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Microbial Genomics

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Papers1428
Citations5567
Journal Papers 1409
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Reducing mapping reference and lineage bias in Mycobacterium tuberculosis
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delete2026-04-01
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deleteOrtiz, Arturo Torres; Didelot, Xavier; Grandjean, Louis
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Rolling out Plaque-2-seq: a single plaque sequencing approach enabling rapid, low-cost sequencing of phages directly from plaques
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delete2026-04-01
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deleteMichniewski, Slawomir; Glenny, Rebecca; Kinsella, Andrew; Porter, Kane; Wright, Kayne; Harrison, Sophie; Ugokwe, Nzubechukwu, I; Alrashidi, Amani; Rashid, Srwa. J.; Eke, Chisomaga; Lee, Jack C. D.; Patel, Faizal; Josephs, Theo; Pedramfar, Arezoo; Coleman, Max; Al-Dahash, Hasanain F. Y.; Sabuholo, Gibson A.; Roemer, Navodya S.; Sampson, Hannah; Misol Jr, Gerald N.; Rihtman, Branko; Scanlan, David J.; Smith, Elspeth; Stafford, Graham; van Schaik, Willem; Puxty, Richard J.; Galyov, Edouard; Clokie, Martha R. J.; Megremis, Spyridon; Millard, Andrew
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Integrative profiling of Helicobacter pylori clinical isolates: virulence genes, antimicrobial susceptibility and genetic diversity in gastric cancer risk stratification
deleteMicrobial Genomics
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delete2026-03-01
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deleteZhang, Ying; Shang, Yanyan; Li, Zhenkai; Kuang, Zupeng; Huang, Shixuan; Ye, Qinghua; Chen, Jianhui; Huang, Zhixin; Chen, Ling; Li, Ying; Wu, Qingping
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Genomic characterization of invasive disease-causing Streptococcus pneumoniae in Lebanon, 2003-2025
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delete2026-03-01
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deleteDakroub, Fatima; King, Alannah C.; Akl, Fata; Zaghlout, Alissar; Hourani, Nancy; Hung, Harry; Barada, Sarah; Boutros, Celina F.; Ferreira, Ana D. S.; McGee, Lesley; Reslan, Lina; Damaj, Stephanie; Ghosn, Nada; Matar, Ghassan M.; Araj, George F.; Abou Fayad, Antoine; Bentley, Stephen D.; Lo, Stephanie W.; Dbaibo, Ghassan S.
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Global population structure of Shiga toxin-producing Escherichia coli O103:H2 and the variation in their major virulence factor-encoding genetic elements (vol 12, 10.1099/mgen.0.001625, 2026)
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delete2026-03-01
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deleteTaniguchi, Itsuki; Morimoto, Yo; Kimura, Yoko; Seto, Junji; Kawai, Yuko; Kitahashi, Tomoko; Aoki, Junko; Terai, Katsuya; Furuta, Toshihiko; Wakabayashi, Yuki; Tanabe, Sumiko; Hamasaki, Mitsuhiro; Abe, Yuri; Sasaki, Mari; Narimatsu, Hiroshi; Yokoyama, Eiji; Iyoda, Sunao; Hayashi, Tetsuya; Nakamura, Keiji
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Structural and functional characteristics of faecal, vaginal and colostrum microbiota in high- yielding sows
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delete2026-03-01
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deletePi, Yu; Wei, Zixi; Xu, Lei; Yin, Chenggang; Li, Yanpin; Li, Xilong
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Genetic traits of IncK2 plasmids and the Escherichia coli host underlying the association to the chicken gut
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delete2026-03-01
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deleteRozwandowicz, Marta; Abuoun, Manal; Alba, Patricia; Anjum, Muna F.; Zajac, Magdalena; Brouwer, Michael S. M.; Borjesson, Stefan; Canica, Manuela; Carfora, Virginia; Diaconu, Elena L.; Doublet, Benoit; Gates, Daisy; Hammerl, Jens-Andre; Hasman, Henrik; Haverkamp, Thomas H. A.; Hendrickx, Antoni P. A.; Lindsjo, Oskar K.; Manageiro, Vera; Mo, Soleveig S.; Myrenas, Mattias; Rizzardi, Kristina; Slettemeas, Jannice Schau; Sunde, Marianne; van Duijkeren, Engeline; Van Hoek, Angela H. A. M.; Veldman, Kees T.; Bomba, Arkadiusz; Nord, Emma; Ceyssens, Pieter-Jan; Hordijk, Joost
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Vitamin B12-associated interactions between Mesorhizobium sp. TaiHu and Synechococcus sp. PCC 7002 revealed by multiomics analysis
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delete2026-03-01
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deleteLiu, Gaopeng; Bai, Peng; Ren, Minglei; Li, Qi; Li, Tao
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Sequence type and strain-level detection of Klebsiella pneumoniae in culture-enriched bacterial metagenomes: comparative performance of mSWEEP and StrainGE bioinformatic tools
deleteMicrobial Genomics
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delete2026-02-01
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deleteBuczek, Dorota Julia; Kabir, Wasifa; Lindstedt, Kenneth; Maklin, Tommi; Thorpe, Harry A.; Suzuki, Yutaka; Corander, Jukka; Samuelsen, Orjan; Sundsfjord, Arnfinn
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Pathogenic potential and phylogenomic analysis of stx2-carrying O26:H11 Shiga toxin-producing Escherichia coli isolated from dairy products in France (2014-2024)
