{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T20:51:07Z","timestamp":1781643067492,"version":"3.54.5"},"reference-count":136,"publisher":"Elsevier BV","issue":"1-2","license":[{"start":{"date-parts":[[2011,11,1]],"date-time":"2011-11-01T00:00:00Z","timestamp":1320105600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2011,11,1]],"date-time":"2011-11-01T00:00:00Z","timestamp":1320105600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2011,11,1]],"date-time":"2011-11-01T00:00:00Z","timestamp":1320105600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2011,11,1]],"date-time":"2011-11-01T00:00:00Z","timestamp":1320105600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2011,11,1]],"date-time":"2011-11-01T00:00:00Z","timestamp":1320105600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2011,11,1]],"date-time":"2011-11-01T00:00:00Z","timestamp":1320105600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2011,11,1]],"date-time":"2011-11-01T00:00:00Z","timestamp":1320105600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Veterinary Microbiology"],"published-print":{"date-parts":[[2011,11]]},"DOI":"10.1016\/j.vetmic.2011.06.014","type":"journal-article","created":{"date-parts":[[2011,6,29]],"date-time":"2011-06-29T01:53:38Z","timestamp":1309312418000},"page":"13-26","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":12,"title":["Everything at once: Comparative analysis of the genomes of bacterial pathogens"],"prefix":"10.1016","volume":"153","author":[{"given":"Chad R.","family":"Laing","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongxiang","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James E.","family":"Thomas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor P.J.","family":"Gannon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.vetmic.2011.06.014_bib0005","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/1471-2180-10-79","article-title":"Analysis of the genome content of Lactococcus garvieae by genomic interspecies microarray hybridization","volume":"10","author":"Aguado-Urda","year":"2010","journal-title":"BMC Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0010","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1038\/16495","article-title":"Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori","volume":"397","author":"Alm","year":"1999","journal-title":"Nature"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0015","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"issue":"3","key":"10.1016\/j.vetmic.2011.06.014_bib0020","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1093\/bioinformatics\/btq665","article-title":"Mugsy: fast multiple alignment of closely related whole genomes","volume":"27","author":"Angiuoli","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0025","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1186\/1471-2164-11-688","article-title":"Comparative genomics of the bacterial genus Listeria: genome evolution is characterized by limited gene acquisition and limited gene loss","volume":"11","author":"den Bakker","year":"2010","journal-title":"BMC Genomics"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0030","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1093\/ajcp\/45.4_ts.493","article-title":"Antibiotic susceptibility testing by a standardized single disk method","volume":"45","author":"Bauer","year":"1966","journal-title":"Am. J. Clin. Pathol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0035","doi-asserted-by":"crossref","first-page":"1653","DOI":"10.1128\/JCM.36.6.1653-1659.1998","article-title":"Assessment of resolution and intercenter reproducibility of results of genotyping Staphylococcus aureus by pulsed-field gel electrophoresis of SmaI macrorestriction fragments: a multicenter study","volume":"36","author":"van Belkum","year":"1998","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0040","doi-asserted-by":"crossref","first-page":"4371","DOI":"10.1073\/pnas.0911295107","article-title":"Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics","volume":"107","author":"Beres","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0045","doi-asserted-by":"crossref","first-page":"10078","DOI":"10.1073\/pnas.152298499","article-title":"Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence","volume":"99","author":"Beres","year":"2002","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0050","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1139\/m82-149","article-title":"Involvement of plasmids in determining bacteriophage sensitivity in Salmonella typhimurium: genetic and physical analysis of phagovar 204","volume":"28","author":"Bezanson","year":"1982","journal-title":"Can. J. