptomycin. All of the VISA isolates were susceptible to linezolid and quinupristin-dalfopristin. CONCLUSION: Although VRSA is still rare, continuous monitoring of VRSA occurrence is needed, as well as VISA prevalence, epidemic clonal shift, and antimicrobial resistance.
Agar ; Anti-Infective Agents ; Brain ; Clone Cells ; Daptomycin ; Erythromycin ; Genotype ; Heart ; Hospitals, General ; Korea* ; Linezolid ; Methicillin-Resistant Staphylococcus aureus ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Molecular Typing* ; Multilocus Sequence Typing ; Prevalence ; Staphylococcus aureus* ; Staphylococcus* ; Trimethoprim, Sulfamethoxazole Drug Combination ; Vancomycin

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

Wonkeun SONG ; Han Sung KIM ; Jae Seok KIM ; Hyun Soo KIM ; Dong Hoon SHIN ; Saeam SHIN ; Min Jeong PARK

Annals of Clinical Microbiology.2016;19(4):83-87. doi:10.5145/ACM.2016.19.4.83

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 positivity and >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.
Agar ; Enterobacteriaceae* ; Escherichia coli ; Methods* ; Pseudomonas* ; Sensitivity and Specificity

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Erratum: Comparison of the BACTEC Peds Plus Pediatric Blood Culture Bottle to the BacT/Alert PF Pediatric Blood Culture Bottle for Culturing Blood from Pediatric Patients.

Kon Hee LEE ; Wonkeun SONG ; Min Jeong PARK ; Jeongwon HYUN ; Hyun Soo KIM ; Kyu Man LEE

Annals of Clinical Microbiology.2013;16(3):152-152. doi:10.5145/ACM.2013.16.3.152

English abstract of the paper, there is an error in the following to correct it.

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Analysis of JSCM General Meeting Program during the Last Three Years.

Sunjoo KIM

Annals of Clinical Microbiology.2013;16(3):149-151. doi:10.5145/ACM.2013.16.3.149

Several members of the Korean Society of Clinical Microbiology (KSCM) have attended general meetings of the Japanese Society for Clinical Microbiology (JSCM) for more than 6 years. Although the composition of the JSCM is quite different from that of the KSCM and the formal language of the meeting is Japanese, it is worth reviewing the program to gain an overview of the direction and progress of the JSCM. The author is convinced that there is a lot to learn from the JSCM, especially in terms of how to maintain a very low antibiotic resistance rate, and how to prevent hospital-acquired infections. I hope that both academic societies will develop further and create a continuous exchange of helpful information, which could act as a good model for exchange between other specialty groups in separate countries.
Asian Continental Ancestry Group ; Drug Resistance, Microbial ; Humans

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Urinary Isolates and Antimicrobial Resistance in the Urine Collected from Patients Admitted into Primary-Care Hospital in Shiheung District.

Jeongsook YOON

Annals of Clinical Microbiology.2013;16(3):145-148. doi:10.5145/ACM.2013.16.3.145

Urinary isolates and antimicrobial resistance of a primary hospital representing community were analyzed. The beta-lactam and aminoglycoside resistances of E. coli and P. aeruginosa were lower than that seen in a tertiary hospital. Imipenem-resistant P.aeruginosa or VRE was not isolated; however the prevalence of ESBL was thought to be similar to that observed in a tertiary hospital.
Anti-Infective Agents ; Drug Resistance ; Humans ; Prevalence ; Tertiary Care Centers

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Evaluation of the Xpert Flu for the Detection of Influenza A Virus and Influenza A/H1N1/2009 Strain.

