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2. Index

Author

Henry, Matthew S.

Published
2022

4. Notes

Author

Henry, Matthew S.

Published
2022

11. Cover

Author

Henry, Matthew S.

Published
2022

16. Pseudomonas aeruginosa ventricular assist device infections: findings from ineffective phage therapies in five cases.

Author

Aslam, Saima, Roach, Dwayne, Nikolich, Mikeljon P, Biswas, Biswajit, Schooley, Robert T, Lilly-Bishop, Kimberley A, Rice, Gregory K, Cer, Regina Z, Hamilton, Theron, Henry, Matthew, Luong, Tiffany, Salabarria, Ann-Charlott, Sisk-Hackworth, Laura, Filippov, Andrey A, Lebreton, Francois, Hall, Lindsey, Nir-Paz, Ran, Onallah, Hadil, Livni, Gilat, Shostak, Eran, Wieder-Finesod, Anat, Yahav, Dafna, Yerushalmy, Ortal, Alkalay-Oren, Sivan, Braunstein, Ron, Khalifa, Leron, Rimon, Amit, Gelman, Daniel, and Hazan, Ronen

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Clinical Sciences, Biodefense, Assistive Technology, Antimicrobial Resistance, Infectious Diseases, Prevention, Cardiovascular, Rare Diseases, Heart Disease, Vaccine Related, Bioengineering, Emerging Infectious Diseases, Infection, LVAD, MDRO, Pseudomonas aeruginosa, device-related infection, phage therapy, Microbiology, Pharmacology and Pharmaceutical Sciences, Medical microbiology, Pharmacology and pharmaceutical sciences
Abstract

Left ventricular assist devices (LVAD) are increasingly used for management of heart failure; infection remains a frequent complication. Phage therapy has been successful in a variety of antibiotic refractory infections and is of interest in treating LVAD infections. We performed a retrospective review of four patients that underwent five separate courses of intravenous (IV) phage therapy with concomitant antibiotic for treatment of endovascular Pseudomonas aeruginosa LVAD infection. We assessed phage susceptibility, bacterial strain sequencing, serum neutralization, biofilm activity, and shelf-life of phage preparations. Five treatments of one to four wild-type virulent phage(s) were administered for 14-51 days after informed consent and regulatory approval. There was no successful outcome. Breakthrough bacteremia occurred in four of five treatments. Two patients died from the underlying infection. We noted a variable decline in phage susceptibility following three of five treatments, four of four tested developed serum neutralization, and prophage presence was confirmed in isolates of two tested patients. Two phage preparations showed an initial titer drop. Phage biofilm activity was confirmed in two. Phage susceptibility alone was not predictive of clinical efficacy in P. aeruginosa endovascular LVAD infection. IV phage was associated with serum neutralization in most cases though lack of clinical effect may be multifactorial including presence of multiple bacterial isolates with varying phage susceptibility, presence of prophages, decline in phage titers, and possible lack of biofilm activity. Breakthrough bacteremia occurred frequently (while the organism remained susceptible to administered phage) and is an important safety consideration.

Published
2024

21. Evaluation of the Feasibility of Phosphorene for Electronic DNA Sequencing Using Density Functional Theory Calculations

Author

Henry, Matthew B., Tumbapo, Mukesh, Wilson, Kolby, and Tayo, Benjamin O.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Electronic DNA sequencing using two-dimensional (2D) materials such as graphene has recently emerged as the next-generation of DNA sequencing technology. Owing to its commercial availability and remarkable physical and conductive properties, graphene has been widely investigated for DNA sequencing by several theoretical and experimental groups. Despite this progress, sequencing using graphene remains a major challenge. This is due to the hydrophobic nature of graphene, which causes DNA bases to stick to its surface via strong {\pi}-{\pi} interactions, reducing translocation speed and increasing error rates. To circumvent this challenge, the scientific community has turned its attention to other 2D materials beyond graphene. One such material is phosphorene. In this article, we performed first-principle computational studies using density functional theory (DFT) to evaluate the ability of phosphorene to distinguish individual DNA bases using two detection principles, namely, nanopore and nanoribbon modalities. We observe that binding energies of DNA bases are lower in phosphorene compared to graphene. The energy gap modulations due to interaction with DNA bases are very significant in phosphorene compared to graphene. Our studies show that phosphorene is superior to graphene, and hence a promising alternative for electronic DNA sequencing., Comment: 6 pages, 2 figures, 2 tables

