keyword
https://read.qxmd.com/read/38466776/computationally-inferred-cell-type-specific-epigenome-wide-dna-methylation-analysis-unveils-distinct-methylation-patterns-among-immune-cells-for-hiv-infection-in-three-cohorts
#21
JOURNAL ARTICLE
Xinyu Zhang, Ying Hu, Ral E Vandenhoudt, Chunhua Yan, Vincent C Marconi, Mardge H Cohen, Zuoheng Wang, Amy C Justice, Bradley E Aouizerat, Ke Xu
BACKGROUND: Epigenome-wide association studies (EWAS) have identified CpG sites associated with HIV infection in blood cells in bulk, which offer limited knowledge of cell-type specific methylation patterns associated with HIV infection. In this study, we aim to identify differentially methylated CpG sites for HIV infection in immune cell types: CD4+ T-cells, CD8+ T-cells, B cells, Natural Killer (NK) cells, and monocytes. METHODS: Applying a computational deconvolution method, we performed a cell-type based EWAS for HIV infection in three independent cohorts (Ntotal = 1,382)...
March 11, 2024: PLoS Pathogens
https://read.qxmd.com/read/38463963/distinct-escherichia-coli-transcriptional-profiles-in-the-guts-of-recurrent-uti-sufferers-revealed-by-pan-genome-hybrid-selection
#22
Mark G Young, Timothy J Straub, Colin J Worby, Hayden C Metsky, Andreas Gnirke, Ryan A Bronson, Lucas R van Dijk, Christopher A Desjardins, Christian Matranga, James Qu, Karen Dodson, Henry L Schreiber, Abigail L Manson, Scott J Hultgren, Ashlee M Earl
Low-abundance members of microbial communities are difficult to study in their native habitat. This includes Escherichia coli , a minor, but common inhabitant of the gastrointestinal tract and opportunistic pathogen, including of the urinary tract, where it causes most infections. While our understanding of the interactions between uropathogenic Escherichia coli (UPEC) and the bladder is increasing, comparatively little is known about UPEC in its pre-infection reservoir, partly due to its low abundance there (<1% relative abundance)...
February 29, 2024: bioRxiv
https://read.qxmd.com/read/38459466/genome-mining-of-escherichia-coli-wg5d-from-drinking-water-source-unraveling-antibiotic-resistance-genes-virulence-factors-and-pathogenicity
#23
JOURNAL ARTICLE
Oluwaseyi Samuel Olanrewaju, Lesego G Molale-Tom, Rinaldo K Kritzinger, Cornelius Carlos Bezuidenhout
BACKGROUND: Escherichia coli, a ubiquitous inhabitant of the gut microbiota, has been recognized as an indicator of fecal contamination and a potential reservoir for antibiotic resistance genes. Its prevalence in drinking water sources raises concerns about the potential dissemination of antibiotic resistance within aquatic ecosystems and the subsequent impact on public health. The ability of E. coli to acquire and transfer resistance genes, coupled with the constant exposure to low levels of antibiotics in the environment, underscores the need for comprehensive surveillance and rigorous antimicrobial stewardship strategies to safeguard the quality and safety of drinking water supplies, ultimately mitigating the escalation of antibiotic resistance and its implications for human well-being...
March 8, 2024: BMC Genomics
https://read.qxmd.com/read/38447128/design-and-optimization-of-a-yst-pcr-to-detect-yersinia-enterocolitica-in-meat-food
#24
JOURNAL ARTICLE
Anna C Mastrodonato, Walter Lapadula, Maximiliano Juri-Ayub, María E Escudero, Gabriela I Favier, Cecilia S M Lucero-Estrada
In this study, a polymerase chain reaction (PCR) directed to the yst chromosomal gene ( yst -PCR) was used as a rapid, sensitive, and specific method to detect Yersinia enterocolitica strains belonging to different biotypes in foods; a competitive Internal Amplification Control (cIAC) is also developed. The cIAC had a molecular weight of 417 bp and was detected until a concentration of 0.85 ng/μL. No other strains of other Yersinia species, nor Enterobacteriales order were detected by this PCR...
March 6, 2024: Foodborne Pathogens and Disease
https://read.qxmd.com/read/38445858/strengthening-bordetella-pertussis-genomic-surveillance-by-direct-sequencing-of-residual-positive-specimens
#25
JOURNAL ARTICLE
Yanhui Peng, Margaret M Williams, Lingzi Xiaoli, Ashley Simon, Heather Fueston, Maria L Tondella, Michael R Weigand
Whole-genome sequencing (WGS) of microbial pathogens recovered from patients with infectious disease facilitates high-resolution strain characterization and molecular epidemiology. However, increasing reliance on culture-independent methods to diagnose infectious diseases has resulted in few isolates available for WGS. Here, we report a novel culture-independent approach to genome characterization of Bordetella pertussis , the causative agent of pertussis and a paradigm for insufficient genomic surveillance due to limited culture of clinical isolates...
