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1. Multiple sclerosis patient-derived spontaneous B cells have distinct EBV and host gene expression profiles in active disease

Author

Soldan, Samantha S., Su, Chenhe, Monaco, Maria Chiara, Yoon, Leena, Kannan, Toshitha, Zankharia, Urvi, Patel, Rishi J., Dheekollu, Jayaraju, Vladimirova, Olga, Dowling, Jack W., Thebault, Simon, Brown, Natalie, Clauze, Annaliese, Andrada, Frances, Feder, Andries, Planet, Paul J., Kossenkov, Andrew, Schäffer, Daniel E., Ohayon, Joan, Auslander, Noam, Jacobson, Steven, and Lieberman, Paul M.

Published
2024
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5. Antimicrobial sensing coupled with cell membrane remodeling mediates antibiotic resistance and virulence in Enterococcus faecalis

Author

Khan, Ayesha, Davlieva, Milya, Panesso, Diana, Rincon, Sandra, Miller, William R, Diaz, Lorena, Reyes, Jinnethe, Cruz, Melissa R, Pemberton, Orville, Nguyen, April H, Siegel, Sara D, Planet, Paul J, Narechania, Apurva, Latorre, Mauricio, Rios, Rafael, Singh, Kavindra V, Ton-That, Hung, Garsin, Danielle A, Tran, Truc T, Shamoo, Yousif, and Arias, Cesar A

Subjects
Vaccine Related, Biodefense, Prevention, Emerging Infectious Diseases, Infectious Diseases, Antimicrobial Resistance, Development of treatments and therapeutic interventions, Aetiology, 5.1 Pharmaceuticals, 2.2 Factors relating to the physical environment, Infection, antibiotic resistance, Enterococcus faecalis, daptomycin, cell membrane adaptation, antimicrobial peptides
Abstract

Bacteria have developed several evolutionary strategies to protect their cell membranes (CMs) from the attack of antibiotics and antimicrobial peptides (AMPs) produced by the innate immune system, including remodeling of phospholipid content and localization. Multidrug-resistant Enterococcus faecalis, an opportunistic human pathogen, evolves resistance to the lipopeptide daptomycin and AMPs by diverting the antibiotic away from critical septal targets using CM anionic phospholipid redistribution. The LiaFSR stress response system regulates this CM remodeling via the LiaR response regulator by a previously unknown mechanism. Here, we characterize a LiaR-regulated protein, LiaX, that senses daptomycin or AMPs and triggers protective CM remodeling. LiaX is surface exposed, and in daptomycin-resistant clinical strains, both LiaX and the N-terminal domain alone are released into the extracellular milieu. The N-terminal domain of LiaX binds daptomycin and AMPs (such as human LL-37) and functions as an extracellular sentinel that activates the cell envelope stress response. The C-terminal domain of LiaX plays a role in inhibiting the LiaFSR system, and when this domain is absent, it leads to activation of anionic phospholipid redistribution. Strains that exhibit LiaX-mediated CM remodeling and AMP resistance show enhanced virulence in the Caenorhabditis elegans model, an effect that is abolished in animals lacking an innate immune pathway crucial for producing AMPs. In conclusion, we report a mechanism of antibiotic and AMP resistance that couples bacterial stress sensing to major changes in CM architecture, ultimately also affecting host-pathogen interactions.

