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Items: 1 to 50 of 72

1.

A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network.

Williamson CHD, Stone NE, Nunnally AE, Hornstra HM, Wagner DM, Roe CC, Vazquez AJ, Nandurkar N, Vinocur J, Terriquez J, Gillece J, Travis J, Lemmer D, Keim P, Sahl JW.

Microb Genom. 2019 Jul;5(7). doi: 10.1099/mgen.0.000271. Epub 2019 May 20.

2.

Phylogenetic Analysis of Francisella tularensis Group A.II Isolates from 5 Patients with Tularemia, Arizona, USA, 2015-2017.

Birdsell DN, Yaglom H, Rodriguez E, Engelthaler DM, Maurer M, Gaither M, Vinocur J, Weiss J, Terriquez J, Komatsu K, Ormsby ME, Gebhardt M, Solomon C, Nienstadt L, Williamson CHD, Sahl JW, Keim PS, Wagner DM.

Emerg Infect Dis. 2019 May;25(5):944-946. doi: 10.3201/eid2505.180363.

3.

Diversity, Virulence, and Antimicrobial Resistance in Isolates From the Newly Emerging Klebsiella pneumoniae ST101 Lineage.

Roe CC, Vazquez AJ, Esposito EP, Zarrilli R, Sahl JW.

Front Microbiol. 2019 Apr 2;10:542. doi: 10.3389/fmicb.2019.00542. eCollection 2019.

4.

Domestic canines do not display evidence of gut microbial dysbiosis in the presence of Clostridioides (Clostridium) difficile, despite cellular susceptibility to its toxins.

Stone NE, Nunnally AE, Jimenez V Jr, Cope EK, Sahl JW, Sheridan K, Hornstra HM, Vinocur J, Settles EW, Headley KC, Williamson CHD, Rideout JR, Bolyen E, Caporaso JG, Terriquez J, Monroy FP, Busch JD, Keim P, Wagner DM.

Anaerobe. 2019 Aug;58:53-72. doi: 10.1016/j.anaerobe.2019.03.017. Epub 2019 Apr 1. Review.

5.

A single introduction of Yersinia pestis to Brazil during the 3rd plague pandemic.

Vogler AJ, Sahl JW, Leal NC, Sobreira M, Williamson CHD, Bollig MC, Birdsell DN, Rivera A, Thompson B, Nottingham R, Rezende AM, Keim P, Almeida AMP, Wagner DM.

PLoS One. 2019 Jan 9;14(1):e0209478. doi: 10.1371/journal.pone.0209478. eCollection 2019.

6.

Burkholderia pseudomallei distribution in Australasia is linked to paleogeographic and anthropogenic history.

Baker AL, Pearson T, Sahl JW, Hepp C, Price EP, Sarovich DS, Mayo M, Tuanyok A, Currie BJ, Keim P, Warner J.

PLoS One. 2018 Nov 5;13(11):e0206845. doi: 10.1371/journal.pone.0206845. eCollection 2018.

7.

Phenotypic characterization and whole genome analysis of extended-spectrum beta-lactamase-producing bacteria isolated from dogs in Germany.

Boehmer T, Vogler AJ, Thomas A, Sauer S, Hergenroether M, Straubinger RK, Birdsell D, Keim P, Sahl JW, Williamson CHD, Riehm JM.

PLoS One. 2018 Oct 26;13(10):e0206252. doi: 10.1371/journal.pone.0206252. eCollection 2018.

8.

Proteomic analysis of four Clostridium botulinum strains identifies proteins that link biological responses to proteomic signatures.

Deatherage Kaiser BL, Hill KK, Smith TJ, Williamson CHD, Keim P, Sahl JW, Wahl KL.

PLoS One. 2018 Oct 15;13(10):e0205586. doi: 10.1371/journal.pone.0205586. eCollection 2018.

9.

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.

10.

Variant site strain typer (VaST): efficient strain typing using a minimal number of variant genomic sites.

Furstenau TN, Cocking JH, Sahl JW, Fofanov VY.

BMC Bioinformatics. 2018 Jun 11;19(1):222. doi: 10.1186/s12859-018-2225-z.

