keyword
https://read.qxmd.com/read/36804427/phylogenomic-analyses-reveal-incongruences-between-divergence-times-and-fossil-records-of-freshwater-snails-in-east-asia
#21
JOURNAL ARTICLE
Takahiro Hirano, Takumi Saito, Shun Ito, Bin Ye, T Mason Linscott, Do Van Tu, Zhengzhong Dong, Satoshi Chiba
Fossils provide important insight into our understanding of phylogenetic history by serving as calibration points for divergence time estimation. However, uncertainties in the fossil record due to parallel evolution and convergent evolution can critically affect estimates of node ages. Here, we compare and contrast estimates of phylogenetic divergence with geologic and fossil history for two freshwater snail genera of the family Viviparidae in East Asia (Cipangopaludina and Margarya). Cipangopaludina species are commonly widely distributed species in East Asia, but extant Margarya species are endemic to the ancient lakes in Yunnan, China...
February 15, 2023: Molecular Phylogenetics and Evolution
https://read.qxmd.com/read/36778153/genomic-relatedness-and-dissemination-of-bla-ndm-5-among-acinetobacter-baumannii-isolated-from-hospital-environments-and-clinical-specimens-in-thailand
#22
JOURNAL ARTICLE
Thawatchai Kitti, Suphattra Manrueang, Udomluk Leungtongkam, Supat Khongfak, Rapee Thummeepak, Surat Wannalerdsakun, Thanyasiri Jindayok, Sutthirat Sitthisak
BACKGROUND: Acinetobacter baumannii ( A. baumannii ) is an important cause of nosocomial infection, especially in intensive care units (ICUs). It has the propensity to tolerate various environments and multiple classes of antibiotics. Our study aimed to characterize the comparative genomes of A. baumannii from hospital environments and clinical isolates. METHODS: Clinical and environmental A. baumannii isolates were collected from a university hospital. Antibiotic susceptibility testing was performed, antibiotic resistance genes (ARGs) were characterized, and repetitive element palindromic-PCR (rep-PCR) typing was performed...
2023: PeerJ
https://read.qxmd.com/read/36768792/genetic-diversity-and-population-structure-of-a-wide-pisum-spp-core-collection
#23
JOURNAL ARTICLE
Nicolas Rispail, Osman Zakaria Wohor, Salvador Osuna-Caballero, Eleonora Barilli, Diego Rubiales
Peas ( Pisum sativum ) are the fourth most cultivated pulses worldwide and a critical source of protein in animal feed and human food. Developing pea core collections improves our understanding of pea evolution and may ease the exploitation of their genetic diversity in breeding programs. We carefully selected a highly diverse pea core collection of 325 accessions and established their genetic diversity and population structure. DArTSeq genotyping provided 35,790 polymorphic DArTseq markers, of which 24,279 were SilicoDArT and 11,511 SNP markers...
January 27, 2023: International Journal of Molecular Sciences
https://read.qxmd.com/read/36752781/nanopore-only-assemblies-for-genomic-surveillance-of-the-global-priority-drug-resistant-pathogen-klebsiella-pneumoniae
#24
JOURNAL ARTICLE
Ebenezer Foster-Nyarko, Hugh Cottingham, Ryan R Wick, Louise M Judd, Margaret M C Lam, Kelly L Wyres, Thomas D Stanton, Kara K Tsang, Sophia David, David M Aanensen, Sylvain Brisse, Kathryn E Holt
Oxford Nanopore Technologies (ONT) sequencing has rich potential for genomic epidemiology and public health investigations of bacterial pathogens, particularly in low-resource settings and at the point of care, due to its portability and affordability. However, low base-call accuracy has limited the reliability of ONT data for critical tasks such as antimicrobial resistance (AMR) and virulence gene detection and typing, serotype prediction, and cluster identification. Thus, Illumina sequencing remains the standard for genomic surveillance despite higher capital and running costs...
