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James Edward Kirby, M.D.

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Mentoring
Available: 12/01/22, Expires: 07/31/27

Antibiotic resistance is a major impediment to successful treatment of patients. Multidrug efflux pumps contribute to broad-spectrum antimicrobial resistance. This mechanism of resistance is particular important in certain pathogen groups like Pseudomonas, Acinetobacter, Burkholderia and Stenotrophomonas, sometimes leaving few if any treatment options. The goal of this student project is to understand how these efflux pumps function. Based on structural understanding of efflux pumps and cross comparisons among efflux pumps and the known efflux substrates, we will generate hypothesis about mechanisms of specific substrate recognition, and test these hypothesis by directed mutation of the pump amino acid sequence, and then measuring efflux of antibiotics of interest. This is a great project for a several month to a one year commitment as the questions are well defined and will allow the student to generate their own hypotheses and test them. Techniques would include highly efficient directed mutagenesis, structural predictions based on programs such as Pymol, Maestro, and alphafold2 to drive hypothesis generation and interpret results, and minimal inhibitory concentration analysis. We collaborate extensively with Ed Yu (Case Western Reserve University School of Medcine) who solved the first structure of a bacterial efflux pump, and is a leader in the structural biology of RND efflux pumps of interest. In collaboration with Dr. Yu, we also may also express and isolate the efflux pump proteins, and Dr. Yu's laboratory will solve the structures of the pumps by cryo-EM allowing us to confirm predicted hypotheses related to structure function correlations. Our long-term goal in underestanding, structure function correlations of efflux pumps is for future design of therapeutics that can inactivate pumps and thereby restore activity of existing antibiotics. Conversely, with a better understanding of pump substrate binding we can apply this knowledge to development of antibiotics that are no longer pump substrates and can then function in pump activated organisms. We are actively interested in design of such antibiotics. I have had other Harvard Medicla Students in the laboratory, and would welcome involvement of medical students. More information about he laboratory can be found at https://www.kirbylab.org


Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. R01AI157208 (KIRBY, JAMES E) Sep 23, 2020 - Aug 31, 2025
    NIH
    Use of De Novo Synthesis Approaches and Structure-guided Design to Optimize Therapeutic Properties of Streptothricin Class Antimicrobials
    Role: Principal Investigator
  2. R01AI154860 (KIRBY, JAMES E) Aug 20, 2020 - Jul 31, 2024
    NIH
    De Novo Synthesis, and Functional and Structural Characterization of Novel Aminoglycoside Analogues to Bypass Resistance Mechanisms and Optimize Selectivity
    Role: Principal Investigator
  3. R21AI146485 (KIRBY, JAMES E) May 15, 2019 - Apr 30, 2021
    NIH
    Fusidic acid derivatization to enhance entry into Gram-negative pathogens
    Role: Principal Investigator
  4. R21AI140212 (MANETSCH, ROMAN) Mar 1, 2019 - Feb 28, 2021
    NIH
    Development of Streptothricin Class Antimicrobials as Novel Therapeutics
    Role: Co-Principal Investigator
  5. R03AI144196 (KIRBY, JAMES E) Feb 8, 2019 - Jan 31, 2021
    NIH
    Targeted modification of the apramycin 2-deoxystreptamine ring to block aminoglycoside modifying enzyme-based inactivation and enhance potency against multidrug-resistant Gram-negative pathogens
    Role: Principal Investigator

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Burg L, Crewe G, DiMeo J, Guo X, Li CG, Mayol M, Tempesta A, Lauzier W, Markham R, Crissy K, Barry C, Walsh B, Kirby JE, Straus D. Rapid pathogen identification and phenotypic antimicrobial susceptibility directly from urine specimens. Sci Rep. 2022 11 15; 12(1):18315. PMID: 36380053; PMCID: PMC9666529.
    Citations:    Fields:    Translation:HumansCells
  2. Callahan C, Ditelberg S, Dutta S, Littlehale N, Cheng A, Kupczewski K, McVay D, Riedel S, Kirby JE, Arnaout R. Reply to Li et al., "Kappa Values in Testing the Concordance: Comments on a Recent Article about Nasopharyngeal Swabs for SARS-CoV-2 Detection". Microbiol Spectr. 2022 12 21; 10(6):e0341822. PMID: 36318026; PMCID: PMC9769801.
    Citations:    Fields:    Translation:HumansCells
  3. Kirby JE, Riedel S, Dutta S, Arnaout R, Cheng A, Ditelberg S, Hamel DJ, Chang CA, Kanki PJ. Sars-Cov-2 antigen tests predict infectivity based on viral culture: comparison of antigen, PCR viral load, and viral culture testing on a large sample cohort. Clin Microbiol Infect. 2023 Jan; 29(1):94-100. PMID: 35863629; PMCID: PMC9293398.
    Citations:    Fields:    
  4. Doern CD, Miller MB, Alby K, Bachman MA, Brecher SM, Casiano-Colon A, Couturier MR, Johnson JK, Kirby JE, McElvania E, Newton DW, Nolte FS, Pancholi P, McNult P, Dharmarha V, Dunbar S. Proceedings of the Clinical Microbiology Open 2018 and 2019 - a Discussion about Emerging Trends, Challenges, and the Future of Clinical Microbiology. J Clin Microbiol. 2022 07 20; 60(7):e0009222. PMID: 35638361; PMCID: PMC9297828.