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0055","doi-asserted-by":"crossref","first-page":"2180","DOI":"10.1128\/aem.58.7.2180-2187.1992","article-title":"Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria","volume":"58","author":"de Bruijn","year":"1992","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0060","series-title":"DNA Markers: Protocols, Applications and Overviews","author":"Caetano-Anoll\u00e9s","year":"1997"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0065","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0070","doi-asserted-by":"crossref","first-page":"3957","DOI":"10.1128\/JCM.01548-08","article-title":"Multilocus sequence typing analysis of Clostridium perfringens isolates from necrotic enteritis outbreaks in broiler chicken populations","volume":"46","author":"Chalmers","year":"2008","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0075","doi-asserted-by":"crossref","first-page":"e1000459","DOI":"10.1371\/journal.ppat.1000459","article-title":"Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence Subspecies","volume":"5","author":"Champion","year":"2009","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0080","doi-asserted-by":"crossref","first-page":"2643","DOI":"10.1099\/00221287-147-10-2643","article-title":"FindTarget: software for subtractive genome analysis","volume":"147","author":"Chetouani","year":"2001","journal-title":"Microbiology"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0085","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1056\/NEJMoa1012928","article-title":"The origin of the Haitian cholera outbreak strain","volume":"364","author":"Chin","year":"2011","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0090","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1007\/978-1-60327-565-1_17","article-title":"Phage typing","volume":"502","author":"Chirakadze","year":"2009","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0095","doi-asserted-by":"crossref","first-page":"e1159","DOI":"10.1371\/journal.pone.0001159","article-title":"Incidence and tracking of Escherichia coli O157:H7 in a major produce production region in California","volume":"2","author":"Cooley","year":"2007","journal-title":"PLoS ONE"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0100","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1128\/AEM.02215-09","article-title":"Comparison of PCR binary typing (P-BIT), a new approach to epidemiological subtyping of Campylobacter jejuni, with serotyping, pulsed-field gel electrophoresis, and multilocus sequence typing methods","volume":"76","author":"Cornelius","year":"2010","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0105","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1126\/science.1198545","article-title":"Rapid pneumococcal evolution in response to clinical interventions","volume":"331","author":"Croucher","year":"2011","journal-title":"Science"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0110","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1093\/genetics\/165.4.1641","article-title":"Amelioration of the cost of conjugative plasmid carriage in Eschericha coli K12","volume":"165","author":"Dahlberg","year":"2003","journal-title":"Genetics"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0115","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: multiple alignment of conserved genomic sequence with rearrangements","volume":"14","author":"Darling","year":"2004","journal-title":"Genome Res."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0120","doi-asserted-by":"crossref","first-page":"e11147","DOI":"10.1371\/journal.pone.0011147","article-title":"progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement","volume":"5","author":"Darling","year":"2010","journal-title":"PLoS ONE"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0125","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1186\/1471-2164-11-500","article-title":"Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification","volume":"11","author":"Deng","year":"2010","journal-title":"BMC Genomics"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0130","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.jbiotec.2008.03.021","article-title":"The Genome Sequencer FLX System\u2014longer reads, more applications, straight forward bioinformatics and more complete data sets","volume":"136","author":"Droege","year":"2008","journal-title":"J. Biotechnol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0135","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.vetmic.2007.10.018","article-title":"Diagnostic and typing options for investigating diseases associated with Pasteurella multocida","volume":"128","author":"Dziva","year":"2008","journal-title":"Vet. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0140","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-5-113","article-title":"MUSCLE: a multiple sequence alignment method with reduced time and space complexity","volume":"5","author":"Edgar","year":"2004","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0145","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0150","doi-asserted-by":"crossref","first-page":"1685","DOI":"10.1128\/JB.01518-09","article-title":"Genome sequence of the deep-rooted Yersinia pestis strain angola reveals new insights into the evolution and pangenome of the plague bacterium","volume":"192","author":"Eppinger","year":"2010","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0155","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1111\/j.1365-294X.1993.tb00014.x","article-title":"Use of random amplified polymorphic DNA (RAPD) for generating specific DNA probes for microorganisms","volume":"2","author":"Fani","year":"1993","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0160","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1093\/genetics\/154.4.1439","article-title":"Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data","volume":"154","author":"Feil","year":"2000","journal-title":"Genetics"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0165","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1186\/1471-2164-10-166","article-title":"Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction","volume":"10","author":"Fournier","year":"2009","journal-title":"BMC Genomics"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0170","unstructured":"Fratamico, P.M., Bhunia, A.K., Smith, J.L., 2005 Foodborne pathogens: microbiology and molecular biology. Caister Academic Press, Wymondham. ISBN: 190445500X, in press."