Publications

A current list of Rasko publications can be found here.

Selected Publications

COMPARATIVE GENOMICS

E. coli and Shigella

D.A. Rasko, M.J. Rosovitz, G.S.A. Myers, E.F. Mongodin, W.F. Fricke, P. Gajer, J. Crabtree, V. Sperandio and J. Ravel. 2008. The pan-genome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol. 190(20):6881-93.

J.W. Sahl, H. Steinsland, J.C. Redman, S.V. Angiuoli, J.P. Nataro, H. Sommerfelt and D.A. Rasko. 2011. A comparative genomic analysis of diverse clonal types of enterotoxigenic Escherichia coli reveals pathovar-specific conservation. Infection and Immunity. 79(2):950-60.

D.A. Rasko, D.R. Webster, J.W. Sahl, A. Bashir, N. Boisen, F. Scheutz, E.E. Paxinos, R.Sebra, C.-S. Chin, D. Iliopoulos, A. Klammer, P. Peluso, L. Lee, A.O. Kislyuk, J. Bullard, A. Kasarskis, S. Wang, J. Eid, D. Rank, J.C. Redman, S.R. Steyert, J. Frimodt-Møller, C. Struve, A.M. Petersen, K.A. Krogfelt, J.P. Nataro, E.E. Schadt, M.K. Waldor. 2011. Origins of the E. coli strain causing a large outbreak of HUS in Germany. New England Journal of Medicine. 365(8):709-17.

S.R. Steyert, J.W. Sahl, C.M. Fraser, L.D. Teel, F. Scheutz and D.A. Rasko. 2012. Comparative genomics and stx phage characterization of LEE-negative Shiga toxin-producing Escherichia coli. Front Cell Infect Microbiol. 2012;2:133. (Open Access article)

T.H. Hazen, J.W. Sahl, C.M. Fraser, M.S. Donnenberg, F. Scheutz and D.A Rasko. 2013. Refining the pathovar paradigm via phylogenomics of the attaching and effacing Escherichia coli. Proc Natl Acad Sci USA. 110(31):12810-5.

A. von Mentzer, T.R. Connor, L.H. Wieler, T. Semmler, A. Iguchi, N.R. Thomson, D.A. Rasko, E. Joffre, J. Corander, D. Pickard, G. Wiklund, A.M. Svennerholm, A. Sjöling and G. Dougan. 2014. Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution. Nat Genet. 46(12):1321-6.

T.H. Hazen, S.R. Leonard, K.A. Lampel, D.W. Lacher, A.T. Maurelli and D.A. Rasko. 2016. Investigating the relatedness of enteroinvasive Escherichia coli to other E. coli and Shigella using comparative genomics. Infect Immun. 84(8):2362-71.

M.S. Donnenberg*, T.H. Hazen, T.H. Fang, S. Panchalingam, M. Antonio, A. Hossain, I. Mandomando, J.B. Ochieng, T. Ramamurthy, B. Tamboura, A. Zaidi, M.M. Levine, K. Kotloff, D.A. Rasko* and J.P. Nataro. 2015. Bacterial factors associated with lethal outcome of Enteropathogenic Escherichia coli infection: genomic case-control studies. PLoS Negl Trop Dis. 2015 May 15;9(5):e000379. (*co-corresponding authors)

J.W. Sahl, J.R. Sistrunk, C.M. Fraser, E. Hine, N. Baby, Y. Begum, Q. Luo, A. Sheikh, F. Qadri, J.M. Fleckenstein and D.A. Rasko. 2015. Examination of the enterotoxigenic Escherichia coli population structure during human infection. MBio. 2015 Jun 9;6(3). pii: e00501-15. doi: 10.1128/mBio.00501-15.

T.H. Hazen, J.B. Kaper, J.P. Nataro and D.A. Rasko. 2015. Comparative genomics provides insight into the diversity of the attaching and effacing Escherichia coli virulence plasmids. Infect Immun. 83(10):4103-17.