    Citations:    Fields:    Translation:HumansPHPublic Health
  5. Stanley S, Hamel DJ, Wolf ID, Riedel S, Dutta S, Contreras E, Callahan CJ, Cheng A, Arnaout R, Kirby JE, Kanki PJ. Limit of Detection for Rapid Antigen Testing of the SARS-CoV-2 Omicron and Delta Variants of Concern Using Live-Virus Culture. J Clin Microbiol. 2022 05 18; 60(5):e0014022. PMID: 35440165; PMCID: PMC9116160.
    Citations: 3     Fields:    Translation:HumansCells
  6. Salamzade R, Manson AL, Walker BJ, Brennan-Krohn T, Worby CJ, Ma P, He LL, Shea TP, Qu J, Chapman SB, Howe W, Young SK, Wurster JI, Delaney ML, Kanjilal S, Onderdonk AB, Bittencourt CE, Gussin GM, Kim D, Peterson EM, Ferraro MJ, Hooper DC, Shenoy ES, Cuomo CA, Cosimi LA, Huang SS, Kirby JE, Pierce VM, Bhattacharyya RP, Earl AM. Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance. Genome Med. 2022 04 05; 14(1):37. PMID: 35379360; PMCID: PMC8981930.
    Citations:    Fields:    Translation:Humans
  7. Dowgiallo MG, Miller BC, Kassu M, Smith KP, Fetigan AD, Guo JJ, Kirby JE, Manetsch R. The convergent total synthesis and antibacterial profile of the natural product streptothricin F. Chem Sci. 2022 Mar 24; 13(12):3447-3453. PMID: 35432870; PMCID: PMC8943883.
    Citations:    
  8. Brennan-Krohn T, Grote A, Rodriguez S, Kirby JE, Earl AM. Transcriptomics Reveals How Minocycline-Colistin Synergy Overcomes Antibiotic Resistance in Multidrug-Resistant Klebsiella pneumoniae. Antimicrob Agents Chemother. 2022 03 15; 66(3):e0196921. PMID: 35041511; PMCID: PMC8923212.
    Citations:    Fields:    Translation:Cells
  9. Matos M, McEwan K, Kanovský M, Halamová J, Steindl SR, Ferreira N, Linharelhos M, Rijo D, Asano K, Márquez MG, Gregório S, Vilas SP, Brito-Pons G, Lucena-Santos P, da Silva Oliveira M, de Souza EL, Llobenes L, Gumiy N, Costa MI, Habib N, Hakem R, Khrad H, Alzahrani A, Cheli S, Petrocchi N, Tholouli E, Issari P, Simos G, Lunding-Gregersen V, Elklit A, Kolts R, Kelly AC, Bortolon C, Delamillieure P, Paucsik M, Wahl JE, Zieba M, Zatorski M, Komendzinski T, Zhang S, Basran J, Kagialis A, Kirby J, Gilbert P. Compassion Protects Mental Health and Social Safeness During the COVID-19 Pandemic Across 21 Countries. Mindfulness (N Y). 2022; 13(4):863-880. PMID: 35003380; PMCID: PMC8724602.
    Citations: 5     
  10. Arnaout R, Lee RA, Lee GR, Callahan C, Cheng A, Yen CF, Smith KP, Arora R, Kirby JE. The Limit of Detection Matters: The Case for Benchmarking Severe Acute Respiratory Syndrome Coronavirus 2 Testing. Clin Infect Dis. 2021 11 02; 73(9):e3042-e3046. PMID: 33532847.
    Citations: 29     Fields:    Translation:HumansCells
  11. Cheng A, Riedel S, Arnaout R, Kirby JE. Verification of the Abbott Alinity m Resp-4-Plex assay for detection of SARS-CoV-2, influenza A/B, and respiratory syncytial virus. Diagn Microbiol Infect Dis. 2022 Feb; 102(2):115575. PMID: 34839127; PMCID: PMC8532379.
    Citations: 3     Fields:    Translation:HumansCells
  12. Callahan C, Ditelberg S, Dutta S, Littlehale N, Cheng A, Kupczewski K, McVay D, Riedel S, Kirby JE, Arnaout R. Saliva is Comparable to Nasopharyngeal Swabs for Molecular Detection of SARS-CoV-2. Microbiol Spectr. 2021 09 03; 9(1):e0016221. PMID: 34406838; PMCID: PMC8552668.
    Citations: 6     Fields:    Translation:HumansCells
  13. Callahan C, Lee RA, Lee GR, Zulauf K, Kirby JE, Arnaout R. Nasal Swab Performance by Collection Timing, Procedure, and Method of Transport for Patients with SARS-CoV-2. J Clin Microbiol. 2021 08 18; 59(9):e0056921. PMID: 34076471.
    Citations: 3     Fields:    Translation:HumansCells
  14. Brennan-Krohn T, Friar L, Ditelberg S, Kirby JE. Evaluation of the Synergistic Activity of Antibacterial and Antifungal Drugs against Candida auris Using an Inkjet Printer-Assisted Method. Antimicrob Agents Chemother. 2021 09 17; 65(10):e0026821. PMID: 34252295; PMCID: PMC8448112.
