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Items: 1 to 50 of 63

1.

Coinfections identified from metagenomic analysis of cervical lymph nodes from tularemia patients.

Birdsell DN, Özsürekci Y, Rawat A, Aycan AE, Mitchell CL, Sahl JW, Johansson A, Colman RE, Schupp JM, Ceyhan M, Keim PS, Wagner DM.

BMC Infect Dis. 2018 Jul 11;18(1):319. doi: 10.1186/s12879-018-3218-2.

2.

Direct detection of Coccidioides from Arizona soils using CocciENV, a highly sensitive and specific real-time PCR assay.

Bowers JR, Parise KL, Kelley EJ, Lemmer D, Schupp JM, Driebe EM, Engelthaler DM, Keim P, Barker BM.

Med Mycol. 2019 Feb 1;57(2):246-255. doi: 10.1093/mmy/myy007.

PMID:
29534236
3.

First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ.

Muller EEL, Narayanasamy S, Zeimes M, Laczny CC, Lebrun LA, Herold M, Hicks ND, Gillece JD, Schupp JM, Keim P, Wilmes P.

Stand Genomic Sci. 2017 Oct 18;12:64. doi: 10.1186/s40793-017-0274-y. eCollection 2017.

4.

Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis.

Price EP, Sarovich DS, Webb JR, Hall CM, Jaramillo SA, Sahl JW, Kaestli M, Mayo M, Harrington G, Baker AL, Sidak-Loftis LC, Settles EW, Lummis M, Schupp JM, Gillece JD, Tuanyok A, Warner J, Busch JD, Keim P, Currie BJ, Wagner DM.

PLoS Negl Trop Dis. 2017 Sep 14;11(9):e0005928. doi: 10.1371/journal.pntd.0005928. eCollection 2017 Sep.

5.

Mechanisms of Resistance to Folate Pathway Inhibitors in Burkholderia pseudomallei: Deviation from the Norm.

Podnecky NL, Rhodes KA, Mima T, Drew HR, Chirakul S, Wuthiekanun V, Schupp JM, Sarovich DS, Currie BJ, Keim P, Schweizer HP.

MBio. 2017 Sep 5;8(5). pii: e01357-17. doi: 10.1128/mBio.01357-17.

6.

Mapping and comparing bacterial microbiota in the sinonasal cavity of healthy, allergic rhinitis, and chronic rhinosinusitis subjects.

Lal D, Keim P, Delisle J, Barker B, Rank MA, Chia N, Schupp JM, Gillece JD, Cope EK.

Int Forum Allergy Rhinol. 2017 Jun;7(6):561-569. doi: 10.1002/alr.21934. Epub 2017 May 8.

PMID:
28481057
7.

NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats.

Sahl JW, Lemmer D, Travis J, Schupp JM, Gillece JD, Aziz M, Driebe EM, Drees KP, Hicks ND, Williamson CHD, Hepp CM, Smith DE, Roe C, Engelthaler DM, Wagner DM, Keim P.

Microb Genom. 2016 Aug 25;2(8):e000074. doi: 10.1099/mgen.0.000074. eCollection 2016 Aug.

8.

A microbiome assessment of medical marijuana.

Thompson GR 3rd, Tuscano JM, Dennis M, Singapuri A, Libertini S, Gaudino R, Torres A, Delisle JM, Gillece JD, Schupp JM, Engelthaler DM.

Clin Microbiol Infect. 2017 Apr;23(4):269-270. doi: 10.1016/j.cmi.2016.12.001. Epub 2016 Dec 9. No abstract available.

9.

VNTR diversity in Yersinia pestis isolates from an animal challenge study reveals the potential for in vitro mutations during laboratory cultivation.

Vogler AJ, Nottingham R, Busch JD, Sahl JW, Shuey MM, Foster JT, Schupp JM, Smith SR, Rocke TE, Keim P, Wagner DM.

Infect Genet Evol. 2016 Nov;45:297-302. doi: 10.1016/j.meegid.2016.09.019. Epub 2016 Sep 21.

PMID:
27664903
10.