Published
2022

22. Identification of DNA Bases Using Nanopores Created in Finite-Size Nanoribbons from Graphene, Phosphorene, and Silicene

Author

Henry, Matthew B., Tumbapo, Mukesh, and Tayo, Benjamin O.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

The success of graphene for nanopore DNA sequencing has shown that it is possible to explore other potential single-atom and few-atom thick layers of elemental 2D materials beyond graphene (e.g., phosphorene and silicene). Using density functional theory, we studied the interaction of DNA bases with nanopores created in finite-size nanoribbons from graphene, phosphorene, and silicene. We observe that binding energies of DNA bases using nanopores from phosphorene and silicene are generally smaller compared to graphene. The band gaps of phosphorene and silicene are significantly altered due to interaction with DNA bases compared to graphene. Our findings show that phosphorene and silicene are promising alternatives to graphene for DNA base detection using advanced detection principles such as transverse tunneling current measurement., Comment: 14 pages

Published
2021
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23. Physisorption of DNA bases on finite-size nanoribbons from graphene, phosphorene, and silicene: Insights from density functional theory

Author

Tumbapo, Mukesh, Henry, Matthew B., Jha, Sanjiv K., and Tayo, Benjamin O.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

The ability to detect and discriminate DNA bases by reading it directly using simple and cost-effective methods is an important problem whose solution can produce significant value for areas such as cancer and human genetic disorders. Two-dimensional (2D) materials have emerged as revolutionary materials for electronic DNA sequencing with strong potentials for fast, single-nucleotide direct-read DNA sequencing with a minimum amount of consumables. Among 2D materials, graphene is the most explored for DNA sequencing. This is due to its commercial availability. The major hindrance of graphene is its hydrophobicity, which causes DNA bases to stick to its surface, slowing down translocation speed, and making single-base discrimination difficult as multiple bases interact with graphene at any given time. It is therefore essential that other elemental 2D materials beyond graphene be investigated. Using density functional theory (DFT), we studied the electronic interaction of DNA bases physisorped onto the surface of nanoribbons from graphene, phosphorene, and silicene. By comparing the change in energy band gap, binding energy and density of states (DOS), we observe that phosphorene performs better than graphene and silicene for DNA sequencing using the physisorption modality., Comment: 9

