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2. Multiple Introductions of Yersinia pestis during Urban Pneumonic Plague Epidemic, Madagascar, 2017

Author

Andrianaivoarimanana, Voahangy, Savin, Cyril, Birdsell, Dawn N., Vogler, Amy J., Guern, Anne-Sophie Le, Rahajandraibe, Soloandry, Bremont, Sylvie, Rahelinirina, Soanandrasana, Sahl, Jason W., Ramasindrazana, Beza, Rakotonanahary, Rado Jean Luc, Rakotomanana, Fanjasoa, Randremanana, Rindra, Maheriniaina, Viviane, Razafimbia, Vaoary, Kwasiborski, Aurelia, Baliere, Charlotte, Ratsitorahina, Maherisoa, Baril, Laurence, Keim, Paul, Caro, Valerie, Rasolofo, Voahangy, Spiegel, Andre, Pizarro- Cerda, Javier, Wagner, David M., and Rajerison, Minoarisoa

Subjects
Plague -- Genetic aspects -- Health aspects, Health
Abstract

Madagascar reports more human plague (causative agent: Yersinia pestis) cases annually than any other country (1), often several hundred each season (typically September-March) (2). Y. pestis persists in multiple rural [...]

Published
2024
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3. Factor Xa cleaves SARS-CoV-2 spike protein to block viral entry and infection

Author

Dong, Wenjuan, Wang, Jing, Tian, Lei, Zhang, Jianying, Settles, Erik W., Qin, Chao, Steinken-Kollath, Daniel R., Itogawa, Ashley N., Celona, Kimberly R., Yi, Jinhee, Bryant, Mitchell, Mead, Heather, Jaramillo, Sierra A., Lu, Hongjia, Li, Aimin, Zumwalt, Ross E., Dadwal, Sanjeet, Feng, Pinghui, Yuan, Weiming, Whelan, Sean P. J., Keim, Paul S., Barker, Bridget Marie, Caligiuri, Michael A., and Yu, Jianhua

Published
2023
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4. Burkholderia thailandensis Isolated from the Environment, United States

Author

Hall, Carina M., Stone, Nathan E., Martz, Madison, Hutton, Shelby M., Santana- Propper, Ella, Versluis, Lora, Guidry, Kieston, Ortiz, Marielisa, Busch, Joseph D., Maness, Trevor, Stewart, Jonathan, Sidwa, Tom, Gee, Jay E., Elrod, Mindy G., Petras, Julia K., Ty, Maureen C., Gulvik, Christopher, Weiner, Zachary P., Salzer, Johanna S., Hoffmaster, Alex R., Rivera-Garcia, Sarai, Keim, Paul, Kieffer, Amanda, Sahl, Jason W., Soltero, Fred, and Wagner, David M.

Subjects
Bacteria, Pathogenic -- Identification and classification -- Environmental aspects -- Genetic aspects, Pseudomonas infections -- Risk factors, Burkholderia -- Identification and classification -- Environmental aspects -- Genetic aspects, Health
Abstract

Burkholderia thailandensis, a gram-negative bacterium found in the environment, poses a public health threat both because of its ability to cause infections as an opportunistic pathogen and potential misidentification as [...]

Published
2023
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5. Using source-associated mobile genetic elements to identify zoonotic extraintestinal E. coli infections

Author

Liu, Cindy M., Aziz, Maliha, Park, Daniel E., Wu, Zhenke, Stegger, Marc, Li, Mengbing, Wang, Yashan, Schmidlin, Kara, Johnson, Timothy J., Koch, Benjamin J., Hungate, Bruce A., Nordstrom, Lora, Gauld, Lori, Weaver, Brett, Rolland, Diana, Statham, Sally, Hall, Brantley, Sariya, Sanjeev, Davis, Gregg S., Keim, Paul S., Johnson, James R., and Price, Lance B.