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0175","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1186\/1471-2105-10-176","article-title":"PolyMin\u201d: software for identification of the minimum number of polymorphisms required for haplotype and genotype differentiation","volume":"10","author":"Frei","year":"2009","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0180","doi-asserted-by":"crossref","first-page":"6779","DOI":"10.1128\/JB.00661-08","article-title":"Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5","volume":"190","author":"Fricke","year":"2008","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0185","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1056\/NEJMoa1003176","article-title":"Whole-genome sequencing and social-network analysis of a tuberculosis outbreak","volume":"364","author":"Gardy","year":"2011","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0190","doi-asserted-by":"crossref","first-page":"2977","DOI":"10.1128\/jcm.35.11.2977-2980.1997","article-title":"Rapid pulsed-field gel electrophoresis protocol for typing of Escherichia coli O157:H7 and other gram-negative organisms in 1 day","volume":"35","author":"Gautom","year":"1997","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0195","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1186\/1471-2164-11-120","article-title":"High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak","volume":"11","author":"Gilmour","year":"2010","journal-title":"BMC Genomics"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0200","doi-asserted-by":"crossref","DOI":"10.1111\/j.1755-0998.2011.03024.x","article-title":"Field guide to next-generation DNA sequencers","author":"Glenn","year":"2011","journal-title":"Mol. Ecol. Resour."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0205","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/S0732-8893(98)00103-5","article-title":"Comparative study of five different techniques for epidemiological typing of Escherichia coli O157","volume":"32","author":"Grif","year":"1998","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0210","first-page":"500","article-title":"Method of colicin typing of Enterobacteriaceae","author":"Grishchenko","year":"1976","journal-title":"Lab. Delo"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0215","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1017\/S0022172400065001","article-title":"Conversion by corynephages and its role in the natural history of diphtheria","volume":"93","author":"Groman","year":"1984","journal-title":"J. Hyg."},{"issue":"1","key":"10.1016\/j.vetmic.2011.06.014_bib0220","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1099\/13500872-142-1-3","article-title":"New approaches to typing and identification of bacteria using the 16S\u201323S rDNA spacer region","volume":"142","author":"G\u00fcrtler","year":"1996","journal-title":"Microbiology"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0225","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1093\/genetics\/162.4.1533","article-title":"Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains","volume":"162","author":"Gutacker","year":"2002","journal-title":"Genetics"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0230","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1089\/fpd.2009.0394","article-title":"Re-evaluation, optimization, and multilaboratory validation of the PulseNet-standardized pulsed-field gel electrophoresis protocol for Listeria monocytogenes","volume":"7","author":"Halpin","year":"2010","journal-title":"Foodborne Pathog. Dis."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0235","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1128\/JCM.01432-08","article-title":"Genomics-based molecular epidemiology of Campylobacter jejuni isolates from feedlot cattle and from people in Alberta, Canada","volume":"47","author":"Hannon","year":"2009","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0240","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1126\/science.1182395","article-title":"Evolution of MRSA during hospital transmission and intercontinental spread","volume":"327","author":"Harris","year":"2010","journal-title":"Science"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0245","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1093\/dnares\/8.1.11","article-title":"Complete genome sequence of enterohemorrhagic Eschelichia coli O157:H7 and genomic comparison with a laboratory strain K-12","volume":"8","author":"Hayashi","year":"2001","journal-title":"DNA Res."