Review
- MINIREVIEW] Rapid and robust MALDI-TOF MS techniques for microbial identification: a brief overview of their diverse applications
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Kyoung-Soon Jang , Young Hwan Kim
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J. Microbiol. 2018;56(4):209-216. Published online February 28, 2018
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DOI: https://doi.org/10.1007/s12275-018-7457-0
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Abstract
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Advances in mass spectrometry have enabled the investigation
of various biological systems by directly analyzing diverse
sets of biomolecules (i.e., proteins, lipids, and carbohydrates),
thus making a significant impact on the life sciences field.
Over the past decade, matrix-assisted laser desorption ionization
time-of-flight mass spectrometry (MALDI-TOF MS) has
been widely utilized as a rapid and reliable method for the
identification of microorganisms. MALDI-TOF MS has come
into widespread use despite its relatively low resolving power
(full width at half maximum, FWHM: < 5,000) and its incompatibility
with tandem MS analysis, features with which other
high-resolution mass spectrometers are equipped. Microbial
identification is achieved by searching databases containing
mass spectra of peptides and proteins extracted from microorganisms
of interest, using scoring algorithms to match analyzed
spectra with reference spectra. In this paper, we give
a brief overview of the diverse applications of rapid and robust
MALDI-TOF MS-based techniques for microbial identification
in a variety of fields, such as clinical diagnosis and environmental
and food monitoring. We also describe the fundamental
principles of MALDI-TOF MS. The general specifications
of the two major MS-based microbial identification
systems available in the global market (BioTyper® and VITEK®
MS Plus) and the distribution of these instruments in Republic
of Korea are also discussed. The current review provides an
understanding of this emerging microbial identification and
classification technology and will help bacteriologists and
cell biologists take advantage of this powerful technique.
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Citations
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BioMed Research International.2018; 2018: 1. CrossRef
Journal Article
- Identification of cyst wall proteins of the hypotrich ciliate Euplotes encysticus using a proteomics approach
-
Bangzheng Wang , Tao Niu , Muhammad Zeeshan Bhatti , Fenfen Chen , Lin Wu , Jiwu Chen
-
J. Microbiol. 2017;55(7):545-553. Published online June 30, 2017
-
DOI: https://doi.org/10.1007/s12275-017-6422-7
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44
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11
Crossref
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Abstract
-
Euplotes encysticus is a species of Hypotrich ciliates, which
form cyst wall by secreting the special substances on encounter
of adverse environment. It has critical significance to study
the component and mechanism underlying resting cyst, during
resisting unfavorable conditions in dormancy induction.
The present study was aimed to investigate the effects of cyst
wall proteins of Euplotes encysticus by using biochemical
methods
. Therefore, protein extracts were separated by SDSPAGE,
identified and analyzed by MALDI-TOF MS and Bioinformatics
tools. We detected 42 cyst wall proteins, 26 were
functional proteins and 16 proteins consist of unknown function;
which is consistent with cyst wall specificity. These results
partially revealed the components of resting cyst wall
formed after the cells differentiation of Euplotes encysticus.
In addition, our data suggested that the function of cyst wall
proteins are more likely involved in the mechanical protection,
signal transduction, material transport, protein degradation
and energy metabolism to survival, with potentially
importance implications in the molecular mechanism of eukaryocyte
dormancy under stress condition.
-
Citations
Citations to this article as recorded by

- Decryption of the survival “black box”: gene family expansion promotes the encystment in ciliated protists
Didi Jin, Chao Li, Xiao Chen, Yurui Wang, Khaled A. S. Al-Rasheid, Naomi A. Stover, Chen Shao, Tengteng Zhang
BMC Genomics.2024;[Epub] CrossRef - Role of chitin synthases CHS1 and CHS2 in biosynthesis of the cyst wall of Cryptocaryon irritans
Huicheng Wu, Yihao Cen, Yipei Lu, Pengbo Dan, Yanwei Li, Xueming Dan, Zequan Mo
International Journal of Biological Macromolecules.2024; 280: 136143. CrossRef - Water temperature affects Cryptocaryon irritans development, cryptocaryoniasis occurrence and an auxiliary treatment decision-making webpage
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European Journal of Protistology.2022; 86: 125922. CrossRef - How Ciliated Protists Survive by Cysts: Some Key Points During Encystment and Excystment
Yuqing Li, Yurui Wang, Shijing Zhang, Xyrus X. Maurer-Alcalá, Ying Yan
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Research Support, Non-U.S. Gov'ts
- Pregnancy - associated human listeriosis: Virulence and genotypic analysis of Listeria monocytogenes from clinical samples
-
Dharmendra Kumar Soni , Durg Vijai Singh , Suresh Kumar Dubey
-
J. Microbiol. 2015;53(9):653-660. Published online August 1, 2015
-
DOI: https://doi.org/10.1007/s12275-015-5243-9
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48
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0
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21
Crossref
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Abstract
-
Listeria monocytogenes, a life-threatening pathogen, poses
severe risk during pregnancy, may cause abortion, fetal death
or neonatal morbidity in terms of septicemia and meningitis.