March 6, 2024: Journal of Clinical Microbiology
https://read.qxmd.com/read/38445851/genomic-insights-into-local-scale-evolution-of-ocular-chlamydia-trachomatis-strains-within-and-between-individuals-in-gambian-trachoma-endemic-villages
#26
JOURNAL ARTICLE
Ehsan Ghasemian, Nkoyo Faal, Harry Pickering, Ansumana Sillah, Judith Breuer, Robin L Bailey, David Mabey, Martin J Holland
Trachoma, a neglected tropical disease caused by Chlamydia trachomatis (Ct) serovars A-C, is the leading infectious cause of blindness worldwide. Africa bears the highest burden, accounting for over 86 % of global trachoma cases. We investigated Ct serovar A (SvA) and B (SvB) whole genome sequences prior to the induction of mass antibiotic drug administration in The Gambia. Here, we explore the factors contributing to Ct strain diversification and the implications for Ct evolution within the context of ocular infection...
March 2024: Microbial Genomics
https://read.qxmd.com/read/38443809/characterization-of-rumen-microbiome-and-immune-genes-expression-of-crossbred-beef-steers-with-divergent-residual-feed-intake-phenotypes
#27
JOURNAL ARTICLE
Godstime Taiwo, Olanrewaju B Morenikeji, Modoluwamu Idowu, Taylor Sidney, Ajiboye Adekunle, Andres Pech Cervantes, Sunday Peters, Ibukun M Ogunade
We investigated whole blood and hepatic mRNA expressions of immune genes and rumen microbiome of crossbred beef steers with divergent residual feed intake phenotype to identify relevant biological processes underpinning feed efficiency in beef cattle. Low-RFI beef steers (n = 20; RFI = - 1.83 kg/d) and high-RFI beef steers (n = 20; RFI = + 2.12 kg/d) were identified from a group of 108 growing crossbred beef steers (average BW = 282 ± 30...
March 5, 2024: BMC Genomics
https://read.qxmd.com/read/38438962/identification-and-validation-of-rna-binding-protein-slc3a2-regulates-melanocyte-ferroptosis-in-vitiligo-by-integrated-analysis-of-single-cell-and-bulk-rna-sequencing
#28
JOURNAL ARTICLE
Jingzhan Zhang, Fang Xiang, Yuan Ding, Wen Hu, Hongjuan Wang, Xiangyue Zhang, Zixian Lei, Tingting Li, Peng Wang, Xiaojing Kang
BACKGROUND: The pathogenesis of vitiligo remains unclear. The genes encoding vitiligo-related RNA-binding proteins (RBPs) and their underlying pathogenic mechanism have not been determined. RESULTS: Single-cell transcriptome sequencing (scRNA-seq) data from the CNCB database was obtained to identify distinct cell types and subpopulations and the relative proportion changes in vitiligo and healthy samples. We identified 14 different cell types and 28 cell subpopulations...
March 4, 2024: BMC Genomics
https://read.qxmd.com/read/38438430/assessment-of-parental-mosaicism-rates-in-neurodevelopmental-disorders-caused-by-apparent-de-novo-pathogenic-variants-using-deep-sequencing
#29
JOURNAL ARTICLE
François Lecoquierre, Kévin Cassinari, Nathalie Drouot, Angèle May, Steeve Fourneaux, Francoise Charbonnier, Celine Derambure, Sophie Coutant, Pascale Saugier-Veber, Alexander Hoischen, Camille Charbonnier, Gaël Nicolas
While de novo variants (DNV) are overall at low risk of recurrence in subsequent pregnancies, a subset is at high risk due to parental mosaicism. Accurately identifying cases of parental mosaicism is therefore important for genetic counseling in clinical care. Some studies have investigated the rate of parental mosaics, but most were either limited by the sensitivity of the techniques (i.e. exome or genome sequencing), or focused on specific types of disease such as epileptic syndromes. This study aimed to determine the proportion of parental mosaicism among the DNV causing neurodevelopmental disorders (NDDs) in a series not enriched in epilepsy syndromes...
