Search Results (52)

Herpes simplex virus 1 (HSV-1) is a rare cause of acute hepatitis, especially in patients with chronic immunosuppression. We performed whole-genome HSV-1 sequencing with a metagenomics approach on peripheral blood samples from an Italian case of fatal acute liver failure with high circulating HSV-1 (1,129,900,000 copies/mL), followed by phylogenetic analysis. After multiple sequence alignment, a final dataset of 182 whole-genome sequences was selected. The sequenced HSV-1 strain belonged to a phylogenetic clade isolated in Florida in 2002 (OQ724868.1). A characterization of single nucleotide polymorphisms and indels was performed to determine their effects on the viral genome: only one variant, classified as an indel, was detected with a high impact effect (c.905_906insGTTTT) in the UL49A gene, which is known to encode a membrane protein regulating virion morphogenesis, replication and assembly. In addition, this study also detected variants in other genes involved in crucial steps of the HSV-1 life cycle, like alpha-regulation (US7), capsid transport (UL36) and viral polymerase function (UL30). In conclusion, the results of this variant analysis confirmed that in HSV-1 hepatitis, some viral regions may be hotspots for adaptive mutations with a substantial impact on viral replication or immune evasion. Full article

Brevibacillus laterosporus strain B.O.D. is a well-established commercial probiotic and antimicrobial microorganism that finds use in human health and in agriculture as a biofertilizer. On the other hand, while B. laterosporus is a well-known entomopathogenic species, the possible insecticidal potential of strain B.O.D. remains unexplored. To address this knowledge gap, this study combined genome sequencing and comparative analysis with other B. laterospours strains and insect bioassays. The genome of B. laterosporus B.O.D. was found to harbor a wide range of genes related to entomopathogenicity encoding putative proteases, chitinases, collagenase-like proteases, mosquitocidal proteins, bacillolysin, and spore-surface proteins. Antimicrobial compounds such as gramicidin and surfactin were also found. Sequence alignment with other well-characterized B. laterosporus strains and analysis revealed significant differences, which support the corresponding differences in insecticidal activity observed when comparing strain B.O.D. with others against a variety of lepidopteran and dipteran pest species. This study reports for the first time the genome of strain B.O.D., providing a comparative analysis and highlighting its insecticidal properties, which appear more moderate compared to previously characterized entomopathogenic strains of the same species. Everything considered, B. laterosporus strain B.O.D. appears to be remarkably versatile, underscoring wide biotechnological potential. Full article

Polyglutamine expansion in Ataxin-2 (ATXN2) is responsible for rare, dominantly inherited Spinocerebellar Ataxia type 2 (SCA2). Together with its paralog Ataxin-2-like (ATXN2L), both proteins have received much interest, since the deletion of their yeast and fly orthologs alleviates TDP-43-triggered neurotoxicity in Amyotrophic Lateral Sclerosis models. Their typical structure across evolution combines LSm with LSm-Associated Domains and a PAM2 motif. To understand the physiological regulation and functions of Ataxin-2 homologs, the phylogenesis of sequences was analyzed. Human ATXN2 harbors multiple alternative start codons, e.g., from an intrinsically disordered sequence (IDR) present since armadillo, or from the polyQ sequence that arose since amphibians, or from the LSm domain since primitive eukaryotes. Multiple smaller isoforms also exist across the C-terminus. Therapeutic knockdown of polyQ expansions in human ATXN2 should selectively target exon 1B. PolyQ repeats developed repeatedly, usually framed and often interrupted by (poly)Pro, originally near PAM2. The LSmAD sequence appeared in algae as the characteristic Ataxin-2 feature with strong conservation. Frequently, Ataxin-2 has added domains, likely due to transcriptional readthrough of neighbor genes during cell stress. These chimerisms show enrichment of rRNA processing; nutrient store mobilization; membrane strengthening via lipid, protein, and glycosylated components; and cell protrusions. Thus, any mutation of Ataxin-2 has complex effects, also affecting membrane resilience. Full article