The present study aimed at characterizing L. monocytogenes
isolated from pregnant women based on serotyping, antibiotic
susceptibility, virulence genes, in vivo pathogenicity test and
ERIC- and REP-PCR fingerprint analyses. The results revealed
that out of 3700 human clinical samples, a total of 30 (0.81%)
isolates [12 (0.80%) from placental bit (1500), 18 (0.81%) from
vaginal swab (2200)] were positive for L. monocytogenes. All
the isolates belonged to serogroup 4b, and were + ve for
virulence genes tested i.e. inlA, inlC, inlJ, plcA, prfA, actA,
hlyA, and iap. Based on the mice inoculation tests, 20 isolates
showed 100% and 4 isolates 60% relative virulence while
6 isolates were non-pathogenic. Moreover, 2 and 10 isolates
were resistant to ciprofloxacin and cefoxitin, respectively,
while the rest susceptible to other antibiotics used in this
study. ERIC- and REP-PCR collectively depicted that the isolates
from placental bit and vaginal swab had distinct PCR
fingerprints except a few isolates with identical patterns. This
study demonstrates prevalence of pathogenic strains mostly
resistant to cefoxitin and/or ciprofloxacin. The results indicate
the importance of isolating and characterizing the pathogen
from human clinical samples as the pre-requisite for accurate
epidemiological investigations.
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Citations
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- Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform
-
Yoon-Seong Jeon , Sang-Cheol Park , Jeongmin Lim , Jongsik Chun , Bong-Soo Kim
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J. Microbiol. 2015;53(1):60-69. Published online January 4, 2015
-
DOI: https://doi.org/10.1007/s12275-015-4601-y
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-
54
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0
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34
Crossref
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Abstract
-
The cost of DNA sequencing has decreased due to advancements
in Next Generation Sequencing. The number of sequences
obtained from the Illumina platform is large, use of
this platform can reduce costs more than the 454 pyrosequencer.
However, the Illumina platform has other challenges,
including bioinformatics analysis of large numbers
of sequences and the need to reduce erroneous nucleotides
generated at the 3-ends of the sequences. These erroneous
sequences can lead to errors in analysis of microbial communities.
Therefore, correction of these erroneous sequences
is necessary for accurate taxonomic identification. Several
studies that have used the Illumina platform to perform metagenomic
analyses proposed curating pipelines to increase
accuracy. In this study, we evaluated the likelihood of obtaining
an erroneous microbial composition using the MiSeq
250 bp paired sequence platform and improved the pipeline
to reduce erroneous identifications. We compared different
sequencing conditions by varying the percentage of control
phiX added, the concentration of the sequencing library, and
the 16S rRNA gene target region using a mock community
sample composed of known sequences. Our recommended
method
corrected erroneous nucleotides and improved identification
accuracy. Overall, 99.5% of the total reads shared
95% similarity with the corresponding template sequences
and 93.6% of the total reads shared over 97% similarity. This
indicated that the MiSeq platform can be used to analyze microbial
communities at the genus level with high accuracy.
The improved analysis method recommended in this study
can be applied to amplicon studies in various environments
using high-throughput reads generated on the MiSeq platform.