More than 50% of Clostridium difficile Isolates from Pet Dogs in Flagstaff, USA, Carry Toxigenic Genotypes.

Stone NE, Sidak-Loftis LC, Sahl JW, Vazquez AJ, Wiggins KB, Gillece JD, Hicks ND, Schupp JM, Busch JD, Keim P, Wagner DM.

PLoS One. 2016 Oct 10;11(10):e0164504. doi: 10.1371/journal.pone.0164504. eCollection 2016.

11.

A Bacillus anthracis Genome Sequence from the Sverdlovsk 1979 Autopsy Specimens.

Sahl JW, Pearson T, Okinaka R, Schupp JM, Gillece JD, Heaton H, Birdsell D, Hepp C, Fofanov V, Noseda R, Fasanella A, Hoffmaster A, Wagner DM, Keim P.

MBio. 2016 Sep 27;7(5). pii: e01501-16. doi: 10.1128/mBio.01501-16.

12.

The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers.

Sahl JW, Vazquez AJ, Hall CM, Busch JD, Tuanyok A, Mayo M, Schupp JM, Lummis M, Pearson T, Shippy K, Colman RE, Allender CJ, Theobald V, Sarovich DS, Price EP, Hutcheson A, Korlach J, LiPuma JJ, Ladner J, Lovett S, Koroleva G, Palacios G, Limmathurotsakul D, Wuthiekanun V, Wongsuwan G, Currie BJ, Keim P, Wagner DM.

MBio. 2016 Sep 20;7(5). pii: e00846-16. doi: 10.1128/mBio.00846-16.

13.

High Leptospira Diversity in Animals and Humans Complicates the Search for Common Reservoirs of Human Disease in Rural Ecuador.

Barragan V, Chiriboga J, Miller E, Olivas S, Birdsell D, Hepp C, Hornstra H, Schupp JM, Morales M, Gonzalez M, Reyes S, de la Cruz C, Keim P, Hartskeerl R, Trueba G, Pearson T.

PLoS Negl Trop Dis. 2016 Sep 13;10(9):e0004990. doi: 10.1371/journal.pntd.0004990. eCollection 2016 Sep.

14.

Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study.

Colman RE, Anderson J, Lemmer D, Lehmkuhl E, Georghiou SB, Heaton H, Wiggins K, Gillece JD, Schupp JM, Catanzaro DG, Crudu V, Cohen T, Rodwell TC, Engelthaler DM.

J Clin Microbiol. 2016 Aug;54(8):2058-67. doi: 10.1128/JCM.00535-16. Epub 2016 May 25.

15.

Local Population Structure and Patterns of Western Hemisphere Dispersal for Coccidioides spp., the Fungal Cause of Valley Fever.

Engelthaler DM, Roe CC, Hepp CM, Teixeira M, Driebe EM, Schupp JM, Gade L, Waddell V, Komatsu K, Arathoon E, Logemann H, Thompson GR 3rd, Chiller T, Barker B, Keim P, Litvintseva AP.

MBio. 2016 Apr 26;7(2):e00550-16. doi: 10.1128/mBio.00550-16.

16.

Genetic variation at the MHC DRB1 locus is similar across Gunnison's prairie dog (Cynomys gunnisoni) colonies regardless of plague history.

Cobble KR, Califf KJ, Stone NE, Shuey MM, Birdsell DN, Colman RE, Schupp JM, Aziz M, Van Andel R, Rocke TE, Wagner DM, Busch JD.

Ecol Evol. 2016 Mar 16;6(8):2624-51. doi: 10.1002/ece3.2077. eCollection 2016 Apr.

17.

Diverse Burkholderia Species Isolated from Soils in the Southern United States with No Evidence of B. pseudomallei.

Hall CM, Busch JD, Shippy K, Allender CJ, Kaestli M, Mayo M, Sahl JW, Schupp JM, Colman RE, Keim P, Currie BJ, Wagner DM.

PLoS One. 2015 Nov 23;10(11):e0143254. doi: 10.1371/journal.pone.0143254. eCollection 2015.

18.

