Journal of Microbiology

Journal Articles

Epidemiological relationships of Campylobacter jejuni strains isolated from humans and chickens in South Korea: Jae-Young Oh , Yong-Kuk Kwon , Bai Wei , Hyung-Kwan Jang , Suk-Kyung Lim , Cheon-Hyeon Kim , Suk-Chan Jung , Min-Su Kang; J. Microbiol. 2017;55(1):13-20. Published online December 30, 2016; DOI: https://doi.org/10.1007/s12275-017-6308-8

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Thirty-nine human isolates of Campylobacter jejuni obtained from a national university hospital during 2007–2010 and 38 chicken isolates of C. jejuni were collected from poultry farms during 2009–2010 in South Korea were used in this study. Campylobacter genomic species and virulence-associated genes were identified by PCR. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were performed to compare their genetic relationships. All isolates were highly resistant to ciprofloxacin, nalidixic acid, and tetracycline. Of all isolates tested, over 94% contained seven virulence associated genes (flaA, cadF, racR, dnaJ, cdtA, cdtB, and cdtC). All isolates were classified into 39 types by PFGE clustering with 90% similarity. Some chicken isolates were incorporated into some PFGE types of human isolates. MLST analysis for the 39 human isolates and 38 chicken isolates
result
ed in 14 and 23 sequence types (STs), respectively, of which 10 STs were new. STs overlapped in both chicken and human isolates included ST-21, ST-48, ST-50, ST-51, and ST-354, of which ST-21 was the predominant ST in both human and chicken isolates. Through combined analysis of PFGE types and STs, three chicken isolates were clonally related to the three human isolates associated with food poisoning (VII-ST-48, XXII-ST-354, and XXVIII-ST-51). They were derived from geographically same or distinct districts. Remarkably, clonal spread of food poisoning pathogens between animals and humans was confirmed by population genetic analysis. Consequently, contamination of campylobacters with quinolone resistance and potential virulence genes in poultry production and consumption may increase the risk of infections in humans.