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delete2026-02-01
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deleteSoleau, Nathan; Bruto, Maxime; Ganet, Sarah; Bonacorsi, Stephane; Cointe, Aurelie; Sergentet, Delphine
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Genome sequencing reveals variation of African swine fever virus in Nigerian outbreaks and identification of two major West African viral lineages
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delete2026-02-01
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deleteJoel, Ganih S.; Jambol, Anvou R.; Jahota, Nenfort Daniel; Li, Fengyi; Njuki, Ruth N.; Odongo, Lameck A.; Ruth, Morenikeji Oluwatoyin; Ayuba, Gyang Godwill; Thankgod, Daniel Geofrey; Jagab, Shuaibu Hafsat; Cai, Zheng-Fei; Oluwole, Olufunke O.; Boladuro, Bamidele; Oladele-Buloka, M. O.; Bishop, Richard P.; Li, Jianbo; Yang, Xinlou; Adedeji, Adeyinka J.; Luka, Pam D.; Zhang, Ya-Ping; Adeola, Adeniyi C.; Peng, Min-Sheng
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Genomic insights into the functional and metabolic versatility of gut microbiome Anaerostipes species
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delete2026-02-01
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deleteBhattacharjee, Disha; Millman, Lindsey C.; Seesengood, Meagan L.; Martineau, Lindsey M.; Seekatz, Anna M.
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Two different genotypes of Vibrio parahaemolyticus serotype O10:K4 have been co-circulating in Shanghai since 2020
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delete2026-02-01
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deleteWang, Chaonan; Zhang, Wanju; Lin, Qingneng; Chen, Yong; Jiang, Hui; Zhou, Jing; Li, Bowen; Li, Peixuan; Zhuang, Yuan; Chen, Min; Chen, Hongyou
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A One Health study of Klebsiella pneumoniae species complex plasmids shows a highly diverse and ecologically adaptable plasmidome
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delete2026-02-01
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deleteWinkler, Mia A.; Hetland, Marit A. K.; Kaspersen, Hakon Pedersen; Bakksjo, Ragna-Johanne; Bernhoff, Eva; Fostervold, Aasmund; Hawkey, Jane; Lunestad, Bjorn-Tore; Marathe, Nachiket P.; Raffelsberger, Niclas; Samuelsen, Orjan; Sunde, Marianne; Sundsfjord, Arnfinn; Lam, Margaret M. C.; Lohr, Iren H.
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Phylogenomic and functional insights into Staphylococcus shinii from blueberry production environments: intra-species structure, probiotic traits and antimicrobial resistance
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delete2026-02-01
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deleteValadez-Cano, Cecilio; Wallace, Rhiannonn L.; Chuan, Jiacheng; Mahoney, David; Yin, Xianhua; Clairmont, Lindsey; Lepp, Dion; Li, Sean; Diarra, Moussa S.; Chen, Wen
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Acinetobacter variabilis represents a diverse species with novel regions associated with antibiotic resistance and surface polysaccharides
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delete2026-02-01
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deletePatterson, Lucy L.; Hatje, Eva; Katouli, Mohammad; Kenyon, Johanna J.; Hamidian, Mehrad
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Evaluation of Oxford Nanopore Technologies workflows for genomic epidemiology of outbreak-associated bacterial isolates in the clinical setting
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delete2026-02-01
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deleteNeuenschwander, Stefan; Borcard, Loic; Gempeler, Sonja; Miani, Miguel A. Terrazos; Casanova, Carlo; Ramette, Alban
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Genomic surveillance of Salmonella enterica serotype Minnesota strains from poultry products imported into South Africa
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delete2026-02-01
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deleteRaghuram, Vishnu; Mafuna, Thendo; Ramnath, Vignesh; Blom, Josefin; Magwedere, Kudakwashe; Carroll, Laura M.; Matle, Itumeleng
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Persistence and spread of fluconazole-resistant Candida parapsilosis clinical isolates associated with increased ERG11 copies in Qatar
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delete2026-02-01
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deleteZhang, Zhu; Wang, Yue; Ben Abid, Fatma; Salah, Husam; Al Ismail, Khalil; Eldos, Haneen; Samuel, Bincy; Zhou, Ruwen; Sundararaju, Sathyavathi; Suleimen, Mohammed; Wang, Kun; Lee, Bernett; Al Maslamani, Muna; Sultan, Ali A.; Perez-Lopez, Andres; Xu, Jianping; Tsui, Clement K. M.
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Comparative genomics of Pantoea allii lineages and distribution of ecologically relevant traits
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delete2026-02-01
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deleteShin, Gi Yoon; De Armas, Stefanie; Galvan, Guillermo A.; Siri, Maria I.; Rojas, Mariah; Vinatzer, Boris A.; Asselin, Jo Ann E.; Stodghill, Paul; Zhao, Mei; Dutta, Bhabesh; Tambong, James; Kvitko, Brian H.
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