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Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis.

Wilson MR, Sample HA, Zorn KC, Arevalo S, Yu G, Neuhaus J, Federman S, Stryke D, Briggs B, Langelier C, Berger A, Douglas V, Josephson SA, Chow FC, Fulton BD, DeRisi JL, Gelfand JM, Naccache SN, Bender J, Dien Bard J, Murkey J, Carlson M, Vespa PM, Vijayan T, Allyn PR, Campeau S, Humphries RM, Klausner JD, Ganzon CD, Memar F, Ocampo NA, Zimmermann LL, Cohen SH, Polage CR, DeBiasi RL, Haller B, Dallas R, Maron G, Hayden R, Messacar K, Dominguez SR, Miller S, Chiu CY.

N Engl J Med. 2019 Jun 13;380(24):2327-2340. doi: 10.1056/NEJMoa1803396.


A Laboratory Medicine Best Practices Systematic Review and Meta-analysis of Nucleic Acid Amplification Tests (NAATs) and Algorithms Including NAATs for the Diagnosis of Clostridioides (Clostridium) difficile in Adults.

Kraft CS, Parrott JS, Cornish NE, Rubinstein ML, Weissfeld AS, McNult P, Nachamkin I, Humphries RM, Kirn TJ, Dien Bard J, Lutgring JD, Gullett JC, Bittencourt CE, Benson S, Bobenchik AM, Sautter RL, Baselski V, Atlas MC, Marlowe EM, Miller NS, Fischer M, Richter SS, Gilligan P, Snyder JW.

Clin Microbiol Rev. 2019 May 29;32(3). pii: e00032-18. doi: 10.1128/CMR.00032-18. Print 2019 Jun 19.


The New, New Daptomycin Breakpoint for Enterococcus spp.

Humphries RM.

J Clin Microbiol. 2019 Jun 25;57(7). pii: e00600-19. doi: 10.1128/JCM.00600-19. Print 2019 Jul.


CIM City: the Game Continues for a Better Carbapenemase Test.

Humphries RM.

J Clin Microbiol. 2019 Jun 25;57(7). pii: e00353-19. doi: 10.1128/JCM.00353-19. Print 2019 Jul.


Understanding and Addressing CLSI Breakpoint Revisions: a Primer for Clinical Laboratories.

Humphries RM, Abbott AN, Hindler JA.

J Clin Microbiol. 2019 May 24;57(6). pii: e00203-19. doi: 10.1128/JCM.00203-19. Print 2019 Jun. Review.


Ceftazidime/avibactam resistance associated with L169P mutation in the omega loop of KPC-2.

Hemarajata P, Humphries RM.

J Antimicrob Chemother. 2019 Feb 7. doi: 10.1093/jac/dkz026. [Epub ahead of print]


A multisite implementation of a real-time polymerase chain reaction assay to predict ciprofloxacin susceptibility in Neisseria gonorrhoeae.

Ellis O, Hemarajata P, Shahkolahi A, Masinde G, Buchs K, Humphries RM, Klausner JD.

Diagn Microbiol Infect Dis. 2019 Jul;94(3):213-217. doi: 10.1016/j.diagmicrobio.2018.12.018. Epub 2019 Jan 14.


Evaluation of the Accelerate Pheno System for Identification of Acinetobacter Clinical Isolates and Minocycline Susceptibility Testing.

Bowler SL, Towne JW, Humphries RM, Doi Y.

J Clin Microbiol. 2019 Feb 27;57(3). pii: e01711-18. doi: 10.1128/JCM.01711-18. Print 2019 Mar.


Public Health Efforts Can Impact Adoption of Current Susceptibility Breakpoints, but Closer Attention from Regulatory Bodies Is Needed.

McKinnell JA, Bhaurla S, Marquez-Sung P, Pucci A, Baron M, Kamali T, Bugante J, Schwartz B, Balter S, Terashita D, Butler-Wu S, Gunzenhauser J, Hindler J, Humphries RM.

J Clin Microbiol. 2019 Feb 27;57(3). pii: e01488-18. doi: 10.1128/JCM.01488-18. Print 2019 Mar.


Evaluation of Ciprofloxacin and Levofloxacin Disk Diffusion and Etest Using the 2019 Enterobacteriaceae CLSI Breakpoints.

Humphries RM, Hindler JA, Shaffer K, Campeau SA.