March 4, 2024: Scientific Reports
https://read.qxmd.com/read/38436750/tips-and-tools-to-obtain-and-assess-mosquito-viromes
#30
REVIEW
Amanda Gonzalez Da Silva, Evelise Bach, Joel Henrique Ellwanger, José Artur Bogo Chies
Due to their vectorial capacity, mosquitoes (Diptera: Culicidae) receive special attention from health authorities and entomologists. These cosmopolitan insects are responsible for the transmission of many viral diseases, such as dengue and yellow fever, causing huge impacts on human health and justifying the intensification of research focused on mosquito-borne diseases. In this context, the study of the virome of mosquitoes can contribute to anticipate the emergence and/or the reemergence of infectious diseases...
March 1, 2024: Archives of Microbiology
https://read.qxmd.com/read/38428609/comparative-genomic-analysis-and-multilocus-sequence-typing-of-staphylococcus-aureus-reveals-candidate-genes-for-low-temperature-tolerance
#31
JOURNAL ARTICLE
Peng Guan, Shijia Fan, Wenjing Dong, Xiaojie Wang, Zhen Li, Miao Song, Biao Suo
Staphylococcus aureus is one of the most frequently detected foodborne pathogens in cold chain foods. Worryingly, small colony variants (SCVs) can survive in cold environments for a long time and can revert to rapidly growing cells in suitable environments, causing serious food safety issues. This study investigated the underlying mechanism of SCV formation at low temperature (4 °C) via comparative genomics. Multilocus sequence typing (MLST) of 105 strains of S. aureus was divided into 9 sequence types...
February 28, 2024: Science of the Total Environment
https://read.qxmd.com/read/38414197/first-report-of-alternaria-alternata-causing-leaf-spot-on-coffea-arabica-in-china
#32
JOURNAL ARTICLE
Tingping Zhang, Hao Zhao, Zhifeng Xue, Yukai Suo, Shiwen Qin, Feifei He
Yunnan Province is the major region for coffee (Coffea arabica) cultivation in China, contributing to over 98% of the national yield and total production value (Ma et al. 2022). In May 2023, brown spot symptoms were observed only on the leaves of coffee plants in a field located in Baoshan City (98°52'37.988400"E, 24°58'17.673600"N), Yunnan Province. Notably, brown and irregularly shaped spots initially started on the leaf bases. The spots enlarged and developed concentric rings with dark brown margins, which are often surrounded by yellow halos...
February 27, 2024: Plant Disease
https://read.qxmd.com/read/38412041/genomic-revisitation-and-reclassification-of-the-genus-providencia
#33
JOURNAL ARTICLE
Xu Dong, Huiqiong Jia, Yuyun Yu, Yanghui Xiang, Ying Zhang
Members of Providencia , although typically opportunistic, can cause severe infections in immunocompromised hosts. Recent advances in genome sequencing provide an opportunity for more precise study of this genus. In this study, we first identified and characterized a novel species named Providencia zhijiangensis sp. nov. It has ≤88.23% average nucleotide identity (ANI) and ≤31.8% in silico DNA-DNA hybridization (dDDH) values with all known Providencia species, which fall significantly below the species-defining thresholds...
February 27, 2024: MSphere
https://read.qxmd.com/read/38410387/phenotypic-heterogeneity-unveils-a-negative-correlation-between-antibiotic-resistance-and-quorum-sensing-in-pseudomonas-aeruginosa-clinical-isolates
#34
JOURNAL ARTICLE
Xiting Yang, Qianglin Zeng, Shiyi Gou, Yi Wu, Xiaoling Ma, Hang Zou, Kelei Zhao
Colonization of Pseudomonas aeruginosa in the lung environments frequently leads to the enrichment of strains displaying enhanced antibiotic resistance and reduced production of quorum-sensing (QS) controlled products. However, the relationship between the emergence of QS deficient variants and antibiotic resistance remains less understood. In this study, 67 P. aeruginosa strains were isolated from the lungs of 14 patients with chronic obstructive pulmonary disease, followed by determining their genetic relationship, QS-related phenotypes and resistance to commonly used antibiotics...
2024: Frontiers in Microbiology
https://read.qxmd.com/read/38410192/characterization-of-pathogenic-microbiome-on-removable-prostheses-with-different-levels-of-cleanliness-using-2brad-m-metagenomic-sequencing
#35
JOURNAL ARTICLE
Tong Wah Lim, Shi Huang, Yuesong Jiang, Yufeng Zhang, Michael Francis Burrow, Colman McGrath
BACKGROUND: The microbiomes on the surface of unclean removable prostheses are complex and yet largely underexplored using metagenomic sequencing technology. OBJECTIVES: To characterize the microbiome of removable prostheses with different levels of cleanliness using Type IIB Restriction-site Associated DNA for Microbiome (2bRAD-M) sequencing and compare the Microbial Index of Pathogenic Bacteria (MIP) between clean and unclean prostheses. MATERIALS AND METHODS: Ninety-seven removable prostheses were classified into 'clean' and 'unclean' groups...
