Specimens In Korea Research Articles

Phylogenetic Assessment of Understudied Families in Hymenochaetales (Basidiomycota, Fungi)—Reporting Uncovered Species and Reflecting the Recent Taxonomic Updates in the Republic of Korea

Hymenochaetales Oberw. is an order classified in Basidiomycota of Fungi, and species in this order display notable diversity. They exhibit various fruiting body shapes, including clavarioid, effused-reflexed, and resupinate basidiomes. Few mycorrhizal species have been reported in Hymenochaetales, but wood-decaying species dominate the order. Hymenochaetaceae Imazeki & Toki and Schizoporaceae Jülich are the most species-rich families within Hymenochaetales, and most species in the Republic of Korea belong to these two families. As such, current taxonomic classification and nomenclature are not reflected upon species in the remaining Hymenochaetales families. For this study, a multifaceted morphological and multigenetic marker-based phylogenetic investigation was conducted to, firstly, comprehensively identify understudied Hymenochaetales specimens in Korea and, secondly, reflect the updates on the species classification. Five genetic markers were assessed for the phylogenetic analysis: nuclear small subunit ribosomal DNA (nSSU), internal transcribed spacer (ITS), nuclear large subunit ribosomal DNA (nLSU), RNA polymerase II subunit 2 gene (RPB2), and translation elongation factor 1 gene (TEF1). The results from phylogenetic analysis supported 18 species classified under eight families (excluding Hymenochaetaceae and Schizoporaceae) in Korea. Species formerly placed in Rickenellaceae and Trichaptum sensu lato have been systematically revised based on recent taxonomic reconstructions. In addition, our findings revealed one new species, Rickenella umbelliformis, and identified five formerly nationally unreported species classified under five understudied families. Our findings contribute to a better understanding of Hymenochaetales diversity and highlight the need for continued research.

A parasitological study on the possible toilet ruins of the Japanese colonial period in Korea.

In the past decade, experts have conducted parasitological research on archaeological specimens in Korea to collect historical parasite infection data. In these studies, parasitologists successfully described the infection pattern of each parasite species in history. However, in the first half of the 20th century, archaeoparasitological reports have been scant. In 2021, we conducted a parasitological examination of a toilet-like structure that emerged in the early 20th century. This structure was built by stacking 2 wooden barrels; and in the study samples, we found ancient Trichuris trichiura, Ascaris lumbricoides (unfertilized), and Taenia spp. eggs and therefore proposed a higher possibility that the barrels could have been used as a toilet at the time. To understand how the antihelminthic campaign since the 1960s helped reduce parasite infection rates in Korea, more research should focus on early-20th-century toilet ruins.

Histological characteristics of the largest and secondary tumors in radical prostatectomy specimens and implications for focal therapy

BackgroundPathological features of prostate cancer in Korean men were analyzed to determine whether identification of tumor volume, Gleason score (GS), focality, and location using radical prostatectomy (RP) specimens can provide useful information for the application of focal therapy (hemiablation).MethodsFrom January 2016 to December 2017, 913 patients who underwent RP at a single center were selected for analysis. Patients with prostate-specific antigen levels > 15 ng/mL or those who had received hormone therapy prior to surgery were excluded. Preoperative data and the number, volume, location, and GS of each tumor were recorded.ResultsOverall, 762 RP specimens were examined, and 1448 tumors were identified. The majority of the cases were multifocal (60.5%) and bilateral (82%) in nature. Among the 686 secondary tumors, 250 (36.4%) had a GS ≥7 and 122 (17.8%) had a tumor volume ≥ 0.5 mL. Among the 435 bilateral multifocal cases, secondary tumors on the lobes contralateral to the largest tumor were significant by volume (≥0.5 mL) in 91 (20.9%) cases and by grade (GS ≥7) in 179 (41.1%) cases. There were 102 (23.4%) tumors with a small tumor volume (< 0.5 mL) and Gleason pattern 4 on the lobe contralateral to the largest tumor.ConclusionsBilateral and multifocal tumors are a common feature and secondary tumors frequently exhibit clinically significant prostate cancer on RP specimens in Korea. In many cases, secondary tumors on the lobe contralateral to the largest tumor had a high GS and small tumor volume.

