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2. SARS-CoV-2 Outbreak Dynamics in an Isolated US Military Recruit Training Center With Rigorous Prevention Measures

Author

Lizewski, Rhonda A., Sealfon, Rachel S. G., Park, Sang Woo, Smith, Gregory R., Porter, Chad K., Gonzalez-Reiche, Ana S., Ge, Yongchao, Miller, Clare M., Goforth, Carl W., Pincas, Hanna, Termini, Michael S., Ramos, Irene, Nair, Venugopalan D., Lizewski, Stephen E., Alshammary, Hala, Cer, Regina Z., Chen, Hua Wei, George, Mary-Catherine, Arnold, Catherine E., Glang, Lindsay A., Long, Kyle A., Malagon, Francisco, Marayag, Jan J., Nunez, Edgar, Rice, Gregory K., Santa Ana, Ernesto, Schilling, Megan A., Smith, Darci R., Sugiharto, Victor A., Sun, Peifang, van de Guchte, Adriana, Khan, Zenab, Dutta, Jayeeta, Vangeti, Sindhu, Voegtly, Logan J., Weir, Dawn L., Metcalf, C. Jessica E., Troyanskaya, Olga G., Bishop-Lilly, Kimberly A., Grenfell, Bryan T., van Bakel, Harm, Letizia, Andrew G., and Sealfon, Stuart C.

Published
2022
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3. A proof of concept for a targeted enrichment approach to the simultaneous detection and characterization of rickettsial pathogens from clinical specimens

Author

Paskey, Adrian C., primary, Schully, Kevin L., additional, Voegtly, Logan J., additional, Arnold, Catherine E., additional, Cer, Regina Z., additional, Frey, Kenneth G., additional, Blair, Paul W., additional, Clark, Danielle V., additional, Ge, Hong, additional, Richards, Allen L., additional, Farris, Christina M., additional, and Bishop-Lilly, Kimberly A., additional

Published
2024
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4. Immune and behavioral correlates of protection against symptomatic post-vaccination SARS-CoV-2 infection

Author

Goguet, Emilie, primary, Olsen, Cara H., additional, Meyer, William A., additional, Ansari, Sara, additional, Powers, John H., additional, Conner, Tonia L., additional, Coggins, Si’Ana A., additional, Wang, Wei, additional, Wang, Richard, additional, Illinik, Luca, additional, Sanchez Edwards, Margaret, additional, Jackson-Thompson, Belinda M., additional, Hollis-Perry, Monique, additional, Wang, Gregory, additional, Alcorta, Yolanda, additional, Wong, Mimi A., additional, Saunders, David, additional, Mohammed, Roshila, additional, Balogun, Bolatito, additional, Kobi, Priscilla, additional, Kosh, Lakeesha, additional, Bishop-Lilly, Kimberly, additional, Cer, Regina Z., additional, Arnold, Catherine E., additional, Voegtly, Logan J., additional, Fitzpatrick, Maren, additional, Luquette, Andrea E., additional, Malagon, Francisco, additional, Ortega, Orlando, additional, Parmelee, Edward, additional, Davies, Julian, additional, Lindrose, Alyssa R., additional, Haines-Hull, Hannah, additional, Moser, Matthew S., additional, Samuels, Emily C., additional, Rekedal, Marana S., additional, Graydon, Elizabeth K., additional, Malloy, Allison M. W., additional, Tribble, David R., additional, Burgess, Timothy H., additional, Campbell, Wesley, additional, Robinson, Sara, additional, Broder, Christopher C., additional, O’Connell, Robert J., additional, Weiss, Carol D., additional, Pollett, Simon, additional, Laing, Eric D., additional, and Mitre, Edward, additional

Published
2024
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8. Comprehensive Microbiological and Metagenomic Analysis of the Guillain–Barré Syndrome Outbreak in Lima, 2019.

