Journal of Microbiology

Journal Articles

Prevalence of human Norovirus by genotype in contaminated groundwater in Korea over the last decade (2007–2016): Siwon Lee , Junhyeong Jang , Kyungseon Bae , Wonseok Lee , Hyenmi Chung , Sangjung Park; J. Microbiol. 2018;56(12):926-931. Published online November 27, 2018; DOI: https://doi.org/10.1007/s12275-018-8340-8

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This study investigated the occurrence of human Norovirus (HuNoV) by genotype in 1,486 groundwater samples collected from 843 groundwater wells suspected of contamination during 2007–2016, in South Korea. We identified and genotyped 186 HuNoV sequences in 178 HuNoV-positive samples using the RIVM-NoroNet norovirus genotyping tool (NGT) and phylogenetic tree analysis based on RIVM-NoroNet reference sequences. HuNoV GII was more prevalent than GI. The major genotypes detected were HuNoV GII.4 (43.0%), GII.22 (15.6%), GI.5 (10.2%), and GI.1 (8.6%); several genotypes accounted for < 5.0% of all HuNoVs, including GII.17, GI.6, GI.4, GII.6, GI.8, GII.3, GII.13, GI.3, GI.7, GI.2, GI.9, GII.1, GII.8, and GII.10. The prevalence of HuNoVs and number of genotypes detected has drastically decreased over the last decade. HuNoV GII.17, the emerging genotype worldwide including Europe and Asia, appeared in Korean groundwater from 2010, dominated in 2013–2014, and continued to be observed. HuNoV GII.4, the major type occurred last decade from Korean groundwater except 2013–2014, continued to be detected and prevalent similar to HuNoV GII.17 in 2016.

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Development of diagnostic systems for wide range and highly sensitive detection of two waterborne hepatitis viruses from groundwater using the conventional reverse transcription nested PCR assay
Kyung-Seon Bae, Siwon Lee, Jin-Young Lee, Ji-Hye Kim, Youn-Lee Joo, Soo Hyung Lee, Hyen-Mi Chung, Kyung-A You
Journal of Virological Methods.2022; 299: 114344. CrossRef
Assessment of Genetic Diversity of Noroviruses Circulating in Temporary Accommodation Centers for Refugees in the Rostov Region in 2022 Using the NoroNetRus Online Software
Alexey S. Vodop’ianov, Ruslan V. Pisanov, Sergey O. Vodop’ianov, Olga S. Chemisova, Artem A. Gerasimenko, Aleksey K. Noskov, Sergey S. Slis, Svetlana A. Nenadskaya, Anastasia D. Koreneva, Alina V. Kolomoitseva, Evgeny V. Kovalev, Anna R. Litovko, Nina V.
ЗДОРОВЬЕ НАСЕЛЕНИЯ И СРЕДА ОБИТАНИЯ - ЗНиСО / PUBLIC HEALTH AND LIFE ENVIRONMENT.2022; : 82. CrossRef
Enteric virus presence in green vegetables and associated irrigation waters in a rural area from Argentina. A quantitative microbial risk assessment
Prez Verónica Emilse, Victoria Matías, Martínez Laura Cecilia, Giordano Miguel Oscar, Masachessi Gisela, DiCola Guadalupe, Ré Viviana Elizabeth, Paván Jorge Victorio, Colina Rodney, Nates Silvia Viviana, Barril Patricia Angélica
LWT.2021; 144: 111201. CrossRef
Characteristics of Norovirus Food Poisoning Outbreaks in Korea in the 2000s
Jong-Gyu Kim, Joong-Soon Kim, Jeong-Gyoo Kim
Journal of Food Protection.2021; 84(3): 472. CrossRef
Prevalence of emerging torque teno virus (TTV) in drinking water, natural waters and wastewater networks (DWNWWS): A systematic review and meta-analysis of the viral pollution marker of faecal and anthropocentric contaminations
Temitope C. Ekundayo
Science of The Total Environment.2021; 771: 145436. CrossRef
Development and Evaluation of a SYBR Green-Based, Real-time Polymerase Chain Reaction for Rapid and Specific Detection of Human Coxsackievirus B5
Kyu Bong Cho
Biomedical Science Letters.2020; 26(4): 302. CrossRef