Best practices for evaluating single nucleotide variant calling methods for microbial genomics.

Olson ND, Lund SP, Colman RE, Foster JT, Sahl JW, Schupp JM, Keim P, Morrow JB, Salit ML, Zook JM.

Front Genet. 2015 Jul 7;6:235. doi: 10.3389/fgene.2015.00235. eCollection 2015. Review.

19.

Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus.

Driebe EM, Sahl JW, Roe C, Bowers JR, Schupp JM, Gillece JD, Kelley E, Price LB, Pearson TR, Hepp CM, Brzoska PM, Cummings CA, Furtado MR, Andersen PS, Stegger M, Engelthaler DM, Keim PS.

PLoS One. 2015 Jul 10;10(7):e0130955. doi: 10.1371/journal.pone.0130955. eCollection 2015.

20.

Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data.

Sahl JW, Schupp JM, Rasko DA, Colman RE, Foster JT, Keim P.

Genome Med. 2015 Jun 9;7(1):52. doi: 10.1186/s13073-015-0176-9. eCollection 2015.

21.

Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks.

Roume H, Heintz-Buschart A, Muller EEL, May P, Satagopam VP, Laczny CC, Narayanasamy S, Lebrun LA, Hoopmann MR, Schupp JM, Gillece JD, Hicks ND, Engelthaler DM, Sauter T, Keim PS, Moritz RL, Wilmes P.

NPJ Biofilms Microbiomes. 2015 Jun 17;1:15007. doi: 10.1038/npjbiofilms.2015.7. eCollection 2015.

22.

Detection of Low-Level Mixed-Population Drug Resistance in Mycobacterium tuberculosis Using High Fidelity Amplicon Sequencing.

Colman RE, Schupp JM, Hicks ND, Smith DE, Buchhagen JL, Valafar F, Crudu V, Romancenco E, Noroc E, Jackson L, Catanzaro DG, Rodwell TC, Catanzaro A, Keim P, Engelthaler DM.

PLoS One. 2015 May 13;10(5):e0126626. doi: 10.1371/journal.pone.0126626. eCollection 2015.

23.

Genomic characterization of Burkholderia pseudomallei isolates selected for medical countermeasures testing: comparative genomics associated with differential virulence.

Sahl JW, Allender CJ, Colman RE, Califf KJ, Schupp JM, Currie BJ, Van Zandt KE, Gelhaus HC, Keim P, Tuanyok A.

PLoS One. 2015 Mar 24;10(3):e0121052. doi: 10.1371/journal.pone.0121052. eCollection 2015.

24.

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage.

Muller EE, Pinel N, Laczny CC, Hoopmann MR, Narayanasamy S, Lebrun LA, Roume H, Lin J, May P, Hicks ND, Heintz-Buschart A, Wampach L, Liu CM, Price LB, Gillece JD, Guignard C, Schupp JM, Vlassis N, Baliga NS, Moritz RL, Keim PS, Wilmes P.

Nat Commun. 2014 Nov 26;5:5603. doi: 10.1038/ncomms6603.

25.

Phylogeography of Bacillus anthracis in the country of Georgia shows evidence of population structuring and is dissimilar to other regional genotypes.

Khmaladze E, Birdsell DN, Naumann AA, Hochhalter CB, Seymour ML, Nottingham R, Beckstrom-Sternberg SM, Beckstrom-Sternberg J, Nikolich MP, Chanturia G, Zhgenti E, Zakalashvili M, Malania L, Babuadze G, Tsertsvadze N, Abazashvili N, Kekelidze M, Tsanava S, Imnadze P, Ganz HH, Getz WM, Pearson O, Gajer P, Eppinger M, Ravel J, Wagner DM, Okinaka RT, Schupp JM, Keim P, Pearson T.

PLoS One. 2014 Jul 21;9(7):e102651. doi: 10.1371/journal.pone.0102651. eCollection 2014.

26.

Cryptococcus gattii in North American Pacific Northwest: whole-population genome analysis provides insights into species evolution and dispersal.

