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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Lopinavir and Ritonavir have High Affinity Toward the SARS-CoV-2 S-protein Receptor-binding Domain Sequenced in Brazil by Aline Diogo Marinho, Helyson Lucas Bezerra Braz, João Alison de Moraes Silveira, Danilo Galvão Rocha, Roberta Jeane Bezerra Jorge, Geanne Matos de Andrade

“…Methods: In this study, we employed in silico docking models to investigate the molecular interactions between the receptor-binding domain (RBD) of the SARS-CoV-2 spike glycoprotein, derived from the Brazilian genome sequence, and seven clinically approved drugs: umifenovir, darunavir, lopinavir, ritonavir, remdesivir, pirfenidone, and oseltamivir. …”
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Emergence and polyclonal dissemination of NDM-5/OXA-181 carbapenemase-producing Escherichia coli in the French Indian Ocean territories by Thibaut Vedani, Matthieu Pot, Thomas Garrigos, Loïk Sababadichetty, Marion Daniel, David Wilkinson, Thierry Benoit-Cattin, Olivier Belmonte, Patrick Mavingui, Laurent Dortet, Guillaume Miltgen

“…Results A total of 92 isolates of NDM-5 (n = 67) and OXA-181 (n = 25) CPEc was collected from Reunion (n = 55) and Mayotte (n = 37) islands. Whole-genome sequencing identified 4 majors STs (ST58, ST167, ST405 and ST410). …”
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Enhancing diagnostic outcomes in kidney genetic disorders: the KidGen national kidney genomics study protocol by Amali Mallawaarachchi, Hugh McCarthy, Thomas A. Forbes, Kushani Jayasinghe, Chirag Patel, Stephen I. Alexander, Tiffany Boughtwood, Jeffrey Braithwaite, Aron Chakera, Sam Crafter, Ira W. Deveson, Randall Faull, Trudie Harris, Lilian Johnstone, Matthew Jose, Anna Leaver, Melissa H. Little, Daniel MacArthur, Tessa Mattiske, Christine Mincham, Kathy Nicholls, Catherine Quinlan, Michael C. J. Quinn, Gopala Rangan, Jessica Ryan, Cas Simons, Ian Smyth, Madhivanan Sundaram, Peter Trnka, Laura Wedd, Erik Biros, Zornitza Stark, Andrew Mallett

“…These include re-analysing existing data and/or undergoing advanced genomic testing methods, including short and long-read whole-genome sequencing, RNA sequencing, and functional genomics strategies using mouse modelling or kidney organoids. …”
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Genomic analysis and replication kinetics of the closely related EHV-1 neuropathogenic 21P40 and abortigenic 97P70 strains by Eslam Mohamed, Ines Zarak, Nick Vereecke, Sebastiaan Theuns, Kathlyn Laval, Hans Nauwynck

“…Cases of EHM have significantly increased since the beginning of the twenty-first century. The genomic sequences of five isolates associated with the fatal neurological outbreak in Valencia, Spain, in 2021 were analyzed and documented. …”
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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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Molecular Epidemiology of Escherichia coli Resistant to Carbapenems, Fluoroquinolones, and Aminoglycosides Isolated from One of the Largest Hospitals in Vietnam in 2014–2019 by Tohru Miyoshi-Akiyama, Do Van Thanh, Truong Thai Phuong, Nguyen Quang Huy, Pham Thi Phuong Thuy, Teruo Kirikae, Pham Hong Nhung, Norio Ohmagari

“…This study was designed to clarify the molecular epidemiology of Escherichia coli isolates resistant to carbapenems, fluoroquinolones, and aminoglycosides isolated from patients admitted to one of the largest hospitals in Vietnam in 2014–2019 based on both whole-genome sequencing (WGS) and phenotypic data. Methodology. …”
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Carbon monoxide-oxidising Pseudomonadota on volcanic deposits by Robin A. Dawson, Nicola Fantom, Tamara Martin-Pozas, Patricia Aguila, Gary M. King, Marcela Hernández

“…Both strains oxidise CO across a broad range of concentrations (< 100 ppmv – 10,000 ppmv), and genome sequence analysis revealed a candidate form-I carbon monoxide dehydrogenase (CODH), which is likely to catalyse this process. …”
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Analysis of the Genomes and Adaptive Traits of <i>Skermanella cutis</i> sp. nov., a Human Skin Isolate, and the Type Strains <i>Skermanella rosea</i> and <i>Skermanella mucosa</i> by Yujin Choi, Munkhtsatsral Ganzorig, Kyoung Lee

“…TT6^T, isolated from human skin, with a focus on its metabolic and environmental adaptations. Genome sequencing and phylogenomic analyses revealed that the strain TT6^T is most closely related to <i>S. rosea</i> M1^T, with average nucleotide identity and digital DNA–DNA hybridization values of 94.14% (±0.5%) and 64.7%, respectively. …”
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High-Resolution Melting Analysis to Detect Antimicrobial Resistance Determinants in South African Neisseria gonorrhoeae Clinical Isolates and Specimens by Nireshni Mitchev, Ravesh Singh, Veron Ramsuran, Arshad Ismail, Mushal Allam, Stanford Kwenda, Florah Mnyameni, Nigel Garrett, Khine Swe Swe-Han, Abraham J. Niehaus, Koleka P. Mlisana