Author

Rojas, Jesús D., Ramos, Mariana, Cruz, Cristopher, Long, Kyle A., Voegtly, Logan J., Meza, Rina, Espinoza, Nereyda, Ttito, Ana Ramos, Cáceres, Hugo Umeres, Cuentas, Alejandro Llanos, Meza, Yocelinda, Troncos, Gilda, Poly, Frédéric M., Paskey, Adrian C., Lueder, Matthew R., Rice, Gregory K., Cer, Regina Z., Bishop-Lilly, Kimberly A., Silva, María, and Grogl, Max

Subjects
GENOMICS, CAMPYLOBACTER jejuni, METAGENOMICS, PUBLIC health, MIXED infections
Abstract

In 2018/2019, two large Guillain–Barré Syndrome (GBS) outbreaks took place in Peru. Here, we report a comprehensive analysis of biological samples from GBS patients from the 2019 outbreak. We applied metagenomic, microbiologic, and serological analyses to different biological samples collected from GBS patients. Further phenotypic and genomic characterization was conducted on Campylobacter jejuni isolates from GBS samples. Microbiologic and metagenomic analyses revealed several patients with multiple co-infections, yet no common infectious agents were found other than C. jejuni. Four C. jejuni isolates were isolated from rectal swabs. Twenty-one patients had detectable IgG serum antibodies related to C. jejuni, of whom seven had IgM antibodies. Genomic analyses showed that these four strains were clonal (ST2993) and contained the class A lipooligosaccharide biosynthesis locus. These results further support the idea that that C. jejuni is the etiological agent that triggered the GBS outbreak in Peru in 2019 and that the strains are not restricted to Peru, hence could be regarded as a broad public health concern. Furthermore, though we cannot delineate the role played by co-infections in GBS development, results obtained herein highlight metagenomic analysis as a potential new tool for depicting a yet unknown area of research in GBS. [ABSTRACT FROM AUTHOR]

Published
2024
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9. Phylogenetic and phenotypic characterization of Burkholderia pseudomallei isolates from Ghana reveals a novel sequence type and common phenotypes.

Author

Schully, Kevin L., Voegtly, Logan J., Rice, Gregory K., Drumm, Hannah, Fitzpatrick, Maren C., Malagon, Francisco, Shea, April, Ming Dong, Oduro, George, Robberts, F. J. Lourens, Dartey, Paul K. A., Owusu-Ofori, Alex, Clark, Danielle V., Cer, Regina Z., and Bishop-Lilly, Kimberly A.

Subjects
BURKHOLDERIA pseudomallei, PHENOTYPES, WHOLE genome sequencing, MELIOIDOSIS, GRAM-negative bacteria, CONTINENTS, COASTS
Abstract

Melioidosis is a potentially severe disease caused by the gram-negative soil-dwelling bacterium called Burkholderia pseudomallei. The true breadth of the distribution of this tropical pathogen is starting to emerge with environmental and clinical isolates frequently characterized in new countries and regions. Even so, isolates, clinical cases, and genetic data from the continent of Africa remain scant. We previously confirmed the presence of B. pseudomallei in the environment of Ghana, unmasking a new area of endemicity for this pathogen. Here, we describe the genetic characteristics of isolates obtained from that environmental survey. Twenty-one isolates were subjected to whole genome sequencing and found to represent three discrete sequence types (ST), one of which was novel, and designated ST2058. Phylogenetic analysis places this novel isolate within a B. pseudomallei clade that includes genomes derived from the Americas, although it is closely related to a sub-clade that includes isolates from Africa. Importantly, phenotypic characterization demonstrates common features including API 20NE profiles and B. pseudomallei CPS to support existing diagnostics, and susceptibility to standard of care antibiotics often used in the clinical management of melioidosis. These findings add to our knowledge about the presence and distribution of B. pseudomallei in Africa and represent the first published genomes out of Ghana. [ABSTRACT FROM AUTHOR]

Published
2024
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11. SARS-CoV-2 Infections in Vaccinated and Unvaccinated Populations in Camp Lemonnier, Djibouti, from April 2020 to January 2022

