Genomic Approaches for Understanding the Characteristics of Salmonella enterica subsp. enterica Serovar Typhimurium ST1120, Isolated from Swine Feces in Korea |
Kim, Seongok
(Department of Molecular Science and Technology, Ajou University)
Kim, Eunsuk (Department of Molecular Science and Technology, Ajou University) Park, Soyeon (College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University) Hahn, Tae-Wook (College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University) Yoon, Hyunjin (Department of Molecular Science and Technology, Ajou University) |
1 | Reeves P. 1995. Role of O-antigen variation in the immune response. Trends Microbiol. 3: 381-386. DOI |
2 | Anjum MF, Choudhary S, Morrison V, Snow LC, Mafura M, Slickers P, et al. 2011. Identifying antimicrobial resistance genes of human clinical relevance within Salmonella isolated from food animals in Great Britain. J. Antimicrob. Chemother. 66: 550-559. DOI |
3 | Patterson SK, Borewicz K, Johnson T, Xu W, Isaacson RE. 2012. Characterization and differential gene expression between two phenotypic phase variants in Salmonella enterica serovar Typhimurium. PLoS One 7: e43592. DOI |
4 | Fortier LC, Sekulovic O. 2013. Importance of prophages to evolution and virulence of bacterial pathogens. Virulence 4:354-365. DOI |
5 | Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J. 2005. ACT: the artemis comparison tool. Bioinformatics 21: 3422-3423. DOI |
6 | Roer L, Hendriksen RS, Leekitcharoenphon P, Lukjancenko O, Kaas RS, Hasman H, et al. 2016. Is the evolution of Salmonella enterica subsp. enterica linked to restriction-modification systems? mSystems. 1: e00009-e00016. |
7 | Kim E, Lee S-H, Lee S-J, Kwon O-P, Yoon H. 2017. New antibacterial-core structures based on styryl quinolinium. Food Sci. Biotechnol. 26: 521-529. DOI |
8 | Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, Jin Q. 2005. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 33: D325-D328. DOI |
9 | Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, et al. 2017. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 45: D566-D573. DOI |
10 | Brumell JH, Rosenberger CM, Gotto GT, Marcus SL, Finlay BB. 2001. SifA permits survival and replication of Salmonella typhimurium in murine macrophages. Cell. Microbiol. 3: 75-84. DOI |
11 | Bowe F, Lipps CJ, Tsolis RM, Groisman E, Heffron F, Kusters JG. 1998. At least four percent of the Salmonella typhimurium genome is required for fatal infection of mice. Infect. Immun. 66: 3372-3377. |
12 | Marcus SL, Brumell JH, Pfeifer CG, Finlay BB. 2000. Salmonella pathogenicity islands: big virulence in small packages. Microb. Infect. 2: 145-156. DOI |
13 | Sullivan MJ, Petty NK, Beatson SA. 2011. Easyfig: a genome comparison visualizer. Bioinformatics 27: 1009-1010. DOI |
14 | Addwebi TM, Call DR, Shah DH. 2014. Contribution of Salmonella Enteritidis virulence factors to intestinal colonization and systemic dissemination in 1-day-old chickens. Poult. Sci. 93: 871-881. DOI |
15 | Tsolis RM, Baumler AJ, Heffron F. 1995. Role of Salmonella typhimurium Mn-superoxide dismutase (SodA) in protection against early killing by J774 macrophages. Infect. Immun. 63:1739-1744. |
16 | Timme RE, Pettengill JB, Allard MW, Strain E, Barrangou R, Wehnes C, et al. 2013. Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters. Genome Biol. Evol. 5: 2109-2123. DOI |
17 | CDC. 2007. Bacterial foodborne and diarrheal disease national case surveillance, annual report, 2005. CDC, Atlanta, GA. |