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Trends, clinical characteristics, antimicrobial susceptibility patterns, and outcomes of Campylobacter bacteraemia: a multicentre retrospective study
Yae Jee Baek, Je Eun Song, Eun Jin Kim, Heun Choi, Yujin Sohn, Yong Duk Jeon, Eun Hwa Lee, Jin Young Ahn, Su Jin Jeong, Nam Su Ku, Jun Yong Choi, Joon-Sup Yeom, Young Goo Song, Jung Ho Kim
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Molecular Detection of Virulence‐Associated Markers in Campylobacter coli and Campylobacter jejuni Isolates From Water, Cattle, and Chicken Faecal Samples From Kajiado County, Kenya
Daniel W. Wanja, Christine M. Mbindyo, Paul G. Mbuthia, Lilly C. Bebora, Gabriel O. Aboge, Kalman Imre
BioMed Research International.2024;[Epub] CrossRef
Epidemiological and Genomic Characterization of a Campylobacter jejuni Outbreak in Lishui, China
Yumei Ge, Youqi Ji, Jianhua Mei, Maojun Zhang, Yumin Li, Bifeng Ye, Honghu Chen, Xiuying Chen
Foodborne Pathogens and Disease.2024;[Epub] CrossRef
Virulence Genes, Antimicrobial Resistance, and Genotypes of Campylobacter jejuni Isolated from Chicken Slaughterhouses in South Korea
Jiyeon Jeong, Ji-Youn Lee, Jin-San Moon, Min-Su Kang, Sung-Il Kang, O-Mi Lee, So-Hee Lee, Yong-Kuk Kwon, Myeongju Chae, Seongbeom Cho
Foodborne Pathogens and Disease.2024;[Epub] CrossRef
Antimicrobial Susceptibility Patterns and Genetic Diversity of Campylobacter spp. Isolates from Patients with Diarrhea in South Korea
So Yeon Kim, Dongheui An, Hyemi Jeong, Jonghyun Kim
Microorganisms.2024; 12(1): 94. CrossRef
Campylobacterspp. isolated from poultry in Iran: Antibiotic resistance profiles, virulence genes, and molecular mechanisms
Seyedeh Bita Mousavinafchi, Ebrahim Rahimi, Amir Shakerian
Food Science & Nutrition.2023; 11(2): 1142. CrossRef
Persistence of Campylobacter spp. in Poultry Flocks after Disinfection, Virulence, and Antimicrobial Resistance Traits of Recovered Isolates
Manel Gharbi, Awatef Béjaoui, Safa Hamrouni, Amel Arfaoui, Abderrazak Maaroufi
Antibiotics.2023; 12(5): 890. CrossRef
Relationships between Virulence Genes and Antibiotic Resistance Phenotypes/Genotypes in Campylobacter spp. Isolated from Layer Hens and Eggs in the North of Tunisia: Statistical and Computational Insights
Manel Gharbi, Selim Kamoun, Chaima Hkimi, Kais Ghedira, Awatef Béjaoui, Abderrazak Maaroufi
Foods.2022; 11(22): 3554. CrossRef
Prevalence and Antimicrobial Susceptibility of Campylobacter Species with Particular Focus on the Growth Promoting, Immunostimulant and Anti-Campylobacter jejuni Activities of Eugenol and Trans-Cinnamaldehyde Mixture in Broiler Chickens
Ahmed Aljazzar, Marwa I. Abd El-Hamid, Rania M. S. El-Malt, Waleed Rizk El-Gharreb, Sherief M. Abdel-Raheem, Abdelazim M. Ibrahim, Adel M. Abdelaziz, Doaa Ibrahim
Animals.2022; 12(7): 905. CrossRef
Genotypical Relationship Between Human and Poultry Strains of Campylobacter jejuni
Roberta Torres de Melo, Carolyne Ferreira Dumont, Raquelline Figueiredo Braz, Guilherme Paz Monteiro, Micaela Guidotti Takeuchi, Eduarda Cristina Alves Lourenzatto, Jandra Pacheco dos Santos, Daise Aparecida Rossi
Current Microbiology.2021; 78(8): 2980. CrossRef
Genomic Characterization of Fluoroquinolone-Resistant Thermophilic Campylobacter Strains Isolated from Layer Chicken Feces in Gangneung, South Korea by Whole-Genome Sequencing
Noel Gahamanyi, Dae-Geun Song, Kye-Yoon Yoon, Leonard E. G. Mboera, Mecky I. Matee, Dieudonné Mutangana, Erick V. G. Komba, Cheol-Ho Pan, Raghavendra G. Amachawadi
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Xiaoqi Zang, Pingyu Huang, Jie Li, Xinan Jiao, Jinlin Huang
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Antimicrobial Resistance Profiles, Virulence Genes, and Genetic Diversity of Thermophilic Campylobacter Species Isolated From a Layer Poultry Farm in Korea
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Ahmed M. Ammar, El-Sayed Y. El-Naenaeey, Rania M. S. El-Malt, Attia A. El-Gedawy, Eman Khalifa, Shimaa S. Elnahriry, Marwa I. Abd El-Hamid
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Epidemiological and Whole Genomic Sequencing Analysis of a Campylobacter jejuni Outbreak in Zhejiang Province, China, May 2019
Honghu Chen, Yaxin Dai, Jiancai Chen, Yunyi Zhang, Li Zhan, Lingling Mei, Hongling Wang
Foodborne Pathogens and Disease.2020; 17(12): 775. CrossRef
Molecular Characterization and Antibiotic Resistant Profiles of Campylobacter Species Isolated From Poultry and Diarrheal Patients in Southeastern China 2017–2019
Leyi Zhang, Yi Li, Yongqiang Shao, Yuqin Hu, Huihuang Lou, Xiaonan Chen, Yuejin Wu, Lingling Mei, Biao Zhou, Xibin Zhang, Wenwu Yao, Lei Fang, Yanjun Zhang
Frontiers in Microbiology.2020;[Epub] CrossRef
Comparative restriction enzyme mapping of Campylobacter jejuni isolates from turkeys and broilers based on flaA flagellar gene using HpyF3I endonuclease
Elham Atefi Tabar, Hamid Staji, Ali Mahdavi
Folia Microbiologica.2019; 64(2): 189. CrossRef
Genetic Diversity of Campylobacter jejuni Isolated From Avian and Human Sources in Egypt
Marwa I. Abd El-Hamid, Norhan K. Abd El-Aziz, Mohamed Samir, El-sayed Y. El-Naenaeey, Etab M. Abo Remela, Rasha A. Mosbah, Mahmoud M. Bendary
Frontiers in Microbiology.2019;[Epub] CrossRef
Prevalence, antimicrobial resistance profiles and virulence-associated genes of thermophilic Campylobacter spp. isolated from ducks in a Chinese slaughterhouse
Xinfeng Han, Xingai Guan, Hang Zeng, Jiakang Li, Xuelin Huang, Yiping Wen, Qin Zhao, Xiaobo Huang, Qigui Yan, Yong Huang, Sanjie Cao, Rui Wu, Xiaoping Ma, Likou Zou
Food Control.2019; 104: 157. CrossRef
Clinical and microbiological characteristics of patients with bacteremia caused by Campylobacter species with an emphasis on the subspecies of C. fetus
Yen-Hung Liu, Wataru Yamazaki, Yu-Tsung Huang, Chun-Hsing Liao, Wang-Hui Sheng, Po-Ren Hsueh
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Source attribution of Campylobacter jejuni shows variable importance of chicken and ruminants reservoirs in non-invasive and invasive French clinical isolates
Elvire Berthenet, Amandine Thépault, Marianne Chemaly, Katell Rivoal, Astrid Ducournau, Alice Buissonnière, Lucie Bénéjat, Emilie Bessède, Francis Mégraud, Samuel K. Sheppard, Philippe Lehours
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A Review of the Effect of Management Practices on Campylobacter Prevalence in Poultry Farms
Nompilo Sibanda, Aaron McKenna, Anne Richmond, Steven C. Ricke, Todd Callaway, Alexandros Ch. Stratakos, Ozan Gundogdu, Nicolae Corcionivoschi
Frontiers in Microbiology.2018;[Epub] CrossRef
The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2016