Ji Yeon SOHN ; Kyung Sun PARK ; Ji Youn KIM ; Chang Seok KI ; Nam Yong LEE

Annals of Clinical Microbiology.2013;16(3):140-144. doi:10.5145/ACM.2013.16.3.140

BACKGROUND: Xpert Flu (Cepheid, USA) allows for fully automated real-time RT-PCR using a single-use disposable cartridge. The aim of this study was to evaluate Xpert Flu for the detection of influenza A virus and subtype A/H1N1/2009 pandemic virus. METHODS: We conducted a prospective comparison study for Xpert Flu with the RealTime ready Influenza A/H1N1 Detection Set (Roche Diagnostics, Germany). Analytical specificities of the assays were determined by testing commonly encountered respiratory viral pathogens, including parainfluenza virus type 1/2/3, rhinovirus A, rhinovirus B, metapneumovirus, adenovirus, and coronavirus. The analytical sensitivities and workflow of both methods were also assessed. RESULTS: A total of 102 consecutive clinical specimens were tested by both methods. Total agreement between the two methods was estimated to be 99.0% (101/102): 11 A/H1N1/2009 and 3 seasonal influenza A by the RealTime ready Influenza A/H1N1 Detection Set; 10 and 3 by Xpert Flu. No cross-reactivity was observed between influenza A/H1N1/2009 and other respiratory viral pathogens in either method. The limits of detection of the RealTime ready Influenza A/H1N1 Detection Set and Xpert Flu were 500 TCID50/mL and 20 TCID50/mL, respectively. Xpert Flu required 85 minutes (10 minutes of hands-on time) for processing, while RealTime ready Influenza A/H1N1 Detection Set took 128 minutes (30 minutes of handson time). CONCLUSION: The results of Xpert Flu were comparable to those of the RealTime ready Influenza A/H1N1 Detection Set. It is of note that the fully automated and closed system of Xpert Flu could be advantageous for reducing hands-on time and for preventing cross-contamination during the testing process.
Adenoviridae ; Coronavirus ; Influenza A virus ; Influenza A Virus, H1N1 Subtype ; Influenza, Human ; Limit of Detection ; Metapneumovirus ; Pandemics ; Paramyxoviridae Infections ; Prospective Studies ; Rhinovirus ; Seasons ; Sprains and Strains ; Viruses

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A Survey of Intestinal Parasite Infection during a 10-Year Period (2003-2012).

Young Eun KIM ; Hee Jae HUH ; Yu Yean HWANG ; Nam Yong LEE

Annals of Clinical Microbiology.2013;16(3):134-139. doi:10.5145/ACM.2013.16.3.134

BACKGROUND: Due to a reduction in the number of parasite infections, attention paid to the importance of intestinal parasites has decreased. However, intestinal parasite infections remain ubiquitous and have reappeared as a growing problem in recent decades due to changing lifestyles such as increased overseas travel. In this study, we evaluated trends in intestinal parasite infection using stool examination in a single institute. METHODS: From January 2003 to December 2012, we reviewed all stool examination results performed at Samsung Medical Center. Fecal examinations were performed by formalin-ether sedimentation. RESULTS: A total 429,866 stool examinations were performed resulting in 14,672 cases with positive findings of helminth eggs or protozoan cysts, of which the positive rate was 3.41% on average. The annual positive rate decreased from 5.68% in 2003 to 2.43% in 2012. The positive rate of intestinal parasites, excepting Endolimax nana and Entamoeba coli, was 1.52% on average. Positive rates decreased from 2.13% to 1.10% for helminth egg detections and from 2.55% to 1.30% for protozoan cyst detections during the same time period. Among nematodes, Trichuris tricuria was the most common and had an increasing positive rate after 2010. Clonorchis sinensis was the most prevalent trematode parasite, with an annual average of 528 cases. CONCLUSION: Infection rates of intestinal parasites have decreased over the last 10 years. However, Trichuris tricuria has reappeared and has become a major contributor to parasite infections. Further education and control efforts are needed for greater prevention and eventual eradication of parasitic infections.
Clonorchis sinensis ; Eggs ; Endolimax ; Entamoeba ; Helminths ; Korea ; Life Style ; Ovum ; Parasites ; Trichuris

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