Genomic characterization of antimicrobial-resistance and virulence factors in Salmonella isolates obtained from pig farms in Antioquia, Colombia. by María Isabel García-Álvarez, Juana L Vidal, Pilar Donado-Godoy, Jared Smith, Nikki Shariat, María Fernanda Valencia, Luis M Gómez-Osorio, Sara López-Osorio, Jenny J Chaparro-Gutiérrez

“…A total of 28 isolates of Salmonella spp. were included, which presented phenotypic resistance to more than one antibiotic used in pig farms. Whole genome sequencing (WGS) was performed in the Unit of Genomic of Agrosavia using an automated pipeline from the GHRU- Sanger Institute, employing the Illumina MiSeq platform.…”
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Isolation and characterization of a highly pathogenic strain of Vibrio harveyi EFL-2201 from pearl gentian grouper by Biao Yuan, Zhixia Zhuang, Xiaoru Wang, Huabin Huang, Qingpi Yan

“…In vitro assays indicated that the conditions during the outbreak were conducive to the proliferation, motility, biofilm formation, and chemotaxis of EFL-2201. Whole-genome sequencing of the strain revealed that mechanisms related to adhesion, secretion, toxins, and invasion significantly contributed to its pathogenicity. …”
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Studyof resistance of pathogenic and opportunistic fungi toantimycotics by A. D. Kozlova, S. P. Yatsentyuk, V. V. Sokolov, M. G. Manoyan

“…The results obtained can serve as a basis for the use of molecular methods to characterize fungi of Candida and Trichophyton genera, however, taking into account the biological features of pathogens from different groups it is reasonable to use several significant genome regions or the results of the whole genome sequencing, as well as the gene expression analysis for successful forecasting of potential resistance.…”
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Improved 11α-hydroxycanrenone production by modification of cytochrome P450 monooxygenase gene in Aspergillus ochraceus by Li Qianqian, Shi Li, Liu Yingying, Guan Shimin, Zhang Shuo, Cai Baoguo, Rong Shaofeng

“…To improve the efficiency of 11α-hydroxycanrenone production, the CYP monooxygenase-coding gene of MF018 was predicted and cloned based on whole-genome sequencing results. A recombinant A. ochraceus strain MF010 with the high expression of CYP monooxygenase was then obtained through homologous recombination. …”
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Genetic Diversity of Human Enterovirus in Kazakhstan, during 2022 by Dinara Kamalova, Assel Akhmetova, Asylulan Amirgazin, Igor Sytnik, Viktoriya Rudenko, Gulzhan Yessimkhanova, Dinagul Bayesheva, Sergey Yegorov, Alexander Shevtsov

“…We then genotyped enteroviral subtypes associated with AM (n = 50) and HA (n = 9) using next-generation sequencing (NGS) on the viral protein 1 (VP1), followed up by whole-genome sequencing of the isolated viral species. All identified EVs were species B EV, consisting of five echoviruses (E6, E9, E11, E21, and E25) and three coxsackieviruses (CVA9, CVB3, and CVB5) serotypes within the cohort. …”
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Evolution of SARS-CoV-2 in white-tailed deer in Pennsylvania 2021-2024. by Andrew D Marques, Matthew Hogenauer, Natalie Bauer, Michelle Gibison, Beatrice DeMarco, Scott Sherrill-Mix, Carter Merenstein, Ronald G Collman, Roderick B Gagne, Frederic D Bushman

“…From the 165 SARS-CoV-2 positive WTD, we recovered 25 whole genome sequences and an additional 17 spike-targeted amplicon sequences. …”
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A machine learning decision support tool optimizes WGS utilization in a neonatal intensive care unit by Edwin F. Juarez, Bennet Peterson, Erica Sanford Kobayashi, Sheldon Gilmer, Laura E. Tobin, Brandan Schultz, Jerica Lenberg, Jeanne Carroll, Shiyu Bai-Tong, Nathaly M. Sweeney, Curtis Beebe, Lawrence Stewart, Lauren Olsen, Julie Reinke, Elizabeth A. Kiernan, Rebecca Reimers, Kristen Wigby, Chris Tackaberry, Mark Yandell, Charlotte Hobbs, Matthew N. Bainbridge

“…Abstract The Mendelian Phenotype Search Engine (MPSE), a clinical decision support tool using Natural Language Processing and Machine Learning, helped neonatologists expedite decisions to whole genome sequencing (WGS) to diagnose patients in the neonatal intensive care unit. …”
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Genotype imputation in human genomic studies by A. A. Berdnikova, I. V. Zorkoltseva, Y. A. Tsepilov, E. E. Elgaeva

“…When performing imputation, genotype information from the study sample, in which only part of the genetic variants are known, is complemented using the standard (reference) sample, which has more complete genotype data (most often the results of whole-genome sequencing). Imputation has become an integral part of human genomic research due to the benefits it provides and the increasing availability of imputation tools and reference sample data. …”
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Polygenic burden of short tandem repeat expansions promotes risk for Alzheimer’s disease by Michael H. Guo, Wan-Ping Lee, Badri Vardarajan, Gerard D. Schellenberg, Jennifer E. Phillips-Cremins

“…Here, we genotype 312,731 polymorphic STR tracts genome-wide using PCR-free whole genome sequencing data from 2981 individuals (1489 AD case and 1492 control individuals). …”
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Sanger validation of WGS variants by Arina Kopernik, Mariia Sayganova, Gaukhar Zobkova, Natalia Doroschuk, Anna Smirnova, Daria Molodtsova-Zolotukhina, Olesya Sagaydak, Oxana Ryzhkova, Sergey Kutsev, Olga Groznova, Lyusya Melikyan, Elizaveta Bondarchuk, Mary Woroncow, Eugene Albert, Viktor Bogdanov, Pavel Volchkov

