Recent Publications and Other Media
COVID-19
Morgan et al. The Coviral Portal: Multi-Cohort Viral Loads and Antigen-Test Virtual Trials for COVID-19. 2023. MedRXiv. doi: https://doi.org/10.1101/2023.05.05.23289582.
Keynote Address Silverstein Symposium. Link to Talk by Kirby and Arnaout: Innovating out of Crisis: Rising to the Laboratory-Diagnostic Challenges of the SARS-CoV-2 Pandemic at BIDMC. Start at 1 hour 15 minutes 30 seconds.
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. https://www.medrxiv.org/content/10.1101/2021.12.22.21268274v1
Rapid Open Development and Clinical Validation of Multiple New 3D-Printed Nasopharyngeal Swabs in Response to the COVID-19 Pandemic. https://jcm.asm.org/content/early/2020/05/11/JCM.00876-20
https://www.wbur.org/commonhealth/2020/04/17/coronavirus-swab-testing-shortage
https://www.washingtonpost.com/climate-environment/2020/04/22/nasal-swabs-shortage-coronavirus/
Initial discussions with HP, Inc.
Forbes article, swabs now supplying testing needs of Belgium
Iterations of swab design
Microwave-Generated Steam Decontamination of N95 Respirators Utilizing Universally Accessible Materials.
https://mbio.asm.org/content/11/3/e00997-20
American Society of Microbiology Press release
BIDMC Press release
Article by Adele Peters: "How to decontaminate an N95 mask in just 3 minutes".
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
https://jcm.asm.org/content/early/2020/05/11/JCM.00913-20
SARS-CoV2 Testing: The Limit of Detection Matters
Published in Clinical Infectious Diseases, . . .the Case for Benchmarking SARS-CoV-2 Testing
Also: https://hms.harvard.edu/news/apples-apples
Nasal-Swab Testing Misses Patients with Low SARS-CoV-2 Viral Loads
https://www.medrxiv.org/content/10.1101/2020.06.12.20128736v1. J Clin Micro Full Text.
Interview on NBC10. Ramping up COVID-19 Testing at Beth Israel Lahey Health.
https://www.nbcboston.com/news/coronavirus/volunteers-helping-process-coronavirus-tests/2131439/
Webinar on SARS-CoV-2 Diagnostics. Presentation on our data is ~ 1 hour into this program
https://www.labroots.com/ms/webinar/design-implementation-sars-cov-2-diagnostic-testing
Verification of the Abbott Alinity m Resp-4-Plex Assay for detection of SARS-CoV-2, influenza A/B, and respiratory syncytial virus. https://www.medrxiv.org/content/10.1101/2021.04.22.21255133v1
Keynote Address Silverstein Symposium. Link to Talk by Kirby and Arnaout: Innovating out of Crisis: Rising to the Laboratory-Diagnostic Challenges of the SARS-CoV-2 Pandemic at BIDMC. Start at 1 hour 15 minutes 30 seconds.
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. https://www.medrxiv.org/content/10.1101/2021.12.22.21268274v1
Rapid Open Development and Clinical Validation of Multiple New 3D-Printed Nasopharyngeal Swabs in Response to the COVID-19 Pandemic. https://jcm.asm.org/content/early/2020/05/11/JCM.00876-20
https://www.wbur.org/commonhealth/2020/04/17/coronavirus-swab-testing-shortage
https://www.washingtonpost.com/climate-environment/2020/04/22/nasal-swabs-shortage-coronavirus/
Initial discussions with HP, Inc.
Forbes article, swabs now supplying testing needs of Belgium
Iterations of swab design
Microwave-Generated Steam Decontamination of N95 Respirators Utilizing Universally Accessible Materials.
https://mbio.asm.org/content/11/3/e00997-20
American Society of Microbiology Press release
BIDMC Press release
Article by Adele Peters: "How to decontaminate an N95 mask in just 3 minutes".
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
https://jcm.asm.org/content/early/2020/05/11/JCM.00913-20
SARS-CoV2 Testing: The Limit of Detection Matters
Published in Clinical Infectious Diseases, . . .the Case for Benchmarking SARS-CoV-2 Testing
Also: https://hms.harvard.edu/news/apples-apples
Nasal-Swab Testing Misses Patients with Low SARS-CoV-2 Viral Loads
https://www.medrxiv.org/content/10.1101/2020.06.12.20128736v1. J Clin Micro Full Text.