Roles of human apolipoprotein E in the infectivity and replication of hepatitis C virus genotype 2a: Bo-Kyoung Jung , Hye-Ran Kim , Gyu-Nam Park , Guangxiang Luo , Kyung-Soo Chang; J. Microbiol. 2016;54(6):451-458. Published online May 27, 2016; DOI: https://doi.org/10.1007/s12275-016-6099-3

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Abstract

Hepatitis C virus (HCV) infection is associated with lipoproteins, and apolipoprotein E (apoE) plays an essential role in infectious HCV particles. Although the role of apoE in HCV infection is well known, its role in the replication of HCV remains unclear. The aims of this study were to determine the role of apoE in the RNA replication of major HCV genotypes 1b and 2a, and to determine whether this role is HCVgenotype- dependent using HCV genotype 1b replicon cells and HCV genotype 2a producing (HP) cells. HCV infection was blocked in Huh7.5 cells treated with low-density lipoproteins, very low-density lipoproteins, or apoE3. An apoE3- specific monoclonal antibody also efficiently neutralized HCV infectivity, and HCV infection was dramatically suppressed by the knockdown of apoE expression with an apoE-specific small interfering RNA, suggesting a requirement for apoE in infectious HCV particles. HCV RNA replication was not affected in HP cells treated with each apoE isoform or transfected with apoE-specific siRNAs. However, the knockdown of apoE expression suppressed RNA replication of HCV genotype 1b. The siRNA-mediated knockdown of apoE, apoA1, and apoB expression also suppressed the RNA replication of HCV genotype 1b, but not that of HCV genotype 2a. Taken together, these findings indicate that apoE plays an important role in HCV genotype 2a infection and in HCV genotype 1b RNA replication, but not in the replication of HCV genotype 2a. These results provide important information for the future development of HCV-genotypespecific anti-HCV agents.

Citations

Citations to this article as recorded by

The Role of ApoE in HCV Infection and Comorbidity
Yue Gong, Wei Cun
International Journal of Molecular Sciences.2019; 20(8): 2037. CrossRef
How Have Retrovirus Pseudotypes Contributed to Our Understanding of Viral Entry?
Barnabas King, Alexander W Tarr
Future Virology.2017; 12(10): 569. CrossRef

Research Support, Non-U.S. Gov't

Molecular Detection and Genotyping of Fusarium oxysporum f. sp. psidii Isolates from Different Agro-Ecological Regions of India: Rupesh Kumar Mishra , Brajesh Kumar Pandey , Vijai Singh , Amita John Mathew , Neelam Pathak , Mohammad Zeeshan; J. Microbiol. 2013;51(4):405-412. Published online August 30, 2013; DOI: https://doi.org/10.1007/s12275-013-2638-3

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Abstract: Twenty one isolates of Fusarium oxysporum f. sp. psidii (Fop), causing a vascular wilt in guava (Psidium guajava L.), were collected from different agro-ecological regions of India. The pathogenicity test was performed in guava seedlings, where the Fop isolates were found to be highly pathogenic. All 21 isolates were confirmed as F. oxysporum f. sp. psidii by a newly developed, species-specific primer against the conserved regions of 28S rDNA and the intergenic spacer region. RAPD and PCR-RFLP were used for genotyping the isolates to determine their genetic relationships. Fifteen RAPD primers were tested, of which five primers produced prominent, polymorphic, and reproducible bands. RAPD yielded an average of 6.5 polymorphic bands per primer, with the amplified DNA fragments ranging from 200–2,000 bp in size. A dendrogram constructed from these data indicated a 22–74% level of homology. In RFLP analysis, two major bands (350 and 220 bp) were commonly present in all isolates of F. oxysporum. These findings provide new insight for rapid, specific, and sensitive disease diagnosis. However, genotyping could be useful in strain-level discrimination of isolates from different agro-ecological regions of India.

Research Support, U.S. Gov't, Non-P.H.S.

