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- Molecular Typing of
Mycobacterium intracellulare Using Pulsed-Field Gel Electrophoresis, Variable-Number Tandem-Repeat Analysis, Mycobacteria Interspersed Repetitive-Unit-Variable-Number Tandem Repeat Typing, and Multilocus Sequence Typing: Molecular Characterization and Comparison of Each Typing Methods - Semi Jeon, Nara Lim, Seungjik Kwon, Taesun Shim, Misun Park, Bum-Joon Kim, Seonghan Kim
- Osong Public Health Res Perspect. 2014;5(3):119-130. Published online June 30, 2014
- DOI: https://doi.org/10.1016/j.phrp.2014.04.003
- 3,601 View
- 19 Download
- 9 Crossref
-
Abstract
PDF - Objectives
Mycobacterium intracellulare is the major causative agent of nontuberculous mycobacteria-related pulmonary infections. The strain typing of M. intracellulare is important for the treatment and control of its infections. We compared the discrimination capacity and effective value of four different molecular typing methods.
Methods
Antibiotic susceptibility testing, hsp65 and rpoB sequencing, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), mycobacteria interspersed repetitive-unit-variable-number tandem-repeat analysis (MIRU-VNTR), and VNTR assay targeting 44 M. intracellulare isolates obtained from patients with pulmonary infections were performed.
Results
All the antibiotic susceptibility patterns had no association with the molecular and sequence types tested in this study; however, the molecular and sequence types were related with each other. PFGE gave best results for discriminatory capacity, followed by VNTR, MLST, and MIRU-VNTR.
Conclusion
The high discriminatory power of PFGE, VNTR, and MLST is enough for differentiating between reinfection and relapse, as well as for other molecular epidemiological usages. The MLST could be regarded as a representative classification method, because it showed the clearest relation with the sequence types. -
Citations
Citations to this article as recorded by
- Applications and advances in molecular diagnostics: revolutionizing non-tuberculous mycobacteria species and subspecies identification
Haiyang Zhang, Maoting Tang, Deyuan Li, Min Xu, Yusen Ao, Liangkang Lin
Frontiers in Public Health.2024;[Epub] CrossRef - Differential Genotyping of Mycobacterium avium Complex and Its Implications in Clinical and Environmental Epidemiology
Jeong-Ih Shin, Sung Jae Shin, Min-Kyoung Shin
Microorganisms.2020; 8(1): 98. CrossRef - A strategy based on Amplified Fragment Length Polymorphism (AFLP) for routine genotyping of nontuberculous mycobacteria at the clinical laboratory
Sara Blanco-Conde, Carolina González-Cortés, Ramiro López-Medrano, Juan José Palacios-Gutiérrez, Cristina Diez-Tascón, Teresa Nebreda-Mayoral, María Josefa Sierra-García, Octavio Miguel Rivero-Lezcano
Molecular Biology Reports.2020; 47(5): 3397. CrossRef - Comparative Evaluation of Band-Based Genotyping Methods for Mycobacterium intracellulare and Its Application for Epidemiological Analysis
Jeong-Ih Shin, Jong-Hun Ha, Dong-Hae Lee, Jeong-Gyu Choi, Kyu-Min Kim, Seung Jun Lee, Yi Yeong Jeong, Jong Deog Lee, Myunghwan Jung, Seung-Chul Baik, Woo Kon Lee, Hyung-Lyun Kang, Min-Kyoung Shin, Jung-Wan Yoo
Microorganisms.2020; 8(9): 1315. CrossRef - Pulsed Field Gel Electrophoresis: Past, present, and future