Interview on NBC10. Ramping up COVID-19 Testing at Beth Israel Lahey Health.
https://www.nbcboston.com/news/coronavirus/volunteers-helping-process-coronavirus-tests/2131439/
Webinar on SARS-CoV-2 Diagnostics. Presentation on our data is ~ 1 hour into this program
https://www.labroots.com/ms/webinar/design-implementation-sars-cov-2-diagnostic-testing
Verification of the Abbott Alinity m Resp-4-Plex Assay for detection of SARS-CoV-2, influenza A/B, and respiratory syncytial virus. https://www.medrxiv.org/content/10.1101/2021.04.22.21255133v1
Translational Diagnostics
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 Jul 27;62(8). pii: e00433-18. doi: 10.1128/AAC.00433-18. PMCID: PMC6105823. Link to abstract. Link to full text. Link to commentary in New England Journal of Medicine Journal Watch.
Smith KP, Richmond DL, Brennan-Krohn T, Elliott HL, Kirby JE. Development of MAST: a Microscopy-Based Antimicrobial Susceptibility Testing Platform. SLAS Technology, 2017. Link to abstract. Link to Manuscript. Link to Figures (50 MB).
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 Antimicrobial Chemotherapy. 2017 July. https://doi.org/10.1093/jac/dkx241. Link to abstract. Link to Journal Full Text. Technology adopted by the CDC based on our publications for use in its Antimicrobial Resistance Laboratory Network as described under Diagnostics.
Smith KP, Kang AD, Kirby JE. Automated Interpretation of Blood Culture Gram Stains using a Deep Convolutional Neural Network. J Clin Micro. Accepted manuscript posted online 29 November 2017, doi: 10.1128/JCM.01521-17. Link to abstract. Link to Final Accepted Version. Press Release: "BIDMC Researchers Use Artificial Intelligence to Identify Bacteria Quickly and Accurately" . "New microscope uses A.I. smarts to diagnose deadly blood infections."
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 Feb;55(2):470-478. doi: 10.1128/JCM.02128-16. PMCID: PMC5277516. Link to abstract.. Link to PDF..
Brennan-Krohn T, Pironti A, Kirby JE. Synergistic Activity of Colistin-Containing Combinations against Colistin-Resistant Enterobacteriaceae. Antimicrob Agents Chemother. 2018 Sep 24;62(10). pii: e00873-18. doi: 10.1128/AAC.00873-18. Print 2018 Oct. PMCID: PMC6153801. Link to abstract. Link to full text.
Smith KP, Kirby JE. How inkjet printing technology can defeat multidrug-resistant pathogens. Future Microbiol. 2016 Oct;11:1375-1377. Epub 2016 Oct 27. PubMed PMID: 27785916. Link to abstract. Link to Final Submitted Version.
Brennan-Krohn and Kirby JE. Antimicrobial Synergy Testing by the Inkjet Printer-assisted Automated Checkerboard Array and the Manual Time-kill Method. J. Vis. Exp. (146), e58636, doi:10.3791/58636 (2019). Link to Full Text and Video.
Smith KP, Kirby JE. Verification of an automated, digital dispensing platform for at-will broth microdilution-based antimicrobial susceptibility testing. J Clin Microbiol. 2016 Sep;54(9):2288-93. doi: 10.1128/JCM.00932-16. Epub 2016 Jun 22. PubMed PMID: 27335151; PubMed Central PMCID: PMC5005478. HTML full text. PDF full text. Press Release: "Simple Method Quickly Tests Hard-to-Treat Bacteria’s Susceptibility to Different Antibiotics." Technology adopted by the CDC based on our publications for use in its Antimicrobial Resistance Laboratory Network as described under Diagnostics.
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 Apr;55(4):1080-1089. doi: 10.1128/JCM.02336-16. Epub 2017 Jan 18. PubMed PMID:28100597. Link to abstract. Link to PDF.
Smith KP and Kirby JE. Rapid Susceptibility Testing Methods. Clin Lab Med. 2019 Sep;39(3):333-344.
Brennan-Krohn and Kirby JE. When One Drug Is Not Enough: Context, Methodology, and Future Prospects in Antibacterial Synergy Testing. Clin Lab Med. 2019. 39(3):345-358.
Brennan-Krohn and Kirby JE. When One Drug Is Not Enough: Context, Methodology, and Future Prospects in Antibacterial Synergy Testing. Clin Lab Med. 2019. 39(3):345-358.
Harvard Catalyst Interview on "Inkjet Technology Tapped for More Rapid Antimicrobial Testing"
Pathogenesis
Kang YS, Kirby JE. Promotion and rescue of intracellular Brucella neotomae replication during co-infection with Legionella pneumophila. Infect Immun. 2017 Mar 6. pii: IAI.00991-16. doi: 10.1128/IAI.00991-16. [Epub ahead of print] PubMed PMID: 28264909. Link to abstract. Link to HTML full text. PDF full text. Press Release: "Dramatic Cooperation Between Two Infectious Bacteria Revealed by BIDMC Researchers"
Kang YS, Brown DA, Kirby JE. Brucella neotomae recapitulates attributes of zoonotic human disease in a murine infection model. Infect Immun. 2018 Oct 29. pii: IAI.00255-18. doi: 10.1128/IAI.00255-18. [Epub ahead of print] PubMed PMID: 30373892. Link to abstract.