Molecular Characterization of Pseudomonas putida Group Isolates Carrying blaVIM-2 Disseminated in a University Hospital in Korea.

Pseudomonas putida group are Gram-negative bacilli with polar flagellation, which are ubiquitous in the environment, although they are rarely involved in human infections. The aim of this study was to identify the dissemination of VIM-2-producing P. putida group in clinical isolates from a hospital in Korea. Thirteen strains were collected from 2014 to 2015 for the study. The isolates were recovered from urine cultures of both inpatients and outpatients at the hospital. Minimum inhibitory concentrations of antibiotics were determined by Etest. Carbapenemase genes were amplified by polymerase chain reaction and sequenced. Pulsed-field gel electrophoresis was performed for strain typing. Whole-genome sequencing was carried out randomly for two strains chosen from each year of the study to analyze the plasmid structure carrying the blaVIM-2 genes. The 13 isolates carried nine different class I integrons harboring VIM-2 and were resistant to meropenem and imipenem (minimum inhibitory concentrations, ≥32 μg/ml), thus exhibiting a multidrug-resistant phenotype. The blaVIM-2 gene was located on a plasmid in seven of the isolates and on the chromosome in six isolates. Each case of the blaVIM-2 gene was disseminated by clonal spread, horizontal transfer, and was mostly an occasional occurrence. In this study, we demonstrated that multidrug-resistant P. putida group carrying VIM-2 has reemerged in human specimens in Korea.

Distribution of Mycobacterium tuberculosis in Korea in the preceding decade.

Tuberculosis (TB) is an infectious disease caused by the bacillus Mycobacterium tuberculosis (MTB); it is transmitted among people through air. The aim of this study was to assess the prevalence of TB and its clinical trends by collecting and analyzing data on specimens in Korea. All clinical specimens referred to the Dankook University Hospital Laboratory in Cheonan, Korea, from September 2005 to June 2016 were tested to isolate MTB using solid and liquid cultures, acid-fast bacilli (AFB) smears, and polymerase chain reactions (PCR). In total, 146150 specimens were collected; the mean TB positivity rate was 7.8%. The highest positivity rate was observed among patients 30-39years of age (12.6%), followed by those 20-29years of age (12.2%). The mean positivity rate was highest in 2010 and lowest in 2016 (10.7% and 6.7%, respectively). When comparing 2015-2011, we saw a decrease in the number of TB-positive patients of 3.4%; this represented an annual decrease in 0.9%. Our data revealed a trend for a decrease in TB prevalence over time. Moreover, TB positivity rates were highest among the younger age groups in our study. Therefore, rapid diagnosis and treatment of TB in younger individuals are crucial.

Hymenoscyphus fraxineus and two new Hymenoscyphus species identified in Korea

Hymenoscyphus fraxineus is an invasive fungal pathogen that causes ash dieback in Europe. Recent investigations have identified H. fraxineus on herbarium specimens in Korea. In this paper, these specimens, plus five additional collections, were studied by internal transcribed spacer (ITS) screening and subsequent phylogenetic analysis using three additional sequence markers (actin, calmodulin, EF1-α). Using the concept of genealogical concordance phylogenetic species recognition (GCPSR), H. fraxineus was confirmed in five of the collections on petioles of Fraxinus mandshurica and F. chinensis subsp. rhynchophylla. The remaining collections revealed two novel species, both occurring on petioles of F. chinensis subsp. rhynchophylla. They are described as Hymenoscyphus occultus sp. nov. and Hymenoscyphus koreanus sp. nov., based on morphological and molecular data. Both develop a Chalara-like anamorph similar to that of H. fraxineus. Together with the newly described H. albidoides from China and H. linearis from Japan, the clade containing H. fraxineus now consists of six species. Within this clade, H. koreanus forms a sister species to H. albidus and both share highly similar morphological and molecular features. Hymenoscyphus occultus is more distantly related to H. fraxineus and shows proximity to H. linearis. Ascocarp production on ash leaf malt-extract agar could be shown for the two new species, and for H. linearis and H. albidus. The experiment demonstrated these species’ ability to self-fertilize. Our findings suggest the diversity of Hymenoscyphus species on Fraxinus sp. might be higher than currently known, calling for further investigations on petioles of other Fraxinus species.