Shedding of Viral Hemorrhagic Septicemia Virus (Genotype IVb) by Experimentally Infected Muskellunge (Esox masquinongy): Robert K. Kim , Mohamed Faisal; J. Microbiol. 2012;50(2):278-284. Published online April 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1145-2

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Abstract: Previous experimental infection demonstrated that juvenile muskellunge (Esox masquinongy) can survive experimental infection of viral hemorrhagic septicemia virus, Genotype IVb (VHSV IVb) at a low concentration of exposure. Herein we report that survivors of experimental infection with VHSV IVb shed the virus into the surrounding environment for an extended period of time. When muskellunge were exposed to VHSV IVb by immersion at a concentration of 1,400 plaque forming units (PFU)/ml, VHSV IVb was detected in the water of surviving fish for up to 15 weeks postexposure (p.e.) with the highest levels of shedding occurring between weeks 1 and 5 p.e. We estimated that each juvenile muskellunge can shed upwards of 1.36×105 PFU/fish/h after initial exposure signifying the uptake and amplification of VHSV to several orders of magnitude above the original exposure concentration. Muskellunge surviving low concentration exposure were re-infected with VHSV IVb by immersion at week 22 p.e. at concentrations ranging from 0 to 106 PFU/ml. Viral shedding was detected in all re-exposed fish, including mock rechallenged controls up to 15 consecutive weeks. Rates of viral shedding were substantially higher following rechallenge in the first 5 weeks. The highest rate of viral shedding was approximately 4.6×106 PFU/fish/h and shedding did not necessarily correspond to the re-exposure VHSV concentration. The results of this study shed new light into the dynamics of VHSV IVb shedding in a highly susceptible host and provide useful insights to fishery managers to design effective control strategies to this deadly virus.

Research Support, Non-U.S. Gov't

Virulence Determinants in Vancomycin-Resistant Enterococcus faecium vanA Isolated from Different Sources at University Hospital of Londrina, Paraná, Brazil: Flávia Imanishi Ruzon , Suelen Balero de Paula , Renata Lumi Kanoshiki , Jussevania Pereira-Santos , Gilselena Kerbauy , Renata Katsuko Takayama Kobayashi , Lucy Megumi Yamauchi , Márcia Regina Eches Perugini , Sueli Fumie Yamada-Ogatta; J. Microbiol. 2010;48(6):814-821. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0099-5

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Abstract: Enterococcus faecium, especially those showing multidrug resistance, has emerged as a significant cause of healthcare-associated infections worldwide. However, relatively little is known about the virulence and pathogenesis of this species. The aim of this study was to determine the occurrence of four putative virulence determinants of E. faecium and to correlate them with phenotypic traits. Using forty E. faecium vanA-type isolates from hospitalized patients and their environmental vicinity, we determined the following: the antimicrobial susceptibility profile, occurrence of the genes cylA, efaA, esp, and gelE, hemolytic and gelatinase activities, capacity to form biofilm and in vitro adhesion to epithelial cells. All isolates were shown to be resistant to vancomycin and teicoplanin, as well as to two or more other antimicrobials. All isolates harbored at least one putative virulence marker, and the prevalence was as follows: esp, 87.5%; efaA, 82.5%; gelE, 70%; and cylA, 65%. The presence of 4 genes was observed in 32.5% isolates. The presence of the efaA was associated with the presence of esp, regardless of the source of the isolates. A positive association with the presence of cylA and hemolytic activity in the sheep blood agar assay was observed. No association was found for gelE and gelatinase production in the agar plate assay, for efaA and LLC-MK2 cell adhesion, and for esp and biofilm formation on polystyrene surface. These results show the presence of putative virulence genes in multiple antimicrobial resistant E. faecium isolates from different sources in a hospital setting.