EFSA Journal.2018;[Epub] CrossRef
Comparative clustering and genotyping of Campylobacter jejuni strains isolated from broiler and turkey feces by using RAPD-PCR and ERIC-PCR analysis
Hamid Staji, Soghra Farhani Birgani, Behnaz Raeisian
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Antibiotic Susceptibility, Genetic Diversity, and the Presence of Toxin Producing Genes in Campylobacter Isolates from Poultry
Jeeyeon Lee, Jiyeon Jeong, Heeyoung Lee, Jimyeong Ha, Sejeong Kim, Yukyung Choi, Hyemin Oh, Kunho Seo, Yohan Yoon, Soomin Lee
International Journal of Environmental Research and Public Health.2017; 14(11): 1400. CrossRef
Molecular Detection, Typing, and Quantification of Campylobacter spp. in Foods of Animal Origin
Beatriz da Silva Frasao, Victor Augustus Marin, Carlos Adam Conte‐Junior
Comprehensive Reviews in Food Science and Food Safety.2017; 16(4): 721. CrossRef

Inverse PCR for subtyping of Acinetobacter baumannii carrying ISAba1: Shukho Kim , Yun-Ju Park , Jungmin Kim; J. Microbiol. 2016;54(5):376-380. Published online April 20, 2016; DOI: https://doi.org/10.1007/s12275-016-6038-3

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Abstract

Acinetobacter baumannii has been prevalent in nosocomial infections, often causing outbreaks in intensive care units. ISAba1 is an insertion sequence that has been identified only in A. baumannii and its copy number varies among strains. It has been reported that ISAba1 provides a promoter for blaOXA-51-like, blaOXA-23-like, and blaampC, which are associated with the resistance of A. baumannii to carbapenems and cephalosporins. The main purpose of this study was to develop a novel inverse PCR method capable of typing A. baumannii strains. The method involves three major steps: cutting of genomic DNA with a restriction enzyme, ligation, and PCR. In the first step, bacterial genomic DNA was digested with DpnI. In the second step, the digested genomic DNAs were ligated to form intramolecular circular DNAs. In the last step, the ligated circular DNAs were amplified by PCR with primers specific for ISAba1 and the amplified PCR products were electrophoresed. Twenty-two clinical isolates of A. baumannii were used for the evaluation of the inverse PCR (iPCR) typing method. Dendrogram analysis revealed two major clusters, similar to pulsed-field gel electrophoresis (PFGE) results. Three ISAba1-associated genes – blaampC, blaOXA-66-like, and csuD – were amplified and detected in the clinical isolates. This novel iPCR typing method is comparable to PFGE in its ability to discriminate A. baumannii strains, and is a promising molecular epidemiological tool for investigating A. baumannii carrying ISAba1.

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DNA sonication inverse PCR for genome scale analysis of uncharacterized flanking sequences
David E. Alquezar‐Planas, Ulrike Löber, Pin Cui, Claudia Quedenau, Wei Chen, Alex D. Greenwood, Susan Johnston
Methods in Ecology and Evolution.2021; 12(1): 182. CrossRef
Update on the Epidemiological Typing Methods for Acinetobacter Baumannii
Rayane Rafei, Marwan Osman, Fouad Dabboussi, Monzer Hamze
Future Microbiology.2019; 14(12): 1065. CrossRef
Identification and characterization of a novel cold-tolerant extracellular protease from Planococcus sp. CGMCC 8088
Kun Chen, Qingshan Mo, Huan Liu, Feiyan Yuan, Haonan Chai, Fuping Lu, Huitu Zhang
Extremophiles.2018; 22(3): 473. CrossRef

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

Antimicrobial Resistance, Virulence Genes and PFGE-profiling of Escherichia coli Isolates from South Korean Cattle Farms: Seung Won Shin , Jae-Won Byun , Myounghwan Jung , Min-Kyoung Shin , Han Sang Yoo; J. Microbiol. 2014;52(9):785-793. Published online July 30, 2014; DOI: https://doi.org/10.1007/s12275-014-4166-1

