Sabat AJ, Budimir A, Nashev D, Sa-Leao R, van Dijl J, Laurent F, Grundmann H, Friedrich AW, Markers ESGoE: Overview of molecular typing methods for outbreak detection and epidemiological surveillance.Euro Surveill 2013, 18:20380.
Google Scholar
Bertelli C, Greub G: Rapid bacterial genome sequencing: methods and applications in clinical microbiology. Clin Microbiol Infect. 2013, 19: 803-813.
Article
CAS
PubMed
Google Scholar
Maiden MC: Multilocus sequence typing of bacteria. Annu Rev Microbiol. 2006, 60: 561-588.
Article
CAS
PubMed
Google Scholar
Gilmour MW, Graham M, Reimer A, Van Domselaar G: Public health genomics and the new molecular epidemiology of bacterial pathogens. Public Health Genomics. 2013, 16: 25-30.
Article
CAS
PubMed
Google Scholar
Pallen MJ, Loman NJ, Penn CW: High-throughput sequencing and clinical microbiology: progress, opportunities and challenges. Curr Opin Microbiol. 2010, 13: 625-631.
Article
CAS
PubMed
Google Scholar
Joseph SJ, Read TD: Bacterial population genomics and infectious disease diagnostics. Trends Biotechnol. 2010, 28: 611-618.
Article
CAS
PubMed
Google Scholar
Didelot X, Bowden R, Wilson DJ, Peto TE, Crook DW: Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet. 2012, 13: 601-612.
Article
CAS
PubMed
Google Scholar
Didelot X, Eyre DW, Cule M, Ip CL, Ansari MA, Griffiths D, Vaughan A, O °Connor L, Golubchik T, Batty EM, Piazza P, Wilson DJ, Bowden R, Donnelly PJ, Dingle KE, Wilcox M, Walker AS, Crook DW, A Peto TE, Harding RM: Microevolutionary analysis of Clostridium difficile genomes to investigate transmission.Genome Biol 2012, 13:R118.
Google Scholar
Price JR, Didelot X, Crook DW, Llewelyn MJ, Paul J: Whole genome sequencing in the prevention and control of Staphylococcus aureus infection. J Hosp Infect. 2013, 83: 14-21.
Article
CAS
PubMed
Google Scholar
Koser CU, Ellington MJ, Cartwright EJ, Gillespie SH, Brown NM, Farrington M, Holden MT, Dougan G, Bentley SD, Parkhill J, Peacock SJ: Routine use of microbial whole genome sequencing in diagnostic and public health microbiology.PLoS Pathog 2012, 8:e1002824.
Google Scholar
Rohde H, Qin J, Cui Y, Li D, Loman NJ, Hentschke M, Chen W, Pu F, Peng Y, Li J, Xi F, Li S, Li Y, Zhang Z, Yang X, Zhao M, Wang P, Guan Y, Cen Z, Zhao X, Christner M, Kobbe R, Loos S, Oh J, Yang L, Danchin A, Gao GF, Song Y, Li Y, Yang H: Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. New Engl J Med. 2011, 365: 718-724.
Article
CAS
PubMed
Google Scholar
Eyre DW, Golubchik T, Gordon NC, Bowden R, Piazza P, Batty EM, Ip CL, Wilson DJ, Didelot X, O °Connor L, Lay R, Buck D, Kearns AM, Shaw A, Paul J, Wilcox MH, Donnelly PJ, Peto TE, Walker AS, Crook DW: A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance.BMJ Open 2012, 2:e001124.
Google Scholar
Torok ME, Peacock SJ: Rapid whole-genome sequencing of bacterial pathogens in the clinical microbiology laboratory pipe dream or reality?. J Antimicrob Chemother. 2012, 67: 2307-2308.
Article
CAS
PubMed
Google Scholar
Harris SR, Cartwright EJ, Torok ME, Holden MT, Brown NM, Ogilvy-Stuart AL, Ellington MJ, Quail MA, Bentley SD, Parkhill J, Peacock SJ: Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis. 2013, 13: 130-136.
Article
CAS
PubMed
PubMed Central
Google Scholar
Reuter S, Ellington MJ, Cartwright EJ, Koser CU, Torok ME, Gouliouris T, Harris SR, Brown NM, Holden MT, Quail M, Parkhill J, Smith GP, Bentley SD, Peacock SJ: Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology. JAMA Intern Med. 2013, 173: 1397-1404.
