396 results on '"Pearson, Talima"'
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2. Natural reversion promotes LPS elongation in an attenuated Coxiella burnetii strain
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Long, Carrie M., Beare, Paul A., Cockrell, Diane, Binette, Picabo, Tesfamariam, Mahelat, Richards, Crystal, Anderson, Matthew, McCormick-Ell, Jessica, Brose, Megan, Anderson, Rebecca, Omsland, Anders, Pearson, Talima, and Heinzen, Robert A.
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- 2024
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3. Domestic dogs in indigenous Amazonian communities: Key players in Leptospira cycling and transmission?
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Guzmán, Diego A., primary, Diaz, Eduardo, additional, Sáenz, Carolina, additional, Álvarez, Hernán, additional, Cueva, Rubén, additional, Zapata-Ríos, Galo, additional, Prado-Vivar, Belén, additional, Falconí, Mercy, additional, Pearson, Talima, additional, and Barragan, Veronica, additional
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- 2024
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4. SaQuant: a real-time PCR assay for quantitative assessment of Staphylococcus aureus
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Wood, Colin, Sahl, Jason, Maltinsky, Sara, Coyne, Briana, Russakoff, Benjamin, Yagüe, David Panisello, Bowers, Jolene, and Pearson, Talima
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- 2021
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5. Leptospira in river and soil in a highly endemic area of Ecuador
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Miller, Erin, Barragan, Veronica, Chiriboga, Jorge, Weddell, Chad, Luna, Ligia, Jiménez, Dulce J., Aleman, John, Mihaljevic, Joseph R., Olivas, Sonora, Marks, Jane, Izurieta, Ricardo, Nieto, Nathan, Keim, Paul, Trueba, Gabriel, Caporaso, J. Gregory, and Pearson, Talima
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- 2021
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6. Comparative Phylogenomics and Evolution of the Brucellae Reveal a Path to Virulence
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Wattam, Alice R, Foster, Jeffrey T, Mane, Shrinivasrao P, Beckstrom-Sternberg, Stephen M, Beckstrom-Sternberg, James M, Dickerman, Allan W, Keim, Paul, Pearson, Talima, Shukla, Maulik, Ward, Doyle V, Williams, Kelly P, Sobral, Bruno W, Tsolis, Renee M, Whatmore, Adrian M, and O'Callaghan, David
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Microbiology ,Biological Sciences ,Biomedical and Clinical Sciences ,Emerging Infectious Diseases ,Infectious Diseases ,Biotechnology ,Prevention ,Vaccine Related ,Biodefense ,Genetics ,Aetiology ,2.2 Factors relating to the physical environment ,Infection ,Bacterial Proteins ,Biological Evolution ,Brucellaceae ,Gene Expression Regulation ,Bacterial ,Genome ,Bacterial ,Genomics ,Phylogeny ,Virulence ,Agricultural and Veterinary Sciences ,Medical and Health Sciences ,Agricultural ,veterinary and food sciences ,Biological sciences ,Biomedical and clinical sciences - Abstract
Brucella species include important zoonotic pathogens that have a substantial impact on both agriculture and human health throughout the world. Brucellae are thought of as "stealth pathogens" that escape recognition by the host innate immune response, modulate the acquired immune response, and evade intracellular destruction. We analyzed the genome sequences of members of the family Brucellaceae to assess its evolutionary history from likely free-living soil-based progenitors into highly successful intracellular pathogens. Phylogenetic analysis split the genus into two groups: recently identified and early-dividing "atypical" strains and a highly conserved "classical" core clade containing the major pathogenic species. Lateral gene transfer events brought unique genomic regions into Brucella that differentiated them from Ochrobactrum and allowed the stepwise acquisition of virulence factors that include a type IV secretion system, a perosamine-based O antigen, and systems for sequestering metal ions that are absent in progenitors. Subsequent radiation within the core Brucella resulted in lineages that appear to have evolved within their preferred mammalian hosts, restricting their virulence to become stealth pathogens capable of causing long-term chronic infections.
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- 2014
7. Phylogeography of Bacillus anthracis in the country of Georgia shows evidence of population structuring and is dissimilar to other regional genotypes.
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Khmaladze, Ekaterine, Birdsell, Dawn N, Naumann, Amber A, Hochhalter, Christian B, Seymour, Meagan L, Nottingham, Roxanne, Beckstrom-Sternberg, Stephen M, Beckstrom-Sternberg, James, Nikolich, Mikeljon P, Chanturia, Gvantsa, Zhgenti, Ekaterine, Zakalashvili, Mariam, Malania, Lile, Babuadze, Giorgi, Tsertsvadze, Nikoloz, Abazashvili, Natalia, Kekelidze, Merab, Tsanava, Shota, Imnadze, Paata, Ganz, Holly H, Getz, Wayne M, Pearson, Ofori, Gajer, Pawel, Eppinger, Mark, Ravel, Jacques, Wagner, David M, Okinaka, Richard T, Schupp, James M, Keim, Paul, and Pearson, Talima
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Humans ,Bacillus anthracis ,Anthrax ,Phylogeny ,Polymorphism ,Single Nucleotide ,Georgia ,Phylogeography ,General Science & Technology - Abstract
Sequence analyses and subtyping of Bacillus anthracis strains from Georgia reveal a single distinct lineage (Aust94) that is ecologically established. Phylogeographic analysis and comparisons to a global collection reveals a clade that is mostly restricted to Georgia. Within this clade, many groups are found around the country, however at least one subclade is only found in the eastern part. This pattern suggests that dispersal into and out of Georgia has been rare and despite historical dispersion within the country, for at least for one lineage, current spread is limited.