    Citations:    Fields:    Translation:Animals
  15. Kim C, Kassu M, Smith KP, Kirby JE, Manetsch R. Pyrazole-Thiazole Core-Containing Analogs Exhibit Adjunctive Activity with Meropenem against Carbapenem-Resistant Enterobacteriaceae (CRE). ChemMedChem. 2021 09 16; 16(18):2775-2780. PMID: 34096189.
    Citations:    Fields:    Translation:Cells
  16. Pawar RD, Balaji L, Mehta S, Cole A, Liu X, Peradze N, Grossestreuer AV, Issa MS, Patel P, Kirby JE, Rowley CF, Berg KM, Moskowitz A, Donnino MW. Viral load and disease severity in COVID-19. Intern Emerg Med. 2022 03; 17(2):359-367. PMID: 34133005; PMCID: PMC8206885.
    Citations: 1     Fields:    Translation:HumansCells
  17. Matos M, McEwan K, Kanovský M, Halamová J, Steindl SR, Ferreira N, Linharelhos M, Rijo D, Asano K, Gregório S, Márquez MG, Vilas SP, Brito-Pons G, Lucena-Santos P, da Silva Oliveira M, de Souza EL, Llobenes L, Gumiy N, Costa MI, Habib N, Hakem R, Khrad H, Alzahrani A, Cheli S, Petrocchi N, Tholouli E, Issari P, Simos G, Lunding-Gregersen V, Elklit A, Kolts R, Kelly AC, Bortolon C, Delamillieure P, Paucsik M, Wahl JE, Zieba M, Zatorski M, Komendzinski T, Zhang S, Basran J, Kagialis A, Kirby J, Gilbert P. Fears of compassion magnify the harmful effects of threat of COVID-19 on mental health and social safeness across 21 countries. Clin Psychol Psychother. 2021 Nov; 28(6):1317-1333. PMID: 33880832; PMCID: PMC8251194.
    Citations: 6     Fields:    Translation:HumansCellsPHPublic Health
  18. Fuhrmeister ER, Larson JR, Kleinschmit AJ, Kirby JE, Pickering AJ, Bascom-Slack CA. Combating Antimicrobial Resistance Through Student-Driven Research and Environmental Surveillance. Front Microbiol. 2021; 12:577821. PMID: 33679626.
    Citations: 1     
  19. Zulauf KE, Kirby JE. Discovery of small-molecule inhibitors of multidrug-resistance plasmid maintenance using a high-throughput screening approach. Proc Natl Acad Sci U S A. 2020 11 24; 117(47):29839-29850. PMID: 33168749.
    Citations: 2     Fields:    Translation:Cells
  20. Callahan CJ, Lee R, Zulauf KE, Tamburello L, Smith KP, Previtera J, Cheng A, Green A, Abdul Azim A, Yano A, Doraiswami N, Kirby JE, Arnaout RA. Open Development and Clinical Validation of Multiple 3D-Printed Nasopharyngeal Collection Swabs: Rapid Resolution of a Critical COVID-19 Testing Bottleneck. J Clin Microbiol. 2020 07 23; 58(8). PMID: 32393482; PMCID: PMC7383530.
    Citations: 53     Fields:    Translation:HumansCellsPHPublic Health
  21. Smith KP, Cheng A, Chopelas A, DuBois-Coyne S, Mezghani I, Rodriguez S, Talay M, Kirby JE. Large-Scale, In-House Production of Viral Transport Media To Support SARS-CoV-2 PCR Testing in a Multihospital Health Care Network during the COVID-19 Pandemic. J Clin Microbiol. 2020 07 23; 58(8). PMID: 32404481.
    Citations: 12     Fields:    Translation:HumansCellsPHPublic Health
  22. Zulauf KE, Green AB, Nguyen Ba AN, Jagdish T, Reif D, Seeley R, Dale A, Kirby JE. Microwave-Generated Steam Decontamination of N95 Respirators Utilizing Universally Accessible Materials. mBio. 2020 06 25; 11(3). PMID: 32587063.
    Citations: 22     Fields:    Translation:HumansCellsPHPublic Health
  23. Callahan C, Lee R, Lee G, Zulauf KE, Kirby JE, Arnaout R. Nasal-Swab Testing Misses Patients with Low SARS-CoV-2 Viral Loads. medRxiv. 2020 Jun 14. PMID: 32587981; PMCID: PMC7310639.
    Citations:    
  24. Arnaout R, Lee RA, Lee GR, Callahan C, Yen CF, Smith KP, Arora R, Kirby JE. SARS-CoV2 Testing: The Limit of Detection Matters. bioRxiv. 2020 Jun 04. PMID: 32577640; PMCID: PMC7302192.
    Citations:    
  25. Smith KP, Cheng A, Chopelas A, DuBois-Coyne S, Mezghani I, Rodriguez S, Talay M, Kirby JE. Large-scale, in-house production of viral transport media to support SARS-CoV-2 PCR testing in a multi-hospital healthcare network during the COVID-19 pandemic. medRxiv. 2020 May 01. PMID: 32511593.
    Citations:    
  26. Zulauf KE, Green AB, Nguyen AN, Jagdish T, Reif D, Seeley R, Dale A, Kirby JE. Microwave-Generated Steam Decontamination of N95 Respirators Utilizing Universally Accessible Materials. medRxiv. 2020 Apr 25. PMID: 32511577.
