Effectiveness of a Novel Liposomal Methylglyoxal–Tobramycin Formulation in Reducing Biofilm Formation and Bacterial Adhesion by Wed Alluhaim, Manal M. Alkhulaifi, Raghad R. Alzahrani, Bahauddeen M. Alrfaei, Alaa Eldeen B. Yassin, Majed F. Alghoribi, Ahlam M. Alsaadi, Ahmed I. Al-Asmari, Ahmed J. Al-Fahad, Rizwan Ali, Naif M. Alhawiti, Majed A. Halwani

“…<b>Methods:</b> Clinical isolates of <i>Pseudomonas aeruginosa</i> and <i>Klebsiella pneumoniae</i> were characterized using whole-genome sequencing. Liposomes (Lip-MGO-TOB) were formulated using Manuka honey as a surfactant and loaded with MGO and TOB. …”
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Exploring aneuploidies in two-center isolated bovine embryonic stem cell lines: Implications for cultured meat production by Chloë Deelkens, Elly De Vlieghere, Mario Van Poucke, Masaki Kinoshita, Jeffrey Aalders, Lieven Thorrez, Bert Devriendt, Ann Van Soom, Luc Peelman, Björn Menten, Catharina De Schauwer, Jolanda van Hengel

“…Through shallow whole-genome sequencing, we identified various chromosomal anomalies, including mono-, tri-, and tetrasomies, with specific gains in chromosomes 7, 12, 27, and 29, and losses in chromosome 9. …”
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An exceptionally rare case of a diffuse midline glioma with concomitant H3.1 K27M and G34R mutations in the HIST1H3C (H3C3) gene by Zita Reisz, Rita Pereira, Smitha Nevis, Alan Mackay, Leena Bhaw, Yura Grabovska, Ross Laxton, Valeria Molinari, Anna Burford, Barnaby Clark, Cristina Bleil, Bassel Zebian, Erika Pace, Annette Weiser, Fernando Carceller, Lynley Marshall, Andrew King, Istvan Bodi, Safa Al-Sarraj, Chris Jones, Matthew Clarke

“…Further molecular studies (whole exome, whole genome sequencing) revealed concurrent H3.1 K27M and G34R mutations (clonal, in the same reads) of H3C3, FGF11 and PIK3CA somatic variants, and a pathogenic germline NBN variant. …”
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Molecular epidemiology of carbapenem-resistant Acinetobacter baumannii group in Taiwan by Tran Lam Tu Quyen, Yu-Chia Hsieh, Shiao-Wen Li, Lii-Tzu Wu, Ya-Zhu Liu, Yi-Jiun Pan

“…Additionally, KL types showed correlations with ST types, carbapenem resistance, and certain clinical records. Whole-genome sequencing of a blaNDM-1-carrying A. seifertii strain revealed a plasmid transferable via in vitro conjugation, suggesting A. seifertii may be a reservoir for NDM-1 plasmids.IMPORTANCECarbapenem-resistant Acinetobacter spp. have been identified by the World Health Organization as a top priority for new antibiotic development. …”
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Germline structural variant as the cause of Lynch Syndrome in a family from Ecuador by Gemma Llargués-Sistac, Laia Bonjoch, Jenifer Muñoz, Xavier Domínguez-Rovira, Teresa Ocaña, Maria Isabel Alvarez-Mora, Celia Badenas, Anna Esteve-Codina, Carlos Reyes-Silva, Gabriela Jaramillo-Koupermann, Maria Teresa Rodrigo, Sandra López-Prades, Miriam Cuatrecasas, Antoni Castells, Francesc Balaguer, Leticia Moreira, Guerau Fernandez, Sergi Castellví-Bel

“…We report the identification and characterization of a novel germline structural variant encompassing 48.757 kb, involving the 3’-ends of the MLH1 and LRRFIP2 genes, as the cause of LS in a family of Ecuador. Whole-genome sequencing and transcriptomics allowed the identification of the genomic rearrangement and highlights the importance of the use of these additional approaches to achieve a comprehensive molecular diagnosis in some LS patients.…”
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Preparedness, prevention and control related to zoonotic avian influenza by EFSA Panel on Animal Health and Animal Welfare (AHAW), ECDC, Julio Alvarez, Anette Boklund, Sabine Dippel, Fernanda Dórea, Jordi Figuerola, Mette S. Herskin, Virginie Michel, Miguel Ángel Miranda Chueca, Eleonora Nannoni, Søren Saxmose Nielsen, Romolo Nonno, Anja B. Riber, Jan Arend Stegeman, Karl Ståhl, Hans‐Hermann Thulke, Frank Tuyttens, Christoph Winckler, Claire Brugerolles, Thorsten Wolff, Anna Parys, Erika Lindh, Neus Latorre‐Margalef, Marie‐Anne Rameix Welti, Ralf Dürrwald, Ramona Trebbien, Sylvie Van der Werf, Magnus Gisslén, Isabella Monne, Alice Fusaro, Claire Guinat, Alessio Bortolami, Leonidas Alexakis, Theresa Enkirch, Olov Svartstrom, Katriina Willgert, Francesca Baldinelli, Ludovica Preite, Malin Grant, Alessandro Broglia, Angeliki Melidou

