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 Sep 3;9(1):e0016221. doi: 10.1128/Spectrum.00162-21. Epub 2021 Aug 18. PMID: 34406838; PMCID: PMC8552668
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. 2021 Oct 22;102(2):115575. doi: 10.1016/j.diagmicrobio.2021.115575. Epub ahead of print. PMID: 34839127; PMCID: PMC8532379.
Arnaout RA. Cooperation under Pressure: Lessons from the COVID-19 Swab Crisis. J Clin Microbiol. 2021 Sep 20;59(10):e0123921. doi: 10.1128/JCM.01239-21. Epub 2021 Aug 18. PMID: 34406796; PMCID: PMC8451415.
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 Sep 17;65(10):e0026821. doi: 10.1128/AAC.00268-21. Epub 2021 Jul 12. PMID: 34252295; PMCID: PMC8448112.
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 Aug 18;59(9):e0056921. doi: 10.1128/JCM.00569-21. Epub 2021 Aug 18. PMID: 34076471; PMCID: PMC8373031.
Zhang SX, Balada-Llasat JM, Pancholi P, Sullivan KV, Riedel S; Fungal Diagnostic Laboratories Consortium (FDLC). COVID-Associated Pulmonary Aspergillosis in the United States: Is It Rare or Have We Missed the Diagnosis? J Clin Microbiol. 2021 Sep 20;59(10):e0113521. doi: 10.1128/JCM.01135-21. Epub 2021 Jul 21. PMID: 34288730; PMCID: PMC8451424.
Riedel S, Halls J, Dutta S, Toraskar N, Lemon J, Carter K, Sinclair W, Lopansri BK, Styer AM, Wolk DM, Walker GT. Clinical evaluation of the acuitas® AMR gene panel for rapid detection of bacteria and genotypic antibiotic resistance determinants. Diagn Microbiol Infect Dis. 2021 Aug;100(4):115383. doi: 10.1016/j.diagmicrobio.2021.115383. Epub 2021 Mar 26. PMID: 33894657.
Chen AF, Riedel S. A Case Illustrating the Practical Application of the AAOS Clinical Practice Guideline: Diagnosis and Prevention of Periprosthetic Joint Infection. J Am Acad Orthop Surg. 2020 Dec 15;28(24):e1081-e1085. doi: 10.5435/JAAOS-D-20-00438. PMID: 32991385.
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 Feb 3:ciaa1382. doi: 10.1093/cid/ciaa1382. Online ahead of print.
Arnaout RA, Prak ETL, Schwab N, Rubelt F; Adaptive Immune Receptor Repertoire Community. The Future of Blood Testing Is the Immunome. Front Immunol. 2021 Mar 15;12:626793. doi: 10.3389/fimmu.2021.626793. eCollection 2021.
Riedel S, Halls J, Dutta S, Toraskar N, Lemon J, Carter K, Sinclair W, Lopansri BK, Styer AM, Wolk DM, Walker GT. Clinical evaluation of the acuitas® AMR gene panel for rapid detection of bacteria and genotypic antibiotic resistance determinants. Diagn Microbiol Infect Dis. 2021 Mar 26;100(4):115383. doi: 10.1016/j.diagmicrobio.2021.115383.
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 Nov 24;117(47):29839-29850. doi: 10.1073/pnas.2005948117. Epub 2020 Nov
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 Jun 25;11(3):e00997-20. doi: 10.1128/mBio.00997-20.
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 Jul 23;58(8):e00913-20. doi: 10.1128/JCM.00913-20. Print 2020 Jul 23.
Arnaout R. Machine Learning in Clinical Pathology: Seeing the Forest for the Trees. Clin Chem. 2018 Nov;64(11):1553-1554. doi: 10.1373/clinchem.2018.295121. Epub 2018 Sep 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 Jul 23;58(8):e00876-20. doi: 10.1128/JCM.00876-20. Print 2020 Jul 23.
