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USA300 Staphylococcus aureus persists on multiple body sites following an infection.

Read TD, Petit RA 3rd, Yin Z, Montgomery T, McNulty MC, David MZ.

BMC Microbiol. 2018 Dec 5;18(1):206. doi: 10.1186/s12866-018-1336-z.


Human mAbs to Staphylococcus aureus IsdA Provide Protection Through Both Heme-Blocking and Fc-Mediated Mechanisms.

Bennett MR, Bombardi RG, Kose N, Parrish EH, Nagel MB, Petit RA 3rd, Read TD, Schey KL, Thomsen IP, Skaar EP, Crowe JE Jr.

J Infect Dis. 2018 Nov 29. doi: 10.1093/infdis/jiy635. [Epub ahead of print]


Genome-based prediction of bacterial antibiotic resistance.

Su M, Satola SW, Read TD.

J Clin Microbiol. 2018 Oct 31. pii: JCM.01405-18. doi: 10.1128/JCM.01405-18. [Epub ahead of print] Review.


Whole genome sequencing for investigations of meningococcal outbreaks in the United States: a retrospective analysis.

Whaley MJ, Joseph SJ, Retchless AC, Kretz CB, Blain A, Hu F, Chang HY, Mbaeyi SA, MacNeil JR, Read TD, Wang X.

Sci Rep. 2018 Oct 25;8(1):15803. doi: 10.1038/s41598-018-33622-5.


Fine-scale differentiation between Bacillus anthracis and Bacillus cereus group signatures in metagenome shotgun data.

Petit Iii RA, Hogan JM, Ezewudo MN, Joseph SJ, Read TD.

PeerJ. 2018 Aug 22;6:e5515. doi: 10.7717/peerj.5515. eCollection 2018.


Quantitative and qualitative assessment of pollen DNA metabarcoding using constructed species mixtures.

Bell KL, Burgess KS, Botsch JC, Dobbs EK, Read TD, Brosi BJ.

Mol Ecol. 2018 Aug 17. doi: 10.1111/mec.14840. [Epub ahead of print]


Staphylococcus aureus viewed from the perspective of 40,000+ genomes.

Petit RA 3rd, Read TD.

PeerJ. 2018 Jul 12;6:e5261. doi: 10.7717/peerj.5261. eCollection 2018.


Invasive Methicillin-Resistant Staphylococcus aureus USA500 Strains from the U.S. Emerging Infections Program Constitute Three Geographically Distinct Lineages.

Frisch MB, Castillo-Ramírez S, Petit RA 3rd, Farley MM, Ray SM, Albrecht VS, Limbago BM, Hernandez J, See I, Satola SW, Read TD.

mSphere. 2018 May 2;3(3). pii: e00571-17. doi: 10.1128/mSphere.00571-17. eCollection 2018 May-Jun.


Correction to: Protocol for the Emory University African American Vaginal, oral, and gut microbiome in pregnancy cohort study.

Corwin EJ, Hogue CJ, Pearce B, Hill CC, Read TD, Mulle J, Dunlop AL.

BMC Pregnancy Childbirth. 2017 Nov 27;17(1):395. doi: 10.1186/s12884-017-1550-y.


The Female Genital Tract Microbiome Is Associated With Vaginal Antiretroviral Drug Concentrations in Human Immunodeficiency Virus-Infected Women on Antiretroviral Therapy.

Donahue Carlson R, Sheth AN, Read TD, Frisch MB, Mehta CC, Martin A, Haaland RE, Patel AS, Pau CP, Kraft CS, Ofotokun I.

J Infect Dis. 2017 Nov 15;216(8):990-999. doi: 10.1093/infdis/jix420.


Correction: Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants.

Diaz MH, Desai HP, Morrison SS, Benitez AJ, Wolff BJ, Caravas J, Read TD, Dean D, Winchell JM.

PLoS One. 2017 Oct 4;12(10):e0186030. doi: 10.1371/journal.pone.0186030. eCollection 2017.


