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Clinical Impact of Metagenomic Next-Generation Sequencing of Plasma Cell-Free DNA for the Diagnosis of Infectious Diseases: A Multicenter Retrospective Cohort Study.

Hogan CA, Yang S, Garner OB, Green DA, Gomez CA, Dien Bard J, Pinsky BA, Banaei N.

Clin Infect Dis. 2020 Jan 14. pii: ciaa035. doi: 10.1093/cid/ciaa035. [Epub ahead of print]


Simple Processing of Formalin-Fixed Paraffin-Embedded Tissue for Accurate Testing with the Xpert MTB/RIF assay.

Budvytiene I, Banaei N.

J Clin Microbiol. 2019 Dec 18. pii: JCM.01905-19. doi: 10.1128/JCM.01905-19. [Epub ahead of print]


Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly.

Kang JB, Siranosian BA, Moss EL, Banaei N, Andermann TM, Bhatt AS.

BMC Bioinformatics. 2019 Dec 2;20(Suppl 16):585. doi: 10.1186/s12859-019-3073-1.


Rapid identification of pathogenic bacteria using Raman spectroscopy and deep learning.

Ho CS, Jean N, Hogan CA, Blackmon L, Jeffrey SS, Holodniy M, Banaei N, Saleh AAE, Ermon S, Dionne J.

Nat Commun. 2019 Oct 30;10(1):4927. doi: 10.1038/s41467-019-12898-9.


Investigation of Preanalytical Variables Impacting Pathogen Cell-Free DNA in Blood and Urine.

Murugesan K, Hogan CA, Palmer Z, Reeve B, Theron G, Andama A, Somoskovi A, Steadman A, Madan D, Andrews J, Croda J, Sahoo MK, Cattamanchi A, Pinsky BA, Banaei N.

J Clin Microbiol. 2019 Oct 23;57(11). pii: e00782-19. doi: 10.1128/JCM.00782-19. Print 2019 Nov.


Dual Reporting of Clostridioides difficile PCR and Predicted Toxin Result Based on PCR Cycle Threshold Reduces Treatment of Toxin-Negative Patients without Increases in Adverse Outcomes.

Hitchcock MM, Holubar M, Hogan CA, Tompkins LS, Banaei N.

J Clin Microbiol. 2019 Oct 23;57(11). pii: e01288-19. doi: 10.1128/JCM.01288-19. Print 2019 Nov.


Comparing QuantiFERON-TB Gold Plus with Other Tests To Diagnose Mycobacterium tuberculosis Infection.

Venkatappa TK, Punnoose R, Katz DJ, Higgins MP, Banaei N, Graviss EA, Belknap RW, Ho CS.

J Clin Microbiol. 2019 Oct 23;57(11). pii: e00985-19. doi: 10.1128/JCM.00985-19. Print 2019 Nov.


Reproducibility of positive results for rare pathogens on the FilmArray GI Panel.

Hitchcock MM, Hogan CA, Budvytiene I, Banaei N.

Diagn Microbiol Infect Dis. 2019 Sep;95(1):10-14. doi: 10.1016/j.diagmicrobio.2019.03.013. Epub 2019 Mar 29.


Eremothecium coryli bloodstream infection in a patient with acute myeloid leukemia: first case report of human infection.

Multani A, Rustagi A, Epstein DJ, Gomez CA, Budvytiene I, Banaei N, Brown JM, Liu AY.

Diagn Microbiol Infect Dis. 2019 Sep;95(1):77-79. doi: 10.1016/j.diagmicrobio.2019.03.011. Epub 2019 Mar 27.


Rapid antimicrobial susceptibility testing by VITEK®2 directly from blood cultures in patients with Gram-negative rod bacteremia.

Hogan CA, Watz N, Budvytiene I, Banaei N.

Diagn Microbiol Infect Dis. 2019 Jun;94(2):116-121. doi: 10.1016/j.diagmicrobio.2019.01.001. Epub 2019 Jan 16.


Diversity of resistance mechanisms in carbapenem-resistant Enterobacteriaceae at a health care system in Northern California, from 2013 to 2016.

Senchyna F, Gaur RL, Sandlund J, Truong C, Tremintin G, Kültz D, Gomez CA, Tamburini FB, Andermann T, Bhatt A, Tickler I, Watz N, Budvytiene I, Shi G, Tenover FC, Banaei N.

Diagn Microbiol Infect Dis. 2019 Mar;93(3):250-257. doi: 10.1016/j.diagmicrobio.2018.10.004. Epub 2018 Oct 13.


Clinical Impact of Clostridium difficile PCR Cycle Threshold-Predicted Toxin Reporting in Pediatric Patients.