Published
2019

6. Contributors

Author

Abzug, Mark J., primary, Adderson, Elisabeth E., additional, Agarwal, Aastha, additional, Agwu, Allison L., additional, Albenberg, Lindsey, additional, Albert, Jonathan, additional, Alby, Kevin, additional, Aldrovandi, Grace M., additional, Allen, Upton D., additional, Alvarez-Hernndez, Gerardo, additional, Ampofo, Krow, additional, Anderson, Evan J., additional, Appiah, Grace D., additional, Ardura, Monica I., additional, Arnon, Stephen S., additional, Aronson, Naomi E., additional, Arvin, Ann M., additional, Ashkenazi, Shai, additional, Ashkenazi-Hoffnung, Liat, additional, Asturias, Edwin J., additional, Aukstuolis, Kestutis, additional, Badalyan, Vahe, additional, Baker, Carol J., additional, Balakrishnan, Karthik, additional, Barnett, Elizabeth D., additional, Bechtel, Kirsten, additional, Benitz, William E., additional, Berkovich, Rachel, additional, Berman, David M., additional, Bialek, Stephanie R., additional, Bijker, Else M., additional, Bizzarro, Matthew J., additional, Bloch, Karen C., additional, Bocchini, Joseph A., additional, Boyce, Thomas G., additional, Bradley, John S., additional, Bratcher, Denise F., additional, Braverman, Paula K., additional, Brook, Itzhak, additional, Brown, Kevin Edward, additional, Bryant, Kristina P., additional, Camacho-Gonzalez, Andres F., additional, Caete-Gibas, Connie F., additional, Cantey, Joseph B., additional, Cantey, Paul, additional, Cardemil, Cristina V., additional, Caserta, Mary T., additional, Castagnini, Luis A., additional, Cataldi, Jessica R., additional, Chadwick, Ellen Gould, additional, Chancey, Rebecca J., additional, Cherry, Cara C., additional, Chiang, Silvia S., additional, Choi, Mary, additional, Christenson, John C., additional, Coffin, Susan E., additional, Cohn, Amanda, additional, Contopoulos-Ioannidis, Despina G., additional, Conway, James H., additional, Cortese, Margaret M., additional, Creech, C. Buddy, additional, Crews, Jonathan D., additional, Curtis, Donna, additional, Curtis, Nigel, additional, Danziger-Isakov, Lara A., additional, Darville, Toni, additional, Dasch, Gregory A., additional, Daskalaki, Irini, additional, Davies, H. Dele, additional, Dawood, Fatimah S., additional, Day, J. Christopher, additional, Teresa de la Morena, M., additional, DeMuri, Gregory P., additional, Despommier, Dickson D., additional, Dodson, Daniel S., additional, Dolgner, Stephen J., additional, Dunn, Clinton, additional, Dyal, Jonathan, additional, Edwards, Kathryn M., additional, Edwards, Morven S., additional, Eichenfield, Dawn Z., additional, Eichenfield, Lawrence F., additional, Elston, Dirk M., additional, Emerson, Beth, additional, Enane, Leslie A., additional, Ephros, Moshe, additional, Erdem, Guliz, additional, Eremeeva, Marina E., additional, Esposito, Douglas H., additional, Farley, Monica M., additional, Feingold, Anat R., additional, Feja, Kristina N., additional, Finn, Adam, additional, Fischer, Marc, additional, Fisher, Brian T., additional, Fisher, Randall G., additional, Flynn, Patricia Michele, additional, Foster, Monique A., additional, Fox, LeAnne M., additional, Frank, Michael M., additional, Fredrick, Douglas R., additional, Frenck, Robert W., additional, Gaensbauer, James, additional, Gans, Hayley A., additional, Gauthier, Gregory M., additional, Gavigan, Patrick, additional, Gerber, Jeffrey S., additional, Gernez, Yael, additional, Gigliotti, Francis, additional, Gilger, Mark A., additional, Glaser, Carol A., additional, Gould, Jane M., additional, Graziano, James, additional, Green, Amanda M., additional, Green, Michael, additional, Griffin, Daniel, additional, Griffin, Patricia M., additional, Griffith, David C., additional, Gupta, Piyush, additional, Gutelius, Bruce J., additional, Gutman, Julie R., additional, Hall, Aron J., additional, Hamdy, Rana F., additional, Han, Jin-Young, additional, Handy, Lori K., additional, Hanisch, Benjamin, additional, Harper, Marvin B., additional, Harris, Aaron M., additional, Harrison, Christopher J., additional, Haslam, David B., additional, Haston, Julia C., additional, Hawkes, Sarah.J., additional, Heald-Sargent, Taylor, additional, Hendley, J. Owen, additional, Hersh, Adam L., additional, Hilinski, Joseph A., additional, Hills, Susan L., additional, Hong, David K., additional, Hotez, Peter J., additional, Hsu, Katherine K., additional, Huang, Felicia Scaggs, additional, Hunstad, David A., additional, Hunt, W. Garrett, additional, Hwang, Loris Y., additional, Ilboudo, Christelle M., additional, Jaggi, Preeti, additional, Jean, Sophonie, additional, Jhaveri, Ravi, additional, Jirk-Pomajbkov, Kateina, additional, Kadry, Nadia A., additional, Kamb, Mary L., additional, Kapadia, Ronak K., additional, Katz, Ben Z., additional, Katz, Sophie E., additional, Kaur, Ishminder, additional, Kersh, Gilbert J., additional, Khan, Muhammad Ali, additional, Khurana, Ananta, additional, Kimberlin, David W., additional, Klein, Bruce, additional, Kobayashi, Miwako, additional, Kociolek, Larry K., additional, Koh, Andrew Y., additional, Kotloff, Karen L., additional, Kroger, Andrew T., additional, Kronman, Matthew P., additional, Lalor, Leah, additional, Lauren, Christine T., additional, Leber, Amy, additional, Leshem, Eyal, additional, Lewis, David B., additional, Livingston, Robyn A., additional, Llata, Eloisa, additional, Lloyd, Kevin, additional, Loh, Katrina, additional, Long, Sarah S., additional, Lopman, Benjamin A., additional, Lucero, Yalda C., additional, Lugo, Debra