Erratum to: draft sequencing and assembly of the genome of the world's largest fish, the whale shark: Rhincodon typus smith 1828.

Read TD, Petit RA 3rd, Joseph SJ, Alam T, Weil MR, Ahmad M, Bhimani R, Vuong JS, Haase CP, Webb DH, Tan M, Dove ADM.

BMC Genomics. 2017 Sep 25;18(1):755. doi: 10.1186/s12864-017-4138-z. No abstract available.


Draft sequencing and assembly of the genome of the world's largest fish, the whale shark: Rhincodon typus Smith 1828.

Read TD, Petit RA 3rd, Joseph SJ, Alam MT, Weil MR, Ahmad M, Bhimani R, Vuong JS, Haase CP, Webb DH, Tan M, Dove ADM.

BMC Genomics. 2017 Jul 14;18(1):532. doi: 10.1186/s12864-017-3926-9. Erratum in: BMC Genomics. 2017 Sep 25;18(1):755.


Protocol for the Emory University African American Vaginal, Oral, and Gut Microbiome in Pregnancy Cohort Study.

Corwin EJ, Hogue CJ, Pearce B, Hill CC, Read TD, Mulle J, Dunlop AL.

BMC Pregnancy Childbirth. 2017 Jun 1;17(1):161. doi: 10.1186/s12884-017-1357-x. Erratum in: BMC Pregnancy Childbirth. 2017 Nov 27;17 (1):395.


Rapid detection and strain typing of Chlamydia trachomatis using a highly multiplexed microfluidic PCR assay.

Turingan RS, Kaplun L, Krautz-Peterson G, Norsworthy S, Zolotova A, Joseph SJ, Read TD, Dean D, Tan E, Selden RF.

PLoS One. 2017 May 31;12(5):e0178653. doi: 10.1371/journal.pone.0178653. eCollection 2017.


Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants.

Diaz MH, Desai HP, Morrison SS, Benitez AJ, Wolff BJ, Caravas J, Read TD, Dean D, Winchell JM.

PLoS One. 2017 Apr 14;12(4):e0174701. doi: 10.1371/journal.pone.0174701. eCollection 2017. Erratum in: PLoS One. 2017 Oct 4;12 (10 ):e0186030.


Emergence of a new Neisseria meningitidis clonal complex 11 lineage 11.2 clade as an effective urogenital pathogen.

Tzeng YL, Bazan JA, Turner AN, Wang X, Retchless AC, Read TD, Toh E, Nelson DE, Del Rio C, Stephens DS.

Proc Natl Acad Sci U S A. 2017 Apr 18;114(16):4237-4242. doi: 10.1073/pnas.1620971114. Epub 2017 Apr 3.


Lung Tissue Concentrations of Pyrazinamide among Patients with Drug-Resistant Pulmonary Tuberculosis.

Kempker RR, Heinrichs MT, Nikolaishvili K, Sabulua I, Bablishvili N, Gogishvili S, Avaliani Z, Tukvadze N, Little B, Bernheim A, Read TD, Guarner J, Derendorf H, Peloquin CA, Blumberg HM, Vashakidze S.

Antimicrob Agents Chemother. 2017 May 24;61(6). pii: e00226-17. doi: 10.1128/AAC.00226-17. Print 2017 Jun.


Oral microbiome in HIV-associated periodontitis.

Noguera-Julian M, Guillén Y, Peterson J, Reznik D, Harris EV, Joseph SJ, Rivera J, Kannanganat S, Amara R, Nguyen ML, Mutembo S, Paredes R, Read TD, Marconi VC.

Medicine (Baltimore). 2017 Mar;96(12):e5821. doi: 10.1097/MD.0000000000005821.


Tet(C) Gene Transfer between Chlamydia suis Strains Occurs by Homologous Recombination after Co-infection: Implications for Spread of Tetracycline-Resistance among Chlamydiaceae.

Marti H, Kim H, Joseph SJ, Dojiri S, Read TD, Dean D.