Validation Study

Differentiation of Lymphocystis Disease Virus Genotype by Multiplex PCR: Shin-Ichi Kitamura , Sung-Ju Jung , Myung-Joo Oh; J. Microbiol. 2006;44(2):248-253.; DOI: https://doi.org/2358 [pii]

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Abstract: Lymphocystis disease virus (LCDV) is the causative agent of lymphocystis disease. The viruses have been divided into three genotypes (genotype I for LCDV-1, II for Japanese flounder isolates, and III for rockfish isolates) on the basis of major capsid protein (MCP) gene sequences. In this study, we developed a multiplex PCR primer set in order to distinguish these genotypes. We also analyzed the MCP gene of a new LCDV isolate from the sea bass (SB98Yosu). Comparison of sequence identities between SB98Yosu and eight Japanese flounder isolates, revealed identity of more than 90.1% at nucleotide level and 96.5% at deduced amino acid level, respectively. Phylogenetic analyses based on the MCP gene showed that SB98Yosu belongs to genotype II, along with Japanese flounder isolates. Multiplex PCR based on the MCP gene allowed us to identify these genotypes in a simple and rapid manner, even in a sample that contained two genotypes, in this case genotypes II and III.

Research Support, Non-U.S. Gov'ts

Molecular Taxonomy of a Soil Actinomycete Isolate, KCCM10454 Showing Neuroprotective Activity by 16S rRNA and rpoB Gene Analysis: Bong-Hee Lee , Hong Kim , Hyun-Ju Kim , Yoon-Kyu Lim , Kyung-Hee Byun , Brian Hutchinson , Chang-Jin Kim , Young-Hwan Ko , Keun-Hwa Lee , Chang-Yong Cha , Yoon-Hoh Kook , Bum-Joon Kim; J. Microbiol. 2005;43(2):213-218.; DOI: https://doi.org/2158 [pii]

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Abstract: Epilepsy constitutes a significant public health problem, and even the newest drugs and neurosurgical techniques have proven unable to cure the disease. In order to select a group of isolates which could generate an active compound with neuroprotective or antiepileptic properties, we isolated 517 actinomycete strains from soil samples taken from Jeju Island, in South Korea. We then screened these strains for possible anti-apoptotic effects against serum deprivation-induced hippocampal cell death, using the 3-(4, 5-dimethylthiazol-2-yl)2,5-diphenyl-tetrazolium bromide (MTT) assay as an in vitro test. The excitotoxic glutamate analog, kainic acid (KA), was used to induce seizures in experimental mice in our in vivo tests. As a result of this testing, we located one strain which exhibited profound neuroprotective activity. This strain was identified as a Streptomyces species, and exhibited the rifampin-resistant genotype, Asn(AAC)^442, according to the results of 16S rRNA and rpoB gene analyses

Hepatitis C Virus (HCV) Genotyping by Annealing Reverse Transcription-PCR Products with Genotype-Specific Capture Probes: Jungmin Rho , Jong Soon Ryu , Wonhee Hur , Chang Wook Kim , Jeong Won Jang , Si Hyun Bae , Jong Young Choi , Sung Key Jang , Seung Kew Yoon; J. Microbiol. 2008;46(1):81-87.; DOI: https://doi.org/10.1007/s12275-007-0121-8

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18 Scopus

Abstract: The genotype of the hepatitis C virus (HCV) strain infecting a given patient is an important predictive factor for the clinical outcome of chronic liver disease and its response to anti-viral therapeutic agents. We herein sought to develop a new easy, sensitive and accurate HCV genotyping method using annealing genotype- specific capture probes (AGSCP) in an automation-friendly 96-well plate format. The validation of our new AGSCP was performed using the Standard HCV Genotype Panel. We then used both our AGSCP and the commercially available INNO-LiPA assay to analyze the HCV genotypes from 111 Korean patients. Discordant results were analyzed by direct sequencing. AGSCP successfully genotyped the standard panel. The genotypes of 111 patient samples were also obtained successfully by AGSCP and INNO-LiPA. We observed a high concordance rate (93 matched samples, 83.8%) between the two assays. Sequencing analysis of the 18 discordant results revealed that the AGSCP had correctly identified 12 samples, whereas the INNO- LiPA had correctly identified only 6. These results collectively indicate that AGSCP assay is a convenient and sensitive method for large-scale genotyping, and it may be a promising tool for the determination of HCV and other genotypes in clinical settings.

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