J., additional, Lujn-Zilbermann, Jorge, additional, Maldonado, Yvonne A., additional, Manaloor, John J., additional, Manthiram, Kalpana, additional, Martin, Stacey W., additional, Mathew, Roshni, additional, Mazzulli, Tony, additional, McFarland, Elizabeth J., additional, McGann, Kathleen A., additional, McNamara, Lucy A., additional, Meislich, Debrah, additional, Meissner, H. Cody, additional, Mejias, Asuncion, additional, Mertsola, Jussi, additional, Messacar, Kevin, additional, Mhaissen, Mohammad Nael, additional, Michaels, Marian G., additional, Miller, Melissa B., additional, Miller-Handley, Hilary, additional, Mintz, Eric, additional, Mohan, Parvathi, additional, Montgomery, Susan P., additional, Montoya, Jose G., additional, Moorman, Anne C., additional, Moro, Pedro L., additional, Moscicki, Anna-Barbara, additional, Muller, William J., additional, Myers, Angela L., additional, Nadel, Simon, additional, Nayak, Jennifer Lynn, additional, Neely, Michael Noel, additional, Neil, Karen P., additional, Nelson, Christina A., additional, Nelson, Noele P., additional, Nichols, Megin, additional, Nicholson, William, additional, Nopper, Amy Jo, additional, Norton, Laura E., additional, Ochoa, Theresa J., additional, Olarte, Liset, additional, Onarecker, Timothy R., additional, Orenstein, Walter A., additional, ORyan, Miguel, additional, Otto, William R., additional, Ouellette, Christopher P., additional, Paddock, Christopher D., additional, Palazzi, Debra L., additional, Panuganti, Suresh Kumar, additional, Pappas, Diane E., additional, Paret, Michal, additional, Pastula, Daniel M., additional, Patterson, Thomas F., additional, Petersen, Brett W., additional, Petrosyan, Mikael, additional, Pickering, Larry K., additional, Pindyck, Talia, additional, Pinninti, Swetha, additional, Pittet, Laure F., additional, Planet, Paul J., additional, Pollard, Andrew J., additional, Posfay-Barbe, Klara M., additional, Poulsen, Casper S., additional, Poutanen, Susan M., additional, Powers, Ann M., additional, Prasanphanich, Nina Salinger, additional, Pritt, Bobbi S., additional, Prober, Charles G., additional, Puar, Neha, additional, Quilter, Laura A.S., additional, Ramilo, Octavio, additional, Rao, Suchitra, additional, Ratner, Adam J., additional, Rawstron, Sarah A., additional, Read, Jennifer S., additional, Relich, Ryan F., additional, Reller, Megan E., additional, Robinson, Candice L., additional, Romero, Jos R., additional, Rosen, David A., additional, Ross, Shannon A., additional, Rours, G. Ingrid J.G., additional, Rowe, Peter C., additional, Rowley, Anne H., additional, Rubin, Lorry G., additional, Ryan, Edward T., additional, Sacharok, Alexandra, additional, Sandora, Thomas J., additional, Sapp, Sarah G.H., additional, Sardana, Kabir, additional, Sauberan, Jason B., additional, Schaffzin, Joshua K., additional, Schillie, Sarah, additional, Schuster, Jennifer E., additional, Schwartz, Kevin L., additional, Sederdahl, Bethany K., additional, Serpa-Alvarez, Jose, additional, Shah, Kara N., additional, Shah, Samir S., additional, Shaikh, Nader, additional, Shane, Andi L., additional, Shapiro, Eugene D., additional, Shaw, Jana, additional, Shetty, Avinash K., additional, Shope, Timothy R., additional, Dairiki Shortliffe, Linda M., additional, Shulman, Stanford T., additional, Shust, Gail F., additional, Siberry, George Kelly, additional, Siegel, Jane D., additional, Siegel, Robert David, additional, Simonsen, Kari A., additional, Singh, Upinder, additional, Smith, Christiana, additional, Smith, Lauren L., additional, Song, Eunkyung, additional, Souder, Emily, additional, Spearman, Paul, additional, St. Geme, Joseph W., additional, Staat, Mary Allen, additional, Staples, J. Erin, additional, Starke, Jeffrey R., additional, Statler, Victoria A., additional, Steinbach, William J., additional, Stensvold, Christen Rune, additional, Stokes, Erin K., additional, Stoner, Bradley P., additional, Storch, Gregory A., additional, Straily, Anne, additional, Sullivan, Kathleen E., additional, Swanson, Douglas S., additional, Tanz, Robert R., additional, Taormina, Gillian, additional, Tate, Jacqueline E., additional, Taveras, Jeanette, additional, Tebruegge, Marc, additional, Teshale, Eyasu H., additional, Thompson, George R., additional, Thompson-Stone, Robert, additional, Thomsen, Isaac, additional, Thomson, Richard B., additional, Thorell, Emily A., additional, Tien, Vivian, additional, Tobin, Nicole H., additional, Toltzis, Philip, additional, Treat, James, additional, Troy, Stephanie B., additional, Van Dvke, Russell B., additional, Vaz, Louise Elaine, additional, Vijayan, Vini, additional, Vodzak, Jennifer, additional, Wagner, Thor A., additional, Wald, Ellen R., additional, Wallihan, Rebecca, additional, Wang, Huanyu, additional, Wangu, Zoon, additional, Washam, Matthew, additional, Waters, Valerie, additional, Watson, Joshua R., additional, Weatherhead, Jill E., additional, Weinberg, Geoffrey A., additional, Weng, Mark K., additional, Wiederhold, Nathan P., additional, Wiesenfeld, Harold C., additional, Williams, Cydni, additional, Williams, John V., additional, Willoughby, Rodney E., additional, Wittler, Robert R., additional, Wood, James B., additional, Woods, Charles Reece, additional, Workowski, Kimberly A., additional, Wright, Terry W., additional, Wu, Hsi-Yang, additional, Xu, Huan, additional, Yagupsky, Pablo, additional, Yi, Jumi, additional, Yoder, Jonathan, additional, Young, Edward J., additional, Zaenglein, Andrea L., additional, Zimmermann, Petra, additional, and Zong, Wenjing, additional

