This case report describes a patient with prolonged fever following a stay in Kinshasa, Democratic Republic of the Congo (DRC). The patient was initially treated for malaria in Kinshasa but was subsequently hospitalized upon returning to Italy. Comprehensive diagnostic investigations, including serological, microbiological, and imaging studies, were conducted. Ultimately, Next Generation Sequencing (NGS) enabled the identification of Human Pegivirus as the likely causative agent, leading to a definitive diagnosis and clinical improvement. This report highlights the diagnostic challenges posed by tropical febrile illnesses and emphasizes the valuable role of NGS in detecting elusive pathogens.

Background: Seasonal influenza vaccination shows highly variable effectiveness across individuals, particularly in older adults, in whom age-related immune decline compromises protective responses. Methods: This study evaluated immune responses to the 2019/2020 quadrivalent influenza vaccine in 75 individuals aged 25–89 years. Influenza-specific antibody titers and virus-neutralizing activity were measured before and four weeks after vaccination, and participants were stratified as high or low responders. Results: We observed that older individuals exhibited increased frequencies of myeloid-derived suppressor cells (MDSCs) and activated regulatory T cells (Treg) expressing HLA-DR and CD38, consistent with enhanced immunosuppressive activity. Importantly, higher levels of these immunoregulatory populations correlated with poor vaccine responsiveness in both adult and older participants. Additionally, circulating T follicular regulatory (Tfr) cells were elevated in older participants and in low responders, whereas T follicular helper (Tfh) cells remained unchanged, resulting in an increased Tfr/Tfh ratio associated with impaired antibody production. However, when adjusting for possible confounders, most immunoregulatory subsets did not remain independently associated with responder status, except CD38+ Treg cells. Conclusions: These findings suggest that immunoregulatory networks, while essential for controlling chronic inflammation during aging, may limit vaccine-induced immunity. Identifying biomarkers such as MDSC frequency, activated Treg phenotype, and Tfr/Tfh balance may contribute to the identification of individuals with different levels of vaccine responsiveness and could help inform future personalized vaccination strategies.

The complex pathophysiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) involves a hyperinflammatory state with excessive cytokine production, leading to an influenza-like syndrome that may need emergency care. The severity of SARS-CoV-2 varies widely, and collective serum immune factors, evaluated in emergency care patients, have not been shown to correlate with disease progression. We applied a machine learning approach to reassess and define serum immune profiles that could align with clinical laboratory parameters and predict disease outcomes in patients with respiratory virus infections, including those with SARS-CoV-2, seeking emergency care. Sixty-two plasma immune molecules, in a cohort of 67 symptomatic SARS-CoV-2, were analyzed for correlation with antibodies (Abs) to spike (S) and nucleocapsid (N) proteins, as well as with clinical laboratory parameters, to identify early indicators of disease prognosis at hospital admission. This approach allowed us to analyze and cluster unlabeled datasets, delineating three distinct serum immune signatures. Two showed significant and opposite modulations, correlating with poorer disease outcomes, while most patients with moderate disease displayed modest immune factor dysregulation. This highlights the complexity of immune responses in the severity of diseases caused by highly respiratory pathogenic virus like SARS-CoV-2, emphasizing the importance of evaluating overall immune imbalance rather than focusing on a few dysregulated factors.

PURPOSE:In 2023-2024, measles cases progressively increased in Europe. Multiple outbreaks were reported and viral strains with three-nucleotide mutations potentially compromising diagnostic testing were identified. We analyzed the first cases of measles reported in Lazio (Central Italy) from September 2023 to March 2024, combining molecular characterization and phylogenetic analysis with epidemiological investigation to identify transmission chains and evaluate the sensitivity of PCR tests adopted on circulating viral strains. METHODS:We tested samples collected through routine measles and rubella surveillance for IgM, IgG and Real-Time PCR. We sequenced positive samples with higher viral titers using an amplicon-based whole-genome next-generation sequencing (WG-NGS) approach and performed mutational and phylogenetic analysis. Furthermore, we tested the sensitivity of the PCR molecular diagnostic assay adopted in our laboratory to identify the mutated strains. RESULTS:Of the 39 suspected cases, 28 were confirmed. Endemic cases were 82%; of these, 78% were sporadic at epidemiological investigation. From 21 high-titer samples, we obtained 14 strains belonging to the D8 genotype. Phylogenetic analysis identified four distinct clusters: three associating 50% of sporadic cases, and one confirming the epidemiological investigation. Several mutational patterns were identified, one of which had three nucleotide mutations potentially affecting the diagnostic test. However, our routine diagnostic PCR tests are able to detect mutated strains at different dilutions. CONCLUSION:Our results demonstrate that WG-NGS can be used to distinguish transmission chains and identify infection clusters to improve surveillance activity and enable the implementation of more targeted control measures, highlighting the importance of integrated epidemiological and genomic surveillance.