18 | Majowicz SE, Musto J, Scallan E, Angulo FJ, Kirk M, O'Brien SJ, et al. 2010. The global burden of nontyphoidal Salmonella gastroenteritis. Clin. Infect. Dis. 50: 882-889. DOI |
19 | Elder JR, Chiok KL, Paul NC, Haldorson G, Guard J, Shah DH. 2016. The Salmonella pathogenicity island 13 contributes to pathogenesis in streptomycin pre-treated mice but not in day-old chickens. Gut Pathog. 8: 16. DOI |
20 | Boyer E, Bergevin I, Malo D, Gros P, Cellier MF. 2002. Acquisition of Mn(II) in addition to Fe(II) is required for full virulence of Salmonella enterica serovar Typhimurium. Infect. Immun. 70: 6032-6042. DOI |
21 |
Kehres DG, Janakiraman A, Slauch JM, Maguire ME. 2002. Regulation of Salmonella enterica serovar Typhimurium mntH transcription by |
22 | Horsburgh MJ, Wharton SJ, Karavolos M, Foster SJ. 2002. Manganese: elemental defence for a life with oxygen. Trends Microbiol. 10: 496-501. DOI |
23 | Althouse C, Patterson S, Fedorka-Cray P, Isaacson RE. 2003. Type 1 fimbriae of Salmonella enterica serovar Typhimurium bind to enterocytes and contribute to colonization of swine in vivo. Infect. Immun. 71: 6446-6452. DOI |
24 | Costa TR, Felisberto-Rodrigues C, Meir A, Prevost MS, Redzej A, Trokter M, et al. 2015. Secretion systems in gramnegative bacteria: structural and mechanistic insights. Nat. Rev. Microbiol. 13: 343-359. DOI |
25 | Baumler AJ, Tsolis RM, Heffron F. 1996. The lpf fimbrial operon mediates adhesion of Salmonella typhimurium to murine Peyer's patches. Proc. Natl. Acad. Sci. USA 93: 279-283. DOI |
26 | Wood RL, Rose R. 1992. Populations of Salmonella typhimurium in internal organs of experimentally infected carrier swine. Am. J. Vet. Res. 53: 653-658. |
27 | Brodsky IE, Ghori N, Falkow S, Monack D. 2005. Mig-14 is an inner membrane-associated protein that promotes Salmonella typhimurium resistance to CRAMP, survival within activated macrophages and persistent infection. Mol. Microbiol. 55:954-972. |
28 | Gal-Mor O, Boyle EC, Grassl GA. 2014. Same species, different diseases: how and why typhoidal and non-typhoidal Salmonella enterica serovars differ. Front. Microbiol. 5: 391. |
29 | Kim HB, Yoon M, Lee SJ, Jang YH, Choe NH. 2014. Prevalence and antibiotic resistance characteristics of Salmonella spp. isolated from food-producing animals and meat products in Korea. J. Preventive Vet. Med. 38: 85-93. DOI |
30 | Letellier A, Messier S, Quessy S. 1999. Prevalence of Salmonella spp. and Yersinia enterocolitica in finishing swine at Canadian abattoirs. J. Food Prot. 62: 22-25. DOI |
31 | De Busser EV, Maes D, Houf K, Dewulf J, Imberechts H, Bertrand S, De Zutter L. 2011. Detection and characterization of Salmonella in lairage, on pig carcasses and intestines in five slaughterhouses. Int. J. Food Microbiol. 145: 279-286. DOI |
32 | Meunier D, Boyd D, Mulvey MR, Baucheron S, Mammina C, Nastasi A, et al. 2002. Salmonella enterica serotype Typhimurium DT 104 antibiotic resistance genomic island I in serotype paratyphi B. Emerg. Infect. Dis. 8: 430-433. DOI |
33 | Berends BR, Van Knapen F, Snijders JM, Mossel DA. 1997. Identification and quantification of risk factors regarding Salmonella spp. on pork carcasses. Int. J. Food Microbiol. 36:199-206. DOI |
34 | Aarestrup FM. 2005. Veterinary drug usage and antimicrobial resistance in bacteria of animal origin. Basic Clin. Pharmacol. Toxicol. 96: 271-281. DOI |
35 | Zhao EY, Bao HX, Tang L, Zou QH, Liu WQ, Zhu DL, et al. 2013. Genomic comparison of Salmonella typhimurium DT104 with non-DT104 strains. Mol. Genet. Genomics 288: 549-557. DOI |