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Abstract

To estimate the prevalence of Escherichia coli with potential pathogenicity in cattle farm in South Korea, a total of 290 E. coli isolates were isolated from cattle farms over a period of 2 years in South Korea. These were examined for phenotypic and genotypic characteristics including antimicrobial susceptibility, serotype, and gene profiles of virulence and antimicrobial resistance. The most dominant virulence gene was f17 (26.2%), followed by stx2 (15.9%), ehxA (11.0%), stx1 (8.3%), eae (5.2%), and sta (4.1%). Some shiga-toxin producing E. coli isolates possessed eae (15.9%). All isolates except for one showed resistance to one or more antimicrobials, with 152 isolates exhibiting multidrug-resistance. The most prevalent resistance phenotype detected was streptomycin (63.1%), followed by tetracycline (54.5%), neomycin (40.3%), cephalothin (32.8%), amoxicillin (30.0%), ampicillin (29.7%), and sulphamethoxazole/trimethoprim (16.6%). The associated resistance determinants detected were strAstrB (39.0%), tet(E) (80.0%), tet(A) (27.6%), aac(3)-IV (33.1%), aphA1 (21.4%), blaTEM (23.8%), and sul2 (22.1%). When investigated by O serotyping and PFGE molecular subtyping, the high degree of diversity was exhibited in E. coli isolates. These results suggest that E. coli isolates from South Korean cattle farms are significantly diverse in terms of virulence and antimicrobial resistance. In conclusion, the gastroinstestinal flora of cattle could be a significant reservoir of diverse virulence and antimicrobial resistance determinants, which is potentially hazardous to public health.

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Underrepresented high diversity of class 1 integrons in the environment uncovered by PacBio sequencing using a new primer
Yu Yang, An-Ni Zhang, You Che, Lei Liu, Yu Deng, Tong Zhang
Science of The Total Environment.2021; 787: 147611. CrossRef
The prevalence of causative agents of calf diarrhea in Korean native calves
Jeong-Byoung Chae, Hyeon-Cheol Kim, Jun-Gu Kang, Kyoung-Seong Choi, Joon-Seok Chae, Do-Hyeon Yu, Bae-Keun Park, Yeon-su Oh, Hak-Jong Choi, Jinho Park
Journal of Animal Science and Technology.2021; 63(4): 864. CrossRef
O-serogroups, virulence genes, antimicrobial susceptibility, and MLST genotypes of Shiga toxin-producing Escherichia coli from swine and cattle in Central China
Zhong Peng, Wan Liang, Zizhe Hu, Xiaosong Li, Rui Guo, Lin Hua, Xibiao Tang, Chen Tan, Huanchun Chen, Xiangru Wang, Bin Wu
BMC Veterinary Research.2019;[Epub] CrossRef
Detection and molecular characterization of sorbitol fermenting non-O157 Escherichia coli from goats
Shivasharanappa Nayakvadi, Charlotte Alison Alemao, H.B. Chethan Kumar, R.S. Rajkumar, Susitha Rajkumar, Eaknath B. Chakurkar, Shivaramu Keelara
Small Ruminant Research.2018; 161: 7. CrossRef
Antimicrobial Resistance inEscherichia coli
Laurent Poirel, Jean-Yves Madec, Agnese Lupo, Anne-Kathrin Schink, Nicolas Kieffer, Patrice Nordmann, Stefan Schwarz, Frank Møller Aarestrup, Stefan Schwarz, Jianzhong Shen, Lina Cavaco
Microbiology Spectrum.2018;[Epub] CrossRef
The genetic background of antibiotic resistance among clinical uropathogenic Escherichia coli strains
Wioletta Adamus-Białek, Anna Baraniak, Monika Wawszczak, Stanisław Głuszek, Beata Gad, Klaudia Wróbel, Paulina Bator, Marta Majchrzak, Paweł Parniewski
Molecular Biology Reports.2018; 45(5): 1055. CrossRef
Interrelationship between tetracycline resistance determinants, phylogenetic group affiliation and carriage of class 1 integrons in commensal Escherichia coli isolates from cattle farms
Kuastros Mekonnen Belaynehe, Seung Won Shin, Han Sang Yoo
BMC Veterinary Research.2018;[Epub] CrossRef
Occurrence of aminoglycoside-modifying enzymes among isolates of Escherichia coli exhibiting high levels of aminoglycoside resistance isolated from Korean cattle farms
Kuastros Mekonnen Belaynehe, Seung Won Shin, Park Hong-Tae, Han Sang Yoo
FEMS Microbiology Letters.2017;[Epub] CrossRef
Prevalence of Antimicrobial Resistance and Transfer of Tetracycline Resistance Genes in Escherichia coli Isolates from Beef Cattle
Seung Won Shin, Min Kyoung Shin, Myunghwan Jung, Kuastros Mekonnen Belaynehe, Han Sang Yoo, M. W. Griffiths
Applied and Environmental Microbiology.2015; 81(16): 5560. CrossRef
Profiling of antimicrobial resistance and plasmid replicon types in β-lactamase producingEscherichia coliisolated from Korean beef cattle
Seung Won Shin, Myunghwan Jung, Min-Kyung Shin, Han Sang Yoo
Journal of Veterinary Science.2015; 16(4): 483. CrossRef