Author

Arnold, Catherine E., primary, Voegtly, Logan J., additional, Stefanov, Emily K., additional, Lueder, Matthew R., additional, Luquette, Andrea E., additional, Miller, Robin H., additional, Miner, Haven L., additional, Bennett, Andrew J., additional, Glang, Lindsay, additional, McGinnis, Tara N., additional, Reisinger, Kristie E., additional, Dugan, Jae W., additional, Mangat, Michael A., additional, Silberger, Daniel J., additional, Pavlicek, Rebecca L., additional, Watters, Chaselynn M., additional, Rice, Gregory K., additional, Malagon, Francisco, additional, Cer, Regina Z., additional, Eggan, Stephen M., additional, and Bishop-Lilly, Kimberly A., additional

Published
2022
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12. Genomic and virologic characterization of samples from a shipboard outbreak of COVID-19 reveals distinct variants within limited temporospatial parameters

Author

Cer, Regina Z., primary, Voegtly, Logan J., additional, Adhikari, Bishwo N., additional, Pike, Brian L., additional, Lueder, Matthew R., additional, Glang, Lindsay A., additional, Malagon, Francisco, additional, Ana, Ernesto Santa, additional, Regeimbal, James M., additional, Potts-Szoke, Maria F., additional, Schully, Kevin L., additional, Smith, Darci R., additional, and Bishop-Lilly, Kimberly A., additional

Published
2022
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13. Outbreak of COVID-19 Among a Highly Vaccinated Population Aboard a U.S. Navy Ship After a Port Visit--Reykjavik, Iceland, July 2021

Author

Servies, Tammy E., Larsen, Eric C., Lindsay, Rodney C., Jones, Jonathan S., Cer, Regina Z., Voegtly, Logan J., Lueder, Matthew R., Malagon, Francisco, Bishop-Lilly, Kimberly A., and Riegodedios, Asha J.

Subjects
United States. Navy, Health aspects, Naval vessels -- Health aspects, Vaccination -- Health aspects, COVID-19 -- Health aspects, Warships -- Health aspects
Abstract

On July 27, 2021, a fully vaccinated* crew member on a U.S. Navy ship who had been symptomatic with cough and congestion for 4 days was evaluated in the ship's [...]

Published
2022

14. Notes from the Field: Outbreak of COVID-19 Among a Highly Vaccinated Population Aboard a U.S. Navy Ship After a Port Visit — Reykjavik, Iceland, July 2021

Author

Servies, Tammy E., primary, Larsen, Eric C., additional, Lindsay, Rodney C., additional, Jones, Jonathan S., additional, Cer, Regina Z., additional, Voegtly, Logan J., additional, Lueder, Matthew R., additional, Malagon, Francisco, additional, Bishop-Lilly, Kimberly A., additional, and Riegodedios, Asha J., additional

Published
2022
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15. Prospective Assessment of Symptoms to Evaluate Asymptomatic SARS-CoV-2 Infections in a Cohort of Health Care Workers

Author

Goguet, Emilie, primary, Powers, John H, additional, Olsen, Cara H, additional, Tribble, David R, additional, Davies, Julian, additional, Illinik, Luca, additional, Jackson-Thompson, Belinda M, additional, Hollis-Perry, Monique, additional, Maiolatesi, Santina E, additional, Pollett, Simon, additional, Duplessis, Christopher A, additional, Wang, Gregory, additional, Ramsey, Kathleen F, additional, Reyes, Anatalio E, additional, Alcorta, Yolanda, additional, Wong, Mimi A, additional, Ortega, Orlando, additional, Parmelee, Edward, additional, Lindrose, Alyssa R, additional, Moser, Matthew, additional, Samuels, Emily C, additional, Coggins, Si’Ana A, additional, Graydon, Elizabeth, additional, Robinson, Sara, additional, Campbell, Wesley, additional, Malloy, Allison M W, additional, Voegtly, Logan J, additional, Arnold, Catherine E, additional, Cer, Regina Z, additional, Malagon, Francisco, additional, Bishop-Lilly, Kimberly A, additional, Burgess, Timothy H, additional, Broder, Christopher C, additional, Laing, Eric D, additional, and Mitre, Edward, additional