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0250","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1017\/S0950268800004908","article-title":"Genomic fingerprinting of shigatoxin-producing Escherichia coli (STEC) strains: comparison of pulsed-field gel electrophoresis (PFGE) and fluorescent amplified-fragment-length polymorphism (FAFLP)","volume":"125","author":"Heir","year":"2000","journal-title":"Epidemiol. Infect."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0255","doi-asserted-by":"crossref","first-page":"3600","DOI":"10.1128\/JCM.01039-10","article-title":"Comparison of two multilocus variable-number tandem-repeat methods and pulsed-field gel electrophoresis for differentiating highly clonal methicillin-resistant Staphylococcus aureus isolates","volume":"48","author":"Holmes","year":"2010","journal-title":"J. Clin. Microbiol."},{"issue":"8","key":"10.1016\/j.vetmic.2011.06.014_bib0260","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1038\/ng.195","article-title":"High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi","volume":"40","author":"Holt","year":"2008","journal-title":"Nat. Genet."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0265","doi-asserted-by":"crossref","first-page":"R45","DOI":"10.1186\/gb-2009-10-4-r45","article-title":"Microbial co-habitation and lateral gene transfer: what transposases can tell us","volume":"10","author":"Hooper","year":"2009","journal-title":"Genome Biol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0270","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1089\/fpd.2006.3.118","article-title":"Second generation subtyping: a proposed PulseNet protocol for multiple-locus variable-number tandem repeat analysis of Shiga toxin-producing Escherichia coli O157 (STEC O157)","volume":"3","author":"Hyyti\u00e4-Trees","year":"2006","journal-title":"Foodborne Pathog. Dis."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0275","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1006\/viro.1999.9888","article-title":"Characterization of wild lambdoid bacteriophages: detection of a wide distribution of phage immunity groups and identification of a Nus-dependent, nonlambdoid phage group","volume":"263","author":"Kameyama","year":"1999","journal-title":"Virology"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0280","doi-asserted-by":"crossref","first-page":"2928","DOI":"10.1128\/JB.182.10.2928-2936.2000","article-title":"Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis","volume":"182","author":"Keim","year":"2000","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0285","doi-asserted-by":"crossref","first-page":"5033","DOI":"10.1073\/pnas.1018444108","article-title":"Helicobacter pylori genome evolution during human infection","volume":"108","author":"Kennemann","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0290","first-page":"656","article-title":"BLAT\u2014the BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0295","doi-asserted-by":"crossref","first-page":"7286","DOI":"10.1128\/AEM.01398-06","article-title":"Toward a more robust assessment of intraspecies diversity, using fewer genetic markers","volume":"72","author":"Konstantinidis","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0300","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1186\/1471-2105-11-142","article-title":"MISHIMA\u2014a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data","volume":"11","author":"Kryukov","year":"2010","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0305","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1128\/MMBR.00027-10","article-title":"The accessory genome of Pseudomonas aeruginosa","volume":"74","author":"Kung","year":"2010","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0310","doi-asserted-by":"crossref","first-page":"2821","DOI":"10.1128\/JCM.00137-10","article-title":"Genome-wide single nucleotide polymorphism typing method for identification of Bacillus anthracis species and strains among B. cereus group species","volume":"48","author":"Kuroda","year":"2010","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0315","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0320","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1186\/1471-2105-11-461","article-title":"Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions","volume":"11","author":"Laing","year":"2010","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0325","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1186\/1471-2164-10-287","article-title":"In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence","volume":"10","author":"Laing","year":"2009","journal-title":"BMC Genomics"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0330","doi-asserted-by":"crossref","first-page":"6606","DOI":"10.1128\/AEM.00985-08","article-title":"Rapid determination of Escherichia coli O157:H7 lineage types and molecular subtypes by using comparative genomic fingerprinting","volume":"74","author":"Laing","year":"2008","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0335","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1186\/1471-2105-9-329","article-title":"Evaluation of genomic island predictors using a comparative genomics approach","volume":"9","author":"Langille","year":"2008","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0340","first-page":"1","article-title":"Pathogenicity islands and the evolution of bacterial pathogens","volume":"5","author":"Lee","year":"1996","journal-title":"Infect. Agents Dis."