“…Comprehensive surveillance of AIVs targeting adaptive mutations with whole genome sequencing in animals and humans is essential for early detection of zoonotic AIVs and efficient implementation of control measures. …”
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SARS-CoV-2 excretion and genetic evolution in nasopharyngeal and stool samples from primary immunodeficiency and immunocompetent pediatric patients by Haifa Khemiri, Ilhem Ben Fraj, Alessio Lorusso, Najla Mekki, Iolanda Mangone, Mariem Gdoura, Adriano Di Pasqual, Cesare Cammà, Valeria Di Lollo, Asma Cherni, Henda Touzi, Amel Sadraoui, Zina Meddeb, Nahed Hogga, Imen Ben Mustapha, Mohamed-Ridha Barbouche, Monia Ouederni, Henda Triki, Sondes Haddad-Boubaker

“…RNA detection was performed using RT-qPCR, and whole-genome sequencing was conducted with the NexSeq 1000 platform. …”
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Genomic interrogation of invasive group A Streptococcus (iGAS) epidemiology and COVID-19 impacts in Victoria, Australia: a 6-year retrospective studyResearch in context by Jacqueline M. Morris, Jake A. Lacey, Kerrie Stevens, Lamali Sadeesh Kumar, Mathilda Wilmot, Janet Strachan, Marion Easton, Daneeta Hennessy, Tony M. Korman, Andrew J. Daley, Katherine B. Gibney, Adam W.J. Jenney, Steven Y.C. Tong, Benjamin P. Howden, Norelle L. Sherry

“…Methods: To investigate these changes and prepare to implement routine genomic surveillance of iGAS for public health purposes, we performed whole genome sequencing (WGS) on iGAS isolates from Victoria, Australia between 2017 and 2022. …”
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Sources and Transmission Routes of Carbapenem-Resistant <i>Pseudomonas aeruginosa</i>: Study Design and Methodology of the SAMPAN Study by Anneloes van Veen, Selvi N. Shahab, Amber Rijfkogel, Anne F. Voor in ’t holt, Corné H. W. Klaassen, Margreet C. Vos, Yulia Rosa Saharman, Anis Karuniawati, Silvia Zelli, Desy De Lorenzis, Giulia Menchinelli, Giulia De Angelis, Maurizio Sanguinetti, Merel Kemper, Anniek E. E. de Jong, Sima Mohammadi, Valentine Renaud, Irena Kukavica-Ibrulj, Marianne Potvin, Guillaume Q. Nguyen, Jeff Gauthier, Roger C. Levesque, Heike Schmitt, Juliëtte A. Severin

“…Additionally, samples will be taken twice from wet hospital environments and monthly from the hospitals’ (drinking) water system, hospital and municipal wastewater treatment plants, and receiving rivers. Whole-genome sequencing will be performed to characterize CRPA isolates and determine the genetic relatedness among the isolates from different reservoirs. …”
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Assessment of Antibiotic Resistance Among Isolates of <i>Klebsiella</i> spp. and <i>Raoultella</i> spp. in Wildlife and Their Environment from Portugal: A Positive Epidemiologic Ou... by Carolina Sabença, Rani de la Rivière, Paulo Barros, João Alexandre Cabral, Roberto Sargo, Luís Sousa, Maria de Lurdes Enes Dapkevicius, Filipe Silva, Filipa Lopes, Ana Carolina Abrantes, Madalena Vieira-Pinto, Manuela Caniça, Gilberto Igrejas, Carmen Torres, Patrícia Poeta

“…Extended-spectrum β-lactamase (ESBL) production was tested by the double-disc synergy test, and one ESBL-producing <i>K. pneumoniae</i> isolate was screened by PCR and whole-genome sequencing. Biofilm production was analyzed using the microtiter plate method. …”
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Source attribution of human Campylobacter infection: a multi-country model in the European Union by Cecilie Thystrup, Maja Lykke Brinch, Clementine Henri, Lapo Mughini-Gras, Lapo Mughini-Gras, Eelco Franz, Kinga Wieczorek, Montserrat Gutierrez, Deirdre M. Prendergast, Geraldine Duffy, Catherine M. Burgess, Declan Bolton, Julio Alvarez, Julio Alvarez, Vicente Lopez-Chavarrias, Thomas Rosendal, Lurdes Clemente, Ana Amaro, Aldert L. Zomer, Katrine Grimstrup Joensen, Eva Møller Nielsen, Gaia Scavia, Magdalena Skarżyńska, Miguel Pinto, Mónica Oleastro, Wonhee Cha, Amandine Thépault, Katell Rivoal, Martine Denis, Marianne Chemaly, Tine Hald