J Clin Microbiol. 2019 Feb 27;57(3). pii: e01797-18. doi: 10.1128/JCM.01797-18. Print 2019 Mar.


Performance of ceftazidime/avibactam susceptibility testing methods against clinically relevant Gram-negative organisms.

Wenzler E, Lee M, Wu TJ, Meyer KA, Shields RK, Nguyen MH, Clancy CJ, Humphries RM, Harrington AT.

J Antimicrob Chemother. 2019 Mar 1;74(3):633-638. doi: 10.1093/jac/dky483.


Fluoroquinolone Prophylaxis Selects for Meropenem-nonsusceptible Pseudomonas aeruginosa in Patients With Hematologic Malignancies and Hematopoietic Cell Transplant Recipients.

Hakki M, Humphries RM, Hemarajata P, Tallman GB, Shields RK, Mettus RT, Doi Y, Lewis JS.

Clin Infect Dis. 2019 May 30;68(12):2045-2052. doi: 10.1093/cid/ciy825.


The Frequency of Discordant Gyrase A Genotypes Among Cases of Multiple Neisseria gonorrhoeae Infections at Different Anatomic Sites.

Allan-Blitz LT, Ellis OL, Bolan R, Hemarajata P, Humphries RM, Shahkolahi A, McGrath M, Klausner JD.

Sex Transm Dis. 2019 Jan;46(1):e3-e4. doi: 10.1097/OLQ.0000000000000912.


Practical methods for effective vancomycin-resistant enterococci (VRE) surveillance: experience in a liver transplant surgical intensive care unit.

Linfield RY, Campeau S, Injean P, Gregson A, Kaldas F, Rubin Z, Kim T, Kunz D, Chan A, Lee DJ, Humphries RM, McKinnell JA.

Infect Control Hosp Epidemiol. 2018 Oct;39(10):1178-1182. doi: 10.1017/ice.2018.178. Epub 2018 Sep 4.


Pharmacodynamics of Daptomycin against Enterococcus faecium and Enterococcus faecalis in the Murine Thigh Infection Model.

Kidd JM, Abdelraouf K, Asempa TE, Humphries RM, Nicolau DP.

Antimicrob Agents Chemother. 2018 Sep 24;62(10). pii: e00506-18. doi: 10.1128/AAC.00506-18. Print 2018 Oct.


Variability of Daptomycin MIC Values for Enterococcus faecium When Measured by Reference Broth Microdilution and Gradient Diffusion Tests.

Campeau SA, Schuetz AN, Kohner P, Arias CA, Hemarajata P, Bard JD, Humphries RM.

Antimicrob Agents Chemother. 2018 Aug 27;62(9). pii: e00745-18. doi: 10.1128/AAC.00745-18. Print 2018 Sep.


Twenty-first Century Cures Act and Antimicrobial Susceptibility Testing: Clinical Implications in the Era of Multidrug Resistance.

Humphries RM, Hindler J, Jane Ferraro M, Mathers A.

Clin Infect Dis. 2018 Sep 14;67(7):1132-1138. doi: 10.1093/cid/ciy432.


The Continued Value of Disk Diffusion for Assessing Antimicrobial Susceptibility in Clinical Laboratories: Report from the Clinical and Laboratory Standards Institute Methods Development and Standardization Working Group.

Humphries RM, Kircher S, Ferrell A, Krause KM, Malherbe R, Hsiung A, Burnham CA.

J Clin Microbiol. 2018 Jul 26;56(8). pii: e00437-18. doi: 10.1128/JCM.00437-18. Print 2018 Aug. Review.


Duodenoscope-Related Outbreak of a Carbapenem-Resistant Klebsiella pneumoniae Identified Using Advanced Molecular Diagnostics.

Humphries RM, Yang S, Kim S, Muthusamy VR, Russell D, Trout AM, Zaroda T, Cheng QJ, Aldrovandi G, Uslan DZ, Hemarajata P, Rubin ZA.

Clin Infect Dis. 2017 Oct 1;65(7):1159-1166. doi: 10.1093/cid/cix527.


Selection of hyperproduction of AmpC and SME-1 in a carbapenem-resistant Serratia marcescens isolate during antibiotic therapy.

Hemarajata P, Amick T, Yang S, Gregson A, Holzmeyer C, Bush K, Humphries RM.

J Antimicrob Chemother. 2018 May 1;73(5):1256-1262. doi: 10.1093/jac/dky028.


Ciprofloxacin May be Efficacious in Treating Wild-Type Gyrase A Genotype Neisseria gonorrhoeae Infections.

Allan-Blitz LT, Hemarajata P, Humphries RM, Kimble M, Elias S, Klausner JD.

Sex Transm Dis. 2018 Apr;45(4):e18. doi: 10.1097/OLQ.0000000000000758. No abstract available.


Impact of 21st Century Cures Act on Breakpoints and Commercial Antimicrobial Susceptibility Test Systems: Progress and Pitfalls.

Humphries RM, Ferraro MJ, Hindler JA.

J Clin Microbiol. 2018 Apr 25;56(5). pii: e00139-18. doi: 10.1128/JCM.00139-18. Print 2018 May. Review.


CLSI Methods Development and Standardization Working Group Best Practices for Evaluation of Antimicrobial Susceptibility Tests.

Humphries RM, Ambler J, Mitchell SL, Castanheira M, Dingle T, Hindler JA, Koeth L, Sei K; CLSI Methods Development and Standardization Working Group of the Subcommittee on Antimicrobial Susceptibility Testing.

J Clin Microbiol. 2018 Mar 26;56(4). pii: e01934-17. doi: 10.1128/JCM.01934-17. Print 2018 Apr. Review.


A Cost Analysis of Gyrase A Testing and Targeted Ciprofloxacin Therapy Versus Recommended 2-Drug Therapy for Neisseria gonorrhoeae Infection.

Allan-Blitz LT, Hemarajata P, Humphries RM, Wynn A, Segura ER, Klausner JD.

Sex Transm Dis. 2018 Feb;45(2):87-91. doi: 10.1097/OLQ.0000000000000698.


Multicenter Evaluation of the Accelerate PhenoTest BC Kit for Rapid Identification and Phenotypic Antimicrobial Susceptibility Testing Using Morphokinetic Cellular Analysis.

Pancholi P, Carroll KC, Buchan BW, Chan RC, Dhiman N, Ford B, Granato PA, Harrington AT, Hernandez DR, Humphries RM, Jindra MR, Ledeboer NA, Miller SA, Mochon AB, Morgan MA, Patel R, Schreckenberger PC, Stamper PD, Simner PJ, Tucci NE, Zimmerman C, Wolk DM.

J Clin Microbiol. 2018 Mar 26;56(4). pii: e01329-17. doi: 10.1128/JCM.01329-17. Print 2018 Apr.


Direct-from-Blood-Culture Disk Diffusion To Determine Antimicrobial Susceptibility of Gram-Negative Bacteria: Preliminary Report from the Clinical and Laboratory Standards Institute Methods Development and Standardization Working Group.

Chandrasekaran S, Abbott A, Campeau S, Zimmer BL, Weinstein M, Thrupp L, Hejna J, Walker L, Ammann T, Kirn T, Patel R, Humphries RM.

J Clin Microbiol. 2018 Feb 22;56(3). pii: e01678-17. doi: 10.1128/JCM.01678-17. Print 2018 Mar.


Performance of Ceftolozane-Tazobactam Etest, MIC Test Strips, and Disk Diffusion Compared to Reference Broth Microdilution for β-Lactam-Resistant Pseudomonas aeruginosa Isolates.

Humphries RM, Hindler JA, Magnano P, Wong-Beringer A, Tibbetts R, Miller SA.

J Clin Microbiol. 2018 Feb 22;56(3). pii: e01633-17. doi: 10.1128/JCM.01633-17. Print 2018 Mar.


Evaluation of Oxacillin and Cefoxitin Disk Diffusion and MIC Breakpoints Established by the Clinical and Laboratory Standards Institute for Detection of mecA-Mediated Oxacillin Resistance in Staphylococcus schleiferi.

Huse HK, Miller SA, Chandrasekaran S, Hindler JA, Lawhon SD, Bemis DA, Westblade LF, Humphries RM.

J Clin Microbiol. 2018 Jan 24;56(2). pii: e01653-17. doi: 10.1128/JCM.01653-17. Print 2018 Feb.


Carbapenem-Resistant Enterobacteriaceae Detection Practices in California: What Are We Missing?