36 | De E, Basle A, Jaquinod M, Saint N, Mallea M, Molle G, et al. 2001. A new mechanism of antibiotic resistance in Enterobacteriaceae induced by a structural modification of the major porin. Mol. Microbiol. 41: 189-198. DOI |
37 | Hapfelmeier S, Stecher B, Barthel M, Kremer M, Muller AJ, Heikenwalder M, et al. 2005. The Salmonella pathogenicity island (SPI)-2 and SPI-1 type III secretion systems allow Salmonella serovar Typhimurium to trigger colitis via MyD88-dependent and MyD88-independent mechanisms. J. Immunol. 174: 1675-1685. DOI |
38 | Swords WE, Cannon BM, Benjamin WH Jr. 1997. Avirulence of LT2 strains of Salmonella typhimurium results from a defective rpoS gene. Infect. Immun. 65: 2451-2453. |
39 | Wilmes-Riesenberg MR, Foster JW, Curtiss R 3rd. 1997. An altered rpoS allele contributes to the avirulence of Salmonella typhimurium LT2. Infect. Immun. 65: 203-210. |
40 | Sievers F , Wilm A , Dineen D , Gibson T J, K arplus K , L i W, et al. 2011. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7: 539. |
41 | Petkau A, Stuart-Edwards M, Stothard P, Van Domselaar G. 2010. Interactive microbial genome visualization with GView. Bioinformatics 26: 3125-3126. DOI |
42 | Tanaka K, Nishimori K, Makino S, Nishimori T, Kanno T, Ishihara R, et al. 2004. Molecular characterization of a prophage of Salmonella enterica serotype Typhimurium DT104. J. Clin. Microbiol. 42: 1807-1812. DOI |
43 | Reiter WD, Palm P, Yeats S. 1989. Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res. 17: 1907-1914. DOI |
44 | Brussow H, Canchaya C, Hardt WD. 2004. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. 68: 560-602. DOI |
45 | Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30: 2068-2069. DOI |
46 | Ju MS, Kang ZW, Jung JH, Cho SB, Kim SH, Lee YJ, et al. 2011. Genotyping, phage typing, and antimicrobial resistance of Salmonella Typhimurium isolated from pigs, cattle, and humans. Korean J. Food Sci. Anim. Resour. 31: 47-53. DOI |
47 | Bruun T, Sorensen G, Forshell LP, Jensen T, Nygard K, Kapperud G, et al. 2009. An outbreak of Salmonella Typhimurium infections in Denmark, Norway and Sweden, 2008. Euro Surveill. 14: 19147. |
48 | Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10: 563-569. DOI |
49 | Lukashin AV, Borodovsky M. 1998. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 26: 1107-1115. DOI |
50 | Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410. DOI |
51 | Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35: 3100-3108. DOI |
52 | Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964. DOI |
53 | Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. 2009. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25: 119-120. DOI |
54 | Richter M, Rossello-Mora R, Oliver Glockner F, Peplies J. 2016. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32: 929-931. DOI |
55 | Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, et al. 2015. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31: 3691-3693. DOI |
56 | Duerr CU, Zenk SF, Chassin C, Pott J, Gutle D, Hensel M, et al. 2009. O-Antigen delays lipopolysaccharide recognition and impairs antibacterial host defense in murine intestinal epithelial cells. PLoS Pathog. 5: e1000567. DOI |
57 | Allison GE, Verma NK. 2000. Serotype-converting bacteriophages and O-antigen modification in Shigella flexneri. Trends Microbiol. 8: 17-23. DOI |
58 | Kim M, Ryu S. 2012. Spontaneous and transient defence against bacteriophage by phase-variable glucosylation of O-antigen in Salmonella enterica serovar Typhimurium. Mol. Microbiol. 86: 411-425. DOI |
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