Smith KP, Kirby JE. Image analysis and artificial intelligence in infectious disease diagnostics. Clin Microbiol Infect. 2020 Oct;26(10):1318-1323. doi: 10.1016/j.cmi.2020.03.012. Epub 2020 Mar 22. PMID: 32213317
Zhang SX, Babady NE, Hanson KE, Harrington AT, Larkin PMK, Leal SM Jr, Luethy PM, Martin IW, Pancholi P, Procop GW, Riedel S, Seyedmousavi S, Sullivan KV, Walsh TJ, Lockhart SR; Fungal Diagnostics Laboratories Consortium (FDLC).Recognition of Diagnostic Gaps for Laboratory Diagnosis of Fungal Diseases: Expert Opinion from the Fungal Diagnostics Laboratories Consortium (FDLC). J Clin Microbiol. 2021 Jan 27:JCM.01784-20. doi: 10.1128/JCM.01784-20. Online ahead of print. PMID: 33504591
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. doi: 10.1016/j.cll.2019.05.008. Epub 2019 Jul 6.
Smith KP, Kirby JE. Rapid Susceptibility Testing Methods. Clin Lab Med. 2019 Sep;39(3):333-344. doi: 10.1016/j.cll.2019.04.001. Epub 2019 Jun 12.
Brennan-Krohn T, Kirby JE. When One Drug Is Not Enough: Context, Methodology, and Future Prospects in Antibacterial Synergy Testing. Clin Lab Med. 2019 Sep;39(3):345-358. doi: 10.1016/j.cll.2019.04.002. Epub 2019 Jun 12.
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.
Chen AF, Riedel S. A Case Illustrating the Practical Application of the AAOS Clinical Practice Guideline: Diagnosis and Prevention of Periprosthetic Joint Infection.
J Am Acad Orthop Surg. 2020 Dec 15;28(24):e1081-e1085. doi: 10.5435/JAAOS-D-20-00438.
Brennan-Krohn T, Yoon E, Nishino M, Kirby JE, Riedel S. Arthroconidia in Lung Tissue: An Unusual Histopathological Finding in Pulmonary Coccidioidomycosis. Hum Pathol. 2017 Aug 1. pii: S0046-8177(17)30265-4. doi: 10.1016/j.humpath.2017.07.013. [Epub ahead of print] PubMed PMID: 28778515.
Riedel S, Huband MD, Sader HS, Flamm RK, Jones RN. Determination of Disk Diffusion and MIC Quality Control Guidelines for High Dose Cefepime-Tazobactam (WCK 4282), a Novel Antibacterial Combination Consisting of a β-Lactamase Inhibitor and a Fourth-Generation Cephalosporin. J Clin Microbiol. 2017 Aug 9. pii: JCM.00788-17. doi: 10.1128/JCM.00788-17. [Epub ahead of print] PubMed PMID: 28794180.
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.
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.
Riedel S, Carroll KC. Early Identification and Treatment of Pathogens in Sepsis: Molecular Diagnostics and Antibiotic Choice. Clin Chest Med. 2016 Jun;37(2):191-207. http://doi: 10.1016/j.ccm.2016.01.018. Review. PubMed PMID: 27229637.
Kaplinsky J, Arnaout R. Robust estimates of overall immune-repertoire diversity from high-throughput measurements on samples. Nat Commun. 2016 Jun 15;7:11881. doi: 10.1038/ncomms11881. PubMed PMID: 27302887; PubMed Central PMCID: PMC4912625.
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. doi: 10.1016/j.diagmicrobio.2015.10.013. Epub 2015 Oct 21. PubMed PMID: 26602949.
Riedel S, Ross JE, Farrell DJ, Flamm RK, Jones RN. Determination of Disk Diffusion and MIC Quality Control Guidelines for Solithromycin, a Novel Fluoroketolide Antibacterial, against Neisseria gonorrhoeae. J Clin Microbiol. 2015 Dec;53(12):3888-90. doi: 10.1128/JCM.02250-15. Epub 2015 Sep 16. PubMed PMID: 26378286; PubMed Central PMCID: PMC4652126.
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.
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"
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.
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 Submitted Version.
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"
Riedel S, Huband MD, Sader HS, Flamm RK, Jones RN. Determination of Disk Diffusion and MIC Quality Control Guidelines for High-Dose Cefepime-Tazobactam (WCK 4282), a Novel Antibacterial Combination Consisting of a β-Lactamase Inhibitor and a Fourth-Generation Cephalosporin. J Clin Microbiol. 2017 Oct;55(10):3130-3134. doi: 10.1128/JCM.00788-17. Epub 2017 Aug 9. PMID: 28794180
Kaplinsky J, Li A, Sun A, Coffre M, Koralov SB, Arnaout R. Antibody repertoire deep sequencing reveals antigen-independent selection in maturing B cells. Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):E2622-9. doi: 10.1073/pnas.1403278111. Epub 2014 Jun 9. PubMed PMID: 24927543; PubMed Central PMCID: PMC4078805.
