Reply to “Distribution of Genotypes between CTX-M-Producing and Non-Extended-Spectrum-β-Lactamase-Producing <i>Klebsiella pneumoniae</i> Isolates”

Shin, Juyoun,Ko, Kwan Soo American Society for Microbiology 2015 Antimicrobial Agents and Chemotherapy Vol.59 No.7

Comparative Study of Genotype and Virulence in CTX-M-Producing and Non-Extended-Spectrum-β-Lactamase-Producing <i>Klebsiella pneumoniae</i> Isolates

Shin, Juyoun,Ko, Kwan Soo American Society for Microbiology 2014 Antimicrobial Agents and Chemotherapy Vol.58 No.4

<P>Molecular and virulence characteristics of CTX-M-producing and non-extended-spectrum-β-lactamase (non-ESBL)-producing <I>Klebsiella pneumoniae</I> isolates were compared. Lack of shared characteristics between the two groups suggested that most CTX-M-producing <I>K. pneumoniae</I> isolates in South Korea did not occur by transfer of <I>bla</I><SUB>CTX-M</SUB> into susceptible strains. Conjugation assays confirmed that the plasmid with the <I>bla</I><SUB>CTX-M-15</SUB> gene confers virulence as well as antimicrobial resistance, suggesting that a CTX-M-15-producing clone such as ST11 may have a selective advantage even without antibiotic pressure.</P>

Duplex dPCR System for Rapid Identification of Gram-Negative Pathogens in the Blood of Patients with Bloodstream Infection: A Culture-Independent Approach

( Juyoun Shin ),( Sun Shin ),( Seung-hyun Jung ),( Chulmin Park ),( Sung-yeon Cho ),( Dong-gun Lee ),( Yeun-jun Chung ) 한국미생물 · 생명공학회 2021 Journal of microbiology and biotechnology Vol.31 No.11

Early and accurate detection of pathogens is important to improve clinical outcomes of bloodstream infections (BSI), especially in the case of drug-resistant pathogens. In this study, we aimed to develop a culture-independent digital PCR (dPCR) system for multiplex detection of major sepsis-causing gram-negative pathogens and antimicrobial resistance genes using plasma DNA from BSI patients. Our duplex dPCR system successfully detected nine targets (five bacteria-specific targets and four antimicrobial resistance genes) through five reactions within 3 hours. The minimum detection limit was 50 ag of bacterial DNA, suggesting that 1 CFU/ml of bacteria in the blood can be detected. To validate the clinical applicability, cell-free DNA samples from febrile patients were tested with our system and confirmed high consistency with conventional blood culture. This system can support early identification of some drug-resistant gram-negative pathogens, which can help improving treatment outcomes of BSI.

<i>bla</i>_NDM-5-Bearing IncFII-Type Plasmids of <i>Klebsiella pneumoniae</i> Sequence Type 147 Transmitted by Cross-Border Transfer of a Patient

Shin, Juyoun,Baek, Jin Yang,Cho, Sun Young,Huh, Hee Jae,Lee, Nam Yong,Song, Jae-Hoon,Chung, Doo Ryeon,Ko, Kwan Soo American Society for Microbiology 2016 Antimicrobial Agents and Chemotherapy Vol.60 No.3

<P>The two plasmids extracted from Klebsiella pneumoniae sequence type 147 (ST147) isolates were analyzed. The first isolate was obtained from a patient transferred from United Arab Emirates to South Korea. The second isolate was obtained from a Korean patient and was suspected to be transmitted from the first patient. Sequences of two plasmids were almost the same, and genetic structures, including bla(NDM-5), of these plasmids were similar to plasmids of NDM-1-producing Escherichia coli ST131 isolates found in Europe.</P>

Instability of the IncFII-Type Plasmid Carrying bla_NDM-5 in a Klebsiella pneumoniae Isolate

( Juyoun Shin ),( Jin Yang Baek ),( Doo Ryeon Chung ),( Kwan Soo Ko ) 한국미생물생명공학회(구 한국산업미생물학회) 2017 Journal of microbiology and biotechnology Vol.27 No.9

In this study, we characterized the bla_NDM-5-bearing plasmid in a Klebsiella pneumoniae isolate that had lost the plasmid during serial passage. We determined the complete sequences of the plasmid pCC1410-2, which was extracted from a K. pneumoniae ST709 isolate collected at a Korean hospital from which two NDM-5-producing K. pneumoniae isolates were subsequently isolated. As a result, the pCC1410-2 plasmid had a backbone structure that was similar to those of two plasmids previously reported from the same hospital, but lacked some antibiotic resistance genes (bla_TEM-1, rmtB, mphR(A), mrx(A), and mph(A)). A 9-bp repeating unit encoding three amino acids (Gln-Gln-Pro) was inserted in TraD in pCC1410-2. Thus, the pCC1410-2 plasmid might be transferred from the previously identified carbapenem-resistant K. pneumoniae, but some delections and inversions might have occurred during the process. We compared the transfer frequency and stability of the plasmids. The relative frequency of conjugative transfer and stability in the host were significantly lower in pCC1410-2 than in previously reported bla_NDM-5-bearing plasmids in Korea. A low transfer frequency and instability in the host may cause underestimation of carbapenemase-producing Enterobacteriaceae in the clinical setting and in surveillance studies.