},{"issue":"21","key":"10.1016\/j.vetmic.2011.06.014_bib0345","doi-asserted-by":"crossref","first-page":"8713","DOI":"10.1073\/pnas.0812949106","article-title":"A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis","volume":"106","author":"Leopold","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"issue":"8","key":"10.1016\/j.vetmic.2011.06.014_bib0350","doi-asserted-by":"crossref","first-page":"1282","DOI":"10.1016\/j.meegid.2010.07.021","article-title":"Further evidence of constrained radiation in the evolution of pathogenic Escherichia coli O157:H7","volume":"10","author":"Leopold","year":"2010","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0355","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.jhin.2010.01.012","article-title":"High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak","volume":"75","author":"Lewis","year":"2010","journal-title":"J. Hosp. Infect."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0360","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows\u2013Wheeler transform","volume":"26","author":"Li","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0365","doi-asserted-by":"crossref","first-page":"1623","DOI":"10.1128\/JCM.38.4.1623-1627.2000","article-title":"Fluorescent amplified-fragment length polymorphism genotyping of Salmonella enterica subsp. enterica serovars and comparison with pulsed-field gel electrophoresis typing","volume":"38","author":"Lindstedt","year":"2000","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0370","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.mimet.2007.11.012","article-title":"Multiple-locus variable-number tandem-repeats analysis of Listeria monocytogenes using multicolour capillary electrophoresis and comparison with pulsed-field gel electrophoresis typing","volume":"72","author":"Lindstedt","year":"2008","journal-title":"J. Microbiol. Methods"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0375","doi-asserted-by":"crossref","first-page":"3795","DOI":"10.1093\/nar\/gkg573","article-title":"WU-Blast2 server at the European Bioinformatics Institute","volume":"31","author":"Lopez","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0380","doi-asserted-by":"crossref","first-page":"e19054","DOI":"10.1371\/journal.pone.0019054","article-title":"Genome sequencing and analysis of Yersina pestis KIM D27, an avirulent strain exempt from select agent regulation","volume":"6","author":"Losada","year":"2011","journal-title":"PLoS ONE"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0385","doi-asserted-by":"crossref","first-page":"2286","DOI":"10.1128\/aem.60.7.2286-2295.1994","article-title":"Specific genomic fingerprints of phytopathogenic Xanthomonas and Pseudomonas pathovars and strains generated with repetitive sequences and PCR","volume":"60","author":"Louws","year":"1994","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0390","doi-asserted-by":"crossref","first-page":"19545","DOI":"10.1073\/pnas.0909285106","article-title":"Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus","volume":"106","author":"Lowder","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0395","doi-asserted-by":"crossref","first-page":"4868","DOI":"10.1073\/pnas.0710834105","article-title":"Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks","volume":"105","author":"Manning","year":"2008","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0400","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1073\/pnas.74.2.560","article-title":"A new method for sequencing DNA","volume":"74","author":"Maxam","year":"1977","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0405","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/35101614","article-title":"Complete genome sequence of Salmonella enterica serovar Typhimurium LT2","volume":"413","author":"McClelland","year":"2001","journal-title":"Nature"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0410","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1016\/j.gde.2005.09.006","article-title":"The microbial pan-genome","volume":"15","author":"Medini","year":"2005","journal-title":"Curr. Opin. Genet. Dev."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0415","doi-asserted-by":"crossref","first-page":"9452","DOI":"10.1073\/pnas.96.17.9452","article-title":"Bacteriophages in the evolution of pathogen\u2013host interactions","volume":"96","author":"Miao","year":"1999","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0420","first-page":"45","article-title":"The bacterial pan-genome: a new paradigm in microbiology","volume":"13","author":"Mira","year":"2010","journal-title":"Int. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0425","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1126\/science.1166083","article-title":"The peopling of the Pacific from a bacterial perspective","volume":"323","author":"Moodley","year":"2009","journal-title":"Science"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0430","doi-asserted-by":"crossref","first-page":"1140","DOI":"10.1038\/ng.705","article-title":"Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity","volume":"42","author":"Morelli","year":"2010","journal-title":"Nat. Genet."