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54. Polyclonal Campylobacter fetus Infections Among Unrelated Patients, Montevideo, Uruguay, 2013–2018

Author

Costa, Daniela, primary, Betancor, Laura, additional, Gadea, Pilar, additional, Cabezas, Laura, additional, Caiata, Leticia, additional, Palacio, Rosario, additional, Seija, Verónica, additional, Galiana, Antonio, additional, Vieytes, Mariela, additional, Cristophersen, Inés, additional, Calleros, Lucía, additional, and Iraola, Gregorio, additional

Published
2019
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57. Correction: The fecal, oral, and skin microbiota of children with Chagas disease treated with benznidazole

Author

Robello, Carlos, primary, Maldonado, Doris Patricia, additional, Hevia, Anna, additional, Hoashi, Marina, additional, Frattaroli, Paola, additional, Montacutti, Valentina, additional, Heguy, Adriana, additional, Dolgalev, Igor, additional, Mojica, Maricruz, additional, Iraola, Gregorio, additional, and Dominguez-Bello, Maria G., additional

Published
2019
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58. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

Author

Afshinnekoo, Ebrahim, Ahsanuddin, Sofia, Ghedin, Elodie, Read, Timothy, Fraser, Claire, Dudley, Joel, Bowler, Christopher, Mason, Christopher E., Chernomoretz, Ariel, Stolovitzky, Gustavo, Łabaj, Paweł P., Graf, Alexandra B., Darling, Aaron, Burke, Catherine, Noushmehr, Houtan, Dias-Neto, Emmanuel, Guo, Yongli, Xie, Zhi, Lee, Patrick K. H., Shi, Leming, Ruiz-Perez, Carlos A., Zambrano, Maria Mercedes, Siam, Rania, Ouf, Amged, Richard, Hugues, Lafontaine, Ingrid, Wieler, Lothar H., Semmler, Torsten, Prithiviraj, Bharath, Nedunuri, Narasimha, Mehr, Shaadi, Banihashemi, Kambiz, Lista, Florigio, Anselmo, Anna, Suzuki, Haruo, Kuroda, Makoto, Yamashita, Riu, Sato, Yukoto, Kaminuma, Eli, Aranda, Celia M. Alpuche, Martinez, Jesus, Dada, Christopher, Dybwad, Marius, Oliveira, Manuela, Schuster, Stephan, Siwo, Geoffrey H., Jang, Soojin, Seo, Sung Chul, Hwang, Sung Ho, Ossowski, Stephan, Bezdan, Daniela, Chaker, Salama, Chatziefthimiou, Aspassia D., Udekwu, Klas, Liungdahl, Per, Sezerman, Ugur, Meydan, Cem, Elhaik, Eran, Gonnet, Gaston, Schriml, Lynn M., Mongodin, Emmanuel, Huttenhower, Curtis, Gilbert, Jack, Eisen, Jonathan, Hirschberg, David, Hernandez, Mark, McGrath, Ken, McGrath, Leanne, Gray, Andrew, Osuolale, Olayinka, Segata, Nicola, Fillo, Silvia, Iraola, Gregorio, Zhou, Yiming, Chang, Yujun, Li, Yang, Zhend, Yuanting, Hou, Wanwan, Ramirez, Adan, Cepeda, Martha, Desnues, Christelle, Rascovan, Nicolas, Baron, Colin, Nagarajan, Niranjan, Ercolini, Danilo, Menary, Wayne, Tighe, Scott, Donia, Mohamed, Levy, Shawn, Benito, Joseph, Jones, Angela, Kasarskis, Andrew, Maritz, Julia, Jorgensen, Ellen, Neches, Russell, Livelli, Tom, Barnetche, Jesus Martinez, Pasolli, Edoardo, Greenfield, Nick, Hasan, Nur, Brownstein, John, Nozick, Linda, Michels, Harold, Schriml, Lynn, Brownstein, Catherine, Garbarino, Jeanne, Lyons, Abby, Zhu, Jeff, Genome Center [UC Davis], University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), American University in Cairo, Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Robert Koch Institute [Berlin] (RKI), Centre for Infection Medicine, Institute of Microbiology and Epizootics, Health Corps Italian Army, Department of Molecular Biology, Immunology and Experimental Medicine, Army Medical and Veterinary Research Center, Integrative Biology Unit, Parco Tecnologico Padano, Department of Environmental