Published
2023
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11. Maternal and neonatal IgG against Klebsiella pneumoniae are associated with broad protection from neonatal sepsis: a case-control study of hospitalized neonates in Botswana

Author

Zhang, Siqi Linsey, primary, McGann, Carolyn M, additional, Duranova, Tereza, additional, Strysko, Jonathan, additional, Steenhoff, Andrew P., additional, Gezmu, Alemayehu, additional, Nakstad, Britt, additional, Arscott-Mills, Tonya, additional, Bayani, One, additional, Tlhako, Nametso, additional, Richard-Greenblatt, Melissa, additional, Moorad, Banno, additional, Planet, Paul J., additional, Coffin, Susan E., additional, and Silverman, Michael A, additional

Published
2024
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12. Multidrug-Resistant Methicillin-Resistant Staphylococcus aureus Associated with Bacteremia and Monocyte Evasion, Rio de Janeiro, Brazil

Author

Viana, Alice Slotfeldt, Botelho, Ana Maria Nunes, Moustafa, Ahmed M., Boge, Craig L.K., Ferreira, Adriana Lucia Pires, Carvalho, Maria Cicera da Silva, Guimaraes, Marcia Aparecida, de Souza Scramignon Costa, Bruno, de Mattos, Marcos Correa, Maciel, Sabrina Pires, Echevarria-Lima, Juliana, Narechania, Apurva, OBrien, Kelsey, Ryan, Chanelle, Gerber, Jeffrey S., Carvalho, Bernadete Teixeira Ferreira, Figueiredo, Agnes Marie Sa, and Planet, Paul J.

Subjects
Rio de Janeiro, Brazil (City) -- Health aspects, Staphylococcus aureus -- Identification and classification -- Genetic aspects, Staphylococcus aureus infections -- Statistics -- Causes of, Bacteremia -- Statistics -- Causes of, Health
Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) is characterized by the mainly clonal structure of bacterial populations and the worldwide spread of a few highly successful lineages, sequence types (STs), and clonal complexes [...]

Published
2021
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13. Genetic variation of staphylococcal LukAB toxin determines receptor tropism

Author

Perelman, Sofya S., James, David B. A., Boguslawski, Kristina M., Nelson, Chase W., Ilmain, Juliana K., Zwack, Erin E., Prescott, Rachel A., Mohamed, Adil, Tam, Kayan, Chan, Rita, Narechania, Apurva, Pawline, Miranda B., Vozhilla, Nikollaq, Moustafa, Ahmed M., Kim, Sang Y., Dittmann, Meike, Ekiert, Damian C., Bhabha, Gira, Shopsin, Bo, Planet, Paul J., Koralov, Sergei B., and Torres, Victor J.

Published
2021
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18. Sequential evolution of virulence and resistance during clonal spread of community-acquired methicillinresistant Staphylococcus aureus

Author

Copin, Richard, Sause, William E., Fulmer, Yi, Balasubramanian, Divya, Dyzenhaus, Sophie, Ahmed, Jamil M., Kumar, Krishan, Lees, John, Stachel, Anna, Fisher, Jason C., Drlica, Karl, Phillips, Michael, Weiser, Jeffrey N., Planet, Paul J., Uhlemann, Anne-Catrin, Altman, Deena R., Sebra, Robert, van Bakel, Harm, Lighter, Jennifer, Torres, Victor J., and Shopsin, Bo

Published
2019

22. Parallel evolution of linezolid-resistant Staphylococcus aureus in patients with cystic fibrosis

Author

Pitcher, Nicholas J., primary, Feder, Andries, additional, Bolden, Nicholas, additional, Zirbes, Christian F., additional, Pamatmat, Anthony J., additional, Boyken, Linda, additional, Hill, Jared J., additional, Bartels, Alyssa R., additional, Thurman, Andrew L., additional, Reeb, Valerie C., additional, Porterfield, Harry S., additional, Moustafa, Ahmed M., additional, Planet, Paul J., additional, and Fischer, Anthony J., additional

Published
2023
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23. An Analysis of the Epidemic of Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae : Convergence of Two Evolutionary Mechanisms Creates the “Perfect Storm”

Author

Rojas, Laura J., Weinstock, George M., De La Cadena, Elsa, Diaz, Lorena, Rios, Rafael, Hanson, Blake M., Brown, Joseph S., Vats, Purva, Phillips, Daniel S., Nguyen, Hoan, Hujer, Kristine M., Correa, Adriana, Adams, Mark D., Perez, Federico, Sodergren, Erica, Narechania, Apurva, Planet, Paul J., Villegas, Maria V., Bonomo, Robert. A., and Arias, Cesar A.

