Phenotypic and Genomic Properties of Brachybacterium vulturis sp. nov. and Brachybacterium avium sp. nov. by Euon J. Tak, Euon J. Tak, Pil S. Kim, Pil S. Kim, Dong-Wook Hyun, Dong-Wook Hyun, Hyun S. Kim, Hyun S. Kim, June-Young Lee, June-Young Lee, Woorim Kang, Woorim Kang, Hojun Sung, Hojun Sung, Na-Ri Shin, Na-Ri Shin, Min-Soo Kim, Min-Soo Kim, Tae W. Whon, Tae W. Whon, Jin-Woo Bae, Jin-Woo Bae

“…The strains shared 99.3% 16S rRNA gene sequence similarity to each other but were identified as two distinct species based on 89.0-89.2% ANIb, 90.3% ANIm, 89.7% OrthoANI and 38.0% dDDH values calculated using whole genome sequences. Among species with validly published names, Brachybacterium ginsengisoli DCY80T shared high 16S rRNA gene sequence similarities with strains VM2412T (98.7%) and VR2415T (98.4%) and close genetic relatedness with strains VM2412T (83.3–83.5% ANIb, 87.0% ANIm, 84.3% OrthoANI and 27.8% dDDH) and VR2415T (82.8–83.2% ANIb, 86.7% ANIm, 83.9% OrthoANI and 27.2% dDDH). …”
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Persistent Asymptomatic Human Infections by <named-content content-type="genus-species">Salmonella enterica</named-content> Serovar Newport in China by Narayan Paudyal, Hang Pan, Beibei Wu, Xiao Zhou, Xin Zhou, Wenqing Chai, Qingqing Wu, Shuning Li, Fang Li, Guimin Gu, Haoqiu Wang, Qinghua Hu, Xuebin Xu, Yan Li, Min Yue

“…Newport strains with their relevant clinical metadata were analyzed, and the strains were subjected to whole-genome sequence analysis. Among these, 62.4% (n = 181) were from diarrheic patients and 28.9% (n = 84) were from asymptomatic individuals (including adults and youngsters) while 8.6% (n = 25) were from cases of persistent diarrhea in infants (28%, n = 7) and toddlers (72%, n = 18). …”
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Comprehensive Assessment of Subtyping Methods for Improved Surveillance of Foodborne Salmonella by Hang Pan, Chenghao Jia, Narayan Paudyal, Fang Li, Junyong Mao, Xi Liu, Chenghang Dong, Kun Zhou, Xiayi Liao, Jiansen Gong, Weihuan Fang, Xiaoliang Li, Corinna Kehrenberg, Min Yue

“…Using 1,064 samples along a poultry production chain with a considerable level of Salmonella contamination, we collected representative isolates for genome sequencing and comparative analysis by using 12 typing techniques, particularly with whole-genome sequence (WGS) based methods and a recently invented CRISPR multi-virulence locus sequence typing (CRISPR-MVLST) method. …”
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Genome characteristics of the optrA-positive Clostridium perfringens strain QHY-2 carrying a novel plasmid type by Ke Wu, Zhe Li, Mingjin Fang, Yuan Yuan, Edward M. Fox, Yingqiu Liu, Ruichao Li, Li Bai, Wen Zhang, Wei-Min Zhang, Qi Yang, Lingling Chang, Pu Li, Xinglong Wang, Juan Wang, Zengqi Yang

“…The gene optrA is the first gene that confers resistance to the tedizolid, a last-resort antimicrobial agent in human medicine. Herein, we whole-genome sequenced and analyzed one optrA-positive C. perfringens strain QHY-2 from Tibetan sheep in Qinghai province and identified one optrA plasmid pQHY-2. …”
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Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic <italic toggle="yes">Escherichia coli</italic> (ExP... by Sabiha Shaik, Amit Ranjan, Sumeet K. Tiwari, Arif Hussain, Nishant Nandanwar, Narender Kumar, Savita Jadhav, Torsten Semmler, Ramani Baddam, Mohammed Aminul Islam, Munirul Alam, Lothar H. Wieler, Haruo Watanabe, Niyaz Ahmed