Morphological Structure of Propagules and Electrophoretic Karyotype Analysis of False Smut Villosiclava virens in Rice: Rongtao Fu , Lei Ding , Jun Zhu , Ping Li , Ai-ping Zheng; J. Microbiol. 2012;50(2):263-269. Published online April 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1456-3

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Abstract: The target pathogen Villosiclava virens (teleomorph: claviceps oryzae-sativae) was isolated from the infected rice, where it caused false smut. In our study, the forming processes of the chlamydospores, chlamydospore balls, conidiospores, and secondary conidiospores during the asexual reproduction were observed more precisely and in greater detail than previous descriptions. The microstructure of the infected rice kernel showed that the outer dense chlamydospores piled around the false smut balls grown on XBZ medium; moreover the sclerotia consisting of dense mycelium were found. The different morphology was observed across the different growing conditions. In addition, we observed the nuclear numbers of both the conidiospores and hyphae using 4′,6-diamidino-2-phenylindole (DAPI) staining. Because the fungus has small chromosomes and the numbers were not previously known, we analyzed the electrophoretic karyotype using a pulsed field gel electrophoresis (PFGE) technique. The results showed that V. virens has at least 10 chromosomes ranging in size from 0.6 kb to 6 Mb. The V. virens genome size is estimated to be 23 Mb. Here, we report the morphological characteristics of the fungus and the process of asexual spores forming asexual propagules, along with the first analyze the molecular karyotype of V. virens. These
results
supply a foundation for further study of the pathogenicity and biology of this devastating pathogen.

Journal Article

Molecular Characteristics and Resistant Mechanisms of Imipenem-Resistant Acinetobacter baumannii Isolates in Shenyang, China: Jing Ping Zhang , Wan Zhu , Su Fei Tian , Yun Zhuo Chu , Bai Yi Chen; J. Microbiol. 2010;48(5):689-694. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0137-3

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Abstract: The investigation was carried out to elucidate the molecular characteristics and resistant mechanisms of imipenem-resistant Acinetobacter baumannii. Thirty-seven isolates were collected from January 2007 to December 2007. The homology of the isolates was analyzed by both pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The genes of β-lactamases, adeB, and class 1 integron were polymerase chain reaction amplified. Genotype analysis of the 37 A. baumannii isolates by PFGE revealed the circulation of four PFGE types (A-D) ; the A- and B-type accounted for 48.6% and 40.5%, respectively. MLST showed the existence of three allelic profiles. The agar dilution method was carried out to determine the MIC of imipenem, in the absence or presence of carbonyl cyanide m-chlorophenylhydrazone (CCCP, 10 μg/ml). The MICs of the strains to imipenem were between 16 μg/ml and 128 μg/ml. When CCCP was added, a MIC decrease of at least four-fold was observed in 20 isolates, which belonged to the A- or C-type. AdeB and blaPER-1 genes were each detected in 35 isolates, blaOXA-23 gene in 34 isolates and blaOXA-58-like gene in 24 isolates. All isolates harbored blaOXA-51-like genes. No isolates carried the blaIMP-1 gene. Integron was detected in 25 isolates, which mediated the resistance to aminoglycosides and rifampin. The epidemiologic data suggested that the increasing infection of A. baumannii in our hospital was mainly caused by the inter-hospital spread of two epidemic clones. The AdeABC efflux system may be the important factor that leads to the high level of imipenem-resistance in PFGE A-type.