Isolating microorganisms from oil spill-contaminated environments is essential for advancing bioremediation strategies and discovering novel bioprocesses for hydrocarbon degradation. In this study, we report the isolation of a novel strain, Rhodococcus erythropolis LP27217, from Pertusillo Lake (Italy) on february 2017. Water samples were collected during an oil spill event and microbial community was previously characterized using 16S rRNA gene-targeted metagenomic analysis and functional prediction. The Rhodococcus genus was identified as the dominant member of this microbiome, and functional predictive analyses guided the isolation of the R. erythropolis LP27217 strain under various growth conditions, including the presence of hydrocarbons and in Liquid Microbial Fuel Cell (L-MFC) systems. This strain exhibits a versatile hydrocarbon-degrading and transforming metabolism, effectively addressing pollutants such as crude oil, polycyclic aromatic hydrocarbons (PAHs), and dibenzothiophene (DBT), even under psychrophilic conditions. Additionally, R. erythropolis LP27217 demonstrated the ability to produce lipopeptide biosurfactants and lipophilic polymers, with the latter being associated with the formation of an electrogenic hydrocarbonoclastic biofilm at the anoxic oil-water interface. Overall, this study demonstrated that R. erythropolis LP27217 is a promising candidate for sustainable applications, including in situ bioremediation of oil spills in lake ecosystems and the biosynthesis of innovative polymers and biosurfactants for biotechnological and environmental purposes. Furthermore, its ability to operate across oxic and hypoxic conditions, at the oil-water interface and within the water column, highlights a novel microbial mechanism with significant ecological and industrial potential.

In this paper, we analyze the serious environmental accident caused by a massive oil spill on 7 February 2024, off the island of Tobago, using two separate algorithms, namely, the established visible near-red index (VNRI) algorithm and the novel IVI visible reflectance ratio index (IVI), both applied to Sentinel-2 satellite images. These algorithms were specifically designed to monitor oil spills in inner waters. In this paper, where the IVI is presented for the first time, its effectiveness in the open sea is also showcased allowing the identification and subsequent monitoring over time of the oily masses that threaten the coral reef of the island. The analysis suggests that with sufficient cloud-free conditions, high temporal revisit multispectral optical satellites could support the timely detection and tracking of oil masses during environmental incidents near natural sanctuaries.

COVID-19 continues to claim victims in the world, especially among elderly subjects and people suffering from chronic-degenerative pathologies, like cardiovascular diseases. Several vaccines and drugs have been developed to mitigate the infection spread and its deleterious consequences. However, the emergence of new variants requires the identification of solutions to deal with the challenging mutations. In this context, the investigation of phytocomplexes and related compounds used in folk medicine and culinary purposes may lead to unfold nutraceuticals endowed with antiviral, and cardioprotective properties. We have described several vegetal extracts and secondary metabolites that hit the most important viral and host targets and bind them. The connection between SARS-CoV-2 and cardiovascular diseases were also outlined, as well as phytocomplexes with potentials for their mitigation. The review provides both an entry point for new researchers in this area, and a comprehensive overview for further investigation of the natural products presented.

Hepatitis E virus (HEV) infection is prevalent among domestic pigs and wild boar in Europe. This study focused on the genetic diversity of HEV subtypes 3c, 3e and 3f among swine and wild boar in Europe as well as their circulation. Phylogenetic analysis and Bayesian phylogenetic inference were applied on the selected ORF2 capsid HEV sequences to co-estimate the viral circulation, the mean evolutionary rates and the dated trees. The estimated mean values of the HEV ORF2 capsid gene evolutionary rate were 8.29 x 10(-3), 5.96 x 10(-3), and 1.107 x 10(-2) substitutions/site/year, respectively for 3c, 3e and 3f. The majority of the HEV 3c and 3e supported clusters did not show intermixing between swine and wild boar. Thus, although the intermixing observed in a minority of HEV 3c and 3e supported clusters suggests that transmission/circulation of these subtypes between swine and wild boar can potentially occur, 3c and 3e European wild boar HEV populations remained mainly segregated. In contrast, one half of the HEV 3f supported clusters showed intermixing between swine and wild boar, providing evidence for transfer/circulation to swine. The data suggest that continued virologic surveillance in swine and wild boar is necessary, together with targeted measures to reduce the chance of HEV transmission to humans.