Smith KP, Richmond DL, Brennan-Krohn T, Elliott HL, Kirby JE. Development of MAST: a Microscopy-Based Antimicrobial Susceptibility Testing Platform. SLAS Technology, In Press. Link to Manuscript. Link to Figures (50 MB).
Brennan-Krohn T, Pica N, Sandora TJ, McAdam A. Closing the Brief Case: Safe To Go Back in the Water? Vibrio parahaemolyticus Wound Infection Associated with Brackish Water. J Clin Microbiol. 2016 Jun;54(6):1672. doi: 10.1128/JCM.02661-15. PubMed PMID: 27217388; PubMed Central PMCID: PMC4879276.
Kirkcaldy RD, Harvey A, Papp JR, Del Rio C, Soge OO, Holmes KK, Hook EW 3rd, Kubin G, Riedel S, Zenilman J, Pettus K, Sanders T, Sharpe S, Torrone E. Neisseria gonorrhoeae Antimicrobial Susceptibility Surveillance - The Gonococcal Isolate Surveillance Project, 27 Sites, United States, 2014. MMWR Surveill Summ. 2016 Jul 15;65(7):1-19. doi: 10.15585/mmwr.ss6507a1. PubMed PMID: 27414503.
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, 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.o abstract.
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. 2021 Oct 22;102(2):115575. doi: 10.1016/j.diagmicrobio.2021.115575. Epub ahead of print. PMID: 34839127; PMCID: PMC8532379.
Arnaout RA. Cooperation under Pressure: Lessons from the COVID-19 Swab Crisis. J Clin Microbiol. 2021 Sep 20;59(10):e0123921. doi: 10.1128/JCM.01239-21. Epub 2021 Aug 18. PMID: 34406796; PMCID: PMC8451415.
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 Sep 17;65(10):e0026821. doi: 10.1128/AAC.00268-21. Epub 2021 Jul 12. PMID: 34252295; PMCID: PMC8448112.
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 Aug 18;59(9):e0056921. doi: 10.1128/JCM.00569-21. Epub 2021 Aug 18. PMID: 34076471; PMCID: PMC8373031.
Zhang SX, Balada-Llasat JM, Pancholi P, Sullivan KV, Riedel S; Fungal Diagnostic Laboratories Consortium (FDLC). COVID-Associated Pulmonary Aspergillosis in the United States: Is It Rare or Have We Missed the Diagnosis? J Clin Microbiol. 2021 Sep 20;59(10):e0113521. doi: 10.1128/JCM.01135-21. Epub 2021 Jul 21. PMID: 34288730; PMCID: PMC8451424.
Riedel S, Halls J, Dutta S, Toraskar N, Lemon J, Carter K, Sinclair W, Lopansri BK, Styer AM, Wolk DM, Walker GT. Clinical evaluation of the acuitas® AMR gene panel for rapid detection of bacteria and genotypic antibiotic resistance determinants. Diagn Microbiol Infect Dis. 2021 Aug;100(4):115383. doi: 10.1016/j.diagmicrobio.2021.115383. Epub 2021 Mar 26. PMID: 33894657.
Chen AF, Riedel S. A Case Illustrating the Practical Application of the AAOS Clinical Practice Guideline: Diagnosis and Prevention of Periprosthetic Joint Infection. J Am Acad Orthop Surg. 2020 Dec 15;28(24):e1081-e1085. doi: 10.5435/JAAOS-D-20-00438. PMID: 32991385.
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 Feb 3:ciaa1382. doi: 10.1093/cid/ciaa1382. Online ahead of print.
Arnaout RA, Prak ETL, Schwab N, Rubelt F; Adaptive Immune Receptor Repertoire Community. The Future of Blood Testing Is the Immunome. Front Immunol. 2021 Mar 15;12:626793. doi: 10.3389/fimmu.2021.626793. eCollection 2021.