Published
2021

42. List of contributors

Author

Abboud, Rayan, primary, Acharya, Akanksha, additional, Al-Dulaimi, Ragheed, additional, Al-Katib, Sayf, additional, Al-Nowfal, Ahmed, additional, Ali, Omair, additional, Almsaddi, Tarek, additional, Amaral, Joao, additional, Anene, Alvin, additional, Awad, Christopher, additional, Badar, Zain, additional, Balabhadra, Samyuktha, additional, Balon, Amanda Bronte, additional, Bhanot, Shelly, additional, Bircher, Walter G., additional, Bitar, Ryan, additional, Bittle, Scott, additional, Borror, William, additional, Boumezrag, Maryam, additional, Braga, Daniel, additional, Chadha, Sakshum, additional, Chapple, Kristina M., additional, Chiramel, George Koshy, additional, Chitra, R., additional, Chockalingam, Arun, additional, Choudhury, Priyam, additional, Clarke, Geoffrey D., additional, Coffman, Kimberly, additional, Cooper, Sydney, additional, Cooper, Kyle, additional, Cornejo, Santiago M., additional, Cornman-Homonoff, Joshua, additional, Covello, Brian, additional, Dandu, Chaitu, additional, Dennison, Jennifer J., additional, Deshmukh, Ashwin, additional, Dixit, Purushottam K., additional, Drummey, Rachel, additional, Duguay, Sean, additional, Dybicz, Stephanie S., additional, El Sehemawi, N., additional, Espiritu, Marvee, additional, Ewing, Brandon, additional, Farag, Ahmed, additional, Fisher, Jason A., additional, Foss, Wylie T., additional, Fourzali, Roberto, additional, Fu, Katherine Shin-Ying, additional, Gaba, Ron C., additional, Gadodia, Gaurav, additional, Garg, Tushar, additional, Ghorashi, Sona, additional, Gibney, Brianna L., additional, Gilbert, Alexandra, additional, Gordon, Andrew C., additional, Gupta, Aakash N., additional, Henry, Matthew, additional, Hernandez, Mauricio, additional, Hood, Amber, additional, Jain, Neil K., additional, Kalantari, Jalil, additional, Kamireddy, Arun, additional, Katz, Joshua, additional, Kauffman, Nathan D., additional, Kim, Charissa, additional, Kirkpatrick, Daniel, additional, Kogan, Joshua, additional, Konstantinidis, Menelaos, additional, Kovac, Stefan, additional, Krajewski, Adam Christopher, additional, Kruse, Jonas, additional, Lalla, E.A., additional, Le, Rebecca Tuan, additional, Lewandowski, Robert J., additional, Liao, Millie, additional, Liu, Tao, additional, Liu, Abraham, additional, Lopez-Reyes, G., additional, Maguire, Thaddeus, additional, Makris, Gregory C., additional, Martinek, Alexander, additional, McCain Pebror, Travis William, additional, McGuirt, Delaney, additional, Mehta, Capt. Tej Ishaan, additional, Meyer, Travis E., additional, Moattari, Syamak, additional, Mohapatra, Ashutosh, additional, Mohit, Babak, additional, Money, David Bradley, additional, Moon, John T., additional, Morar, Satya K., additional, Mor, Yechiel, additional, Moudgil, Pranav, additional, Murthy, Sandeep, additional, Murthy, Shashidhara, additional, Muthusami, Prakash, additional, Nair, Girish B., additional, Nassar, Mark, additional, Nezami, Nariman, additional, Ngo, Han G., additional, Nourouzpour, S., additional, Olivieri, Brandon, additional, Ovanez, Christopher, additional, Ozen, Merve, additional, Parker, Matt, additional, Patel, Shrey, additional, Patel, Neal, additional, Paturu, Mounica, additional, Pham, Eric, additional, Qamhawi, Zahi, additional, Ragulojan, Ranjan, additional, Raheem, Ishmael, additional, Ramasamy, Shakthi Kumaran, additional, Ramji, Husayn F., additional, Reyes, Daniel, additional, Reynolds, Conner D., additional, Rizk, Tony H., additional, Shah, Karishma, additional, Shah, Raj, additional, Sharma, Jatin, additional, Sheth, Rahul A., additional, Shing, Li Ka, additional, Shrigiriwar, Apurva, additional, Smith, Zachary T., additional, Solomon, Alex J., additional, Sreenivasulu, Kilari, additional, Taghipour, Mehdi, additional, Talluri, Tulasi, additional, Thomson, Benedict, additional, Thukral, Siddhant, additional, Tyagi, Ravi, additional, Veneranda, M., additional, Venkatraman, Siddharth, additional, Vollano, Nicholas, additional, Wagstaff, William, additional, Walker, John, additional, Webster, Linzi Arndt, additional, Windham-Herman, Austin-Marley, additional, Woodhead, Gregory J., additional, and Zhong, Jim, additional

Published
2023
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48. Early clinical experience of bacteriophage therapy in 3 lung transplant recipients

Author

Aslam, Saima, Courtwright, Andrew M, Koval, Christine, Lehman, Susan M, Morales, Sandra, Furr, Carrie-Lynn Langlais, Rosas, Francisco, Brownstein, Michael J, Fackler, Joseph R, Sisson, Brittany M, Biswas, Biswajit, Henry, Matthew, Luu, Truong, Bivens, Brittany N, Hamilton, Theron, Duplessis, Christopher, Logan, Cathy, Law, Nancy, Yung, Gordon, Turowski, Jason, Anesi, Judith, Strathdee, Steffanie A, and Schooley, Robert T

