Understanding the clinical and molecular epidemiological characteristics of carbapenem-resistant Acinetobacter baumannii infections within intensive care units of three teaching ho... by Pengyu Zhang, Jingchen Hao, Yafen Zhang, Junfeng Su, Guozhuang Sun, Jun Xie, Jian Hu, Guocai Li

“…Genome characteristics of isolates were investigated by whole genome sequencing. Multilocus sequence typing and phylogenetic trees were used to assess the genetic similarity of isolates. …”
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Microbial keratitis in Southern Malawi: a microbiological pilot study by Timothy Neal, Dean Everett, Stephen B Kaye, Alistair Darby, Moira Gandiwa, Shaffi Mdala, Caroline E Corless, Rose Herbert, Nicholas A V Beare, Tobi F Somerville, Thokozani Zungu, Malcolm J Horsburgh, Petros C Kayange

“…We investigated the feasibility of using a novel corneal impression membrane (CIM) for obtaining and processing samples by culture, PCR and whole-genome sequencing (WGS) in patients presenting with suspected MK in Malawi.Methods and analysis Samples were collected from patients presenting with suspected MK using a 12 mm diameter polytetrafluoroethylene CIM disc. …”
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The Mla pathway promotes Vibrio cholerae re-expansion from stationary phase by Deborah R. Leitner, Franz G. Zingl, Alexander A. Morano, Hailong Zhang, Matthew K. Waldor

“…By monitoring the abundances of genomically barcoded libraries of WT and ∆mlaE strains, we observed that a few barcodes dominated the mutant culture at 96 h, suggesting that the similarity of the population sizes at this time was caused by expansion of a subpopulation containing a mutation that suppressed the defect of ∆mlaE. Whole genome sequencing revealed that mlaE suppressors inactivated flagellar biosynthesis. …”
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The Presence of Two Distinct Lineages of the Foot-And-Mouth Disease Virus Type A in Russia in 2013–2014 Has Significant Implications for the Epidemiology of the Virus in the Region... by Victor V. Nikiforov, Sergey A. Noskov, Alexander V. Sprygin, Mohammad Abed Alhussen, Anastasia S. Krylova, Taisia V. Erofeeva, Svetlana N. Fomina, Svetlana R. Kremenchugskaya, Fedor I. Korennoy, Maxim V. Patrushev, Ilya A. Chvala, Tamara K. Mayorova, Stepan V. Toshchakov

“…In this study, we investigated the FMDV strains circulating in Russia during the 2013–2014 period in geographically distant regions utilizing whole genome sequencing followed by maximum-likelihood phylogenetic reconstruction of whole genome and VP1 gene sequences. …”
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Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland by Anna Tumeo, Francesca McDonagh, Aneta Kovarova, Kate Ryan, Christina Clarke, Georgios Miliotis

“…Antibiotic susceptibility testing was performed using the Sensititre-EUMDRXXF plate. Whole-genome-sequencing was conducted with NextSeq1000, and genomic analysis identified antibiotic-resistance-genes (ARGs) and virulence-factors (VFs). …”
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Identification and Characterization of a Cryptic Genomic Deletion-Insertion in EYA1 Associated with Branchio-Otic Syndrome by Hao Zheng, Jun Xu, Yu Wang, Yun Lin, Qingqiang Hu, Xing Li, Jiusheng Chu, Changling Sun, Yongchuan Chai, Xiuhong Pang

“…Real-time PCR at multiple regions of EYA1 confirmed the existence of this genomic deletion and extended its 5′ boundary beyond the 5′-UTR. Whole genome sequencing subsequently located the 5′ and 3′ breakpoints to 19268 bp upstream to the ATG initiation codon and 3180 bp downstream to exon 5. …”
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An initial exploration of core collection construction and DNA fingerprinting in Elymus sibiricus L. using SNP markers by Xinrui Li, Xinrui Li, Xinrui Li, Daping Song, Mingfeng Li, Daxu Li, Minghong You, Yan Peng, Jiajun Yan, Shiqie Bai

