Publications
September 8, 2024
Comprehensive Microbiological and Metagenomic Analysis of the Guillain–Barré Syndrome Outbreak in Lima, 2019
Jesús D. Rojas, Mariana Ramos, Cristopher Cruz, Kyle A. Long, Logan J. Voegtly, Rina Meza, Nereyda Espinoza, Ana Ramos Ttito, Hugo Umeres Cáceres, Alejandro Llanos Cuentas, Yocelinda Meza, Gilda Troncos, Frédéric M. Poly, Adrian C. Paskey, Matthew R. Lueder, Gregory K. Rice, Regina Z. Cer, Kimberly A. Bishop-Lilly, María Silva and Max Grogl
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...
July 9, 2024
Phylogenetic and phenotypic characterization of Burkholderia pseudomallei isolates from Ghana reveals a novel sequence type and common phenotypes
Kevin L Schully, Logan J Voegtly, Gregory K Rice, Hannah Drumm, Maren C Fitzpatrick, Francisco Malagon, April Shea, Ming Dong, George Oduro, F J Lourens Robberts, Paul K A Dartey, Alex Owusu-Ofori, Danielle V Clark, Regina Z Cer, Kimberly A Bishop-Lilly
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...
April 10, 204
A proof of concept for a targeted enrichment approach to the simultaneous detection and characterization of rickettsial pathogens from clinical specimens
Adrian C Paskey, Kevin L Schully, Logan J Voegtly, Catherine E Arnold, Regina Z Cer, Kenneth G Frey, Paul W Blair, Danielle V Clark, Hong Ge, Allen L Richards, Christina M Farris, Kimberly A Bishop-Lilly
Infection with either Rickettsia prowazekii or Orientia tsutsugamushi is common, yet diagnostic capabilities are limited due to the short window for positive identification. Until now, although...
March 19, 2024
Immune and behavioral correlates of protection against symptomatic post-vaccination SARS-CoV-2 infection
Emilie Goguet, Cara H. Olsen, William A. Meyer, III, Sara Ansari, John H. Powers, III, Tonia L. Conner, Si’Ana A. Coggins, Wei Wang, Richard Wang, Luca Illinik, Margaret Sanchez Edwards, Belinda M. Jackson-Thompson, Monique Hollis-Perry, Gregory Wang, Yolanda Alcorta, Mimi A. Wong, David Saunders, Roshila Mohammed, Bolatito Balogun, Priscilla Kobi, Lakeesha Kosh, Kimberly Bishop-Lilly, Regina Z. Cer, Catherine E. Arnold, Logan J. Voegtly, Maren Fitzpatrick, Andrea E. Luquette, Francisco Malagon, Orlando Ortega, Edward Parmelee, Julian Davies, Alyssa R. Lindrose, Hannah Haines-Hull, Matthew S. Moser, Emily C. Samuels, Marana S. Rekedal, Elizabeth K. Graydon, Allison M. W. Malloy, David R. Tribble, Timothy H. Burgess, Wesley Campbell, Sara Robinson, Christopher C. Broder, Robert J. O’Connell, Carol D. Weiss, Simon Pollett, Eric D. Laing, and Edward Mitre
Introduction: We sought to determine pre-infection correlates of protection against SARS-CoV-2 post-vaccine inzfections (PVI) acquired during the first Omicron wave in the United States. Methods:...
August 10, 2022
Genomic and virologic characterization of samples from a shipboard outbreak of COVID-19 reveals distinct variants within limited temporospatial parameters
Regina Z Cer, Logan J Voegtly, Bishwo N Adhikari, Brian L Pike, Matthew R Lueder, Lindsay A Glang, Francisco Malagon, Ernesto Santa Ana, James M Regeimbal, Maria F Potts-Szoke, Kevin L Schully, Darci R Smith, Kimberly A Bishop-Lilly
Early in the pandemic, in March of 2020, an outbreak of COVID-19 occurred aboard the aircraft carrier USS Theodore Roosevelt (CVN-71), during deployment in the Western Pacific. Out of the crew of...
