Browsing by Author "Torres, RC"

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    Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Project
    (Taylor and Francis Ltd., 2024) Vale, FF; Roberts, RJ; Kobayashi, I; Camargo, MC; Rabkin, CS; Wang, D; Hicks, B; Zhu, B; Yeager, M; Hutchinson, A; Teshome, K; Jones, K; Luo, W; Goldstein, AM; Hu, N; Taylor, PR; Song, M; Gutiérrez-Escobar, AJ; Yu, K; Abnet, CC; Chanock, SJ; Romero-Gallo, J; Krishna, U; Peek, RM; Piazuelo, MB; Wilson, KT; Loh, JT; Cover, TL; Raaf, N; Aftab, H; Akada, J; Matsumoto, T; Yamaoka, Y; Haesebrouck, F; Bartelli, TF; Nunes, DN; Pelosof, A; Sztokfisz, CZ; Dias-Neto, E; Assumpção, PP; Tishkov, I; Goodman, KJ; Geary, J; Cromarty, TJ; Price, NL; Quilty, D; Corvalan, AH; Serrano, CA; Gonzalez, R; Riquelme, A; García-Cancino, A; Parra-Sepúlveda, C; Castillo, F; Bravo, MM; Pazos, A; Bravo, LE; Fox, JG; Ramírez-Mayorga, V; Molina-Castro, S; Durán-Bermúdez, S; Campos-Núñez, C; Chaves-Cervantes, M; Tshibangu-Kabamba, E; Tumba, GD; Tshimpi-Wola, A; de Jesus Ngoma-Kisoko, P; Ngoyi, DM; Cruz, M; Hosking, C; Abreu, JJ; Varon, C; Benejat, L; Jehanne, Q; Lehours, P; Megraud, F; Secka, O; Link, A; Malfertheiner, P; Adinortey, MB; Bockarie, AS; Adinortey, CA; Ofori, EG; Sgouras, DN; Martinez-Gonzalez, B; Michopoulos, S; Georgopoulos, S; Hernandez, E; Dominguez, RL; Morgan, DR; Harðardóttir, H; Gunnarsdóttir, AI; Guðjónsson, H; Jónasson, JG; Björnsson, ES; Ballal, M; Shetty, V; Miftahussurur, M; Sugihartono, T; Alfaray, RI; Waskito, LA; Fauzia, KA; Syam, AF; Maulahela, H; Malekzadeh, R; Sotoudeh, M; Peretz, A; Azrad, M; On, A; De, Re, V; Zanussi, S; Cannizzaro, R; Canzonieri, V; Shimura, T; Tokunaga, K; Osaki, T; Kamiya, S; Jadallah, K; Matalka, I; Sagynbekuly, IN; Moldobaeva, MS; Rakhat, A; Choi, IJ; Kim, JG; Kim, N; Leja, M; Vangravs, R; Šķenders, Ģ; Rūdule, A; Kikuste, I; Vanags, A; Rudzīte, D; Kupcinskas, J; Skieceviciene, J; Jonaitis, L; Kiudelis, G; Jonaitis, P; Kiudelis, V; Varkalaite, G; Vadivelu, J; Loke, MF; Vellasamy, KM; Herrera-Goepfert, R; Alonso-Larraga, JO; Yee, TT; Htet, K; Matsuhisa, T; Shrestha, PK; Ansari, S; Abiodun, O; Jemilohun, C; Akande, KO; Olu-Abiodun, O; Magaji, FA; Omotoso, A; Okonkwo, U; Osuagwu, CC; Owoseni, OO; Castaneda, C; Castillo, M; Velapatino, B; Gilman, RH; Krzyżek, P; Gościniak, G; Pawełka, D; Korona-Glowniak, I; Cichoz-Lach, H; Oleastro, M; Figueiredo, C; Machado, JC; Ferreira, RM; Bordin, DS; Livzan, MA; Tsukanov, VV; Tan, P; Yeoh, KG; Zhu, F; Ally, R; Haas, R; Fischer, W; Montes, M; Fernández-Reyes, M; Tamayo, E; Lizasoain, J; Bujanda, L; Lario, S; Ramírez-Lázaro, MJ; Calvet, X; Brunet-Mas, E; Domper-Arnal, MJ; García-Mateo, S; Abad-Baroja, D; Delgado-Guillena, P; Moreira, L; Botargues, J; Pérez-Martínez, I; Barreiro-Alonso, E; Flores, V; Gisbert, JP; Muro, EA; Linares, P; Alcoba, L; Martin, V; Fleitas-Kanonnikoff, T; Altayeb, HN; Engstrand, L; Enroth, H; Keller, PM; Wagner, K; Pohl, D; Lee, Y-C; Liou, J-M; Wu, M-S; Kocazeybek, B; Sarıbas, S; Tasçı, İ; Demiryas, S; Kepil, N; Quiel, L; Villagra, M; Norton, M; Johnson, D; Huang, RJ; Hwang, JH; Szymczak, W; Rajagopalan, S; Asare, E; Jacobs, WR; In, H; Bollag, R; Lopez, A; Kruse, EJ; White, J; Graham, DY; Lane, C; Gao, Y; Gold, BD; Cruz-Correa, M; González-Pons, M; Rodriguez, LM; Tuan, VP; Dung, HDQ; Binh, TT; Trang, TTH; Van, Khien, V; Chen, X; Zhao, Y; Raley, C; Kessing, B; Tran, B; Katsura, Y; Gonzalez-Hormazabal, P; Didelot, X; Sheppard, S; Tarazona-Santos, E; Zamudio, R; Mariño-Ramírez, L; Backert, S; Naumann, M; Smet, A; Berg, DE; Chiner-Oms, Á; Comas, I; Martínez-Martínez, FJ; Yahara, K; Blaser, MJ; Vincze, T; Morgan, RD; Dekker, JP; Torres, J; Noureen, M; Cherry, JL; Osada, N; Fukuyo, M; Arita, M; Sandoval-Motta, S; Agostini, RB; Ghirotto, S; Muñoz-Ramírez, ZY; Torres, RC; Falush, D; Thorell, K; Uchiyama, I
    Prophages can have major clinical implications through their ability to change pathogenic bacterial traits. There is limited understanding of the prophage role in ecological, evolutionary, adaptive processes and pathogenicity of Helicobacter pylori, a widespread bacterium causally associated with gastric cancer. Inferring the exact prophage genomic location and completeness requires complete genomes. The international Helicobacter pylori Genome Project (HpGP) dataset comprises 1011 H. pylori complete clinical genomes enriched with epigenetic data. We thoroughly evaluated the H. pylori prophage genomic content in the HpGP dataset. We investigated population evolutionary dynamics through phylogenetic and pangenome analyses. Additionally, we identified genome rearrangements and assessed the impact of prophage presence on bacterial gene disruption and methylome. We found that 29.5% (298) of the HpGP genomes contain prophages, of which only 32.2% (96) were complete, minimizing the burden of prophage carriage. The prevalence of H. pylori prophage sequences was variable by geography and ancestry, but not by disease status of the human host. Prophage insertion occasionally results in gene disruption that can change the global bacterial epigenome. Gene function prediction allowed the development of the first model for lysogenic-lytic cycle regulation in H. pylori. We have disclosed new prophage inactivation mechanisms that appear to occur by genome rearrangement, merger with other mobile elements, and pseudogene accumulation. Our analysis provides a comprehensive framework for H. pylori prophage biological and genomics, offering insights into lysogeny regulation and bacterial adaptation to prophages. © 2024 The Author(s). Published with license by Taylor & Francis Group, LLC.
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    The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes
    (Nature Research, 2023) Thorell, K; Muñoz-Ramírez, ZY; Wang, D; Sandoval-Motta, S; Boscolo-Agostini, R; Ghirotto, S; Torres, RC; Romero-Gallo, J; Krishna, U; Peek, RM; Piazuelo, MB; Raaf, N; Bentolila, F; Aftab, H; Akada, J; Matsumoto, T; Haesebrouck, F; Colanzi, RP; Bartelli, TF; Castaneda, C; Castillo, M; Velapatino, B; Gilman, RH; Krzyżek, P; Gościniak, G; Pawełka, D; Korona-Glowniak, I; Cichoz-Lach, H; Oleastro, M; Figueiredo, C; Machado, JC; Ferreira, RM; Bordin, DS; Camargo, MC; Rabkin, CS
    Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics.