Animal Brucellosis in Egypt: Review on Evolution, Epidemiological Situation, Prevalent <i>Brucella</i> Strains, Genetic Diversity, and Assessment of Implemented National Control Me... by Ahmed M. S. Menshawy, Acacia Ferreira Vicente, Yamen M. Hegazy, Vitomir Djokic, Mahmoud E. R. Hamdy, Luca Freddi, Essam M. Elbauomy, Ashraf E. Sayour, Claire Ponsart, Nour H. Abdel-Hamid

“…This review delves deeply into brucellosis’s current epidemiological situation and potential sources of livestock infection in Egypt during the last two decades. MLVA-16 and Whole Genome Sequencing based on core-genome SNP analyses confirm the presence of different <i>B. abortus</i> and <i>B. melitensis</i> outbreak strains, both older widely disseminated <i>Brucella</i> strains and newly introduced ones. …”
Get full text

Activity of Aztreonam-avibactam and other β-lactamase inhibitor combinations against Gram-negative bacteria isolated from patients hospitalized with pneumonia in United States medi... by Helio S. Sader, Rodrigo E. Mendes, S. J. Ryan Arends, Timothy B. Doyle, Mariana Castanheira

“…Carbapenem-resistant Enterobacterales (CRE; isolates with MIC values of > 2 mg/L for imipenem and/or meropenem) isolates were screened for carbapenemases by whole genome sequencing. Results Gram-negative bacilli represented 71.1% of organisms. …”
Get full text

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). …”
Get full text

Improving genomic prediction accuracy of pig reproductive traits based on genotype imputation using preselected markers with different imputation platforms by J. Sun, J. Wei, Y. Pan, M. Cao, X. Li, J. Xiao, G. Yang, T. Yu

“…In this study, the imputation from 80 k Single Nucleotide Polymorphism chip data of 832 Large White pigs to whole-genome sequencing genotypes was performed by Swine Imputation Server, Pig Haplotypes Reference Panel (PHARP), Animal Genotype Imputation Database and 1k-pig-genomes four thousand-pig imputation panels. …”
Get full text

A gut-derived Streptococcus salivarius produces the novel nisin variant designated nisin G and inhibits Fusobacterium nucleatum in a model of the human distal colon microbiome by Garreth W. Lawrence, Enriqueta Garcia-Gutierrez, A. Kate O’Mahony, Calum J. Walsh, Paula M. O'Connor, Máire Begley, Caitriona M. Guinane, Paul D. Cotter

“…Screening for gut-derived strains that exhibit anti-F. nucleatum activity in vitro revealed Streptococcus salivarius DPC6487 as a strain of interest. Whole-genome sequencing of S. salivarius DPC6487 identified a nisin operon with a novel structural variant designated nisin G. …”
Get full text

Research note: A low-density SNP genotyping panel for Chinese native chickens by Jie Wang, Siyuan Xing, Yan Zhou, Jie Liu, Yan Sun, Qiuxia Lei, Haixia Han, Wei Liu, Dapeng Li, Fuwei Li, Dingguo Cao

“…The panel design was based on whole genome sequencing data from 7 local breeds and a commercial breed. …”
Get full text

Population Genomics Reveals Elevated Inbreeding and Accumulation of Deleterious Mutations in White Raccoon Dogs by Yinping Tian, Yu Lin, Yue Ma, Jiayi Li, Sunil Kumar Sahu, Jiale Fan, Chen Lin, Zhiang Li, Minhui Shi, Fengping He, Lianduo Bai, Yuan Fu, Zhangwen Deng, Huabing Guo, Haimeng Li, Qiye Li, Yanchun Xu, Tianming Lan, Zhijun Hou, Yanling Xia, Shuhui Yang

“…By analyzing and comparing whole-genome sequencing data from 20 white raccoon dogs and 38 normal raccoon dogs, we detected an increased occurrence of loss-of-function (LoF) mutations in white raccoon dogs compared with normal raccoon dogs. …”
Get full text

Biological Characteristics and Whole-Genome Analysis of a Porcine <i>E. coli</i> Phage by Shenghui Wan, Nana Li, Sajid Habib, Pei Zheng, Yanfang Li, Yan Liang, Yonggang Qu

“…Genomic features were analyzed using whole-genome sequencing. (3) Results: A lytic phage named vB_EcoS_Psq-1 (abbreviated as Psq-1) was successfully isolated. …”
Get full text

Significance of KLK7 expression, polymorphisms, and function in sheep horn growth by Mingzhu Shan, Hao Li, Xinyue Li, Guoqing Zhang, Jianxin Shi, Pingjie Feng, Lisheng Zhou, Zhangyuan Pan, Mingxing Chu

“…Potential functional sites of KLK7 were explored using whole-genome sequencing (WGS) data. Allele specific expression sites in the KLK7 gene sequence were identified. …”
Get full text

Genomic epidemiology of third-generation cephalosporin-resistant Escherichia coli from companion animals and human infections in Europe by Adrien Biguenet, Benoit Valot, Farid El Garch, Xavier Bertrand, Didier Hocquet

“…The aim of this study was to compare the genomes of third-generation cephalosporin-resistant (3GC-R) Escherichia coli responsible for human and pet infections in Europe.Whole-genome sequencing data from 3GC-R E. coli isolated from clinical samples of humans, dogs and cats, and published in eight European studies were re-analyzed using bioinformatics tools. …”
Get full text

Characterization of the genomic landscape of canine diffuse large B-cell lymphoma reveals recurrent H3K27M mutations linked to progression-free survival by Anna Darlene van der Heiden, Raphaela Pensch, Sophie Agger, Heather L. Gardner, William Hendricks, Victoria Zismann, Shukmei Wong, Natalia Briones, Bryce Turner, Karin Forsberg-Nilsson, Cheryl London, Kerstin Lindblad-Toh, Maja Louise Arendt