Published
2018

26. Dynamics of the MRSA Population in a Chilean Hospital: a Phylogenomic Analysis (2000–2016)

Author

Martínez, José R. W., primary, Planet, Paul J., additional, Spencer-Sandino, Maria, additional, Rivas, Lina, additional, Díaz, Lorena, additional, Moustafa, Ahmed M., additional, Quesille-Villalobos, Ana, additional, Riquelme-Neira, Roberto, additional, Alcalde-Rico, Manuel, additional, Hanson, Blake, additional, Carvajal, Lina P., additional, Rincón, Sandra, additional, Reyes, Jinnethe, additional, Lam, Marusella, additional, Calderon, Juan F., additional, Araos, Rafael, additional, García, Patricia, additional, Arias, César A., additional, and Munita, José M., additional

Published
2023
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27. Carbapenem-resistantAcinetobacter baumanniiat a hospital in Botswana: Detecting a protracted outbreak using whole genome sequencing

Author

Strysko, Jonathan, primary, Thela, Tefelo, additional, Feder, Andries, additional, Thubuka, Janet, additional, Machiya, Tichaona, additional, Mkubwa, Jack, additional, Mochankana, Kagiso, additional, Tiroyakgosi, Celda, additional, Kgomanyane, Kgomotso, additional, Ntereke, Tlhalefo Dudu, additional, Zankere, Tshiamo, additional, Lechiile, Kwana, additional, Gatonye, Teresia, additional, Tembo, Chimwemwe Viola, additional, Vurayai, Moses, additional, Mannathoko, Naledi, additional, Mokomane, Margaret, additional, Moustafa, Ahmed M, additional, Goldfarb, David M, additional, Richard-Greenblatt, Melissa, additional, McGann, Carolyn, additional, Coffin, Susan E, additional, Cancedda, Corrado, additional, Lautenbach, Ebbing, additional, Bogoshi, Dineo, additional, Smith, Anthony M, additional, and Planet, Paul J, additional

Published
2023
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30. Lung function and microbiota diversity in cystic fibrosis

Author

Cuthbertson, Leah, Walker, Alan W., Oliver, Anna E., Rogers, Geraint B., Rivett, Damian W., Hampton, Thomas H., Ashare, Alix, Elborn, J. Stuart, De Soyza, Anthony, Carroll, Mary P., Hoffman, Lucas R., Lanyon, Clare, Moskowitz, Samuel M., O’Toole, George A., Parkhill, Julian, Planet, Paul J., Teneback, Charlotte C., Tunney, Michael M., Zuckerman, Jonathan B., Bruce, Kenneth D., and van der Gast, Christopher J.

Published
2020
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36. Heavy Metal Pollution From a Major Earthquake and Tsunami in Chile Is Associated With Geographic Divergence of Clinical Isolates of Methicillin-Resistant Staphylococcus aureus in Latin America

Author

Martinez, Jose RW, primary, Alcalde-Rico, Manuel, additional, Jara-Videla, Estefania, additional, Rios, Rafael, additional, Moustafa, Ahmed M, additional, Hanson, Blake, additional, Rivas, Lina, additional, Carvajal, Lina P, additional, Rincon, Sandra, additional, Diaz, Lorena, additional, Reyes, Jinnethe, additional, Quesille-Villalobos, Ana, additional, Riquelme-Neira, Roberto, additional, Undurraga, Eduardo A, additional, Olivares-Pacheco, Jorge, additional, Garcia, Patricia, additional, Araos, Rafael, additional, Planet, Paul J, additional, Arias, Cesar A, additional, and Munita, Jose M, additional

Published
2023
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38. Parallel Evolution of Linezolid ResistantStaphylococcus aureusin Patients with Cystic Fibrosis

Author

Pitcher, Nicholas J., primary, Feder, Andries, additional, Bolden, Nicholas, additional, Zirbes, Christian F., additional, Pamatmat, Anthony J, additional, Boyken, Linda D, additional, Hill, Jared J., additional, Thurman, Andrew, additional, Reeb, Valerie, additional, Porterfield, Harry S., additional, Moustafa, Ahmed M, additional, Planet, Paul J, additional, and Fischer, Anthony John, additional

Published
2023
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39. Arresting microbiome development limits immune system maturation and resistance to infection in mice

Author

Lubin, Jean-Bernard, primary, Green, Jamal, additional, Maddux, Sarah, additional, Denu, Lidiya, additional, Duranova, Tereza, additional, Lanza, Matthew, additional, Wynosky-Dolfi, Meghan, additional, Flores, Julia N., additional, Grimes, Logan P., additional, Brodsky, Igor E., additional, Planet, Paul J., additional, and Silverman, Michael A., additional

Published
2023
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41. Heavy Metal Pollution From a Major Earthquake and Tsunami in Chile Is Associated With Geographic Divergence of Clinical Isolates of Methicillin-ResistantStaphylococcus aureusin Latin America

Author

Martínez, Jose RW, Alcalde-Rico, Manuel, Jara-Videla, Estefanía, Rios, Rafael, Moustafa, Ahmed M., Hanson, Blake, Rivas, Lina, Carvajal, Lina P., Rincon, Sandra, Diaz, Lorena, Reyes, Jinnethe, Quesille-Villalobos, Ana, Riquelme-Neira, Roberto, Undurraga, Eduardo A., Olivares-Pacheco, Jorge, García, Patricia, Araos, Rafael, Planet, Paul J., Arias, César A., and Munita, Jose M.