Kang YS, Kirby JE. A chemical genetics screen reveals influence of p38 map kinase and autophagy on phagosome development and intracellular replication of Brucella neotomae in macrophages. Infect Immun. 2019. IAI.00044-19. Link to abstract.
Antimicrobial Discovery
Dowgialo et al. The convergent total synthesis and antibacterial profile of the natural product streptothricin F. 2022. Chemical Science.
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 Jun 6. doi: 10.1002/cmdc.202100321. Epub ahead of print. PMID: 34096189.
Brennan-Krohn T, Kirby JE. Synergistic combinations and repurposed antibiotics active against the pandrug-resistant Klebsiella pneumoniae Nevada strain. Antimicrob Agents Chemother. 2019. Link to abstract. Link to abstract. Link to final accepted version.
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 Jan 16. PMID: 29339396. Link to full text.
Kang AD, Smith KP, Eliopoulos GM, Berg AH, McCoy C, Kirby JE. In vitro apramycin activity against multidrug-resistant Acinetobacter baumannii and Pseudomonas aeruginosa. Diagn Microbiol Infect Dis. 2017 Mar 16. pii: S0732-8893(17)30082-2. doi: 10.1016/j.diagmicrobio.2017.03.006. [Epub ahead of print] PubMed PMID: 28341099. Link to abstract. Link to final accepted version.
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 May 29. pii: S0732-8893(18)30175-5. doi: 10.1016/j.diagmicrobio.2018.05.018. Link to abstract. Link to final accepted version.
Riedel S, Vijayakumar, Berg G, Kang AD, Kang AD, Smith KP, and Kirby JE. Evaluation of apramycin against spectinomycin-resistant and -susceptible strains of Neisseria gonorrhoeae. Journal of Antimicrobial Chemotherapy. 2019. In Press. https://doi.org/10.1093/jac/dkz012. Link to final accepted version. Link to final full text article.
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 July https://doi.org/10.1177/2472555219859592. [Epub ahead of print] PMID: 31268804
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 Nov 16;(117). doi: 10.3791/54841. PubMed PMID: 27911388. Link to abstract. Link to video and article on JoVE website. Link to full text and associated notice of Copyright © 2016 Journal of Visualized Experiments
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. doi: 10.1016/j.diagmicrobio.2016.09.002. Epub 2016 Sep 8. PubMed PMID: 27745736.. Link to abstract. Link to final accepted version.
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. doi: 10.1089/adt.2016.701. Epub 2016 Apr 5. PubMed PMID: 27045615; PubMed Central PMCID: PMC4841070. Link to abstract. Link to full text. Press Release: "Screening Method Uncovers Drugs that May Combat Deadly Antibiotic-Resistant Bacteria"
Chiaraviglio L, Kirby JE. High-throughput intracellular antimicrobial susceptibility testing of Legionella pneumophila. Antimicrob Agents Chemother. 2015 Dec;59(12):7517-29. doi: 10.1128/AAC.01248-15. Epub 2015 Sep 21. PubMed PMID: 26392509; PubMed Central PMCID: PMC4649152. Full text for comprehensive susceptibility profile of Legionella pneumophila.
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. doi: 10.1089/adt.2014.577. PubMed PMID: 24831788; PubMed Central PMCID: PMC4026211. Link to HTML full text. Press Release.
Contagion Live: "3 Drug Combinations Appear Effective Against Candida auris."
Our review of CRE Therapeutic Pipeline: Brennan-Krohn T, Manetsch R, O'Doherty GA, and Kirby JE. New Strategies and Structural Considerations in Development of Therapeutics for Carbapenem-Resistant Enterobacteriaceae: New Therapies for CRE. Translational Research, In Press. Link to Final Accepted Manuscript. Check out the Figures for structural summary of antibiotics in pipeline and their derivation!
Antimicrobial Resistance
Green AB, Zulauf KE, Truelson K, Chiaraviglio C, Cui M, Zhang Z, Ware MP, Flegel WA, Haspel RL, Yu E, Kirby JE. Amotosalen is a bacterial multidrug efflux pump substrate potentially affecting its pathogen inactivation activity. Link to BioRXiv article. 2021.
Journal of Clinical Microbiology commentary on the past and future of antimicrobial susceptibility testing: 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 May. PMID: 28468856 Link to Abstract. Link to final accepted version.
