• Journal of Preventive Medicine and Public Health
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• v.45 no.1
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• pp.1-7
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• 2012

Using three Austrian case studies, the variegated applications of molecular typing in today's public health laboratories are discussed to help illustrate preventive management strategies relying on DNA subtyping. DNA macrorestriction analysis by pulsed field gel electrophoresis has become the gold standard for subtyping of food borne pathogens like listeria, salmonella, campylobacter and Bacillus cereus. Using a Salmonella Mbandaka outbreak from the year 2010 as example, it is shown how the comparison of patterns from human isolates, food isolates, animal isolates and feed isolates can allow to identify and confirm a source of disease. An epidemiological connection between the simultaneous occurrence of tuberculosis in cattle and deer with cases of human tuberculosis due to Mycobacterium caprae in 2010 was excluded using mycobacterial interspersed repetitive units variable-number tandem repeats subtyping. Also in 2010, multilocus sequence typing with nonselective housekeeping genes, the so-called sequence based typing protocol, was used to elucidate connections between an environmental source (a hospital drinking water system) and a case of legionellosis. During the last decades, molecular typing has evolved to become a routine tool in the daily work of public health laboratories. The challenge is now no longer to simply type microorganisms, but to type them in a way that allows for data exchange between public health laboratories all over the world.

• Microbiology and Biotechnology Letters
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• v.46 no.2
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• pp.162-170
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• 2018

Non-typhoidal Salmonella is one of the main pathogens causing food-borne illness in humans, with up to 20% of cases resulting from consumption of pork products. Over the gastroenteritis signs, multidrug resistant Salmonella has arisen. In this study, pan-susceptible phenotypic strains of Salmonella enterica serotype Weltevreden recovered from pig production chain in Chiang Mai, Thailand during 2012-2014 were chosen for analysis. The aim of this study was to use whole genome sequencing (WGS) data with an emphasis on antimicrobial resistance gene investigation to assess their pathogenic potential and genetic diversity determination based on whole genome Multilocus Sequence Typing (wgMLST) to expand epidemiological knowledge and to provide additional guidance for disease control. Analyis using ResFinder 3.0 for WGS database tracing found that one of pan-susceptible phenotypic strain carried five classes of resistance genes: aminoglycoside, beta-lactam, phenicol, sulfonamide, and tetracycline associated genes. Twenty four and 36 loci differences were detected by core genome Multilocus Sequence Typing (cgMLST) and pan genome Multilocus Sequence Typing (pgMLST), respectively, in two matching strains (44/13 vs A543057 and A543056 vs 204/13) initially assigned by conventional MLST and Pulsed-field Gel Electrophoresis (PFGE). One hundread percent discriminant ability can be achieved using the wgMLST technique. WGS is currently the ultimate molecular technique for various in-depth studies. As the findings stated above, a new of "gold standard typing method era" for routine works in genome study is being set.

• Food Science and Biotechnology
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• v.27 no.6
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• pp.1755-1760
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• 2018

The objective of this study was to perform genetic diversity analysis of 13 strains isolated from South Korean foods by multilocus sequence typing (MLST). For typing, seven housekeeping loci (atpA, dnaA, dnaK, gyrB, pheS, pyrG, and rpoA) were selected, amplified and analyzed. Fifty-one polymorphic sites varying from 1 to 22 in each species were identified. Thirteen sequence types were generated with allele numbers ranged from 2 to 10. The overall relationship between strains was assessed by unweighted pair group method with arithmetic mean dendrogram and minimum spanning tree. In addition, combined spits tree analysis revealed intragenic recombination. No clear relationship was observed between the isolation sources and strains. The developed MLST scheme enhanced our knowledge of the population diversity of Leu. citreum strains and will be used further for the selection of industrially important strain.