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

Genomic Diversity of Legionella pneumophila Serogroup 1 from Environmental Water Sources and Clinical Specimens Using Pulsed-Field Gel Electrophoresis (PFGE) from 1985 to 2007, Korea: Hae Kyung Lee , Yeon Ho Kang , Jae Yon Yu; J. Microbiol. 2010;48(5):547-553. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0031-z

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Abstract: The molecular typing of 202 Legionella pneumophila sg 1 isolates obtained from environmental water sources and clinical specimens from 1985 to 2007 was conducted using pulsed-field gel electrophoresis (PFGE). In this study, a total of 212 isolates were grouped into 35 different PFGE types and Type 1 was the predominant type, accounting for 28.7% in PFGE types. Type 1 and Type 8 were observed continuously from 1985 to 2007. In the analysis of the distribution of PFGE types in six geographic regions (Seoul-Incheon, Gangwon, Chungcheong, Gyeongsang, Jeolla, and Jeju), Type 1 was predominant throughout four regions except for Jeolla and Jeju, and Type 6 was observed in four regions except two regions (Gangwon and Jeju). Six clinical isolates belonged to PFGE Type 1, Type 6, Type 9, and Type 15. Type 1 among these types, was isolated from 3 patients with confirmed nosocomial infection at the hospital and Type 6, Type 9, and Type 15 were isolated 3 patients with suspected community-acquired infection. Type R, PFGE pattern of L. pneumophila sg 1 (ATCC 33152, Philadelphia-1), was not observed in the isolates evaluated in this study. Therefore, our results suggest that PFGE Type 1 was very prevalent in the environmental and clinical isolates in Korea. Type 1 was distributed continuously for many years throughout Korea.

Journal Articles

Antimicrobial Resistance Patterns and Characterization of Integrons of Shigella sonnei Isolates in Seoul, 1999-2008: Young-hee Jin , Young-hee Oh , Ji-hun Jung , Soo-jin Kim , Jin-ah Kim , Ki-young Han , Min-young Kim , Seog-gee Park , Young-ki Lee; J. Microbiol. 2010;48(2):236-242. Published online May 1, 2010; DOI: https://doi.org/10.1007/s12275-010-9220-z

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Abstract: A total of 66 Shigella sonnei isolates from 1999 to 2008 in Seoul was analyzed for their antimicrobial resistance, carriage of integron, and the patterns of Pulsed-field gel electrophoresis (PFGE). A high level of antimicrobial resistance to streptomycin (100%), trimethoprim/sulfamethoxazole (95%), tetracycline (94%), nalidixic acid (65%), and ampicillin (41%) was observed among S. sonnei isolates. Fourteen profiles of antimicrobial resistance were identified with the most common resistance profile being nalidixic acid, streptomycin, tetracycline, and trimethoprim/sulfamethoxazole (35%). PCR and DNA sequencing analysis revealed the presence of class 2 integron in all isolates, and class 1 and 2 integrons in 7 isolates. The class 2 integron carried two types of gene cassettes. One cassette array was dfrI, sat2, and aadA1 (91%), and the other was dfr1 and sat1 (8%). dfrA12 and aadA2 gene cassette was found in one isolate containing class 1 integron. PFGE was carried out to examine the genetic relatedness among isolates. All isolates except for one showed similar PFGE patterns (similarity of 80.1%). These results suggest that the S. sonnei isolated during 1999-2008 in Seoul have similar lineages that have not undergone evolutionary changes with time.

Burkholderia cepacia Complex Infection in a Cohort of Italian Patients with Cystic Fibrosis: Antonietta Lambiase , Valeria Raia , Stefania Stefani , Angela Sepe , Pasqualina Ferri , Paolo Buonpensiero , Fabio Rossano , Mariassunta Del Pezzo; J. Microbiol. 2007;45(3):275-279.; DOI: https://doi.org/2530 [pii]

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Abstract: The aims of this study were to detect Burkholderia cepacia complex (Bcc) strains in a cohort of Cystic Fibrosis patients (n=276) and to characterize Bcc isolates by molecular techniques. The results showed that 11.23% of patients were infected by Bcc. Burkholderia cenocepacia lineage III-A was the most prevalent species (64.3%) and, of these, 10% was cblA positive and 50% esmR positive. Less than half of the strains were sensitive to ceftazidime, meropenem, piperacillin tazobactam, and trimethoprim-sulfamethoxazole. About half of the strains (41%) had homogeneous profiles, suggesting cross-transmission. The infection by B. cenocepacia was associated to a high rate of mortality (p=0.01).

Genetic Diversity of Multi-resistant Salmonella enterica Serotype Typhimurium Isolates from Animals and Humans: Yong-Ku Woo , Su-Hwa Lee; J. Microbiol. 2006;44(1):106-112.; DOI: https://doi.org/2329 [pii]