    Citations:    
  27. Callahan CJ, Lee R, Zulauf K, Tamburello L, Smith KP, Previtera J, Cheng A, Green A, Abdul Azim A, Yano A, Doraiswami N, Kirby J, Arnaout R. Open Development and Clinical Validation of Multiple 3D-Printed Sample-Collection Swabs: Rapid Resolution of a Critical COVID-19 Testing Bottleneck. medRxiv. 2020 Apr 17. PMID: 32511491.
    Citations:    
  28. Kirby JE, Brennan-Krohn T, Smith KP. Reply to Humphries and Simner, "Verification Is an Integral Part of Antimicrobial Susceptibility Test Quality Assurance," and Wojewoda et al., "College of American Pathologists (CAP) Microbiology Committee Perspective: the Need for Verification Studies". J Clin Microbiol. 2020 03 25; 58(4). PMID: 32213577.
    Citations:    Fields:    Translation:Humans
  29. Smith KP, Kirby JE. Image analysis and artificial intelligence in infectious disease diagnostics. Clin Microbiol Infect. 2020 Oct; 26(10):1318-1323. PMID: 32213317.
    Citations: 7     Fields:    Translation:Humans
  30. Brennan-Krohn T, Manetsch R, O'Doherty GA, Kirby JE. New strategies and structural considerations in development of therapeutics for carbapenem-resistant Enterobacteriaceae. Transl Res. 2020 06; 220:14-32. PMID: 32201344.
    Citations: 4     Fields:    Translation:Cells
  31. Yang L, Yildirim E, Kirby JE, Press W, Lee JT. Widespread organ tolerance to Xist loss and X reactivation except under chronic stress in the gut. Proc Natl Acad Sci U S A. 2020 02 25; 117(8):4262-4272. PMID: 32041873; PMCID: PMC7049159.
    Citations: 12     Fields:    Translation:HumansAnimalsCells
  32. Morgan CE, Huang W, Rudin SD, Taylor DJ, Kirby JE, Bonomo RA, Yu EW. Cryo-electron Microscopy Structure of the Acinetobacter baumannii 70S Ribosome and Implications for New Antibiotic Development. mBio. 2020 01 21; 11(1). PMID: 31964740.
    Citations: 14     Fields:    Translation:HumansCells
  33. Kirby JE, Brennan-Krohn T, Smith KP. Bringing Antimicrobial Susceptibility Testing for New Drugs into the Clinical Laboratory: Removing Obstacles in Our Fight against Multidrug-Resistant Pathogens. J Clin Microbiol. 2019 12; 57(12). PMID: 31533983.
    Citations: 8     Fields:    Translation:HumansCells
  34. Kirby JE. Our Pathogens Are Not Standing Still and Neither Can We. Clin Lab Med. 2019 09; 39(3):xiii-xiv. PMID: 31383273.
    Citations: 1     Fields:    Translation:HumansCells
  35. Brennan-Krohn T, Kirby JE. Synergistic Combinations and Repurposed Antibiotics Active against the Pandrug-Resistant Klebsiella pneumoniae Nevada Strain. Antimicrob Agents Chemother. 2019 09; 63(9). PMID: 31307981; PMCID: PMC6709503.
    Citations: 8     Fields:    Translation:HumansCells
  36. Kang YS, Kirby JE. A Chemical Genetics Screen Reveals Influence of p38 Mitogen-Activated Protein Kinase and Autophagy on Phagosome Development and Intracellular Replication of Brucella neotomae in Macrophages. Infect Immun. 2019 08; 87(8). PMID: 31160361; PMCID: PMC6652748.
    Citations: 3     Fields:    Translation:HumansAnimalsCells
  37. Lee RA, Kirby JE. We Cannot Do It Alone: The Intersection of Public Health, Public Policy, and Clinical Microbiology. Clin Lab Med. 2019 09; 39(3):499-508. PMID: 31383271.
    Citations: 2     Fields:    Translation:HumansPHPublic Health
  38. Smith KP, Dowgiallo MG, Chiaraviglio L, Parvatkar P, Kim C, Manetsch R, Kirby JE. A Whole-Cell Screen for Adjunctive and Direct Antimicrobials Active against Carbapenem-Resistant Enterobacteriaceae. SLAS Discov. 2019 09; 24(8):842-853. PMID: 31268804; PMCID: PMC6702050.
    Citations: 2     Fields:    Translation:HumansCells
  39. Brennan-Krohn T, Kirby JE. When One Drug Is Not Enough: Context, Methodology, and Future Prospects in Antibacterial Synergy Testing. Clin Lab Med. 2019 09; 39(3):345-358. PMID: 31383261.
    Citations: 8     Fields:    Translation:HumansAnimals
  40. Smith KP, Kirby JE. Rapid Susceptibility Testing Methods. Clin Lab Med. 2019 09; 39(3):333-344. PMID: 31383260; PMCID: PMC6686868.
    Citations: 6     Fields:    Translation:HumansCells
  41. Riedel S, Vijayakumar D, Berg G, Kang AD, Smith KP, Kirby JE. Evaluation of apramycin against spectinomycin-resistant and -susceptible strains of Neisseria gonorrhoeae. J Antimicrob Chemother. 2019 05 01; 74(5):1311-1316. PMID: 30689929; PMCID: PMC6477976.