Humphries RM, Hindler JA, Epson E, Horwich-Scholefield S, Miller LG, Mendez J, Martinez JB, Sinkowitz J, Sinkowtiz D, Hershey C, Marquez P, Bhaurla S, Moran M, Pandes L, Terashita D, McKinnell JA.

Clin Infect Dis. 2018 Mar 19;66(7):1061-1067. doi: 10.1093/cid/cix942.


Activity of Ceftolozane-Tazobactam and Ceftazidime-Avibactam against Beta-Lactam-Resistant Pseudomonas aeruginosa Isolates.

Humphries RM, Hindler JA, Wong-Beringer A, Miller SA.

Antimicrob Agents Chemother. 2017 Nov 22;61(12). pii: e01858-17. doi: 10.1128/AAC.01858-17. Print 2017 Dec.


Rapid pathogen-specific phenotypic antibiotic susceptibility testing using digital LAMP quantification in clinical samples.

Schoepp NG, Schlappi TS, Curtis MS, Butkovich SS, Miller S, Humphries RM, Ismagilov RF.

Sci Transl Med. 2017 Oct 4;9(410). pii: eaal3693. doi: 10.1126/scitranslmed.aal3693.


Corrigendum: Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility after only 15 Minutes of Antibiotic Exposure.

Schoepp NG, Khorosheva EM, Schlappi TS, Curtis MS, Humphries RM, Hindler JA, Ismagilov RF.

Angew Chem Int Ed Engl. 2017 Sep 18;56(39):11675. doi: 10.1002/anie.201707742. No abstract available.


Real-Time PCR Targeting the penA Mosaic XXXIV Type for Prediction of Extended-Spectrum-Cephalosporin Susceptibility in Clinical Neisseria gonorrhoeae Isolates.

Wong LK, Hemarajata P, Soge OO, Humphries RM, Klausner JD.

Antimicrob Agents Chemother. 2017 Oct 24;61(11). pii: e01339-17. doi: 10.1128/AAC.01339-17. Print 2017 Nov.


Epidemiology of Neisseria gonorrhoeae Gyrase A Genotype, Los Angeles, California, USA.

Bhatti AA, Allan-Blitz LT, Castrejon M, Humphries RM, Hemarajata P, Klausner JD.

Emerg Infect Dis. 2017 Sep;23(9):1581-1584. doi: 10.3201/eid2309.170215.


Induction of β-Lactamase Activity and Decreased β-Lactam Susceptibility by CO2 in Clinical Bacterial Isolates.

Mullen N, Raposo H, Gudis P, Barker L, Humphries RM, Schmitt BH, Relich RF, May M.

mSphere. 2017 Jul 19;2(4). pii: e00266-17. doi: 10.1128/mSphere.00266-17. eCollection 2017 Jul-Aug.


Resistance to Ceftazidime-Avibactam Is Due to Transposition of KPC in a Porin-Deficient Strain of Klebsiella pneumoniae with Increased Efflux Activity.

Nelson K, Hemarajata P, Sun D, Rubio-Aparicio D, Tsivkovski R, Yang S, Sebra R, Kasarskis A, Nguyen H, Hanson BM, Leopold S, Weinstock G, Lomovskaya O, Humphries RM.

Antimicrob Agents Chemother. 2017 Sep 22;61(10). pii: e00989-17. doi: 10.1128/AAC.00989-17. Print 2017 Oct.


Hepatitis E Virus-Associated Meningoencephalitis in a Lung Transplant Recipient Diagnosed by Clinical Metagenomic Sequencing.

Murkey JA, Chew KW, Carlson M, Shannon CL, Sirohi D, Sample HA, Wilson MR, Vespa P, Humphries RM, Miller S, Klausner JD, Chiu CY.

Open Forum Infect Dis. 2017 Jun 13;4(3):ofx121. doi: 10.1093/ofid/ofx121. eCollection 2017 Summer.


Resistance to Ceftazidime-Avibactam in Klebsiella pneumoniae Due to Porin Mutations and the Increased Expression of KPC-3.

Humphries RM, Hemarajata P.

Antimicrob Agents Chemother. 2017 May 24;61(6). pii: e00537-17. doi: 10.1128/AAC.00537-17. Print 2017 Jun. No abstract available.