“…Additionally, we identified 290 SNP loci from among the high-quality SNP loci generated by whole-genome sequencing of the 90 E. sibiricus samples as candidate markers. …”
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Genome-wide analyses of genomic diversity, population structure and selection signatures in Italian turkey populations by Medhat S. Saleh, Vincenzo Landi, Martijn F.L. Derks, Gerardo Centoducati, Martien A.M. Groenen, Pasquale De Palo, Elena Ciani, Maria G. Strillacci, Alessandro Bagnato, Nicola Pugliese, Elena Circella, Antonio Camarda

“…Italian local turkey populations are an important source of genetic diversity that should be preserved through an in vivo approach. Whole genome sequencing (WGS) and genotyping datasets were used to assess genetic variability within and across populations, to perform a genome-wide comparative analysis among populations and to identify selection signatures in Italian turkey populations. …”
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The rapid detection of a neonatal unit outbreak of a wild-type Klebsiella variicola using decentralized Oxford Nanopore sequencing by Rhys T. White, Michelle Balm, Megan Burton, Samantha Hutton, Jamaal Jeram, Matthew Kelly, Donia Macartney-Coxson, Tanya Sinha, Henrietta Sushames, David J. Winter, Maxim G. Bloomfield

“…This triggered investigation with a nanopore-based decentralized whole-genome sequencing (dWGS) system in operation at our laboratory. …”
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Characterization of <i>Streptococcus pyogenes</i> Strains from Tonsillopharyngitis and Scarlet Fever Resurgence, 2023—FIRST Detection of M1_UK in Bulgaria by Emma Keuleyan, Theodor Todorov, Deyan Donchev, Ani Kevorkyan, Radoslava Vazharova, Alexander Kukov, Georgi Todorov, Boriana Georgieva, Iskra Altankova, Yordanka Uzunova

“…Virulence factors were identified using multiplex PCR and whole genome sequencing (WGS). Immune responses were measured through detection of serum complement levels, lymphocyte subsets, and cytokine profiling. …”
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Study on the multidrug resistance and transmission factors of Staphylococcus aureus at the ‘animal–environment–human’ interface in the broiler feeding cycle by Fangyuan Hu, Fangyuan Hu, Yaopeng Liu, Yaopeng Liu, Lin Wang, Juan Wang, Na Liu, Yan Li, Xiaoxiao Duan, Junwei Wang, Mingzhe Lu, Junhui Liu, Zhina Qu, Keguang Han

“…Based on the concept of “One Health,” this study analyzed the multidrug resistance and transmission factors of S. aureus isolated from the “animal–environment–human” interface during one feeding cycle of commercial broilers in China by using antimicrobial susceptibility testing and whole genome sequencing (WGS) technologies. The results showed that in stage 1, the isolation rate of S. aureus was 1.32% (6/453), that of workers was 25.0% (4/16), and that of environmental samples was 0.69% (2/287), and the multidrug resistance rate was 83.33%. …”
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Characterization of Enterobacterales growing on selective CPE screening plates with a focus on non-carbapenemase-producing strains by Reut Efrati Epchtien, Elizabeth Temkin, Mor N. Lurie-Weinberger, Ophir Kastel, Alona Keren-Paz, David Schwartz, Yehuda Carmeli

“…Fourier-transform infrared spectroscopy (FTIR) was used to analyze phenotypic similarity, and whole genome sequencing was conducted on a subset of non-CPE isolates. …”
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Characterizing immune biomarkers and effector CD8+ T-cell exhaustion in pancreatic adenocarcinoma via single-cell RNA sequencing profiling by Rawaa AlChalabi, Raghda Makia, Semaa A. Shaban, Ahmed AbdulJabbar Suleiman

“…Methods: We employed a multi-omics approach, integrating single-cell RNA sequencing data with whole genome sequencing to identify dysregulated exhaustion-related immune markers in CD8+ T-cells in PDAC. …”
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Genomic characterization and radiation tolerance of Naganishia kalamii sp. nov. and Cystobasidium onofrii sp. nov. from Mars 2020 mission assembly facilities by Patrick Leo, Marcus de Melo Texeira, Atul M. Chander, Nitin K. Singh, Anna C. Simpson, Andrey Yurkov, Fathi Karouia, Jason E. Stajich, Christopher E. Mason, Kasthuri Venkateswaran