A number of studies have suggested that influenza vaccination can provide protection against COVID-19, but the underlying mechanisms that could explain this association are still unclear. In this study, the effect of the 2021/2022 seasonal influenza vaccination on the immune response to the booster dose of anti-SARS-CoV-2 vaccination was evaluated in a cohort of healthy individuals. A total of 113 participants were enrolled, 74 of whom had no prior COVID-19 diagnosis or significant comorbidities were considered for the analysis. Participants received the anti-influenza tetravalent vaccine and the booster dose of the anti-SARS-CoV-2 vaccine or the anti-SARS-CoV-2 vaccine alone. Blood was collected before and 4 weeks after each vaccination and 12 weeks after SARS-CoV-2 vaccination and analyzed for anti-flu and anti-spike-specific antibody titers and for in vitro influenza and SARS-CoV-2 neutralization capacity. Results indicated an increased reactivity in subjects who received both influenza and SARS-CoV-2 vaccinations compared to those who received only the SARS-CoV-2 vaccine, with sustained anti-spike antibody titers up to 12 weeks post-vaccination. Immune response to the influenza vaccine was evaluated, and individuals were stratified as high or low responders. High responders showed increased antibody titers against the SARS-CoV-2 vaccine both after 4 and 12 weeks post-vaccination. Conversely, individuals classified as low responders were less responsive to the SARS-CoV-2 vaccine. These data indicate that both external stimuli, such as influenza vaccination, and the host’s intrinsic ability to respond to stimuli play a role in the response to the vaccine.

The planetary crisis regarding water resources means that new methods are needed to monitor large areas of water basins that are threatened by chemical and natural pollutants, together with climate change. With the aim to detect oil spill, we applied an algorithm, which could consistently and reliably confirm the presence of oil in four polluted lake waters analyzed. Combined algorithm application and metagenomic analysis from the spill areas that had been detected by the satellite identified drivers of the microbial response to oil pollution. Based on ortholog abundances, metabolic pathway reconstruction carried out in PICRUSt2 highlighted the degradative capacity of these microorganism. These microorganisms could be suitable candidates for treatment of crude oil, aromatic hydrocarbons and the desulfurization of persistent petroleum substances like dibenzothiophene.Environmental changes have been analysed with the combination of satellite monitoring and metagenomic in other studies. Red snow phenomenon, in Franz Josef Land's Arctic observed by satellite, is the result of a microbial succession dominated by Chlamydomonas nivalis, a unicellular, red-colored photosynthetic green algae. Similarly, satellite monitoring and metagenomic monitoring were used to assess the impact on coral reefs of a huge quantity of mud spill from iron ore mining on the Abrolhos Bank reef in Brazil.In our study, the combination of satellite sensing and metagenomics analyses offer useful tools for the real-time monitoring of water bodies threatened by oil spills, as well as for the design of recovery strategies based on the use of valuable hydrocarbonoclastic microorganisms.

Microbial fuel cells (MFCs) represent a promising technology for sustainable energy generation, which leverages the metabolic activities of microorganisms to convert organic substrates into electrical energy. In oil spill scenarios, hydrocarbonoclastic biofilms naturally form at the water–oil interface, creating a distinct environment for microbial activity. In this work, we engineered a novel MFC that harnesses these biofilms by strategically positioning the positive electrode at this critical junction, integrating the biofilm’s natural properties into the MFC design. These biofilms, composed of specialized hydrocarbon-degrading bacteria, are vital in supporting electron transfer, significantly enhancing the system’s power generation. Next-generation sequencing and scanning electron microscopy were used to characterize the microbial community, revealing a significant enrichment of hydrocarbonoclastic Gammaproteobacteria within the biofilm. Notably, key genera such as Paenalcaligenes, Providencia, and Pseudomonas were identified as dominant members, each contributing to the degradation of complex hydrocarbons and supporting the electrogenic activity of the MFCs. An electrochemical analysis demonstrated that the MFC achieved a stable power output of 51.5 μW under static conditions, with an internal resistance of about 1.05 kΩ. The system showed remarkable long-term stability, which maintained consistent performance over a 5-day testing period, with an average daily energy storage of approximately 216 mJ. Additionally, the MFC effectively recovered after deep discharge cycles, sustaining power output for up to 7.5 h before requiring a recovery period. Overall, the study indicates that MFCs based on hydrocarbonoclastic biofilms provide a dual-functionality system, combining renewable energy generation with environmental remediation, particularly in wastewater treatment. Despite lower power output compared to other hydrocarbon-degrading MFCs, the results highlight the potential of this technology for autonomous sensor networks and other low-power applications, which required sustainable energy sources. Moreover, the hydrocarbonoclastic biofilm-based MFC presented here offer significant potential as a biosensor for real-time monitoring of hydrocarbons and other contaminants in water. The biofilm’s electrogenic properties enable the detection of organic compound degradation, positioning this system as ideal for environmental biosensing applications.