    Citations: 13     Fields:    Translation:HumansCells
  42. Brennan-Krohn T, Kirby JE. Antimicrobial Synergy Testing by the Inkjet Printer-assisted Automated Checkerboard Array and the Manual Time-kill Method. J Vis Exp. 2019 04 18; (146). PMID: 31058886; PMCID: PMC6698365.
    Citations: 8     Fields:    
  43. Kang YS, Brown DA, Kirby JE. Brucella neotomae Recapitulates Attributes of Zoonotic Human Disease in a Murine Infection Model. Infect Immun. 2019 01; 87(1). PMID: 30373892; PMCID: PMC6300638.
    Citations: 7     Fields:    Translation:AnimalsCells
  44. Brennan-Krohn T, Pironti A, Kirby JE. Synergistic Activity of Colistin-Containing Combinations against Colistin-Resistant Enterobacteriaceae. Antimicrob Agents Chemother. 2018 10; 62(10). PMID: 30061285; PMCID: PMC6153801.
    Citations: 39     Fields:    Translation:Cells
  45. Smith KP, Kirby JE. The Inoculum Effect in the Era of Multidrug Resistance: Minor Differences in Inoculum Have Dramatic Effect on MIC Determination. Antimicrob Agents Chemother. 2018 08; 62(8). PMID: 29784837; PMCID: PMC6105823.
    Citations: 28     Fields:    Translation:Cells
  46. Gite S, Archambault D, Cappillino MP, Cunha D, Dorich V, Shatova T, Tempesta A, Walsh B, Walsh JA, Williams A, Kirby JE, Bowers J, Straus D. A Rapid, Accurate, Single Molecule Counting Method Detects Clostridium difficile Toxin B in Stool Samples. Sci Rep. 2018 05 30; 8(1):8364. PMID: 29849171; PMCID: PMC5976643.
    Citations: 6     Fields:    Translation:HumansCells
  47. Truelson KA, Brennan-Krohn T, Smith KP, Kirby JE. Evaluation of apramycin activity against methicillin-resistant, methicillin-sensitive, and vancomycin-intermediate Staphylococcus aureus clinical isolates. Diagn Microbiol Infect Dis. 2018 Oct; 92(2):168-171. PMID: 29934071; PMCID: PMC6131043.
    Citations: 9     Fields:    Translation:HumansCells
  48. Kang AD, Smith KP, Berg AH, Truelson KA, Eliopoulos GM, McCoy C, Kirby JE. Efficacy of Apramycin against Multidrug-Resistant Acinetobacter baumannii in the Murine Neutropenic Thigh Model. Antimicrob Agents Chemother. 2018 04; 62(4). PMID: 29339396; PMCID: PMC5913965.
    Citations: 12     Fields:    Translation:AnimalsCells
  49. Smith KP, Kang AD, Kirby JE. Automated Interpretation of Blood Culture Gram Stains by Use of a Deep Convolutional Neural Network. J Clin Microbiol. 2018 03; 56(3). PMID: 29187563; PMCID: PMC5824030.
    Citations: 18     Fields:    Translation:Humans
  50. Brennan-Krohn T, Truelson KA, Smith KP, Kirby JE. Screening for synergistic activity of antimicrobial combinations against carbapenem-resistant Enterobacteriaceae using inkjet printer-based technology. J Antimicrob Chemother. 2017 10 01; 72(10):2775-2781. PMID: 29091221; PMCID: PMC5890738.
    Citations: 22     Fields:    Translation:HumansCells
  51. Smith KP, Richmond DL, Brennan-Krohn T, Elliott HL, Kirby JE. Development of MAST: A Microscopy-Based Antimicrobial Susceptibility Testing Platform. SLAS Technol. 2017 12; 22(6):662-674. PMID: 28837780.
    Citations: 11     Fields:    Translation:HumansCells
  52. Brennan-Krohn T, Yoon E, Nishino M, Kirby JE, Riedel S. Arthroconidia in lung tissue: an unusual histopathological finding in pulmonary coccidioidomycosis. Hum Pathol. 2018 01; 71:55-59. PMID: 28778515; PMCID: PMC5936468.
    Citations: 1     Fields:    Translation:HumansCells
  53. Chen A, Smith KP, Whitfield BA, Zucchi PC, Lasco TM, Bias TE, Kirby JE, Hirsch EB. Activity of minocycline against Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae clinical isolates, with comparison to doxycycline and tigecycline. Diagn Microbiol Infect Dis. 2017 Aug; 88(4):365-367. PMID: 28535946.
    Citations: 3     Fields:    Translation:HumansCells
  54. Brennan-Krohn T, Smith KP, Kirby JE. The Poisoned Well: Enhancing the Predictive Value of Antimicrobial Susceptibility Testing in the Era of Multidrug Resistance. J Clin Microbiol. 2017 08; 55(8):2304-2308. PMID: 28468856; PMCID: PMC5527407.
    Citations: 14     Fields:    
  55. Kang YS, Kirby JE. Promotion and Rescue of Intracellular Brucella neotomae Replication during Coinfection with Legionella pneumophila. Infect Immun. 2017 05; 85(5). PMID: 28264909; PMCID: PMC5400850.