“…The species-level classification of these two novel strains, using traditional colony and cell morphology methods combined with the phylogenetic reconstructions using multi-locus sequence analysis (MLSA) based on several gene loci (ITS, LSU, SSU, RPB1, RPB2, CYTB and TEF1), and whole genome sequencing (WGS) was carried out. This polyphasic taxonomic approach supported the conclusion that the two basidiomycetous yeasts belong to hitherto undescribed species. …”
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Genomic and virulent characterization of a duck-associated Salmonella serovar Potsdam from China by Hongli An, Xiamei Kang, Chenhu Huang, Chenghao Jia, Jiaqi Chen, Yingying Huang, Qianzhe Cao, Yan Li, Biao Tang, Min Yue

“…Our study aims to fill this gap by providing genomic features of the antimicrobial resistance and virulence potential of Salmonella isolates from dead duck embryos using whole-genome sequencing and in silico toolkits. We also sought to assess the virulent characterization of the major serovar isolates by experimental infection of chicken and duck embryos. …”
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Targeted dual biologic therapy for erythroderma of unknown etiology guided by high-parameter peripheral blood immunophenotyping by Hannah L. Cornman, Martin P. Alphonse, Arbor Dykema, Alexander L. Kollhoff, Kevin K. Lee, Jaya Manjunath, Emily Z Ma, Varsha Parthasarathy, Junwen Deng, Thomas Pritchard, Anusha Kambala, Melika Marani, Kayla A. Parr, Javid P. Mohammed, Madan M. Kwatra, Jay H. Bream, Won Jin Ho, Shawn G. Kwatra

“…We found that the index patient had a novel form of erythroderma characterized by increased interleukin (IL)-13- and IL-17-producing γVδ2 T cells, basophils, and activated platelets. Whole-genome sequencing of PBMCs and immunofluorescence staining of skin biopsies revealed increased expression of Th2- (IL-13, IL-4Rα) and Th17-associated markers (IL-17, IL-17Rα) and non-functional mutations associated with Th2 and Th17 signaling, demonstrating that PBMCs can reflect cutaneous disease pathology. …”
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Insufficient gene expression and lost gene regulatory network may underlie the mechanism of Hirschsprung Disease in 5p–syndrome by Yizhao Luan, Peng Li, Yuanyuan Luo, Hong Zhang, Xiaochun Zhu, Yan Zhang, Aihua Yin, Qiang Wu, Chengwei Chai

“…Here, we conducted a study on two patients with CDC and HSCR using whole genome sequencing (WGS) analyses. Our WGS data confirmed the deletion regions on 5p associated with CDC and indicated potential unknown genetic mechanisms underlying HSCR. …”
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Survival outcome prediction of esophageal squamous cell carcinoma patients based on radiomics and mutation signature by Ting Yan, Zhenpeng Yan, Guohui Chen, Songrui Xu, Chenxuan Wu, Qichao Zhou, Guolan Wang, Ying Li, Mengjiu Jia, Xiaofei Zhuang, Jie Yang, Lili Liu, Lu Wang, Qinglu Wu, Bin Wang, Tianyi Yan

“…The mutation signature was constructed based on whole genome sequencing data and found to be significantly associated with the prognosis of patients with ESCC. …”
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Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds by Bortoluzzi, Chiara, Restoux, Gwendal, Rouger, Romuald, Desnoues, Benoit, Petitjean, Florence, Bosse, Mirte, Tixier-Boichard, Michèle

“…We here used temporal whole-genome sequencing data to assess the effects of a conservation program on the genetic diversity (Δπ), deleterious variation (ΔL), and inbreeding (ΔF) of two local French chicken breeds, the Barbezieux and Gasconne. …”
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Prevalence of β-lactam antibiotic resistance of Escherichia coli isolated from a neonatal intensive care unit by Jian Zhou, Jingqian Zhou, Min Chen, Pan Lü, Chunming Jiang

“…Genomic DNA was extracted for whole genome sequencing, construction of plasmid physical maps, locating resistance genes, and analyzing flanking regions and the resistance gene-related sequences. …”
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