Science and Engineering, Graduate School of Science and Engineering, Department of Population Medicine and Diagnostic Sciences, Cornell University [New York], Dynamique cellulaire et moléculaire de la muqueuse respiratoire, Université de Reims Champagne-Ardenne (URCA)-IFR53-Institut National de la Santé et de la Recherche Médicale (INSERM), Biostatistics Department, Harvard School of Public Health, Institute for genomic and systems biology, Argonne National Laboratory [Lemont] (ANL), Department of Ecology and Evolution [Chicago], University of Chicago, Alfred P. Sloan Foundation [2015-13964], National Institutes of Health [F31GM111053, R01NS076465, R25EB020393], Promega, CosmosID, Illumina, Copan, QIAGEN, University of California-University of California, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Acibadem University Dspace, Afshinnekoo, Ebrahim, Ahsanuddin, Sofia, Ghedin, Elodie, Read, Timothy, Fraser, Claire, Dudley, Joel, Bowler, Christopher, Mason, Christopher E., Chernomoretz, Ariel, Stolovitzky, Gustavo, Łabaj, Paweł P., Graf, Alexandra B., Darling, Aaron, Burke, Catherine, Noushmehr, Houtan, Dias-Neto, Emmanuel, Guo, Yongli, Xie, Zhi, Lee, Patrick K. H., Shi, Leming, Ruiz-Perez, Carlos A., Zambrano, Maria Mercede, Siam, Rania, Ouf, Amged, Richard, Hugue, Lafontaine, Ingrid, Wieler, Lothar H., Semmler, Torsten, Prithiviraj, Bharath, Nedunuri, Narasimha, Mehr, Shaadi, Banihashemi, Kambiz, Lista, Florigio, Anselmo, Anna, Suzuki, Haruo, Kuroda, Makoto, Yamashita, Riu, Sato, Yukoto, Kaminuma, Eli, Aranda, Celia M. Alpuche, Martinez, Jesu, Dada, Christopher, Dybwad, Mariu, Oliveira, Manuela, Schuster, Stephan, Siwo, Geoffrey H., Jang, Soojin, Seo, Sung Chul, Hwang, Sung Ho, Ossowski, Stephan, Bezdan, Daniela, Chaker, Salama, Chatziefthimiou, Aspassia D., Udekwu, Kla, Liungdahl, Per, Sezerman, Ugur, Meydan, Cem, Elhaik, Eran, Gonnet, Gaston, Schriml, Lynn M., Mongodin, Emmanuel, Huttenhower, Curti, Gilbert, Jack, Eisen, Jonathan, Hirschberg, David, Hernandez, Mark, Mcgrath, Ken, Mcgrath, Leanne, Gray, Andrew, Osuolale, Olayinka, Segata, Nicola, Fillo, Silvia, Iraola, Gregorio, Zhou, Yiming, Chang, Yujun, Li, Yang, Zhend, Yuanting, Hou, Wanwan, Ramirez, Adan, Cepeda, Martha, Desnues, Christelle, Rascovan, Nicola, Baron, Colin, Nagarajan, Niranjan, Ercolini, Danilo, Menary, Wayne, Tighe, Scott, Donia, Mohamed, Levy, Shawn, Benito, Joseph, Jones, Angela, Kasarskis, Andrew, Maritz, Julia, Jorgensen, Ellen, Neches, Russell, Livelli, Tom, Barnetche, Jesus Martinez, Pasolli, Edoardo, Greenfield, Nick, Hasan, Nur, Brownstein, John, Nozick, Linda, Michels, Harold, Schriml, Lynn, Brownstein, Catherine, Garbarino, Jeanne, Lyons, Abby, and Zhu, Jeff

Subjects
0301 basic medicine, Microbiology (medical), Built environment, Antimicrobial resistance markers, [SDV]Life Sciences [q-bio], 030106 microbiology, BIOINFORMÁTICA, Biosynthetic gene cluster, Genomics, Biology, Meeting Report, Microbiology, Biosynthetic gene clusters, Microbiome, Next-generation sequencing, 12. Responsible consumption, Metagenomic, 03 medical and health sciences, Data visualization, Urban planning, Databases, Genetic, 11. Sustainability, City Planning, Architecture, Environmental planning, Ecosystem, Metadesign, business.industry, Antimicrobial resistance marker, Biotechnology, 030104 developmental biology, Research Design, 13. Climate action, Metagenomics, Public Health, Sample collection, business, Human
Abstract

International audience; The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities.