Notes on the Unrecorded Species of Subgenus Lepidella in Korean Genus Amanita

Amanita subgenus Lepidella is a well-known group that includes lethal amanitas. However, the taxonomic investigation of Korean Amanita species is still in progress. In this study, we collected Amanita specimens in Korea from 2009 to 2015 and classified 22 of them as subgenus Lepidella based on the morphology. Phylogenetic analysis of the 22 Amanita specimens based on the internal transcribed spacers sequences identified 16 phylogenetic species which included three undescribed Amanita species (A. sepiacea, A. modesta and A. kotohiraensis). Microscopic features of newly recorded Amanita species were photographed and line drawings were made. All collections cited here are deposited in the Herbarium Conservation Center of the National Institute of Agricultural Sciences.

수압파쇄 적용을 위한 셰일의 취성의 개념 고찰 및 취성도 간의 상관관계 분석

Abstract Hydraulic fracturing is the key technology for production of shale gas, which is one of the major unconventional resources. Brittleness index is one of the most important mechanical properties which determine the efficiency of hydraulic fracturing. It was required that the production of shale gas increases with more brittle behavior. Confusingly, there are numerous definitions available for brittleness of rock. This paper summarizes various definitions of brittleness index, and presents correlation analysis of the brittleness indices by using the laboratory experimental results of 48 shale specimens in Korea. Generally, it shows a very weak positive correlation between the brittleness index (B 1 ) which is the ratio of uniaxial compressive strength to tensile strength and the brittleness index (B 3 ) which is calculated by using the Youngs modulus and Poisson’s ratio. In addition, the role of Poissons ratio is not clear in defining brittleness indices. In conclusion, standardization of definition for brittleness index is required to apply it to hydraulic fracturing as a parameter for predicting the efficiency.

In vitro antimicrobial susceptibility of Mycoplasma hyorhinis field isolates collected from swine lung specimens in Korea

Mycoplasma hyorhinis is a very common inhabitant of the respiratory tract of pigs with or without pneumonia. Because there is no vaccine available to control M hyorhinis, chemotherapy is the most practical way to treat disease associated with M hyorhinis infection. Therefore, we tested the antimicrobial susceptibility of M hyorhinis isolates recovered from lung specimens of pigs using the liquid minimum inhibitory concentration (MIC) method in tests with 12 antimicrobial agents. The MIC50, MIC90, and range of MICs against 10 field isolates from Korea and the reference strain (ATCC 17981) were investigated. Mycoplasma hyorhinis field isolates were sensitive to lincomycin and tylosin but resistant to erythromycin, spectinomycin, and streptomycin. The MIC90s for lincomycin and tylosin were 0.5 µg per mL and 1.0 µg per mL, respectively. The MIC90s for amoxicillin, erythromycin, penicillin, spectinomycin, and streptomycin were ≥ 64 µg per mL. The MIC90s for gentamicin, kanamycin, and neomycin were 4.0 µg per mL, 8.0 µg per mL and 16 µg per mL, respectively. For oxytetracycline and tetracycline, the MIC50 was 4.0 µg per mL and the MIC90 was 16 µg per mL. These results provide practical information for treatment of M hyorhinis infection in pigs.

Three New Records of Penicillium Species Isolated from Insect Specimens in Korea

Three Penicillium species have been isolated from insect specimens in Korea; Penicillium sp., P. steckii, and P. polonicum. Penicillium sp. (KNU12-3-2) was isolated from Lixus imperessiventris, while P. polonicum (KNU12-1-8) and Penicillium steckii (KNU12-2-9) were isolated from Muljarus japonicas and Meloe proscarabaeus, respectively. The identification was based on the morphological characteristics of the fungi and in internal transcribed spacer analysis. This is the first report on the isolation of these three species of Penicillium from insects in Korea.

