Anderson ES, Ward LR, Saxe MJ, de Sa JD. Bacteriophage-typing designations of Salmonella Typhimurium. J Hyg. 1977;78(2):297–300.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rabsch W. Salmonella Typhimurium phage typing for pathogens. Methods Mol Biol. 2007;394:177–211.
Article
CAS
PubMed
Google Scholar
Hyman P, Abedon ST. Bacteriophage host range and bacterial resistance. Adv Appl Microbiol. 2010;70:217–48.
Article
CAS
PubMed
Google Scholar
Labrie SJ, Samson JE, Moineau S. Bacteriophage resistance mechanisms. Nat Rev Microbiol. 2010;8(5):317–27.
Article
CAS
PubMed
Google Scholar
Dupuis ME, Villion M, Magadan AH, Moineau S. CRISPR-Cas and restriction-modification systems are compatible and increase phage resistance. Nat Commun. 2013;4:2087.
Article
PubMed
Google Scholar
Noble DJ, Lane C, Little CL, Davies R, De Pinna E, Larkin L, Morgan D. Revival of an old problem: an increase in Salmonella
enterica serovar Typhimurium definitive phage type 8 infections in 2010 in England and Northern Ireland linked to duck eggs. Epidemiol Infect. 2012;140(1):146–9.
Article
CAS
PubMed
Google Scholar
Garvey P, McKeown P, Kelly P, Cormican M, Anderson W, Flack A, Barron S, De Lappe N, Buckley J, Cosgrove C, et al. Investigation and management of an outbreak of Salmonella Typhimurium DT8 associated with duck eggs, Ireland 2009–2011. Euro Surveill Bull Eur Sur Les maladies Transm Eur Commun Dis Bull. 2013;18(16):20454.
CAS
Google Scholar
Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178–92.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res. 2011;39(Web Server issue):W347–52.
Article
PubMed Central
CAS
PubMed
Google Scholar
Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007;35(Web Server issue):W52–7.
Article
PubMed Central
PubMed
Google Scholar
Carattoli A, Zankari E, Garcia-Fernandez A, Voldby Larsen M, Lund O, Villa L, Moller Aarestrup F, Hasman H. In silico detection and typing of plasmids using plasmid finder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58(7):3895–903.
Article
PubMed Central
PubMed
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.
Article
CAS
PubMed
Google Scholar
Shepard SM, Danzeisen JL, Isaacson RE, Seemann T, Achtman M, Johnson TJ. Genome sequences and phylogenetic analysis of K88- and F18-positive porcine enterotoxigenic Escherichia coli. J Bacteriol. 2012;194(2):395–405.
Article
PubMed Central
CAS
PubMed
Google Scholar
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42(Database issue):D222–30.
Article
PubMed Central
CAS
PubMed
Google Scholar
Baggesen DL, Sorensen G, Nielsen EM, Wegener HC. Phage typing of Salmonella Typhimurium—is it still a useful tool for surveillance and outbreak investigation? Euro Surveill Bull Eur Sur Les Mal Transm Eur Commun Dis Bull. 2010;15(4):19471.
CAS
Google Scholar
Roossinck MJ. The good viruses: viral mutualistic symbioses. Nat Rev Microbiol. 2011;9(2):99–108.
Article
CAS
PubMed
Google Scholar
Hiley L, Fang NX, Micalizzi GR, Bates J. Distribution of Gifsy-3 and of variants of ST64B and Gifsy-1 prophages amongst Salmonella enterica Serovar Typhimurium isolates: evidence that combinations of prophages promote clonality. PLoS One. 2014;9(1):e86203.
Article
PubMed Central
PubMed
Google Scholar
McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F, et al. Complete genome sequence of Salmonella
enterica serovar Typhimurium LT2. Nature. 2001;413(6858):852–6.
Article
CAS
PubMed
Google Scholar
Luo Y, Kong Q, Yang J, Mitra A, Golden G, Wanda SY, Roland KL, Jensen RV, Ernst PB, Curtiss R 3rd. Comparative genome analysis of the high pathogenicity Salmonella Typhimurium strain UK-1. PLoS One. 2012;7(7):e40645.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kroger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hebrard M, Handler K, et al. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci USA. 2012;109(20):E1277–86.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hanna LF, Matthews TD, Dinsdale EA, Hasty D, Edwards RA. Characterization of the ELPhiS prophage from Salmonella enterica serovar Enteritidis strain LK5. Appl Environ Microbiol. 2012;78(6):1785–93.