Lilia Lopez-Canovas, Maximo B. Martinez Benitez, Jose A. Herrera Isidron, Eduardo Flores Soto
Analytical Biochemistry.2019; 573: 17. CrossRef - Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis
Zofia Bakuła, Anna Brzostek, Paulina Borówka, Anna Żaczek, Izabela Szulc-Kiełbik, Agata Podpora, Paweł Parniewski, Dominik Strapagiel, Jarosław Dziadek, Małgorzata Proboszcz, Jacek Bielecki, Jakko van Ingen, Tomasz Jagielski
Scientific Reports.2018;[Epub] CrossRef -
Mycobacterium paraintracellulare sp. nov., for the genotype INT-1 of Mycobacterium intracellulare
So-Young Lee, Byoung-Jun Kim, Hong Kim, Yu-Seop Won, Che Ok Jeon, Joseph Jeong, Seon Ho Lee, Ji-Hun Lim, Seung-Heon Lee, Chang Ki Kim, Yoon-Hoh Kook, Bum-Joon Kim
International Journal of Systematic and Evolution.2016; 66(8): 3132. CrossRef - Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria
Tomasz Jagielski, Alina Minias, Jakko van Ingen, Nalin Rastogi, Anna Brzostek, Anna Żaczek, Jarosław Dziadek
Clinical Microbiology Reviews.2016; 29(2): 239. CrossRef - Genetic diversity of clinical Mycobacterium avium subsp. hominissuis and Mycobacterium intracellulare isolates causing pulmonary diseases recovered from different geographical regions
Kazuya Ichikawa, Jakko van Ingen, Won-Jung Koh, Dirk Wagner, Max Salfinger, Takayuki Inagaki, Kei-ichi Uchiya, Taku Nakagawa, Kenji Ogawa, Kiyofumi Yamada, Tetsuya Yagi
Infection, Genetics and Evolution.2015; 36: 250. CrossRef
- Applications and advances in molecular diagnostics: revolutionizing non-tuberculous mycobacteria species and subspecies identification
- A Comparison of Subtyping Methods for Differentiating
Salmonella enterica Serovar Enteritidis Isolates Obtained from Food and Human Sources - Ji-Yeon Hyeon, Jung-Whan Chon, Jun-Ho Park, Moo-Sang Kim, Young-Hee Oh, In-Soo Choi, Kun-Ho Seo
- Osong Public Health Res Perspect. 2013;4(1):27-33. Published online February 28, 2013
- DOI: https://doi.org/10.1016/j.phrp.2012.12.005
- 3,559 View
- 23 Download
- 21 Crossref
-
Abstract
PDF
- Purpose:
To evaluate the abilities of these subtyping methods, we distinguished Salmonella Enteritidis (S. Enteritidis) isolated from food products and human clinical samples between 2009 and 2010 in Seoul using five subtyping methods.
Methods
We determined the subtypes of 20 S. Enteritidis isolates from food and human sources using phage typing, antimicrobial susceptibility, pulsed-field gel electrophoresis (PFGE), repetitive sequence-based PCR (rep-PCR), and multi-locus sequence typing (MLST).
Results
A total of 20 tested isolates were differentiated into six antimicrobial susceptibility patterns, three different phage types, four different PFGE profiles, seven rep-PCR patterns, and one MLST type. Food isolates were considerably more susceptible to antibiotics than human isolates. We were best able to discriminate among S. Enteritidis isolates using rep-PCR, and obtained the highest Simpson’s diversity index of 0.82, whereas other methods produced indices that were less than 0.71. PFGE pattern appeared to be more related to antimicrobial resistance and phage types of S. Enteritidis isolates than rep-PCR. MLST revealed identical alleles in all isolates at all seven loci examined, indicating no resolution.