“…Despite that, no works to date report the concordance between variants from whole genome sequencing and their gold-standard Sanger validation. …”
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A sequencing-based method for quantifying gene-deletion mutants of bacteria in the intracellular environment by Xiao Fei, Xiao Fei, Zengzhi Yuan, Zengzhi Yuan, Sandra Marina Wellner, Yibing Ma, John Elmerdahl Olsen

“…Notably, the simplicity and standardization of the method, rooted in standard whole-genome sequencing protocols, make it easily implementable across various laboratories.…”
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An evaluation of the severe acute respiratory infection surveillance system in Ireland by Louise Marron, Roisin Duffy, Joan O’Donnell, Lisa Domegan

“…Time to receipt of whole genome sequencing (WGS) results was 40 days (IQR 30–61). …”
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Hypermutability bypasses genetic constraints in SCV phenotypic switching in Pseudomonas aeruginosa biofilms by Romina A. Tobares, Román A. Martino, Claudia A. Colque, Gaston L. Castillo Moro, Alejandro J. Moyano, Andrea G. Albarracín Orio, Andrea M. Smania

“…Through experimental evolution and whole-genome sequencing, we show that both wild-type and mutator strains undergo parallel evolution by accumulating compensatory mutations in factors regulating intracellular c-di-GMP levels, particularly in the Wsp and Yfi systems. …”
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Truncated SPAG9 as a novel candidate gene for a new syndrome: Coarse facial features, albinism, cataract and developmental delay (CACD syndrome) by Majid Alfadhel, Bashayr S. Alhubayshi, Muhammad Umair, Ahmed Alfaidi, Deemah Alwadaani, Essra Aloyouni, Safdar Abbas, Abdulkareem Al Abdulrahman, Mohammed Aldrees, Abeer Al Tuwaijri, Ruaa S. Alharithy, Abdulaziz Alajlan, Abdulrahman Alswaid, Saad Almohrij, Sultan Al-Khenaizan

“…We identified two families (A and B) having multisystem features like coarse facial features, albinism, cataracts, skeletal abnormalities, and developmental delay. Whole genome sequencing (WGS) in families A and B revealed a homozygous frameshift variant (c.903del; p.Phe301Leufs*2) in the SPAG9 gene. …”
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Bioinformatics Analysis, Prokaryotic Expression and Biological Activity of Lysin from Vibrio parahaemolyticus Phage vB_VpP_1 by ZHANG Defu, YANG Wenjing, LIU Ke, LIU Qingqing, BAI Wutong, LI Fan, LÜ Xinran, BAI Xue, TAN Xiqian, LI Xuepeng, LI Jianrong

“…To study the in vitro cleavage effect of a recombinant lysin from bacteriophage vB_VpP_1 on Vibrio parahaemolyticus, the gp32 gene fragment of vB_VpP_1 was identified as a lysin gene according to the results of whole-genome sequencing (WGS) and functional analysis. The amino acid sequence and structure of gp32 were analyzed by various tools such as Expasy. …”
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Nematicidal potential of Microbacterium maritypicum Sneb159 against Heterodera glycines and the complete genome sequence analysis by Jing Zhao, Jing Zhao, Jing Zhao, Zhifu Xing, Aatika Sikandar, Yuxi Duan

“…Biological control provides a strategy for sustainable and environmentally friendly nematode management.MethodsIn this study, solid-phase microextraction gas chromatography-mass spectrometry (SPME-GC-MS) was used to reveal the volatile nematicidal compounds of Microbacterium maritypicum Sneb159 and the mode of action was further elucidated via whole genome sequencing.ResultsThe present study demonstrated that M. maritypicum Sneb159 fermentation broth showed strong nematicidal activities against H. glycines. …”
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SMARCA4-related Coffin-Siris syndrome in newborn: a case report and literature review by Yuqian Wang, Li Zhang, Jing Zhu, Liu Yang, Chan Wang, Ning Zou

“…For patients with developmental abnormalities, whole-genome sequencing or whole-exome sequencing is particularly important to assist diagnosis. …”
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On the ability to extract MLVA profiles of Vibrio cholerae isolates from WGS data generated with Oxford Nanopore Technologies by Jérôme Ambroise, Bertrand Bearzatto, Jean-Francois Durant, Leonid M. Irenge, Jean-Luc Gala

“…The MLVAType shiny application was previously designed to extract MLVA profiles of Vibrio cholerae isolates from whole-genome sequencing (WGS) data, and provide backward compatibility with traditional MLVA typing methods. …”
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A chemical genetic screen with the EXO70 inhibitor Endosidin2 uncovers potential modulators of exocytosis in Arabidopsis by Xiaohui Li, Diwen Wang, Xianglin Yin, Mingji Dai, Christopher J. Staiger, Chunhua Zhang

“…This approach led to the identification of 70 ES2‐hypersensitive mutants, named es2s. Through a whole‐genome sequencing‐based mapping strategy, 14 nonallelic es2s mutants were mapped and the candidate mutations reported here. …”
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The Single-Nucleotide Polymorphism (SNP) Validity to Detect Omicron Variants by Lia Gardenia Partakusuma, Luhung Budiailmiawan, null Budiman, Ida Parwati, null Aryati, Basti Andriyoko, Louisa Markus, Corine Niswara, Cut Nur Cinthia Alamanda

“…Variants of SARS-CoV-2 are determined by the whole genome sequencing (WGS) assay, which is time-consuming, with limited availability (only in several laboratories). …”
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