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0435","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1016\/j.mimet.2009.10.005","article-title":"Comparison of the Biolog OmniLog Identification System and 16S ribosomal RNA gene sequencing for accuracy in identification of atypical bacteria of clinical origin","volume":"79","author":"Morgan","year":"2009","journal-title":"J. Microbiol. Methods"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0440","doi-asserted-by":"crossref","first-page":"1574","DOI":"10.1128\/JCM.41.4.1574-1585.2003","volume":"41","author":"Murchan","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0445","doi-asserted-by":"crossref","first-page":"1616","DOI":"10.1126\/science.3029872","article-title":"Variable number of tandem repeat (VNTR) markers for human gene mapping","volume":"235","author":"Nakamura","year":"1987","journal-title":"Science"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0450","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1186\/1471-2164-11-667","article-title":"Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes","volume":"11","author":"Nash","year":"2010","journal-title":"BMC Genomics"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0455","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1128\/JCM.41.2.675-679.2003","article-title":"Multilocus sequence typing reveals a lack of diversity among Escherichia coli O157:H7 isolates that are distinct by pulsed-field gel electrophoresis","volume":"41","author":"Noller","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0460","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1006\/jmbi.2000.4042","article-title":"T-Coffee: a novel method for fast and accurate multiple sequence alignment","volume":"302","author":"Notredame","year":"2000","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0465","doi-asserted-by":"crossref","first-page":"R138","DOI":"10.1186\/gb-2007-8-7-r138","article-title":"Extensive genomic diversity and selective conservation of virulence-determinants in enterohemorrhagic Escherichia coli strains of O157 and non-O157 serotypes","volume":"8","author":"Ogura","year":"2007","journal-title":"Genome Biol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0470","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1073\/pnas.0911811107","article-title":"Decreased necrotizing fasciitis capacity caused by a single nucleotide mutation that alters a multiple gene virulence axis","volume":"107","author":"Olsen","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0475","doi-asserted-by":"crossref","first-page":"2776","DOI":"10.1093\/bioinformatics\/btn512","article-title":"Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications","volume":"24","author":"Ondov","year":"2008","journal-title":"Bioinformatics"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0480","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1128\/MMBR.00033-09","article-title":"Mapping the tree of life: progress and prospects","volume":"73","author":"Pace","year":"2009","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0485","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1186\/1471-2180-9-213","article-title":"Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay","volume":"9","author":"Pandya","year":"2009","journal-title":"BMC Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0490","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/0076-6879(90)83007-V","article-title":"Rapid and sensitive sequence comparison with FASTP and FASTA","volume":"183","author":"Pearson","year":"1990","journal-title":"Methods Enzymol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0495","doi-asserted-by":"crossref","first-page":"58","DOI":"10.7883\/yoken.JJID.2008.58","article-title":"Molecular characterization of enterohemorrhagic Escherichia coli O157:H7 isolates dispersed across Japan by pulsed-field gel electrophoresis and multiple-locus variable-number tandem repeat analysis","volume":"61","author":"Pei","year":"2008","journal-title":"Jpn. J. Infect. Dis."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0500","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/35054089","article-title":"Genome sequence of enterohaemorrhagic Escherichia coli O157:H7","volume":"409","author":"Perna","year":"2001","journal-title":"Nature"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0505","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1186\/1471-2105-8-278","article-title":"Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants","volume":"8","author":"Price","year":"2007","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0510","doi-asserted-by":"crossref","first-page":"7793","DOI":"10.1128\/AEM.01338-06","article-title":"Fingerprinting of Campylobacter jejuni by using resolution-optimized binary gene targets derived from comparative genome hybridization studies","volume":"72","author":"Price","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0515","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1038\/nmeth.1270","article-title":"A large genome center's improvements to the Illumina sequencing system","volume":"5","author":"Quail","year":"2008","journal-title":"Nat. Methods"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0520","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1099\/00207713-50-2-665","article-title":"Comparison