Conclusion
The results of this study suggest that rep-PCR provided the best discriminatory power for phenotypically similar S. Enteritidis isolates of food and human origins, whereas the discriminatory ability of MLST may be problematic because of the high sequence conservation of the targeted genes. -
Citations
Citations to this article as recorded by- Genomic and phylogenetic analysis of Salmonella enterica serovar Enteritidis strains linked to multiple outbreaks in Brazil
Guojie Cao, Maria Balkey, Qing Jin, Eric Brown, Marc Allard, Adma Nadja Ferreira de Melo, Geany Targino de Souza Pedrosa, Tereza Cristina Rocha Moreira de Oliveira, Marciane Magnani, Dumitru Macarisin
Letters in Applied Microbiology.2023;[Epub] CrossRef - Phenotypic and Genotypic Characterization of Salmonella Isolates Recovered from Foods Linked to Human Salmonellosis Outbreaks in Minas Gerais State, Brazil
Leandro L. Faula, Monica M. O.P. Cerqueira, Jovita E. G.C. Madeira, Marcelo R. Souza, Fernando N. Souza, Gláucia C.S. Amancio
Journal of Food Protection.2022; 85(1): 142. CrossRef - Comparison of conventional molecular and whole-genome sequencing methods for subtyping Salmonella enterica serovar Enteritidis strains from Tunisia
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European Journal of Clinical Microbiology & Infect.2021; 40(3): 597. CrossRef - Molecular characterisation of antimicrobial resistance determinants and class 1 integrons of Salmonella enterica subsp. enterica serotype Enteritidis strains from retail food in China
Yu Li, Xiaojuan Yang, Jumei Zhang, Shiyuan Yang, Shuhong Zhang, Moutong Chen, Liang Xue, Yu Ding, Haiyan Zeng, Qihui Gu, Youxiong Zhang, Xianhu Wei, Juan Wang, Qingping Wu
Food Control.2021; 128: 108191. CrossRef - Molecular typing of cephalosporin resistant serovars of Salmonella enterica from poultry and farm animals
A. Rafati Zomorodi, M. Rad, Gh. R. Hashemitabar, H. Salimizand
BULGARIAN JOURNAL OF VETERINARY MEDICINE.2020; 23(2): 178. CrossRef -
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Journal of Food Processing and Preservation.2020;[Epub] CrossRef - Effectiveness of BOX-PCR in Differentiating Genetic Relatedness amongSalmonella entericaSerotype 4,[5],12:i:- Isolates from Hospitalized Patients and Minced Pork Samples in Northern Thailand
Kritchai Poonchareon, Chaiwat Pulsrikarn, Narong Nuanmuang, Phichaya Khamai
International Journal of Microbiology.2019; 2019: 1. CrossRef - A common Salmonella Enteritidis sequence type from poultry and human gastroenteritis in Ibagué, Colombia
Luz Clemencia Fandiño, Noel Verjan
Biomédica.2019; 39: 50. CrossRef - Distribution and Molecular Characterization of Campylobacter Species at Different Processing Stages in Two Poultry Processing Plants
Soo-Kyoung Lee, Hyun-Jung Park, Jin-Hee Lee, Jong-Soo Lim, Kun-Ho Seo, Eun-Jeong Heo, Young-Jo Kim, Sung-Hwan Wee, Jin-San Moon
Foodborne Pathogens and Disease.2017; 14(3): 141. CrossRef - Molecular Characterization of Salmonella from Beef Carcasses and Fecal Samples from an Integrated Feedlot and Abattoir in Mexico
Diana Ayala, Kendra Nightingale, Claudia Narvaez-Bravo, Mindy M. Brashears
Journal of Food Protection.2017; 80(12): 1964. CrossRef - Repetitive sequence-based PCR fingerprinting and the relationship of antimicrobial-resistance characteristics and corresponding genes among Salmonella strains from pig production
Teerarat Prasertsee, Nattakarn Khantaprab, Panuwat Yamsakul, Pannita Santiyanont, Nipa Chokesajjawatee, Prapas Patchanee
Asian Pacific Journal of Tropical Disease.2016; 6(5): 390. CrossRef - Prevalence, Seasonal Occurrence, and Antimicrobial Resistance of Salmonella spp. Isolates Recovered from Chicken Carcasses Sampled at Major Poultry Processing Plants of South Korea
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Foodborne Pathogens and Disease.2016; 13(10): 544. CrossRef - Resistance of Strains Producing Extended-Spectrum β-Lactamases AmongSalmonellafrom Duck Carcasses at Slaughterhouses in Three Major Provinces of South Korea
