Sign in to use this feature.

Years

Between: -

Subjects

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Journals

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Article Types

Countries / Regions

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Search Results (5,416)

Search Parameters:
Keywords = whole genomic sequence

Order results
Result details
Results per page
Select all
Export citation of selected articles as:
14 pages, 1669 KiB  
Article
Guinea Pig X Virus Is a Gammaherpesvirus
by Vy Ngoc Yen Truong, Robert Ellis and Brent A. Stanfield
Viruses 2025, 17(8), 1084; https://doi.org/10.3390/v17081084 - 5 Aug 2025
Abstract
The Guinea Pig X Virus (GPXV), a newly identified gammaherpesvirus, provides an opportunity to study viral evolution and host–virus dynamics. This study characterizes the GPXV genome and investigates its phylogenetic relationships and divergence from related viruses through comparative genomic and phylogenetic analyses. Virus [...] Read more.
The Guinea Pig X Virus (GPXV), a newly identified gammaherpesvirus, provides an opportunity to study viral evolution and host–virus dynamics. This study characterizes the GPXV genome and investigates its phylogenetic relationships and divergence from related viruses through comparative genomic and phylogenetic analyses. Virus propagation was conducted in Vero cells, followed by genomic DNA extraction and pan-herpesvirus nested PCR. Sanger sequencing filled gaps in the initial genome assembly, and whole-genome sequencing was performed using the Illumina MiSeq platform. Phylogenetic analyses focused on ORF8 (glycoprotein B), ORF9 (DNA polymerase catalytic subunit), ORF50 (RTA: replication and transcription activator), and ORF73 (LANA: latency-associated nuclear antigen). Results showed that GPXV ORFs showed variable evolutionary relationships with other gammaherpesviruses, including divergence from primate-associated viruses and clustering with bovine and rodent viruses. In addition to phylogenetics, a comprehensive comparative analysis of protein-coding genes between GPXV and the previously described Guinea Pig Herpes-Like Virus (GPHLV) revealed divergence. Twenty-four non-ORF genomic features were unique to GPXV, while 62 shared ORFs exhibited low to high sequence divergence. These findings highlight GPXV’s distinct evolutionary trajectory and its potential role as a model for studying host-specific adaptations and gammaherpesvirus diversity. Full article
(This article belongs to the Special Issue Animal Herpesvirus 2025)
Show Figures

Graphical abstract

17 pages, 3344 KiB  
Article
Connectiveness of Antimicrobial Resistance Genotype–Genotype and Genotype–Phenotype in the “Intersection” of Skin and Gut Microbes
by Ruizhao Jia, Wenya Su, Wenjia Wang, Lulu Shi, Xinrou Zheng, Youming Zhang, Hai Xu, Xueyun Geng, Ling Li, Mingyu Wang and Xiang Li
Biology 2025, 14(8), 1000; https://doi.org/10.3390/biology14081000 - 5 Aug 2025
Abstract
The perianal skin is a unique “skin–gut” boundary that serves as a critical hotspot for the exchange and evolution of antibiotic resistance genes (ARGs). However, its role in the dissemination of antimicrobial resistance (AMR) has often been underestimated. To characterize the resistance patterns [...] Read more.
The perianal skin is a unique “skin–gut” boundary that serves as a critical hotspot for the exchange and evolution of antibiotic resistance genes (ARGs). However, its role in the dissemination of antimicrobial resistance (AMR) has often been underestimated. To characterize the resistance patterns in the perianal skin environment of patients with perianal diseases and to investigate the drivers of AMR in this niche, a total of 51 bacterial isolates were selected from a historical strain bank containing isolates originally collected from patients with perianal diseases. All the isolates originated from the skin site and were subjected to antimicrobial susceptibility testing, whole-genome sequencing, and co-occurrence network analysis. The analysis revealed a highly structured resistance pattern, dominated by two distinct modules: one representing a classic Staphylococcal resistance platform centered around mecA and the bla operon, and a broad-spectrum multidrug resistance module in Gram-negative bacteria centered around tet(A) and predominantly carried by IncFIB and other IncF family plasmids. Further analysis pinpointed IncFIB-type plasmids as potent vehicles driving the efficient dissemination of the latter resistance module. Moreover, numerous unexplained resistance phenotypes were observed in a subset of isolates, indicating the potential presence of emerging and uncharacterized AMR threats. These findings establish the perianal skin as a complex reservoir of multidrug resistance genes and a hub for mobile genetic element exchange, highlighting the necessity of enhanced surveillance and targeted interventions in this clinically important ecological niche. Full article
(This article belongs to the Section Microbiology)
Show Figures

