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Evaluation of Genotypic Antiviral Resistance Testing as an Alternative to Phenotypic Testing in a Patient with DOCK8 Deficiency and Severe HSV-1 Disease.

Casto AM, Stout SC, Selvarangan R, Freeman AF, Newell BD, Stahl ED, Ahmed AA, Greninger AL, Yin DE.

J Infect Dis. 2020 Jan 23. pii: jiaa020. doi: 10.1093/infdis/jiaa020. [Epub ahead of print]


Trillions and Trillions: Herpes Simplex Virus-1 Hepatitis in an Immunocompetent Adult.

Ikuta K, Roychoudhury P, Xie H, Mcclurkan CL, Walkiewicz M, Makhsous N, Huang ML, Beru Y, Alam M, Shepherd A, Lamotte ED, Patel K, Morris A, Ҫoruh B, Yu L, Bhattacharya R, Cheng R, Walter RB, Limaye AP, Lockwood CM, Holland SM, Rakita RM, Koelle DM, Greninger AL.

Open Forum Infect Dis. 2019 Nov 5;6(11):ofz465. doi: 10.1093/ofid/ofz465. eCollection 2019 Nov.


International Spread of Multidrug-Resistant Campylobacter coli in Men who have Sex with Men in Washington State and Quebec, 2015-2018.

Greninger AL, Addetia A, Starr K, Cybulski RJ, Stewart MK, Salipante SJ, Bryan AB, Cookson B, Gaudreau C, Bekal S, Fang FC.

Clin Infect Dis. 2019 Oct 29. pii: ciz1060. doi: 10.1093/cid/ciz1060. [Epub ahead of print]


Characterization of orally efficacious influenza drug with high resistance barrier in ferrets and human airway epithelia.

Toots M, Yoon JJ, Cox RM, Hart M, Sticher ZM, Makhsous N, Plesker R, Barrena AH, Reddy PG, Mitchell DG, Shean RC, Bluemling GR, Kolykhalov AA, Greninger AL, Natchus MG, Painter GR, Plemper RK.

Sci Transl Med. 2019 Oct 23;11(515). pii: eaax5866. doi: 10.1126/scitranslmed.aax5866.


Metagenomics to Assist in the Diagnosis of Bloodstream Infection.

Greninger AL, Naccache SN.

J Appl Lab Med. 2019 Jan;3(4):643-653. doi: 10.1373/jalm.2018.026120. Epub 2018 Nov 30. Review.


Inherited Chromosomally Integrated Human Herpesvirus 6 Demonstrates Tissue-Specific RNA Expression In Vivo That Correlates with an Increased Antibody Immune Response.

Peddu V, Dubuc I, Gravel A, Xie H, Huang ML, Tenenbaum D, Jerome KR, Tardif JC, Dubé MP, Flamand L, Greninger AL.

J Virol. 2019 Dec 12;94(1). pii: e01418-19. doi: 10.1128/JVI.01418-19. Print 2019 Dec 12.


Closing the Brief Case: Inherited Chromosomally Integrated Human Herpesvirus 6 (HHV-6) in the Age of Multiplex HHV-6 Testing.

Greninger AL, Naccache SN, Pannaraj P, Jerome KR, Dien Bard J, Ruderman JW.

J Clin Microbiol. 2019 Sep 24;57(10). pii: e02018-18. doi: 10.1128/JCM.02018-18. Print 2019 Oct. No abstract available.


The Brief Case: Inherited Chromosomally Integrated Human Herpesvirus 6 (HHV-6) in the Age of Multiplex HHV-6 Testing.

Greninger AL, Naccache SN, Pannaraj P, Jerome KR, Dien Bard J, Ruderman JW.

J Clin Microbiol. 2019 Sep 24;57(10). pii: e02016-18. doi: 10.1128/JCM.02016-18. Print 2019 Oct. No abstract available.


Comparison of Three Adenovirus Quantitative PCR Assays with ATCC Reference Strains and Clinical Samples.