of AFLP and rep-PCR genomic fingerprinting with DNA--DNA homology studies: Xanthomonas as a model system","volume":"50","author":"Rademaker","year":"2000","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0525","doi-asserted-by":"crossref","first-page":"i187","DOI":"10.1093\/bioinformatics\/btn281","article-title":"Segment-based multiple sequence alignment","volume":"24","author":"Rausch","year":"2008","journal-title":"Bioinformatics"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0530","doi-asserted-by":"crossref","first-page":"1397","DOI":"10.1093\/nar\/28.6.1397","article-title":"Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39","volume":"28","author":"Read","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0535","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1038\/nature01586","article-title":"The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria","volume":"423","author":"Read","year":"2003","journal-title":"Nature"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0540","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1038\/35017546","article-title":"Parallel evolution of virulence in pathogenic Escherichia coli","volume":"406","author":"Reid","year":"2000","journal-title":"Nature"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0545","doi-asserted-by":"crossref","first-page":"1008","DOI":"10.3201\/eid1307.060205","article-title":"Ongoing genome reduction in Mycobacterium ulcerans","volume":"13","author":"Rondini","year":"2007","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0550","doi-asserted-by":"crossref","first-page":"5463","DOI":"10.1073\/pnas.74.12.5463","article-title":"DNA sequencing with chain-terminating inhibitors","volume":"74","author":"Sanger","year":"1977","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0555","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/S0378-1119(03)00487-6","article-title":"Distinctiveness of the genomic sequence of Shiga toxin 2-converting phage isolated from Escherichia coli O157:H7 Okayama strain as compared to other Shiga toxin 2-converting phages","volume":"309","author":"Sato","year":"2003","journal-title":"Gene"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0560","doi-asserted-by":"crossref","first-page":"R227","DOI":"10.1093\/hmg\/ddq416","article-title":"A window into third-generation sequencing","volume":"19","author":"Schadt","year":"2010","journal-title":"Hum. Mol. Genet."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0565","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1186\/1471-2105-8-474","article-title":"High-throughput sequence alignment using Graphics Processing Units","volume":"8","author":"Schatz","year":"2007","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0570","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.meegid.2009.10.002","article-title":"The tempo and mode of molecular evolution of Mycobacterium tuberculosis at patient-to-patient scale","volume":"10","author":"Sch\u00fcrch","year":"2010","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0575","doi-asserted-by":"crossref","first-page":"W194","DOI":"10.1093\/nar\/gkq326","article-title":"mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes","volume":"38","author":"Shao","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0580","doi-asserted-by":"crossref","first-page":"e11556","DOI":"10.1371\/journal.pone.0011556","article-title":"Whole-genome sequencing reveals distinct mutational patterns in closely related laboratory and naturally propagated Francisella tularensis strains","volume":"5","author":"Sj\u00f6din","year":"2010","journal-title":"PLoS ONE"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0585","doi-asserted-by":"crossref","first-page":"1631","DOI":"10.1093\/jac\/dkq175","article-title":"A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A","volume":"65","author":"Song","year":"2010","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0590","doi-asserted-by":"crossref","first-page":"382","DOI":"10.3201\/eid0703.017303","article-title":"PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States","volume":"7","author":"Swaminathan","year":"2001","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0595","series-title":"Campylobacter Helicobacter-Related Organisms 2007 Meeting","first-page":"54","article-title":"The use of high-throughput comparative genomics-based molecular typing enhances cluster detection in epidemiological studies of Campylobacter jejejuni","author":"Taboada","year":"2007"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0600","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1186\/1471-2148-8-229","article-title":"Comparative genomic assessment of multi-locus sequence typing: rapid accumulation of genomic heterogeneity among clonal isolates of Campylobacter jejuni","volume":"8","author":"Taboada","year":"2008","journal-title":"BMC Evol. Biol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0605","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1128\/jcm.28.6.1225-1228.1990","article-title":"Plasmid profiling of members of the family Enterobacteriaceae, lactobacilli, and bifidobacteria to study the transmission of bacteria from mother to