11.

Developing Inclusivity and Exclusivity Panels for Testing Diagnostic and Detection Tools Targeting Burkholderia pseudomallei, the Causative Agent of Melioidosis.

Williamson CHD, Wagner DM, Keim P, Sahl JW.

J AOAC Int. 2018 Nov 1;101(6):1920-1926. doi: 10.5740/jaoacint.18-0014. Epub 2018 Apr 20. Review.

PMID:
29678218
12.

Complete Genome Sequence of the Environmental Burkholderia pseudomallei Sequence Type 131 Isolate MSHR1435, Associated with a Chronic Melioidosis Infection.

Sahl JW, Mayo M, Price EP, Sarovich DS, Kaestli M, Pearson T, Williamson CHD, Nottingham R, Sheridan K, Wagner DM, Currie BJ, Keim P.

Genome Announc. 2018 Mar 15;6(11). pii: e00072-18. doi: 10.1128/genomeA.00072-18.

13.

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.

14.

Temporal phylogeography of Yersinia pestis in Madagascar: Insights into the long-term maintenance of plague.

Vogler AJ, Andrianaivoarimanana V, Telfer S, Hall CM, Sahl JW, Hepp CM, Centner H, Andersen G, Birdsell DN, Rahalison L, Nottingham R, Keim P, Wagner DM, Rajerison M.

PLoS Negl Trop Dis. 2017 Sep 5;11(9):e0005887. doi: 10.1371/journal.pntd.0005887. eCollection 2017 Sep.

15.

Differentiating Botulinum Neurotoxin-Producing Clostridia with a Simple, Multiplex PCR Assay.

Williamson CHD, Vazquez AJ, Hill K, Smith TJ, Nottingham R, Stone NE, Sobek CJ, Cocking JH, Fernández RA, Caballero PA, Leiser OP, Keim P, Sahl JW.

Appl Environ Microbiol. 2017 Aug 31;83(18). pii: e00806-17. doi: 10.1128/AEM.00806-17. Print 2017 Sep 15.

16.

Non-Toxin-Producing Bacillus cereus Strains Belonging to the B. anthracis Clade Isolated from the International Space Station.

Venkateswaran K, Singh NK, Checinska Sielaff A, Pope RK, Bergman NH, van Tongeren SP, Patel NB, Lawson PA, Satomi M, Williamson CHD, Sahl JW, Keim P, Pierson D, Perry J.

mSystems. 2017 Jun 27;2(3). pii: e00021-17. doi: 10.1128/mSystems.00021-17. eCollection 2017 May-Jun.

17.

Insights into enterotoxigenic Escherichia coli diversity in Bangladesh utilizing genomic epidemiology.

Sahl JW, Sistrunk JR, Baby NI, Begum Y, Luo Q, Sheikh A, Qadri F, Fleckenstein JM, Rasko DA.

Sci Rep. 2017 Jun 13;7(1):3402. doi: 10.1038/s41598-017-03631-x.

18.

Unexpected Relations of Historical Anthrax Strain.

Antwerpen MH, Sahl JW, Birdsell D, Pearson T, Pearce MJ, Redmond C, Meyer H, Keim PS.

MBio. 2017 Apr 25;8(2). pii: e00440-17. doi: 10.1128/mBio.00440-17.

19.

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.

20.

Burkholderia humptydooensis sp. nov., a New Species Related to Burkholderia thailandensis and the Fifth Member of the Burkholderia pseudomallei Complex.

Tuanyok A, Mayo M, Scholz H, Hall CM, Allender CJ, Kaestli M, Ginther J, Spring-Pearson S, Bollig MC, Stone JK, Settles EW, Busch JD, Sidak-Loftis L, Sahl JW, Thomas A, Kreutzer L, Georgi E, Gee JE, Bowen RA, Ladner JT, Lovett S, Koroleva G, Palacios G, Wagner DM, Currie BJ, Keim P.

Appl Environ Microbiol. 2017 Feb 15;83(5). pii: e02802-16. doi: 10.1128/AEM.02802-16. Print 2017 Mar 1.

21.

17th Century Variola Virus Reveals the Recent History of Smallpox.