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Environmental Entomology.2016; : nvw112. CrossRef - Fecal Microbiota Analysis: An Overview of Sample Collection Methods and Sequencing Strategies
Vincent Thomas, James Clark, Joël Doré
Future Microbiology.2015; 10(9): 1485. CrossRef
- Performance of a real-time PCR assay for the rapid identification of Mycobacterium species
-
Hye-young Wang , Hyunjung Kim , Sunghyun Kim , Do-kyoon Kim , Sang-Nae Cho , Hyeyoung Lee
-
J. Microbiol. 2015;53(1):38-46. Published online January 4, 2015
-
DOI: https://doi.org/10.1007/s12275-015-4495-8
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43
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18
Crossref
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Abstract
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Mycobacteria cause a variety of illnesses that differ in severity
and public health implications. The differentiation of
Mycobacterium tuberculosis (MTB) from nontuberculous
mycobacteria (NTM) is of primary importance for infection
control and choice of antimicrobial therapy. The diagnosis
of diseases caused by NTM is difficult because NTM species
are prevalent in the environment and because they have fastidious
properties. In the present study, we evaluated 279
clinical isolates grown in liquid culture provided by The
Catholic University of Korea, St. Vincent’s Hospital using
real-time PCR based on mycobacterial rpoB gene sequences.
The positive rate of real-time PCR assay accurately discriminated
100% (195/195) and 100% (84/84) between MTB and
NTM species. Comparison of isolates identified using the
MolecuTech REBA Myco-ID? and Real Myco-ID? were completely
concordant except for two samples. Two cases that
were identified as mixed infection (M. intracellulare-M. massiliense
and M. avium-M. massiliense co-infection) by PCRREBA
assay were only detected using M. abscessus-specific
probes by Real Myco-ID?. Among a total of 84 cases, the
most frequently identified NTM species were M. intracellulare
(n=38, 45.2%), M. avium (n=18, 23.7%), M. massiliense
(n=10, 13.2%), M. fortuitum (n=5, 6%), M. abscessus
(n=3, 3.9%), M. gordonae (n=3, 3.9%), M. kansasii (n=2,
2.4%), M. mucogenicum (n=2, 2.4%), and M. chelonae (n=
1, 1.2%). Real Myco-ID? is an efficient tool for the rapid detection
of NTM species as well as MTB and sensitive and
specific and comparable to conventional methods.
-
Citations
Citations to this article as recorded by

- Evaluation of Nanopore Sequencing for Diagnosing Pulmonary Tuberculosis Using Negative Smear Clinical Specimens
Guocan Yu, Yanqin Shen, Liwei Yao, Xudong Xu
Infection and Drug Resistance.2024; Volume 17: 673. CrossRef - Preclinical murine models for the testing of antimicrobials against Mycobacterium abscessus pulmonary infections: Current practices and recommendations
Véronique Dartois, Tracey L. Bonfield, Jim P. Boyce, Charles L. Daley, Thomas Dick, Mercedes Gonzalez-Juarrero, Shashank Gupta, Igor Kramnik, Gyanu Lamichhane, Barbara E. Laughon, Nicola I. Lorè, Kenneth C. Malcolm, Kenneth N. Olivier, Katherine L. Tuggle
Tuberculosis.2024; 147: 102503. CrossRef -
Durlobactam to boost the clinical utility of standard of care β-lactams against
Mycobacterium abscessus
lung disease
Dereje A. Negatu, Wassihun Wedajo Aragaw, Tewodros T. Gebresilase, Sindhuja Paruchuri, Firat Kaya, Sung Jae Shin, Peter Sander, Véronique Dartois, Thomas Dick, Jared A. Silverman
Antimicrobial Agents and Chemotherapy.2024;[Epub] CrossRef - Epidemiology and laboratory detection of non-tuberculous mycobacteria
Nuo Xu, Lihong Li, Shenghai Wu
Heliyon.2024; 10(15): e35311. CrossRef - Molecular identification of non-tuberculous mycobacterial species isolated from extrapulmonary samples using real-time PCR and rpoB sequence analysis
Mohammad Hashemzadeh, Aram Asarehzadegan Dezfuli, Azar Dokht Khosravi, Maryam Moradi Bandbal, Atousa Ghorbani, Mahtab Hamed, Soolmaz Khandan Dezfuli
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DEEPAK SAWANT, LOKHANDE CD, SHARMA RK, CHOUGULE RA
