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JOURNAL ARTICLE
Zaineb Hamzaoui, Sana Ferjani, Ines Medini, Latifa Charaa, Ichrak Landolsi, Roua Ben Ali, Wissal Khaled, Sarra Chammam, Salma Abid, Lamia Kanzari, Asma Ferjani, Ahmed Fakhfakh, Dhouha Kebaier, Zoubeir Bouslah, Mouna Ben Sassi, Sameh Trabelsi, Ilhem Boutiba-Ben Boubaker
OBJECTIVES: This study aimed to construct geographically, temporally, and epidemiologically representative data sets for SARS-CoV-2 in North Africa, focusing on Variants of Concern (VOCs), Variants of Interest (VOIs), and Variants Under Monitoring (VUMs). METHODS: SARS-CoV-2 genomic sequences and metadata from the EpiCoV database via the Global Initiative on Sharing All Influenza Data platform were analyzed. Data analysis included cases, deaths, demographics, patient status, sequencing technologies, and variant analysis...
June 2024: IJID Reg
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JOURNAL ARTICLE
Yi-Ching Liaw, Koichi Matsuda, Yung-Po Liaw
PURPOSE: The purpose of this study was to identify new independent significant SNPs associated with osteoporosis using data from the Taiwan Biobank (TWBB). MATERIAL AND METHODS: The dataset was divided into discovery (60%) and replication (40%) subsets. Following data quality control, genome-wide association study (GWAS) analysis was performed, adjusting for sex, age, and the top 5 principal components, employing the Scalable and Accurate Implementation of the Generalized mixed model approach...
May 2024: JBMR Plus
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JOURNAL ARTICLE
Christoph Buchta, Stephan W Aberle, Irene Görzer, Andrea Griesmacher, Mathias M Müller, Erich Neuwirth, Elisabeth Puchhammer-Stöckl, Lukas Weseslindtner, Jeremy V Camp
BACKGROUND: External quality assessment (EQA) schemes provide objective feedback to participating laboratories about the performance of their analytical systems and information about overall regional analytical performance. The EQAs are particularly important during pandemics as they also assess the reliability of individual test results and show opportunities to improve test strategies. With the end of the COVID-19 pandemic, the testing frequency significantly decreased in Austria. Here, we analyzed whether this decrease had an effect on participation and/or performance in SARS-CoV‑2 virus detection EQAs, as compared to the pandemic era...
April 23, 2024: Wiener Klinische Wochenschrift
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REVIEW
Xueting Shan, Rui Li, Xiang Ma, Guoqiang Qiu, Yi Xiang, Xiaojun Zhang, De Wu, Lu Wang, Jianhong Zhang, Tao Wang, Weifen Li, Yun Xiang, Houhui Song, Dong Niu
Coronaviruses have been identified as pathogens of gastrointestinal and respiratory diseases in humans and various animal species. In recent years, the global spread of new coronaviruses has had profound influences for global public health and economies worldwide. As highly pathogenic zoonotic viruses, coronaviruses have become the focus of current research. Porcine Deltacoronavirus (PDCoV), an enterovirus belonging to the family of coronaviruses, has emerged on a global scale in the past decade and significantly influenced the swine industry...
April 24, 2024: Functional & Integrative Genomics
#5
JOURNAL ARTICLE
Luana Boff, Humberlânia de Sousa Duarte, Gabriela Bergiante Kraychete, Gabriel Taddeucci-Rocha, Bianca Diniz Oliveira, Rodolpho Mattos Albano, Ana Paula D'Alincourt Carvalho-Assef, Silvana Vargas Superti, Ianick Souto Martins, Renata Cristina Picão
Klebsiella pneumoniae is an opportunistic pathogen that can colonize the gastrointestinal tract (GIT) of humans. The mechanisms underlying the successful translocation of this pathogen to cause extra-intestinal infections remain unknown, although virulence and antimicrobial resistance traits likely play significant roles in the establishment of infections. We investigated K. pneumoniae strains isolated from GIT colonization (strains Kp_FZcol-1, Kp_FZcol-2 and Kp_FZcro-1) and from a fatal bloodstream infection (strain Kp_HM-1) in a leukemia patient...