Development of reverse transcription loop-mediated isothermal amplification assays for point-of-care testing of avian influenza virus subtype H5 and H9

Zhang, Songzi,Shin, Juyoun,Shin, Sun,Chung, Yeun-Jun Korea Genome Organization 2020 Genomics & informatics Vol.18 No.4

Avian influenza (AIV) outbreaks can induce fatal human pulmonary infections in addition to economic losses to the poultry industry. In this study, we aimed to develop a rapid and sensitive point-of-care AIV test using loop-mediated isothermal amplification (LAMP) technology. We designed three sets of reverse transcription LAMP (RT-LAMP) primers targeting the matrix (M) and hemagglutinin (HA) genes of the H5 and H9 subtypes. RT-LAMP targeting the universal M gene was designed to screen for the presence of AIV and RT-LAMP assays targeting H5-HA and H9-HA were designed to discriminate between the H5 and H9 subtypes. All three RT-LAMP assays showed specific amplification results without nonspecific reactions. In terms of sensitivity, the detection limits of our RT-LAMP assays were 100 to 1,000 RNA copies per reaction, which were 10 times more sensitive than the detection limits of the reference reverse-transcription polymerase chain reaction (RT-PCR) (1,000 to 10,000 RNA copies per reaction). The reaction time of our RT-LAMP assays was less than 30 min, which was approximately four times quicker than that of conventional RT-PCR. Altogether, these assays successfully detected the existence of AIV and discriminated between the H5 or H9 subtypes with higher sensitivity and less time than the conventional RT-PCR assay.

Rapid and sensitive detection of Salmonella species targeting the hilA gene using a loop-mediated isothermal amplification assay

Chu, Jiyon,Shin, Juyoun,Kang, Shinseok,Shin, Sun,Chung, Yeun-Jun Korea Genome Organization 2021 Genomics & informatics Vol.19 No.3

Salmonella species are among the major pathogens that cause foodborne illness outbreaks. In this study, we aimed to develop a loop-mediated isothermal amplification (LAMP) assay for the rapid and sensitive detection of Salmonella species. We designed LAMP primers targeting the hilA gene as a universal marker of Salmonella species. A total of seven Salmonella species strains and 11 non-Salmonella pathogen strains from eight different genera were used in this study. All Salmonella strains showed positive amplification signals with the Salmonella LAMP assay; however, there was no non-specific amplification signal for the non-Salmonella strains. The detection limit was 100 femtograms (20 copies per reaction), which was ~1,000 times more sensitive than the detection limits of the conventional polymerase chain reaction (PCR) assay (100 pg). The reaction time for a positive amplification signal was less than 20 minutes, which was less than one-third the time taken while using conventional PCR. In conclusion, our Salmonella LAMP assay accurately detected Salmonella species with a higher degree of sensitivity and greater rapidity than the conventional PCR assay, and it may be suitable for point-of-care testing in the field.

PAIVS: prediction of avian influenza virus subtype

Park, Hyeon-Chun,Shin, Juyoun,Cho, Sung-Min,Kang, Shinseok,Chung, Yeun-Jun,Jung, Seung-Hyun Korea Genome Organization 2020 Genomics & informatics Vol.18 No.1

Highly pathogenic avian influenza (HPAI) viruses have caused severe respiratory disease and death in poultry and human beings. Although most of the avian influenza viruses (AIVs) are of low pathogenicity and cause mild infections in birds, some subtypes including hemagglutinin H5 and H7 subtype cause HPAI. Therefore, sensitive and accurate subtyping of AIV is important to prepare and prevent for the spread of HPAI. Next-generation sequencing (NGS) can analyze the full-length sequence information of entire AIV genome at once, so this technology is becoming a more common in detecting AIVs and predicting subtypes. However, an analysis pipeline of NGS-based AIV sequencing data, including AIV subtyping, has not yet been established. Here, in order to support the pre-processing of NGS data and its interpretation, we developed a user-friendly tool, named prediction of avian influenza virus subtype (PAIVS). PAIVS has multiple functions that support the pre-processing of NGS data, reference-guided AIV subtyping, de novo assembly, variant calling and identifying the closest full-length sequences by BLAST, and provide the graphical summary to the end users.