“…Real-time PCR and high-resolution melting analysis were used to detect porA pseudogene (species-specific marker) and resistance-associated targets. Whole-genome sequencing was used as the gold standard for the presence of point mutations. …”
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Taxonomic refinement of Bacillus thuringiensis by Nagham Shiekh Suliman, Reza Talaei-Hassanloui, Hamid Abachi, Sadegh Zarei, Ebrahim Osdaghi

“…By October 2023, whole genome sequences (WGS) of 885 bacterial strains were labeled as B. thuringiensis in the NCBI GenBank database. …”
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Xanthohumol and echinocystic acid induces PSTVd tolerance in tomato by Wenkun Tang, Zhichao Tang, Haiyi Liu, Jinbiao Lu, Qianyun Du, Huan Tian, Jingwei Li

“…We obtained the full‐length genome sequence of previously conserved PSTVd and inoculated it on four genotypes of semi‐cultivated tomatoes selected from a local tomato germplasm resource. …”
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mRNA technology as one of the promising platforms for the SARS-CoV-2 vaccine development by A. A. Ilyichev, L. A. Orlova, S. V. Sharabrin, L. I. Karpenko

“…After the genome sequence of SARS-CoV-2 (Severe acute respiratory syndrome-related coronavirus 2) was published and the number of infected people began to increase rapidly, many global companies began to develop a vaccine. …”
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Composition of the sputum bacterial microbiome of patients with different pathomorphological forms of non-small-cell lung cancer by V. G. Druzhinin, E. D. Baranova, P. S. Demenkov, L. V. Matskova, A. V. Larionov

“…Further research should be devoted to the search for microbiome biomarkers of lung cancer at the level of bacterial species using whole-genome sequencing.…”
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Comparison of Conservation Strategies for California Channel Island Oak (Quercus tomentella) Using Climate Suitability Predicted From Genomic Data by Alayna Mead, Sorel Fitz‐Gibbon, John Knapp, Victoria L. Sork

“…We performed whole‐genome sequencing on Island Oak individuals and Q. chrysolepis, a closely related species that hybridizes with Island Oak (127 total), to characterize genetic structure and introgression across its range and assess the relationship between genomic variation and climate. …”
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Spatio‐Temporal Changes in Effective Population Size in an Expanding Metapopulation of Eurasian Otters by Nia Evelyn Thomas, Elizabeth A. Chadwick, Michael W. Bruford, Frank Hailer

“…We obtained clear bottleneck signals in East England, and signals of recent population expansion in Wales and South West England in some analyses, consistent with national otter surveys and recent findings from whole‐genome sequencing. Analyses that did not account for spatial genetic structuring yielded strong spurious signals of United Kingdom‐wide population expansion, and Ne estimates from these analyses were suppressed by a factor of 3–4. …”
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Genomic and mutational analysis of Pseudomonas syringae pv. tagetis EB037 pathogenicity on sunflower by Jude E. Maul, John Lydon, Dilip Lakshman, Colin Willard, Hyesuk Kong, Daniel P. Roberts

“…Abstract Background Pseudomonas syringae pv. tagetis (Pstag) causes apical chlorosis on sunflower and various other plants of the Asteraceae family. Whole genome sequencing of Pstag strain EB037 and transposon-mutant derivatives, no longer capable of causing apical chlorosis, was conducted to improve understanding of the molecular basis of disease caused by this pathogen. …”
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Allele-specific PCR with fluorescently labeled probes: criteria for selecting primers for genotyping by V. A. Devyatkin, A. A. Shklyar, A. Zh. Fursova, Yu. V. Rumyantseva, O. S. Kozhevnikova

“…Single-nucleotide polymorphisms (SNPs) can serve as reliable markers in genetic engineering, selection, screening examinations, and other fields of science, medicine, and manufacturing. Whole-genome sequencing and genotyping by sequencing can detect SNPs with high specificity and identify novel variants. …”
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Archival and Newly Isolated Historical <i>Bacillus anthracis</i> Strains Populate the Deeper Phylogeny of the A.Br.075(Sterne) Clade by Markus Antwerpen, Peter Braun, Wolfgang Beyer, Dirk Aldenkortt, Michael Seidel, Gregor Grass

“…In this study, we genome-sequenced and analyzed 56 additional <i>B. anthracis</i> isolates of the A.Br.075 clade. …”
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Virulence is not directly related to strain success in planta in Clavibacter nebraskensis by Molly Veregge, Cory D. Hirsch, Matthew J. Moscou, Liana Burghardt, Peter Tiffin, Devanshi Khokhani

“…Here, we used phenotypic assays and a high-throughput whole-genome sequencing approach to explore among-strain variation in virulence and multistrain reproductive success in planta. …”
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