Published
2023
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7. COVID-19 vaccination elicits an evolving, cross-reactive antibody response to epitopes conserved with endemic coronavirus spike proteins

Author

Elko, Evan A., Nelson, Georgia A., Mead, Heather L., Kelley, Erin J., Carvalho, Sophia T., Sarbo, Nathan G., Harms, Caroline E., Le Verche, Virginia, Cardoso, Angelo A., Ely, Jennifer L., Boyle, Annalee S., Piña, Alejandra, Henson, Sierra N., Rahee, Fatima, Keim, Paul S., Celona, Kimberly R., Yi, Jinhee, Settles, Erik W., Bota, Daniela A., Yu, George C., Morris, Sheldon R., Zaia, John A., Ladner, Jason T., and Altin, John A.

Published
2022
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8. A multi-omics strategy to understand PASC through the RECOVER cohorts: a paradigm for a systems biology approach to the study of chronic conditions.

Author

Sun, Jun, Aikawa, Masanori, Ashktorab, Hassan, Beckmann, Noam D., Enger, Michael L., Espinosa, Joaquin M., Gai, Xiaowu, Horne, Benjamin D., Keim, Paul, Lasky-Su, Jessica, Letts, Rebecca, Maier, Cheryl L., Mandal, Meisha, Nichols, Lauren, Roan, Nadia R., Russell, Mark W., Rutter, Jacqueline, Saade, George R., Sharma, Kumar, and Shiau, Stephanie

Subjects
POST-acute COVID-19 syndrome, SYSTEMS biology, SOCIAL determinants of health, TASK forces, CHILD patients, BIOMARKERS
Abstract

Post-Acute Sequelae of SARS-CoV-2 infection (PASC or "Long COVID"), includes numerous chronic conditions associated with widespread morbidity and rising healthcare costs. PASC has highly variable clinical presentations, and likely includes multiple molecular subtypes, but it remains poorly understood from a molecular and mechanistic standpoint. This hampers the development of rationally targeted therapeutic strategies. The NIH-sponsored "Researching COVID to Enhance Recovery" (RECOVER) initiative includes several retrospective/prospective observational cohort studies enrolling adult, pregnant adult and pediatric patients respectively. RECOVER formed an "OMICS" multidisciplinary task force, including clinicians, pathologists, laboratory scientists and data scientists, charged with developing recommendations to apply cutting-edge system biology technologies to achieve the goals of RECOVER. The task force met biweekly over 14 months, to evaluate published evidence, examine the possible contribution of each "omics" technique to the study of PASC and develop study design recommendations. The OMICS task force recommended an integrated, longitudinal, simultaneous systems biology study of participant biospecimens on the entire RECOVER cohorts through centralized laboratories, as opposed to multiple smaller studies using one or few analytical techniques. The resulting multi-dimensional molecular dataset should be correlated with the deep clinical phenotyping performed through RECOVER, as well as with information on demographics, comorbidities, social determinants of health, the exposome and lifestyle factors that may contribute to the clinical presentations of PASC. This approach will minimize lab-to-lab technical variability, maximize sample size for class discovery, and enable the incorporation of as many relevant variables as possible into statistical models. Many of our recommendations have already been considered by the NIH through the peer-review process, resulting in the creation of a systems biology panel that is currently designing the studies we proposed. This system biology strategy, coupled with modern data science approaches, will dramatically improve our prospects for accurate disease subtype identification, biomarker discovery and therapeutic target identification for precision treatment. The resulting dataset should be made available to the scientific community for secondary analyses. Analogous system biology approaches should be built into the study designs of large observational studies whenever possible. [ABSTRACT FROM AUTHOR]

Published
2025
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9. Melioidosis in goats at a single Australian farm was caused by multiple diverse lineages of Burkholderia pseudomallei present in soil.

Author

Busch, Joseph D., Kaestli, Mirjam, Mayo, Mark, Roe, Chandler C., Vazquez, Adam J., Choy, Jodie Low, Harrington, Glenda, Benedict, Suresh, Stone, Nathan E., Allender, Christopher J., Bowen, Richard A., Keim, Paul, Currie, Bart J., Sahl, Jason W., Tuanyok, Apichai, and Wagner, David M.