    Citations: 6     Fields:    Translation:HumansAnimalsCells
  56. Kang AD, Smith KP, Eliopoulos GM, Berg AH, McCoy C, Kirby JE. Invitro Apramycin Activity against multidrug-resistant Acinetobacter baumannii and Pseudomonas aeruginosa. Diagn Microbiol Infect Dis. 2017 Jun; 88(2):188-191. PMID: 28341099.
    Citations: 31     Fields:    Translation:HumansAnimalsCells
  57. Bryan AW, Qian Q, Kirby JE. Answer to February 2017 Photo Quiz. J Clin Microbiol. 2017 02; 55(2):660-661. PMID: 28122997; PMCID: PMC5277542.
    Citations:    Fields:    Translation:Humans
  58. Bryan AW, Qian Q, Kirby JE. Photo Quiz: A Man with Fever and Headache. J Clin Microbiol. 2017 02; 55(2):351. PMID: 28122992; PMCID: PMC5277501.
    Citations:    Fields:    Translation:Humans
  59. Kirby JE, Branch-Elliman W, LaSalvia MT, Longhi L, MacKechnie M, Urman G, Baldini LM, Muriel FR, Sullivan B, Yassa DS, Gold HS, Wagner TK, Diekema DJ, Wright SB. Investigation of a Candida guilliermondii Pseudo-outbreak Reveals a Novel Source of Laboratory Contamination. J Clin Microbiol. 2017 04; 55(4):1080-1089. PMID: 28100597; PMCID: PMC5377835.
    Citations:    Fields:    Translation:HumansAnimalsPHPublic Health
  60. Cerqueira GC, Earl AM, Ernst CM, Grad YH, Dekker JP, Feldgarden M, Chapman SB, Reis-Cunha JL, Shea TP, Young S, Zeng Q, Delaney ML, Kim D, Peterson EM, O'Brien TF, Ferraro MJ, Hooper DC, Huang SS, Kirby JE, Onderdonk AB, Birren BW, Hung DT, Cosimi LA, Wortman JR, Murphy CI, Hanage WP. Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks. Proc Natl Acad Sci U S A. 2017 01 31; 114(5):1135-1140. PMID: 28096418; PMCID: PMC5293017.
    Citations: 61     Fields:    Translation:HumansCellsPHPublic Health
  61. Smith KP, Brennan-Krohn T, Weir S, Kirby JE. Improved Accuracy of Cefepime Susceptibility Testing for Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae with an On-Demand Digital Dispensing Method. J Clin Microbiol. 2017 02; 55(2):470-478. PMID: 27903600; PMCID: PMC5277516.
    Citations: 9     Fields:    Translation:HumansCells
  62. Chiaraviglio L, Kang YS, Kirby JE. High Throughput, Real-time, Dual-readout Testing of Intracellular Antimicrobial Activity and Eukaryotic Cell Cytotoxicity. J Vis Exp. 2016 11 16; (117). PMID: 27911388.
    Citations: 2     Fields:    Translation:AnimalsCells
  63. Smith KP, Kirby JE. How inkjet printing technology can defeat multidrug-resistant pathogens. Future Microbiol. 2016 10; 11:1375-1377. PMID: 27785916.
    Citations: 4     Fields:    Translation:HumansCells
  64. Smith KP, Kirby JE. Evaluation of apramycin activity against carbapenem-resistant and -susceptible strains of Enterobacteriaceae. Diagn Microbiol Infect Dis. 2016 Dec; 86(4):439-441. PMID: 27745736.
    Citations: 21     Fields:    Translation:HumansCells
  65. Hale AJ, LaSalvia M, Kirby JE, Kimball A, Baden R. Fatal purpura fulminans and Waterhouse-Friderichsen syndrome from fulminant Streptococcus pneumoniae sepsis in an asplenic young adult. IDCases. 2016; 6:1-4. PMID: 27583208; PMCID: PMC4995527.
    Citations: 6     
  66. Yang L, Kirby JE, Sunwoo H, Lee JT. Female mice lacking Xist RNA show partial dosage compensation and survive to term. Genes Dev. 2016 08 01; 30(15):1747-60. PMID: 27542829; PMCID: PMC5002979.
    Citations: 33     Fields:    Translation:AnimalsCells
  67. Smith KP, Kirby JE. Verification of an Automated, Digital Dispensing Platform for At-Will Broth Microdilution-Based Antimicrobial Susceptibility Testing. J Clin Microbiol. 2016 09; 54(9):2288-93. PMID: 27335151; PMCID: PMC5005478.
    Citations: 25     Fields:    Translation:HumansCells
  68. Hale A, Kirby JE, Albrecht M. Fatal Spontaneous Clostridium bifermentans Necrotizing Endometritis: A Case Report and Literature Review of the Pathogen. Open Forum Infect Dis. 2016 Apr; 3(2):ofw095. PMID: 27419167; PMCID: PMC4943541.
    Citations: 5     
  69. Hirsch EB, Zucchi PC, Chen A, Raux BR, Kirby JE, McCoy C, Eliopoulos GM. Susceptibility of Multidrug-Resistant Gram-Negative Urine Isolates to Oral Antibiotics. Antimicrob Agents Chemother. 2016 05; 60(5):3138-40. PMID: 26883704; PMCID: PMC4862536.