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Clinical Sciences, Pneumonia & Influenza, Infectious Diseases, Transplantation, Patient Safety, Rare Diseases, Lung, Emerging Infectious Diseases, Pneumonia, Antimicrobial Resistance, Development of treatments and therapeutic interventions, 5.1 Pharmaceuticals, Infection, Adult, Aged, Anti-Bacterial Agents, Bacterial Infections, Burkholderia, Drug Resistance, Multiple, Bacterial, Female, Humans, Lung Diseases, Lung Transplantation, Male, Middle Aged, Phage Therapy, Postoperative Complications, Pseudomonas aeruginosa, Respiratory Tract Infections, Transplant Recipients, antibiotic drug resistance, antibiotic, antibacterial, clinical research, practice, infection and infectious agents - bacterial, infectious disease, lung disease, infectious, lung transplantation, pulmonology, translational research, science, antibiotic: antibacterial, clinical research/practice, lung disease: infectious, lung transplantation/pulmonology, translational research/science, Medical and Health Sciences, Surgery, Clinical sciences, Immunology
Abstract

Bacteriophage therapy (BT) uses bacteriophages to treat pathogenic bacteria and is an emerging strategy against multidrug-resistant (MDR) infections. Experience in solid organ transplant is limited. We describe BT in 3 lung transplant recipients (LTR) with life-threatening MDR infections caused by Pseudomonas aeruginosa (n = 2) and Burkholderia dolosa (n = 1). For each patient, lytic bacteriophages were selected against their bacterial isolates. BT was administered for variable durations under emergency Investigational New Drug applications and with patient informed consent. Safety was assessed using clinical/laboratory parameters and observed clinical improvements described, as appropriate. All patients received concurrent antibiotics. Two ventilator-dependent LTR with large airway complications and refractory MDR P. aeruginosa pneumonia received BT. Both responded clinically and were discharged from the hospital off ventilator support. A third patient had recurrent B. dolosa infection following transplant. Following BT initiation, consolidative opacities improved and ventilator weaning was begun. However, infection relapsed on BT and the patient died. No BT-related adverse events were identified in the 3 cases. BT was well tolerated and associated with clinical improvement in LTRs with MDR bacterial infection not responsive to antibiotics alone. BT may be a viable adjunct to antibiotics for patients with MDR infections.

Published
2019

49. Erratum for Schooley et al., “Development and Use of Personalized Bacteriophage-Based Therapeutic Cocktails To Treat a Patient with a Disseminated Resistant Acinetobacter baumannii Infection”

Author

Schooley, Robert T, Biswas, Biswajit, Gill, Jason J, Hernandez-Morales, Adriana, Lancaster, Jacob, Lessor, Lauren, Barr, Jeremy J, Reed, Sharon L, Rohwer, Forest, Benler, Sean, Segall, Anca M, Taplitz, Randy, Smith, Davey M, Kerr, Kim, Kumaraswamy, Monika, Nizet, Victor, Lin, Leo, McCauley, Melanie D, Strathdee, Steffanie A, Benson, Constance A, Pope, Robert K, Leroux, Brian M, Picel, Andrew C, Mateczun, Alfred J, Cilwa, Katherine E, Regeimbal, James M, Estrella, Luis A, Wolfe, David M, Henry, Matthew S, Quinones, Javier, Salka, Scott, Bishop-Lilly, Kimberly A, Young, Ry, and Hamilton, Theron

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Microbiology, Clinical Sciences, Medical Microbiology, Good Health and Well Being, Pharmacology and Pharmaceutical Sciences, Medical microbiology, Pharmacology and pharmaceutical sciences
Abstract

Volume 61, no. 10, e00954-17, 2017, https://doi.org/10.1128/AAC.00954-17. Materials and Methods, 2nd paragraph, 2nd sentence: “Phages provided by the Biological Defense Research Directorate (BDRD) of the Naval Medical Research Center (AB-Navy1, AB-Navy4, AB-Navy71, AB-Navy97, and AbTP31) were isolated from various environmental samples by using routine isolation techniques, as previously described (9)” should read “Phages provided by the Biological Defense Research Directorate (BDRD) of the Naval Medical Research Center (AB-Navy1, AB-Navy4, AB-Navy97, and AbTP31) were isolated from various environmental samples by using routine isolation techniques, as previously described (9), except for one phage (AB-Navy71, also known as phage vB_Ab-M-G7, DSM strain no. 25639), which was purchased from Liebniz Institute DSMZ (Germany).”

Published
2018

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