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Abstract: In this study, the genetic diversities of multi-resistant Salmonella typhimurium (ST) isolates were analyzed via the application of both pulsed field gel electrophoresis (PFGE) and Polymerase chain reaction (PCR) analysis methods, using 6 kinds of primers (REP, ERIC, SERE, BOX, P-1254 and OPB-17). And their discriminative abilities (DA) were also compared in order to determine the most effective and reliable analysis method. 118 S. typhimurium isolates, cultured from diverse animals and human patients in Korea beginning in 1993, were analyzed and subjected to a comparison of Simpson’s index of diversity (SID), using both PFGE and PCR methods. PFGE by XbaI enzyme digestion allowed for discrimination into 9 pulsotypes, with high SID values (0.991) on the genomic DNA level. This shows that PFGE is a very discriminative genotypic tool, and also that multiple clones of S. typhimurium isolates had existed in domestic animals and humans in Korea since 1993. However, we could ultimately not to trace the definitive sources or animal reservoirs of specific S. typhimurium isolates examined in this study. Depending on the SID values, the combined
method
(7 kinds of method) was found to be the most discriminative method, followed by (in order) SERE-PCR, REP-PCR, ERIC-PCR, PFGE & OPB-17 (RAPD), P-1254 (RAPD), and BOX-PCR at the 80% clone cut-off value. This finding suggests that the REP-PCR method (which utilizes 4 primer types) may be an alternative tool to PFGE for the genotyping of S. typhimurium isolates, with comparable cost, time, and labor requirement. The establishment of a highly reliable and discriminatory method for epidemiologic analysis is considered necessary in order for researchers to trace the sources of specific pathogens and, consequently, to control and prevent the spread of epidemic S. typhimurium isolates to humans.

Molecular Epidemiological Analysis of Bloodstream Isolates of Candida albicans from a University Hospital over a Five-Year Period: Jong Hee Shin , Yu Gyung Og , Duck Cho , Seung Jung Kee , Myung Geun Shin , Soon Pal Suh , Dong Wook Ryang; J. Microbiol. 2005;43(6):546-554.; DOI: https://doi.org/2291 [pii]

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Abstract: We assessed the genetic relations and epidemiological links among bloodstream isolates of Candida albicans, which were obtained from a university hospital over a period of five years. The 54 bloodstream isolates from the 38 patients yielded 14 different karyotypes, 29 different patterns after digestion with SfiI (REAG-S), and 31 different patterns after digestion with BssHII (REAG-B) when analyzed using three different pulsed-field gel electrophoresis (PFGE) typing methods. In 11 patients with serial bloodstream isolates, all strains from each patient had the same PFGE pattern. The dendrograms for all of the strains revealed that the distribution of similarity values ranged from 0.70 to 1.0 in the REAG-S patterns, and from 0.35 to 1.0 in the REAG-B patterns. Overall, the combination of the three different PFGE methods identified 31 distinct types, reflecting the results obtained using the REAG-B alone different. different Five PFGE types were shared among 22 isolates from 12 patients. These types of strains were more frequently associated with central venous catheter-related fungemia than the other 26 type strains (92% versus 31%; P < 0.005). Of five PFGE types, four isolates were determined to be epidemiologically related: each of these types was primarily from two or three patients who had been hospitalized concurrently within the same intensive care unit. Our results suggest that the REAG-B constitutes perhaps the most useful PFGE method for investigating C. albicans candidemia and also shows that a relatively high proportion of C. albicans candidemia may be associated with exogenous acquisition of clonal strains.

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

Finding the Sources of Korean Salmonella enterica Serovar Enteritidis PT4 Isolates by Pulsed-field Gel Electrophoresis: Yong-Ku Woo; J. Microbiol. 2005;43(5):424-429.; DOI: https://doi.org/2280 [pii]

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Abstract: In previous studies, it has been reported that both S. enteritidis, the most common serotype, and S. enteritidis Phage Type 4 (SEPT 4) isolates were identified as the most prevalent PT in domestic poultry and also in humans in Korea until 2002. The aim of this study was to analyze the genetic diversity and epidemiological properties of both PT isolates, and also to trace the source of SEPT 4 isolates from domestic poultry and humans by Pulsed-field gel electrophoresis (PFGE). In order to understand the molecular epidemiologic properties of SEPT 4 isolates, which have very similar phenotypic properties to our preliminary investigations (serotyping, phage typing, large plasmids and antibiograms), PFGE analysis with XbaI enzyme was performed on the representative SEPT 4 isolates. Thirty-six SEPT 4 isolates were analyzed and differentiated with 10 pulsed-field profiles (PFP) expressing very high discriminative ability (SID: 0.921). In PFP, SEPT 4 isolates from human patients showed a perfect genetic match with those from broiler chickens and meats. Therefore, this study was able to successfully trace the major source of SEPT 4 isolates and also to determine the usefulness of the PFGE method for genetic analysis of epidemic strains.