“…The aim of this study was to predict the sources of human campylobacteriosis cases across multiple countries using available whole-genome sequencing (WGS) data and explore the impact of data availability and sample size distribution in a multi-country source attribution model.MethodsWe constructed a machine-learning model using k-mer frequency patterns as input data to predict human campylobacteriosis cases per source. …”
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Duckweed: a starch-hyperaccumulating plant under cultivation with a combination of nutrient limitation and elevated CO2 by Ling Guo, Ling Guo, Yang Fang, Songhu Wang, Yao Xiao, Yanqiang Ding, Yanling Jin, Xueping Tian, Anping Du, Zhihua Liao, Kaize He, Shuang Chen, Yonggui Zhao, Li Tan, Zhuolin Yi, Yuqing Che, Lanchai Chen, Jinmeng Li, Leyi Zhao, Peng Zhang, Zhengbiao Gu, Fangyuan Zhang, Yan Hong, Qing Zhang, Hai Zhao

“…In this study, we integrated whole-genome sequencing, epigenomics, transcriptomics, enzyme activity, and composition variation to elucidate the mechanisms of efficient starch accumulation in duckweed in terms of starch accumulation and carbon partitioning, regulation of the expression of genes in the starch metabolic pathway, and sucrose biosynthesis and transportation.Results and discussionAlthough Landoltia punctata exhibits dramatic gene family contraction, its starch content and productivity reached 72.2% (dry basis) and 10.4 g m-2 d-1, respectively, in 10 days, equivalent to a yield of 38.0 t ha-1 y-1, under nutrient limitation treatment with elevated CO2 levels. …”
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Comparative Genomics Reveals Pathogenicity-Related Loci in Shewanella algae by Jui-Hsing Wang, Guo-Cheng He, Yao-Ting Huang, Po-Yu Liu

“…In this study, we aim to determine the occurrence of common virulence genes in S. algae using whole-genome sequence and comparative genomic analysis. Comparative genomics reveals putative-virulence genes related to bile resistance, chemotaxis, hemolysis, and motility. …”
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misMM: An Integrated Pipeline for Misassembly Detection Using Genotyping-by-Sequencing and Its Validation with BAC End Library Sequences and Gene Synteny by Young-Joon Ko, Jung Sun Kim, Sangsoo Kim

“…As next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. …”
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First isolation and characterization of SARS-CoV-2 from COVID-19 patient of North East India by Aniruddha Jakharia, Biswajyoti Borkakoty, Sumi Pait, Gautam Baruah, Rahul Hazarika, Dipankar Biswas

“…Phylogenetic analyses of the whole genome sequences of the SARS-CoV-2 isolate (EPI_ISL_2501532 | 2020-05-19) showed monophyletic clade G and lineage B.1.1.…”
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Research Note: Novel reassortant avian influenza A(H9N2) Viruses in Wild Birds in Shanghai, China, 2020–2023 by Jie Hu, Yuting Xu, Min Ma, Chenyao Zhao, Yue Yuan, Guimei He

“…To better understand the genetic characteristics of these H9N2 viruses in Shanghai, the whole genome sequences were analyzed. Phylogenetical analysis showed that the nine H9N2 viruses have undergone complicated reassortment with waterfowl viruses along the East Asian-Australasian flyways. …”
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Urinary Catheter Colonization by Multidrug-Resistant Cedecea neteri in Patient with Benign Prostatic Hyperplasia by Peter S. Ginn, Serina B. Tart, Stephen M. Sharkady, Dorothea K. Thompson

“…This C. neteri isolate was resistant or intermediate to second-generation cephalosporins, penicillins, and certain β-lactamase inhibitor/β-lactam combinations. Analysis of whole genome sequence information for a representative C. neteri strain indicated the presence of multiple open reading frames with sequence similarity to β-lactamases, including a chromosome-encoded AmpC β-lactamase and metallo-β-lactamases, consistent with the resistance phenotype of this bacterium. …”
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Chromosome-level reference genome assembly of the gyrfalcon (Falco rusticolus) and population genomics offer insights into the falcon population in Mongolia by Farooq Omar Al-Ajli, Giulio Formenti, Olivier Fedrigo, Alan Tracey, Ying Sims, Kerstin Howe, Ikdam M. Al-Karkhi, Asmaa Ali Althani, Erich D. Jarvis, Sadequr Rahman, Qasim Ayub

“…Here, we generated a chromosome-level gyrfalcon reference genome using the Vertebrate Genomes Project (VGP) assembly pipeline. Using whole genome sequences of 49 falcons from different species and populations, including “Altai” falcons, we analyzed their population structure, admixture patterns, and demographic history. …”
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Mining the Proteome of subsp. ATCC 25586 for Potential Therapeutics Discovery: An Approach by Abdul Musaweer Habib, Md. Saiful Islam, Md. Sohel, Md. Habibul Hasan Mazumder, Mohd. Omar Faruk Sikder, Shah Md. Shahik

“…In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. …”
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Genome analysis and prevalence of SARS-CoV-2 Indonesian variants and the correlation with the outbreak timeline by Maria Prevyolita Indra Muliawan, Timotius Christopher Tantokusumo, Amalda Siti Anisa, Kholis Abdurachim Audah

“…Methods: We analyzed whole genome sequences of SARS-CoV-2 wild type and variants isolated from Indonesian samples, sourced from GenBank and the GISAID EpiCoV database. …”
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