Article
PubMed Central
CAS
PubMed
Google Scholar
Barrangou R, Horvath P. CRISPR: new horizons in phage resistance and strain identification. Annu Rev Food Sci Technol. 2012;3:143–62.
Article
CAS
PubMed
Google Scholar
Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct. 2006;1:7.
Article
PubMed Central
PubMed
Google Scholar
Shariat N, Timme RE, Pettengill JB, Barrangou R, Dudley EG. Characterization and evolution of Salmonella CRISPR-Cas systems. Microbiology. 2015;161(Pt 2):374–86.
Article
CAS
PubMed
Google Scholar
Fabre L, Zhang J, Guigon G, Le Hello S, Guibert V, Accou-Demartin M, de Romans S, Lim C, Roux C, Passet V, et al. CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections. PLoS One. 2012;7(5):e36995.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pang S, Octavia S, Feng L, Liu B, Reeves PR, Lan R, Wang L. Genomic diversity and adaptation of Salmonella enterica serovar Typhimurium from analysis of six genomes of different phage types. BMC Genom. 2013;14:718.
Article
CAS
Google Scholar
Pang S, Octavia S, Reeves PR, Wang Q, Gilbert GL, Sintchenko V, Lan R. Genetic relationships of phage types and single nucleotide polymorphism typing of Salmonella
enterica Serovar Typhimurium. J Clin Microbiol. 2012;50(3):727–34.
Article
PubMed Central
CAS
PubMed
Google Scholar
Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev S, Dryden DT, Dybvig K, et al. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res. 2003;31(7):1805–12.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wilson GG, Murray NE. Restriction and modification systems. Annu Rev Genet. 1991;25:585–627.
Article
CAS
PubMed
Google Scholar
Fang G, Munera D, Friedman DI, Mandlik A, Chao MC, Banerjee O, Feng Z, Losic B, Mahajan MC, Jabado OJ, et al. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat Biotechnol. 2012;30(12):1232–9.
Article
CAS
PubMed
Google Scholar
Yamaichi Y, Chao MC, Sasabe J, Clark L, Davis BM, Yamamoto N, Mori H, Kurokawa K, Waldor MK. High-resolution genetic analysis of the requirements for horizontal transmission of the ESBL plasmid from Escherichia coli O104:H4. Nucleic Acids Res. 2015;43(1):348–60.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kruger DH, Bickle TA. Bacteriophage survival: multiple mechanisms for avoiding the deoxyribonucleic acid restriction systems of their hosts. Microbiol Rev. 1983;47(3):345–60.
PubMed Central
CAS
PubMed
Google Scholar
Warren RA. Modified bases in bacteriophage DNAs. Annu Rev Microbiol. 1980;34:137–58.
Article
CAS
PubMed
Google Scholar
Hattman S. DNA methyltransferase-dependent transcription of the phage Mu mom gene. Proc Natl Acad Sci USA. 1982;79(18):5518–21.
Article
PubMed Central
CAS
PubMed
Google Scholar
Frost JA, Ward LR, Rowe B. Acquisition of a drug resistance plasmid converts Salmonella enteritidis phage type 4 to phage type 24. Epidemiol Infect. 1989;103(2):243–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
Burrus V, Waldor MK. Shaping bacterial genomes with integrative and conjugative elements. Res Microbiol. 2004;155(5):376–86.
Article
CAS
PubMed
Google Scholar
Burrus V, Pavlovic G, Decaris B, Guedon G. Conjugative transposons: the tip of the iceberg. Mol Microbiol. 2002;46(3):601–10.
Article
CAS
PubMed
Google Scholar
Okoro CK, Kingsley RA, Connor TR, Harris SR, Parry CM, Al-Mashhadani MN, Kariuki S, Msefula CL, Gordon MA, de Pinna E, et al. Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat Genet. 2012;44(11):1215–21.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25(14):1754–60.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
Article
PubMed Central
PubMed
Google Scholar
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Posada D. jModelTest: phylogenetic model averaging. Mol Biol Evol. 2008;25(7):1253–6.
Article
CAS
PubMed
Google Scholar
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18(5):821–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. The RAST server: rapid annotations using subsystems technology. BMC Genom. 2008;9:75.
Article
Google Scholar
Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE—a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res. 2010;38(Database issue):D234–6.
Article
PubMed Central
CAS
PubMed
Google Scholar