Schwenk HT, Bio LL, Kruger JF, Banaei N.

J Pediatric Infect Dis Soc. 2018 Nov 22. doi: 10.1093/jpids/piy117. [Epub ahead of print]


Toward the Development of a Circulating Free DNA-Based In Vitro Diagnostic Test for Infectious Diseases: a Review of Evidence for Tuberculosis.

Fernández-Carballo BL, Broger T, Wyss R, Banaei N, Denkinger CM.

J Clin Microbiol. 2019 Mar 28;57(4). pii: e01234-18. doi: 10.1128/JCM.01234-18. Print 2019 Apr. Review.


1H, 13C and 15N resonance assignments and structure prediction of translation initiation factor 1 from Clostridium difficile.

Aguilar F, Banaei N, Zhang Y.

Biomol NMR Assign. 2019 Apr;13(1):91-95. doi: 10.1007/s12104-018-9858-8. Epub 2018 Oct 28.


Higher Positivity Rate with Fourth-Generation QuantiFERON-TB Gold Plus Assay in Low-Risk U.S. Health Care Workers.

Hogan CA, Tien S, Pai M, Banaei N.

J Clin Microbiol. 2019 Jan 2;57(1). pii: e01688-18. doi: 10.1128/JCM.01688-18. Print 2019 Jan. No abstract available.


Precision identification of diverse bloodstream pathogens in the gut microbiome.

Tamburini FB, Andermann TM, Tkachenko E, Senchyna F, Banaei N, Bhatt AS.

Nat Med. 2018 Dec;24(12):1809-1814. doi: 10.1038/s41591-018-0202-8. Epub 2018 Oct 15.


Ultrasensitive Detection of Clostridioides difficile Toxins A and B by Use of Automated Single-Molecule Counting Technology.

Sandlund J, Bartolome A, Almazan A, Tam S, Biscocho S, Abusali S, Bishop JJ, Nolan N, Estis J, Todd J, Young S, Senchyna F, Banaei N.

J Clin Microbiol. 2018 Oct 25;56(11). pii: e00908-18. doi: 10.1128/JCM.00908-18. Print 2018 Nov.


Rapid and specific labeling of single live Mycobacterium tuberculosis with a dual-targeting fluorogenic probe.

Cheng Y, Xie J, Lee KH, Gaur RL, Song A, Dai T, Ren H, Wu J, Sun Z, Banaei N, Akin D, Rao J.

Sci Transl Med. 2018 Aug 15;10(454). pii: eaar4470. doi: 10.1126/scitranslmed.aar4470.


Development of colorimetric sensor array for diagnosis of tuberculosis through detection of urinary volatile organic compounds.

Sandlund J, Lim S, Queralto N, Huang R, Yun J, Taba B, Song R, Odero R, Ouma G, Sitati R, Murithi W, Cain KP, Banaei N.

Diagn Microbiol Infect Dis. 2018 Dec;92(4):299-304. doi: 10.1016/j.diagmicrobio.2018.06.014. Epub 2018 Jun 22.


Liquid biopsy for infectious diseases: sequencing of cell-free plasma to detect pathogen DNA in patients with invasive fungal disease.

Hong DK, Blauwkamp TA, Kertesz M, Bercovici S, Truong C, Banaei N.

Diagn Microbiol Infect Dis. 2018 Nov;92(3):210-213. doi: 10.1016/j.diagmicrobio.2018.06.009. Epub 2018 Jun 22.


Spiking of intravenous bags does not cause time-dependent microbial contamination: a preliminary report.

Brock-Utne JG, Smith SC, Banaei N, Chang SC, Alejandro-Harper D, Jaffe RA.

Infect Control Hosp Epidemiol. 2018 Sep;39(9):1129-1130. doi: 10.1017/ice.2018.143. Epub 2018 Jul 2. No abstract available.


Trypanosoma cruzi Reactivation in the Brain.

Gomez CA, Banaei N.

N Engl J Med. 2018 May 10;378(19):1824. doi: 10.1056/NEJMicm1703763. No abstract available.


Intramolecular substitution uncages fluorogenic probes for detection of metallo-carbapenemase-expressing bacteria.

Song A, Cheng Y, Xie J, Banaei N, Rao J.

Chem Sci. 2017 Nov 1;8(11):7669-7674. doi: 10.1039/c7sc02416a. Epub 2017 Sep 21.


Evaluation of the Xpert MTB/RIF Performance on Tissues: Potential Impact on Airborne Infection Isolation at a Tertiary Cancer Care Center.

McMillen T, Usiak SC, Chen LH, Gomez L, Ntiamoah P, Hameed MR, Budvytiene I, Banaei N, Kamboj M, Babady NE.