Duggan AT, Perdomo MF, Piombino-Mascali D, Marciniak S, Poinar D, Emery MV, Buchmann JP, Duchêne S, Jankauskas R, Humphreys M, Golding GB, Southon J, Devault A, Rouillard JM, Sahl JW, Dutour O, Hedman K, Sajantila A, Smith GL, Holmes EC, Poinar HN.

Curr Biol. 2016 Dec 19;26(24):3407-3412. doi: 10.1016/j.cub.2016.10.061. Epub 2016 Dec 8.

22.

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
23.

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.

24.

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.

25.

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.

26.

KlebSeq, a Diagnostic Tool for Surveillance, Detection, and Monitoring of Klebsiella pneumoniae.

Bowers JR, Lemmer D, Sahl JW, Pearson T, Driebe EM, Wojack B, Saubolle MA, Engelthaler DM, Keim P.

J Clin Microbiol. 2016 Oct;54(10):2582-96. doi: 10.1128/JCM.00927-16. Epub 2016 Aug 10.

27.

Draft Genome Sequence of the First Pathogenic Leptospira Isolates from Ecuador.

Barragan V, Sahl JW, Wiggins K, Chiriboga J, Salinas A, Cantos NE, Loor MN, Intriago BI, Morales M, Trueba G, Pearson T.

Genome Announc. 2016 May 5;4(3). pii: e00271-16. doi: 10.1128/genomeA.00271-16.

28.

Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia.

Williamson CH, Sahl JW, Smith TJ, Xie G, Foley BT, Smith LA, Fernández RA, Lindström M, Korkeala H, Keim P, Foster J, Hill K.

BMC Genomics. 2016 Mar 3;17:180. doi: 10.1186/s12864-016-2502-z.

29.

Unprecedented Melioidosis Cases in Northern Australia Caused by an Asian Burkholderia pseudomallei Strain Identified by Using Large-Scale Comparative Genomics.

Price EP, Sarovich DS, Smith EJ, MacHunter B, Harrington G, Theobald V, Hall CM, Hornstra HM, McRobb E, Podin Y, Mayo M, Sahl JW, Wagner DM, Keim P, Kaestli M, Currie BJ.

Appl Environ Microbiol. 2015 Nov 25;82(3):954-63. doi: 10.1128/AEM.03013-15. Print 2016 Feb 1.

30.

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.

31.

Water as Source of Francisella tularensis Infection in Humans, Turkey.

Kilic S, Birdsell DN, Karagöz A, Çelebi B, Bakkaloglu Z, Arikan M, Sahl JW, Mitchell C, Rivera A, Maltinsky S, Keim P, Üstek D, Durmaz R, Wagner DM.

Emerg Infect Dis. 2015 Dec;21(12):2213-6. doi: 10.3201/eid2112.150634.

32.

Whole-genome sequencing investigation of animal-skin-drum-associated UK anthrax cases reveals evidence of mixed populations and relatedness to a US case.

Pullan ST, Pearson TR, Latham J, Mason J, Atkinson B, Silman NJ, Marston CK, Sahl JW, Birdsell D, Hoffmaster AR, Keim P, Vipond R.

Microb Genom. 2015 Nov 7;1(5):e000039. doi: 10.1099/mgen.0.000039. eCollection 2015 Nov.

33.

Phylogenetic and genomic diversity in isolates from the globally distributed Acinetobacter baumannii ST25 lineage.

Sahl JW, Del Franco M, Pournaras S, Colman RE, Karah N, Dijkshoorn L, Zarrilli R.

Sci Rep. 2015 Oct 14;5:15188. doi: 10.1038/srep15188.

34.

Redefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics.

Califf KJ, Keim PS, Wagner DM, Sahl JW.

Microb Genom. 2015 Aug 3;1(2):e000028. doi: 10.1099/mgen.0.000028. eCollection 2015 Aug.

35.

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.

36.

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.

37.

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.

38.

Examination of the Enterotoxigenic Escherichia coli Population Structure during Human Infection.

Sahl JW, Sistrunk JR, Fraser CM, Hine E, Baby N, Begum Y, Luo Q, Sheikh A, Qadri F, Fleckenstein JM, Rasko DA.