February 2023: Microbial Genomics
https://read.qxmd.com/read/36743821/rt-rpa-cas12a-based-assay-facilitates-the-discrimination-of-sars-cov-2-variants-of-concern
#25
JOURNAL ARTICLE
Guiyue Tang, Zilong Zhang, Wei Tan, Fei Long, Jingxian Sun, Yingying Li, Siwei Zou, Yujiao Yang, Kezhu Cai, Shenwei Li, Zhiyi Wang, Jiakun Liu, Guobing Mao, Yingxin Ma, Guo-Ping Zhao, Zhen-Gan Tian, Wei Zhao
Timely and accurate detection of SARS-CoV-2 variants of concern (VOCs) is urgently needed for pandemic surveillance and control. Great efforts have been made from a mass of scientists in increasing the detection sensitivity and operability, and reducing the turn-around time and cost. Here, we report a nucleic acid testing-based method aiming to detect and discriminate SARS-CoV-2 mutations by combining RT-RPA and CRISPR-Cas12a detecting assays (RRCd). With a detection limit of 10 copies RNA/reaction, RRCd was validated in 194 clinical samples, showing 89% positive predictive agreement and 100% negative predictive agreement, respectively...
April 15, 2023: Sensors and Actuators. B, Chemical
https://read.qxmd.com/read/36718463/association-of-single-nucleotide-polymorphisms-in-nucleotide-binding-domain-leucine-rich-repeat-protein-1-with-clostridioides-difficile-colonization-or-infection
#26
JOURNAL ARTICLE
Bo-Yang Tsai, Pei-Jane Tsai, Ching-Chi Lee, Chun-Wei Chiu, Yi-Hsin Lai, Jen-Chieh Lee, Wen-Chien Ko, Yuan-Pin Hung
INTRODUCTION: Nucleotide-binding domain leucine-rich repeat protein (NLRP) is critical in the inflammasome-activation pathway, which is important for host survival and the clearance of Clostridioides difficile . Therefore, the influence of NLRP1 polymorphisms on C. difficile colonization (CdC) or infection (CDI) was analyzed. MATERIALS AND METHODS: A prospective cohort study consisted of hospitalized adults was conducted from January 2011 to January 2013. Single nucleotide polymorphisms (SNPs) of NLRP1, including rs12150220, rs2670660, rs6502867, rs878329, rs8182352, rs3744717, and rs11078571, were incorporating in analyses...
2023: Infection and Drug Resistance
https://read.qxmd.com/read/36716318/therapeutic-potential-of-il6r-blockade-for-the-treatment-of-sepsis-and-sepsis-related-death-a-mendelian-randomisation-study
#27
JOURNAL ARTICLE
Fergus W Hamilton, Matt Thomas, David Arnold, Tom Palmer, Ed Moran, Alexander J Mentzer, Nick Maskell, Kenneth Baillie, Charlotte Summers, Aroon Hingorani, Alasdair MacGowan, Golam M Khandaker, Ruth Mitchell, George Davey Smith, Peter Ghazal, Nicholas J Timpson
BACKGROUND: Sepsis is characterised by dysregulated, life-threatening immune responses, which are thought to be driven by cytokines such as interleukin 6 (IL-6). Genetic variants in IL6R known to down-regulate IL-6 signalling are associated with improved Coronavirus Disease 2019 (COVID-19) outcomes, a finding later confirmed in randomised trials of IL-6 receptor antagonists (IL6RAs). We hypothesised that blockade of IL6R could also improve outcomes in sepsis. METHODS AND FINDINGS: We performed a Mendelian randomisation (MR) analysis using single nucleotide polymorphisms (SNPs) in and near IL6R to evaluate the likely causal effects of IL6R blockade on sepsis (primary outcome), sepsis severity, other infections, and COVID-19 (secondary outcomes)...