Infect Control Hosp Epidemiol. 2018 Apr;39(4):462-466. doi: 10.1017/ice.2018.7. Epub 2018 Feb 15.


Low Yield of FilmArray GI Panel in Hospitalized Patients with Diarrhea: an Opportunity for Diagnostic Stewardship Intervention.

Hitchcock MM, Gomez CA, Banaei N.

J Clin Microbiol. 2018 Feb 22;56(3). pii: e01558-17. doi: 10.1128/JCM.01558-17. Print 2018 Mar.


Microfluidics for Combating Antimicrobial Resistance.

Liu Z, Banaei N, Ren K.

Trends Biotechnol. 2017 Dec;35(12):1129-1139. doi: 10.1016/j.tibtech.2017.07.008. Epub 2017 Nov 15. Review.


Performance of Targeted Fungal Sequencing for Culture-Independent Diagnosis of Invasive Fungal Disease.

Gomez CA, Budvytiene I, Zemek AJ, Banaei N.

Clin Infect Dis. 2017 Nov 29;65(12):2035-2041. doi: 10.1093/cid/cix728.


Multiplex detection of pancreatic cancer biomarkers using a SERS-based immunoassay.

Banaei N, Foley A, Houghton JM, Sun Y, Kim B.

Nanotechnology. 2017 Nov 10;28(45):455101. doi: 10.1088/1361-6528/aa8e8c.


Small Colony Variants of Pseudomonas aeruginosa Display Heterogeneity in Inhibiting Aspergillus fumigatus Biofilm.

Anand R, Moss RB, Sass G, Banaei N, Clemons KV, Martinez M, Stevens DA.

Mycopathologia. 2018 Feb;183(1):263-272. doi: 10.1007/s11046-017-0186-9. Epub 2017 Aug 7.


Detecting New Mycobacterium tuberculosis Infection. Time for a More Nuanced Interpretation of QuantiFERON Conversions.

Banaei N, Pai M.

Am J Respir Crit Care Med. 2017 Sep 1;196(5):546-547. doi: 10.1164/rccm.201707-1543ED. No abstract available.


Malaria and Chikungunya Detected Using Molecular Diagnostics Among Febrile Kenyan Children.

Waggoner J, Brichard J, Mutuku F, Ndenga B, Heath CJ, Mohamed-Hadley A, Sahoo MK, Vulule J, Lefterova M, Banaei N, Mukoko D, Pinsky BA, LaBeaud AD.

Open Forum Infect Dis. 2017 May 29;4(3):ofx110. doi: 10.1093/ofid/ofx110. eCollection 2017 Summer.


Clostridium difficile PCR Cycle Threshold Predicts Free Toxin.

Senchyna F, Gaur RL, Gombar S, Truong CY, Schroeder LF, Banaei N.

J Clin Microbiol. 2017 Sep;55(9):2651-2660. doi: 10.1128/JCM.00563-17. Epub 2017 Jun 14.


Delayed Diagnosis of Tuberculous Meningitis Misdiagnosed as Herpes Simplex Virus-1 Encephalitis With the FilmArray Syndromic Polymerase Chain Reaction Panel.

Gomez CA, Pinsky BA, Liu A, Banaei N.

Open Forum Infect Dis. 2016 Dec 7;4(1):ofw245. doi: 10.1093/ofid/ofw245. eCollection 2017 Winter.


Metagenomic DNA Sequencing for the Diagnosis of Intraocular Infections.

Doan T, Acharya NR, Pinsky BA, Sahoo MK, Chow ED, Banaei N, Budvytiene I, Cevallos V, Zhong L, Zhou Z, Lietman TM, DeRisi JL.

Ophthalmology. 2017 Aug;124(8):1247-1248. doi: 10.1016/j.ophtha.2017.03.045. Epub 2017 May 16. No abstract available.


Susceptibility of Candida albicans from Cystic Fibrosis Patients.

Sabino R, Carolino E, Moss RB, Banaei N, Verissimo C, Stevens DA.

Mycopathologia. 2017 Oct;182(9-10):863-867. doi: 10.1007/s11046-017-0133-9. Epub 2017 Apr 18.


Evaluation of QuantiFERON-TB Gold-Plus in Health Care Workers in a Low-Incidence Setting.

Moon HW, Gaur RL, Tien SS, Spangler M, Pai M, Banaei N.

J Clin Microbiol. 2017 Jun;55(6):1650-1657. doi: 10.1128/JCM.02498-16. Epub 2017 Mar 15.


Real-Time Electronic Tracking of Diarrheal Episodes and Laxative Therapy Enables Verification of Clostridium difficile Clinical Testing Criteria and Reduction of Clostridium difficile Infection Rates.