Helicobacter pylori (H. pylori) is a Gram-negative bacterium that colonizes the human stomach and is associated with several gastric diseases, including gastritis, peptic ulcer disease, and gastric cancer. The bacterium’s ability to thrive in the harsh gastric environment is due, to some extent, to its stress response mechanisms, with its heat shock proteins (HSPs) playing a putative, yet not fully understood, role in these adaptive processes. HSPs are a family of molecules, highly conserved throughout phylogenesis, that assist in protein folding, prevent aggregation, and ensure cellular homeostasis under stressful conditions. In H. pylori, HSPs contribute to survival in the stomach’s acidic environment and oxidative stress. Furthermore, they aid in the bacterium’s ability to adhere to gastric epithelial cells, modulate the host immune response, and form biofilms, all contributing to chronic infection and pathogenicity. The role of microbial HSPs in antibiotic resistance has also emerged as a critical area of research, as these proteins help stabilize efflux pumps, protect essential proteins targeted by antibiotics, and promote biofilm formation, thereby reducing the efficacy of antimicrobial treatments. Among bacterial HSPs, GroEL and DnaK are probably the major proteins that control most of the H. pylori’s functioning. Indeed, both proteins possess remarkable acid resistance, high substrate affinity, and dual roles in protein homeostasis and host interaction. These features make them critical for H. pylori’s adaptation, persistence, and pathogenicity in the gastric niche. In addition, recent findings have also highlighted the involvement of HSPs in the crosstalk between H. pylori and gastric epithelial cells mediated by the release of bacterial outer membrane vesicles and host-derived exosomes, both of these extracellular vesicles being part of the muco-microbiotic layer of the stomach and influencing cellular signalling and immune modulation. Considering their critical role in the survival and persistence of bacteria, microbial HSPs also represent potential therapeutic targets. Strategies aimed at inhibiting microbial HSP function, combined with conventional antibiotics or developing vaccines targeting microbial HSPs, could provide new avenues for the treatment of H. pylori infections and combat antibiotic resistance. This review explores the multifaceted roles of microbial HSPs in the pathogenesis of H. pylori, highlighting their contributions to bacterial adhesion, immune evasion, stress response, and antibiotic resistance. Full article

Low pathogenic H9N2 avian influenza viruses have become widespread in wild birds and poultry worldwide, raising concerns about their potential to spark pandemics or their role in enhancing the virulence and infectivity of H5Nx viruses through genetic reassortment. Therefore, influenza monitoring studies, including those of H9N2 viruses, are crucial for understanding, evaluating, and mitigating the risks associated with avian infections, and have broader implications for global public health. Although H9N2 viruses are not considered enzootic in Kazakhstan, they have been repeatedly detected in wild waterfowls and domestic poultry. In this study, all eight gene segments of influenza A/H9N2 viruses isolated in various regions of Kazakhstan between 2014 and 2020 were sequenced and analyzed. Molecular characterization revealed the presence of genetic markers associated with mammalian infectivity and disease potential. Furthermore, their predicted receptor binding site sequences indicate their potential capacity to attach to human-type receptors. These findings highlight the importance of continued surveillance and molecular investigation to better understand the evolution and zoonotic potential of H9N2 viruses in Kazakhstan. Full article

This study reports on the whole genome sequencing of the hazelnut endophytic Fusarium isolate Hzn5 from Poland. It was identified as a member of the Fusarium citricola species complex based on a phylogenetic analysis which also pointed out that other hazelnut isolates, previously identified as F. lateritium and F. tricinctum, actually belong to this species complex. Genome annotation allowed the mapping of 4491 different protein sequences to the genome assembly. A further in silico search for their potential biosynthetic activity showed that predicted genes are involved in 1110 metabolic pathways. Moreover, the analysis of the genome sequence carried out in comparison to another isolate, previously identified as an agent of hazelnut gray necrosis in Italy, revealed a homology to several regions containing biosynthetic gene clusters for bioactive secondary metabolites. The resulting indications for the biosynthetic aptitude concerning some emerging mycotoxins, such as the enniatins and culmorin, should be taken into consideration with reference to the possible contamination of hazelnuts and derived products. Full article

Blastocystis is a common intestinal protist with a global distribution, frequently found in humans and various animals. Despite its prevalence, its role in human health remains debated, oscillating between being a harmless commensal and a potential pathogen. It has also been associated with gastrointestinal disorders such as irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). In Italy, the genetic and spatial diversity of Blastocystis remains understudied, despite the country’s diverse urbanized and environmental landscapes. This study investigates the haplotypic and spatial diversity of clinical isolates of Blastocystis across two different Italian regions, with an emphasis on subtype distribution and genetic variation. Using a network-based haplotype analysis, the study reveals a heterogeneous subtype distribution, with subtype ST4 (47.3%) being the most prevalent, followed by ST3 (20%), ST1 (16.4%), ST2 (12.7%), ST6 (1.8%) and ST7 (1.8%). The overall infection rate detected from symptomatic patients is 9.75%. Notably, ST4 shows limited haplotypic variation, suggesting a more stable population structure that is potentially linked to a human-adapted lineage. In contrast, ST1 and ST2 exhibit greater haplotypic diversity, likely due to ongoing zoonotic transmission. These findings enhance our understanding of the epidemiology of Blastocystis in Italy and underscore the need for further research on its pathogenic potential and transmission dynamics. Full article