Journal Articles

Molecular Investigation of Two Consecutive Nosocomial Clusters of Candida tropicalis Candiduria Using Pulsed-Field Gel Electrophoresis: Joon Rho , Jong Hee Shin , Jeong Won Song , Mi-Ra Park , Seung Jung Kee , Sook Jin Jang , Young Kyu Park , Soon Pal Suh , Dong Wook Ryang; J. Microbiol. 2004;42(2):80-86.; DOI: https://doi.org/2041 [pii]

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Abstract: Pulsed-field gel electrophoresis (PFGE) typing was applied to the epidemiological investigation of 21 Candida tropicalis isolates collected from urine specimens of 11 patients and one healthcare worker, in an intensive care unit (ICU) over a 4-month period. Seventeen epidemiologically unrelated strains from 14 patients were also tested to determine the discriminatory power of PFGE. PFGE typing consisted of electrophoretic karyotyping (EK) and restriction endonuclease analysis of genomic DNA (REAG), using two restriction enzymes (BssHII and SfiI). The EK pattern was the same in all 38 isolates, while REAG using SfiI separated the isolates into nine types. However, 16 different PFGE types were identified by REAG with BssHII, and the same results were obtained when the results of both REAG tests were combined. In serial urinary isolates from 10 patients, all strains from each patient had the same PFGE pattern. While the epidemiologically unrelated strains from 14 patients consisted of 13 different PFGE types, the 20 isolates from the 11 ICU patients fell into only two PFGE types (types C1 and C2), and these apparently originated from the two different outbreaks. All strains of type C1 (n = 12) were isolated from six patients, between November 1999 and January 2000, and all of the type C2 strains (n=8) were isolated from five patients, during January and February 2000. This study shows two consecutive clusters of C. tropicalis candiduria in an ICU, defined by PFGE typing, and also demonstrates that a PFGE typing method using BssHII is perhaps the most useful method for investigating C. tropicalis candiduria.

Genomic Relationship of Salmonella enterica Serovar Typhimurium DT104 Isolates from Korea and the United States: Shukho Kim , Sung Guen Chun , Ok Young Lim , Mi Sun Park , Yeon Ho Kang , Yong Ho Park , Bok Kwon Lee; J. Microbiol. 2004;42(1):14-19.; DOI: https://doi.org/2007 [pii]

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Abstract: Salmonella enterica serovar Typhimurium DT104 (Salmonella Typhimurium DT104 or DT104) hasbeen emerging as a common pathogen for human in Korea since 1997. In order to compare the genomic relationship and to search for the dominant strains in Korea, we conducted pulsed-field gel electrophoresis (PFGE) and IS200 fingerprinting of 25 epidemiological unrelated isolates from human and animals from Korea and cattle from America. Two Salmonella Typhimurium DT104 isolates from human in Korea and all 8 isolates from American cattle had indistinguishable patterns from the PFGE and IS200 fingerprinting but multidrug-resistant Salmonella Typhimurium isolates, including DT104, from Korean animals had diverse genetic patterns. The data suggest that a dominant DT104 strain might have circulated between Korean and American cattle and that it had a high level of clonality.

Megabase-sized DNA Isolation and Electrophoretic Karyotype of Fusarium oxysporum Schlecht: Park, Min Seon , Min, Byung Re; J. Microbiol. 1995;33(2):132-135.

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Abstract: To investigate the electrophoretic karytype of Fusarium oxysporum, intact chromosomal DNA was separated by pulsed-field gel electrophoresis (PEGE). DNA extraction from nulcei, mycelia and protoplasts were compared with one another and with the quantity and the suitability for PFGE separation in agarose gel. As a result, the most useful extracting method for intact DNA was found to be that from protoplasts. By varying the electrophoretic conditions, 8 chromosomal DNA bounds were resolved. Using the Schizosaccharomyces pombe and Saccharomyces cerevisiae as size standards, the size of Fusarium oxysporum chromosomes was estimated to range from approximately 0.6 Mb TO 6.7 Mb, and total genome size was 26.7 Mb. The suitability of electrophoretic karyotyping as a tool for strain characterization is discussed.

Characterization of an Escherichia coli O157:H7 Strain Producing Verotoxin 2 Isolated from a Patient in Korea: Chang-Kyu Sohn , Wan Huh , Byung-Chun Kim , Wan Park; J. Microbiol. 2000;38(2):93-98.

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Abstract: Nine hundred patients diagnosed with diarrhea or hemorrhagic uremic syndrome in the Kyungpook Province, Korea, were examined from November 1998 to February 2000. One patient in Kumi appeared to possess the Escherichia coli O157:H7 strain, which is very important in clinical decision making and public health action. The isolated strain, an E. coli O157:H7 KM, contained a 60 MDa plasmid and typical virulence genes including the verotoxin 2 gene, ehxA gene (encoding enterohemorrhagic hemolysin), and eae (encoding attaching and effacing protein-intimin) gene. This strain produced only verotoxin 2. Pulsed field gel electrophoretic analysis showed that the genomic organization of the E. coli O157:H7 KM strain may differ greatly from those of representative strains previously reported in the United States and Japan.

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