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- 2014
8. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
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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
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- 2019
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9. Phylogenetic Discovery Bias in Bacillus anthracis Using Single-Nucleotide Polymorphisms from Whole-Genome Sequencing
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Pearson, Talima, Busch, Joseph D., Ravel, Jacques, Read, Timothy D., Rhoton, Shane D., Simonson, Tatum S., Kachur, Sergey M., Leadem, Rebecca R., Cardon, Michelle L., Van Ert, Matthew N., Huynh, Lynn Y., Fraser, Claire M., Keim, Paul, and Falkow, Stanley
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- 2004
10. Cross-sectional study of the association of social relationship resources with Staphylococcus aureus colonization in naturally occurring social groups along the US/Mexico border
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Barger, Steven D., primary, Lininger, Monica R., additional, Trotter, Robert T., additional, Mbegbu, Mimi, additional, Kyman, Shari, additional, Tucker-Morgan, Kara, additional, Wood, Colin, additional, Coyne, Briana, additional, Russakoff, Benjamin, additional, Ceniceros, Kathya, additional, Padilla, Cristina, additional, Maltinsky, Sara, additional, and Pearson, Talima, additional
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- 2023
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11. First detection of Leptospira santarosai in the reproductive track of a boar: A potential threat to swine production and public health
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Diaz, Eduardo A., primary, Luna, Ligia, additional, Burgos-Mayorga, Ana, additional, Donoso, Gustavo, additional, Guzman, Diego A., additional, Baquero, María Ines, additional, Pearson, Talima, additional, and Barragan, Veronica Alexandra, additional
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- 2022
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12. Diverse lineages of pathogenic Leptospira species are widespread in the environment in Puerto Rico, USA
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Stone, Nathan E., primary, Hall, Carina M., additional, Ortiz, Marielisa, additional, Hutton, Shelby M., additional, Santana-Propper, Ella, additional, Celona, Kimberly R., additional, Williamson, Charles H. D., additional, Bratsch, Nicole, additional, Fernandes, Luis G. V., additional, Busch, Joseph D., additional, Pearson, Talima, additional, Rivera-Garcia, Sarai, additional, Soltero, Fred, additional, Galloway, Renee, additional, Sahl, Jason W., additional, Nally, Jarlath E., additional, and Wagner, David M., additional
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- 2022
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13. When Outgroups Fail; Phylogenomics of Rooting the Emerging Pathogen, Coxiella burnetii
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Pearson, Talima, Hornstra, Heidie M., Sahl, Jason W., Schaack, Sarah, Schupp, James M., Beckstrom-Sternberg, Stephen M., O'Neill, Matthew W., Priestley, Rachael A., Champion, Mia D., Beckstrom-Sternberg, James S., Kersh, Gilbert J., Samuel, James E., Massung, Robert F., and Keim, Paul
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- 2013
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14. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
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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
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- 2019
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15. Francisella tularensis subsp. tularensis group A.I, United States
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Birdsell, Dawn N., Johansson, Anders, Ohrman, Caroline, Kaufman, Emily, Molins, Claudia, Pearson, Talima, Gyuranecz, Miklos, Naumann, Amber, Vogler, Amy J., Myrtennas, Kerstin, Larsson, Par, Forsman, Mats, Sjodin, Andreas, Gillece, John D., Schupp, James, Petersen, Jeannine M., Keim, Paul, and Wagner, David M.
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Francisella tularensis -- Health aspects ,Tularemia -- Causes of -- Care and treatment -- Patient outcomes -- Genetic aspects ,Phylogeny -- Analysis ,Health - Abstract
Tularemia, caused by the bacterium Francisella tularensis, is a potentially severe disease that often causes unspecific symptoms; because of its low infectious dose and ease of dissemination, F. tularensis is [...]
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- 2014
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16. Genome Sequences of Community Carriage Strains of Staphylococcus aureus from Yuma, Arizona
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Pearson, Talima, primary, Hepp, Crystal, additional, Trotter, Robert T., additional, Mbegbu, Mimi, additional, Russakoff, Benjamin, additional, Panisello Yagüe, David, additional, Wood, Colin, additional, Tucker-Morgan, Kara, additional, Ceniceros, Kathya, additional, Padilla, Cristina, additional, Kyman, Shari, additional, and Villa, Francisco, additional
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- 2021
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17. Impact Of Different Exercise Modalities On The Human Gut Microbiome
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Bycura, Dierdra, primary, Santos, Anthony, additional, Shiffer, Arron, additional, Kyman, Shari, additional, Winfree, Kyle, additional, Sutliffe, Jay, additional, Pearson, Talima, additional, Sonderegger, Derek, additional, Cope, Emily, additional, and Caporaso, J Greg, additional
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- 2021
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18. Molecular epidemiologic investigation of an anthrax outbreak among heroin users, Europe
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Price, Erin P., Seymour, Meagan L., Sarovich, Derek S., Latham, Jennie, Wolken, Spenser R., Mason, Joanne, Vincent, Gemma, Drees, Kevin P., Beckstrom-Sternberg, Stephen M., Phillippy, Adam M., Koren, Sergey, Okinaka, Richard T., Chung, Wai-Kwan, Schupp, James M., Wagner, David M., Vipond, Richard, Foster, Jeffrey T., Bergman, Nicholas H., Burans, James, Pearson, Talima, Brooks, Tim, and Keim, Paul
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Illumina Inc. -- Investigations ,Biotechnology industry -- Investigations ,Genomes -- Investigations ,Anthrax -- Investigations ,Company legal issue ,Health - Abstract
Bacillus anthracis is a gram-positive endosporeforming bacterium that causes the disease anthrax in livestock, wildlife, and humans. Because of its hardy spores, B. anthracis can survive for extended periods in [...]