August 5, 2022
SARS-CoV-2 Outbreak Dynamics in an Isolated US Military Recruit Training Center With Rigorous Prevention Measures
Rhonda A Lizewski, Rachel S G Sealfon, Sang Woo Park, Gregory R Smith, Chad K Porter, Ana S Gonzalez-Reiche, Yongchao Ge, Clare M Miller, Carl W Goforth, Hanna Pincas, Michael S Termini, Irene Ramos, Venugopalan D Nair, Stephen E Lizewski, Hala Alshammary, Regina Z Cer, Hua Wei Chen, Mary-Catherine George, Catherine E Arnold, Lindsay A Glang, Kyle A Long, Francisco Malagon, Jan J Marayag, Edgar Nunez, Gregory K Rice, Ernesto Santa Ana, Megan A Schilling, Darci R Smith, Victor A Sugiharto, Peifang Sun, Adriana van de Guchte, Zenab Khan, Jayeeta Dutta, Sindhu Vangeti, Logan J Voegtly, Dawn L Weir, C Jessica E Metcalf, Olga G Troyanskaya, Kimberly A Bishop-Lilly, Bryan T Grenfell, Harm van Bakel, Andrew G Letizia, Stuart C Sealfon
Background: Marine recruits training at Parris Island experienced an unexpectedly high rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, despite preventive measures...
August 30, 2022
SARS-CoV-2 Infections in Vaccinated and Unvaccinated Populations in Camp Lemonnier, Djibouti, from April 2020 to January 2022
Catherine E Arnold, Logan J Voegtly, Emily K Stefanov, Matthew R Lueder, Andrea E Luquette, Robin H Miller, Haven L Miner, Andrew J Bennett, Lindsay Glang, Tara N McGinnis, Kristie E Reisinger, Jae W Dugan, Michael A Mangat, Daniel J Silberger, Rebecca L Pavlicek, Chaselynn M Watters, Gregory K Rice, Francisco Malagon, Regina Z Cer, Stephen M Eggan, Kimberly A Bishop-Lilly
The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the disparity between developed and developing countries for infectious disease...
June 30, 2022
Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy
Mei Liu #, Adriana Hernandez-Morales #, James Clark, Tram Le, Biswajit Biswas, Kimberly A Bishop-Lilly, Matthew Henry, Javier Quinones, Logan J Voegtly, Regina Z Cer, Theron Hamilton, Robert T Schooley, Scott Salka, Ry Young, Jason J Gill
In 2016, a 68-year-old patient with a disseminated multidrug-resistant Acinetobacter baumannii infection was successfully treated using lytic bacteriophages. Here we report the genomes of the nine...
February 14, 2022
Prospective Assessment of Symptoms to Evaluate Asymptomatic SARS-CoV-2 Infections in a Cohort of Health Care Workers
Emilie Goguet, John H Powersrd, Cara H Olsen, David R Tribble, Julian Davies, Luca Illinik, Belinda M Jackson-Thompson, Monique Hollis-Perry, Santina E Maiolatesi, Simon Pollett, Christopher A Duplessis, Gregory Wang, Kathleen F Ramsey, Anatalio E Reyes, Yolanda Alcorta, Mimi A Wong, Orlando Ortega, Edward Parmelee, Alyssa R Lindrose, Matthew Moser, Emily C Samuels, Si'Ana A Coggins, Elizabeth Graydon, Sara Robinson, Wesley Campbell, Allison M W Malloy, Logan J Voegtly, Catherine E Arnold, Regina Z Cer, Francisco Malagon, Kimberly A Bishop-Lilly, Timothy H Burgess, Christopher C Broder, Eric D Laing, Edward Mitre
Background: The frequency of asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is unclear and may be influenced by how symptoms are evaluated. In this study, we...