Engelthaler DM, Hicks ND, Gillece JD, Roe CC, Schupp JM, Driebe EM, Gilgado F, Carriconde F, Trilles L, Firacative C, Ngamskulrungroj P, Castañeda E, Lazera Mdos S, Melhem MS, Pérez-Bercoff A, Huttley G, Sorrell TC, Voelz K, May RC, Fisher MC, Thompson GR 3rd, Lockhart SR, Keim P, Meyer W.

MBio. 2014 Jul 15;5(4):e01464-14. doi: 10.1128/mBio.01464-14.

27.

Whole-genome analysis of Exserohilum rostratum from an outbreak of fungal meningitis and other infections.

Litvintseva AP, Hurst S, Gade L, Frace MA, Hilsabeck R, Schupp JM, Gillece JD, Roe C, Smith D, Keim P, Lockhart SR, Changayil S, Weil MR, MacCannell DR, Brandt ME, Engelthaler DM.

J Clin Microbiol. 2014 Sep;52(9):3216-22. doi: 10.1128/JCM.00936-14. Epub 2014 Jun 20.

28.

Real-time PCR assays for genotyping of Cryptococcus gattii in North America.

Kelley EJ, Driebe EM, Etienne K, Brandt ME, Schupp JM, Gillece JD, Trujillo JS, Lockhart SR, Deak E, Keim PS, Engelthaler DM.

BMC Microbiol. 2014 May 13;14:125. doi: 10.1186/1471-2180-14-125.

29.

High prevalence and two dominant host-specific genotypes of Coxiella burnetii in U.S. milk.

Pearson T, Hornstra HM, Hilsabeck R, Gates LT, Olivas SM, Birdsell DM, Hall CM, German S, Cook JM, Seymour ML, Priestley RA, Kondas AV, Clark Friedman CL, Price EP, Schupp JM, Liu CM, Price LB, Massung RF, Kersh GJ, Keim P.

BMC Microbiol. 2014 Feb 17;14:41. doi: 10.1186/1471-2180-14-41.

30.

The innate immune response may be important for surviving plague in wild Gunnison's prairie dogs.

Busch JD, Van Andel R, Stone NE, Cobble KR, Nottingham R, Lee J, VerSteeg M, Corcoran J, Cordova J, Van Pelt W, Shuey MM, Foster JT, Schupp JM, Beckstrom-Sternberg S, Beckstrom-Sternberg J, Keim P, Smith S, Rodriguez-Ramos J, Williamson JL, Rocke TE, Wagner DM.

J Wildl Dis. 2013 Oct;49(4):920-31. doi: 10.7589/2012-08-209.

PMID:
24502719
31.

Rapid and robust phylotyping of spa t003, a dominant MRSA clone in Luxembourg and other European countries.

Engelthaler DM, Kelley E, Driebe EM, Bowers J, Eberhard CF, Trujillo J, Decruyenaere F, Schupp JM, Mossong J, Keim P, Even J.

BMC Infect Dis. 2013 Jul 23;13:339. doi: 10.1186/1471-2334-13-339.

32.

When outgroups fail; phylogenomics of rooting the emerging pathogen, Coxiella burnetii.

Pearson T, Hornstra HM, Sahl JW, Schaack S, Schupp JM, Beckstrom-Sternberg SM, O'Neill MW, Priestley RA, Champion MD, Beckstrom-Sternberg JS, Kersh GJ, Samuel JE, Massung RF, Keim P.

Syst Biol. 2013 Sep;62(5):752-62. doi: 10.1093/sysbio/syt038. Epub 2013 Jun 4.

33.

Evolution of a pathogen: a comparative genomics analysis identifies a genetic pathway to pathogenesis in Acinetobacter.

Sahl JW, Gillece JD, Schupp JM, Waddell VG, Driebe EM, Engelthaler DM, Keim P.

PLoS One. 2013;8(1):e54287. doi: 10.1371/journal.pone.0054287. Epub 2013 Jan 24.

34.

Necrotizing cutaneous mucormycosis after a tornado in Joplin, Missouri, in 2011.