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- 2012
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19. Molecular epidemiology of glanders, Pakistan
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Hornstra, Heidie, Pearson, Talima, Georgia, Shalamar, Liguori, Andrew, Dale, Julia, Price, Erin, ONeill, Matthew, DeShazer, David, Muhammad, Ghulam, Saqib, Muhammad, Naureen, Abeera, and Keim, Paul
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Infection -- Health aspects ,Epidemiology -- Health aspects ,Horses -- Health aspects - Abstract
Glanders is an equine disease that was recognized by Hippocrates and Aristotle (1). It is caused by the bacterium Burkholderia mallei, an obligate pathogen of horses, donkeys, and mules (Equidae), [...]
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- 2009
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20. Whole-genome-based phylogeny and divergence of the genus Brucella
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Foster, Jeffrey T., Beckstrom-Sternberg, Stephen M., Pearson, Talima, Beckstrom-Sternberg, James S., Chain, Patrick S.G., Roberto, Francisco F., Hnath, Jonathan, Brettin, Tom, and Keim, Paul
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Phylogeny -- Research ,Biological sciences - Abstract
Brucellae are worldwide bacterial pathogens of livestock and wildlife, but phylogenetic reconstructions have been challenging due to limited genetic diversity. We assessed the taxonomic and evolutionary relationships of five Brucella species--Brucella abortus, B. melitensis, B. suis, B. canis, and B. ovis--using whole-genome comparisons. We developed a phylogeny using single nucleotide polymorphisms (SNPs) from 13 genomes and rooted the tree using the closely related soil bacterium and opportunistic human pathogen, Ochrobactrum anthropi. Whole-genome sequencing and a SNP-based approach provided the requisite level of genetic detail to resolve species in the highly conserved brucellae. Comparisons among the Brucella genomes revealed 20,154 orthologous SNPs that were shared in all genomes. Rooting with Ochrobactrum anthropi reveals that the B. ovis lineage is basal to the rest of the Brucella lineage. We found that B. suis is a highly divergent clade with extensive intraspecific genetic diversity. Furthermore, B. suis was determined to be paraphyletic in our analyses, only forming a monophyletic clade when the B. canis genome was included. Using a molecular clock with these data suggests that most Brucella species diverged from their common B. ovis ancestor in the past 86,000 to 296,000 years, which precedes the domestication of their livestock hosts. Detailed knowledge of the Brucella phylogeny will lead to an improved understanding of the ecology, evolutionary history, and host relationships for this genus and can be used for determining appropriate genotyping approaches for rapid detection and diagnostic assays for molecular epidemiological and clinical studies.
- Published
- 2009
21. Phylogeography of Francisella tularensis: global expansion of a highly fit clone
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Vogler, Amy J., Birdsell, Dawn, Price, Lance B., Bowers, Jolene R., Beckstrom-Sternberg, Stephen M., Auerbach, Raymond K., Beckstrom-Sternberg, James S., Johansson, Anders, Clare, Ashley, Buchhagen, Jordan L., Petersen, Jeannine M., Pearson, Talima, Vaissaire, Josee, Dempsey, Michael P., Foxall, Paul, Engelthaler, David M., Wagner, David M., and Keim, Paul
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Francisella tularensis -- Genetic aspects ,Phylogeny -- Research ,Biological sciences - Abstract
Francisella tularensis contains several highly pathogenic subspecies, including Francisella tularensis subsp. holarctica, whose distribution is circumpolar in the northern hemisphere. The phylogeography of these subspecies and their subclades was examined using whole-genome single nucleotide polymorphism (SNP) analysis, high-density microarray SNP genotyping, and real-time-PCR-based canonical SNP (canSNP) assays. Almost 30,000 SNPs were identified among 13 whole genomes for phylogenetic analysis. We selected 1,655 SNPs to genotype 95 isolates on a high-density microarray platform. Finally, 23 clade- and subclade-specific canSNPs were identified and used to genotype 496 isolates to establish global geographic genetic patterns. We confirm previous findings concerning the four subspecies and two Francisella tularensis subsp. tularensis subpopulations and identify additional structure within these groups. We identify 11 subclades within F. tularensis subsp. holarctica, including a new, genetically distinct subclade that appears intermediate between Japanese F. tularensis subsp. holarctica isolates and the common F. tularensis subsp. holarctica isolates associated with the radiation event (the B radiation) wherein this subspecies spread throughout the northern hemisphere. Phylogenetic analyses suggest a North American origin for this B-radiation clade and multiple dispersal events between North America and Eurasia. These findings indicate a complex transmission history for F. tularensis subsp. holarctica.
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- 2009
22. Identification of melioidosis outbreak by multilocus variable number tandem repeat analysis
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Currie, Bart J., Haslem, Asha, Pearson, Talima, Hornstra, Heidie, Leadem, Benjamin, Mayo, Mark, Gal, Daniel, Ward, Linda, Godoy, Daniel, Spratt, Brian G., and Keim, Paul
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Pseudomonas infections -- Analysis ,Biological warfare -- Analysis - Abstract
Endemic melioidosis is caused by genetically diverse Burkholderia pseudomallei strains. However, clonal outbreaks (multiple cases caused by 1 strain) have occurred, such as from contaminated potable water. B. pseudomallei is [...]