MBio. 2015 Jun 9;6(3):e00501. doi: 10.1128/mBio.00501-15.

39.

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.

40.

CRISPR-cas subtype I-Fb in Acinetobacter baumannii: evolution and utilization for strain subtyping.

Karah N, Samuelsen Ø, Zarrilli R, Sahl JW, Wai SN, Uhlin BE.

PLoS One. 2015 Feb 23;10(2):e0118205. doi: 10.1371/journal.pone.0118205. eCollection 2015.

41.

Defining the phylogenomics of Shigella species: a pathway to diagnostics.

Sahl JW, Morris CR, Emberger J, Fraser CM, Ochieng JB, Juma J, Fields B, Breiman RF, Gilmour M, Nataro JP, Rasko DA.

J Clin Microbiol. 2015 Mar;53(3):951-60. doi: 10.1128/JCM.03527-14. Epub 2015 Jan 14.

42.

The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes.

Sahl JW, Caporaso JG, Rasko DA, Keim P.

PeerJ. 2014 Apr 1;2:e332. doi: 10.7717/peerj.332. eCollection 2014.

43.

High frequency, spontaneous motA mutations in Campylobacter jejuni strain 81-176.

Mohawk KL, Poly F, Sahl JW, Rasko DA, Guerry P.

PLoS One. 2014 Feb 18;9(2):e88043. doi: 10.1371/journal.pone.0088043. eCollection 2014.

44.

Yersinia pestis and the plague of Justinian 541-543 AD: a genomic analysis.

Wagner DM, Klunk J, Harbeck M, Devault A, Waglechner N, Sahl JW, Enk J, Birdsell DN, Kuch M, Lumibao C, Poinar D, Pearson T, Fourment M, Golding B, Riehm JM, Earn DJ, Dewitte S, Rouillard JM, Grupe G, Wiechmann I, Bliska JB, Keim PS, Scholz HC, Holmes EC, Poinar H.

Lancet Infect Dis. 2014 Apr;14(4):319-26. doi: 10.1016/S1473-3099(13)70323-2. Epub 2014 Jan 28.

PMID:
24480148
45.

Characterization of Klebsiella sp. strain 10982, a colonizer of humans that contains novel antibiotic resistance alleles and exhibits genetic similarities to plant and clinical Klebsiella isolates.

Hazen TH, Zhao L, Sahl JW, Robinson G, Harris AD, Rasko DA, Johnson JK.

Antimicrob Agents Chemother. 2014;58(4):1879-88. doi: 10.1128/AAC.01605-13. Epub 2014 Jan 6.

46.

Draft Genome Sequences of Three O157 Enteropathogenic Escherichia coli Isolates.

Hazen TH, Sahl JW, Fraser CM, Donnenberg MS, Scheutz F, Rasko DA.

Genome Announc. 2013 Jul 18;1(4). pii: e00516-13. doi: 10.1128/genomeA.00516-13.

47.

Refining the pathovar paradigm via phylogenomics of the attaching and effacing Escherichia coli.

Hazen TH, Sahl JW, Fraser CM, Donnenberg MS, Scheutz F, Rasko DA.

Proc Natl Acad Sci U S A. 2013 Jul 30;110(31):12810-5. doi: 10.1073/pnas.1306836110. Epub 2013 Jul 15.

48.

Characterization of intracellular growth regulator icgR by utilizing transcriptomics to identify mediators of pathogenesis in Shigella flexneri.

Morris CR, Grassel CL, Redman JC, Sahl JW, Barry EM, Rasko DA.

Infect Immun. 2013 Sep;81(9):3068-76. doi: 10.1128/IAI.00537-13. Epub 2013 Jun 10.

49.

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.

50.

Genome Sequence of Burkholderia pseudomallei NCTC 13392.

Sahl JW, Stone JK, Gelhaus HC, Warren RL, Cruttwell CJ, Funnell SG, Keim P, Tuanyok A.

Genome Announc. 2013 May 23;1(3). pii: e00183-13. doi: 10.1128/genomeA.00183-13.

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