Riedel S, Halls J, Dutta S, Toraskar N, Lemon J, Carter K, Sinclair W, Lopansri BK, Styer AM, Wolk DM, Walker GT. Clinical evaluation of the acuitas® AMR gene panel for rapid detection of bacteria and genotypic antibiotic resistance determinants. Diagn Microbiol Infect Dis. 2021 Mar 26;100(4):115383. doi: 10.1016/j.diagmicrobio.2021.115383.
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 Nov 24;117(47):29839-29850. doi: 10.1073/pnas.2005948117. Epub 2020 Nov
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 Jun 25;11(3):e00997-20. doi: 10.1128/mBio.00997-20.
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 Jul 23;58(8):e00913-20. doi: 10.1128/JCM.00913-20. Print 2020 Jul 23.
Arnaout R. Machine Learning in Clinical Pathology: Seeing the Forest for the Trees. Clin Chem. 2018 Nov;64(11):1553-1554. doi: 10.1373/clinchem.2018.295121. Epub 2018 Sep 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 Jul 23;58(8):e00876-20. doi: 10.1128/JCM.00876-20. Print 2020 Jul 23.
Smith KP, Kirby JE. Image analysis and artificial intelligence in infectious disease diagnostics. Clin Microbiol Infect. 2020 Oct;26(10):1318-1323. doi: 10.1016/j.cmi.2020.03.012. Epub 2020 Mar 22. PMID: 32213317
Zhang SX, Babady NE, Hanson KE, Harrington AT, Larkin PMK, Leal SM Jr, Luethy PM, Martin IW, Pancholi P, Procop GW, Riedel S, Seyedmousavi S, Sullivan KV, Walsh TJ, Lockhart SR; Fungal Diagnostics Laboratories Consortium (FDLC).Recognition of Diagnostic Gaps for Laboratory Diagnosis of Fungal Diseases: Expert Opinion from the Fungal Diagnostics Laboratories Consortium (FDLC). J Clin Microbiol. 2021 Jan 27:JCM.01784-20. doi: 10.1128/JCM.01784-20. Online ahead of print. PMID: 33504591
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. doi: 10.1016/j.cll.2019.05.008. Epub 2019 Jul 6.
Smith KP, Kirby JE. Rapid Susceptibility Testing Methods. Clin Lab Med. 2019 Sep;39(3):333-344. doi: 10.1016/j.cll.2019.04.001. Epub 2019 Jun 12.
Brennan-Krohn T, Kirby JE. When One Drug Is Not Enough: Context, Methodology, and Future Prospects in Antibacterial Synergy Testing. Clin Lab Med. 2019 Sep;39(3):345-358. doi: 10.1016/j.cll.2019.04.002. Epub 2019 Jun 12.
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.
Chen AF, Riedel S. A Case Illustrating the Practical Application of the AAOS Clinical Practice Guideline: Diagnosis and Prevention of Periprosthetic Joint Infection.
J Am Acad Orthop Surg. 2020 Dec 15;28(24):e1081-e1085. doi: 10.5435/JAAOS-D-20-00438.
Brennan-Krohn T, Yoon E, Nishino M, Kirby JE, Riedel S. Arthroconidia in Lung Tissue: An Unusual Histopathological Finding in Pulmonary Coccidioidomycosis. Hum Pathol. 2017 Aug 1. pii: S0046-8177(17)30265-4. doi: 10.1016/j.humpath.2017.07.013. [Epub ahead of print] PubMed PMID: 28778515.
Riedel S, Huband MD, Sader HS, Flamm RK, Jones RN. Determination of Disk Diffusion and MIC Quality Control Guidelines for High Dose Cefepime-Tazobactam (WCK 4282), a Novel Antibacterial Combination Consisting of a β-Lactamase Inhibitor and a Fourth-Generation Cephalosporin. J Clin Microbiol. 2017 Aug 9. pii: JCM.00788-17. doi: 10.1128/JCM.00788-17. [Epub ahead of print] PubMed PMID: 28794180.
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.
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.
Riedel S, Carroll KC. Early Identification and Treatment of Pathogens in Sepsis: Molecular Diagnostics and Antibiotic Choice. Clin Chest Med. 2016 Jun;37(2):191-207. http://doi: 10.1016/j.ccm.2016.01.018. Review. PubMed PMID: 27229637.
Kaplinsky J, Arnaout R. Robust estimates of overall immune-repertoire diversity from high-throughput measurements on samples. Nat Commun. 2016 Jun 15;7:11881. doi: 10.1038/ncomms11881. PubMed PMID: 27302887; PubMed Central PMCID: PMC4912625.