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- 2009
23. Single nucleotide polymorphism typing of Bacillus anthracis from Sverdlovsk tissue
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Okinaka, Richard T., Henrie, Melinda, Hill, Karen K., Lowery, Kristin S., Van Ert, Matthew, Pearson, Talima, Schupp, James, Kenefic, Leo, Beaudry, Jodi, Hofstadler, Steven A., Jackson, Paul J., and Keim, Paul
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Bacillus anthracis -- Genetic aspects ,Bacillus anthracis -- Research ,Single nucleotide polymorphisms -- Health aspects ,Single nucleotide polymorphisms -- Research - Abstract
A small number of conserved canonical single nucleotide polymorphisms (canSNP) that define major phylogenetic branches for Bacillus anthracis were used to place a Sverdlovsk patient's B. anthracis genotype into 1 [...]
- Published
- 2008
24. A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions
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Tuanyok, Apichai, Auerbach, Raymond K., Brettin, Thomas S., Bruce, David C., Munk, A. Christine, Detter, J. Chris, Pearson, Talima, Hornstra, Heidie, Sermswan, Rasana W., Wuthiekanun, Vanaporn, Peacock, Sharon J., Currie, Bart J., Keim, Paul, and Wagner, David M.
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Bacterial genetics -- Research ,Gram-negative bacteria -- Genetic aspects ,Gram-negative bacteria -- Distribution ,Gram-negative bacteria -- Varieties ,Genetic transformation -- Research ,Company distribution practices ,Biological sciences - Abstract
Burkholderia pseudomallei is the etiologic agent of melioidosis. Many disease manifestations are associated with melioidosis, and the mechanisms causing this variation are unknown; genomic differences among strains offer one explanation. We compared the genome sequences of two strains of B. pseudomallei: the original reference strain K96243 from Thailand and strain MSHR305 from Australia. We identified a variable homologous region between the two strains. This region was previously identified in comparisons of the genome of B. pseudomallei strain K96243 with the genome of strain E264 from the closely related B. thailandensis. In that comparison, K96243 was shown to possess a horizontally acquired Yersinia-like fimbrial (YLF) gene cluster. Here, we show that the homologous genomic region in B. pseudomallei strain 305 is similar to that previously identified in B. thailandensis strain E264. We have named this region in B. pseudomallei strain 305 the B. thailandensis-like flagellum and chemotaxis (BTFC) gene cluster. We screened for these different genomic components across additional genome sequences and 571 B. pseudomallei DNA extracts obtained from regions of endemicity. These alternate genomic states define two distinct groups within B. pseudomallei: all strains contained either the BTFC gene cluster (group BTFC) or the YLF gene cluster (group YLF). These two groups have distinct geographic distributions: group BTFC is dominant in Australia, and group YLF is dominant in Thailand and elsewhere. In addition, clinical isolates are more likely to belong to group YLF, whereas environmental isolates are more likely to belong to group BTFC. These groups should be further characterized in an animal model.
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- 2007
25. Fine-scale genetic diversity among Burkholderia pseudomallei soil isolates in northeast Thailand
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U'Ren, Jana M., Hornstra, Heidie, Pearson, Talima, Schupp, James M., Leadem, Benjamin, Georgia, Shalamar, Sermswam, Rasana W., and Keim, Paul
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Bacteria -- Research ,Bacteria -- Genetic aspects ,Genotype -- Observations ,Biological sciences - Abstract
Burkholderia pseudomallei soil isolates from northeast Thailand are genotyped using multiple-locus variable number tandem repeat analysis (MLVA) and multilocus sequence typing (MLST). MLVA identified 19 genotypes within three clades, while MLST revealed two genotypes.
- Published
- 2007
26. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
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Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, 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, 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, Caporaso, J. Gregory, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, 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, 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
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- 2020
27. Predicting the current and future distribution of the western black-legged tick, Ixodes pacificus, across the Western US using citizen science collections
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Porter, W. Tanner, primary, Barrand, Zachary A., additional, Wachara, Julie, additional, DaVall, Kaila, additional, Mihaljevic, Joseph R., additional, Pearson, Talima, additional, Salkeld, Daniel J., additional, and Nieto, Nathan C., additional
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- 2021
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28. Educational Attainment and Staphylococcus aureus Colonization in a Hispanic Border Community: Testing Fundamental Cause Theory
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Barger, Steven D., primary, Lininger, Monica R., additional, Trotter, Robert T., additional, Wayment, Heidi A., additional, Mbegbu, Mimi, additional, Kyman, Shari, additional, and Pearson, Talima, additional
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- 2020
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29. Draft Genome Sequence of a Streptococcus suis Isolate from a Case of Cattle Meningitis
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Okwumabua, Ogi, primary, Williamson, Charles H. D., additional, Pearson, Talima R., additional, and Sahl, Jason W., additional
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- 2020
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30. Pathogen to commensal? Longitudinal within-host population dynamics, evolution, and adaptation during a chronic >16-year Burkholderia pseudomallei infection