Article
PubMed
PubMed Central
Google Scholar
Sherry NL, Porter JL, Seemann T, Watkins A, Stinear TP, Howden BP: Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory. J Clin Microbiol. 2013, 51: 1396-1401.
Article
PubMed
PubMed Central
Google Scholar
D'Auria G, Schneider MV, Moya A: Live Genomics for Pathogen Monitoring in Public Health. Pathogens. 2014, 3: 93-108. 10.3390/pathogens3010093.
Article
PubMed
PubMed Central
Google Scholar
Gupta SK, Padmanabhan BR, Diene SM, Lopez-Rojas R, Kempf M, Landraud L, Rolain JM: ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother. 2014, 58: 212-220.
Article
PubMed
PubMed Central
Google Scholar
Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV: Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012, 67: 2640-2644.
Article
CAS
PubMed
PubMed Central
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 PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014, 58: 3895-3903.
Article
PubMed
PubMed Central
Google Scholar
Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Ponten TS, Ussery DW, Aarestrup FM, Lund O: Multilocus sequence typing of total genome sequenced bacteria. J Clin Microbiol. 2012, 50: 1355-1361.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jolley KA, Maiden MC: Automated extraction of typing information for bacterial pathogens from whole genome sequence data: Neisseria meningitidis as an exemplar.Euro Surveill 2013, 18:20379.
Google Scholar
Cody AJ, McCarthy ND, Jansen van Rensburg M, Isinkaye T, Bentley SD, Parkhill J, Dingle KE, Bowler IC, Jolley KA, Maiden MC: Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing. J Clin Microbiol. 2013, 51: 2526-2534.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zerbino DR, Birney E: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008, 18: 821-829.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA: SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012, 19: 455-477.
Article
CAS
PubMed
PubMed Central
Google Scholar
Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM: Automated ensemble assembly and validation of microbial genomes.BMC Bioinformatics 2014, 15:126.
Google Scholar
Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marcais G, Pop M, Yorke JA: GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res. 2012, 22: 557-567.
Article
CAS
PubMed
PubMed Central
Google Scholar
Inouye M, Conway TC, Zobel J, Holt KE: Short read sequence typing (SRST): multi-locus sequence types from short reads.BMC Genomics 2012, 13:338.
Google Scholar
Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012, 9: 357-359.
Article
CAS
PubMed
PubMed Central
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: 2078-2079.
Article
PubMed
PubMed Central
Google Scholar
Loman NJ, Constantinidou C, Chan JZ, Halachev M, Sergeant M, Penn CW, Robinson ER, Pallen MJ: High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol. 2012, 10: 599-606.
Article
CAS
PubMed
Google Scholar
Meacham F, Boffelli D, Dhahbi J, Martin DI, Singer M, Pachter L: Identification and correction of systematic error in high-throughput sequence data.BMC Bioinformatics 2011, 12:451.
Google Scholar
Ragon M, Wirth T, Hollandt F, Lavenir R, Lecuit M, Le Monnier A, Brisse S: A new perspective on Listeria monocytogenes evolution.PLoS Pathog 2008, 4:e1000146.
Google Scholar
Listeria monocytogenes MLST Database. http://www.pasteur.fr/recherche/genopole/PF8/mlst/Lmono.html
SRST2 - Short Read Sequence Typing for Bacterial Pathogens. http://katholt.github.io/srst2/
Holden MT, Hsu LY, Kurt K, Weinert LA, Mather AE, Harris SR, Strommenger B, Layer F, Witte W, de Lencastre H, Skov R, Westh H, Zemlickova H, Coombs G, Kearns AM, Hill RL, Edgeworth J, Gould I, Gant V, Cooke J, Edwards GF, McAdam PR, Templeton KE, McCann A, Zhou Z, Castillo-Ramirez S, Feil EJ, Hudson LO, Enright MC, Balloux F: A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic. Genome Res. 2013, 23: 653-664.
Article
CAS
PubMed
PubMed Central
Google Scholar
Castillo-Ramirez S, Corander J, Marttinen P, Aldeljawi M, Hanage WP, Westh H, Boye K, Gulay Z, Bentley SD, Parkhill J, Holden MT, Feil EJ: Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus.Genome Biol 2012, 13:R126.