Published
2022
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16. Genomic and Virological Characterization of SARS-CoV-2 Variants in a Subset of Unvaccinated and Vaccinated U.S. Military Personnel

Author

Smith, Darci R., primary, Singh, Christopher, additional, Green, Jennetta, additional, Lueder, Matthew R., additional, Arnold, Catherine E., additional, Voegtly, Logan J., additional, Long, Kyle A., additional, Rice, Gregory K., additional, Luquette, Andrea E., additional, Miner, Haven L., additional, Glang, Lindsay, additional, Bennett, Andrew J., additional, Miller, Robin H., additional, Malagon, Francisco, additional, Cer, Regina Z., additional, and Bishop-Lilly, Kimberly A., additional

Published
2022
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17. EDGE 2017 R&D 100 Entry with Appendix

Author

Chain, Patrick Sam Guy, primary, Davenport, Karen Walston, additional, Li, Po-E, additional, Lo, Chien-Chi, additional, Xu, Yan, additional, Senin, Pavel, additional, Shakya, Migun, additional, Ahmed, Sanaa Afroz, additional, Hamilton, Theron C., additional, Bishop-Lilly, Kimberly A., additional, Anderson, Joseph J., additional, Voegtly, Logan J., additional, and Philipson, Casandra W., additional

Published
2017
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18. Genomic and Virological Characterization of SARS-CoV-2 Variants in a Subset of Unvaccinated and Vaccinated U.S. Military Personnel

Author

Smith, Darci R., primary, Singh, Christopher, additional, Green, Jennetta, additional, Lueder, Matthew R., additional, Arnold, Catherine E., additional, Voegtly, Logan J., additional, Long, Kyle A., additional, Rice, Gregory K., additional, Luquette, Andrea, additional, Miner, Haven, additional, Glang, Lindsay, additional, Bennett, Andrew, additional, Miller, Robin, additional, Malagon, Francisco, additional, Cer, Regina Z., additional, and Bishop-Lilly, Kimberly A., additional

Published
2021
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19. Immunological and Genetic Investigation of SARS-CoV-2 Reinfection in an Otherwise Healthy, Young Marine Recruit

Author

Letizia, Andrew G., primary, Arnold, Catherine E., additional, Adhikari, Bishwo N., additional, Voegtly, Logan J., additional, Glang, Lindsay, additional, Rice, Gregory K., additional, Goforth, Carl W., additional, Schilling, Megan A., additional, Weir, Dawn L., additional, Malagon, Francisco, additional, Ramos, Irene, additional, Vangeti, Sindhu, additional, Gonzalez-Reiche, Ana S., additional, Cer, Regina Z., additional, Sealfon, Stuart C., additional, van Bakel, Harm, additional, and Bishop-Lilly, Kimberly A., additional

Published
2021
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20. A Case of Early Re-infection with SARS-CoV-2

Author

Larson, Derek, Brodniak, Sterling L, Voegtly, Logan J, Cer, Regina Z, Glang, Lindsay A, Malagon, Francisco J, Long, Kyle A, Potocki, Ronald, Smith, Darci R, Lanteri, Charlotte, Burgess, Timothy, and Bishop-Lilly, Kimberly A

Subjects
AcademicSubjects/MED00290, Correspondence
Published
2020

21. A Department of Defense Laboratory Consortium Approach to Next Generation Sequencing and Bioinformatics Training for Infectious Disease Surveillance in Kenya

Author

Maljkovic Berry, Irina, primary, Rutvisuttinunt, Wiriya, additional, Voegtly, Logan J., additional, Prieto, Karla, additional, Pollett, Simon, additional, Cer, Regina Z., additional, Kugelman, Jeffrey R., additional, Bishop-Lilly, Kimberly A., additional, Morton, Lindsay, additional, Waitumbi, John, additional, and Jarman, Richard G., additional

Published
2020
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22. A Case of Early Reinfection With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Author