Subjects
IRRIGATED soils, ANIMAL herds, BURKHOLDERIA pseudomallei, SOIL depth, AGRICULTURE
Abstract

Background: Burkholderia pseudomallei, causative agent of melioidosis, is a One Health concern as it is acquired directly from soil and water and causes disease in humans and agricultural and wild animals. We examined B. pseudomallei in soil and goats at a single farm in the Northern Territory of Australia where >30 goats acquired melioidosis over nine years. Methodology/Principal findings: We cultured 45 B. pseudomallei isolates from 35 goats and sampled soil in and around goat enclosures to isolate and detect B. pseudomallei and evaluate characteristics associated with its occurrence; 33 soil isolates were obtained from 1993–1994 and 116 in 2006. Ninety-two goat and soil isolates were sequenced; mice were challenged with six soil isolates to evaluate virulence. Sampling depth and total N/organic C correlated with B. pseudomallei presence. Twelve sequence types (STs) were identified. Most goat infections (74%) were ST617, some with high similarity to 2006 soil isolates, suggesting ST617 was successful at persisting in soil and infecting goats. ST260 and ST266 isolates were highly virulent in mice but other isolates produced low/intermediate virulence; three of these were ST326 isolates, the most common soil ST in 2006. Thus, virulent and non-virulent lineages can co-occur locally. Three genes associated with virulence were present in ST260 and ST266, absent in most ST326 isolates, and present or variably present in ST617. Conclusions/Significance: Agricultural animals can influence B. pseudomallei abundance and diversity in local environments. This effect may persist, as B. pseudomallei was detected more often from soil collected inside and adjacent to goat enclosures years after most goats were removed. Following goat removal, the low virulence ST326, which was not isolated from soil when goats were present, became the predominant ST in soil by 2006. Although multiple diverse lineages of B. pseudomallei may exist in a given location, some may infect mammals more efficiently than others. Author summary: We studied genomic diversity in the environmental bacterial pathogen, Burkholderia pseudomallei, which caused the disease melioidosis in goats at a small farm in northern Australia. By comparing genomes from 92 B. pseudomallei isolates from goats and soil, we discovered 12 diverse lineages at this location, three of which infected the majority of goats and were cultured from the soil of goat enclosures. We also conducted a mouse challenge experiment using six isolates from this farm and determined that two soil isolates displayed much greater virulence than the others. Finally, we investigated soil factors associated with B. pseudomallei occurrence and found 1) most B. pseudomallei isolates were sampled from irrigated soils, and 2) B. pseudomallei was much more likely to be encountered at soil depths of 30 cm than 10 cm. The presence of this pathogen in the soil severely impacted maintenance of the goat herd due to high mortality and emphasizes its One Health implications for other livestock operations in tropical countries where B. pseudomallei is endemic. Our findings provide insight into the importance of more fully understanding soil habitats that promote B. pseudomallei presence, thereby increasing the risk of melioidosis to humans and agricultural animals. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics

Author

Martínez Arbas, Susana, Narayanasamy, Shaman, Herold, Malte, Lebrun, Laura A., Hoopmann, Michael R., Li, Sujun, Lam, Tony J., Kunath, Benoît J., Hicks, Nathan D., Liu, Cindy M., Price, Lance B., Laczny, Cedric C., Gillece, John D., Schupp, James M., Keim, Paul S., Moritz, Robert L., Faust, Karoline, Tang, Haixu, Ye, Yuzhen, Skupin, Alexander, May, Patrick, Muller, Emilie E. L., and Wilmes, Paul

Published
2021
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15. Domestic canines do not display evidence of gut microbial dysbiosis in the presence of Clostridioides (Clostridium) difficile, despite cellular susceptibility to its toxins

Author

Stone, Nathan E., Nunnally, Amalee E., Jimenez, Victor, Jr., Cope, Emily K., Sahl, Jason W., Sheridan, Krystal, Hornstra, Heidie M., Vinocur, Jacob, Settles, Erik W., Headley, Kyle C., Williamson, Charles H.D., Rideout, Jai Ram, Bolyen, Evan, Caporaso, J. Gregory, Terriquez, Joel, Monroy, Fernando P., Busch, Joseph D., Keim, Paul, and Wagner, David M.