Asian Journal of Pharmaceutical and Clinical Research.2023; : 167. CrossRef - Factors Associated with the Performance of Direct PCR Detection of Mycobacteria in Clinical Specimens: Retrospective Real-world Data
Chang-Hun Park
Laboratory Medicine Online.2023; 13(3): 205. CrossRef - Evaluation of a new assay for nontuberculous mycobacteria species identification in diagnostic material and cultures
Tatiana Smirnova, Vera Ustinova, Sofya Andreevskaya, Elena Larionova, Ekaterina Kiseleva, Larisa Chernousova, Dmitry Varlamov, Dmitry Sochivko, Atadzhan Ergeshov
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Cas12a/Guide RNA-Based Platform for Rapid and Accurate Identification of Major
Mycobacterium
Species
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Journal of Clinical Microbiology.2020;[Epub] CrossRef - Diagnostic Performance of the GENEDIA MTB/NTM Detection Kit for Detecting Mycobacterium tuberculosis and Nontuberculous Mycobacteria With Sputum Specimens
Sunghwan Shin, In Young Yoo, Hyang Jin Shim, On Kyun Kang, Byung Woo Jhun, Won-Jung Koh, Hee Jae Huh, Nam Yong Lee
Annals of Laboratory Medicine.2020; 40(2): 169. CrossRef - Diagnostic performance of real time PCR and MALDI-TOF in the detection of nontuberculous mycobacteria from clinical isolates
Ellappan Kalaiarasan, Kalpana Thangavelu, Krishnakumariamma Krishnapriya, Muthaiah Muthuraj, Maria Jose, Noyal Mariya Joseph
Tuberculosis.2020; 125: 101988. CrossRef - Comparison of the Three Molecular Diagnostic Assays for Molecular Identification ofMycobacterium tuberculosisand Nontuberculous Mycobacteria Species in Sputum Samples
Jinyoung Bae, Sung-Bae Park, Ji-Hoi Kim, Mi Ran Kang, Kyung Eun Lee, Sunghyun Kim, Hyunwoo Jin
Biomedical Science Letters.2020; 26(3): 170. CrossRef -
Rapid Identification of Clinically Relevant
Mycobacterium
Species by Multicolor Melting Curve Analysis
Ye Xu, Bin Liang, Chen Du, Xueshan Tian, Xingshan Cai, Yanjie Hou, Hui Li, Rongrong Zheng, Junlian Li, Yuqin Liu, Kaili Wang, Muhammad Ammar Athar, Yaoju Tan, Qingge Li, Melissa B. Miller
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Ruben Porudominsky, Eduardo H. Gotuzzo
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Hsin-Chih Lai, Yu-Tze Horng, Pen-Fang Yeh, Jann-Yuan Wang, Chin-Chung Shu, Chia-Chen Lu, Jang-Jih Lu, Jen-Jyh Lee, Po-Chi Soo
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Jean Sebastian Hurtado Hurtado
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Jean Sebastian Hurtado Hurtado
Reumatología Clínica (English Edition).2016; 12(2): 118. CrossRef - Nontuberculous Mycobacterial Lung Disease Caused byMycobacterium shinjukuense: The First Reported Case in Korea
Seong Mi Moon, Su-Young Kim, Myung Jin Chung, Seung Heon Lee, Sung Jae Shin, Won-Jung Koh
Tuberculosis and Respiratory Diseases.2015; 78(4): 416. CrossRef
- Characterization of Thermostable Deblocking Aminopeptidases of Archaeon Thermococcus onnurineus NA1 by Proteomic and Biochemical Approaches
-
Yeol Gyun Lee , Sun-Hee Leem , Young-Ho Chung , Seung Il Kim
-
J. Microbiol. 2012;50(5):792-797. Published online November 4, 2012
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DOI: https://doi.org/10.1007/s12275-012-2461-2
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38
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2
Scopus
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Abstract
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Thermococcus onnurineus NA1 is a hyperthermophilic archaeon that grows optimally at >80°C. The deblocking aminopeptidase (DAP) (TNA1-DAP1) encoded in Ton_1032 of T. onnurineus NA1 is considered a major DAP. However, four genes encoding putative DAP have been identified from a genomic analysis of T. onnurineus NA1. A proteomic analysis revealed that all four DAPs were differentially induced in YPS culture medium and, particularly, two DAPs (TNA1-DAP1 and TNA1-DAP2) were dominantly expressed in T. onnurineus NA1. The biochemical properties and enzyme activity of DAPs induced in an E. coli expression system suggested that the two major DAPs play complementary roles in T. onnurineus NA1.