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Pearson, Talima, primary, Sahl, Jason W., additional, Hepp, Crystal M., additional, Handady, Karthik, additional, Hornstra, Heidie, additional, Vazquez, Adam J., additional, Settles, Erik, additional, Mayo, Mark, additional, Kaestli, Mirjam, additional, Williamson, Charles H. D., additional, Price, Erin P., additional, Sarovich, Derek S., additional, Cook, James M., additional, Wolken, Spenser R., additional, Bowen, Richard A., additional, Tuanyok, Apichai, additional, Foster, Jeffrey T., additional, Drees, Kevin P., additional, Kidd, Timothy J., additional, Bell, Scott C., additional, Currie, Bart J., additional, and Keim, Paul, additional
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- 2020
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31. Selective whole genome amplification and sequencing of Coxiella burnetii directly from environmental samples
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Cocking, Jill Hager, primary, Deberg, Michael, additional, Schupp, Jim, additional, Sahl, Jason, additional, Wiggins, Kristin, additional, Porty, Ariel, additional, Hornstra, Heidie M., additional, Hepp, Crystal, additional, Jardine, Claire, additional, Furstenau, Tara N., additional, Schulte-Hostedde, Albrecht, additional, Fofanov, Viacheslav Y., additional, and Pearson, Talima, additional
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- 2020
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32. Author Correction:Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 (Nature Biotechnology, (2019), 37, 8, (852-857), 10.1038/s41587-019-0209-9)
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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, 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, Caporaso, J. Gregory, 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, 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
- Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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- 2019
33. Epidemiology and investigation of melioidosis, southern Arizona
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Stewart, Tasha, Engelthaler, David M., Blaney, David D., Tuanyok, Apichai, Wangsness, Eric, Smith, Theresa L., Pearson, Talima, Komatsu, Kenneth K., Keim, Paul, Currie, Bart J., Levy, Craig, and Sunenshine, Rebecca
- Subjects
Pseudomonas infections -- Health aspects -- Investigations ,Infection -- Health aspects -- Investigations ,Disease transmission -- Health aspects -- Investigations ,Epidemiology -- Health aspects -- Investigations ,Company legal issue ,Health - Abstract
Burkholderia pseudomallei is endemic to Southeast Asia and northern Australia; the organism has also been identified on other continents and islands but not North America (1). B. pseudomallei is present [...]
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- 2011
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34. Texas isolates closely related to Bacillus anthracis Ames
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Kenefic, Leo J., Pearson, Talima, Okinaka, Richard T., Chung, Wai-Kwan, Max, Tamara, Van Ert, Matthew N., Marston, Chung K., Gutierrez, Kathy, Swinford, Amy K., Hoffmaster, Alex R., and Keim, Paul
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Bacillus anthracis -- Identification and classification ,Bacillus anthracis -- Health aspects ,Bacillus anthracis -- Research ,Nucleotide sequencing -- Methods ,Nucleotide sequencing -- Health aspects ,Single nucleotide polymorphisms -- Physiological aspects ,Single nucleotide polymorphisms -- Research - Abstract
To the Editor: Forensic and epidemiologic investigation of the 2001 bioterrorism-associated anthrax attacks used multiple-locus variable-number tandem-repeat analysis (MLVA) to identify the attack strain as Ames (1). Strain identity was [...]
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- 2008
35. Genotyping of Brucella species using clade specific SNPs
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Foster Jeffrey T, Price Lance B, Beckstrom-Sternberg Stephen M, Pearson Talima, Brown William D, Kiesling Danika M, Allen Christina A, Liu Cindy M, Beckstrom-Sternberg James, Roberto Frank F, and Keim Paul
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Microbiology ,QR1-502 - Abstract
Abstract Background Brucellosis is a worldwide disease of mammals caused by Alphaproteobacteria in the genus Brucella. The genus is genetically monomorphic, requiring extensive genotyping to differentiate isolates. We utilized two different genotyping strategies to characterize isolates. First, we developed a microarray-based assay based on 1000 single nucleotide polymorphisms (SNPs) that were identified from whole genome comparisons of two B. abortus isolates , one B. melitensis, and one B. suis. We then genotyped a diverse collection of 85 Brucella strains at these SNP loci and generated a phylogenetic tree of relationships. Second, we developed a selective primer-extension assay system using capillary electrophoresis that targeted 17 high value SNPs across 8 major branches of the phylogeny and determined their genotypes in a large collection ( n = 340) of diverse isolates. Results Our 1000 SNP microarray readily distinguished B. abortus, B. melitensis, and B. suis, differentiating B. melitensis and B. suis into two clades each. Brucella abortus was divided into four major clades. Our capillary-based SNP genotyping confirmed all major branches from the microarray assay and assigned all samples to defined lineages. Isolates from these lineages and closely related isolates, among the most commonly encountered lineages worldwide, can now be quickly and easily identified and genetically characterized. Conclusions We have identified clade-specific SNPs in Brucella that can be used for rapid assignment into major groups below the species level in the three main Brucella species. Our assays represent SNP genotyping approaches that can reliably determine the evolutionary relationships of bacterial isolates without the need for whole genome sequencing of all isolates.
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- 2012
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36. Health Disparities in Staphylococcus aureus Transmission and Carriage in a Border Region of the United States Based on Cultural Differences in Social Relationships: Protocol for a Survey Study
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Pearson, Talima, primary, Barger, Steven D, additional, Lininger, Monica, additional, Wayment, Heidi, additional, Hepp, Crystal, additional, Villa, Francisco, additional, Tucker-Morgan, Kara, additional, Kyman, Shari, additional, Cabrera, Melissa, additional, Hurtado, Kevin, additional, Menard, Ashley, additional, Fulbright, Kelly, additional, Wood, Colin, additional, Mbegbu, Mimi, additional, Zambrano, Yesenia, additional, Fletcher, Annette, additional, Medina-Rodriguez, Sarah, additional, Manone, Mark, additional, Aguirre, Amanda, additional, Milner, Trudie, additional, and Trotter II, Robert T, additional
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- 2019
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37. Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development
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Pearson, Talima, primary, Caporaso, J. Gregory, additional, Yellowhair, Monica, additional, Bokulich, Nicholas A., additional, Padi, Megha, additional, Roe, Denise J., additional, Wertheim, Betsy C., additional, Linhart, Mark, additional, Martinez, Jessica A., additional, Bilagody, Cherae, additional, Hornstra, Heidie, additional, Alberts, David S., additional, Lance, Peter, additional, and Thompson, Patricia A., additional
- Published
- 2019
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38. An attenuated strain of Bacillus anthracis (CDC 684) has a large chromosomal inversion and altered growth kinetics
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Ivins Bruce E, Challacombe Jean, Hill Karen K, Munk Chris, Xie Gary, Pearson Talima, Chung Wai, Gruendike Jeffrey M, Wolken Spenser R, Price Erin P, Okinaka Richard T, Schupp James M, Beckstrom-Sternberg Stephen M, Friedlander Arthur, and Keim Paul
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background An isolate originally labeled Bacillus megaterium CDC 684 was found to contain both pXO1 and pXO2, was non-hemolytic, sensitive to gamma-phage, and produced both the protective antigen and the poly-D-glutamic acid capsule. These phenotypes prompted Ezzell et al., (J. Clin. Microbiol. 28:223) to reclassify this isolate to Bacillus anthracis in 1990. Results We demonstrate that despite these B. anthracis features, the isolate is severely attenuated in a guinea pig model. This prompted whole genome sequencing and closure. The comparative analysis of CDC 684 to other sequenced B. anthracis isolates and further analysis reveals: a) CDC 684 is a close relative of a virulent strain, Vollum A0488; b) CDC 684 defines a new B. anthracis lineage (at least 51 SNPs) that includes 15 other isolates; c) the genome of CDC 684 contains a large chromosomal inversion that spans 3.3 Mbp; d) this inversion has caused a displacement of the usual spatial orientation of the origin of replication (ori) to the termination of replication (ter) from 180° in wild-type B. anthracis to 120° in CDC 684 and e) this isolate also has altered growth kinetics in liquid media. Conclusions We propose two alternative hypotheses explaining the attenuated phenotype of this isolate. Hypothesis 1 suggests that the skewed ori/ter relationship in CDC 684 has altered its DNA replication and/or transcriptome processes resulting in altered growth kinetics and virulence capacity. Hypothesis 2 suggests that one or more of the single nucleotide polymorphisms in CDC 684 has altered the expression of a regulatory element or other genes necessary for virulence.
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- 2011
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39. Phylogeography of Francisella tularensis subspecies holarctica from the country of Georgia
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Busch Joseph D, Kaufman Emily L, Pettus Amanda H, Farlow Jason, Gyuranecz Miklos, Sinari Shripad, Champion Mia D, Beckstrom-Sternberg James S, Beckstrom-Sternberg Stephen M, Imnadze Paata, Tsanava Shota, Tsertsvadze Nikoloz, Babuadze George, Zhgenti Ekaterine, Kekelidze Merab, Birdsell Dawn N, Chanturia Gvantsa, Pearson Talima, Foster Jeffrey T, Vogler Amy J, Wagner David M, and Keim Paul
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Microbiology ,QR1-502 - Abstract
Abstract Background Francisella tularensis, the causative agent of tularemia, displays subspecies-specific differences in virulence, geographic distribution, and genetic diversity. F. tularensis subsp. holarctica is widely distributed throughout the Northern Hemisphere. In Europe, F. tularensis subsp. holarctica isolates have largely been assigned to two phylogenetic groups that have specific geographic distributions. Most isolates from Western Europe are assigned to the B.Br.FTNF002-00 group, whereas most isolates from Eastern Europe are assigned to numerous lineages within the B.Br.013 group. The eastern geographic extent of the B.Br.013 group is currently unknown due to a lack of phylogenetic knowledge about populations at the European/Asian juncture and in Asia. In this study, we address this knowledge gap by describing the phylogenetic structure of F. tularensis subsp. holarctica isolates from the country of Georgia, and by placing these isolates into a global phylogeographic context. Results We identified a new genetic lineage of F. tularensis subsp. holarctica from Georgia that belongs to the B.Br.013 group. This new lineage is genetically and geographically distinct from lineages previously described from the B.Br.013 group from Central-Eastern Europe. Importantly, this new lineage is basal within the B.Br.013 group, indicating the Georgian lineage diverged before the diversification of the other known B.Br.013 lineages. Although two isolates from the Georgian lineage were collected nearby in the Ukrainian region of Crimea, all other global isolates assigned to this lineage were collected in Georgia. This restricted geographic distribution, as well as the high levels of genetic diversity within the lineage, is consistent with a relatively older origin and localized differentiation. Conclusions We identified a new lineage of F. tularensis subsp. holarctica from Georgia that appears to have an older origin than any other diversified lineages previously described from the B.Br.013 group. This finding suggests that additional phylogenetic studies of F. tularensis subsp. holarctica populations in Eastern Europe and Asia have the potential to yield important new insights into the evolutionary history and phylogeography of this broadly dispersed F. tularensis subspecies.
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- 2011
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40. Lack of evidence that ursodeoxycholic acids effects on the gut microbiome influence colorectal adenoma risk
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Pearson, Talima, Caporaso, J. Gregory, Yellowhair, Monica, Bokulich, Nicholas, Roe, Denise J., Wertheim, Betsy C., Linhart, Mark, Martinez, Jessica A., Bilagody, Cherae, Hornstra, Heidie, Alberts, David S., Lance, Peter, and Thompson, Patricia A.