Published
2016
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59. Additional file 1: Figure S1. of Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates

Author

Lasserre, Moira, Fresia, Pablo, Greif, Gonzalo, Iraola, Gregorio, Castro-Ramos, Miguel, Juambeltz, Arturo, Nuñez, Álvaro, Naya, Hugo, Robello, Carlos, and Berná, Luisa

Subjects
body regions, nervous system, fungi
Abstract

Sequencing and genome annotation statistics for the 23 Uruguayan strains of M. bovis. (PDF 115 kb)

Published
2018
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60. Additional file 6: Figure S3a. of Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates

Author

Lasserre, Moira, Fresia, Pablo, Greif, Gonzalo, Iraola, Gregorio, Castro-Ramos, Miguel, Juambeltz, Arturo, Nuñez, Álvaro, Naya, Hugo, Robello, Carlos, and Berná, Luisa

Subjects
genetic structures
Abstract

Interactive Genome Visualizer (IGV) visualization of reads aligned to reference genome AF2122/97 (exemplified by strains MbURU-002, MbURU-003 and MbURU-010), showing a region containing glycosyltransferase-coding genes Mb1551 and Mb1553c (wbbL2). Coverage is represented in the upper track of each strain as a gray bar chart, and SNPs are showed as colored bars. The average coverage for these genes can reach up to 10 times the average genome coverage. Figure S3b. IGV visualization of reads from strain MbURU-002 aligned to reference genome AF2122/97, showing a region containing polyketide synthase pks12 gene. The lower alignment represents only reads with mapping qualities higher than 0 and show therefore no multimapping reads, while the upper alignment represents the original data from MbURU-002. Coverage is represented in the upper track of each strain as a gray bar chart, and SNPs are showed as colored bars. Note that there are very few called SNPs in this region and some are still present once multimapping reads have been removed. (PDF 2630 kb)

Published
2018
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61. Additional file 7: Figure S4a. of Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates

Author

Lasserre, Moira, Fresia, Pablo, Greif, Gonzalo, Iraola, Gregorio, Castro-Ramos, Miguel, Juambeltz, Arturo, Nuñez, Álvaro, Naya, Hugo, Robello, Carlos, and Berná, Luisa

Abstract

Validation of in silico RD typing with PCR on 21 of the Uruguayan M. bovis strains. Figure S4b. Alignment of the sequenced reads of strain MbURU-003 against the assembled genome of the same strain. Selected pair of reads in red exemplify one of the reads that flanks both sides of a region of difference (RDbov145a) that is absent in this strain. (PDF 1643 kb)

Published
2018
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62. Additional file 3: Figure S2. of Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates

Author

Lasserre, Moira, Fresia, Pablo, Greif, Gonzalo, Iraola, Gregorio, Castro-Ramos, Miguel, Juambeltz, Arturo, Nuñez, Álvaro, Naya, Hugo, Robello, Carlos, and Berná, Luisa

Subjects
body regions, nervous system, fungi, environment and public health
Abstract

List of tRNAs and corresponding codons in the Uruguayan genomes under study. (PDF 66 kb)

Published
2018
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66. Polyclonal Campylobacter fetus Infections Among Unrelated Patients, Montevideo, Uruguay, 2013–2018.