Truong CY, Gombar S, Wilson R, Sundararajan G, Tekic N, Holubar M, Shepard J, Madison A, Tompkins L, Shah N, Deresinski S, Schroeder LF, Banaei N.

J Clin Microbiol. 2017 May;55(5):1276-1284. doi: 10.1128/JCM.02319-16. Epub 2017 Mar 1.


New and developing diagnostic technologies for urinary tract infections.

Davenport M, Mach KE, Shortliffe LMD, Banaei N, Wang TH, Liao JC.

Nat Rev Urol. 2017 May;14(5):296-310. doi: 10.1038/nrurol.2017.20. Epub 2017 Mar 1. Review.


Is Follow-Up Testing with the FilmArray Gastrointestinal Multiplex PCR Panel Necessary?

Park S, Hitchcock MM, Gomez CA, Banaei N.

J Clin Microbiol. 2017 Apr;55(4):1154-1161. doi: 10.1128/JCM.02354-16. Epub 2017 Jan 25.


Fatal Emmonsia sp. Infection and Fungemia after Orthotopic Liver Transplantation.

Kappagoda S, Adams JY, Luo R, Banaei N, Concepcion W, Ho DY.

Emerg Infect Dis. 2017 Feb;23(2):346-349. doi: 10.3201/eid2302.160799.


Clostridium difficile rates in asymptomatic and symptomatic hospitalized patients using nucleic acid testing.

Truong C, Schroeder LF, Gaur R, Anikst VE, Komo I, Watters C, McCalley E, Kulik C, Pickham D, Lee NJ, Banaei N.

Diagn Microbiol Infect Dis. 2017 Apr;87(4):365-370. doi: 10.1016/j.diagmicrobio.2016.12.014. Epub 2017 Jan 3.


Are Cystic Fibrosis Aspergillus fumigatus Isolates Different? Intermicrobial Interactions with Pseudomonas.

Nazik H, Moss RB, Karna V, Clemons KV, Banaei N, Cohen K, Choudhary V, Stevens DA.

Mycopathologia. 2017 Apr;182(3-4):315-318. doi: 10.1007/s11046-016-0087-3. Epub 2016 Nov 7.


Adenosine triphosphate bioluminescence for bacteriologic surveillance and reprocessing strategies for minimizing risk of infection transmission by duodenoscopes.

Sethi S, Huang RJ, Barakat MT, Banaei N, Friedland S, Banerjee S.

Gastrointest Endosc. 2017 Jun;85(6):1180-1187.e1. doi: 10.1016/j.gie.2016.10.035. Epub 2016 Nov 3.


Determining the cause of recurrent Clostridium difficile infection using whole genome sequencing.

Sim JH, Truong C, Minot SS, Greenfield N, Budvytiene I, Lohith A, Anikst V, Pourmand N, Banaei N.

Diagn Microbiol Infect Dis. 2017 Jan;87(1):11-16. doi: 10.1016/j.diagmicrobio.2016.09.023. Epub 2016 Oct 5.


Serial testing for latent tuberculosis using QuantiFERON-TB Gold In-Tube: A Markov model.

Moses MW, Zwerling A, Cattamanchi A, Denkinger CM, Banaei N, Kik SV, Metcalfe J, Pai M, Dowdy D.

Sci Rep. 2016 Jul 29;6:30781. doi: 10.1038/srep30781.


Rapid Diagnosis of Tuberculosis from Analysis of Urine Volatile Organic Compounds.

Lim SH, Martino R, Anikst V, Xu Z, Mix S, Benjamin R, Schub H, Eiden M, Rhodes PA, Banaei N.

ACS Sens. 2016 Jul 22;1(7):852-856. doi: 10.1021/acssensors.6b00309. Epub 2016 Jun 9.


Toxin Immunoassays and Clostridium difficile Infection.

Banaei N, Schroeder LF.

JAMA Intern Med. 2016 Mar;176(3):413. doi: 10.1001/jamainternmed.2015.8525. No abstract available.


Organism burden, toxin concentration, and lactoferrin concentration do not distinguish between clinically significant and nonsignificant diarrhea in patients with Clostridium difficile.

Anikst VE, Gaur RL, Schroeder LF, Banaei N.

Diagn Microbiol Infect Dis. 2016 Apr;84(4):343-6. doi: 10.1016/j.diagmicrobio.2015.11.022. Epub 2015 Nov 30.


Interferon Gamma Release Assays for Latent Tuberculosis: What Are the Sources of Variability?

Banaei N, Gaur RL, Pai M.

J Clin Microbiol. 2016 Apr;54(4):845-50. doi: 10.1128/JCM.02803-15. Epub 2016 Jan 13. Review.

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