infant","volume":"28","author":"Tannock","year":"1990","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0610","doi-asserted-by":"crossref","first-page":"13950","DOI":"10.1073\/pnas.0506758102","article-title":"Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial \u201cpan-genome\u201d","volume":"102","author":"Tettelin","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0615","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0620","doi-asserted-by":"crossref","first-page":"e5519","DOI":"10.1371\/journal.pone.0005519","article-title":"Genome degradation in Brucella ovis corresponds with narrowing of its host range and tissue tropism","volume":"4","author":"Tsolis","year":"2009","journal-title":"PLoS ONE"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0625","doi-asserted-by":"crossref","first-page":"5568","DOI":"10.1128\/JB.187.16.5568-5577.2005","article-title":"Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae","volume":"187","author":"Vasconcelos","year":"2005","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0630","doi-asserted-by":"crossref","first-page":"4407","DOI":"10.1093\/nar\/23.21.4407","article-title":"AFLP: a new technique for DNA fingerprinting","volume":"23","author":"Vos","year":"1995","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0635","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1093\/bioinformatics\/btq644","article-title":"GPU-BLAST: using graphics processors to accelerate protein sequence alignment","volume":"27","author":"Vouzis","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0640","doi-asserted-by":"crossref","first-page":"1910","DOI":"10.1126\/science.272.5270.1910","article-title":"Lysogenic conversion by a filamentous phage encoding cholera toxin","volume":"272","author":"Waldor","year":"1996","journal-title":"Science"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0645","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: a revolutionary tool for transcriptomics","volume":"10","author":"Wang","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0650","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1016\/S0959-437X(02)00361-1","article-title":"Inferences from whole-genome sequences of bacterial pathogens","volume":"12","author":"Whittam","year":"2002","journal-title":"Curr. Opin. Genet. Dev."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0655","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1128\/mr.51.2.221-271.1987","article-title":"Bacterial evolution","volume":"51","author":"Woese","year":"1987","journal-title":"Microbiol. Rev."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0660","doi-asserted-by":"crossref","first-page":"5625","DOI":"10.1128\/JB.00535-10","article-title":"Comparative genomic characterization of Actinobacillus pleuropneumoniae","volume":"192","author":"Xu","year":"2010","journal-title":"J. Bacteriol."},{"issue":"1","key":"10.1016\/j.vetmic.2011.06.014_bib0665","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/j.ijfoodmicro.2010.11.038","article-title":"Extended MLST-based population genetics and phylogeny of Vibrio parahaemolyticus with high levels of recombination","volume":"145","author":"Yan","year":"2010","journal-title":"Int. J. Food Microbiol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0670","doi-asserted-by":"crossref","first-page":"195","DOI":"10.3233\/ISB-00290","article-title":"nWayComp: a genome-wide sequence comparison tool for multiple strains\/species of phylogenetically related microorganisms","volume":"7","author":"Yao","year":"2007","journal-title":"In Silico Biol."},{"key":"10.1016\/j.vetmic.2011.06.014_bib0675","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.jgg.2011.02.003","article-title":"The impact of next-generation sequencing on genomics","volume":"38","author":"Zhang","year":"2011","journal-title":"J. Genet. Genomics"},{"key":"10.1016\/j.vetmic.2011.06.014_bib0680","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/1471-2180-4-12","article-title":"Library on a slide for bacterial comparative genomics","volume":"4","author":"Zhang","year":"2004","journal-title":"BMC Microbiol."}],"container-title":["Veterinary Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0378113511003427?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0378113511003427?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T22:59:00Z","timestamp":1759877940000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0378113511003427"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,11]]},"references-count":136,"journal-issue":{"issue":"1-2","published-print":{"date-parts":[[2011,11]]}},"alternative-id":["S0378113511003427"],"URL":"https:\/\/doi.org\/10.1016\/j.vetmic.2011.06.014","relation":{},"ISSN":["0378-1135"],"issn-type":[{"value":"0378-1135","type":"print"}],"subject":[],"published":{"date-parts":[[2011,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Everything at once: Comparative analysis of the genomes of bacterial pathogens","name":"articletitle","label":"Article Title"},{"value":"Veterinary Microbiology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.vetmic.2011.06.014","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Crown copyright \u00a9 2011 Published by Elsevier B.V. All rights reserved.","name":"copyright","label":"Copyright"}]}}