    Citations: 4     Fields:    
  70. Smith KP, Kirby JE. Validation of a High-Throughput Screening Assay for Identification of Adjunctive and Directly Acting Antimicrobials Targeting Carbapenem-Resistant Enterobacteriaceae. Assay Drug Dev Technol. 2016 Apr; 14(3):194-206. PMID: 27045615.
    Citations: 8     Fields:    Translation:Cells
  71. Qian Q, Urman G, Cederroth T, Najarian R, Kirby JE. Photo Quiz: A Man with Fever and Cough. J Clin Microbiol. 2016 Apr; 54(4):825; discussion 1177. PMID: 27016589; PMCID: PMC4809913.
    Citations:    Fields:    Translation:HumansAnimals
  72. Qian Q, Urman G, Cederroth T, Najarian R, Kirby JE. Answer to April 2016 Photo Quiz. J Clin Microbiol. 2016 Apr; 54(4):1177. PMID: 27016595; PMCID: PMC4809941.
    Citations:    
  73. Sells RE, Chen CA, Wong MT, Zimarowski MJ, Kirby JE, Joyce RM, Wu PA. Continuous positive airway pressure-associated cutaneous amoebiasis in an immunosuppressed patient. Br J Dermatol. 2016 Mar; 174(3):625-8. PMID: 26474324.
    Citations:    Fields:    Translation:HumansAnimals
  74. Harris RM, Arnaout R, Koziel H, Folch E, Majid A, Kirby JE. Utility of microbiological testing of thoracic lymph nodes sampled by endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) in patients with mediastinal lymphadenopathy. Diagn Microbiol Infect Dis. 2016 Feb; 84(2):170-4. PMID: 26602949.
    Citations: 5     Fields:    Translation:Humans
  75. Hirsch EB, Raux BR, Zucchi PC, Kim Y, McCoy C, Kirby JE, Wright SB, Eliopoulos GM. Activity of fosfomycin and comparison of several susceptibility testing methods against contemporary urine isolates. Int J Antimicrob Agents. 2015 Dec; 46(6):642-7. PMID: 26498988.
    Citations: 16     Fields:    Translation:HumansCells
  76. Chiaraviglio L, Kirby JE. High-Throughput Intracellular Antimicrobial Susceptibility Testing of Legionella pneumophila. Antimicrob Agents Chemother. 2015 Dec; 59(12):7517-29. PMID: 26392509; PMCID: PMC4649152.
    Citations: 9     Fields:    Translation:HumansCells
  77. Harris RM, Stillman IE, Goldsmith JD, Qian Q, Kirby JE. Pathological rib fracture and soft tissue mass simulating malignancy--Cryptococcus, an unsuspected culprit. Diagn Microbiol Infect Dis. 2015 Mar; 81(3):189-91. PMID: 25583128.
    Citations:    Fields:    Translation:HumansAnimals
  78. Chiaraviglio L, Kirby JE. Evaluation of impermeant, DNA-binding dye fluorescence as a real-time readout of eukaryotic cell toxicity in a high throughput screening format. Assay Drug Dev Technol. 2014 May; 12(4):219-28. PMID: 24831788.
    Citations: 18     Fields:    Translation:HumansCells
  79. Cheng A, Kirby JE. Evaluation of the Hologic gen-probe PANTHER, APTIMA Combo 2 assay in a tertiary care teaching hospital. Am J Clin Pathol. 2014 Mar; 141(3):397-403. PMID: 24515768.
    Citations: 7     Fields:    Translation:HumansCells
  80. Qian Q, Eichelberger K, Kirby JE. Rapid identification of Staphylococcus aureus directly from Bactec blood culture broth by the BinaxNOW S. aureus test. J Clin Microbiol. 2014 Jan; 52(1):319-20. PMID: 24153135.
    Citations: 3     Fields:    Translation:HumansCells
  81. Yildirim E, Kirby JE, Brown DE, Mercier FE, Sadreyev RI, Scadden DT, Lee JT. Xist RNA is a potent suppressor of hematologic cancer in mice. Cell. 2013 Feb 14; 152(4):727-42. PMID: 23415223; PMCID: PMC3875356.
    Citations: 245     Fields:    Translation:AnimalsCells
  82. Anguera MC, Sadreyev R, Zhang Z, Szanto A, Payer B, Sheridan SD, Kwok S, Haggarty SJ, Sur M, Alvarez J, Gimelbrant A, Mitalipova M, Kirby JE, Lee JT. Molecular signatures of human induced pluripotent stem cells highlight sex differences and cancer genes. Cell Stem Cell. 2012 Jul 06; 11(1):75-90. PMID: 22770242.
    Citations: 72     Fields:    Translation:HumansAnimalsCells
  83. Cheng A, Qian Q, Kirby JE. Evaluation of the Abbott RealTime CT/NG assay in comparison to the Roche Cobas Amplicor CT/NG assay. J Clin Microbiol. 2011 Apr; 49(4):1294-300. PMID: 21325546.
    Citations: 21     Fields:    Translation:HumansCells
  84. Chiaraviglio L, Duong S, Brown DA, Birtles RJ, Kirby JE. An immunocompromised murine model of chronic Bartonella infection. Am J Pathol. 2010 Jun; 176(6):2753-63. PMID: 20395436; PMCID: PMC2877837.