- NOTE] A Rapid PCR-Based Approach for Molecular Identification of Filamentous Fungi
-
Yuanyuan Chen , Bernard A. Prior , Guiyang Shi , Zhengxiang Wang
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J. Microbiol. 2011;49(4):675-679. Published online September 2, 2011
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DOI: https://doi.org/10.1007/s12275-011-0525-3
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28
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13
Scopus
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Abstract
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In this study, a novel rapid and efficient DNA extraction method based on alkaline lysis, which can deal
with a large number of filamentous fungal isolates in the same batch, was established. The filamentous
fungal genomic DNA required only 20 min to prepare and can be directly used as a template for PCR
amplification. The amplified internal transcribed spacer regions were easy to identify by analysis. The extracted
DNA also can be used to amplify other protein-coding genes for fungal identification. This method
can be used for rapid systematic identification of filamentous fungal isolates.
Journal Articles
- NOTE] Taxonomy of Eurotium Species Isolated from Meju
-
Seung-Beom Hong , Dae-Ho Kim , Mina Lee , Seong-Yeol Baek , Soon-Wo Kwon , Robert A. Samson
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J. Microbiol. 2011;49(4):669-674. Published online September 2, 2011
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DOI: https://doi.org/10.1007/s12275-011-0376-y
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26
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0
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30
Scopus
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Abstract
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Eurotium strains were isolated from 77 loaves of meju (dried fermented soybeans), in various regions of
Korea from 2008 to 2010. Morphological characteristics and DNA sequences of β-tubulin were examined.
They were identified as Eurotium amstelodami, E. chevalieri, E. herbariorum, E. repens, E. rubrum, and
E. tonophilum. Of these species, E. chevalieri and E. tonophilum had not been previously reported in association
with meju. E. chevalieri and E. repens were the species isolated most frequently. This paper summarizes
the morphological characteristics of six Eurotium species and provides key to identify the species from meju.
- Re-identification of Aspergillus fumigatus sensu lato Based on a New Concept of Species Delimitation
-
Seung-Beom Hong , Dae-Ho Kim , In-Cheol Park , Young-Joon Choi , Hyeon-Dong Shin , Robert Samson
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J. Microbiol. 2010;48(5):607-615. Published online November 3, 2010
-
DOI: https://doi.org/10.1007/s12275-010-0084-z
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34
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16
Scopus
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Abstract
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The species concept of Aspergillus fumigatus sensu stricto has recently been defined by polyphasic taxonomy. Based on the new concept of species delimitations, 146 worldwide strains of Aspergillus fumigatus sensu lato were re-identified. Of those 146 strains, 140 (95.8%) could be identified as A. fumigatus sensu stricto, 3 (2.1%) as A. lentulus, and the remaining 3 strains as A. viridinutans complex, Neosartorya udagawae, and N. cf. nishimurae. Of 98 clinical strains, only 1 from dolphin nostril was identified as A. lentulus and not A. fumigatus sensu stricto. Random amplification of polymorphic DNA-polymerase chain reaction (RAPD-PCR) with primers PELF and URP1F produced nearly the same band patterns among 136 strains of A. fumigatus sensu stricto while discriminated the species from its related species. We also discussed about identification of several atypical A. fumigatus strains from clinical environments.
- Development of a Method Based on Surface Enhanced Laser Desorption and Ionization Time of Flight Mass Spectrometry for Rapid Identification of Klebsiella pneumoniae
-
Daiwen Xiao , Yongchang Yang , Hua Liu , Hua Yu , Yingjun Yan , Wenfang Huang , Wei Jiang , Weijin Liao , Qi Hu , Bo Huang
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J. Microbiol. 2009;47(5):646-650. Published online October 24, 2009
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DOI: https://doi.org/10.1007/s12275-009-0092-z
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29
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4
Scopus
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Abstract
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A method based on surface enhanced laser desorption and ionization time of flight mass spectrometry (SELDI-TOF MS) was developed for the rapid identification of Klebsiella pneumoniae by directly applying bacterial colonies without further protein extraction. A total of 40 K. pneumoniae and 114 other related microorganisms isolated clinically were analyzed by SELDI-TOF MS. An identification model for K. pneumoniae was established by artificial neural networks (ANNs) with classification accuracy of 100%. The model was blindly tested with 43 K. pneumoniae and 53 control bacteria again. The results showed that the model was successful with accuracy of 96.9%, sensitivity of 100% and specificity of 94.3%. This strategy is potential for rapid identification of K. pneumoniae.