Journal of Clinical Microbiology: Commentary on impediments to use of new effect antibiotics in treating highly resistant infections. Kirby JE, Brennan-Krohn T and Smith KP. Bringing antimicrobial susceptibility testing for new drugs into the clinical laboratory: removing obstacles in our fight against multidrug-resistant pathogens. J Clin MIcro. Link to full text. And our addendum final accepted manuscript to make inadequacies of current verification hurdles even more explicit.
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 Jan 31;114(5):1135-1140. doi: 10.1073/pnas.1616248114. Epub 2017 Jan 17. PubMed PMID: 28096418; PubMed Central PMCID: PMC5293017. HTML full text. Press Release: "Drug-resistant ‘nightmare bacteria’ show worrisome ability to diversify and spread"
Panel Discussion, Harvard Medical School Live, Longwood Seminar: "Resistance movement: Drugs, bugs and the fight against über-germs."
Clinical Microbiology and Public Policy
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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 Sep 18. pii: JCM.01270-19. doi: 10.1128/JCM.01270-19. Full text final accepted manuscript.
Lee RA, Kirby JE. We Cannot Do It Alone: The Intersection of Public Health,
Public Policy, and Clinical Microbiology. Clin Lab Med. 2019 Sep;39(3):499-508. Full text final accepted manuscript.
Kirby JE. Our Pathogens Are Not Standing Still and Neither Can We. Clin Lab Med. 2019 Sep;39(3):xiii-xiv. doi: 10.1016/j.cll.2019.06.001. PubMed PMID: 31383273. Full text final accepted manuscript.
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Our inkjet printer-based pathogen and AST testing method as portrayed on the ABC Sitcom, "The Good Doctor." |
Kirby Lab Plasmids
Bibliography
ASM Website Articles by Current and Former Fellows
Note, ASM is currently updating their website. There are many more articles that are currently offline, but will become available again by the end of 2019.
Thea Brennan-Krohn
Eastern Equine Encephalitis Virus (EEV): The Role of Diagnostics
Urine Good Hands: Diagnosing UTIs With Urine Cultures
Rabies and Roundworm: Raccoon-Associated Infectious Diseases
Combination Antibiotic Testing: When Two Drugs Are Better Than One (or Two).
Rabies and Roundworm: Raccoon-Associated Infectious Diseases
Diagnosing Measles in the Post-Elimination Era
Measles Vaccination and Infection: Questions and Misconceptions
Some Good News in the Field of Antimicrobial Resistance
Making Sense of Respiratory Viral Panel Results
Infections in Animals and Humans Caused by Bacterial 'Cousins
Rose Lee
C. diff Diagnosis versus Detection: Why Tests Remain Ambiguous
KP Smith
Opening the Black Box of Phenotypic Carbapenemase Detection
Who Are the HACEK Organisms?
Predictive Value of Blood Culture Time to Positivity
Opening the Black Box of MALDI-TOF MS
The Origin of MacConkey Agar
Jennifer Tsang
The One Health of Animals, Humans, and Our Planet: It’s All Microbially Connected
Changing CO2 Levels Require Microbial Coping Strategies
Snow Is Coming - What’s That Have to Do with Microbes?
Does a Minimal Genome Exist
Yeast through the Years: from Hidden Fermenters to Synthetic Biology
Thea Brennan-Krohn
Eastern Equine Encephalitis Virus (EEV): The Role of Diagnostics
Urine Good Hands: Diagnosing UTIs With Urine Cultures
Rabies and Roundworm: Raccoon-Associated Infectious Diseases
Combination Antibiotic Testing: When Two Drugs Are Better Than One (or Two).
Rabies and Roundworm: Raccoon-Associated Infectious Diseases
Diagnosing Measles in the Post-Elimination Era
Measles Vaccination and Infection: Questions and Misconceptions
Some Good News in the Field of Antimicrobial Resistance
Making Sense of Respiratory Viral Panel Results
Infections in Animals and Humans Caused by Bacterial 'Cousins
Rose Lee
C. diff Diagnosis versus Detection: Why Tests Remain Ambiguous
KP Smith
Opening the Black Box of Phenotypic Carbapenemase Detection
Who Are the HACEK Organisms?
Predictive Value of Blood Culture Time to Positivity
Opening the Black Box of MALDI-TOF MS
The Origin of MacConkey Agar
Jennifer Tsang
The One Health of Animals, Humans, and Our Planet: It’s All Microbially Connected
Changing CO2 Levels Require Microbial Coping Strategies
Snow Is Coming - What’s That Have to Do with Microbes?
Does a Minimal Genome Exist
Yeast through the Years: from Hidden Fermenters to Synthetic Biology