Front Microbiol. 2017 Feb 7;8:156. doi: 10.3389/fmicb.2017.00156. eCollection 2017.


The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data.

Joseph SJ, Li B, Petit Iii RA, Qin ZS, Darrow L, Read TD.

PeerJ. 2016 Oct 18;4:e2571. eCollection 2016.


Dynamics of genome change among Legionella species.

Joseph SJ, Cox D, Wolff B, Morrison SS, Kozak-Muiznieks NA, Frace M, Didelot X, Castillo-Ramirez S, Winchell J, Read TD, Dean D.

Sci Rep. 2016 Sep 16;6:33442. doi: 10.1038/srep33442.


Tetracycline Selective Pressure and Homologous Recombination Shape the Evolution of Chlamydia suis: A Recently Identified Zoonotic Pathogen.

Joseph SJ, Marti H, Didelot X, Read TD, Dean D.

Genome Biol Evol. 2016 Sep 2;8(8):2613-23. doi: 10.1093/gbe/evw182.


Antibiotic failure mediated by a resistant subpopulation in Enterobacter cloacae.

Band VI, Crispell EK, Napier BA, Herrera CM, Tharp GK, Vavikolanu K, Pohl J, Read TD, Bosinger SE, Trent MS, Burd EM, Weiss DS.

Nat Microbiol. 2016 May 9;1(6):16053. doi: 10.1038/nmicrobiol.2016.53.


Draft Genome Sequence of the Pandoraea apista LMG 16407 Type Strain.

Millard AD, Westblade LF, LiPuma JJ, Vavikolanu K, Read TD, Pallen MJ, Burd EM, Constantinidou CI.

Genome Announc. 2015 Nov 12;3(6). pii: e01300-15. doi: 10.1128/genomeA.01300-15.


Chlamydiaceae Genomics Reveals Interspecies Admixture and the Recent Evolution of Chlamydia abortus Infecting Lower Mammalian Species and Humans.

Joseph SJ, Marti H, Didelot X, Castillo-Ramirez S, Read TD, Dean D.

Genome Biol Evol. 2015 Oct 27;7(11):3070-84. doi: 10.1093/gbe/evv201.


Characterization of a spermine/spermidine transport system reveals a novel DNA sequence duplication in Neisseria gonorrhoeae.

Goytia M, Hawel L 3rd, Dhulipala VL, Joseph SJ, Read TD, Shafer WM.

FEMS Microbiol Lett. 2015 Aug;362(16). pii: fnv125. doi: 10.1093/femsle/fnv125. Epub 2015 Jul 30.


'SEEDY' (Simulation of Evolutionary and Epidemiological Dynamics): An R Package to Follow Accumulation of Within-Host Mutation in Pathogens.

Worby CJ, Read TD.

PLoS One. 2015 Jun 15;10(6):e0129745. doi: 10.1371/journal.pone.0129745. eCollection 2015.


USA300 and USA500 clonal lineages of Staphylococcus aureus do not produce a capsular polysaccharide due to conserved mutations in the cap5 locus.

Boyle-Vavra S, Li X, Alam MT, Read TD, Sieth J, Cywes-Bentley C, Dobbins G, David MZ, Kumar N, Eells SJ, Miller LG, Boxrud DJ, Chambers HF, Lynfield R, Lee JC, Daum RS.

MBio. 2015 Apr 7;6(2). pii: e02585-14. doi: 10.1128/mBio.02585-14.


Population structure of Neisseria gonorrhoeae based on whole genome data and its relationship with antibiotic resistance.

Ezewudo MN, Joseph SJ, Castillo-Ramirez S, Dean D, Del Rio C, Didelot X, Dillon JA, Selden RF, Shafer WM, Turingan RS, Unemo M, Read TD.

PeerJ. 2015 Mar 5;3:e806. doi: 10.7717/peerj.806. eCollection 2015.


Transmission and microevolution of USA300 MRSA in U.S. households: evidence from whole-genome sequencing.