Chandipura virus (CHPV) is an arthropod-borne virus linked to encephalitis in humans, primarily in India. Its evolutionary dynamics and transmission pathways remain poorly understood due to limited genomic data. This study analyzed 23 publicly available CHPV genomes, including isolates from humans, sandflies, and a hedgehog, retrieved from GenBank. Phylogenetic analyses were conducted to explore host-specific and geographic evolutionary patterns. Phylogenetic analysis revealed distinct evolutionary lineages. Human-derived genomes collected in India between 2003 and 2024 formed a well-supported monophyletic clade, suggesting a unique evolutionary lineage. In contrast, sandfly-derived genomes exhibited diverse clustering patterns. Notably, Kenyan sandfly isolates from 2016–2017 were phylogenetically closer to human-derived sequences, suggesting possible shared evolutionary pressures. These findings provide preliminary insights into CHPV evolution and emphasize the need for enhanced genomic surveillance in both human and non-human populations. Expanding genomic data is essential to validate these observations and inform public health strategies. Full article

Toxoplasma gondii is a widespread foodborne parasite that affects both humans and animals worldwide. The genetic characterization of this parasite has become crucial due to its epidemiological and clinical implications. The present study focused on the direct genetic characterization of T. gondii-positive DNA samples from Northern Italy, using three standardized genotyping methods. Of the 87 PCR-positive DNA samples obtained from livestock, wild, and captive animals, 9 were confirmed, quantified, and subsequently subjected to typing procedures: microsatellite analysis, PCR-RFLP, and partial sequencing of GRA6 and SAG3 genes. Most of the typed samples, derived from clinical cases of toxoplasmosis, specifically related to abortion outbreaks in small ruminants, as well as one case of systemic toxoplasmosis in lemur (Lemur catta). Predominantly, Type II strains were observed, with non-clonal variants identified in a sheep and a lemur. Sequencing of SAG3 revealed specific single nucleotide polymorphism, previously documented in European type-II variants, with phylogenesis suggesting a potential genetic relatedness between T. gondii population in Italy, Spain, and France. By utilizing three distinct genotyping methods, this study provides the first comprehensive microsatellite profiles of T. gondii in Italy, and additional insights into the molecular variability of T. gondii strains circulating in this country from different epidemiological settings. Full article

Small ruminant lentiviruses (SRLVs) are responsible for chronic and progressive multisystemic clinical forms, which significantly reduce flocks’ productivity and have a considerable economic impact on the small ruminant industry. Due to the increase in genetic analysis studies and the potential for misclassification of certain strains, owing to the high genetic variability of these viruses, a systematic review was deemed necessary. This review explores the types of matrices used for molecular detection and phylogenetic studies, the genomic regions selected as targets, and the software utilized for phylogenetic analysis, assessing the geographical distribution of identified genotypes and subgenotypes over time. A thorough comparison of the diagnostic approaches highlights the strengths and limitations of each method, identifying gaps that need to be addressed. Additionally, recombination events and compartmentalization are examined to provide an updated, detailed, and comprehensive overview of SRLV phylogenesis. Full article

The molecular classification of Acanthamoeba is currently based on the analysis of 18S rDNA sequences, delimiting around twenty genotypes (T1–T23). In some cases, however, the resolution of 18S is limited, and other genetic markers could be useful for unravelling poorly resolved lineages. In this study, the partial large subunit (LSU) of rDNA and ITS were used to re-examine the Acanthamoeba palestinensis group (T2/T6 lineage), which consists of various poorly defined lineages, including the T2 and T6 genotypes. New sequences overlapping 18S, ITS, and LSU were recovered. The analysis placed previously identified partial ITS-LSU sequences as T2/T6 and further confirmed the separation of the OX1 lineage from T2. In addition, analysis of the second internal transcribed spacer (ITS-2) suggests that multiple species may be present within the T6 and OX1 lineages. The results obtained from the T2/T6 lineage analysis confirm the utility of partial LSU and ITS for the study of Acanthamoeba, suggesting their advantage for disentangling complex lineages. Full article