“…Our study aimed to characterize the mutational landscape of cDLBCL using whole-genome sequencing of matched tumor-normal samples obtained from a cohort of 43 dogs previously enrolled in a clinical trial for which longitudinal follow-up was available. …”
Get full text

Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63 by Tamila Musaeva, Artem Fadeev, Maria Pisareva, Veronika Eder, Andrey Ksenafontov, Margarita Korzhanova, Valery Tsvetkov, Alexander Perederiy, Irina Kiseleva, Daria Danilenko, Dmitry Lioznov, Andrey Komissarov

“…In this study, we developed a two-pool, long-amplicon (900–1100 bp) PCR primer panel for the whole-genome sequencing of four seasonal hCoV species. The panel was validated using nasopharyngeal swab samples collected within the Global Influenza Hospital Surveillance Network (GIHSN) project. …”
Get full text

A novel compound heterozygous mutation in the DYNC2H1 gene in a Chinese family with Jeune syndrome by Sujie Xiong, Guangyao Hu, Yao Zhou, Fei Sun, Yanlin Ma

“…Methods Cytogenetic and molecular genetic analyses of amniotic fluid via whole-genome sequencing (WGS), routine G-banded karyotype analysis, fluorescent quantitative polymerase chain reaction, and whole-exome sequencing (WES) were performed at 19 weeks. …”
Get full text

Cancer phylogenetic tree inference at scale from 1000s of single cell genomes by Salehi, Sohrab, Dorri, Fatemeh, Chern, Kevin, Kabeer, Farhia, Rusk, Nicole, Funnell, Tyler, Williams, Marc J., Lai, Daniel, Andronescu, Mirela, Campbell, Kieran R., McPherson, Andrew, Aparicio, Samuel, Roth, Andrew, Shah, Sohrab P., Bouchard-Côté, Alexandre

“…A new generation of scalable single cell whole genome sequencing (scWGS) methods allows unprecedented high resolution measurement of the evolutionary dynamics of cancer cell populations. …”
Get full text

Outbreak of carbapenem resistant Klebsiella pneumoniae in a neurorehabilitation unit: Genomic epidemiology reveals complex transmission pattern in a tertiary care hospital by Maria Grazia Silvotti, Erika Scaltriti, Luca Bolzoni, Beatrice Zerbi, Gabriella Tocci, Andrea Zappavigna, Gianfranco Lamberti, Federico Donati, Franco Federici, Stefano Pongolini, Giuliana Lo Cascio

“…We report an outbreak by KPC-Kp, in a neurorehabilitation unit in Italy, analysed through whole-genome sequencing (WGS) for transmission routes reconstruction to improve management of KPC-Kp infections in rehabilitation units. …”
Get full text

Genomic characteristics of ST6115 carbapenem-resistant Klebsiella pneumoniae coharboring blaNDM-1 and blaIMP-4 by Xiaofang Xie, Xiaofang Xie, Yaxuan Zhai, Zhichen Zhu, Feinan Qian, Feinan Qian, Jie Zhu, Qizhao Gao, Hong Du, Hong Du

“…ObjectivesThe aim of this study is to characterize the genomic features of ST6115 carbapenem-resistant Klebsiella pneumoniae (CRKP) co-harboring blaNDM-1 and blaIMP-4.MethodsThe genome sequences of one ST6115 Klebsiella pneumoniae (KP) strain and 12 ST17 KP strain were obtained through whole genome sequencing (WGS). Subsequently, a phylogenetic analysis was employed to ascertain the clonal relationship of these strains. …”
Get full text

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. …”
Get full text

Phenotypic and genotypic characterization of clinical carbapenem-resistant Acinetobacter species harboring the metallo-beta-lactamases IMP-8 or NDM-1 in China by Qingye Xu, Xinli Mu, Jintao He, Haiyang Liu, Xiaochen Liu, Yanfei Wang, Xiaoting Hua, Yunsong Yu

“…The blaIMP-8-carrying A1014 was the first identified CRAB among all known STPas150 isolates worldwide. Through whole-genome sequencing and the southern blot analysis, we determined that blaIMP-8 was located on a pR4WN-type plasmid and blaNDM-1 was located on four distinct pSU1904NDM-type plasmids. …”
Get full text

Molecular characterization of ST15 carbapenem-resistant Klebsiella pneumoniae isolated in a single patient by Yongjin Hu, Rong Tang, Shanshan Jin, Jiahao Guan, Xiaoxiao Meng, Zengpeijie Dan, Ruilan Wang, Hong-Yu Ou, Jian Lu

“…Pulsed-field gel electrophoresis (PFGE) was used to investigate the homology relationship between the strains. The whole genome sequencing and phylogenetic analysis of 9 representative isolates was also performed. …”
Get full text

Emerging Resistance and Virulence Patterns in <i>Salmonella enterica</i>: Insights into Silver Nanoparticles as an Antimicrobial Strategy by Irina Gheorghe-Barbu, Ilda Czobor Barbu, Rareș-Ionuț Dragomir, Ioana Cristina Marinaș, Miruna Silvia Stan, Radu Pericleanu, Andreea Ștefania Dumbravă, Liviu-Iulian Rotaru, Simona Paraschiv, Leontina Mirela Bănică, Ionuț Pecete, Dan Oțelea, Violeta Corina Cristea, Mircea Ioan Popa, Marilena Monica Țânțu, Marius Surleac

“…., <i>invA</i>, <i>spvC</i>, <i>pldA</i>, and <i>held</i>). Whole-genome sequencing (WGS) was performed on 19 selected isolates. …”
Get full text