Figure 1

18 pages, 2678 KiB  
Article
Pre-Conception Maternal Obesity Confers Autism Spectrum Disorder-like Behaviors in Mice Offspring Through Neuroepigenetic Dysregulation
by Nina P. Allan, Amada Torres, Michael J. Corley, Brennan Y. Yamamoto, Chantell Balaan, Yasuhiro Yamauchi, Rafael Peres, Yujia Qin, Vedbar S. Khadka, Youping Deng, Monika A. Ward and Alika K. Maunakea
Cells 2025, 14(15), 1201; https://doi.org/10.3390/cells14151201 (registering DOI) - 5 Aug 2025
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with early-life origins. Maternal obesity has been associated with increased ASD risk, yet the mechanisms and timing of susceptibility remain unclear. Using a mouse model combining in vitro fertilization (IVF) and embryo transfer, we [...] Read more.
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with early-life origins. Maternal obesity has been associated with increased ASD risk, yet the mechanisms and timing of susceptibility remain unclear. Using a mouse model combining in vitro fertilization (IVF) and embryo transfer, we separated the effects of pre-conception and gestational obesity. We found that maternal high fat diet (HFD) exposure prior to conception alone was sufficient to induce ASD-like behaviors in male offspring—including altered vocalizations, reduced sociability, and increased repetitive grooming—without anxiety-related changes. These phenotypes were absent in female offspring and those exposed only during gestation. Cortical transcriptome analysis revealed dysregulation and isoform shifts in genes implicated in ASD, including Homer1 and Zswim6. Whole-genome bisulfite sequencing of hippocampal tissue showed hypomethylation of an alternative Homer1 promoter, correlating with increased expression of the short isoform Homer1a, which is known to disrupt synaptic scaffolding. This pattern was specific to mice with ASD-like behaviors. Our findings show that pre-conceptional maternal obesity can lead to lasting, isoform-specific transcriptomic and epigenetic changes in the offspring’s brain. These results underscore the importance of maternal health before pregnancy as a critical and modifiable factor in ASD risk. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Autism Spectrum Disorder)
Show Figures

Figure 1

28 pages, 5831 KiB  
Article
An Italian Single-Center Genomic Surveillance Study: Two-Year Analysis of SARS-CoV-2 Spike Protein Mutations
by Riccardo Cecchetto, Emil Tonon, Asia Palmisano, Anna Lagni, Erica Diani, Virginia Lotti, Marco Mantoan, Livio Montesarchio, Francesca Palladini, Giona Turri and Davide Gibellini
Int. J. Mol. Sci. 2025, 26(15), 7558; https://doi.org/10.3390/ijms26157558 (registering DOI) - 5 Aug 2025
Abstract
The repeated occurrence of SARS-CoV-2 variants, largely driven by virus–host interactions, was and will remain a public health concern. Spike protein mutations shaped viral infectivity, transmissibility, and immune escape. From February 2022 to April 2024, a local genomic surveillance program in Verona, Italy, [...] Read more.
The repeated occurrence of SARS-CoV-2 variants, largely driven by virus–host interactions, was and will remain a public health concern. Spike protein mutations shaped viral infectivity, transmissibility, and immune escape. From February 2022 to April 2024, a local genomic surveillance program in Verona, Italy, was conducted on 1333 SARS-CoV-2-positive nasopharyngeal swabs via next generation full-length genome sequencing. Spike protein mutations were classified based on their prevalence over time. Mutations were grouped into five categories: fixed, emerging, fading, transient, and divergent. Notably, some divergent mutations displayed a “Lazarus effect,” disappearing and later reappearing in new lineages, indicating potential adaptive advantages in specific genomic contexts. This two-year surveillance study highlights the dynamic nature of spike protein mutations and their role in SARS-CoV-2 evolution. The findings underscore the need for ongoing mutation-focused genomic monitoring to detect early signals of variant emergence, especially among mutations previously considered disadvantageous. Such efforts are critical for driving public health responses and guiding future vaccine and therapeutic strategies. Full article
(This article belongs to the Special Issue The Interaction Between Cell and Virus, 3rd Edition)
Show Figures