Neblett Fanfair R, Benedict K, Bos J, Bennett SD, Lo YC, Adebanjo T, Etienne K, Deak E, Derado G, Shieh WJ, Drew C, Zaki S, Sugerman D, Gade L, Thompson EH, Sutton DA, Engelthaler DM, Schupp JM, Brandt ME, Harris JR, Lockhart SR, Turabelidze G, Park BJ.

N Engl J Med. 2012 Dec 6;367(23):2214-25. doi: 10.1056/NEJMoa1204781.

35.

Whole genome sequence typing to investigate the Apophysomyces outbreak following a tornado in Joplin, Missouri, 2011.

Etienne KA, Gillece J, Hilsabeck R, Schupp JM, Colman R, Lockhart SR, Gade L, Thompson EH, Sutton DA, Neblett-Fanfair R, Park BJ, Turabelidze G, Keim P, Brandt ME, Deak E, Engelthaler DM.

PLoS One. 2012;7(11):e49989. doi: 10.1371/journal.pone.0049989. Epub 2012 Nov 27.

36.

Genome sequence of "Candidatus Microthrix parvicella" Bio17-1, a long-chain-fatty-acid-accumulating filamentous actinobacterium from a biological wastewater treatment plant.

Muller EE, Pinel N, Gillece JD, Schupp JM, Price LB, Engelthaler DM, Levantesi C, Tandoi V, Luong K, Baliga NS, Korlach J, Keim PS, Wilmes P.

J Bacteriol. 2012 Dec;194(23):6670-1. doi: 10.1128/JB.01765-12.

37.

Molecular epidemiologic investigation of an anthrax outbreak among heroin users, Europe.

Price EP, Seymour ML, Sarovich DS, Latham J, Wolken SR, Mason J, Vincent G, Drees KP, Beckstrom-Sternberg SM, Phillippy AM, Koren S, Okinaka RT, Chung WK, Schupp JM, Wagner DM, Vipond R, Foster JT, Bergman NH, Burans J, Pearson T, Brooks T, Keim P.

Emerg Infect Dis. 2012 Aug;18(8):1307-13. doi: 10.3201/eid1808.111343.

38.

Comparison of TaqMan PCR assays for detection of the melioidosis agent Burkholderia pseudomallei in clinical specimens.

Kaestli M, Richardson LJ, Colman RE, Tuanyok A, Price EP, Bowers JR, Mayo M, Kelley E, Seymour ML, Sarovich DS, Pearson T, Engelthaler DM, Wagner DM, Keim PS, Schupp JM, Currie BJ.

J Clin Microbiol. 2012 Jun;50(6):2059-62. doi: 10.1128/JCM.06737-11. Epub 2012 Mar 21.

39.

Whole genome sequence analysis of Cryptococcus gattii from the Pacific Northwest reveals unexpected diversity.

Gillece JD, Schupp JM, Balajee SA, Harris J, Pearson T, Yan Y, Keim P, DeBess E, Marsden-Haug N, Wohrle R, Engelthaler DM, Lockhart SR.

PLoS One. 2011;6(12):e28550. doi: 10.1371/journal.pone.0028550. Epub 2011 Dec 7.

40.

An attenuated strain of Bacillus anthracis (CDC 684) has a large chromosomal inversion and altered growth kinetics.

Okinaka RT, Price EP, Wolken SR, Gruendike JM, Chung WK, Pearson T, Xie G, Munk C, Hill KK, Challacombe J, Ivins BE, Schupp JM, Beckstrom-Sternberg SM, Friedlander A, Keim P.

BMC Genomics. 2011 Sep 30;12:477. doi: 10.1186/1471-2164-12-477.

41.

Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak.

Hendriksen RS, Price LB, Schupp JM, Gillece JD, Kaas RS, Engelthaler DM, Bortolaia V, Pearson T, Waters AE, Upadhyay BP, Shrestha SD, Adhikari S, Shakya G, Keim PS, Aarestrup FM.

MBio. 2011 Sep 1;2(4):e00157-11. doi: 10.1128/mBio.00157-11. Print 2011.

42.