January 2023: PLoS Medicine
https://read.qxmd.com/read/36623443/causal-association-between-iron-deficiency-anemia-and-chronic-obstructive-pulmonary-disease-a-bidirectional-two-sample-mendelian-randomization-study
#28
JOURNAL ARTICLE
Yi Wei, Lei Sun, Chao Liu, Lujia Li
BACKGROUND: Observational studies have found an association between iron deficiency anemia (IDA) and chronic obstructive pulmonary disease (COPD) risk. However, whether IDA plays a role in COPD development remains unclear. OBJECTIVES: This study was performed to explore the causal association between IDA and COPD. METHODS: We obtained summary statistics for IDA from 6087 cases and 211,115 controls of European ancestry in an open genome-wide association study (GWAS) to select strongly associated single nucleotide polymorphisms that could serve as instrumental variables for IDA (P < 5 × 10-8)...
January 7, 2023: Heart & Lung: the Journal of Critical Care
https://read.qxmd.com/read/36602845/idiopathic-pulmonary-fibrosis-is-associated-with-common-genetic-variants-and-limited-rare-variants
#29
JOURNAL ARTICLE
Anna L Peljto, Rachel Z Blumhagen, Avram D Walts, Jonathan Cardwell, Julia Powers, Tamera J Corte, Joanne L Dickinson, Ian Glaspole, Yuben P Moodley, Martina Koziar Vasakova, Elisabeth Bendstrup, Jesper R Davidsen, Raphael Borie, Bruno Crestani, Philippe Dieude, Francesco Bonella, Ulrich Costabel, Gunnar Gudmundsson, Seamas C Donnelly, Jim Egan, Michael T Henry, Michael P Keane, Marcus P Kennedy, Cormac McCarthy, Aoife N McElroy, Joshua A Olaniyi, Katherine M A O'Reilly, Luca Richeldi, Paolo M Leone, Venerino Poletti, Francesco Puppo, Sara Tomassetti, Valentina Luzzi, Nurdan Kokturk, Nesrin Mogulkoc, Christine A Fiddler, Nikhil Hirani, Gisli Jenkins, Toby M Maher, Philip L Molyneaux, Helen Parfrey, Rebecca Braybrooke, Timothy S Blackwell, Peter D Jackson, Steven D Nathan, Mary K Porteous, Kevin K Brown, Jason D Christie, Harold R Collard, Oliver Eickelberg, Elena E Foster, Kevin F Gibson, Marilyn Glassberg, Daniel Kass, Jonathan A Kropski, David Lederer, Angela L Linderholm, Jim Loyd, Susan K Mathai, Sydney B Montesi, Imre Noth, Justin M Oldham, Amy J Palmisciano, Cristina A Reichner, Mauricio Rojas, Jesse Roman, Neil Schluger, Barry S Shea, Jeffrey J Swigris, Paul J Wolters, Yingze Zhang, Cecilia M A Prele, Juan I Enghelmayer, Maria Otaola, Christopher J Ryerson, Mauricio Salinas, Martina Sterclova, Tewodros H Gebremariam, Marjukka Myllärniemi, Roberto Carbone, Haruhiko Furusawa, Masaki Hirose, Yoshikazu Inoue, Yasunari Miyazaki, Ken Ohta, Shin Ohta, Tsukasa Okamoto, Dong Soon Kim, Annie Pardo, Moises Selman, Alvaro U Aranda, Moo Suk Park, Jong Sun Park, Jin Woo Song, Maria Molina-Molina, Lurdes Planas-Cerezales, Gunilla Westergren-Thorsson, Albert V Smith, Ani W Manichaikul, John S Kim, Stephen S Rich, Elizabeth C Oelsner, R Graham Barr, Jerome I Rotter, Josee Dupuis, George O'Connor, Ramachandran S Vasan, Michael H Cho, Edwin K Silverman, Marvin I Schwarz, Mark P Steele, Joyce S Lee, Ivana V Yang, Tasha E Fingerlin, David A Schwartz
RATIONALE: Idiopathic pulmonary fibrosis is a rare, irreversible, and progressive disease of the lungs. Common genetic variants, in addition to non-genetic factors, have been consistently associated with IPF. Rare variants identified by candidate gene, family-based, and exome studies have also been reported to associate with IPF. However, the extent to which rare variants genome-wide may contribute to the risk of IPF remains unknown. OBJECTIVES: We used whole-genome sequencing to investigate the role of rare variants, genome-wide, on IPF risk...