Figure 1

22 pages, 884 KiB  
Article
Mitochondrial Dysregulation in Male Infertility: A Preliminary Study for Infertility-Specific lncRNA Variants
by Georgios Stamatellos, Maria-Anna Kyrgiafini, Aris Kaltsas and Zissis Mamuris
DNA 2025, 5(3), 38; https://doi.org/10.3390/dna5030038 - 5 Aug 2025
Abstract
Background/Objectives: Male infertility is a major health concern with a complex etiopathology, yet a substantial proportion of cases remain idiopathic. Mitochondrial dysfunction and non-coding RNA (ncRNA) deregulation have both been implicated in impaired spermatogenesis, but their interplay remains poorly understood. This study aimed [...] Read more.
Background/Objectives: Male infertility is a major health concern with a complex etiopathology, yet a substantial proportion of cases remain idiopathic. Mitochondrial dysfunction and non-coding RNA (ncRNA) deregulation have both been implicated in impaired spermatogenesis, but their interplay remains poorly understood. This study aimed to identify infertility-specific variants in ncRNAs that affect mitochondrial dynamics and homeostasis and to explore their roles. Methods: Whole-genome sequencing (WGS) was performed on genomic DNA samples from teratozoospermic, asthenozoospermic, oligozoospermic, and normozoospermic men. Variants uniquely present in infertile individuals and mapped to ncRNAs that affect mitochondrial dynamics were selected and prioritized using bioinformatics tools. An independent transcriptomic validation was conducted using RNA-sequencing data from testicular biopsies of men with non-obstructive azoospermia (NOA) to determine whether the ncRNAs harboring WGS-derived variants were transcriptionally altered. Results: We identified several infertility-specific variants located in lncRNAs known to interact with mitochondrial regulators, including GAS5, HOTAIR, PVT1, MEG3, and CDKN2B-AS1. Transcriptomic analysis confirmed significant deregulation of these lncRNAs in azoospermic testicular samples. Bioinformatic analysis also implicated the disruption of lncRNA–miRNA–mitochondria networks, potentially contributing to mitochondrial membrane potential loss, elevated reactive oxygen species (ROS) production, impaired mitophagy, and germ cell apoptosis. Conclusions: Our integrative genomic and transcriptomic analysis highlights lncRNA–mitochondrial gene interactions as a novel regulatory layer in male infertility, while the identified lncRNAs hold promise as biomarkers and therapeutic targets. However, future functional studies are warranted to elucidate their mechanistic roles and potential for clinical translation in reproductive medicine. Full article
Show Figures

Figure 1

15 pages, 9663 KiB  
Article
Hidden in the Genome: The First Italian Family with North Carolina Macular Dystrophy Carrying a Novel PRDM13 and CCNC Duplication
by Beatrice Spedicati, Domizia Pasquetti, Aurora Santin, Stefania Zampieri, Anna Morgan, Stefania Lenarduzzi, Giuseppe Giovanni Nardone, Elisa Paccagnella, Stefania Cappellani, Laura Diplotti, Stefano Pensiero, Fulvio Parentin, Paolo Gasparini, Maurizio Battaglia Parodi and Giorgia Girotto
Biomedicines 2025, 13(8), 1904; https://doi.org/10.3390/biomedicines13081904 - 5 Aug 2025
Abstract
Background: North Carolina Macular Dystrophy (NCMD) is a non-progressive inherited macular dystrophy characterized by marked phenotypic variability. The genetic etiology of NCMD remains largely unknown, and only a limited number of families have been reported in Europe. Methods: We performed an in-depth investigation [...] Read more.
Background: North Carolina Macular Dystrophy (NCMD) is a non-progressive inherited macular dystrophy characterized by marked phenotypic variability. The genetic etiology of NCMD remains largely unknown, and only a limited number of families have been reported in Europe. Methods: We performed an in-depth investigation of an Italian family affected by NCMD using an integrated approach that combined SNP-array analysis, whole-exome sequencing, and long-read whole-genome sequencing. Additionally, we conducted a comprehensive review of NCMD-related literature. Results: We identified a novel 98 Kb duplication involving both PRDM13 and CCNC genes in a three-generation kindred, where the proband exhibited severe macular alterations, while all other affected family members presented with a milder clinical phenotype. A review of the literature suggests different genotype–phenotype correlations and similar penetrance for duplications and single-nucleotide variants (SNVs) in described families. Specifically, smaller duplications may be associated with more severe phenotypes, while SNVs exhibit high phenotypic variability. Conclusions: In this study, we describe the first NCMD Italian family, in which the integration of second- and third-generation sequencing methods enabled the identification of a novel pathogenic PRDM13 and CCNC duplication, thereby expanding the mutational spectrum of NCMD. Overall, these findings, together with the literature review, highlight the importance of selecting appropriate genetic testing approaches that allow the detection of non-coding variants and CNVs and thus enable accurate diagnosis and effective clinical management of patients and their families. Full article
(This article belongs to the Special Issue Ophthalmic Genetics: Unraveling the Genomics of Eye Disorders)
Show Figures