T.H. Hazen, M.S. Donnenberg*, S. Panchalingam, M. Antonio, A. Hossain, I. Mandomando, J.B. Ochieng, T. Ramamurthy, B. Tamboura, S. Qureshi, F. Quadri, A. Zaidi, K. Kotloff, M.M. Levine, E.M. Barry, J.B. Kaper, D.A. Rasko* and J.P. Nataro. 2016. Genomic diversity of EPEC associated with clinical presentations of differing severity. Nature Microbiology 1, Article number: 15014 doi:10.1038/nmicrobiol.2015.14. (*co-corresponding authors)

Forensic applications

D.A. Rasko, P. Worsham, T.G. Abshire, S.T. Stanley, J.D. Bannan, M.R. Wilson, R.J. Langham, R.S. Decker, L. Jiang, A.M. Phillipy, S.L. Salzberg, M. Pop, M.N. VanErt, L.J. Kenefic, P.S. Keim, C.M. Fraser-Liggett, J. Ravel. 2011. Microbial forensic applications of comparative genome analysis: Identification of Bacillus anthracis genetic markers in the Amerithrax investigation. Proceedings of the National Academy of Sciences. 108(12):5027-32.

Antimicrobial Resistance

J.W. Sahl, J.K. Johnson, A.D. Harris, A.M. Phillippy, W.W. Hsiao, K.A. Thom, and D.A. Rasko. 2011. Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity. BMC Genomics. 4;12:291.

T.H. Hazen, G.L. Robinson, A.D. Harris, D.A. Rasko and J.K. Johnson. 2012. Genome sequence of Klebsiella oxytoca 11492-1, a nosocomial isolate possessing a FOX-5 AmpC β-Lactamase. Journal of Bacteriology. 194(11):3028-9. (PMC3370625)

T.H. Hazen, L. Zhao, J.W. Sahl, G. Robinson, A.D. Harris, D.A. Rasko and J.K. Johnson. 2014. Characterization of Klebsiella sp. 10982, a colonizer of humans that contains novel antibiotic resistance alleles and exhibits genetic similarities to plant and clinical Klebsiella isolates. Antimicrob Agents Chemother. 58(4):1879-88

T.H. Hazen, L. Zhao, M.A. Boutin, A. Stancil, G. Robinson, A.D. Harris, D.A. Rasko and J.K. Johnson. 2014. Comparative genomics of an IncA/C multidrug resistance plasmid from Escherichia coli and Klebsiella species isolated from ICU patients: the utility of whole genome sequencing in healthcare settings. Antimicrob Agents Chemother. 58(8):4814-2.

Y. Doi, T.H. Hazen, M. Boitano, Y.C. Tsai, T.A. Clark, J. Korlach and D.A. Rasko. 2014. Whole genome assembly of Klebsiella pneumoniae co-producing NDM-1 and OXA-232 carbapenemases using Single-Molecule, Real-Time Sequencing. Antimicrob Agents Chemother. 58(10):5947-53.

L. Wallace, S.C. Daugherty, S. Nagaraj, J.K. Johnson, A.D. Harris and D.A. Rasko. 2016. The use of comparative genomics to characterize the diversity of Acinetobacter baumannii surveillance isolates in a health care institution. Antimicrob Agents Chemother. 60(10):5933-41.

TRANSCRIPTIONAL STUDIES

J.W. Sahl and D.A. Rasko. 2012. Analysis of the global transcriptional profiles of enterotoxigenic Escherichia coli (ETEC) isolate E24377A. Infection and Immunity. 80(3):1232-42.