Subjects
Article
Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) is a priority pathogen listed by the World Health Organization. The global spread of MRSA is characterized by successive waves of epidemic clones that predominate in specific geographical regions. The acquisition of genes encoding resistance to heavy-metals is thought to be a key feature in the divergence and geographical spread of MRSA. Increasing evidence suggests that extreme natural events, such as earthquakes and tsunamis, could release heavy-metals into the environment. However, the impact of environmental exposition to heavy-metals on the divergence and spread of MRSA clones has been insufficiently explored. We assess the association between a major earthquake and tsunami in an industrialized port in southern Chile and MRSA clone divergence in Latin America. We performed a phylogenomic reconstruction of 113 MRSA clinical isolates from seven Latin American healthcare centers, including 25 isolates collected in a geographic area affected by an earthquake and tsunami that led to high levels of heavy-metal environmental contamination. We found a divergence event strongly associated with the presence of a plasmid harboring heavy-metal resistance genes in the isolates obtained in the area where the earthquake and tsunami occurred. Moreover, clinical isolates carrying this plasmid showed increased tolerance to mercury, arsenic, and cadmium. We also observed a physiological burden in the plasmid-carrying isolates in absence of heavy-metals. Our results are the first evidence that suggests that heavy-metal contamination, in the aftermath of an environmental disaster, appears to be a key evolutionary event for the spread and dissemination of MRSA in Latin America.

Published
2023

42. Parallel Epidemics of Community-Associated Methicillin-Resistant Staphylococcus aureus USA300 Infection in North and South America

Author

Planet, Paul J., Diaz, Lorena, Kolokotronis, Sergios-Orestis, Narechania, Apurva, Reyes, Jinnethe, Xing, Galen, Rincon, Sandra, Smith, Hannah, Panesso, Diana, Ryan, Chanelle, Smith, Dylan P., Guzman, Manuel, Zurita, Jeannete, Sebra, Robert, Deikus, Gintaras, Nolan, Rathel L., Tenover, Fred C., Weinstock, George M., Robinson, D. Ashley, and Arias, Cesar A.

Published
2015

43. Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change

Author

Narechania, Apurva, Bobo, Dean, Deitz, Kevin, DeSalle, Rob, Planet, Paul J., and Mathema, Barun

Abstract

The COVID-19 pandemic has highlighted the critical role of genomic surveillance for guiding policy and control. Timeliness is key, but sequence alignment and phylogeny slow most surveillance techniques. Millions of SARS-CoV-2 genomes have been assembled. Phylogenetic methods are ill equipped to handle this sheer scale. We introduce a pangenomic measure that examines the information diversity of a k-mer library drawn from a country's complete set of clinical, pooled, or wastewater sequence. Quantifying diversity is central to ecology. Hill numbers, or the effective number of species in a sample, provide a simple metric for comparing species diversity across environments. The more diverse the sample, the higher the Hill number. We adopt this ecological approach and consider each k-mer an individual and each genome a transect in the pangenome of the species. Structured in this way, Hill numbers summarize the temporal trajectory of pandemic variants, collapsing each day's assemblies into genome equivalents. For pooled or wastewater sequence, we instead compare days using survey sequence divorced from individual infections. Across data from the UK, USA, and South Africa, we trace the ascendance of new variants of concern as they emerge in local populations well before these variants are named and added to phylogenetic databases. Using data from San Diego wastewater, we monitor these same population changes from raw, unassembled sequence. This history of emerging variants senses all available data as it is sequenced, intimating variant sweeps to dominance or declines to extinction at the leading edge of the COVID-19 pandemic.

Published
2024
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45. Contributors