January 5, 2023: American Journal of Respiratory and Critical Care Medicine
https://read.qxmd.com/read/36574772/immunoglobulin-germline-gene-polymorphisms-influence-the-function-of-sars-cov-2-neutralizing-antibodies
#30
JOURNAL ARTICLE
Pradeepa Pushparaj, Andrea Nicoletto, Daniel J Sheward, Hrishikesh Das, Xaquin Castro Dopico, Laura Perez Vidakovics, Leo Hanke, Mark Chernyshev, Sanjana Narang, Sungyong Kim, Julian Fischbach, Simon Ekström, Gerald McInerney, B Martin Hällberg, Ben Murrell, Martin Corcoran, Gunilla B Karlsson Hedestam
The human immunoglobulin heavy-chain (IGH) locus is exceptionally polymorphic, with high levels of allelic and structural variation. Thus, germline IGH genotypes are personal, which may influence responses to infection and vaccination. For an improved understanding of inter-individual differences in antibody responses, we isolated SARS-CoV-2 spike-specific monoclonal antibodies from convalescent health care workers, focusing on the IGHV1-69 gene, which has the highest level of allelic variation of all IGHV genes...
December 12, 2022: Immunity
https://read.qxmd.com/read/36557273/evaluation-of-the-association-between-single-nucleotide-polymorphisms-of-metabolizing-enzymes-with-the-serum-concentration-of-paracetamol-and-its-metabolites
#31
JOURNAL ARTICLE
Kannan Sridharan, Ali Mohamed Qader, Mustafa Hammad, Anfal Jassim, Diab Eltayeb Diab, Betsy Abraham, Hasan M S N Hasan, Sheikh Abdul Azeez Pasha, Shamik Shah
Intravenous paracetamol is a commonly administered analgesic and antipyretic in inpatient settings. Paracetamol is metabolized by cytochrome P450 (CYP) enzymes followed by conjugating enzymes to mainly glucuronide but to a lesser extent, sulphate metabolites, and oxidative metabolites. Single nucleotide polymorphisms (SNPs) in the CYP enzymes result in modified enzymatic activity. The present study was carried out to evaluate the prevalence of SNPs related to paracetamol metabolism and principal metabolites in critically ill patients, and those with chronic kidney disease...
December 9, 2022: Metabolites
https://read.qxmd.com/read/36521397/the-association-of-il-10-1082g-a-gene-polymorphism-with-the-risk-of-acute-lung-injury-respiratory-distress-syndrome-ali-rds-a-meta-analysis
#32
REVIEW
Renye Yao, Ting Chen, Feng Xue
BACKGROUND: Several records have reported that single nucleotide polymorphism (SNP) at the interleukin 10 (IL-10)-1082G/A locus affects the risk of acute lung injury/respiratory distress syndrome (ALI/RDS), but the exact association between them has not been elucidated. OBJECTIVE: This systematic review aims to elucidate the relationship between SNP at the IL-10-1082G/A locus and susceptibility to ALI/RDS by the method of meta-analysis, to identify the early warning indicators of ALI/RDS...
December 13, 2022: Heart & Lung: the Journal of Critical Care
https://read.qxmd.com/read/36445147/outbreak-of-klebsiella-pneumoniae-st11-resistant-to-ceftazidime-avibactam-producing-kpc-31-and-the-novel-variant-kpc-115-during-covid-19-pandemic-in-argentina
#33
JOURNAL ARTICLE
Federico Nicola, Daniela Cejas, Francisco González-Espinosa, Silvia Relloso, Fabián Herrera, Pablo Bonvehí, Jorgelina Smayevsky, Roque Figueroa-Espinosa, Gabriel Gutkind, Marcela Radice
We describe an outbreak of Klebsiella pneumoniae sequence type 11 (ST11) producing KPC variants resistant to ceftazidime-avibactam. Six patients hospitalized in the intensive care unit (mostly due to critical COVID pneumonia) presented infection or colonization by this bacterium. They had several comorbidities and required mechanical ventilation, central venous catheters, and urinary catheters. All 6 patients had a history of fecal colonization with KPC-producing Enterobacterales (KPC-E). Three of them had previous episodes of infection with ceftazidime-avibactam-susceptible KPC-producing K...