Figure 1

13 pages, 2127 KiB  
Article
Assessing SARS-CoV-2 Rare Mutations and Transmission in New York City by NGS
by Dakai Liu, Harlan Pietz, George D. Rodriguez, Yuexiu Wu, Yihan Cao, Vishnu Singh, Hui Li, Eric Konadu, Keither K. James, Calvin Lui, Bright Varghese, Mingyu Shao, Gary Chen, Andrew Schreiner, Jiankun Tong, Carl Urban, Nishant Prasad, Ameer Hassoun, Manish Sharma and William Harry Rodgers
Microorganisms 2025, 13(8), 1821; https://doi.org/10.3390/microorganisms13081821 - 4 Aug 2025
Abstract
SARS-CoV-2 undergoes frequent mutations that drive viral evolution and genomic diversity, influencing transmissibility, immune escape, and disease severity. In this study, we performed whole-genome sequencing on SARS-CoV-2 isolates from patients in New York City and identified several globally rare mutations across multiple viral [...] Read more.
SARS-CoV-2 undergoes frequent mutations that drive viral evolution and genomic diversity, influencing transmissibility, immune escape, and disease severity. In this study, we performed whole-genome sequencing on SARS-CoV-2 isolates from patients in New York City and identified several globally rare mutations across multiple viral lineages. The isolates analyzed for rare mutations belonged to three lineages: B.1.1.7 (Alpha), B.1.526 (Iota), and B.1.623. We identified 16 rare mutations (global incidence <1000) in non-structural protein genes, including nsp2, nsp3, nsp4, nsp6, nsp8, nsp13, nsp14, ORF7a, and ORF8. Three of these mutations—located in nsp2, nsp13, and ORF8—have been reported in fewer than 100 individuals worldwide. We also detected five rare mutations in structural proteins (S, M, and N), including two—one in M and one in N—previously reported in fewer than 100 cases globally. We present clinical profiles of three patients, each infected with genetically distinct viral isolates from the three lineages studied. Furthermore, we illustrate a local transmission chain inferred from unique mutation patterns identified in the Omicron genome. These findings underscore the importance of whole-genome sequencing for detecting rare mutations, tracking community spread, and identifying emerging variants with clinical and public health significance. Full article
(This article belongs to the Special Issue The Molecular Epidemiology of Infectious Diseases)
Show Figures

Figure 1

18 pages, 1942 KiB  
Article
Surveillance and Characterization of Vancomycin-Resistant and Vancomycin-Variable Enterococci in a Hospital Setting
by Claudia Rotondo, Valentina Antonelli, Alberto Rossi, Silvia D’Arezzo, Marina Selleri, Michele Properzi, Silvia Turco, Giovanni Chillemi, Valentina Dimartino, Carolina Venditti, Sara Guerci, Paola Gallì, Carla Nisii, Alessia Arcangeli, Emanuela Caraffa, Stefania Cicalini and Carla Fontana
Antibiotics 2025, 14(8), 795; https://doi.org/10.3390/antibiotics14080795 (registering DOI) - 4 Aug 2025
Abstract
Background/Objectives: Enterococci, particularly Enterococcus faecalis and Enterococcus faecium, are Gram-positive cocci that can cause severe infections in hospitalized patients. The rise of vancomycin-resistant enterococci (VRE) and vancomycin-variable enterococci (VVE) poses significant challenges in healthcare settings due to their resistance to multiple [...] Read more.
Background/Objectives: Enterococci, particularly Enterococcus faecalis and Enterococcus faecium, are Gram-positive cocci that can cause severe infections in hospitalized patients. The rise of vancomycin-resistant enterococci (VRE) and vancomycin-variable enterococci (VVE) poses significant challenges in healthcare settings due to their resistance to multiple antibiotics. Methods: We conducted a point prevalence survey (PPS) to assess the prevalence of VRE and VVE colonization in hospitalized patients. Rectal swabs were collected from 160 patients and analyzed using molecular assays (MAs) and culture. Whole-genome sequencing (WGS) and core-genome multilocus sequence typing (cgMLST) were performed to identify the genetic diversity. Results: Of the 160 rectal swabs collected, 54 (33.7%) tested positive for the vanA and/or vanB genes. Culture-based methods identified 47 positive samples (29.3%); of these, 44 isolates were identified as E. faecium and 3 as E. faecalis. Based on the resistance profiles, 35 isolates (74.5%) were classified as VRE, while 12 (25.5%) were classified as VVE. WGS and cgMLST analyses identified seven clusters of E. faecium, with sequence type (ST) 80 being the most prevalent. Various resistance genes and virulence factors were identified, and this study also highlighted intra- and inter-ward transmission of VRE strains. Conclusions: Our findings underscore the potential for virulence and resistance of both the VRE and VVE strains, and they highlight the importance of effective infection control measures to prevent their spread. VVE in particular should be carefully monitored as they often escape detection. Integrating molecular data with clinical information will hopefully enhance our ability to predict and prevent future VRE infections. Full article
(This article belongs to the Special Issue Hospital-Associated Infectious Diseases and Antibiotic Therapy)
Show Figures