Cyclopropavir inhibits the normal function of the human cytomegalovirus UL97 kinase.

James SH, Hartline CB, Harden EA, Driebe EM, Schupp JM, Engelthaler DM, Keim PS, Bowlin TL, Kern ER, Prichard MN.

Antimicrob Agents Chemother. 2011 Oct;55(10):4682-91. doi: 10.1128/AAC.00571-11. Epub 2011 Jul 25.

43.

Cost-effective interrogation of single nucleotide polymorphisms using the mismatch amplification mutation assay and capillary electrophoresis.

Price EP, Matthews MA, Beaudry JA, Allred JL, Schupp JM, Birdsell DN, Pearson T, Keim P.

Electrophoresis. 2010 Dec;31(23-24):3881-8. doi: 10.1002/elps.201000379.

44.

Selective isolation of Yersinia pestis from plague-infected fleas.

Sarovich DS, Colman RE, Price EP, Chung WK, Lee J, Schupp JM, Cobble KR, Busch JD, Alexander J, Keim P, Wagner DM.

J Microbiol Methods. 2010 Jul;82(1):95-7. doi: 10.1016/j.mimet.2010.03.019. Epub 2010 Apr 10.

45.

The genome and variation of Bacillus anthracis.

Keim P, Gruendike JM, Klevytska AM, Schupp JM, Challacombe J, Okinaka R.

Mol Aspects Med. 2009 Dec;30(6):397-405. doi: 10.1016/j.mam.2009.08.005. Epub 2009 Sep 1. Review.

46.

Bacillus anthracis in China and its relationship to worldwide lineages.

Simonson TS, Okinaka RT, Wang B, Easterday WR, Huynh L, U'Ren JM, Dukerich M, Zanecki SR, Kenefic LJ, Beaudry J, Schupp JM, Pearson T, Wagner DM, Hoffmaster A, Ravel J, Keim P.

BMC Microbiol. 2009 Apr 15;9:71. doi: 10.1186/1471-2180-9-71.

47.

Pre-Columbian origins for North American anthrax.

Kenefic LJ, Pearson T, Okinaka RT, Schupp JM, Wagner DM, Hoffmaster AR, Trim CB, Chung WK, Beaudry JA, Jiang L, Gajer P, Foster JT, Mead JI, Ravel J, Keim P.

PLoS One. 2009;4(3):e4813. doi: 10.1371/journal.pone.0004813. Epub 2009 Mar 13. Erratum in: PLoS One.2009;4(5):10.1371/annotation/9e8af820-8037-4f98-86b3-6581e16c2ae6. Jiang, Lingxia [added]; Gajer, Pawel [added]; Trim, Carla P [corrected to Trim, Carla B].

48.

Texas isolates closely related to Bacillus anthracis Ames.

Kenefic LJ, Pearson T, Okinaka RT, Chung WK, Max T, Trim CP, Beaudry JA, Schupp JM, Van Ert MN, Marston CK, Gutierrez K, Swinford AK, Hoffmaster AR, Keim P.

Emerg Infect Dis. 2008 Sep;14(9):1494-6. doi: 10.3201/eid1409.080076. No abstract available. Erratum in: Emerg Infect Dis. 2008 Nov;14(11):1825. Trim, Carla P [added]; Beaudry, Jodi A [added]; Schupp, James M [added].

49.

Fine-scale genetic diversity among Burkholderia pseudomallei soil isolates in northeast Thailand.

U'ren JM, Hornstra H, Pearson T, Schupp JM, Leadem B, Georgia S, Sermswan RW, Keim P.

Appl Environ Microbiol. 2007 Oct;73(20):6678-81. Epub 2007 Aug 24.

50.

Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping.

U'Ren JM, Schupp JM, Pearson T, Hornstra H, Friedman CL, Smith KL, Daugherty RR, Rhoton SD, Leadem B, Georgia S, Cardon M, Huynh LY, DeShazer D, Harvey SP, Robison R, Gal D, Mayo MJ, Wagner D, Currie BJ, Keim P.

BMC Microbiol. 2007 Mar 30;7:23.

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