November 29, 2022: Microbiology Spectrum
https://read.qxmd.com/read/36277105/human-pandemic-k27-st392-ctx-m-15-extended-spectrum-%C3%AE-lactamase-positive-klebsiella-pneumoniae-a-one-health-clone-threatening-companion-animals
#34
JOURNAL ARTICLE
Luciano C B A da Silva, Brenda Cardoso, Herrison Fontana, Fernanda Esposito, Silvia R G Cortopassi, Fábio P Sellera, Nilton Lincopan
Extended spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae is a medically important pathogen that commonly causes human nosocomial infections. Since veterinary emergency and critical care services have also significantly progressed over the last decades, there are increasing reports of ESBL-producing K. pneumoniae causing hospital-associated infections in companion animals. We present microbiological and genomic analysis of a multidrug-resistant ESBL-positive K. pneumoniae (LCKp01) isolated from a fatal infection in a dog admitted to a veterinary intensive care unit...
December 2022: One Health
https://read.qxmd.com/read/36129475/small-wards-in-the-icu-a-favorable-measure-for-controlling-the-transmission-of-carbapenem-resistant-klebsiella-pneumoniae
#35
JOURNAL ARTICLE
Xiaohui Chi, Xiaohua Meng, Luying Xiong, Tao Chen, Yanzi Zhou, Jinru Ji, Beiwen Zheng, Yonghong Xiao
PURPOSE: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is one of the leading causes of healthcare-associated infections (HAIs) and is particularly pervasive in intensive care units (ICUs). This study takes ICU layout as the research object, and integrates clinical data and bacterial genome analysis to clarify the role of separate, small wards within the ICU in controlling the transmission of CRKP. METHODS: This study prospectively observed the carriage and spread of CRKP from a long-term in-hospital patient (hereafter called the Patient) colonized with CRKP in the gut and located in a separate, small ward within the ICU...
November 2022: Intensive Care Medicine
https://read.qxmd.com/read/35986912/ddx58-is-associated-with-susceptibility-to-severe-influenza-virus-infection-in-children-and-adolescents
#36
JOURNAL ARTICLE
Sanghun Lee, Yu Zhang, Margaret Newhams, Tanya Novak, Paul G Thomas, Peter M Mourani, Mark W Hall, Laura L Loftis, Natalie Z Cvijanovich, Keiko M Tarquinio, Adam J Schwarz, Scott L Weiss, Neal J Thomas, Barry Markovitz, Melissa L Cullimore, Ronald C Sanders, Matt S Zinter, Janice E Sullivan, Natasha B Halasa, Melania M Bembea, John S Giuliano, Katri V Typpo, Ryan A Nofziger, Steven L Shein, Michele Kong, Bria M Coates, Scott T Weiss, Christoph Lange, Helen C Su, Adrienne G Randolph
BACKGROUND: Seasonal influenza virus infection causes a range of disease severity, including lower respiratory tract infection with respiratory failure. We evaluated the association of common variants in interferon (IFN) regulatory genes with susceptibility to critical influenza infection in children. METHODS: We performed targeted sequencing of 69 influenza-associated candidate genes in 348 children from 24 U.S. centers admitted to the intensive care unit with influenza infection and lacking risk factors for severe influenza infection (PICFlu cohort, 59...