February 18, 2022
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
Tammy E. Servies, MD1; Eric C. Larsen, MD1; Rodney C. Lindsay, MPH1; Jonathan S. Jones, MS1; Regina Z. Cer, MS2; Logan J. Voegtly, MS2,3; Matthew R. Lueder, MS2,3; Francisco Malagon, PhD2,3; Kimberly A. Bishop-Lilly, PhD2; Asha J. Riegodedios, MSPH4
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 onboard medical department and...
January 27, 2022
Genomic and Virological Characterization of SARS-CoV-2 Variants in a Subset of Unvaccinated and Vaccinated U.S. Military Personnel
Darci R Smith, Christopher Singh, Jennetta Green, Matthew R Lueder, Catherine E Arnold, Logan J Voegtly, Kyle A Long, Gregory K Rice, Andrea E Luquette, Haven L Miner, Lindsay Glang, Andrew J Bennett, Robin H Miller, Francisco Malagon, Regina Z Cer, Kimberly A Bishop-Lilly
The emergence of SARS-CoV-2 variants complicates efforts to control the COVID-19 pandemic. Increasing genomic surveillance of SARS-CoV-2 is imperative for early detection of emerging variants, to...
December 8, 2021
Immunological and Genetic Investigation of SARS-CoV-2 Reinfection in an Otherwise Healthy, Young Marine Recruit
Andrew G Letizia, Catherine E Arnold, Bishwo N Adhikari, Logan J Voegtly, Lindsay Glang, Gregory K Rice, Carl W Goforth, Megan A Schilling, Dawn L Weir, Francisco Malagon, Irene Ramos, Sindhu Vangeti, Ana S Gonzalez-Reiche, Regina Z Cer, Stuart C Sealfon, Harm van Bakel, Kimberly A Bishop-Lilly
We used epidemiologic and viral genetic information to identify a case of likely reinfection in an otherwise healthy, young Marine recruit enrolled in the prospective, longitudinal COVID-19 Health...
November 2, 2021
A Case of Early Reinfection With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
Derek Larson, Sterling L Brodniak, Logan J Voegtly, Regina Z Cer, Lindsay A Glang, Francisco J Malagon, Kyle A Long, Ronald Potocki, Darci R Smith, Charlotte Lanteri, Timothy Burgess, Kimberly A Bishop-Lilly
It is with great interest that we read the first report of reinfection from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which represented an important data point in the ongoing...
October 9, 2021
Manual Annotation Studio (MAS): a collaborative platform for manual functional annotation of viral and microbial genomes
Matthew R Lueder, Regina Z Cer, Miles Patrick, Logan J Voegtly, Kyle A Long, Gregory K Rice, Kimberly A Bishop-Lilly
Background: Functional genome annotation is the process of labelling functional genomic regions with descriptive information. Manual curation can produce higher quality genome annotations than...
February 3, 2021
A Sarcina bacterium linked to lethal disease in sanctuary chimpanzees in Sierra Leone
Leah A. Owens, Barbara Colitti, Ismail Hirji, Andrea Pizarro, Jenny E. Jaffe, Sophie Moittié, Kimberly A. Bishop-Lilly, Luis A. Estrella, Logan J. Voegtly, Jens H. Kuhn, Garret Suen, Courtney L. Deblois, Christopher D. Dunn, Carles Juan-Sallés & Tony L. Goldberg
Human and animal infections with bacteria of the genus Sarcina (family Clostridiaceae) are associated with gastric dilation and emphysematous gastritis. However, the potential roles of sarcinae as...
September 25, 2020
A Department of Defense Laboratory Consortium Approach to Next Generation Sequencing and Bioinformatics Training for Infectious Disease Surveillance in Kenya
Irina Maljkovic Berry, Wiriya Rutvisuttinunt, Logan J Voegtly, Karla Prieto, Simon Pollett, Regina Z Cer, Jeffrey R Kugelman, Kimberly A Bishop-Lilly, Lindsay Morton, John Waitumbi, Richard G Jarman
Epidemics of emerging and re-emerging infectious diseases are a danger to civilian and military populations worldwide. Health security and mitigation of infectious disease threats is a priority of...