    Citations: 10     Fields:    Translation:HumansAnimalsCells
  85. Soscia SJ, Kirby JE, Washicosky KJ, Tucker SM, Ingelsson M, Hyman B, Burton MA, Goldstein LE, Duong S, Tanzi RE, Moir RD. The Alzheimer's disease-associated amyloid beta-protein is an antimicrobial peptide. PLoS One. 2010 Mar 03; 5(3):e9505. PMID: 20209079.
    Citations: 398     Fields:    Translation:HumansAnimals
  86. Qian Q, Venkataraman L, Kirby JE, Gold HS, Yamazumi T. Direct detection of methicillin resistance in Staphylococcus aureus in blood culture broth by use of a penicillin binding protein 2a latex agglutination test. J Clin Microbiol. 2010 Apr; 48(4):1420-1. PMID: 20129965.
    Citations: 4     Fields:    Translation:HumansCells
  87. Pollock NR, Duong S, Cheng A, Han LL, Smole S, Kirby JE. Ruling out novel H1N1 influenza virus infection with direct fluorescent antigen testing. Clin Infect Dis. 2009 Sep 15; 49(6):e66-8. PMID: 19681710.
    Citations: 20     Fields:    Translation:HumansCells
  88. Wang Y, Kirby JE, Qian Q. Effective use of JC virus PCR for diagnosis of progressive multifocal leukoencephalopathy. J Med Microbiol. 2009 Feb; 58(Pt 2):253-255. PMID: 19141745.
    Citations: 12     Fields:    Translation:HumansCells
  89. Kirby JE, Delaney M, Qian Q, Gold HS. Optimal use of Myco/F lytic and standard BACTEC blood culture bottles for detection of yeast and mycobacteria. Arch Pathol Lab Med. 2009 Jan; 133(1):93-6. PMID: 19123744.
    Citations: 7     Fields:    Translation:AnimalsCells
  90. Chiaraviglio L, Brown DA, Kirby JE. Infection of cultured human endothelial cells by Legionella pneumophila. PLoS One. 2008 Apr 23; 3(4):e2012. PMID: 18431493.
    Citations: 6     Fields:    Translation:HumansCells
  91. Wang Y, Doucette S, Qian Q, Kirby JE. Yield of primary and repeat induced sputum testing for Pneumocystis jiroveci in human immunodeficiency virus-positive and -negative patients. Arch Pathol Lab Med. 2007 Oct; 131(10):1582-4. PMID: 17922597.
    Citations: 2     Fields:    Translation:HumansAnimals
  92. Qian Q, Eichelberger K, Kirby JE. Rapid identification of Staphylococcus aureus in blood cultures by use of the direct tube coagulase test. J Clin Microbiol. 2007 Jul; 45(7):2267-9. PMID: 17522280; PMCID: PMC1932990.
    Citations: 15     Fields:    Translation:HumansCells
  93. Konstantinopoulos PA, Kirby JE, Miller KB, Dezube BJ. Babesiosis masquerading as recurrent immune thrombocytopenic purpura in a splenectomized patient. Ann Hematol. 2006 Oct; 85(10):739-40. PMID: 16705453.
    Citations:    Fields:    Translation:HumansCells
  94. Duong S, Chiaraviglio L, Kirby JE. Histopathology in a murine model of anthrax. Int J Exp Pathol. 2006 Apr; 87(2):131-7. PMID: 16623757.
    Citations: 10     Fields:    Translation:AnimalsCells
  95. Kirby JE. In vitro model of Bartonella henselae-induced angiogenesis. Infect Immun. 2004 Dec; 72(12):7315-7. PMID: 15557658; PMCID: PMC529148.
    Citations: 9     Fields:    Translation:HumansCells
  96. Kirby JE. Anthrax lethal toxin induces human endothelial cell apoptosis. Infect Immun. 2004 Jan; 72(1):430-9. PMID: 14688124.
    Citations: 66     Fields:    Translation:HumansCells
  97. Kirby JE, Nekorchuk DM. Bartonella-associated endothelial proliferation depends on inhibition of apoptosis. Proc Natl Acad Sci U S A. 2002 Apr 02; 99(7):4656-61. PMID: 11904386; PMCID: PMC123703.
    Citations: 37     Fields:    Translation:AnimalsCells
  98. Kirby JE, Isberg RR. Legionnaires' disease: the pore macrophage and the legion of terror within. Trends Microbiol. 1998 Jul; 6(7):256-8. PMID: 9717211.
    Citations: 17     Fields:    Translation:HumansCells
  99. Kirby JE, Vogel JP, Andrews HL, Isberg RR. Evidence for pore-forming ability by Legionella pneumophila. Mol Microbiol. 1998 Jan; 27(2):323-36. PMID: 9484888.
    Citations: 95     Fields:    Translation:AnimalsCells
  100. Kirby JE, Laposata M. The nature and extent of training activities in clinical pathology required for effective consultation on laboratory test selection and interpretation. Arch Pathol Lab Med. 1997 Nov; 121(11):1163-7. PMID: 9372742.
    Citations:    Fields:    Translation:Humans
  101. Harris MG, Kirby JE, Tornatore CW, Wrightnour JA. Microwave disinfection of soft contact lenses. Optom Vis Sci. 1989 Feb; 66(2):82-6. PMID: 2710514.
    Citations:    Fields:    Translation:PHPublic Health
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.