Starr K, Greninger AL, Makhsous N, Jerome KR, Cook L.

J Clin Microbiol. 2019 Oct 23;57(11). pii: e00735-19. doi: 10.1128/JCM.00735-19. Print 2019 Nov.


One future of clinical metagenomic sequencing for infectious diseases.

Shean RC, Greninger AL.

Expert Rev Mol Diagn. 2019 Oct;19(10):849-851. doi: 10.1080/14737159.2019.1658524. Epub 2019 Aug 22. No abstract available.


Authentic Modeling of Human Respiratory Virus Infection in Human Pluripotent Stem Cell-Derived Lung Organoids.

Porotto M, Ferren M, Chen YW, Siu Y, Makhsous N, Rima B, Briese T, Greninger AL, Snoeck HW, Moscona A.

mBio. 2019 May 7;10(3). pii: e00723-19. doi: 10.1128/mBio.00723-19.


Genome-Wide Approach to the CD4 T-Cell Response to Human Herpesvirus 6B.

Hanson DJ, Tsvetkova O, Rerolle GF, Greninger AL, Sette A, Jing L, Campbell VL, Koelle DM.

J Virol. 2019 Jun 28;93(14). pii: e00321-19. doi: 10.1128/JVI.00321-19. Print 2019 Jul 15.


Whole-genome analysis of extraintestinal pathogenic Escherichia coli (ExPEC) MDR ST73 and ST127 isolated from endangered southern resident killer whales (Orcinus orca).

Melendez D, Roberts MC, Greninger AL, Weissman S, No D, Rabinowitz P, Wasser S.

J Antimicrob Chemother. 2019 Aug 1;74(8):2176-2180. doi: 10.1093/jac/dkz159.


Large, stable, contemporary interspecies recombination events in circulating human herpes simplex viruses.

Casto AM, Roychoudhury P, Xie H, Selke S, Perchetti GA, Wofford H, Huang ML, Verjans GMGM, Gottlieb GS, Wald A, Jerome KR, Koelle DM, Johnston C, Greninger AL.

J Infect Dis. 2019 Apr 23. pii: jiz199. doi: 10.1093/infdis/jiz199. [Epub ahead of print]


A Novel, Widespread qacA Allele Results in Reduced Chlorhexidine Susceptibility in Staphylococcus epidermidis.

Addetia A, Greninger AL, Adler A, Yuan S, Makhsous N, Qin X, Zerr DM.

Antimicrob Agents Chemother. 2019 May 24;63(6). pii: e02607-18. doi: 10.1128/AAC.02607-18. Print 2019 Jun.


Societal Implications of the Internet of Pathogens.

Greninger AL.

J Clin Microbiol. 2019 May 24;57(6). pii: e01914-18. doi: 10.1128/JCM.01914-18. Print 2019 Jun.


VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank.

Shean RC, Makhsous N, Stoddard GD, Lin MJ, Greninger AL.

BMC Bioinformatics. 2019 Jan 23;20(1):48. doi: 10.1186/s12859-019-2606-y.


Prospective, Real-time Metagenomic Sequencing During Norovirus Outbreak Reveals Discrete Transmission Clusters.

Casto AM, Adler AL, Makhsous N, Crawford K, Qin X, Kuypers JM, Huang ML, Zerr DM, Greninger AL.

Clin Infect Dis. 2019 Aug 30;69(6):941-948. doi: 10.1093/cid/ciy1020.


Mycobacterium talmoniae, a Potential Pulmonary Pathogen Isolated from Multiple Patients with Bronchiectasis in the United States, Including the First Case of Clinical Disease in a Patient with Cystic Fibrosis.

Vasireddy R, Vasireddy S, Brown-Elliott BA, Greninger AL, Davidson RM, Ard KL, Turenne CY, Wallace RJ Jr.

J Clin Microbiol. 2019 Jan 30;57(2). pii: e00906-18. doi: 10.1128/JCM.00906-18. Print 2019 Feb.