Google Scholar
Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, van der Linden M, McGee L, von Gottberg A, Song JH, Ko KS, Pichon B, Baker S, Parry CM, Lambertsen LM, Shahinas D, Pillai DR, Mitchell TJ, Dougan G, Tomasz A, Klugman KP, Parkhill J, Hanage WP, Bentley SD: Rapid pneumococcal evolution in response to clinical interventions. Science. 2011, 331: 430-434.
Article
CAS
PubMed
PubMed Central
Google Scholar
Okoro CK, Kingsley RA, Connor TR, Harris SR, Parry CM, Al-Mashhadani MN, Kariuki S, Msefula CL, Gordon MA, de Pinna E, Wain J, Heyderman RS, Obaro S, Alonso PL, Mandomando I, MacLennan CA, Tapia MD, Levine MM, Tennant SM, Parkhill J, Dougan G: Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat Genet. 2012, 44: 1215-1221.
Article
CAS
PubMed
PubMed Central
Google Scholar
Holt KE, Baker S, Weill FX, Holmes EC, Kitchen A, Yu J, Sangal V, Brown DJ, Coia JE, Kim DW, Choi SY, Kim SH, da Silveira WD, Pickard DJ, Farrar JJ, Parkhill J, Dougan G, Thomson NR: Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat Genet. 2012, 44: 1056-1059.
Article
CAS
PubMed
PubMed Central
Google Scholar
Howden BP, Holt KE, Lam MM, Seemann T, Ballard S, Coombs GW, Tong SY, Grayson ML, Johnson PD, Stinear TP: Genomic insights to control the emergence of vancomycin-resistant enterococci. MBio. 2013, 4: e00412-e00413.
Article
PubMed
PubMed Central
Google Scholar
Stoesser N, Batty EM, Eyre DW, Morgan M, Wyllie DH, Del Ojo EC, Johnson JR, Walker AS, Peto TE, Crook DW: Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J Antimicrob Chemother. 2013, 68: 2234-2244.
CAS
PubMed
PubMed Central
Google Scholar
ARG-ANNOT - Antibiotic Resistance Gene-ANNOTation. http://www.mediterranee-infection.com/article.php?laref=282&titer=arg-annot
Li W, Godzik A: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006, 22: 1658-1659.
Article
CAS
PubMed
Google Scholar
Carattoli A, Bertini A, Villa L, Falbo V, Hopkins KL, Threlfall EJ: Identification of plasmids by PCR-based replicon typing. J Microbiol Methods. 2005, 63: 219-228.
Article
CAS
PubMed
Google Scholar
Arenas M, Posada D: Coalescent simulation of intracodon recombination. Genetics. 2010, 184: 429-437.
Article
CAS
PubMed
PubMed Central
Google Scholar
Feil EJ, Cooper JE, Grundmann H, Robinson DA, Enright MC, Berendt T, Peacock SJ, Smith JM, Murphy M, Spratt BG, Moore CE, Day NP: How clonal is Staphylococcus aureus?. J Bacteriol. 2003, 185: 3307-3316.
Article
CAS
PubMed
PubMed Central
Google Scholar
VelvetOptimiser. [], http://bioinformatics.net.au/software.velvetoptimiser.shtml
Victorian Life Sciences Computation Initiative. http://www.vlsci.org.au/
Stinear TP, Olden DC, Johnson PD, Davies JK, Grayson ML: Enterococcal vanB resistance locus in anaerobic bacteria in human faeces. Lancet. 2001, 357: 855-856.
Article
CAS
PubMed
Google Scholar
Athey TB, Teatero S, Li A, Marchand-Austin A, Beall BW, Fittipaldi N: Deriving group A Streptococcus typing information from short-read whole genome sequencing data. J Clin Microbiol. 2014, 52: 1871-1876.
Article
CAS
PubMed
PubMed Central
Google Scholar
Johnson PD, Ballard SA, Grabsch EA, Stinear TP, Seemann T, Young HL, Grayson ML, Howden BP: A sustained hospital outbreak of vancomycin-resistant Enterococcus faecium bacteremia due to emergence of vanB E. faecium sequence type 203. J Infect Dis. 2010, 202: 1278-1286.
Article
PubMed
Google Scholar