Research Support, Non-U.S. Gov'ts
- High Infectivity of an Endoparasitic Fungus Strain, Esteya vermicola, against Nematodes
-
Chun Yan Wang , Zhe Ming Fang , Bai Shen Sun , Li Juan Gu , Ke Qin Zhang , Chang-Keun Sung
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J. Microbiol. 2008;46(4):380-389. Published online August 31, 2008
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DOI: https://doi.org/10.1007/s12275-007-0122-7
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49
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0
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49
Crossref
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Abstract
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Esteya vermicola, as the first recorded endoparasitic fungus of pinewood nematodes, exhibits great potential as a biological agent against nematodes. However, only two strains of this species have been described so far. In this study, we identified a novel endoparasitic fungal strain, CNU 120806, isolated from infected nematodes in forest soil samples during a survey of nematophagous fungi in Korea. This strain showed similar morphological characteristics and infection mode with the two previously described strains of E. vermicola. All strains are characterized by the ability to produce two types of conidiogenous cells and conidia, and to parasitize nematodes with lunate adhesive conidia. Moreover, the CNU 120806 strain showed 100% identity with E. vermicola CBS 115803 when their partial sequences of 28S rRNA gene were compared. Molecular phylogenetic analysis further identified CNU 120806 as a strain of E. vermicola, by clustering CNU 120806 and E. vermicola CBS 115803 into a single subclade. Culture medium influenced the proportion of dimorphic CNU 120806 conidia, and further changed the adhesive and mortality rates of nematodes. The CNU 120806 strain exhibits high infection activity against nematodes on nutrient-rich PDA medium. Almost all tested nematodes were killed within 8~10 days after inoculation. This study provides justification for further research of E. vermicola, and the application and formulation of this fungus as a bio-control agent against nematodes.
-
Citations
Citations to this article as recorded by

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Jingang Hou, Jianjie Xue, Chunyan Wang, Lei Liu, Dongliang Zhang, Zhen Wang, Wei Li, Yinan Zheng, Changkeun Sung
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Zhen Wang, Chun Yan Wang, Li Juan Gu, Yun Bo Wang, Yong An Zhang, Chang Keun Sung
Canadian Journal of Microbiology.2011; 57(10): 838. CrossRef - Variabilities of Two Drechslerella dactyloides Isolates in Korea and High Predacity Against Bursaphelenchus xylophilus
Zhen Wang, Chun-Yan Wang, Li-Juan Gu, Bai-Shen Sun, Dong-Liang Zhang, Lei Liu, Mi-Ra Lee, Chun-Ling Wang, Zheng Li, Eun-Kyung Mo, Chang-Keun Sung
Current Microbiology.2011; 62(2): 472. CrossRef - Viability and pathogenicity ofEsteya vermicolain pine trees
Zhen Wang, Chun Yan Wang, Zhi Hong Yang, Zhe Ming Fang, Young Ja Moon, Bai Shen Sun, Mi Ra Lee, Chang Keun Sung
Biocontrol Science and Technology.2011; 21(4): 387. CrossRef - Effects of mineral salts on the growth, sporulation and virulence ofEsteya vermicola, an endoparasitic fungus of the pinewood nematode,Bursaphelenchus xylophilus
Zhen Wang, Chunyan Wang, Min Liu, Yongan Zhang, Jianjie Xue, Yunbo Wang, Zheng Li, Jingang Hou, Jingjie Li, Changkeun Sung
Biocontrol Science and Technology.2011; 21(12): 1485. CrossRef - Biological control of the pinewood nematode Bursaphelenchus xylophilus by application of the endoparasitic fungus Esteya vermicola
Chun Yan Wang, Zhe Ming Fang, Zhen Wang, Dong Liang Zhang, Li Juan Gu, Mi Ra Lee, Lei Liu, Chang Keun Sung
BioControl.2011; 56(1): 91. CrossRef - Influence of Pinewood Nematode, Bursaphelenchus xylophilus, on the Growth of Endoparasitic Fungus Esteya vermicola
Journal of Life Science.2010; 20(5): 644. CrossRef - Attraction of Pinewood Nematode to Endoparasitic Nematophagous Fungus Esteya vermicola
Chun Yan Wang, Zhen Wang, Zhe Ming Fang, Dong Liang Zhang, Li Juan Gu, Lei Liu, Chang Keun Sung
Current Microbiology.2010; 60(5): 387. CrossRef
- Development of Strain-specific PCR Primers Based on a DNA Probe Fu12 for the Identification of Fusobacterium nucleatum subsp. nucleatum ATCC 25586^T
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Hwa-Sook Kim , Soo Keun Song , So Young Yoo , Dong Chun Jin , Hwan Seon Shin , Chae Kwang Lim , Myung-Soo Kim , Jin-Soo Kim , Son-Jin Choe , Joong-Ki Kook
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J. Microbiol. 2005;43(4):331-336.