Figure 1

10 pages, 2785 KiB  
Article
Integration of Genome and Epigenetic Testing in the Diagnostic Evaluation of Developmental Delay: Differentiating Börjeson–Forssman–Lehmann (BFLS) and White–Kernohan (WHIKERS) Syndromes
by Keri Ramsey, Supraja Prakash, Jennifer Kerkhof, Bekim Sadikovic, Susan White, Marcus Naymik, Jennifer Sloan, Anna Bonfitto, Newell Belnap, Meredith Sanchez-Castillo, Wayne Jepsen, Matthew Huentelman, Saunder Bernes, Vinodh Narayanan and Shagun Kaur
Genes 2025, 16(8), 933; https://doi.org/10.3390/genes16080933 (registering DOI) - 4 Aug 2025
Abstract
Background: More than 1500 genes are associated with developmental delay and intellectual disability, with variants in many of these genes contributing to a shared phenotype. The discovery of variants of uncertain significance (VUS) found in these genes during genetic testing can lead [...] Read more.
Background: More than 1500 genes are associated with developmental delay and intellectual disability, with variants in many of these genes contributing to a shared phenotype. The discovery of variants of uncertain significance (VUS) found in these genes during genetic testing can lead to ambiguity and further delay in diagnosis and medical management. Phenotyping, additional genetic testing, and functional studies can all add valuable information to help reclassify these variants. Here we demonstrate the clinical utility of epigenetic signatures in prioritizing variants of uncertain significance in genes associated with developmental delay (DD) and intellectual disability (ID). Methods: Genome sequencing was performed in a male with developmental delay. He was found to have VUSs in both PHF6 and DDB1 genes, linked with Börjeson–Forssman–Lehmann syndrome (BFLS) and White–Kernohan syndrome (WHIKERS), respectively. These two disorders share a similar phenotype but have distinct inheritance patterns and molecular pathogenic mechanisms. DNA methylation profiling (DNAm) of whole blood was performed using the clinically validated EpiSign assay. Results: The proband’s methylation profile demonstrated a strong correlation with the BFLS methylation signature, supporting the PHF6 variant as a likely cause of his neurodevelopmental disorder. Conclusions: Epigenetic testing for disorders with distinct methylation patterns can provide diagnostic utility when a patient presents with variants of uncertain significance in genes associated with developmental delay. Epigenetic signatures can also guide genetic counselling and family planning. Full article
(This article belongs to the Special Issue Genetics and Genomics of Heritable Pediatric Disorders)
Show Figures

