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artículo

The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

Publicado por
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

Publicado 2023

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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 populatio...

artículo

Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Project

Publicado por
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

Publicado 2024

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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 ...