- Abstract
Objective We previously reported that Ursodeoxycholic acid (UDCA), a therapeutic bile acid, reduces risk for advanced colorectal adenoma in men but not women. Interactions between the gut microbiome and fecal bile acid composition as a factor in colon cancer neoplasia have been postulated but evidence is limited to small cohorts and animal studies. Design Using banked stool samples collected as part of a phase III randomized clinical trial of UDCA for the prevention of colorectal neoplasia, we compared change in the microbiome composition after 3 years intervention in a subset of participants randomized to 8–10 mg/kg of body weight UDCA (n=198) to placebo (n=203). UDCA effects on the microbiome, sex and adenoma outcome were investigated. Results Study participants randomized to UDCA experienced compositional changes in their microbiome that were statistically more similar to other individuals in the UDCA arm than to those in the placebo arm. This change reflected an UDCA-associated shift in microbial community distance metrics (P 0.05). These UDCA-associated shifts in microbial community distance metrics from baseline to end-of-study were not associated with risk of any or advanced adenoma (all P> 0.05) in men or women. Conclusion Despite a large sampling of randomized clinical trial participants, daily UDCA use only modestly influenced the relative abundance of microbial species in stool with no evidence for effects of UDCA on stool microbial community composition as a modifier of colorectal adenoma risk.
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- 2017
41. Burkholderia pseudomallei distribution in Australasia is linked to paleogeographic and anthropogenic history
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Baker, Anthony L., primary, Pearson, Talima, additional, Sahl, Jason W., additional, Hepp, Crystal, additional, Price, Erin P., additional, Sarovich, Derek S., additional, Mayo, Mark, additional, Tuanyok, Apichai, additional, Currie, Bart J., additional, Keim, Paul, additional, and Warner, Jeffrey, additional
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- 2018
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42. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer
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Kaul Rajinder, Chang Jean, Wu Zaining, Pearson Ofori, Sim Siew, Okinaka Richard T, Wagner David M, Allan Gerard J, Foster Jeffrey T, Beckstrom-Sternberg James S, Leadem Benjamin, Glass Mindy B, Price Erin P, Tuanyok Apichai, Hornstra Heidie, Auerbach Raymond, Beckstrom-Sternberg Stephen, Giffard Philip, Pearson Talima, Hoffmaster Alex R, Brettin Thomas S, Robison Richard A, Mayo Mark, Gee Jay E, Tan Patrick, Currie Bart J, and Keim Paul
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Biology (General) ,QH301-705.5 - Abstract
Abstract Background Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer.
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- 2009
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43. Bacillus anthracis in China and its relationship to worldwide lineages
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Schupp James M, Beaudry Jodi, Kenefic Leo J, Zanecki Shaylan R, Dukerich Meghan, U'Ren Jana M, Huynh Lynn, Easterday W Ryan, Wang Bingxiang, Okinaka Richard T, Simonson Tatum S, Pearson Talima, Wagner David M, Hoffmaster Alex, Ravel Jacques, and Keim Paul
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Microbiology ,QR1-502 - Abstract
Abstract Background The global pattern of distribution of 1033 B. anthracis isolates has previously been defined by a set of 12 conserved canonical single nucleotide polymorphisms (canSNP). These studies reinforced the presence of three major lineages and 12 sub-lineages and sub-groups of this anthrax-causing pathogen. Isolates that form the A lineage (unlike the B and C lineages) have become widely dispersed throughout the world and form the basis for the geographical disposition of "modern" anthrax. An archival collection of 191 different B. anthracis isolates from China provides a glimpse into the possible role of Chinese trade and commerce in the spread of certain sub-lineages of this pathogen. Canonical single nucleotide polymorphism (canSNP) and multiple locus VNTR analysis (MLVA) typing has been used to examine this archival collection of isolates. Results The canSNP study indicates that there are 5 different sub-lineages/sub-groups in China out of 12 previously described world-wide canSNP genotypes. Three of these canSNP genotypes were only found in the western-most province of China, Xinjiang. These genotypes were A.Br.008/009, a sub-group that is spread across most of Europe and Asia; A.Br.Aust 94, a sub-lineage that is present in Europe and India, and A.Br.Vollum, a lineage that is also present in Europe. The remaining two canSNP genotypes are spread across the whole of China and belong to sub-group A.Br.001/002 and the A.Br.Ames sub-lineage, two closely related genotypes. MLVA typing adds resolution to the isolates in each canSNP genotype and diversity indices for the A.Br.008/009 and A.Br.001/002 sub-groups suggest that these represent older and established clades in China. Conclusion B. anthracis isolates were recovered from three canSNP sub-groups (A.Br.008/009, A.Br.Aust94, and A.Br.Vollum) in the western most portion of the large Chinese province of Xinjiang. The city of Kashi in this province appears to have served as a crossroads for not only trade but the movement of diseases such as anthrax along the ancient "silk road". Phylogenetic inference also suggests that the A.Br.Ames sub-lineage, first identified in the original Ames strain isolated from Jim Hogg County, TX, is descended from the A.Br.001/002 sub-group that has a major presence in most of China. These results suggest a genetic discontinuity between the younger Ames sub-lineage in Texas and the large Western North American sub-lineage spread across central Canada and the Dakotas.