August 17, 2020
An Observational Study of Sepsis in Takeo Province Cambodia: An in-depth examination of pathogens causing severe infections
Michelle Rozo, Kevin L Schully, Casandra Philipson, Amitha Fitkariwala, Dararith Nhim, Tin Som, Darith Sieng, Bora Huot, Sokha Dul, Michael J Gregory, Vireak Heang, Andrew Vaughn, Te Vantha, Angela M Prouty, Chien-Chung Chao, Zhiwen Zhang, Tatyana Belinskaya, Logan J Voegtly, Regina Z Cer, Kimberly A Bishop-Lilly, Chris Duplessis, James V Lawler, Danielle V Clark
The world's most consequential pathogens occur in regions with the fewest diagnostic resources, leaving the true burden of these diseases largely under-represented. During a prospective...
October 28, 2019
Direct-from-blood RNA sequencing identifies the cause of post-bronchoscopy fever
Emily R Ko, Casandra W Philipson, Thomas W Burke, Regina Z Cer, Kimberly A Bishop-Lilly, Logan J Voegtly, Ephraim L Tsalik, Christopher W Woods, Danielle V Clark, Kevin L Schully
Background: Antibiotic resistance is rising at disturbing rates and contributes to the deaths of millions of people yearly. Antibiotic resistant infections disproportionately affect those with...
January 3, 2019
High-Quality Draft Genome Sequence of Pseudomonas aeruginosa 268 Isolated from a Patient with a Left Ventricular Assist Device
Logan J Voegtly, Gregory K Rice, Regina Z Cer, Kenneth G Frey, Biswajit Biswas, Theron Hamilton, Saima Aslam, Kimberly A Bishop-Lilly
Pseudomonas aeruginosa is known to cause persistent bloodstream infections associated with left ventricular assist devices (LVAD). Here, we present the high-quality draft genome assembly for a...
April 18, 2018
Characterizing Phage Genomes for Therapeutic Applications
Casandra W Philipson, Logan J Voegtly, Matthew R Lueder, Kyle A Long, Gregory K Rice, Kenneth G Frey, Biswajit Biswas, Regina Z Cer, Theron Hamilton, Kimberly A Bishop-Lilly
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...
December 5, 2017
Brief Protocol for EDGE Bioinformatics: Analyzing Microbial and Metagenomic NGS Data
Casandra Philipson, Karen Davenport, Logan Voegtly, Chien-Chi Lo, Po-E Li, Yan Xu, Migun Shakya, Regina Z Cer, Kimberly A Bishop-Lilly, Theron Hamilton, Patrick S G Chain
Next-generation sequencing (NGS) offers unparalleled resolution for untargeted organism detection and characterization. However, the majority of NGS analysis programs require users to be proficient...
January 22, 2013
Genome evolution and phylogenomic analysis of Candidatus Kinetoplastibacterium, the betaproteobacterial endosymbionts of Strigomonas and Angomonas.
João M P Alves, Myrna G Serrano, Flávia Maia da Silva, Logan J Voegtly, Andrey V Matveyev, Marta M G Teixeira, Erney P Camargo, Gregory A Buck
Candidatus Kinetoplastibacterium or TPE [trypanosomatid proteobacterial endosymbiont] that supplement the host metabolism. Based on previous analyses of other bacterial endosymbiont genomes from...
August 11, 2011
Identification and phylogenetic analysis of heme synthesis genes in trypanosomatids and their bacterial endosymbionts.
João M P Alves, Logan Voegtly, Andrey V Matveyev, Ana M Lara, Flávia Maia da Silva, Myrna G Serrano, Gregory A Buck, Marta M G Teixeira, Erney P Camargo
It has been known for decades that some insect-infecting trypanosomatids can survive in culture without heme supplementation while others cannot, and that this capability is associated with the...