Abstract 4225: PNA mediated real-time PCR clamping assay to detect IDH1 mutations .

Abstract The hotspot mutations in codon 132 of isocitrate dehydrogenase 1 (IDH1) is a frequent DNA alteration in gliomas and astrocytomas. IDH mutations are prognostic and diagnostic for tumors with mutation, associated with a proneural subclass, and have longer survival compared with those without the mutation. We have developed a highly sensitive and simple method to detect hotspot mutations in codon 132 of IDH1 using PNA-mediated real-time PCR clamping, PNAClampTM. PNAClampTM is based on unique properties of PNA probes that PNA oligomers are not recognized by DNA that can serve as sequence-selective clamps during PCR amplification. This method can also detect 5 mutations through only one tube reactions simultaneously, which requires only 10 ng of the target DNA each. Data analysis was much faster and easier to perform than analysis of the sequencing data, and results could be obtained in 3hr from DNA extraction to analysis. Furthermore, we could readily identify a mixture of 1% mutant allele vs. 99% wild type allele with our PNAClamp assay, in comparison to direct sequencing assay which have detection limit of approximately 20% mutant allele. We performed the assay on 191 paraffin-embedded glioma specimens in Korea for diagnosing IDH mutation. The results showed that the PNAClampTM IDH1 detected higher number of mutation (27.2%, 52/191) than of direct sequencing (20.9%, 40/191) in 191 giloma samples in Korea. The result was not in agreement with the sequencing in12 (6.3%) samples. This result was likely due to the high sensitivity of PNAClampTM. PNAClampTM is a fast, sensitive and easy to perform method which can reliably detect common mutations of IDH genes in gliomas or other tumors. Citation Format: Jihye Yoon, jae jin Choi, Woohyung Choi, Heekyung Park. PNA mediated real-time PCR clamping assay to detect IDH1 mutations . [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4225. doi:10.1158/1538-7445.AM2013-4225

Fecal Colonization ofEnterobacteriaceaeCarrying Plasmid-Mediated Quinolone Resistance Determinants in Korea

The aims of the current study were to investigate the prevalence and molecular characteristics of plasmid-mediated quinolone resistance (PMQR) genes from colonizing fecal organisms and to compare the incidence and subtype of these genes according to bacterial species and hospital at five tertiary-care hospitals in Korea. A total of 500 nonduplicated clinical isolates of Enterobacteriaceae were obtained from fecal specimens at five tertiary-care hospitals between March and May 2008. The PMQR genes (qnrA, qnrB, qnrS, aac(6')-Ib-cr, and qepA) were amplified by PCR and confirmed by direct sequencing of the PCR products. A total of 83 (16.6%) qnr-positive isolates were detected. The prevalence rates of qnrA, qnrB, and qnrS were 1.4%, 13.6%, and 1.6%, respectively. The species distributions of qnrB-positive isolates were Klebsiella pneumoniae (37/109; 33.9%), Citrobacter freundii (10/34; 29.4%), Citrobacter braakii (8/13; 61.5%), and Escherichia coli (8/275; 2.9%). Sixteen subtypes of qnrB were detected, including seven novel variants. The prevalences of aac(6')-Ib-cr and qepA were 15.6% (n=78) and 0.6% (n=3), respectively. The aac(6')-Ib-cr gene was detected in 39 (47.0%) of 83 qnr-positive isolates and 39 (9.4%) of 417 qnr-negative isolates There was one qepA variant containing a novel mutation (Ala231Val). The prevalence of PMQR genes was high in Enterobacteriaceae from stool specimens in Korea, and there was a close relation between qnr and aac(6')-Ib-cr.