Author

Costa, Daniela, Betancor, Laura, Gadea, Pilar, Cabezas, Laura, Caiata, Leticia, Palacio, Rosario, Seija, Verónica, Galiana, Antonio, Vieytes, Mariela, Cristophersen, Inés, Calleros, Lucía, and Iraola, Gregorio

Subjects
CAMPYLOBACTER infections, GENOMES, INTESTINAL diseases, GUT microbiome, SEQUENCE analysis, BACTERIAL contamination, INFECTIOUS disease transmission
Abstract

In Montevideo (2013-2018), 8 Campylobacter fetus extraintestinal infections were reported. The polyclonal nature of strains revealed by whole-genome sequencing and the apparent lack of epidemiological links was incompatible with a single contamination source, supporting alternative routes of transmission. [ABSTRACT FROM AUTHOR]

Published
2020
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69. First Release of the Bacterial Biobank of the Urban Environment (BBUE)

Author

Antelo, Verónica, primary, Salazar, Cecilia, additional, Martínez, Arací, additional, D’Alessandro, Bruno, additional, Castro, Marta, additional, Betancor, Laura, additional, Barcala, María Victoria, additional, Míguez, Diana, additional, Gonnet, Gastón H., additional, and Iraola, Gregorio, additional

Published
2018
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78. Inter- and intracontinental migrations and local differentiation have shaped the contemporary epidemiological landscape of canine parvovirus in South America

Author

Grecco, Sofía, primary, Iraola, Gregorio, additional, Decaro, Nicola, additional, Alfieri, Alice, additional, Alfieri, Amauri, additional, Gallo Calderón, Marina, additional, da Silva, Ana Paula, additional, Name, Daniela, additional, Aldaz, Jaime, additional, Calleros, Lucía, additional, Marandino, Ana, additional, Tomás, Gonzalo, additional, Maya, Leticia, additional, Francia, Lourdes, additional, Panzera, Yanina, additional, and Pérez, Ruben, additional

Published
2018
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80. Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota

Author

Iraola, Gregorio, primary, Forster, Samuel C., additional, Kumar, Nitin, additional, Lehours, Philippe, additional, Bekal, Sadjia, additional, García-Peña, Francisco J., additional, Paolicchi, Fernando, additional, Morsella, Claudia, additional, Hotzel, Helmut, additional, Hsueh, Po-Ren, additional, Vidal, Ana, additional, Lévesque, Simon, additional, Yamazaki, Wataru, additional, Balzan, Claudia, additional, Vargas, Agueda, additional, Piccirillo, Alessandra, additional, Chaban, Bonnie, additional, Hill, Janet E., additional, Betancor, Laura, additional, Collado, Luis, additional, Truyers, Isabelle, additional, Midwinter, Anne C., additional, Dagi, Hatice T., additional, Mégraud, Francis, additional, Calleros, Lucía, additional, Pérez, Ruben, additional, Naya, Hugo, additional, and Lawley, Trevor D., additional

Published
2017
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87. Tritryps Comparative Repeatome: Insights on Repetitive Element Evolution in Trypanosomatid Pathogens.

Author

Pita, Sebastián, Díaz-Viraqué, Florencia, Iraola, Gregorio, and Robello, Carlos

Subjects
MICROBIAL genomes, TRYPANOSOMATIDAE, TRYPANOSOMA cruzi, LEISHMANIA, REPEATED sequence (Genetics), TRANSPOSONS
Abstract

The major human pathogens Trypanosoma cruzi, Trypanosoma brucei, and Leishmania major are collectively known as the Tritryps. The initial comparative analysis of their genomes has uncovered that Tritryps share a great number of genes, but repetitive DNA seems to be extremely variable between them. However, the in-depth characterization of repetitive DNA in these pathogens has been in part neglected, mainly due to the well-known technical challenges of studying repetitive sequences from de novo assemblies using short reads. Here, we compared the repetitive DNA repertories between the Tritryps genomes using genome-wide, low-coverage Illumina sequencing coupled to RepeatExplorer analysis. Our work demonstrates that this extensively implemented approach for studying higher eukaryote repeatomes is also useful for protozoan parasites like trypanosomatids, as we recovered previously observed differences in the presence and amount of repetitive DNA families. Additionally, our estimations of repetitive DNA abundance were comparable to those obtained from enhanced-quality assemblies using longer reads. Importantly, our methodology allowed us to describe a previously undescribed transposable element in Leishmania major (TATE element), highlighting its potential to accurately recover distinctive features from poorly characterized repeatomes. Together, our results support the application of this low-cost, low-coverage sequencing approach for the extensive characterization of repetitive DNA evolutionary dynamics in trypanosomatid and other protozoan genomes. [ABSTRACT FROM AUTHOR]