“…This is perhaps the first study that employs the high-throughput whole-genome sequence-based approach to compare and study the genomic features of these four ExPEC lineages in relation to their functional properties. …”
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Comparative Genomic Analyses of New and Old World Viscerotropic Leishmanine Parasites: Further Insights into the Origins of Visceral Leishmaniasis Agents by Fernando Tobias Silveira, Edivaldo Costa Sousa Junior, Rodrigo Vellasco Duarte Silvestre, Thiago Vasconcelos dos Santos, Wilfredo Sosa-Ochoa, Concepción Zúniga Valeriano, Patrícia Karla Santos Ramos, Samir Mansour Moraes Casseb, Luciana Vieira do Rêgo Lima, Marliane Batista Campos, Vania Lucia da Matta, Claudia Maria Gomes, Gabriela V. Araujo Flores, Carmen M. Sandoval Pacheco, Carlos Eduardo Corbett, Márcia Dalastra Laurenti

“…However, in light of ecological evidence from the NW parasite’s enzootic cycle involving a wild phlebotomine vector (<i>Lutzomyia longipalpis</i>) and a wild mammal reservoir (the fox, <i>Cerdocyon thous</i>), we have recently analyzed by molecular clock comparisons of the DNA polymerase alpha subunit gene the whole-genome sequence of <i>L. (L.) infantum chagasi</i> of the most prevalent clinical form, atypical dermal leishmaniasis (ADL), from Honduras (Central America) with that of the same parasite from Brazil (South America), as well as those of <i>L. …”
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Comparative Genomic Analysis of 19 Clinical Isolates of Tigecycline-Resistant Acinetobacter baumannii by Lin Liu, Lin Liu, Ping Shen, Ping Shen, Beiwen Zheng, Beiwen Zheng, Wei Yu, Wei Yu, Jinru Ji, Jinru Ji, Yonghong Xiao, Yonghong Xiao

“…Compared with 26 other whole-genome sequences of A. baumannii deposited in GeneBank, TgcR strains in this study commonly lacked the EF-Tu mutation for elfamycin resistance. …”
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Incidence and Genomic Background of Antibiotic Resistance in Food-Borne and Clinical Isolates of <i>Salmonella enterica</i> Serovar Derby from Spain by Xenia Vázquez, Raquel García-Fierro, Javier Fernández, Margarita Bances, Ana Herrero-Fresno, John E. Olsen, Rosaura Rodicio, Víctor Ladero, Vanesa García, M. Rosario Rodicio

“…Derby isolates (36) collected between 2006 and 2018 in a Spanish region (Asturias) from human clinical samples (20) as well as from pig carcasses, pork- or pork and beef-derived products, or wild boar (16) were phenotypically characterized with regard to resistance, and 22 (12 derived from humans and 10 from food-related samples) were also subjected to whole genome sequence analysis. The sequenced isolates belonged to ST40, a common <i>S</i>. …”
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Comparison of Primary Virus Isolation in Pulmonary Alveolar Macrophages and Four Different Continuous Cell Lines for Type 1 and Type 2 Porcine Reproductive and Respiratory Syndrome... by Jiexiong Xie, Nick Vereecke, Sebastiaan Theuns, Dayoung Oh, Nathalie Vanderheijden, Ivan Trus, Jannes Sauer, Philip Vyt, Caroline Bonckaert, Christian Lalonde, Chantale Provost, Carl A. Gagnon, Hans Nauwynck

“…Further, a possible correlation between cell tropism and viral genotype was assessed using PRRSV whole genome sequences in a Genome-Wide-Association Study (GWAS). …”
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Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Ama... by Felipe Gomes Naveca, Valdinete Nascimento, Victor Souza, André de Lima Corado, Fernanda Nascimento, George Silva, Matilde Contreras Mejía, Maria Júlia Brandão, Ágatha Costa, Débora Duarte, Karina Pessoa, Michele Jesus, Luciana Gonçalves, Cristiano Fernandes, Tirza Mattos, Ligia Abdalla, João Hugo Santos, Alex Martins, Fabiola Mendonça Chui, Fernando Fonseca Val, Gisely Cardoso de Melo, Mariana Simão Xavier, Vanderson de Souza Sampaio, Maria Paula Mourão, Marcus Vinícius Lacerda, Érika Lopes Rocha Batista, Alessandro Leonardo Álvares Magalhães, Nathânia Dábilla, Lucas Carlos Gomes Pereira, Fernando Vinhal, Fabio Miyajima, Fernando Braga Stehling Dias, Eduardo Ruback dos Santos, Danilo Coêlho, Matheus Ferraz, Roberto Lins, Gabriel Luz Wallau, Edson Delatorre, Tiago Gräf, Marilda Mendonça Siqueira, Paola Cristina Resende, Gonzalo Bello