Species Distribution and Antifungal Susceptibilities of Yeast Clinical Isolates from Three Hospitals in Korea, 2001 to 2007

We utilized results from the ARTEMIS DISK Global Antifungal Surveillance Program to evaluate the species distribution and fluconazole and voriconazole susceptibilities of yeast isolates from clinical specimens in South Korea from 2001 to 2007. Data were collected on 5,665 yeast isolates from all body sites at three locations. All investigators tested clinical yeast isolates using the CLSI M44-A disk diffusion method. Test plates were automatically read and results were recorded using the BIOMIC image analysis plate reader system (Giles Scientific, USA). Species, drug, zone diameter, susceptibility category, and quality control results were collected quarterly via e-mail for analysis. Candida albicans was the most common isolate, but a progressive increase in non-C. albicans Candida and noncandidal yeast species has been observed in recent years. The overall percentages of isolates in each category (susceptible, susceptible dose dependent, and resistant) were 98.8%, 0.5%, and 0.7% and 99.2%, 0.2%, and 0.6% for fluconazole and voriconazole, respectively. Candida of 3 species exhibited decreased susceptibility to fluconazole (<90% S) in the order of that seen with the resistant (R) species: C. krusei, C. guilliermondii, and C. glabrata. Emerging resistance to fluconazole or voriconazole was documented among isolates of Cryptococcus neoformans, Trichosporon spp., and Rhodotorula spp. The species distribution and antifungal susceptibilities of yeasts may differ according to specimen type, testing method, hospital, and geographic region. Therefore, further large-scaled, long-term surveillance studies are needed to isolate yeasts and to confirm the species distribution and antifungal susceptibilities of yeast isolates from clinical specimens in Korea.

임상검체로부터 분리한 플라스미드 매개성 SHV-11 β-lactamase 유전자의 특성

In this study, we characterized extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae isolated from clinical specimens in Korea and found two strains harboring plasmid-mediated blaSHV-11, Klebsiella pneumoniae. First, the isolates were detected using the Vitek system and confirmed by the double-disk synergy test. The classification of gene coding for ESBL was also performed by polymerase chain reactions and followed by DNA sequencing. The transmission of genes was confirmed by transconjugation and transformation. Resistant expression of transformants was determined by broth microdilution minimal inhibitory concentration test. Genotypic analysis revealed that one strain harbored the bla TEM-1 , bla SHV-11 and blaCTX-M-15 and the other strain harbored the bla SHV-11 and bla CTX-M-15 . They showed high resistance to oxyiminocephalosphorins (3rd-generation cephalosporins), while the transformant containing only bla SHV-11 did not show any resistance to the antibiotics.

Clinical Significance of Nontuberculous Mycobacteria Isolated From Respiratory Specimens in Korea

Precise epidemiologic data regarding nontuberculous mycobacterial (NTM) lung infection in many Asian countries have been relatively unavailable. In order to determine the clinical significance of NTM isolated from respiratory specimens, we reviewed medical records from all patients from whom NTM isolates were recovered within a 2-year period. We identified all NTM isolates from respiratory specimens at the Samsung Medical Center (Seoul, South Korea) obtained from January 2002 to December 2003. We then reviewed the clinical and radiologic characteristics of the patients from whom NTM was isolated. Patients were classified as having either definite, probable, or unlikely NTM lung disease, as defined by the guidelines of both the American Thoracic Society and the British Thoracic Society. During the study period, 1,548 NTM isolates were recovered from 794 patients. Of these 794 patients, 131 patients (17%) were determined to have definite NTM lung disease, and 64 patients (8%) were designated as probable disease candidates. The most commonly involved organisms in the definite and probable NTM lung disease cases were Mycobacterium avium complex (n = 94, 48%) and Mycobacterium abscessus (n = 64, 33%). In 195 patients with NTM lung disease, 82 patients (42%) manifested the upper lobe cavitary form, 101 patients (52%) exhibited the nodular bronchiectatic form, and 12 patients (6%) exhibited the unclassifiable form. About one fourth of the patients in whom NTM was isolated from respiratory specimens were found to have clinically significant NTM lung infections. The spectrum of organisms responsible for the NTM lung disease in these Korean patients differed from those reported in other regions of the world. However, the estimates of clinical significance in this study may be underestimates due to the retrospective analysis. Some of the patients might have "true" NTM lung disease that could be diagnosed with continued evaluation and follow-up.