The planetary crisis regarding water resources means that new methods are needed to monitor large areas of water basins that are threatened by chemical and natural pollutants, together with climate change. With the aim to monitor the pollution status of some Sites of National Interest (SIN) which represent very large contaminated Italian areas classified as dangerous, we are applying new or already well established algorithms to optical satellite images. In particular, a recently introduced oil spill detection algorithm [1] was able to, consistently and reliably, confirm the presence of oil in five polluted lake waters analysed. The combination of this algorithm with metagenomic analysis of the spill areas detected by the satellite allowed to identify drivers of the microbial response to oil pollution. Based on ortholog abundances, metabolic pathway reconstruction carried out in Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) software highlighted the degradative capacity of these microorganisms. These microorganisms could be suitable candidates for treatment of crude oil, aromatic hydrocarbons and the desulfurization of persistent petroleum substances like dibenzothiophene. Building upon this recent algorithmic development, the SatellOmic project funded by the Italian Space Agency (ASI) focuses on the pre-operational application of such integrated approach combining satellite sensing and metagenomics analyses for real-time monitoring of water bodies threatened by oil spills, as well as for the design of recovery strategies based on the use of valuable hydrocarbonoclastic microorganisms.

Understanding environmental microbiomes is central to furthering strategies for the restoration of polluted habitats. Such studies allow us to gather important information on the native microbiota, as well as possible microbial responses to remediation procedures. In recent years, metagenomics has emerged as a reliable method to enable the holistic characterization of diverse microbiomes including those from soil, oceans, lakes, and animal gut, among others. Indeed, metagenomics has been used to identify microbial proxies from contaminated environments and elaborate taxonomic and functional changes in microbial communities during pollution events. Coupled with continually decreasing sequencing costs, metagenomics, and associated bioinformatic tools/pipelines now constitute routinely used methods in laboratories worldwide. This necessitates an adequate understanding of metagenomic shotgun sequencing and various other related sequencing applications, as well as the constantly evolving bioinformatic milieu, to ensure proper interpretation of microbiome data. To this end, we review the various massively parallel sequencing-based applications for studying microbiomes in this chapter and discuss the bioinformatic tools, strategies, and approaches available to analyze the sequencing data generated. To provide context, we additionally discuss studies where next-generation sequencing-based applications have been employed in investigating contaminated environments.

Natural products are a rich source of bioactive molecules that have potential pharmacotherapeutic applications. In this study, we focused on Artemisia annua (A. annua) and its enriched extracts which were biologically evaluated in vitro as virucidal, antiviral, and antioxidant agents, with a potential application against the COVID-19 infection. The crude extract showed virucidal, antiviral and antioxidant effects in concentrations that did not affect cell viability. Scopoletin, arteannuin B and artemisinic acid (single fractions isolated from A. annua) exerted a considerable virucidal and antiviral effect in vitro starting from a concentration of 50 µg/mL. Data from Surface Plasmon Resonance (SPR) showed that the inhibition of the viral infection was due to the interaction of these compounds with the 3CLpro and Spike proteins of SARS-CoV-2, suggesting that the main interaction of compounds may interfere with the viral pathways during the insertion and the replication process. The present study suggests that natural extract of A. annua and its components could have a key role as antioxidants and antiviral agents and support the fight against SARS-CoV-2 variants and other possible emerging Coronaviruses.