Viral Genetics Modulate Orolabial Herpes Simplex Virus Type 1 Shedding in Humans.

Ramchandani MS, Jing L, Russell RM, Tran T, Laing KJ, Magaret AS, Selke S, Cheng A, Huang ML, Xie H, Strachan E, Greninger AL, Roychoudhury P, Jerome KR, Wald A, Koelle DM.

J Infect Dis. 2019 Mar 15;219(7):1058-1066. doi: 10.1093/infdis/jiy631.


Limited Marginal Utility of Deep Sequencing for HIV Drug Resistance Testing in the Age of Integrase Inhibitors.

Dalmat RR, Makhsous N, Pepper GG, Magaret A, Jerome KR, Wald A, Greninger AL.

J Clin Microbiol. 2018 Nov 27;56(12). pii: e01443-18. doi: 10.1128/JCM.01443-18. Print 2018 Dec.


Epidemiological and genomic characterization of community-acquired Clostridium difficile infections.

Thornton CS, Rubin JE, Greninger AL, Peirano G, Chiu CY, Pillai DR.

BMC Infect Dis. 2018 Aug 31;18(1):443. doi: 10.1186/s12879-018-3337-9.


Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation.

Iketani S, Shean RC, Ferren M, Makhsous N, Aquino DB, des Georges A, Rima B, Mathieu C, Porotto M, Moscona A, Greninger AL.

mBio. 2018 Jul 3;9(4). pii: e00898-18. doi: 10.1128/mBio.00898-18.


An optimized methodology for whole genome sequencing of RNA respiratory viruses from nasopharyngeal aspirates.

Goya S, Valinotto LE, Tittarelli E, Rojo GL, Nabaes Jodar MS, Greninger AL, Zaiat JJ, Marti MA, Mistchenko AS, Viegas M.

PLoS One. 2018 Jun 25;13(6):e0199714. doi: 10.1371/journal.pone.0199714. eCollection 2018.


Distribution of Staphylococcus species in dairy cows, workers and shared farm environments.

Roberts MC, Garland-Lewis G, Trufan S, Meschke SJ, Fowler H, Shean RC, Greninger AL, Rabinowitz PM.

FEMS Microbiol Lett. 2018 Aug 1;365(15). doi: 10.1093/femsle/fny146.


Ultrasensitive Capture of Human Herpes Simplex Virus Genomes Directly from Clinical Samples Reveals Extraordinarily Limited Evolution in Cell Culture.

Greninger AL, Roychoudhury P, Xie H, Casto A, Cent A, Pepper G, Koelle DM, Huang ML, Wald A, Johnston C, Jerome KR.

mSphere. 2018 Jun 13;3(3). pii: e00283-18. doi: 10.1128/mSphereDirect.00283-18. Print 2018 Jun 27.


The challenge of diagnostic metagenomics.

Greninger AL.

Expert Rev Mol Diagn. 2018 Jul;18(7):605-615. doi: 10.1080/14737159.2018.1487292. Epub 2018 Jun 18. Review.


Orally Efficacious Broad-Spectrum Ribonucleoside Analog Inhibitor of Influenza and Respiratory Syncytial Viruses.

Yoon JJ, Toots M, Lee S, Lee ME, Ludeke B, Luczo JM, Ganti K, Cox RM, Sticher ZM, Edpuganti V, Mitchell DG, Lockwood MA, Kolykhalov AA, Greninger AL, Moore ML, Painter GR, Lowen AC, Tompkins SM, Fearns R, Natchus MG, Plemper RK.

Antimicrob Agents Chemother. 2018 Jul 27;62(8). pii: e00766-18. doi: 10.1128/AAC.00766-18. Print 2018 Aug.


The human clone ST22 SCCmec IV methicillin-resistant Staphylococcus aureus isolated from swine herds and wild primates in Nepal: is man the common source?

Roberts MC, Joshi PR, Greninger AL, Melendez D, Paudel S, Acharya M, Bimali NK, Koju NP, No D, Chalise M, Kyes RC.