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- 2009
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44. Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping
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Harvey Steven P, DeShazer David, Huynh Lynn Y, Cardon Michelle, Georgia Shalamar, Leadem Ben, Rhoton Shane D, Daugherty Rebecca, Smith Kimothy L, Friedman Christine, Hornstra Heidie, Pearson Talima, Schupp James M, U'Ren Jana M, Robison Richard, Gal Daniel, Mayo Mark J, Wagner David, Currie Bart J, and Keim Paul
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Microbiology ,QR1-502 - Abstract
Abstract Background The facultative, intracellular bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized tandem repeat arrays and their distribution throughout the genome of B. pseudomallei strain K96243 in order to develop a genetic typing method for B. pseudomallei. We then screened 104 of the potentially polymorphic loci across a diverse panel of 31 isolates including B. pseudomallei, B. mallei and B. thailandensis in order to identify loci with varying degrees of polymorphism. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to examine 66 B. pseudomallei and 21 B. mallei isolates from around the world, as well as 95 lineages from a serial transfer experiment encompassing ~18,000 generations. Results B. pseudomallei contains a preponderance of tandem repeat loci throughout its genome, many of which are duplicated elsewhere in the genome. The majority of these loci are composed of repeat motif lengths of 6 to 9 bp with 4 to 10 repeat units and are predominately located in intergenic regions of the genome. Across geographically diverse B. pseudomallei and B.mallei isolates, the 32 VNTR loci displayed between 7 and 28 alleles, with Nei's diversity values ranging from 0.47 and 0.94. Mutation rates for these loci are comparable (>10-5 per locus per generation) to that of the most diverse tandemly repeated regions found in other less diverse bacteria. Conclusion The frequency, location and duplicate nature of tandemly repeated regions within the B. pseudomallei genome indicate that these tandem repeat regions may play a role in generating and maintaining adaptive genomic variation. Multiple-locus VNTR analysis revealed extensive diversity within the global isolate set containing B. pseudomallei and B. mallei, and it detected genotypic differences within clonal lineages of both species that were identical using previous typing methods. Given the health threat to humans and livestock and the potential for B. pseudomallei to be released intentionally, MLVA could prove to be an important tool for fine-scale epidemiological or forensic tracking of this increasingly important environmental pathogen.
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- 2007
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45. Prevalence and strain identification of Coxiella burnetii on dairy goat farms and in associated wildlife
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Porty, Ariel, Jardine, Claire, Pearson, Talima, Menzies, Paula, Jones-Bitton, Andria, and Schulte‐Hostedde, Albrecht
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livestock ,Coxiella burnetii ,animal diseases ,wildlife ,transmission ,bacteria ,dairy goat ,bacterial infections and mycoses - Abstract
Presentation Abstract: To control Coxiella burnetii in goats and lower risk to humans, we need to determine the role wildlife may play. While the genotyping results for this project are still pending, we know that wildlife on the farms and in nearby natural areas are infected with C. burnetii. The genotyping results will help us get one step closer in identifying the role that wildlife play in the transmission of C. burnetii. In the event that wildlife are infected with the same bacterial strain as the dairy goats then we will suggest extra farm bio-security to prevent future transmission between livestock and wildlife. Managing this disease on the farm is not only important for livestock and other farm animals, but also for the farm producers. Laurentian University and Northern Arizona University
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- 2017
46. Corrigendum: Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity
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Fleshman, Amy, primary, Mullins, Kristin, additional, Sahl, Jason, additional, Hepp, Crystal, additional, Nieto, Nathan, additional, Wiggins, Kristin, additional, Hornstra, Heidie, additional, Kelly, Daryl, additional, Chan, Teik-Chye, additional, Phetsouvanh, Rattanaphone, additional, Dittrich, Sabine, additional, Panyanivong, Phonepasith, additional, Paris, Daniel, additional, Newton, Paul, additional, Richards, Allen, additional, and Pearson, Talima, additional
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- 2018
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47. Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity
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Fleshman, Amy, primary, Mullins, Kristin, additional, Sahl, Jason, additional, Hepp, Crystal, additional, Nieto, Nathan, additional, Wiggins, Kristin, additional, Hornstra, Heidie, additional, Kelly, Daryl, additional, Chan, Teik-Chye, additional, Phetsouvanh, Rattanaphone, additional, Dittrich, Sabine, additional, Panyanivong, Phonepasith, additional, Paris, Daniel, additional, Newton, Paul, additional, Richards, Allen, additional, and Pearson, Talima, additional
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- 2018
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48. Complete Genome Sequence of the Environmental Burkholderia pseudomallei Sequence Type 131 Isolate MSHR1435, Associated with a Chronic Melioidosis Infection
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Sahl, Jason W., primary, Mayo, Mark, additional, Price, Erin P., additional, Sarovich, Derek S., additional, Kaestli, Mirjam, additional, Pearson, Talima, additional, Williamson, Charles H. D., additional, Nottingham, Roxanne, additional, Sheridan, Krystal, additional, Wagner, David M., additional, Currie, Bart J., additional, and Keim, Paul, additional
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- 2018
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49. Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome
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Drees, Kevin P., primary, Lorch, Jeffrey M., additional, Puechmaille, Sebastien J., additional, Parise, Katy L., additional, Wibbelt, Gudrun, additional, Hoyt, Joseph R., additional, Sun, Keping, additional, Jargalsaikhan, Ariunbold, additional, Dalannast, Munkhnast, additional, Palmer, Jonathan M., additional, Lindner, Daniel L., additional, Marm Kilpatrick, A., additional, Pearson, Talima, additional, Keim, Paul S., additional, Blehert, David S., additional, and Foster, Jeffrey T., additional
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- 2017
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50. Critical Knowledge Gaps in Our Understanding of Environmental Cycling and Transmission of Leptospira spp
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Barragan, Veronica, primary, Olivas, Sonora, additional, Keim, Paul, additional, and Pearson, Talima, additional
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- 2017
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