Alam MT, Read TD, Petit RA 3rd, Boyle-Vavra S, Miller LG, Eells SJ, Daum RS, David MZ.

MBio. 2015 Mar 10;6(2):e00054. doi: 10.1128/mBio.00054-15.


Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology.

Read TD, Massey RC.

Genome Med. 2014 Nov 22;6(11):109. doi: 10.1186/s13073-014-0109-z. eCollection 2014.


Overproduction of the MtrCDE efflux pump in Neisseria gonorrhoeae produces unexpected changes in cellular transcription patterns.

Ohneck EA, Goytia M, Rouquette-Loughlin CE, Joseph SJ, Read TD, Jerse AE, Shafer WM.

Antimicrob Agents Chemother. 2015 Jan;59(1):724-6. doi: 10.1128/AAC.04148-14. Epub 2014 Nov 3.


Using genomics to standardize population analysis profile-area under the curve ratio for vancomycin-intermediate Staphylococcus aureus.

Read TD, Satola SW.

J Clin Microbiol. 2014 Oct;52(10):3824-6. doi: 10.1128/JCM.01536-14. Epub 2014 Jul 23. No abstract available.


Using crude whole-genome assemblies of Neisseria gonorrhoeae as a platform for strain analysis: clonal spread of gonorrhea infection in Saskatchewan, Canada.

Vidovic S, Caron C, Taheri A, Thakur SD, Read TD, Kusalik A, Dillon JA.

J Clin Microbiol. 2014 Oct;52(10):3772-6. doi: 10.1128/JCM.01502-14. Epub 2014 Jul 23.


Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples.

Joseph SJ, Li B, Ghonasgi T, Haase CP, Qin ZS, Dean D, Read TD.

PLoS One. 2014 Jun 27;9(6):e99290. doi: 10.1371/journal.pone.0099290. eCollection 2014.


Development of oxacillin resistance in a patient with recurrent Staphylococcus aureus bacteremia.

Burd EM, Alam MT, Passalacqua KD, Kalokhe AS, Eaton ME, Satola SW, Kraft CS, Read TD.

J Clin Microbiol. 2014 Aug;52(8):3114-7. doi: 10.1128/JCM.00615-14. Epub 2014 May 21.


Phase-variable expression of lptA modulates the resistance of Neisseria gonorrhoeae to cationic antimicrobial peptides.

Kandler JL, Joseph SJ, Balthazar JT, Dhulipala V, Read TD, Jerse AE, Shafer WM.

Antimicrob Agents Chemother. 2014 Jul;58(7):4230-3. doi: 10.1128/AAC.03108-14. Epub 2014 May 12.


Functional genomic characterization of virulence factors from necrotizing fasciitis-causing strains of Aeromonas hydrophila.

Grim CJ, Kozlova EV, Ponnusamy D, Fitts EC, Sha J, Kirtley ML, van Lier CJ, Tiner BL, Erova TE, Joseph SJ, Read TD, Shak JR, Joseph SW, Singletary E, Felland T, Baze WB, Horneman AJ, Chopra AK.

Appl Environ Microbiol. 2014 Jul;80(14):4162-83. doi: 10.1128/AEM.00486-14. Epub 2014 May 2.


Dissecting vancomycin-intermediate resistance in staphylococcus aureus using genome-wide association.

Alam MT, Petit RA 3rd, Crispell EK, Thornton TA, Conneely KN, Jiang Y, Satola SW, Read TD.

Genome Biol Evol. 2014 Apr 30;6(5):1174-85. doi: 10.1093/gbe/evu092.


Predicting the virulence of MRSA from its genome sequence.

Laabei M, Recker M, Rudkin JK, Aldeljawi M, Gulay Z, Sloan TJ, Williams P, Endres JL, Bayles KW, Fey PD, Yajjala VK, Widhelm T, Hawkins E, Lewis K, Parfett S, Scowen L, Peacock SJ, Holden M, Wilson D, Read TD, van den Elsen J, Priest NK, Feil EJ, Hurst LD, Josefsson E, Massey RC.