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Journal of Bacteriology and Virology.2015; 45(4): 314. CrossRef - Molecular Characterization of Salmonella Paratyphi B dT + and Salmonella Heidelberg from Poultry and Retail Chicken Meat in Colombia by Pulsed-Field Gel Electrophoresis
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Journal of Food Protection.2015; 78(4): 802. CrossRef - Prevalence Analysis and Molecular Characterization of Salmonella at Different Processing Steps in Broiler Slaughter Plants in South Korea
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Poultry Science.2013; 92(10): 2789. CrossRef
- Genomic and phylogenetic analysis of Salmonella enterica serovar Enteritidis strains linked to multiple outbreaks in Brazil
- Multilocus Sequence Analysis of Housekeeping Genes and Antigenic Determinant Genes in
Bordetella pertussis Strains Isolated in Korea - Sang-Oun Jung, Yu Mi Moon, So-Hyeon Kim, Hwa Young Sung, Seung-Jik Kwon, Yeon Ho Kang, Jae Yon Yu
- Osong Public Health Res Perspect. 2011;2(2):115-126. Published online June 30, 2011
- DOI: https://doi.org/10.1016/j.phrp.2011.08.003
- 3,581 View
- 20 Download
- 3 Crossref
-
Abstract
PDF
- Objectives
To confirm genotype diversities of clinical isolates of Bordetella pertussis and to evaluate the risk of pertussis outbreak in Korea.
Methods
Seven housekeeping genes and 10 antigenic determinant genes from clinical B. pertussis isolates were analyzed by Multilocus sequence typing (MLST).
Results
More variant pattern was observed in antigenic determinant genes. Especially, PtxS1 gene was the most variant gene; five genotypes were observed from eight global genotypes. In the bacterial type, the number of observed sequence types in the isolates was seven and the most frequent form was type 1 (79.6%). This major sequence type also showed a time-dependent transition pattern. Older isolates (1968 and 1975) showed type 1 and 6 in housekeeping genes and antigenic determinant genes, respectively. However, these were changed to type 2 and 1 in isolates 1999–2008. This transition was mainly attributed to genotype change of PtxS1 and Fim3 gene; the tendency of genotype change was to avoid vaccine-derived genotype. In addition, there was second transition in 2009. In this period, only the sequence type of antigenic determinant genes was changed to type 2. Based Upon Related Sequence Types (BURST) analysis confirmed that there were two clonal complexes (ACCI and ACCII) in the Korean isolates. Moreover, the recently increased sequence type was revealed as AST2 derived from AST 3 in ACCI.
Conclusions
Genotype changes in Korean distributing strains are still progressing and there was a specific driving force in antigenic determinant genes. Therefore continuous surveillance of genotype change of the distributing strains should be performed to confirm interrelationship of genotype change with vaccine immunity. -
Citations
Citations to this article as recorded by- Characterization of Bordetella pertussis Strains Isolated from India
Shweta Alai, Manish Gautam, Sonali Palkar, Jitendra Oswal, Sunil Gairola, Dhiraj P. Dhotre
Pathogens.2022; 11(7): 794. CrossRef - Variation in Bordetella pertussis Susceptibility to Erythromycin and Virulence-Related Genotype Changes in China (1970-2014)
Ying Yang, Kaihu Yao, Xiang Ma, Wei Shi, Lin Yuan, Yonghong Yang, Daniela Flavia Hozbor
PLOS ONE.2015; 10(9): e0138941. CrossRef - Recent Trends of Antigenic Variation inBordetella pertussisIsolates in Korea
So-Hyun Kim, Jin Lee, Hwa Young Sung, Jae Yon Yu, Seong Han Kim, Mi Sun Park, Sang-Oun Jung
Journal of Korean Medical Science.2014; 29(3): 328. CrossRef
- Characterization of Bordetella pertussis Strains Isolated from India
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