Published
2019
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19. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Author

Bolyen, Evan, Rideout, Jai Ram, Dillon, Matthew R., Bokulich, Nicholas A., Abnet, Christian C., Al-Ghalith, Gabriel A., Alexander, Harriet, Alm, Eric J., Arumugam, Manimozhiyan, Asnicar, Francesco, Bai, Yang, Bisanz, Jordan E., Bittinger, Kyle, Brejnrod, Asker, Brislawn, Colin J., Brown, C. Titus, Callahan, Benjamin J., Caraballo-Rodríguez, Andrés Mauricio, Chase, John, Cope, Emily K., Da Silva, Ricardo, Diener, Christian, Dorrestein, Pieter C., Douglas, Gavin M., Durall, Daniel M., Duvallet, Claire, Edwardson, Christian F., Ernst, Madeleine, Estaki, Mehrbod, Fouquier, Jennifer, Gauglitz, Julia M., Gibbons, Sean M., Gibson, Deanna L., Gonzalez, Antonio, Gorlick, Kestrel, Guo, Jiarong, Hillmann, Benjamin, Holmes, Susan, Holste, Hannes, Huttenhower, Curtis, Huttley, Gavin A., Janssen, Stefan, Jarmusch, Alan K., Jiang, Lingjing, Kaehler, Benjamin D., Kang, Kyo Bin, Keefe, Christopher R., Keim, Paul, Kelley, Scott T., Knights, Dan, Koester, Irina, Kosciolek, Tomasz, Kreps, Jorden, Langille, Morgan G. I., Lee, Joslynn, Ley, Ruth, Liu, Yong-Xin, Loftfield, Erikka, Lozupone, Catherine, Maher, Massoud, Marotz, Clarisse, Martin, Bryan D., McDonald, Daniel, McIver, Lauren J., Melnik, Alexey V., Metcalf, Jessica L., Morgan, Sydney C., Morton, Jamie T., Naimey, Ahmad Turan, Navas-Molina, Jose A., Nothias, Louis Felix, Orchanian, Stephanie B., Pearson, Talima, Peoples, Samuel L., Petras, Daniel, Preuss, Mary Lai, Pruesse, Elmar, Rasmussen, Lasse Buur, Rivers, Adam, Robeson, II, Michael S., Rosenthal, Patrick, Segata, Nicola, Shaffer, Michael, Shiffer, Arron, Sinha, Rashmi, Song, Se Jin, Spear, John R., Swafford, Austin D., Thompson, Luke R., Torres, Pedro J., Trinh, Pauline, Tripathi, Anupriya, Turnbaugh, Peter J., Ul-Hasan, Sabah, van der Hooft, Justin J. J., Vargas, Fernando, Vázquez-Baeza, Yoshiki, Vogtmann, Emily, von Hippel, Max, Walters, William, Wan, Yunhu, Wang, Mingxun, Warren, Jonathan, Weber, Kyle C., Williamson, Charles H. D., Willis, Amy D., Xu, Zhenjiang Zech, Zaneveld, Jesse R., Zhang, Yilong, Zhu, Qiyun, Knight, Rob, and Caporaso, J. Gregory

Published
2019
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21. Microevolution and History of the Plague Bacillus, Yersinia pestis

Author

Achtman, Mark, Morelli, Giovanna, Zhu, Peixuan, Wirth, Thierry, Diehl, Ines, Kusecek, Barica, Vogler, Amy J., Wagner, David M., Allender, Christopher J., Easterday, W. Ryan, Chenal-Francisque, Viviane, Worsham, Patricia, Thomson, Nicholas R., Parkhill, Julian, Lindler, Luther E., Carniel, Elisabeth, Keim, Paul, and Meselson, M. S.

Published
2004

27. Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance

Author

Herold, Malte, Martínez Arbas, Susana, Narayanasamy, Shaman, Sheik, Abdul R., Kleine-Borgmann, Luise A. K., Lebrun, Laura A., Kunath, Benoît J., Roume, Hugo, Bessarab, Irina, Williams, Rohan B. H., Gillece, John D., Schupp, James M., Keim, Paul S., Jäger, Christian, Hoopmann, Michael R., Moritz, Robert L., Ye, Yuzhen, Li, Sujun, Tang, Haixu, Heintz-Buschart, Anna, May, Patrick, Muller, Emilie E. L., Laczny, Cedric C., and Wilmes, Paul

Published
2020
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42. Phylogenetic Analysis of Francisella tularensis Group A.II Isolates from 5 Patients with Tularemia, Arizona, USA, 2015-2017

Author

Birdsell, Dawn N., Yaglom, Hayley, Rodriguez, Edwin, Engelthaler, David M., Maurer, Matthew, Gaither, Marlene, Vinocur, Jacob, Weiss, Joli, Terriquez, Joel, Komatsu, Kenneth, Ormsby, Mary Ellen, Gebhardt, Marette, Solomon, Catherine, Nienstadt, Linus, Williamson, Charles H.D., Sahl, Jason W., Keim, Paul S., and Wagner, David M.