The purpose of this study was to combine all available information on the state of Lake Pertusillo (Basilicata, Italy), both in the field and published, which included Sentinel-2A satellite data, to understand algal blooms in a lacustrine environment impacted by petroleum hydrocarbons. Sentinel-2A data was retrospectively used to monitor the state of the lake, which is located near the largest land-based oil extraction plant in Europe, with particular attention to chlorophyll a during algal blooms and petroleum hydrocarbons. In winter 2017, a massive dinoflagellate bloom (10.4 × 106 cell/L) of Peridinium umbonatum and a simultaneous presence of hydrocarbons were observed at the lake surface. Furthermore, a recent study using metagenomic analyses carried out three months later identified a hydrocarbonoclastic microbial community specialized in the degradation aromatic and nitroaromatic hydrocarbons. In this study, Sentinel-2A imagery was able to detect the presence of chlorophyll a in the waters, while successfully distinguishing the signal from that of hydrocarbons. Remotely sensed results confirmed surface reference measurements of lacustrine phytoplankton, chlorophyll a, and the presence of hydrocarbons during algal blooms, thereby explaining the presence of the hydrocarbonoclastic microbial community found in the lake three months after the oil spill event. The combination of emerging methodologies such as satellite systems and metagenomics represent an important support methodology for describing complex contaminations in diverse ecosystems.

Biofilm at water-oil interface of hypoxic water columns of microcosms, prepared from a lacustrine sample, that used diesel as a carbon source was found to show electrogenic properties. These microcosms named, Liquid Microbial Fuel Cells (L-MFCs) were electrically characterized using a custom electronic analyzer; accurate determination of voltage (V), power density (W/m 2), and current density (A/m2) for both charge and discharge phases was carried out. The instrument made it possible to carry out cell characterizations using resistive loads between 0 Ω (Ohm) and 10 kΩ. During the hypoxic and electrogenic phase, the synthesis of a system of “bacterial piping induction”, produced filaments of hundreds of micrometers in which the microbial cells are hosted. Ultrastructural microscopy collected by scanning (SEM), transmission (TEM), immunofluorescence, Thunder Imager 3D, confocal laser scanning (CLSM) microscopy revealed a “myelin like“ structure during filamentation processes; this “myelin like” structure exhibited cross-reactivity towards different epitopes of the myelin basic protein (MBP) and Claudin 11 (O4) of human oligodendrocytes. The disclosure of these filamentation processes could be helpful to describe further unconventional microbial structures in aquatic ecosystems and of the animal world.The data that support the findings of this study are openly available in at https://data.mendeley.com/datasets/7d35tj3j96/1.

COronaVIrus Disease 2019 (COVID-19) is a newly emerging infectious disease that spread across the world, caused by the novel coronavirus Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2). Despite the advancements in science that led to the creation of the vaccine, there is still an urgent need for new antiviral drugs effective against SARS-CoV-2. This study aimed to investigate the antiviral effect of Paulownia tomentosa Steud extract against SARS-CoV-2 and to evaluate its antioxidant properties, including respiratory smooth muscle relaxant effects. Our results showed that P. tomentosa extract can inhibit viral replication by directly interacting with both the 3-chymotrypsin-like protease and spike protein. In addition, the phyto complex does not reduce lung epithelial cell viability and exerts a protective action in those cells damaged by tert-butyl hydroperoxide , a toxic agent able to alter cells' functions via increased oxidative stress. These data suggest the potential role of P. tomentosa extract in COVID-19 treatment, since this extract is able to act both as an antiviral and a cytoprotective agent in vitro.

Microbiomes of freshwater basins intended for human use remain poorly studied, with very little known about the microbial response to in situ oil spills. Lake Pertusillo is an artificial freshwater reservoir in Basilicata, Italy, and serves as the primary source of drinking water for more than one and a half million people in the region. Notably, it is located in close proximity to one of the largest oil extraction plants in Europe. The lake suffered a major oil spill in 2017, where approximately 400 tons of crude oil spilled into the lake; importantly, the pollution event provided a rare opportunity to study how the lacustrine microbiome responds to petroleum hydrocarbon contamination. Water samples were collected from Lake Pertusillo 10 months prior to and 3 months after the accident. The presence of hydrocarbons was verified and the taxonomic and functional aspects of the lake microbiome were assessed. The analysis revealed specialized successional patterns of lake microbial communities that were potentially capable of degrading complex, recalcitrant hydrocarbons, including aromatic, chloroaromatic, nitroaromatic, and sulfur containing aromatic hydrocarbons. Our findings indicated that changes in the freshwater microbial community were associated with the oil pollution event, where microbial patterns identified in the lacustrine microbiome 3 months after the oil spill were representative of its hydrocarbonoclastic potential and may serve as effective proxies for lacustrine oil pollution.