Author

Abzug, Mark J., primary, Adderson, Elisabeth E., additional, Agwu, Allison L., additional, Alby, Kevin, additional, Aldrovandi, Grace M., additional, Allen, Upton D., additional, Alvarez-Hernández, Gerardo, additional, Ampofo, Krow, additional, Anderson, Evan J., additional, Anderson, Margot, additional, Antonara, Stella, additional, Ardura, Monica I., additional, Arguin, Paul M., additional, Arnold, John C., additional, Aronson, Naomi E., additional, Arvin, Ann M., additional, Ashkenazi, Shai, additional, Asturias, Edwin J., additional, Badalyan, Vahe, additional, Baker, Carol J., additional, Balakrishnan, Karthik, additional, Barros, Brittany S., additional, Barson, William J., additional, Bausch, Daniel G., additional, Bechtel, Kirsten, additional, Benjamin, Daniel K., additional, Berman, David M., additional, Blanco, David A., additional, Bloch, Karen C., additional, Blythe, Margaret J., additional, Bocchini, Joseph A., additional, Bowen, Anna, additional, Bowie, William R., additional, Boyce, Thomas G., additional, Bradley, John S., additional, Brady, Michael T., additional, Bratcher, Denise F., additional, Braverman, Paula K., additional, Bresee, Joseph, additional, Brook, Itzhak, additional, Brown, Kevin E., additional, Bryant, Kristina, additional, Buescher, E. Stephen, additional, Burns, Jane L., additional, Byington, Carrie L., additional, Camacho-Gonzalez, Andres F., additional, Cantey, Paul, additional, Carter, Bryan D., additional, Caserta, Mary T., additional, Castagnini, Luis A., additional, Cerini, Chiara, additional, Chadwick, Ellen Gould, additional, Chiang, Silvia S., additional, Christenson, John C., additional, Coffin, Susan E., additional, Collier, Melissa G., additional, Collins, Jennifer P., additional, Conklin, Laurie S., additional, Connelly, Beverly L., additional, Contopoulos-Ioannidis, Despina, additional, Conway, James H., additional, Cortese, Margaret M., additional, Cox, Elaine G., additional, Creech, C. Buddy, additional, Crews, Jonathan D., additional, Cunningham, Dennis J., additional, Curtis, Nigel, additional, Dailey, Natalie J.M., additional, Danziger-Isakov, Lara A., additional, Darville, Toni, additional, Dasch, Gregory A., additional, Daskalaki, Irini, additional, Daum, Robert S., additional, Davenport, Michael, additional, Davies, H. Dele, additional, Dawood, Fatimah S., additional, Day, J. Christopher, additional, de la Morena, Maite, additional, Demmler-Harrison, Gail J., additional, DeMuri, Gregory P., additional, Despommier, Dickson D., additional, Diefenbach, Karen A., additional, Edwards, Kathryn M., additional, Edwards, Morven S., additional, Eichenfield, Lawrence F., additional, Elston, Dirk M., additional, Emerson, Beth, additional, Ephros, Moshe, additional, Erdem, Guliz, additional, Eremeeva, Marina E., additional, Ericson, Jessica E., additional, Esposito, Douglas H., additional, Farley, Monica M., additional, Feingold, Anat R., additional, Feja, Kristina N., additional, Finn, Adam, additional, Fischer, Marc, additional, Flynn, Patricia M., additional, Fox, LeAnne M., additional, Frank, Michael M., additional, Fredrick, Douglas R., additional, Frenck, Robert W., additional, Friedlander, Sheila Fallon, additional, Gans, Hayley A., additional, Gauthier, Gregory M., additional, Gerber, Jeffrey S., additional, Gigliotti, Francis, additional, Gilger, Mark A., additional, Glaser, Carol A., additional, Goddard, Amanda F., additional, Gold, Benjamin D., additional, Gould, Jane M., additional, Green, Michael, additional, Greenberg, David, additional, Greywal, Tanya, additional, Griffin, Daniel, additional, Griffin, Patricia M., additional, Grom, Alexei A., additional, Gutierrez, Kathleen, additional, Gutman, Julie, additional, Guzman-Cottrill, Judith A., additional, Hall, Aron J., additional, Han, Jin-Young, additional, Harper, Marvin B., additional, Harris, Julie R., additional, Harrison, Christopher J., additional, Haslam, David B., additional, Hawkes, Sarah J., additional, Hendley, J. Owen, additional, Henry, Marion C.W., additional, Hilinski, Joseph A., additional, Hills, Susan L., additional, Holmberg, Scott D., additional, Holtzman, Deborah, additional, Hong, David K., additional, Hotez, Peter J., additional, Hsu, Katherine K., additional, Hunstad, David A., additional, Hwang, Loris Y., additional, Jackson, Mary Anne, additional, Jacobs, Richard F., additional, Jhaveri, Ravi, additional, Jirků-Pomajbíková, Kateřina, additional, Jones, Jeffrey L., additional, Karki, Mahima, additional, Karlowicz, M. Gary, additional, Katz, Ben Z., additional, Kaur, Ishminder, additional, Kersh, Gilbert J., additional, Keystone, Jay S., additional, Khan, Muhammad Ali, additional, Kimberlin, David W., additional, Kleiman, Martin B., additional, Klein, Bruce S., additional, Klontz, Karl, additional, Knust, Barbara, additional, Koh, Andrew Y., additional, Korgenski, E. Kent, additional, Krogstad, Paul, additional, Kutty, Preeta Krishnan, additional, Lauren, Christine T., additional, Lawrence, Hillary S., additional, Leber, Amy, additional, Lee, Grace M., additional, Leibovitz, Eugene, additional, Leshem, Eyal, additional, Levasseur, Stéphanie, additional, Lewis, David B., additional, Livingston, Robyn A., additional, Llata, Eloisa, additional, Long, Sarah S., additional, Lopman, Ben A., additional, Lucero, Yalda C., additional, Luján-Zilbermann, Jorge, additional, Luzuriaga, Katherine, additional, MacDonald, Noni E., additional, Maldonado, Yvonne A., additional, Manaloor, John, additional, Mani, Chitra S., additional, Manthiram, Kalpana, additional, Marshall, Gary