Figure 1

14 pages, 1805 KiB  
Data Descriptor
Mediterranean-DASH Intervention for Neurodegenerative Delay (MIND) Trial: Genetic Resource for Precision Nutrition
by Yuxi Liu, Hailie Fowler, Dong D. Wang, Lisa L. Barnes and Marilyn C. Cornelis
Nutrients 2025, 17(15), 2548; https://doi.org/10.3390/nu17152548 - 4 Aug 2025
Abstract
Background: The Mediterranean-DASH Intervention for Neurodegenerative Delay (MIND) was a 3-year, multicenter, randomized controlled trial to test the effects of the MIND diet on cognitive decline in 604 individuals at risk for Alzheimer’s dementia. Here, we describe the genotyping, imputation, and quality control [...] Read more.
Background: The Mediterranean-DASH Intervention for Neurodegenerative Delay (MIND) was a 3-year, multicenter, randomized controlled trial to test the effects of the MIND diet on cognitive decline in 604 individuals at risk for Alzheimer’s dementia. Here, we describe the genotyping, imputation, and quality control (QC) procedures for the genetic data of trial participants. Methods: DNA was extracted from either whole blood or serum, and genotyping was performed using the Infinium Global Diversity Array. Established sample and SNP QC procedures were applied to the genotyping data, followed by imputation using the 1000 Genomes Phase 3 v5 reference panel. Results: Significant study-site, specimen type, and batch effects were observed. A total of 494 individuals of inferred European ancestry and 58 individuals of inferred African ancestry were included in the final imputed dataset. Evaluation of the imputed APOE genotype against gold-standard sequencing data showed high concordance (98.2%). We replicated several known genetic associations identified from previous genome-wide association studies, including SNPs previously linked to adiponectin (rs16861209, p = 1.5 × 10−5), alpha-linolenic acid (rs174547, p = 1.3 × 10−7), and alpha-tocopherol (rs964184, p = 0.003). Conclusions: This dataset represents the first genetic resource derived from a dietary intervention trial focused on cognitive outcomes. It enables investigation of genetic contributions to variability in cognitive response to the MIND diet and supports integrative analyses with other omics data types to elucidate the biological mechanisms underlying cognitive decline. These efforts may ultimately inform precision nutrition strategies to promote cognitive health. Full article
(This article belongs to the Section Nutrigenetics and Nutrigenomics)
Show Figures

Figure 1

14 pages, 3361 KiB  
Article
Bacteremia Caused by a Putative Novel Species in the Genus Erwinia: A Case Report and Genomic Analysis
by Jiwoo Lee, Taek Soo Kim, Hyunwoong Park and Jae Hyeon Park
Life 2025, 15(8), 1227; https://doi.org/10.3390/life15081227 - 3 Aug 2025
Viewed by 49
Abstract
We report a case of catheter-associated bloodstream infection caused by a putative novel species in the genus Erwinia, identified using whole-genome sequencing (WGS). A female adolescent receiving long-term home parenteral nutrition via a central venous catheter (CVC) presented with a fever. Gram-negative [...] Read more.
We report a case of catheter-associated bloodstream infection caused by a putative novel species in the genus Erwinia, identified using whole-genome sequencing (WGS). A female adolescent receiving long-term home parenteral nutrition via a central venous catheter (CVC) presented with a fever. Gram-negative rods were isolated from two CVC-derived blood culture sets, while peripheral cultures remained negative. Conventional identification methods, including VITEK 2, Phoenix M50, MALDI-TOF MS, and 16S rRNA and rpoB gene sequencing, failed to achieve species-level identification. WGS was performed on the isolate using Illumina MiSeq. Genomic analysis revealed a genome size of 5.39 Mb with 56.8% GC content and high assembly completeness. The highest average nucleotide identity (ANI) was 90.3% with Pantoea coffeiphila, and ≤85% with known Erwinia species, suggesting that it represents a distinct taxon. Phylogenetic analyses placed the isolate within the Erwinia clade but separate from any known species. Antimicrobial susceptibility testing showed broad susceptibility. This case highlights the utility of WGS for the identification of rare or novel organisms not captured by conventional methods and expands the clinical spectrum of Erwinia species. While the criteria for species delineation were met, the phenotypic characterization remains insufficient to formally propose a new species. Full article
Show Figures

Figure 1

19 pages, 9488 KiB  
Article
Proteus mirabilis from Captive Giant Pandas and Red Pandas Carries Diverse Antimicrobial Resistance Genes and Virulence Genes Associated with Mobile Genetic Elements
by Yizhou Yang, Yan Liu, Jiali Wang, Caiwu Li, Ruihu Wu, Jialiang Xin, Xue Yang, Haohong Zheng, Zhijun Zhong, Hualin Fu, Ziyao Zhou, Haifeng Liu and Guangneng Peng
Microorganisms 2025, 13(8), 1802; https://doi.org/10.3390/microorganisms13081802 - 1 Aug 2025
Viewed by 148
Abstract
Proteus mirabilis is a zoonotic pathogen that poses a growing threat to both animal and human health due to rising antimicrobial resistance (AMR). It is widely found in animals, including China’s nationally protected captive giant and red pandas. This study isolated Proteus mirabilis [...] Read more.
Proteus mirabilis is a zoonotic pathogen that poses a growing threat to both animal and human health due to rising antimicrobial resistance (AMR). It is widely found in animals, including China’s nationally protected captive giant and red pandas. This study isolated Proteus mirabilis from panda feces to assess AMR and virulence traits, and used whole-genome sequencing (WGS) to evaluate the spread of resistance genes (ARGs) and virulence genes (VAGs). In this study, 37 isolates were obtained, 20 from red pandas and 17 from giant pandas. Multidrug-resistant (MDR) strains were present in both hosts. Giant panda isolates showed the highest resistance to ampicillin and cefazolin (58.8%), while red panda isolates were most resistant to trimethoprim/sulfamethoxazole (65%) and imipenem (55%). Giant panda-derived strains also exhibited stronger biofilm formation and swarming motility. WGS identified 31 ARGs and 73 VAGs, many linked to mobile genetic elements (MGEs) such as plasmids, integrons, and ICEs. In addition, we found frequent co-localization of drug resistance genes/VAGs with MGEs, indicating a high possibility of horizontal gene transfer (HGT). This study provides crucial insights into AMR and virulence risks in P. mirabilis from captive pandas, supporting targeted surveillance and control strategies. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and the Use of Antibiotics in Animals)
Show Figures