Candida auris is an emerging yeast considered a serious threat to global health. We report the first case of C. auris candidemia in Southern Italy, characterized using whole genome sequencing (WGS), and compared with a second strain isolated from a patient who presented as C. auris-colonized following screening. The C. auris strain was isolated from clinical samples, identified via MALDI-TOF, and subjected to WGS. Antifungal susceptibility testing was performed using commercial broth microdilution plates, and resistance protein sequences were evaluated with TBLASTN-2.15.0. Following the initial C. auris isolation from patient A, active surveillance and environmental investigations were implemented for all ICU patients. Of the 26 ICU surfaces sampled, 46.1% tested positive for C. auris via real-time PCR. Screening identified a second patient (patient B) as C. auris-colonized. The phylogenetic characterization of strains from patients A and B, based on the D1/D2 region of the 28s rDNA and the internal transcribed spacer (ITS) region, showed high similarity with strains from Lebanon. SNP analysis revealed high clonality, assigning both strains to clade I, indicating a significant similarity with Lebanese strains. This case confirms the alarming spread of C. auris infections and highlights the need for stringent infection control measures to manage outbreaks. Full article

The protein S100B is a part of the S100 protein family, which consists of at least 25 calcium-binding proteins. S100B is highly conserved across different species, supporting important biological functions. The protein was shown to play a role in gut microbiota eubiosis and is secreted in human breast milk, suggesting a physiological trophic function in newborn development. This study explores the possible presence of the S100B motif in plant genomes, and of S100B-like immunoreactive material in different plant extracts, opening up potential botanical uses for dietary supplementation. To explore the presence of the S100B motif in plants, a bioinformatic workflow was used. In addition, the immunoreactivity of S100B from vegetable and fruit samples was tested using an ELISA assay. The S100B motif was expected in silico in the genome of different edible plants belonging to the Viridiplantae clade, such as Durio zibethinus or Malus domestica and other medicinal species. S100B-like immunoreactive material was also detected in samples from fruits or leaves. The finding of S100B-like molecules in plants sheds new light on their role in phylogenesis and in the food chain. This study lays the foundation to elucidate the possible beneficial effects of plants or derivatives containing the S100B-like principle and their potential use in nutraceuticals. Full article

Enteroviruses (EVs) are ubiquitous viruses that circulate worldwide, causing sporadic or epidemic infections, typically during the summer and fall. They cause a broad spectrum of illnesses, ranging from an unspecified febrile clinical presentation to a severe illness. EVs are recognized to be the most frequent etiological agents of aseptic meningitis in children. However, as the infection is usually mild and self-limiting, it remains underestimated, and the epidemiology of EVs is poorly understood. To date, no vaccine or effective therapy for all types of enteroviruses is available, and EVs constitute a public health concern. Here, we investigated the molecular epidemiology of EV strains circulating in the Lazio region over a 10-year time span (2012–2023) by using a sequence-typing approach and phylogenetic analysis. The epidemiological trend of EV infection has undergone changes during the SARS-CoV-2 pandemic (2020–2021), which resulted in a modification in terms of the number of diagnosed cases and seasonality. From 2022, the circulation of EVs showed a behavior typical of the pre-pandemic period, although changes in predominantly circulating strains have been noted. Both epidemic and sporadic circulation events have been characterized in the Lazio region. Further analyses are needed to better characterize any strain with higher potential pathogenic power and to identify possible recombinant strains. Full article

Equine hepacivirus (EqHV, Flaviviridae, hepacivirus) is a small, enveloped RNA virus generally causing sub-clinical hepatitis with occasional fatalities. EqHV is reported in equids worldwide, but for Italy data are limited. To address this, a survey study was set up to estimate prevalence at a national level and among different production categories (equestrian; competition; work and meat; reproduction) and national macro-regions (North, Central, South, and Islands). Data obtained testing 1801 horse serum samples by Real-Time RT PCR were compared within the categories and regions. The NS3 fragment of the PCR-positive samples was sequenced by Sanger protocol for phylogenetic and mutational analysis. The tertiary structure of the NS3 protein was also assessed. The estimated national prevalence was 4.27% [1.97–6.59, 95% CI] and no statistical differences were detected among production categories and macro-regions. The phylogenesis confirmed the distribution in Italy of the three known EqHV subtypes, also suggesting a possible fourth sub-type that, however, requires further confirmation. Mutational profiles that could also affect the NS3 binding affinity to the viral RNA were detected. The present paper demonstrates that EqHV should be included in diagnostic protocols when investigating causes of hepatitis, and in quality control protocols for blood derived products due to its parental transmission. Full article