• Korean Journal of Poultry Science
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• v.47 no.2
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• pp.115-119
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• 2020

Fowl cholera is an infectious disease caused by Pasteurella multocida that contributes to high economic loss in the commercial chicken industry. Three Pasteurella multocida strains were isolated from outbreaks of acute fowl cholera in the Korean layer farms from 2018 to 2019. One strain was identified and serotyped using capsular PCR typing. This strain was also genotyped by lipopolysaccharide (LPS) PCR typing as A: L3, whereas other strains were non-typable. The multilocus sequence typing (MLST) result showed that the A: L3 strain is sequence type (ST) 134; the non-typable strains were recorded as the following new STs: ST 366 and ST 374. Using phylogenetic tree analysis based on MLST sequences, we determined that ST 366 and ST 374 are closely related to the reference strains that were previously isolated from duck and chicken in Korea, and they were highly prevalent within the Korean cluster. In conclusion, Pasteurella multocida strains were identified and isolated in this study. Furthermore, this is the first report of using MLST to determine the prevalence of fowl cholera in Korea.

• Food Science of Animal Resources
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• v.40 no.5
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• pp.758-771
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• 2020

This study was to investigate the prevalence and characteristics of antimicrobial-resistant Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) from 4,264 retail meat samples including beef, pork, and chicken in Korea between 2013 and 2018. A broth microdilution antimicrobial susceptibility testing was performed for S. aureus. Molecular typing by multilocus sequence typing (MLST), spa typing, and pulsed-field gel electrophoresis (PFGE), was performed on mecA-positive S. aureus strain. S. aureus was isolated at a rate of 18.2% (777/4,264), of which MRSA comprised 0.7% (29 strains). MLST analysis showed that 11 out of the 29 MRSA isolates were predominantly sequence type (ST) 398 (37.9%). In addition, ST72, ST692, ST188, ST9, and ST630 were identified in the MRSA isolates. The spa typing results were classified into 11 types and showed a high correlation with MLST. The antimicrobial resistance assays revealed that MRSA showed 100% resistance to cefoxitin and penicillin. In addition, resistance to tetracycline (62.1%), clindamycin (55.2%), and erythromycin (55.2%) was relatively high; 27 of the 29 MRSA isolates exhibited multidrug resistance. PFGE analysis of the 18 strains excluding the 11 ST398 strains exhibited a maximum of 100% homology and a minimum of 64.0% homology. Among these, three pairs of isolates showed 100% homology in PFGE; these results were consistent with the MLST and spa typing results. Identification of MRSA at the final consumption stage has potential risks, suggesting that continuous monitoring of retail meat products is required.

• Mycobiology
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• v.43 no.3
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• pp.360-365
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• 2015

Multilocus sequence typing analysis was applied to determine the genotypes of 147 (137 clinical and 10 environmental) Cryptococcus neoformans and three clinical Cryptococcus gattii isolates from 1993 to 2014 in Korea. Among the 137 clinical isolates of C. neoformans, the most prevalent genotype was ST5 (n = 131), followed by ST31 (n = 5) and ST127 (n = 1). Three C. gattii strains were identified as ST57, ST7, and ST113. All environmental isolates were identified as C. neoformans with two genotypes, ST5 (n = 7) and ST31 (n = 3). Our results show that C. neoformans isolates in Korea are genetically homogeneous, and represent a close genetic relationship between clinical and environmental isolates.

• Journal of Digital Convergence
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• v.14 no.4
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• pp.371-378
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• 2016

An aim of current study was to investigate the prevalence and the mechanism of quinolone-resistance in E. coli isolates obtained from chicken cecum in Korea. In addition, multilocus sequence typing (MLST) was also performed for the molecular characterization of E. coli isolates. In an antimicrobial susceptibility test by the disk diffusion method, the 63.5% (54/85) of E. coli isolates showed the resistance to quinolone group of antimicrobial agents. All of the 54 E. coli isolates showing resistant to quinolone group had sense mutations in gyrA gene and point mutations at the $57^{th}$, $80^{th}$, or $84^{th}$ residues in parC gene were detected in 90.7% of the isolates. Interestingly, E. coli ST was closely related to amino acid substitutions in parE gene. Our results indicated that the long-term use of antimicrobial agents in food-producing animals was strongly associated with a prevalence of antimicrobial resistance in commensal Enterobacteriaceae, suggesting the need for continuous surveillance and monitoring of antimicrobial resistant determinants in bacterial isolates from food animals.