Figure 1

15 pages, 2636 KiB  
Article
Genome-Wide Identification of DNA Methyltransferase and Demethylase in Populus sect. Turanga and Their Potential Roles in Heteromorphic Leaf Development in Populus euphratica
by Chen Qiu, Jianhao Sun, Mingyu Jia, Xiaoli Han, Jia Song, Zhongshuai Gai and Zhijun Li
Plants 2025, 14(15), 2370; https://doi.org/10.3390/plants14152370 - 1 Aug 2025
Viewed by 188
Abstract
DNA methylation, mediated by DNA methyltransferases (DMTs) and demethylases (DMLs), is an important epigenetic modification that maintains genomic stability and regulates gene expression in plant growth, development, and stress responses. However, a comprehensive characterization of these gene families in Populus sect. Turanga remains [...] Read more.
DNA methylation, mediated by DNA methyltransferases (DMTs) and demethylases (DMLs), is an important epigenetic modification that maintains genomic stability and regulates gene expression in plant growth, development, and stress responses. However, a comprehensive characterization of these gene families in Populus sect. Turanga remains lacking. In this study, eight PeDMT and two PeDML genes were identified in Populus euphratica, and six PpDMT and three PpDML genes in Populus pruinosa. Phylogenetic analysis revealed that DMTs and DMLs could be classified into four and three subfamilies, respectively. The analysis of cis-acting elements indicated that the promoter regions of both DMTs and DMLs were enriched with elements responsive to growth and development, light, phytohormones, and stress. Collinearity analysis detected three segmentally duplicated gene pairs (PeDMT5/8, PeDML1/2, and PpDML2/3), suggesting potential functional diversification. Transcriptome profiling showed that several PeDMTs and PeDMLs exhibited leaf shape- and developmental stage-specific expression patterns, with PeDML1 highly expressed during early stages and in broad-ovate leaves. Whole-genome bisulfite sequencing revealed corresponding decreases in DNA methylation levels, suggesting that active demethylation may contribute to heteromorphic leaf formation. Overall, this study provides significant insights for exploring the functions and expression regulation of plant DMTs and DMLs and will contribute to future research unraveling the molecular mechanisms of epigenetic regulation in P. euphratica. Full article
Show Figures