FEMS Microbiol Ecol. 2018 May 1;94(5). doi: 10.1093/femsec/fiy052.


Heterogeneous Antimicrobial Susceptibility Characteristics in Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients.

Qin X, Zhou C, Zerr DM, Adler A, Addetia A, Yuan S, Greninger AL.

mSphere. 2018 Mar 14;3(2). pii: e00615-17. doi: 10.1128/mSphere.00615-17. eCollection 2018 Mar-Apr.


Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6.

Greninger AL, Knudsen GM, Roychoudhury P, Hanson DJ, Sedlak RH, Xie H, Guan J, Nguyen T, Peddu V, Boeckh M, Huang ML, Cook L, Depledge DP, Zerr DM, Koelle DM, Gantt S, Yoshikawa T, Caserta M, Hill JA, Jerome KR.

BMC Genomics. 2018 Mar 20;19(1):204. doi: 10.1186/s12864-018-4604-2.


Model-based estimation of superinfection prevalence from limited datasets.

Reeves DB, Magaret AS, Greninger AL, Johnston C, Schiffer JT.

J R Soc Interface. 2018 Feb;15(139). pii: 20170968. doi: 10.1098/rsif.2017.0968.


Copy Number Heterogeneity, Large Origin Tandem Repeats, and Interspecies Recombination in Human Herpesvirus 6A (HHV-6A) and HHV-6B Reference Strains.

Greninger AL, Roychoudhury P, Makhsous N, Hanson D, Chase J, Krueger G, Xie H, Huang ML, Saunders L, Ablashi D, Koelle DM, Cook L, Jerome KR.

J Virol. 2018 Apr 27;92(10). pii: e00135-18. doi: 10.1128/JVI.00135-18. Print 2018 May 15.


Continued in vitro cefazolin susceptibility in methicillin-susceptible Staphylococcus aureus.

Gern BH, Greninger AL, Weissman SJ, Stapp JR, Tao Y, Qin X.

Ann Clin Microbiol Antimicrob. 2018 Feb 20;17(1):5. doi: 10.1186/s12941-018-0257-x.


The Unstructured Paramyxovirus Nucleocapsid Protein Tail Domain Modulates Viral Pathogenesis through Regulation of Transcriptase Activity.

Thakkar VD, Cox RM, Sawatsky B, da Fontoura Budaszewski R, Sourimant J, Wabbel K, Makhsous N, Greninger AL, von Messling V, Plemper RK.

J Virol. 2018 Mar 28;92(8). pii: e02064-17. doi: 10.1128/JVI.02064-17. Print 2018 Apr 15.


Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples.

Xue KS, Greninger AL, Pérez-Osorio A, Bloom JD.

mSphere. 2018 Jan 3;3(1). pii: e00552-17. doi: 10.1128/mSphereDirect.00552-17. eCollection 2018 Jan-Feb.


Dual-strain genital herpes simplex virus type 2 (HSV-2) infection in the US, Peru, and 8 countries in sub-Saharan Africa: A nested cross-sectional viral genotyping study.

Johnston C, Magaret A, Roychoudhury P, Greninger AL, Reeves D, Schiffer J, Jerome KR, Sather C, Diem K, Lingappa JR, Celum C, Koelle DM, Wald A.

PLoS Med. 2017 Dec 27;14(12):e1002475. doi: 10.1371/journal.pmed.1002475. eCollection 2017 Dec.


Myeloablation-associated deletion of ORF4 in a human coronavirus 229E infection.

Greninger AL, Pepper G, Shean RC, Cent A, Palileo I, Kuypers JM, Schiffer JT, Jerome KR.

NPJ Genom Med. 2017 Oct 9;2:30. doi: 10.1038/s41525-017-0033-4. eCollection 2017.


A decade of RNA virus metagenomics is (not) enough.

Greninger AL.

Virus Res. 2018 Jan 15;244:218-229. doi: 10.1016/j.virusres.2017.10.014. Epub 2017 Oct 18. Review.