Nontuberculous Mycobacterial Pulmonary Infection in Immunocompetent Patients

Background : Nontuberculous mycobacteria (NTM) have usually been considered to be contaminants of colonizers when isolated from respiratory specimens in Korea, where there is a high prevalence of tuberculosis and a low rate of HIV infections. Therefore, there has been few studies on the clinical significance of NTM species in immunocompetent patients were investigated. Methods : Thirty-five NTM isolates, for which species identification was requested by the treating physicians during 1999 at the Asan Medical Center, were retrospectively analyzed. They were identified to the species level by mycolic acid analysis using high-performance liquid chromatography. The medical records of the patients with the NTM isolates were reviewed to identify those patients who met the American Thoracic Society (ATS)'s criteria for mycobacterial pulmonary infection. Their antimicrobial susceptibility data were compared with the clinical outcomes. Results : The NTM were identified as M. intracellulare (6 isolates), M. avium (5), M. abscessus (5), M. gordonae (5), M. terrae complex (4), M. szulgai (2), M. kansasii (2), M. fortuitum (2), M. peregrinum (1), M. mucogenicum (1), M. celatum (1), and M. chelonae (1). All 35 patients showed clinical symptoms and signs of chronic lung disease, but none had a HIV infections; 16 (45.7%) patients were found to be compatible with a NTM pulmonary infection according to the ATS criteria, 5 and 4 cases were affected with M. intracellulare and M. abscessus, respectively; 8 patients had a history of pulmonary tuberculosis. 13 patients received antimycobacterial therapy for an average of 21 months and 9 patients were treated with second-line drugs. Only 4 patients had improved radiologically. Conclusion : A NTM should be considered a potential pathogen of pulmonary infections in immunocompetent patients with chronic pulmonary diseases. Most NTM infections were left untreated for a prolonged period and showed a poor outcome as a result, M. intracellulare and M. abscessus were the two most frequent causes of NTM pulmonary infections in this study. Species identification and antimycobacterial susceptibility tests based on the species are needed for the optimum management of a NTM pulmonary infection in patients.

Cellular fatty acid profiles of ninety-five strains of Vibrio vulnificus isolated from clinical specimens in Korea.

There have been many reports of primary Vibrio vulnificus septicemia in Korea since 1987. This study was undertaken to determine the cellular fatty acid (CFA) compositions of 95 clinical strains of V. vulnificus isolated in Korea during 1985-1995. We compared these results with the CFA profile of V. vulnificus in the Microbial Identification System (MIS) (CLIN library version 3.9; Microbial ID Inc., Newark, DE, U.S.A.), and the grouping of V. vulnificus by CFA analysis was also performed. The relationship between groups and serotypes of V. vulnificus was described. Although most of the CFAs in V. vulnificus strains were similar to the CFA profile of V. vulnificus in the MIS, some distinctive differences were observed between the results of this study and the MIS CFA profile of V. vulnificus. First, the means of 2 major CFAs, 16 : 0 and 16 : 1w7c, were 22.16 and 18.26% in this study but 23.52 and 25.44% in the MIS, respectively. Second, all isolates had 11 : 0iso3OH, which was not present in the MIS. Of 95 strains, 10 strains (10.5%) showed 'NO MATCH' results by the MIS identification. Eighty five strains (89.5%) were identified as V. vulnificus by the MIS (the first choice identification), but they disclosed low SI values of <0.6 (not 'EXCELLENT MATCH') except 2 strains (2.1%). This showed that V. vulnificus strains isolated in Korea had different characteristics in CFA composition in comparison with the MIS V. vulnificus library. Nine groups comprising all the strains were obtained by cluster analysis and were further characterized by principal-component analysis. There was heterogeneity between the groups by CFA and serotypes of V. vulnificus. The same serovars were distributed into diverse groups.