April 21, 2024: Infection, Genetics and Evolution
#6
JOURNAL ARTICLE
Soo Heon Kwak, Ryan B Hernandez-Cancela, Daniel A DiCorpo, David E Condon, Jordi Merino, Peitao Wu, Jennifer A Brody, Jie Yao, Xiuqing Guo, Fariba Ahmadizar, Mariah Meyer, Murat Sincan, Josep M Mercader, Sujin Lee, Jeffrey Haessler, Ha My T Vy, Zhaotong Lin, Nicole D Armstrong, Shaopeng Gu, Noah L Tsao, Leslie A Lange, Ningyuan Wang, Kerri L Wiggins, Stella Trompet, Simin Liu, Ruth J F Loos, Renae Judy, Philip H Schroeder, Natalie R Hasbani, Maxime M Bos, Alanna C Morrison, Rebecca D Jackson, Alexander P Reiner, JoAnn E Manson, Ninad S Chaudhary, Lynn K Carmichael, Yii-Der Ida Chen, Kent D Taylor, Mohsen Ghanbari, Joyce van Meurs, Achilleas N Pitsillides, Bruce M Psaty, Raymond Noordam, Ron Do, Kyong Soo Park, J Wouter Jukema, Maryam Kavousi, Adolfo Correa, Stephen S Rich, Scott M Damrauer, Catherine Hajek, Nam H Cho, Marguerite R Irvin, James S Pankow, Girish N Nadkarni, Robert Sladek, Mark O Goodarzi, Jose C Florez, Daniel I Chasman, Susan R Heckbert, Charles Kooperberg, Josée Dupuis, Rajeev Malhotra, Paul S de Vries, Ching-Ti Liu, Jerome I Rotter, James B Meigs
OBJECTIVE: To identify genetic risk factors for incident cardiovascular disease (CVD) among people with type 2 diabetes (T2D). RESEARCH DESIGN AND METHODS: We conducted a multiancestry time-to-event genome-wide association study for incident CVD among people with T2D. We also tested 204 known coronary artery disease (CAD) variants for association with incident CVD. RESULTS: Among 49,230 participants with T2D, 8,956 had incident CVD events (event rate 18...
April 23, 2024: Diabetes Care
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JOURNAL ARTICLE
Anne-Sophie Le Guern, Cyril Savin, Fanny Chereau, Sabrina Tessier, Julien Guglielmini, Sylvie Brémont, Javier Pizarro-Cerdá
UNLABELLED: Enteric yersiniosis, the third most common food-borne zoonosis in Europe, is mainly caused by the pathogen Yersinia enterocolitica . In France , the yersiniosis microbiological surveillance is conducted at the Yersinia National Reference Laboratory (YNRL). Since 2017, isolates have been characterized by whole genome sequencing (WGS) followed by a 500-gene Yersinia -cgMLST. We report here the data of the WGS-based surveillance on Y. enterocolitica isolates for the 2017-2021 period...
April 23, 2024: Microbiology Spectrum
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JOURNAL ARTICLE
Lais Ceschini Machado, Filipe Zimmer Dezordi, Gustavo Barbosa de Lima, Raul Emídio de Lima, Lilian Caroliny Amorim Silva, Leandro de Mattos Pereira, Alexandre Freitas da Silva, Antonio Marinho da Silva Neto, André Luiz Sá de Oliveira, Anderson da Costa Armstrong, Rômulo Pessoa-E-Silva, Rodrigo Moraes Loyo, Barbara de Oliveira Silva, Anderson Rodrigues de Almeida, Maira Galdino da Rocha Pitta, Francisco de Assis da Silva Santos, Marilda Mendonça Siqueira, Paola Cristina Resende, Edson Delatorre, Felipe Gomes Naveca, Fabio Miyajima, Tiago Gräf, Rodrigo Feliciano do Carmo, Michelly Cristiny Pereira, Tulio de Lima Campos, Matheus Filgueira Bezerra, Marcelo Henrique Santos Paiva, Gabriel da Luz Wallau
SARS-CoV-2 virus emerged as a new threat to humans and spread around the world, leaving a large death toll. As of January 2023, Brazil is among the countries with the highest number of registered deaths. Nonpharmacological and pharmacological interventions have been heterogeneously implemented in the country, which, associated with large socioeconomic differences between the country regions, has led to distinct virus spread dynamics. Here, we investigate the spatiotemporal dispersion of SARS-CoV-2 lineages in the Pernambuco state (Northeast Brazil) throughout the distinct epidemiological scenarios that unfolded in the first 2 years of the pandemic...
April 23, 2024: Microbiology Spectrum
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JOURNAL ARTICLE
Melissa Mariana, Amadeu M V M Soares, Miguel Castelo-Branco, Elisa Cairrao
Hypertensive disorders in pregnancy (HDP) are the most prevalent diseases during pregnancy. In addition to the already identified risk factors, exposure to environmental contaminants has been also considered a new one. Phthalates, which are classified as priority environmental pollutants due to their ubiquitousness and endocrine disrupting properties, have been implicated in HDP in some epidemiological studies. Nevertheless, phthalates' vascular impacts still need to be clarified. Thus, we aimed to understand the connection between phthalates exposure and the occurrence of gestational hypertension, as well as the pathway involved in the pathological vascular effects...
April 18, 2024: Journal of Xenobiotics
#10
JOURNAL ARTICLE
Xuemin Zhao, Linfei Liu
INTRODUCTION: There are insufficient epidemiological studies on the impact of age at first sexual intercourse (AFS) and age at first live birth (AFB) on postpartum depression (PPD) in pregnant women, and the conclusions of these studies are inconsistent. METHODS: We performed a Mendelian randomization (MR) study to determine the causal relationship between AFS or AFB and the risk of PPD. The summary data were extracted from genome-wide association study (GWAS) summary datasets...
2024: Frontiers in Psychiatry
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JOURNAL ARTICLE
Ntelekwane George Khasapane, Jane Nkhebenyane, Zamantungwa Mnisi, Stanford Kwenda, Oriel Thekisoe
Staphylococcus species are the primary cause of mastitis in dairy cows across the world. Staphylococcus aureus has recently become a pathogen that is zoonotic and multidrug resistant. This study aimed to sequence whole genomes of 38 S. aureus isolates from 55 subclinical mastitis dairy cows of 7 small-scale farmers in the Free State Province, South Africa and document and their antimicrobial and virulence genes. The 38 isolates were grouped by the in silico multi-locus sequencing types (MLST) into seven sequence types (STs), that is (ST 97, 352, 152, 243) and three new STs (ST8495, ST8500, and ST8501)...
2024: Frontiers in Microbiology
#12
JOURNAL ARTICLE
Anett Illés, Henriett Pikó, Kristóf Árvai, Veronika Donka, Olívia Szepesi, János Kósa, Péter Lakatos, Artúr Beke
BACKGROUND: Premature ovarian insuffiency (POI) is one of the main cause behind infertility. The genetic analysis of POI should be part of the clinical diagnostics, as several genes have been implicated in the genetic background of it. The aim of our study was to analyse the genetic background of POI in a Hungarian cohort. METHODS: The age of onset was between 15 and 39 years. All patients had the 46,XX karyotype and they were prescreened for the most frequent POI associated FMR1 premutation...
April 22, 2024: BMC Medical Genomics
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JOURNAL ARTICLE
Hye Sun Lee, Hong Il Lim, Tae Ju Moon, So Young Lee, Jun-Hyuk Lee
BACKGROUND: The relationship between atherosclerosis and renal function is well established. Atherosclerotic cardiovascular disease (ASCVD) risk scores reflect atherosclerotic burden, which changes over time. We investigated the association between ASCVD risk trajectories and incident chronic kidney disease (CKD) using data from a large community-based Korean cohort with up to 16 years of follow-up. METHODS: We analyzed data from 5032 participants without CKD from the baseline survey of the Korean Genome and Epidemiology Study Ansan-Ansung cohort...
April 22, 2024: BMC Nephrology
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JOURNAL ARTICLE
Xiaofeng Zhu, Yihe Yang, Noah Lorincz-Comi, Gen Li, Amy R Bentley, Paul S de Vries, Michael Brown, Alanna C Morrison, Charles N Rotimi, W James Gauderman, Dabeeru C Rao, Hugues Aschard
There is a long-standing debate about the magnitude of the contribution of gene-environment interactions to phenotypic variations of complex traits owing to the low statistical power and few reported interactions to date. To address this issue, the Gene-Lifestyle Interactions Working Group within the Cohorts for Heart and Aging Research in Genetic Epidemiology Consortium has been spearheading efforts to investigate G × E in large and diverse samples through meta-analysis. Here, we present a powerful new approach to screen for interactions across the genome, an approach that shares substantial similarity to the Mendelian randomization framework...