Mycobacterium grossiae sp. nov., a rapidly growing, scotochromogenic species isolated from human clinical respiratory and blood culture specimens.

Paniz-Mondolfi AE, Greninger AL, Ladutko L, Brown-Elliott BA, Vasireddy R, Jakubiec W, Vasireddy S, Wallace RJ Jr, Simmon KE, Dunn BE, Jackoway G, Vora SB, Quinn KK, Qin X, Campbell S.

Int J Syst Evol Microbiol. 2017 Nov;67(11):4345-4351. doi: 10.1099/ijsem.0.002216. Epub 2017 Oct 6.


Acute Liver Failure Due to Echovirus 9 Associated With Persistent B-Cell Depletion From Rituximab.

Bajema KL, Simonson PD, Greninger AL, Çoruh B, Pottinger PS, Bhattacharya R, Liou IW, Jalikis FG, Fligner CL, Rakita RM.

Open Forum Infect Dis. 2017 Aug 14;4(3):ofx174. doi: 10.1093/ofid/ofx174. eCollection 2017 Summer.


Conservation and Recombination in the Genome Sequence of Haemophilus influenzae Type f WAPHL1.

Bateman AC, Perez-Osorio AC, Li Z, Tran M, Greninger AL.

Genome Announc. 2017 Sep 21;5(38). pii: e00929-17. doi: 10.1128/genomeA.00929-17.


Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses.

Niyonzima N, Lambert AR, Werther R, De Silva Feelixge H, Roychoudhury P, Greninger AL, Stone D, Stoddard BL, Jerome KR.

Protein Eng Des Sel. 2017 Jul 1;30(7):503-522. doi: 10.1093/protein/gzx037.


Isolation and characterization of the fall Chinook aquareovirus.

Makhsous N, Jensen NL, Haman KH, Batts WN, Jerome KR, Winton JR, Greninger AL.

Virol J. 2017 Sep 5;14(1):170. doi: 10.1186/s12985-017-0839-9.


Prolonged Shedding of Human Coronavirus in Hematopoietic Cell Transplant Recipients: Risk Factors and Viral Genome Evolution.

Ogimi C, Greninger AL, Waghmare AA, Kuypers JM, Shean RC, Xie H, Leisenring WM, Stevens-Ayers TL, Jerome KR, Englund JA, Boeckh M.

J Infect Dis. 2017 Jul 15;216(2):203-209. doi: 10.1093/infdis/jix264.


Highly conserved intragenic HSV-2 sequences: Results from next-generation sequencing of HSV-2 UL and US regions from genital swabs collected from 3 continents.

Johnston C, Magaret A, Roychoudhury P, Greninger AL, Cheng A, Diem K, Fitzgibbon MP, Huang ML, Selke S, Lingappa JR, Celum C, Jerome KR, Wald A, Koelle DM.

Virology. 2017 Oct;510:90-98. doi: 10.1016/j.virol.2017.06.031. Epub 2017 Jul 13.


Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory.

Kozyreva VK, Truong CL, Greninger AL, Crandall J, Mukhopadhyay R, Chaturvedi V.

J Clin Microbiol. 2017 Aug;55(8):2502-2520. doi: 10.1128/JCM.00361-17. Epub 2017 Jun 7.


Clostridium perfringens sepsis masquerading as a hemolytic transfusion reaction.

Greninger AL, Hess JR.

Transfusion. 2017 May;57(5):1112. doi: 10.1111/trf.13863. No abstract available.


Rule-Out Outbreak: 24-Hour Metagenomic Next-Generation Sequencing for Characterizing Respiratory Virus Source for Infection Prevention.

Greninger AL, Waghmare A, Adler A, Qin X, Crowley JL, Englund JA, Kuypers JM, Jerome KR, Zerr DM.

J Pediatric Infect Dis Soc. 2017 Jun 1;6(2):168-172. doi: 10.1093/jpids/pix019.

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