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. doi: 10.1016/j.diagmicrobio.2015.10.013. Epub 2015 Oct 21. PubMed PMID: 26602949.
Riedel S, Ross JE, Farrell DJ, Flamm RK, Jones RN. Determination of Disk Diffusion and MIC Quality Control Guidelines for Solithromycin, a Novel Fluoroketolide Antibacterial, against Neisseria gonorrhoeae. J Clin Microbiol. 2015 Dec;53(12):3888-90. doi: 10.1128/JCM.02250-15. Epub 2015 Sep 16. PubMed PMID: 26378286; PubMed Central PMCID: PMC4652126.
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.
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"
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.
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 Submitted Version.
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"
Riedel S, Huband MD, Sader HS, Flamm RK, Jones RN. Determination of Disk Diffusion and MIC Quality Control Guidelines for High-Dose Cefepime-Tazobactam (WCK 4282), a Novel Antibacterial Combination Consisting of a β-Lactamase Inhibitor and a Fourth-Generation Cephalosporin. J Clin Microbiol. 2017 Oct;55(10):3130-3134. doi: 10.1128/JCM.00788-17. Epub 2017 Aug 9. PMID: 28794180
Kaplinsky J, Li A, Sun A, Coffre M, Koralov SB, Arnaout R. Antibody repertoire deep sequencing reveals antigen-independent selection in maturing B cells. Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):E2622-9. doi: 10.1073/pnas.1403278111. Epub 2014 Jun 9. PubMed PMID: 24927543; PubMed Central PMCID: PMC4078805.
Smith KP, Richmond DL, Brennan-Krohn T, Elliott HL, Kirby JE. Development of MAST: a Microscopy-Based Antimicrobial Susceptibility Testing Platform. SLAS Technology, In Press. Link to Manuscript. Link to Figures (50 MB).
Brennan-Krohn T, Pica N, Sandora TJ, McAdam A. Closing the Brief Case: Safe To Go Back in the Water? Vibrio parahaemolyticus Wound Infection Associated with Brackish Water. J Clin Microbiol. 2016 Jun;54(6):1672. doi: 10.1128/JCM.02661-15. PubMed PMID: 27217388; PubMed Central PMCID: PMC4879276.
Kirkcaldy RD, Harvey A, Papp JR, Del Rio C, Soge OO, Holmes KK, Hook EW 3rd, Kubin G, Riedel S, Zenilman J, Pettus K, Sanders T, Sharpe S, Torrone E. Neisseria gonorrhoeae Antimicrobial Susceptibility Surveillance - The Gonococcal Isolate Surveillance Project, 27 Sites, United States, 2014. MMWR Surveill Summ. 2016 Jul 15;65(7):1-19. doi: 10.15585/mmwr.ss6507a1. PubMed PMID: 27414503.
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, 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.o abstract.
From our Fellowship Affiliated Faculty at Boston Children's Hospital and The Massachusetts State Laboratory Institute
Sigal GB, Novak T, Mathew A, Chou J, Zhang Y, Manjula N, Bathala P, Joe J, Padmanabhan N, Romero D, Allegri-Machado G, Joerger J, Loftis LL, Schwartz SP, Walker TC, Fitzgerald JC, Tarquinio KM, Zinter MS, Schuster JE, Halasa NB, Cullimore ML, Maddux AB, Staat MA, Irby K, Flori HR, Coates BM, Crandall H, Gertz SJ, Randolph AG, Pollock NR. Measurement of SARS-CoV-2 antigens in plasma of pediatric patients with acute COVID-19 or MIS-C using an ultrasensitive and quantitative immunoassay. medRxiv [Preprint]. 2021 Dec 9:2021.12.08.21267502. doi: 10.1101/2021.12.08.21267502. PMID: 34909787; PMCID: PMC8669854.
Pollock NR, Lee F, Ginocchio CC, Yao JD, Humphries RM. Considerations for Assessment and Deployment of Rapid Antigen Tests for Diagnosis of Coronavirus Disease 2019. Open Forum Infect Dis. 2021 Mar 7;8(6):ofab110. doi: 10.1093/ofid/ofab110. PMID: 34258309; PMCID: PMC7989197.