Larson, Derek, primary, Brodniak, Sterling L, additional, Voegtly, Logan J, additional, Cer, Regina Z, additional, Glang, Lindsay A, additional, Malagon, Francisco J, additional, Long, Kyle A, additional, Potocki, Ronald, additional, Smith, Darci R, additional, Lanteri, Charlotte, additional, Burgess, Timothy, additional, and Bishop-Lilly, Kimberly A, additional

Published
2020
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23. An Observational Study of Sepsis in Takeo Province Cambodia: An in-depth examination of pathogens causing severe infections

Author

Rozo, Michelle, primary, Schully, Kevin L., additional, Philipson, Casandra, additional, Fitkariwala, Amitha, additional, Nhim, Dararith, additional, Som, Tin, additional, Sieng, Darith, additional, Huot, Bora, additional, Dul, Sokha, additional, Gregory, Michael J., additional, Heang, Vireak, additional, Vaughn, Andrew, additional, Vantha, Te, additional, Prouty, Angela M., additional, Chao, Chien-Chung, additional, Zhang, Zhiwen, additional, Belinskaya, Tatyana, additional, Voegtly, Logan J., additional, Cer, Regina Z., additional, Bishop-Lilly, Kimberly A., additional, Duplessis, Chris, additional, Lawler, James V., additional, and Clark, Danielle V., additional

Published
2020
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26. Case of Early Reinfection With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).

Author

Larson, Derek, Brodniak, Sterling L, Voegtly, Logan J, Cer, Regina Z, Glang, Lindsay A, Malagon, Francisco J, Long, Kyle A, Potocki, Ronald, Smith, Darci R, Lanteri, Charlotte, Burgess, Timothy, and Bishop-Lilly, Kimberly A

Subjects
BLOOD serum analysis, PHYSICAL diagnosis, REVERSE transcriptase polymerase chain reaction, COVID-19, FEVER, CHEST X rays, SEQUENCE analysis, MILITARY medicine, SICK people, REINFECTION, MEDICAL personnel, GASTROINTESTINAL diseases, RNA, DYSPNEA, COUGH, POLYMERASE chain reaction, ENVIRONMENTAL exposure, SYMPTOMS
Abstract

The article explores reinfection from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which represented an important data point in the ongoing coronavirus disease 2019 (COVID-19) pandemic. Questions have arisen regarding the timing and severity of reinfections, for which we offer a case report of symptomatic reinfection within 90 days.

Published
2021
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27. Characterizing Phage Genomes for Therapeutic Applications.

Author

Philipson, Casandra W., Voegtly, Logan J., Lueder, Matthew R., Long, Kyle A., Rice, Gregory K., Frey, Kenneth G., Biswas, Biswajit, Cer, Regina Z., Hamilton, Theron, and Bishop-Lilly, Kimberly A.

Subjects
*VIRAL genetics, *BACTERIOPHAGES, *NUCLEOTIDE sequence, *MULTIDRUG resistance in bacteria
Abstract

Multi-drug resistance is increasing at alarming rates. The efficacy of phage therapy, treating bacterial infections with bacteriophages alone or in combination with traditional antibiotics, has been demonstrated in emergency cases in the United States and in other countries, however remains to be approved for wide-spread use in the US. One limiting factor is a lack of guidelines for assessing the genomic safety of phage candidates. We present the phage characterization workflow used by our team to generate data for submitting phages to the Federal Drug Administration (FDA) for authorized use. Essential analysis checkpoints and warnings are detailed for obtaining high-quality genomes, excluding undesirable candidates, rigorously assessing a phage genome for safety and evaluating sequencing contamination. This workflow has been developed in accordance with community standards for high-throughput sequencing of viral genomes as well as principles for ideal phages used for therapy. The feasibility and utility of the pipeline is demonstrated on two new phage genomes that meet all safety criteria. We propose these guidelines as a minimum standard for phages being submitted to the FDA for review as investigational new drug candidates. [ABSTRACT FROM AUTHOR]

Published
2018
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