August 20, 2022: Journal of Infectious Diseases
https://read.qxmd.com/read/35899207/-cyp2c19-gene-profiling-as-a-tool-for-personalized-stress-ulcer-prophylaxis-with-proton-pump-inhibitors-in-critically-ill-patients-recommendations-proposal
#37
JOURNAL ARTICLE
Petra Bořilová Linhartová, Ondřej Zendulka, Jaroslav Janošek, Natálie Mlčůchová, Michaela Cvanová, Zdeněk Daněk, Radek Kroupa, Ladislava Bartošová, Břetislav Lipový
To this date, there are no recommendations for personalized stress ulcer prophylaxis (SUP) in critical care that would take the patient's individual genetic predispositions into account. Of drugs used for this purpose, proton pump inhibitors (PPIs) are the first-choice drugs in intensive care unit patients. The degradation of proton pump inhibitors is mediated by cytochrome P450 (CYP) enzymes; in particular, CYP2C19 and, to a lesser extent, CYP3A4 are involved. Expression and metabolic activity of, namely in, CYP2C19 is significantly affected by single nucleotide polymorphisms, the drug metabolization rate varies greatly from ultrarapid to poor and likely influences the optimal dosage...
2022: Frontiers in Medicine
https://read.qxmd.com/read/35832565/the-pharmacogenetics-of-opiates-and-its-impact-on-delirium-in-mechanically-ventilated-adults-a-pilot-study
#38
JOURNAL ARTICLE
C Adrian Austin, Andy Szeto, Apoorva Gupta, Timothy Wiltshire, Daniel J Crona, Christine Kistler
Background: Pharmacogenetics may explain a substantial proportion of the variation seen in the efficacy and risk profile of analgesosedative drugs and the incidence of delirium in critically ill adults. Objectives: Conduct a feasibility study to demonstrate the reliability of collecting and analyzing pharmacogenetic information from critically ill patients and to assess the impact of pharmacogenetics on intensive care unit (ICU) outcomes. Methods: We prospectively enrolled subjects from the Medical ICU at the University of North Carolina (UNC)...
August 2022: Journal of Pharmacy Technology: JPT: Official Publication of the Association of Pharmacy Technicians
https://read.qxmd.com/read/35822078/association-of-interferon-gamma-inducible-protein-10-monocyte-chemoattractant-protein-1-macrophage-inflammatory-protein-1-alpha-interleukin-6-and-rs12252-single-nucleotide-polymorphism-of-interferon-induced-transmembrane-protein-3-gene-with-the-severity-of
#39
JOURNAL ARTICLE
Shafia Mulla, Md Maruf Ahmed Molla, S M Ali Ahmed, A K M Akhtaruzzaman, Ahmed Abu Saleh, Shaheda Anwar
Background: Evaluating the serum levels of IP-10, MCP-1, MIP-1α, and IL-6 and genotyping of rs12252 SNP of IFITM3 gene among different categories of COVID-19 patients might aid in understanding the pathogenesis of COVID-19 and contribute to developing disease-specific biomarkers and therapeutic strategies. Methods: This is a cross-sectional study involving a total of 84 COVID-19 patients confirmed by positive RT-PCR and 28 healthy controls. COVID-19 patients were recruited from the intensive care unit (ICU) and COVID unit of Bangabandhu Sheikh Mujib Medical University, Shahbag, Dhaka...
2022: Egyptian Journal of Internal Medicine
https://read.qxmd.com/read/35770811/interplay-between-demographic-clinical-and-polygenic-risk-factors-for-severe-covid-19
#40
JOURNAL ARTICLE
Samantha S R Crossfield, Natalie J M Chaddock, Mark M Iles, Mar Pujades-Rodriguez, Ann W Morgan
BACKGROUND: We aimed to identify clinical, socio-demographic and genetic risk factors for severe COVID-19 (hospitalization, critical care admission or death) in the general population. METHODS: In this observational study, we identified 9560 UK Biobank participants diagnosed with COVID-19 during 2020. A polygenic risk score (PRS) for severe COVID-19 was derived and optimized using publicly available European and trans-ethnic COVID-19 genome-wide summary statistics...
June 30, 2022: International Journal of Epidemiology
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