Use of Ancillary Carbapenemase Tests To Improve Specificity of Phenotypic Definitions for Carbapenemase-Producing Enterobacteriaceae.

Miller SA, Hindler JA, Chengcuenca A, Humphries RM.

J Clin Microbiol. 2017 Jun;55(6):1827-1836. doi: 10.1128/JCM.00157-17. Epub 2017 Mar 29.


Reply to "Burkholderia pseudomallei: Challenges for the Clinical Microbiology Laboratory-a Response from the Front Line".

Hemarajata P, Humphries RM.

J Clin Microbiol. 2017 Mar;55(3):983-984. doi: 10.1128/JCM.02438-16. No abstract available.


Can Ceftazidime-Avibactam and Aztreonam Overcome β-Lactam Resistance Conferred by Metallo-β-Lactamases in Enterobacteriaceae?

Marshall S, Hujer AM, Rojas LJ, Papp-Wallace KM, Humphries RM, Spellberg B, Hujer KM, Marshall EK, Rudin SD, Perez F, Wilson BM, Wasserman RB, Chikowski L, Paterson DL, Vila AJ, van Duin D, Kreiswirth BN, Chambers HF, Fowler VG Jr, Jacobs MR, Pulse ME, Weiss WJ, Bonomo RA.

Antimicrob Agents Chemother. 2017 Mar 24;61(4). pii: e02243-16. doi: 10.1128/AAC.02243-16. Print 2017 Apr.


Implementation of a Rapid Genotypic Assay to Promote Targeted Ciprofloxacin Therapy of Neisseria gonorrhoeae in a Large Health System.

Allan-Blitz LT, Humphries RM, Hemarajata P, Bhatti A, Pandori MW, Siedner MJ, Klausner JD.

Clin Infect Dis. 2017 May 1;64(9):1268-1270. doi: 10.1093/cid/ciw864.


Clinical and Microbiological Aspects of β-Lactam Resistance in Staphylococcus lugdunensis.

McHardy IH, Veltman J, Hindler J, Bruxvoort K, Carvalho MM, Humphries RM.

J Clin Microbiol. 2017 Feb;55(2):585-595. doi: 10.1128/JCM.02092-16. Epub 2016 Dec 7.


Multicenter Evaluation of a Modified Cefoxitin Disk Diffusion Method and PBP2a Testing To Predict mecA-Mediated Oxacillin Resistance in Atypical Staphylococcus aureus.

Miller SA, Karichu J, Kohner P, Cole N, Hindler JA, Patel R, Richter S, Humphries RM.

J Clin Microbiol. 2017 Feb;55(2):485-494. doi: 10.1128/JCM.02211-16. Epub 2016 Nov 30.


Graft Loss and CLAD-Onset Is Hastened by Viral Pneumonia After Lung Transplantation.

Allyn PR, Duffy EL, Humphries RM, Injean P, Weigt SS, Saggar R, Shino MY, Lynch JP 3rd, Ardehali A, Kubak B, Tseng CH, Belperio JA, Ross DJ, Gregson AL.

Transplantation. 2016 Nov;100(11):2424-2431.


Burkholderia pseudomallei: Challenges for the Clinical Microbiology Laboratory.

Hemarajata P, Baghdadi JD, Hoffman R, Humphries RM.

J Clin Microbiol. 2016 Dec;54(12):2866-2873. Epub 2016 Sep 21. Review.


Reply to Kircher et al.

Humphries RM, Hindler JA.

Clin Infect Dis. 2016 Dec 1;63(11):1532-1533. Epub 2016 Aug 31. No abstract available.


Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility after only 15 Minutes of Antibiotic Exposure.

Schoepp NG, Khorosheva EM, Schlappi TS, Curtis MS, Humphries RM, Hindler JA, Ismagilov RF.

Angew Chem Int Ed Engl. 2016 Aug 8;55(33):9557-61. doi: 10.1002/anie.201602763. Epub 2016 Jun 30. Erratum in: Angew Chem Int Ed Engl. 2017 Sep 18;56(39):11675.


Clinical laboratory detection of carbapenem-resistant and carbapenemase-producing Enterobacteriaceae.

Miller S, Humphries RM.

Expert Rev Anti Infect Ther. 2016 Aug;14(8):705-17. doi: 10.1080/14787210.2016.1206815. Epub 2016 Jul 11. Review.


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