Figure 1

11 pages, 1914 KiB  
Case Report
Case Report of Nephrogenic Diabetes Insipidus with a Novel Mutation in the AQP2 Gene
by Alejandro Padilla-Guzmán, Vanessa Amparo Ochoa-Jiménez, Jessica María Forero-Delgadillo, Karen Apraez-Murillo, Harry Pachajoa and Jaime M. Restrepo
Int. J. Mol. Sci. 2025, 26(15), 7415; https://doi.org/10.3390/ijms26157415 - 1 Aug 2025
Viewed by 113
Abstract
Nephrogenic diabetes insipidus (NDI) is a rare hereditary disorder characterized by renal resistance to arginine vasopressin (AVP), resulting in the kidneys’ inability to concentrate urine. Approximately 90% of NDI cases follow an X-linked inheritance pattern and are associated with pathogenic variants in the [...] Read more.
Nephrogenic diabetes insipidus (NDI) is a rare hereditary disorder characterized by renal resistance to arginine vasopressin (AVP), resulting in the kidneys’ inability to concentrate urine. Approximately 90% of NDI cases follow an X-linked inheritance pattern and are associated with pathogenic variants in the AVPR2 gene, which encodes the vasopressin receptor type 2. The remaining 10% are attributed to mutations in the AQP2 gene, which encodes aquaporin-2, and may follow either autosomal dominant or recessive inheritance patterns. We present the case of a male infant, younger than nine months of age, who was clinically diagnosed with NDI at six months. The patient presented recurrent episodes of polydipsia, polyuria, dehydration, hypernatremia, and persistently low urine osmolality. Despite adjustments in pharmacologic treatment and strict monitoring of urinary output, the clinical response remained suboptimal. Given the lack of improvement and the radiological finding of an absent posterior pituitary (neurohypophysis), the possibility of coexistent central diabetes insipidus (CDI) was raised, prompting a therapeutic trial with desmopressin. Nevertheless, in the absence of clinical improvement, desmopressin was discontinued. The patient’s management was continued with hydrochlorothiazide, ibuprofen, and a high-calorie diet restricted in sodium and protein, resulting in progressive clinical stabilization. Whole-exome sequencing identified a novel homozygous missense variant in the AQP2 gene (c.398T > A; p.Val133Glu), classified as likely pathogenic according to the American College of Medical Genetics and Genomics (ACMG) criteria: PM2 (absent from population databases), PP2 (missense variant in a gene with a low rate of benign missense variation), and PP3 (multiple lines of computational evidence supporting a deleterious effect)]. NDI is typically diagnosed during early infancy due to the early onset of symptoms and the potential for severe complications if left untreated. In this case, although initial clinical suspicion included concomitant CDI, the timely initiation of supportive management and the subsequent incorporation of molecular diagnostics facilitated a definitive diagnosis. The identification of a previously unreported homozygous variant in AQP2 contributed to diagnostic confirmation and therapeutic decision-making. The diagnosis and comprehensive management of NDI within the context of polyuria-polydipsia syndrome necessitates a multidisciplinary approach, integrating clinical evaluation with advanced molecular diagnostics. The novel AQP2 c.398T > A (p.Val133Glu) variant described herein was associated with early and severe clinical manifestations, underscoring the importance of genetic testing in atypical or treatment-refractory presentations of diabetes insipidus. Full article
(This article belongs to the Special Issue A Molecular Perspective on the Genetics of Kidney Diseases)
Show Figures

Figure 1

11 pages, 1419 KiB  
Article
Genetic Evidence of Yersinia pestis from the First Pandemic
by Swamy R. Adapa, Karen Hendrix, Aditya Upadhyay, Subhajeet Dutta, Andrea Vianello, Gregory O’Corry-Crowe, Jorge Monroy, Tatiana Ferrer, Elizabeth Remily-Wood, Gloria C. Ferreira, Michael Decker, Robert H. Tykot, Sucheta Tripathy and Rays H. Y. Jiang
Genes 2025, 16(8), 926; https://doi.org/10.3390/genes16080926 (registering DOI) - 31 Jul 2025
Viewed by 448
Abstract
Background/Objectives: The Plague of Justinian marked the beginning of the First Pandemic (541–750 CE), yet no genomic evidence of Yersinia pestis has previously been recovered from the Eastern Mediterranean, where the outbreak was first recorded. This study aimed to determine whether Y. pestis [...] Read more.
Background/Objectives: The Plague of Justinian marked the beginning of the First Pandemic (541–750 CE), yet no genomic evidence of Yersinia pestis has previously been recovered from the Eastern Mediterranean, where the outbreak was first recorded. This study aimed to determine whether Y. pestis was present in a mid-6th to early 7th century mass grave in Jerash, Jordan, and to characterize its genome within the broader context of First Pandemic strains. Methods: We analyzed samples from multiple individuals recovered from the Jerash mass grave. Initial screening for potential pathogen presence was conducted using proteomics. Select samples were subjected to ancient DNA extraction and whole genome sequencing. Comparative genomic and phylogenetic analyses were conducted to assess strain identity and evolutionary placement. Results: Genomic sequencing recovered Y. pestis DNA from five individuals, revealing highly similar genomes. All strains clustered tightly with other First Pandemic lineages but were notably recovered from a region geographically close to the pandemic’s historical epicenter for the first time. The near-identical genomes across diverse individuals suggest an outbreak of a single circulating lineage at the time of this outbreak. Conclusions: This study provides the first genomic evidence of Y. pestis in the Eastern Mediterranean during the First Pandemic, linking archaeological findings with pathogen genomics near the origin point of the Plague of Justinian. Summary Sentence: Genomic evidence links Y. pestis to the First Pandemic in an ancient city. Full article
(This article belongs to the Section Microbial Genetics and Genomics)
Show Figures

Figure 1

Back to TopTop