Pollock NR, Tran K, Jacobs JR, Cranston AE, Smith S, O'Kane CY, Roady TJ, Moran A, Scarry A, Carroll M, Volinsky L, Perez G, Patel P, Gabriel S, Lennon NJ, Madoff LC, Brown C, Smole SC. Performance and Operational Evaluation of the Access Bio CareStart Rapid Antigen Test in a High-Throughput Drive-Through Community Testing Site in Massachusetts. Open Forum Infect Dis. 2021 May 26;8(7):ofab243. doi: 10.1093/ofid/ofab243. PMID: 34250188; PMCID: PMC8244626.
Pollock NR, Berlin D, Smole SC, Madoff LC, Brown C, Henderson K, Larsen E, Hay J, Gabriel S, Gawande AA, Lennon NJ. Implementation of SARS-CoV2 Screening in K-12 Schools Using In-School Pooled Molecular Testing and Deconvolution by Rapid Antigen Test. J Clin Microbiol. 2021 Aug 18;59(9):e0112321. doi: 10.1128/JCM.01123-21. Epub 2021 Aug 18. PMID: 34191585; PMCID: PMC8373013.
Pollock NR, MacIntyre AT, Blauwkamp TA, Blair L, Ho C, Calderon R, Franke MF. Detection of Mycobacterium tuberculosis cell-free DNA to diagnose TB in pediatric and adult patients. Int J Tuberc Lung Dis. 2021 May 1;25(5):403-405. doi: 10.5588/ijtld.21.0055. PMID: 33977910; PMCID: PMC8174651.
Performance and Implementation Evaluation of the Abbott BinaxNOW Rapid Antigen Test in a High-Throughput Drive-Through Community Testing Site in Massachusetts. J Clin Microbiol. 2021 Apr 20;59(5):e00083-21. doi: 10.1128/JCM.00083-21. PMID: 33622768; PMCID: PMC8091851.
Pollock NR, Savage TJ, Wardell H, Lee RA, Mathew A, Stengelin M, Sigal GB. Correlation of SARS-CoV-2 Nucleocapsid Antigen and RNA Concentrations in Nasopharyngeal Samples from Children and Adults Using an Ultrasensitive and Quantitative Antigen Assay. J Clin Microbiol. 2021 Mar 19;59(4):e03077-20. doi: 10.1128/JCM.03077-20. PMID: 33441395; PMCID: PMC8092747.
Kociolek LK, Muller WJ, Yee R, Dien Bard J, Brown CA, Revell PA, Wardell H, Savage TJ, Jung S, Dominguez S, Parikh BA, Jerris RC, Kehl SC, Campigotto A, Bender JM, Zheng X, Muscat E, Linam M, Abuogi L, Smith C, Graff K, Hernandez-Leyva A, Williams D, Pollock NR. Comparison of Upper Respiratory Viral Load Distributions in Asymptomatic and Symptomatic Children Diagnosed with SARS-CoV-2 Infection in Pediatric Hospital Testing Programs. J Clin Microbiol. 2020 Dec 17;59(1):e02593-20. doi: 10.1128/JCM.02593-20. PMID: 33093026; PMCID: PMC7771452.
Branda JA, Lemieux JE, Blair L, Ahmed AA, Hong DK, Bercovici S, Blauwkamp TA, Hollemon D, Ho C, Strle K, Damle NS, Lepore TJ, Pollock NR. Detection of Borrelia burgdorferi Cell-free DNA in Human Plasma Samples for Improved Diagnosis of Early Lyme Borreliosis. Clin Infect Dis. 2021 Oct 5;73(7):e2355-e2361. doi: 10.1093/cid/ciaa858. PMID: 32584965; PMCID: PMC8492203.
Brock M, Hanlon D, Zhao M, Pollock NR. Detection of mycobacterial lipoarabinomannan in serum for diagnosis of active tuberculosis. Diagn Microbiol Infect Dis. 2020 Feb;96(2):114937. doi: 10.1016/j.diagmicrobio.2019.114937. Epub 2019 Nov 13. PMID: 31785971.
Kelly CP, Chen X, Williams D, Xu H, Cuddemi CA, Daugherty K, Barrett C, Miller M, Foussadier A, Lantz A, Banz A, Pollock NR. Host Immune Markers Distinguish Clostridioides difficile Infection From Asymptomatic Carriage and Non-C. difficile Diarrhea. Clin Infect Dis. 2020 Mar 3;70(6):1083-1093. doi: 10.1093/cid/ciz330. PMID: 31211839; PMCID: PMC8204484.