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DOI: https://doi.org/2257 [pii]
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Abstract
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The objective of this study was to assess the strain-specificity of a DNA probe, Fu12, for Fusobacterium nucleatum subsp. nucleatum ATCC 25586^T (F. nucleatum ATCC 25586^T), and to develop sets of strain-specific polymerase chain reaction (PCR) primers. Strain-specificity was tested against 16 strains of F. nucleatum and 3 strains of distinct Fusobacterium species. Southern blot hybridization revealed that the Fu12 reacted exclusively with the HindIII-digested genomic DNA of F. nucleatum ATCC 25586^T. The results of PCR revealed that three pairs of PCR primers, based on the nucleotide sequence of Fu12, generated the strain-specific amplicons from F. nucleatum ATCC 25586^T. These results suggest that the DNA probe Fu12 and the three pairs of PCR primers could be useful in the identification of F. nucleatum ATCC 25586^T, especially with regard to the determination of the authenticity of the strain.
- Rapid Detection of Bacteria from Blood Culture by an Electronic Nose
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Peter Lykos , Pravin H. Patel , Christopher Morong , Asha Joseph
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J. Microbiol. 2001;39(3):213-218.
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Abstract
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The treatment of patients with bacteraemia and septicemia requires accurate and rapid identification of the pathogen so that the physician can be guided regarding the selection of the proper antimicrobial therapy. The usual procedure is to withdraw an aliquot of the positive blood culture sample for gram staining and subculturing on the media for the growth and subsequent identification, and susceptibility determinations. It was noticed that during the process some microbiologists would sniff the effluent gases that are products of metabolism and in some cases guess the identity of the bacterium. That prompted us to engage in systematic investigation of two gram positive and two gram negative bacteria using an electronic nose that had been proven successful in distinguishing the aroma of coffee beans from different sources. The investigation was successful in illustrating the efficacy of such a device in this clinical setting to distinguish Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Enterococcus faecalis. A representative set of patterns obtained with this apparatus is displayed as well. No effort was made to determine an optimal set of sensors for some specific set of bacterial metabolism gaseous products.
- Genotyping of Six Pathogenic Vibrio Species Based on RFLP of 16S rDNAs for Rapid Identification
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Young-Jun Yoon , Kyung-Hwan Im , Young-Hwan Koh , Seong-Kon Kim , Jung-Wan Kim
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J. Microbiol. 2003;41(4):312-319.
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Abstract
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In an attempt to develop a method for rapid and accurate identification of six Vibrio species that are clinically important and most frequently detected in Korea, 16S rDNA restriction fragment length polymorphism (RFLP) of Vibrio type strains, as well as environmental isolates obtained from the Korean coastal area, was analyzed using ten restriction endonucleases. Digestion of the 16S rDNA fragments amplified by polymerase chain reaction (PCR) with the enzymes gave rise to 2~6 restriction patterns for each digestion for 47 Vibrio strains and isolates. An additional 2~3 restriction patterns were observed for five reference species, including Escherichia coli, Aeromonas hydrophila, A. salmonicida, Photobacterium phosphoreum, and Plesiomonas shigelloides. A genetic distance tree based on RFLP of the bacterial species correlated well with that based on 16S rDNA sequences. The very small 16S rDNA sequence difference (0.1%) between V. alginolyticus and V. parahaemolyticus was resolved clearly by RFLP with a genetic distance of more than 2%. RFLP variation within a species was also detected in the cases of V. parahaemolyticus, V. proteolyticus, and V. vulnificus. According to the RFLP analysis, six Vibrio and five reference species were assigned to 12 genotypes. Using three restriction endonucleases to analyze RFLP proved sufficient to identify the six pathogenic Vibrio species.