Subjects
Resveratrol -- Analysis, Phylogeny -- Analysis, Tularemia -- Analysis, Health
Abstract

Francisella tularensis, a Tier 1 select agent (7), has 3 subspecies: tularensis (type A), holarctica (type B), and mediasiatica (Appendix 1 Figure, https://wwwnc. cdc.gov/EID/article/25/5/18-0363-App1.pdf). In humans, disease is caused by [...]

Published
2019
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44. Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis

Author

Wagner, David M, Klunk, Jennifer, Harbeck, Michaela, Devault, Alison, Waglechner, Nicholas, Sahl, Jason W, Enk, Jacob, Birdsell, Dawn N, Kuch, Melanie, Lumibao, Candice, Poinar, Debi, Pearson, Talima, Fourment, Mathieu, Golding, Brian, Riehm, Julia M, Earn, David J D, DeWitte, Sharon, Rouillard, Jean-Marie, Grupe, Gisela, Wiechmann, Ingrid, Bliska, James B, Keim, Paul S, Scholz, Holger C, Holmes, Edward C, and Poinar, Hendrik

Published
2014
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48. Water as source of Francisella tularensis infection in humans, Turkey

Author

Kilic, Selcuk, Birdsell, Dawn N., Karagoz, Alper, Qelebi, Bekir, Bakkaloglu, Zekiye, Arikan, Muzaffer, Sahl, Jason W., Mitchell, Cedar, Rivera, Andrew, Maltinsky, Sara, Keim, Paul, Ustek, Duran, Durmaz, Rlza, and Wagner, David M.

Subjects
Francisella tularensis -- Research -- Development and progression -- Genetic aspects -- Care and treatment -- Patient outcomes, Single nucleotide polymorphisms -- Health aspects -- Research, Health
Abstract

Tularemia is a disease caused primarily by 2 subspecies of Francisella tularensis: F. tularensis subsp. tularensis, which is restricted to North America; and F. tularensis subsp. holarctica, which is found [...]

Published
2015
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49. High Prevalence of intermediate Leptospira spp. DNA in febrile humans from Urban and Rural Ecuador

Author

Chiriboga, Jorge, Barragan, Veronica, Arroyo, Gabriela, Sosa, Andrea, Birdsell, Dawn N., Espana, Karool, Mora, Ana, Espin, Emilia, Mejia, Maria Eugenia, Morales, Melba, Pinargote, Carmina, Gonzalez, Manuel, Hartskeerl, Rudy, Keim, Paul, Bretas, Gustavo, Eisenberg, Joseph N.S., and Trueba, Gabriel

Subjects
Prevalence studies (Epidemiology) -- Research, Leptospirosis -- Research -- Development and progression -- Care and treatment -- Patient outcomes -- Complications and side effects, Gram-negative bacteria -- Research, Health
Abstract

Leptospirosis, caused by spirochetes of the genus Leptospira, is a neglected and potentially fatal disease that burdens impoverished communities of developing nations in tropical regions (1-4). The bacteria cause 1.7 [...]

Published
2015
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50. Adaptations of Avian Flu Virus Are a Cause for Concern

Author

Berns, Kenneth I., Casadevall, Arturo, Cohen, Murray L., Ehrlich, Susan A., Enquist, Lynn W., Fitch, J. Patrick, Franz, David R., Fraser-Liggett, Claire M., Grant, Christine M., Imperiale, Michael J., Kanabrocki, Joseph, Keim, Paul S., Lemon, Stanley M., Levy, Stuart B., Lumpkin, John R., Miller, Jeffery F., Murch, Randall, Nance, Mark E., Osterholm, Michael T., Relman, David A., Roth, James A., and Vidaver, Anne K.

Published
2012
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