S., additional, Martin, Stacey W., additional, Matanock, Almea, additional, Matiz, Catalina, additional, Mawle, Alison C., additional, Mazzulli, Tony, additional, McGann, Kathleen A., additional, McIntosh, Kenneth, additional, McNamara, Lucy A., additional, Meir, Michal, additional, Meislich, Debrah, additional, Meissner, H. Cody, additional, Meites, Elissa, additional, Mejías, Asunción, additional, Mertsola, Jussi, additional, Messacar, Kevin, additional, Mhaissen, Mohammed Nael, additional, Michaels, Marian G., additional, Miller, Melissa B., additional, Mintz, Eric D., additional, Modlin, John F., additional, Mohan, Parvathi, additional, Montgomery, Susan P., additional, Montoya, José G., additional, Moro, Pedro L., additional, Moscicki, Anna-Barbara, additional, Moss, R. Lawrence, additional, Myers, Angela L., additional, Nadel, Simon, additional, Neely, Michael N., additional, Neil, Karen P., additional, Nelson, Joanna, additional, Nelson, Noele P., additional, Nicholson, William L., additional, Nizet, Victor, additional, Nopper, Amy Jo, additional, Ochoa, Theresa J., additional, Orenstein, Walter A., additional, O'Ryan, Miguel, additional, Paddock, Christopher D., additional, Pall, Harpreet, additional, Panuganti, Suresh Kumar, additional, Pappas, Diane E., additional, Pass, Robert F., additional, Patterson, Thomas F., additional, Patton, Monica E., additional, Pelton, Stephen I., additional, Petersen, Brett W., additional, Pickering, Larry K., additional, Pinninti, Swetha, additional, Planet, Paul J., additional, Pollard, Andrew J., additional, Posfay-Barbe, Klara M., additional, Poulsen, Casper S., additional, Poutanen, Susan M., additional, Powers, Ann M., additional, Prober, Charles G., additional, Ramilo, Octavio, additional, Rangel, Shawn J., additional, Rao, Suchitra, additional, Rawstron, Sarah A., additional, Read, Jennifer S., additional, Reed, Michael D., additional, Relich, Ryan F., additional, Reller, Megan E., additional, Rellosa, Neil, additional, Rempe, Katherine A., additional, Reyes, Melissa A., additional, Rice-Townsend, Samuel E., additional, Richards, Frank O., additional, Romero, José R., additional, Rosen, David A., additional, Rostad, Christina A., additional, Rours, G. Ingrid J.G., additional, Routh, Janell A., additional, Rowley, Anne H., additional, Rubin, Lorry G., additional, Ryan, Edward T., additional, Saiman, Lisa, additional, Sammons, Julia S., additional, Sass, Laura, additional, Sauberan, Jason B., additional, Schillie, Sarah, additional, Schulert, Grant S., additional, Schuster, Jennifer E., additional, Schwartz, Kevin L., additional, Sederdahl, Bethany K., additional, Serpa, Jose A., additional, Shah, Kara N., additional, Shah, Samir S., additional, Shane, Andi L., additional, Shapiro, Eugene D., additional, Shaw, Jana, additional, Shetty, Avinash K., additional, Dairiki, Linda M., additional, Siberry, George Kelly, additional, Siegel, Jane D., additional, Siegel, Robert David, additional, Simonsen, Kari A., additional, Singh, Nalini, additional, Singh, Upinder, additional, Smith, P. Brian, additional, Snyder, John D., additional, Song, Eunkyung, additional, Sorrell, Jennifer L., additional, Souder, Emily, additional, St. Geme, Joseph W., additional, Staat, Mary Allen, additional, Staples, J. Erin, additional, Starke, Jeffrey R., additional, Steinbach, William J., additional, Stensvold, Christen R., additional, Stoner, Bradley P., additional, Strikas, Raymond A., additional, Strober, Jonathan B., additional, Sue, Paul K., additional, Sutton, Deanna A., additional, Swanson, Douglas, additional, Tate, Jacqueline E., additional, Tebruegge, Marc, additional, Teshale, Eyasu H., additional, Thompson, Amelia B., additional, Thompson, George R., additional, Thompson-Stone, Robert, additional, Thomson, Richard B., additional, Thorell, Emily A., additional, Tobin, Nicole H., additional, Toltzis, Philip, additional, Treat, James, additional, Troy, Stephanie B., additional, Van, Russell B., additional, Vaz, Louise Elaine, additional, Vodzak, Jennifer, additional, Wald, Ellen R., additional, Wallihan, Rebecca, additional, Wangu, Zoon, additional, Washam, Matthew, additional, Watson, Joshua R., additional, Wattier, Rachel L., additional, Weinberg, Geoffrey A., additional, White, A. Clinton, additional, Wiesenfeld, Harold C., additional, Williams, John V., additional, Willoughby, Rodney E., additional, Wingerter, Sarah L., additional, Wittler, Robert R., additional, Wong, Karen K., additional, Workowski, Kimberly A., additional, Wright, Terry W., additional, Yagupsky, Pablo, additional, Yen, Catherine, additional, Yi, Jumi, additional, Yoder, Jonathan S., additional, Young, Edward J., additional, Zaenglein, Andrea L., additional, and Zimmerman, Kanecia, additional

Published
2018
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47. Dynamics of the MRSA Population in A Chilean Hospital: A Phylogenomic Analysis (2000-2016)

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Martínez, José RW, primary, Planet, Paul J., additional, Maria, Spencer-Sandino, additional, Lina, Rivas, additional, Lorena, Díaz, additional, Ana, Quesille-Villalobos, additional, Roberto, Riquelme-Neira, additional, Manuel, Alcalde-Rico, additional, Blake, Hanson, additional, Carvajal, Lina P, additional, Sandra, Rincón, additional, Jinnethe, Reyes, additional, Marusella, Lam, additional, Rafael, Araos, additional, Patricia, García, additional, Arias, César A., additional, and Munita, José M., additional

Published
2023
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