Overexpression of integrin αv correlates with poor prognosis in colorectal cancer

Ha, Sang Yun,Shin, Juyoun,Kim, Jeong Hoon,Kang, Myung Soo,Yoo, Hae-Yong,Kim, Hyeon-Ho,Um, Sung-Hee,Kim, Seok-Hyung BMJ Publishing Group Ltd 2014 Journal of clinical pathology Vol.67 No.7

<P>Aims Integrin alpha v subunits are involved in tumour angiogenesis and tumour progression in various types of cancers. Clinical trials evaluating agents targeting integrin alpha v are ongoing. Integrin alpha v expression has been reported in several cancers in association with tumour progression or poor survival. However, no study has addressed the prognostic influence of integrin alpha v expression on survival of patients with colorectal cancer (CRC). Methods Immunohistochemical staining of integrin alpha v was performed in 198 CRC samples to evaluate its prognostic significance. Results High expression of integrin alpha v was observed in 58.1% (115/189) of colorectal adenocarcinoma samples, while only in 11.5% (3/26) of tubular adenoma samples and in none of normal mucosa or hyperplastic polyp samples. It was more frequently found in female patients and less frequently observed in well differentiated tumours. The proportion of cases with high expression of integrin alpha v showed an increasing trend with increased T stage (p=0.032), N stage (p=0.006) and TNM stage (p=0.001). Patients displaying exuberant expression of integrin alpha v showed shorter overall survival (p=0.001) and disease-free survival (p=0.004). Elevated integrin alpha v expression was an independent prognostic factor for overall survival (HR: 2.04, 95% CI 1.16 to 3.56; p=0.013) and disease-free survival (HR: 2.19, 95% CI 1.16 to 4.13; p=0.015). Conclusions Overexpression of integrin alpha v is associated with advanced T and N stage and as an independent prognostic factor in CRC.</P>

多時期 위성영상을 이용한 두만강 하류지역의 농경지 개간의 공간적 특성분석

이민부(Min-Boo Lee),한욱(Uk Han),김남신(Nam-Shin Kim),한주연(Juyoun Han),신근하(Keun-Ha Shin),강철성(Chul-Sung Kang) 대한지리학회 2003 대한지리학회지 Vol.38 No.4

본 연구는 두만강 하류의 온성, 새별, 은덕 지역을 대상으로 1992년 Landsat TM과 2000년 Landsat ETM 자료 및 수치고도자료를 이용하여 농경지와 산림지의 분포와 변화, 변화과정의 공간적 특성을 분석한 것이다. 1:5만 수치지형도 분석, 영상밴드조합, 주성분 분석 등 감독분류를 통하여 농경지, 산림, 취락 및 건물, 강과 저수지 등의 수체를 주요 항목으로 하여 분류를 시도하였다. 대상 지역에 대한 분석의 결과를 보면, 온성과 은덕 지역에서는 1992년에서 2000년 사이에 농경지가 각각 22.8%, 14.7% 증가하였으며, 상대적으로 산림은 각각 24.0%, 13.6% 감소하<br/> 였다. 또한 경작지의 평균고도를 보면 온성, 새별, 은덕의 경우, 각각 157m, 85m, 78m에서 192m, 95m, 91m로 높아졌으며, 경사도의 경우는, 각각 5.2˚, 2.5˚, 3.0˚에서 6.6˚, 3.0˚, 4.4˚로, 고도와 경사도 모두 약 30% 증가세를 보여주고 있다. 특히 신개간지 만을 보면 평균고도는 각각 255m, 122m, 127m, 평균경사도는 9.4˚, 5.1˚, 8.0˚로 나타나고 있다. 이러한 개간지들은 구릉지대나 산록완사면을 따라 경사변환점까지 확대되고 있으며, 산림이 제거된 나대지들은 불규칙한 패치모양을 띠면서 rill과 gully 등의 사면침식과 하천의 토사퇴적의 원인을 제공하고 있다. 이러한 위성영상분석은 지표확인을 할 수 없는 한계점은 있으나 농업과 관련된 북한의 환경문제에 대한 실태파악에 도움을 줄 수 있다. This study aims to analysis the distribution and change of cropland and forest, the Onseong, Saebyeol, and Eundeok counties on the lower reach of Duman(Tumen) river, northeast Korea, using 1992 year Landsat TM data, 2000 year Landsat ETM data, and digital terrain elevation data(DTED). Land cover and land use of the study areas are classified into cropland, forest, village, and water body, using the supervised classification method including 1:50,000 DTED analysis, image band composition, and principal component<br/> analysis(PCA). Results of quantitative analysis present that each growth rate of cropland of Onseong and Eundeok are 22.8% and 14.7% corresponding to decreasing rates of forest, 8% and 13.6% during 8 years from 1992 to 2000. In Onseong, Saebyeol, and Eundeok, each values of mean elevations and slope gradients increased to 192m, 95m, and 91m from 157m, 85m, and 78m, and to 6.6°, 3.0°, and 4.4° from 5.2°, 2.5°, and 3.0°. Especially, in case of newly developed cropland, the values of mean elevation and mean gradient have 225m, 122m, and 127m, and 9.4°, 5.1°, and 8.0°, in above three regions. These new croplands were developing along to deeper valleys and toward lower hill and mountain slope up to knickpoint zone of gradient change. Deforested lands for cropland have formed irregular pattern of patch-type, and become sources for the sheet erosion, rilling and gulleying in mountain slope and sedimentation in local river channel. Though there were no field checking, analysis using landsat images and GIS mapping can help understand actual environmental problems relating to cropland development of mountain slope in North Korea.