R. Kansal, D.A. Rasko, J.W. Sahl, G.P. Munson, K. Roy, Q. Luo, A. Sheikh, K.J. Kuhne and J.M. Fleckenstein. 2013. Transcriptional modulation of Enterotoxigenic Escherichia coli virulence genes in response to epithelial cell interactions. Infect Immun. 81(1):259-70. (PMC3536156)

T.H. Hazen, J.W. Sahl, J.C. Redman, C.R. Morris, S.C. Daugherty, M.C. Chibucos, N.A. Sengamalay, C.M. Fraser-Liggett, H. Steinsland, T.S. Whittam, B. Whittam, S.D. Manning, D.A Rasko. 2012. Draft genome sequences of the Diarrheagenic Escherichia coli collection. Journal of Bacteriology. 194(11):3026-7. (PMC3370608)

T.H. Hazen, S.C Daugherty, A. Shetty, A.A. Mahurkar, O. White, J.B. Kaper JB and D.A Rasko. 2015. RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates. Front Microbiol. 2015 Jun 12;6:569. doi: 10.3389/fmicb.2015.00569. eCollection 2015.

MICROBIOME

E.A. Eloe-Fadrosh and D.A. Rasko. 2013. The human microbiome: from symbiosis to pathogenesis. Annu Rev Med. 2013;64:145-63. (NIHMSID 460863)

E.A. Eloe-Fadrosh, M.A. McArthur, A.M. Seekatz, E.F. Drabek, D.A Rasko, M.B. Sztein and C.M. Fraser. 2013. Impact of oral typhoid vaccination on the human gut microbiota and correlations with S. Typhi-specific immunological responses. PLoS One. 8(4):e62026. (PMC3634757)

A.M. Seekatz, A. Panda, D.A. Rasko, F.R. Toapanta, E.A. Eloe-Fadrosh, A.Q. Khan, Z. Liu, S.T. Shipley, L.J. Detolla, M.B. Sztein and C.M. Fraser. 2013. Differential response of the cynomolgus macaque gut microbiota to Shigella infection. PLoS One. 8(6):e64212. (PMC in progress, publisher provided)

MICROBIAL PATHOGENESIS

D.A. Rasko, C.G. Moreira, D.R. Li, N.C. Reading, J.M. Ritchie, M.K. Waldor, N. Williams, R. Taussig, S. Wei, M. Roth, D.T. Hughes, J.F. Huntley, M.W. Fina, J.R. Falck and V. Sperandio. 2008. Targeting QseC signaling and virulence for antibiotic development. Science. 321(5892):1078-80.

C.R. Morris, C.L. Grassel, J.C. Redman, J.W. Sahl, E.M. Barry and D.A. Rasko. 2013. Utilizing transcriptomics to identify mediators of pathogenesis in Shigella flexneri: characterization of intracellular growth regulator, icgR. Infect Immun. 81(9):3068-76.

J.R. Sistrunk, K.P. Nickerson, R.B. Chanin, D.A. Rasko and C.S. Faherty. 2016. Survival of the fittest: how bacterial pathogens utilize bile to enhance infection. Clinical Microbiology Reviews. 29(4):819-836.

TOOL DEVELOPMENT

D.A. Rasko, G.S. Myers, J. Ravel. 2005. Visualization of comparative genomic analyses by BLAST score ratio. BMC Bioinformatics. 6:2

J.W. Sahl, M.N. Matalka and D.A. Rasko. 2012. Phylomark: a tool to find conserved, phylogenetic markers from whole-genome alignments. Applied and Environmental Microbiology. 78(14):4884-92. (PMC3416384)

J.W. Sahl, J.G. Caporaso, D.A. Rasko and P. Keim. 2014. The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes. PeerJ. 2:e332. doi: 10.7717/peerj.332. eCollection 2014.

J. Crabtree, S. Agrawal, A. Mahurkar, G.S. Myers, D.A. Rasko and O. White. 2014. Circleator: Flexible Circular Visualization of Genome-Associated Data with BioPerl and SVG. Bioinformatics. 30(21):3125-7.

USING GENOMICS FOR DIAGNIOSTIC DEVELOPMENT

J.W. Sahl, C.M. Morris, J. Emberger, C.M. Fraser, J.B. Ochieng, J. Juma, B. Fields, B.F. Breiman, M. Gilmour, J.P. Nataro and D.A. Rasko. 2015. Defining the phylogenomics of Shigella species: A pathway to diagnostics. J Clin Microbiol. 53(3):951-60.

Rasko Lab

Est. 2008