2024: Journal of Oral Microbiology
https://read.qxmd.com/read/38402218/implications-of-the-three-dimensional-chromatin-organization-for-genome-evolution-in-a-fungal-plant-pathogen
#36
JOURNAL ARTICLE
David E Torres, H Martin Kramer, Vittorio Tracanna, Gabriel L Fiorin, David E Cook, Michael F Seidl, Bart P H J Thomma
The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae, known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation...
February 24, 2024: Nature Communications
https://read.qxmd.com/read/38399804/african-swine-fever-virus-i267l-is-a-hemorrhage-related-gene-based-on-transcriptome-analysis
#37
JOURNAL ARTICLE
Yuan Wen, Xianghan Duan, Jingjing Ren, Jing Zhang, Guiquan Guan, Yi Ru, Dan Li, Haixue Zheng
African swine fever (ASF) is an acute and severe disease transmitted among domestic pigs and wild boars. This disease is notorious for its high mortality rate and has caused great losses to the world's pig industry in the past few years. After infection, pigs can develop symptoms such as high fever, inflammation, and acute hemorrhage, finally leading to death. African swine fever virus (ASFV) is the causal agent of ASF; it is a large DNA virus with 150-200 genes. Elucidating the functions of each gene could provide insightful information for developing prevention and control methods...
February 17, 2024: Microorganisms
https://read.qxmd.com/read/38397113/screening-for-rare-mitochondrial-genome-variants-reveals-a-potentially-novel-association-between-mt-co1-and-mt-tl2-genes-and-diabetes-phenotype
#38
JOURNAL ARTICLE
Tomasz Płoszaj, Sebastian Skoczylas, Karolina Gadzalska, Paulina Jakiel, Ewa Juścińska, Monika Gorządek, Agnieszka Robaszkiewicz, Maciej Borowiec, Agnieszka Zmysłowska
Variations in several nuclear genes predisposing humans to the development of MODY diabetes have been very well characterized by modern genetic diagnostics. However, recent reports indicate that variants in the mtDNA genome may also be associated with the diabetic phenotype. As relatively little research has addressed the entire mitochondrial genome in this regard, the aim of the present study is to evaluate the genetic variations present in mtDNA among individuals susceptible to MODY diabetes. In total, 193 patients with a MODY phenotype were tested with a custom panel with mtDNA enrichment...
February 19, 2024: International Journal of Molecular Sciences
https://read.qxmd.com/read/38384961/rapid-detection-of-high-consequence-and-emerging-viral-pathogens-in-pigs
#39
JOURNAL ARTICLE
Alison C Neujahr, Duan S Loy, John Dustin Loy, Bruce W Brodersen, Samodha C Fernando
INTRODUCTION: An increasing emergence of novel animal pathogens has been observed over the last decade. Viruses are a major contributor to the increased emergence and therefore, veterinary surveillance and testing procedures are greatly needed to rapidly and accurately detect high-consequence animal diseases such as Foot and Mouth Disease, Highly Pathogenic Avian Influenza, Classical Swine Fever, and African Swine Fever. The major detection methods for such diseases include real-time PCR assays and pathogen-specific antibodies among others...
2024: Frontiers in Veterinary Science
https://read.qxmd.com/read/38376152/detection-of-salmonella-enterica-and-listeria-monocytogenes-in-alternative-irrigation-water-by-culture-and-qpcr-based-methods-in-the-mid-atlantic-u-s
#40
JOURNAL ARTICLE
Chanelle L Acheamfour, Salina Parveen, Alan Gutierrez, Eric T Handy, Sara Behal, Donghyun Kim, Seongyun Kim, Cheryl East, Ray Xiong, Joseph R Haymaker, Shirley A Micallef, Rachel E Rosenberg Goldstein, Kalmia E Kniel, Amy R Sapkota, Fawzy Hashem, Manan Sharma
Alternative irrigation waters (rivers, ponds, and reclaimed water) can harbor bacterial foodborne pathogens like Salmonella enterica and Listeria monocytogenes , potentially contaminating fruit and vegetable commodities. Detecting foodborne pathogens using qPCR-based methods may accelerate testing methods and procedures compared to culture-based methods. This study compared detection of S. enterica and L. monocytogenes by qPCR (real-time PCR) and culture methods in irrigation waters to determine the influence of water type (river, pond, and reclaimed water), season (winter, spring, summer, and fall), or volume (0...
February 20, 2024: Microbiology Spectrum
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