• Clinical and Experimental Pediatrics
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• v.58 no.1
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• pp.20-27
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• 2015

Purpose: We investigated the molecular types of uropathogenic Escherichia coli (UPEC) by using conventional phylogrouping, multilocus sequence typing (MLST), and fimH genotyping. Methods: Samples of patients younger than 18 years of age were collected from the Chung-Ang University Hospital over 2 years. Conventional phylogenetic grouping for UPEC strains was performed by polymerase chain reaction (PCR). Bacterial strain sequence types (STs) were classified on the basis of the results of partial sequencing of seven housekeeping genes. In addition, we analyzed nucleotide variations in a 424-base pair fragment of fimH, a major virulence factor in UPEC. Results: Sixty-four UPEC isolates were analyzed in this study. Phylogenetic grouping revealed that group B2 was the most common type (n=54, 84%). We identified 16 distinctive STs using MLST. The most common STs were ST95 (35.9%), ST73 (15.6%), ST131 (12.5%), ST69 (7.8%), and ST14 (6.3%). Fourteen fimH allele types were identified, of which 11 had been previously reported, and the remaining three were identified in this study. f1 (n=28, 45.2%) was found to be the most common allele type, followed by f6 and f9 (n=7, 11.3% each). Comparative analysis of the results from the three different molecular typing techniques revealed that both MLST and fimH typing generated more discriminatory UPEC types than did PCR-based phylogrouping. Conclusion: We characterized UPEC molecular types isolated from Korean children by MLST and fimH genotyping. fimH genotyping might serve as a useful molecular test for large epidemiologic studies of UPEC isolates.

• Journal of Microbiology and Biotechnology
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• v.22 no.11
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• pp.1467-1470
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• 2012

We compared rapid fingerprinting using repetitive sequencebased PCR (rep-PCR) for subtyping Campylobacter jejuni isolates to the widely used multilocus sequence typing (MLST). Representative C. jejuni isolates (n = 16) from broilers were analyzed using MLST and rep-PCR. Both techniques demonstrated an equal discriminatory power of 0.8917, and 9 subgroups were identified. Clonal identification of all 16 isolates was identical for both techniques. The rep-PCR as described in this study may be used as a rapid and cost-effective alternative for subtyping of C. jejuni isolates, or as an effective screening tool in large epidemiological studies.

• Journal of Microbiology and Biotechnology
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• v.27 no.5
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• pp.916-924
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• 2017

Eighty-five Enterococcus faecalis isolates collected from animals (40 isolates), meju (a Korean fermented soybean product; 27 isolates), humans (10 isolates), and various environmental samples (8 isolates) were subjected to multilocus sequence typing (MLST) to identify genetic differences between samples of different origins. MLST analysis resulted in 44 sequence types (STs), and the eBURST algorithm clustered the STs into 21 clonal complexes (CCs) and 17 singletons. The predominant STs, ST695 (21.1%, 18/85) and ST694 (9.4%, 8/85), were singletons, and only contained isolates originating from meju. None of the STs in the current study belonged to CC2 or CC9, which comprise clinical isolates with high levels of antibiotic resistance. The E. faecalis isolates showed the highest rates of resistance to tetracycline (32.9%), followed by erythromycin (9.4%) and vancomycin (2.4%). All isolates from meju were sensitive to these three antibiotics. Hence, MLST uncovered genetic diversity within E. faecalis, and clustering of the STs using eBURST revealed a correlation between the genotypes and origins of the isolates.