April 22, 2024: Nature Communications
#15
JOURNAL ARTICLE
Qiuju Liang, Jiajun Jing, Huiming He, Xiaofeng Huang, Jianing Liu, Mingjun Wang, Zijuan Qi, Li'e Zhang, Ziang Huang, Yuanliang Yan, Sijin Liu, Ming Gao, Yunfeng Zou
Manganese (Mn) is an essential micronutrient required for various biological processes but excess exposure to Mn can cause neurotoxicity. However, there are few reports regarding the toxicity effect of Mn on the kidney as well as the underlying molecule mechanism. Herein, in vivo experiments were adopted to assess the toxicity effects associated with Mn, and found that chronic Mn treatment induced the injury of glomerular podocytes but not renal tubule in rats. Genome-wide CRISPR/Cas9 knockout screen was then employed to explore the biotargets of the toxic effect of Mn on podocytes...
April 18, 2024: Environment International
#16
JOURNAL ARTICLE
Ziying Qiu, Rongkun Huang, Yuxuan Wu, Xinghao Li, Chunyu Sun, Yunqi Ma
The escalating crisis of antimicrobial resistance (AMR) underscores the urgent need for novel antimicrobials. One promising strategy is the exploration of structural diversity, as diverse structures can lead to diverse biological activities and mechanisms of action. This review delves into the role of structural diversity in antimicrobial discovery, highlighting its influence on factors such as target selectivity, binding affinity, pharmacokinetic properties, and the ability to overcome resistance mechanisms...
April 22, 2024: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
#17
JOURNAL ARTICLE
Qianying Lin, Emma E Goldberg, Thomas Leitner, Carmen Molina-París, Aaron A King, Ethan O Romero-Severson
Reassortment is an evolutionary process common in viruses with segmented genomes. These viruses can swap whole genomic segments during cellular co-infection, giving rise to novel progeny formed from the mixture of parental segments. Because large-scale genome rearrangements have the potential to generate new phenotypes, reassortment is important to both evolutionary biology and public health research. However, statistical inference of the pattern of reassortment events from phylogenetic data is exceptionally difficult, potentially involving inference of general graphs in which individual segment trees are embedded...
April 22, 2024: Molecular Biology and Evolution
#18
JOURNAL ARTICLE
Cristian Arbey Velarde, Uriel Hurtado, Andres Fernando Cardona Rios, Celeny Ortiz, Idabely Betancur
Introduction. During the development of the SARS-CoV-2 pandemic in Antioquia, we experienced epidemiological peaks related to the α, ɣ, β, ƛ, and δ variants. δ had the highest incidence and prevalence. This lineage is of concern due to its clinical manifestations and epidemiological characteristics. A total of 253 δ sublineages have been reported in the PANGOLIN database. The sublineage identification through genomic analysis has made it possible to trace their evolution and propagation...
March 31, 2024: Biomédica: Revista del Instituto Nacional de Salud
#19
JOURNAL ARTICLE
Chris Lauber, Xiaoyu Zhang, Josef Vaas, Franziska Klingler, Pascal Mutz, Arseny Dubin, Thomas Pietschmann, Olivia Roth, Benjamin W Neuman, Alexander E Gorbalenya, Ralf Bartenschlager, Stefan Seitz
Virus discovery by genomics and metagenomics empowered studies of viromes, facilitated characterization of pathogen epidemiology, and redefined our understanding of the natural genetic diversity of viruses with profound functional and structural implications. Here we employed a data-driven virus discovery approach that directly queries unprocessed sequencing data in a highly parallelized way and involves a targeted viral genome assembly strategy in a wide range of sequence similarity. By screening more than 269,000 datasets of numerous authors from the Sequence Read Archive and using two metrics that quantitatively assess assembly quality, we discovered 40 nidoviruses from six virus families whose members infect vertebrate hosts...
April 22, 2024: PLoS Pathogens
#20
REVIEW
Mohamed Chakkour, Zeinab Hammoud, Solay Farhat, Ali El Roz, Zeinab Ezzeddine, Ghassan Ghssein
Proteus mirabilis is a Gram-negative bacterium with exclusive molecular and biological features. It is a versatile pathogen acclaimed for its distinct urease production, swarming behavior, and rapid multicellular activity. Clinically, P. mirabilis is a frequent pathogen of the human urinary system where it causes urinary tract infections (UTIs) and catheter-associated urinary tract infections (CAUTIs). This review explores the epidemiology, risk factors, clinical manifestations, and treatment of P. mirabilis infections, emphasizing its association with UTIs...
2024: Frontiers in Microbiology
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