“…To understand how SARS-CoV-2 persisted in a human population with a high immunity barrier, we generated 1,188 SARS-CoV-2 whole-genome sequences from individuals diagnosed in the Amazonas state from 1st January to 6th July 2021, of which 38 were vaccine breakthrough infections. …”
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Genetic and Structural Variation in the O-Antigen of Salmonella enterica Serovar Typhimurium Isolates Causing Bloodstream Infections in the Democratic Republic of the Congo by Sandra Van Puyvelde, Gianmarco Gasperini, Michael Biggel, Marie-France Phoba, Maria Michelina Raso, Tessa de Block, Leen N. Vanheer, Stijn Deborggraeve, Olivier Vandenberg, Nicholas Thomson, Neil Ravenscroft, Calman A. Maclennan, Barbara Bellich, Paola Cescutti, Gordon Dougan, Jan Jacobs, Octavie Lunguya, Francesca Micoli

“…In this study, we Illumina whole-genome sequenced 354 Salmonella Typhimurium isolates from the DRC, which were isolated between 2002 and 2017. …”
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Comparison of the genetic characteristics of directly measured and Fourier-transform mid-infrared-predicted bovine milk fatty acids and proteins by Kathryn M. Tiplady, Thomas J. Lopdell, Richard G. Sherlock, Thomas J.J. Johnson, Richard J. Spelman, Bevin L. Harris, Stephen R. Davis, Mathew D. Littlejohn, Dorian J. Garrick

“…A genome-wide association study was undertaken using imputed whole-genome sequence, and quantitative trait loci (QTL) from directly measured traits were compared with QTL from the corresponding FT-MIR predicted traits. …”
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Horizontal Gene Transfer and Loss of Serotype-Specific Genes in Listeria monocytogenes Can Lead to Incorrect Serotype Designations with a Commonly-Employed Molecular Serotyping Sch... by Phillip Brown, Zuzana Kucerova, Lisa Gorski, Yi Chen, Mirena Ivanova, Pimlapas Leekitcharoenphon, Cameron Parsons, Jeffrey Niedermeyer, James Jackson, Sophia Kathariou

“…However, for certain strains, the DS serotype designations are in conflict with those relying on antibody-based schemes or whole-genome sequence (WGS) analysis. In the current study, all 27 tested serotype 4b strains with sequence type 782 (ST782) within the hypervirulent clonal complex 2 (CC2) were designated 1/2b/3b using the DS. …”
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Genetic determinants of risk in pulmonary arterial hypertension: international genome-wide association studies and meta-analysis by Rhodes, CJ, Batai, K, Bleda, M, Haimel, M, Southgate, L, Germain, M, Pauciulo, MW, Hadinnapola, C, Aman, J, Girerd, B, Arora, A, Knight, J, Hanscombe, KB, Karnes, JH, Kaakinen, M, Gall, H, Ulrich, A, Harbaum, L, Cebola, I, Ferrer, J, Lutz, K, Swietlik, EM, Ahmad, F, Amouyel, P, Archer, SL, Argula, R, Austin, ED, Badesch, D, Bakshi, S, Barnett, C, Benza, R, Bhatt, N, Bogaard, HJ, Burger, CD, Chakinala, M, Church, C, Coghlan, JG, Condliffe, R, Corris, PA, Danesino, C, Debette, S, Elliott, CG, Elwing, J, Eyries, M, Fortin, T, Franke, A, Frantz, RP, Frost, A, Garcia, JGN, Ghio, S, Ghofrani, H-A, Gibbs, JSR, Harley, J, He, H, Hill, NS, Hirsch, R, Houweling, AC, Howard, LS, Ivy, D, Kiely, DG, Klinger, J, Kovacs, G, Lahm, T, Laudes, M, Machado, RD, Ross, RV, Marsolo, K, Martin, LJ, Moledina, S, Montani, D, Nathan, SD, Newnham, M, Olschewski, A, Olschewski, H, Oudiz, RJ, Ouwehand, WH, Peacock, AJ, Pepke-Zaba, J, Rehman, Z, Robbins, I, Roden, DM, Rosenzweig, EB, Saydain, G, Scelsi, L, Schilz, R, Seeger, W, Shaffer, CM, Simms, RW, Simon, M, Sitbon, O, Suntharalingam, J, Tang, H, Tchourbanov, AY, Thenappan, T, Torres, F, Toshner, MR, Treacy, CM, Noordegraaf, A, Waisfisz, Q, Walsworth, AK, Walter, RE, Wharton, J, White, RJ, Wilt, J, Wort, SJ, Yung, D, Lawrie, A, Humbert, M, Soubrier, F, Trégouët, D-A, Prokopenko, I, Kittles, R, Gräf, S, Nichols, WC, Trembath, RC, Desai, AA, Morrell, NW, Wilkins, MR, UK NIHR Bioresource Rare Diseases Consortium, UK PAH Cohort Study Consortium, US PAH Biobank Consortium, McCarthy, M

“…One GWAS used genotypes from 5895 whole-genome sequences and the other GWAS used genotyping array data from an additional 5849 individuals. …”

Multidrug-resistant tuberculosis control in Rwanda overcomes a successful clone that causes most disease over a quarter century by Jean Claude S. Ngabonziza, Leen Rigouts, Gabriela Torrea, Tom Decroo, Eliane Kamanzi, Pauline Lempens, Aniceth Rucogoza, Yves M. Habimana, Lies Laenen, Belamo E. Niyigena, Cécile Uwizeye, Bertin Ushizimpumu, Wim Mulders, Emil Ivan, Oren Tzfadia, Claude Mambo Muvunyi, Patrick Migambi, Emmanuel Andre, Jean Baptiste Mazarati, Dissou Affolabi, Alaine N. Umubyeyi, Sabin Nsanzimana, Françoise Portaels, Michel Gasana, Bouke C. de Jong, Conor J. Meehan

“…Methods: We analysed whole genome sequences of a longitudinal collection of nationwide RR-TB isolates. …”
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Comparison of the NG-Test Carba 5, Colloidal Gold Immunoassay (CGI) Test, and Xpert Carba-R for the Rapid Detection of Carbapenemases in Carbapenemase-Producing Organisms by Danxia Gu, Zelin Yan, Chang Cai, Jiaping Li, Yanyan Zhang, Yuchen Wu, Jiaxing Yang, Yonglu Huang, Rong Zhang, Yongning Wu

“…The presence or absence of carbapenemase genes in the whole-genome sequences was used as the gold standard for evaluating the accuracy of the above-mentioned three methods. …”
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<italic toggle="yes">Escherichia coli</italic> Sequence Type 410 Is Causing New International High-Risk Clones by Louise Roer, Søren Overballe-Petersen, Frank Hansen, Kristian Schønning, Mikala Wang, Bent L. Røder, Dennis S. Hansen, Ulrik S. Justesen, Leif P. Andersen, David Fulgsang-Damgaard, Katie L. Hopkins, Neil Woodford, Linda Falgenhauer, Trinad Chakraborty, Ørjan Samuelsen, Karin Sjöström, Thor B. Johannesen, Kim Ng, Jens Nielsen, Steen Ethelberg, Marc Stegger, Anette M. Hammerum, Henrik Hasman

“…Furthermore, E. coli ST410 was investigated in a global context to provide further insight into the acquisition of the carbapenemase genes blaOXA-181 and blaNDM-5 of this successful lineage. From 127 whole-genome-sequenced isolates, we reconstructed an evolutionary framework of E. coli ST410 which portrays the antimicrobial-resistant clades B2/H24R, B3/H24Rx, and B4/H24RxC. …”
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Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016–2018 by Jijoho Michel Agbla, Mathew D. Esona, Jose Jaimes, Rashi Gautam, Alidéhou Jerrold Agbankpé, Eric Katz, Tamegnon Victorien Dougnon, Annick Capo-Chichi, Nafissatou Ouedraogo, Osseni Razack, Honoré Sourou Bankolé, Michael D. Bowen

“…This analysis of whole genome sequences of RVA strains circulating in Benin described genetic point mutations and reassortment events as well as novel alleles. …”
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Genome wide association study based on gene-set enrichment analysis of growth traits in a Chicken advanced intercross line by H Mohammadi , A H Khaltabadi Farahani , M H Moradi and I Hajkhodadadi

“…The use of very high density SNP data or even whole genome sequence data could alleviate some of these issues. …”
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Conceptual design blueprint for the DiSSCo digitization infrastructure - DELIVERABLE D8.1 by Alex Hardisty, Hannu Saarenmaa, Ana Casino, Mathias Dillen, Karsten Gödderz, Quentin Groom, Helen Hardy, Dimitris Koureas, Abraham Nieva de la Hidalga, Deborah Paul, Veljo Runnel, Xavier Vermeersch, Myriam van Walsum, Luc Willemse

“…These new data include DNA barcodes, whole genome sequences, proteomics and metabolomics data, chemical data, trait data, and imaging data (Computer-assisted Tomography (CT), Synchrotron, etc.), to name but a few; and will lead to a wide range of end-user services that begins with finding, accessing, using and improving data. …”
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