Published
2019
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90. Genetic characterization of South American infectious bursal disease virus reveals the existence of a distinct worldwide-spread genetic lineage

Author

Hernández, Martín, primary, Tomás, Gonzalo, additional, Marandino, Ana, additional, Iraola, Gregorio, additional, Maya, Leticia, additional, Mattion, Nora, additional, Hernández, Diego, additional, Villegas, Pedro, additional, Banda, Alejandro, additional, Panzera, Yanina, additional, and Pérez, Ruben, additional

Published
2015
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91. Phylogenetic and Genome-Wide Deep-Sequencing Analyses of Canine Parvovirus Reveal Co-Infection with Field Variants and Emergence of a Recent Recombinant Strain

Author

Pérez, Ruben, primary, Calleros, Lucía, additional, Marandino, Ana, additional, Sarute, Nicolás, additional, Iraola, Gregorio, additional, Grecco, Sofia, additional, Blanc, Hervé, additional, Vignuzzi, Marco, additional, Isakov, Ofer, additional, Shomron, Noam, additional, Carrau, Lucía, additional, Hernández, Martín, additional, Francia, Lourdes, additional, Sosa, Katia, additional, Tomás, Gonzalo, additional, and Panzera, Yanina, additional

Published
2014
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94. Comparative genomics identifies potential virulence factors in Clostridium tertiumand C. paraputrificum

Author

Muñoz, Marina, Restrepo-Montoya, Daniel, Kumar, Nitin, Iraola, Gregorio, Herrera, Giovanny, Ríos-Chaparro, Dora I., Díaz-Arévalo, Diana, Patarroyo, Manuel A., Lawley, Trevor D., and Ramírez, Juan David

Abstract

ABSTRACTSome well-known Clostridiales species such as Clostridium difficileand C. perfringensare agents of high impact diseases worldwide. Nevertheless, other foreseen Clostridiales species have recently emerged such as Clostridium tertiumand C. paraputrificum. Three fecal isolates were identified as Clostridium tertium(Gcol.A2 and Gcol.A43) and C. paraputrificum(Gcol.A11) during public health screening for C. difficileinfections in Colombia. C. paraputrificumgenomes were highly diverse and contained large numbers of accessory genes. Genetic diversity and accessory gene percentage were lower among the C. tertiumgenomes than in the C. paraputrificumgenomes. C. difficile tcdAand tcdBtoxins encoding homologous sequences and other potential virulence factors were also identified. EndoAinterferase, a toxic component of the type II toxin-antitoxin system, was found among the C. tertiumgenomes. toxAwas the only toxin encoding gene detected in Gcol.A43, the Colombian isolate with an experimentally-determined high cytotoxic effect. Gcol.A2 and Gcol.A43 had higher sporulation efficiencies than Gcol.A11 (84.5%, 83.8% and 57.0%, respectively), as supported by the greater number of proteins associated with sporulation pathways in the C. tertiumgenomes compared with the C. paraputrificumgenomes (33.3 and 28.4 on average, respectively). This work allowed complete genome description of two clostridiales species revealing high levels of intra-taxa diversity, accessory genomes containing virulence-factors encoding genes (especially in C. paraputrificum), with proteins involved in sporulation processes more highly represented in C. tertium. These finding suggest the need to advance in the study of those species with potential importance at public health level.

Published
2019
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97. Complete Genome Sequence of Campylobacter fetus subsp. venerealis Biovar Intermedius, Isolated from the Prepuce of a Bull

Author

Iraola, Gregorio, primary, Pérez, Ruben, additional, Naya, Hugo, additional, Paolicchi, Fernando, additional, Harris, David, additional, Lawley, Trevor D., additional, Rego, Natalia, additional, Hernández, Martín, additional, Calleros, Lucía, additional, Carretto, Luis, additional, Velilla, Alejandra, additional, Morsella, Claudia, additional, Méndez, Alejandra, additional, and Gioffre, Andrea, additional

Published
2013
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