Genome Res. 2014 May;24(5):839-49. doi: 10.1101/gr.165415.113. Epub 2014 Apr 9.


The complete mitochondrial genome sequence of the world's largest fish, the whale shark (Rhincodon typus), and its comparison with those of related shark species.

Alam MT, Petit RA 3rd, Read TD, Dove AD.

Gene. 2014 Apr 10;539(1):44-9. doi: 10.1016/j.gene.2014.01.064. Epub 2014 Feb 4.


Genetic evidence for the involvement of the S-layer protein gene sap and the sporulation genes spo0A, spo0B, and spo0F in Phage AP50c infection of Bacillus anthracis.

Plaut RD, Beaber JW, Zemansky J, Kaur AP, George M, Biswas B, Henry M, Bishop-Lilly KA, Mokashi V, Hannah RM, Pope RK, Read TD, Stibitz S, Calendar R, Sozhamannan S.

J Bacteriol. 2014 Mar;196(6):1143-54. doi: 10.1128/JB.00739-13. Epub 2013 Dec 20.


IsdB-dependent hemoglobin binding is required for acquisition of heme by Staphylococcus aureus.

Pishchany G, Sheldon JR, Dickson CF, Alam MT, Read TD, Gell DA, Heinrichs DE, Skaar EP.

J Infect Dis. 2014 Jun 1;209(11):1764-72. doi: 10.1093/infdis/jit817. Epub 2013 Dec 13.


Genome Sequencing of Four Strains of Rickettsia prowazekii, the Causative Agent of Epidemic Typhus, Including One Flying Squirrel Isolate.

Bishop-Lilly KA, Ge H, Butani A, Osborne B, Verratti K, Mokashi V, Nagarajan N, Pop M, Read TD, Richards AL.

Genome Announc. 2013 Jun 27;1(3). pii: e00399-13. doi: 10.1128/genomeA.00399-13.


Characterization of Aeromonas hydrophila wound pathotypes by comparative genomic and functional analyses of virulence genes.

Grim CJ, Kozlova EV, Sha J, Fitts EC, van Lier CJ, Kirtley ML, Joseph SJ, Read TD, Burd EM, Tall BD, Joseph SW, Horneman AJ, Chopra AK, Shak JR.

MBio. 2013 Apr 23;4(2):e00064-13. doi: 10.1128/mBio.00064-13.


Comparative analysis of Chlamydia psittaci genomes reveals the recent emergence of a pathogenic lineage with a broad host range.

Read TD, Joseph SJ, Didelot X, Liang B, Patel L, Dean D.

MBio. 2013 Mar 26;4(2). pii: e00604-12. doi: 10.1128/mBio.00604-12.


A multiplexed microfluidic PCR assay for sensitive and specific point-of-care detection of Chlamydia trachomatis.

Dean D, Turingan RS, Thomann HU, Zolotova A, Rothschild J, Joseph SJ, Read TD, Tan E, Selden RF.

PLoS One. 2012;7(12):e51685. doi: 10.1371/journal.pone.0051685. Epub 2012 Dec 14.


Whole genome sequencing of phage resistant Bacillus anthracis mutants reveals an essential role for cell surface anchoring protein CsaB in phage AP50c adsorption.

Bishop-Lilly KA, Plaut RD, Chen PE, Akmal A, Willner KM, Butani A, Dorsey S, Mokashi V, Mateczun AJ, Chapman C, George M, Luu T, Read TD, Calendar R, Stibitz S, Sozhamannan S.

Virol J. 2012 Oct 26;9:246. doi: 10.1186/1743-422X-9-246.


Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis.

Passalacqua KD, Varadarajan A, Weist C, Ondov BD, Byrd B, Read TD, Bergman NH.

PLoS One. 2012;7(8):e43350. doi: 10.1371/journal.pone.0043350. Epub 2012 Aug 22.

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