Pollock NR, Banz A, Chen X, Williams D, Xu H, Cuddemi CA, Cui AX, Perrotta M, Alhassan E, Riou B, Lantz A, Miller MA, Kelly CP. Comparison of Clostridioides difficile Stool Toxin Concentrations in Adults With Symptomatic Infection and Asymptomatic Carriage Using an Ultrasensitive Quantitative Immunoassay. Clin Infect Dis. 2019 Jan 1;68(1):78-86. doi: 10.1093/cid/ciy415. PMID: 29788296; PMCID: PMC6293008.
Roldan GA, Cui AX, Pollock NR. Assessing the Burden of Clostridium difficile Infection in Low- and Middle-Income Countries. J Clin Microbiol. 2018 Feb 22;56(3):e01747-17. doi: 10.1128/JCM.01747-17. PMID: 29305541; PMCID: PMC5824057.
Sauer-Budge AF, Brookfield SJ, Janzen R, McGray S, Boardman A, Wirz H, Pollock NR. A novel device for collecting and dispensing fingerstick blood for point of care testing. PLoS One. 2017 Aug 24;12(8):e0183625. doi: 10.1371/journal.pone.0183625. PMID: 28837616; PMCID: PMC5570352.
Pollock NR, Wonderly B. Evaluating Novel Diagnostics in an Outbreak Setting: Lessons Learned from Ebola. J Clin Microbiol. 2017 May;55(5):1255-1261. doi: 10.1128/JCM.00053-17. Epub 2017 Mar 1. PMID: 28250002; PMCID: PMC5405244.
Broadhurst MJ, Brooks TJ, Pollock NR. Diagnosis of Ebola Virus Disease: Past, Present, and Future. Clin Microbiol Rev. 2016 Oct;29(4):773-93. doi: 10.1128/CMR.00003-16. PMID: 27413095; PMCID: PMC5010747.
Semper AE, Broadhurst MJ, Richards J, Foster GM, Simpson AJ, Logue CH, Kelly JD, Miller A, Brooks TJ, Murray M, Pollock NR. Performance of the GeneXpert Ebola Assay for Diagnosis of Ebola Virus Disease in Sierra Leone: A Field Evaluation Study. PLoS Med. 2016 Mar 29;13(3):e1001980. doi: 10.1371/journal.pmed.1001980. PMID: 27023868; PMCID: PMC4811569.
Broadhurst MJ, Semper A, Bailey D, Pollock NR. ReEBOV Antigen Rapid Test kit for Ebola - Authors' reply. Lancet. 2015 Dec 5;386(10010):2255-6. doi: 10.1016/S0140-6736(15)01109-5. PMID: 26681290.
Pollock NR. Ultrasensitive Detection and Quantification of Toxins for Optimized Diagnosis of Clostridium difficile Infection. J Clin Microbiol. 2016 Feb;54(2):259-64. doi: 10.1128/JCM.02419-15. Epub 2015 Dec 9. PMID: 26659205; PMCID: PMC4733189.
Broadhurst MJ, Kelly JD, Miller A, Semper A, Bailey D, Groppelli E, Simpson A, Brooks T, Hula S, Nyoni W, Sankoh AB, Kanu S, Jalloh A, Ton Q, Sarchet N, George P, Perkins MD, Wonderly B, Murray M, Pollock NR. ReEBOV Antigen Rapid Test kit for point-of-care and laboratory-based testing for Ebola virus disease: a field validation study. Lancet. 2015 Aug 29;386(9996):867-74. doi: 10.1016/S0140-6736(15)61042-X. Epub 2015 Jun 25. PMID: 26119838.
And of course the micro comic strip summary of the ins and outs of the microbiology field by Editor-In-Chief of the Journal of Clinical Microbiology, Alex McAdam. I could populate with many examples.
McAdam AJ. What Is Needed for the Response to COVID-19? A Micro-Comic Strip. J Clin Microbiol. 2020 Jul 23;58(8):e01011-20. doi: 10.1128/JCM.01011-20. PMID: 32703888; PMCID: PMC7383553.
ASM Blogs written by current and former fellows:
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
The Origin of MacConkey Agar
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