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Analysis of class I integrons responsible for antibiotics resistance in Pseudomonas aeruginosa
오만환,이장원,최승규,손승렬 한국유전학회 2015 Genes & Genomics Vol.37 No.3
An increase in resistance to antibiotics inPseudomonas aeruginosa has become a major worldwideconcern. Particularly, P. aeruginosa which produces carbapenemases,versatile metallo-b-lactamases (MBLs),causes limitation to treat infection. Class I integrons playan important role in the spread of antibiotic resistancedeterminants such as MBLs in P. aeruginosa. In thepresent study, we identified and characterized geneticcontents of class I integrons in P. aeruginosa DK45 thatwas isolated from catheterized urine of patients atChungbuk National University Hospital in South Koreaand strongly exhibited carbapenemase activity. The correlationbetween integron-associated gene cassettes andantibiotics resistance was also investigated. Screening ofthe integrons in P. aeruginosa was performed by PCR andthe integron-associated gene cassettes were further characterizedby DNA sequencing. It was confirmed that threeintegrons (class I) harboring VIM-2, OXA-10, and OXA-30 type b-lactamase genes, respectively, existed on thebacterial plasmid. Each integron also contained genesencoding resistance determinants to various antibioticssuch as aminoglycoside, fluoroquinolone and folate pathwayinhibitors. Functional analysis by recombinant plasmidsbearing each integron in Escherichia coli indicatedthat each integron was associated to a high resistance rateto b-lactam and aminoglycoside antibiotics. The combinedresults suggest that genetic diversity of class I integrons is amajor factor capable of increasing a broad spectrumresistance to the antibiotics.
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Genes Involved in the Biosynthesis and Transport of Acinetobactin in Acinetobacter baumannii
Tarik Hasan,최철희,오만환 한국유전체학회 2015 Genomics & informatics Vol.13 No.1
Pathogenic bacteria survive in iron-limited host environments by using several iron acquisition mechanisms. Acinetobacterbaumannii, causing serious infections in compromised patients, produces an iron-chelating molecule, called acinetobactin,which is composed of equimolar quantities of 2,3-dihydroxybenzoic acid (DHBA), L-threonine, and N-hydroxyhistamine, tocompete with host cells for iron. Genes that are involved in the production and transport of acinetobactin are clusteredwithin the genome of A. baumannii. A recent study showed that entA, located outside of the acinetobactin gene cluster,plays important roles in the biosynthesis of the acinetobactin precursor DHBA and in bacterial pathogenesis. Therefore,understanding the genes that are associated with the biosynthesis and transport of acinetobactin in the bacterial genome isrequired. This review is intended to provide a general overview of the genes in the genome of A. baumannii that are requiredfor acinetobactin biosynthesis and transport.
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Investigation of Hanwoo-specific structural variations using wholegenome sequencing data
박장호,신원석,문세영,오만환,임다정,오동엽,박영준,박종화,박용수,한규동 한국유전학회 2019 Genes & Genomics Vol.41 No.2
Background The total length of the cattle genome is approximately ~ 3 billion base pairs. About half of the bovine genome (46.5%) is composed of transposable elements (TEs). The TEs could be a major source of genomic structural variations (SVs) between cattle breeds. These SVs have led to genomic fluidity and rearrangements between interspecies. Objective TE-mediated insertion and deletion events could have a strong influence on the bovine genome. This study aimed to investigate TE-mediated deletion events that are common to 12 Hanwoo genome resequencing data. Results We compared 12 Hanwoo genome resequencing data with the cattle reference genome (Bos taurus_UMD_3.1.1) and six other open source data (2 Jersey, 2 Holstein, 2 Angus). By using BreakDancer program, the common SVs to the 12 Hanwoo genomes were detected. A total of 299 Hanwoo-specific SV candidates were detected. Among them, 56 Hanwoospecific TE-mediated deletion candidate loci were validated by PCR and Sanger sequencing. Finally, we identified one locus, DEL_96, which is an authentic Hanwoo-specific deletion. The DEL_96 event occurred by nonallelic homologous end-joining between LINE (BovB) and unique sequence with 1 bp microhomology. The 370 bp deletion event appeared to be only in the Hanwoo individuals after the divergence of Hanwoo and Holstein lineages. Conclusion Our study showed that one of the SVs, TE-mediated deletion, could be utilized as a molecular maker to distinguish between Hanwoo and Holstein.
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Complete genome sequence of uropathogenic Escherichia coli isolate UPEC 26-1
Bindu Subhadra,김동호,김재석,우경호,손경목,김화중,한규동,오만환,최철희 한국유전학회 2018 Genes & Genomics Vol.40 No.6
Urinary tract infections (UTIs) are among the most common infections in humans, predominantly caused by uropathogenic Escherichia coli (UPEC). The diverse genomes of UPEC strains mostly impede disease prevention and control measures. In this study, we comparatively analyzed the whole genome sequence of a highly virulent UPEC strain, namely UPEC 26-1, which was isolated from urine sample of a patient suffering from UTI in Korea. Whole genome analysis showed that the genome consists of one circular chromosome of 5,329,753 bp, comprising 5064 protein-coding genes, 122 RNA genes (94 tRNA, 22 rRNA and 6 ncRNA genes), and 100 pseudogenes, with an average G+C content of 50.56%. In addition, we identified 8 prophage regions comprising 5 intact, 2 incomplete and 1 questionable ones and 63 genomic islands, suggesting the possibility of horizontal gene transfer in this strain. Comparative genome analysis of UPEC 26-1 with the UPEC strain CFT073 revealed an average nucleotide identity of 99.7%. The genome comparison with CFT073 provides major differences in the genome of UPEC 26-1 that would explain its increased virulence and biofilm formation. Nineteen of the total GIs were unique to UPEC 26-1 compared to CFT073 and nine of them harbored unique genes that are involved in virulence, multidrug resistance, biofilm formation and bacterial pathogenesis. The data from this study will assist in future studies of UPEC strains to develop effective control measures.
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