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Abstract Background The impact of the microbiota on host fitness has so far mainly been demonstrated for the bacterial microbiome. We know much less about host-associated protist and viral communities, largely due to technical issues. However, all microorganisms within a microbiome potentially interact with each other as well as with the host and the environment, therefore likely affecting the host health. Results We set out to explore how environmental and host factors shape the composition and diversity of bacterial, protist and viral microbial communities in the Pacific oyster hemolymph, both in health and disease. To do so, five oyster families differing in susceptibility to the Pacific oyster mortality syndrome were reared in hatchery and transplanted into a natural environment either before or during a disease outbreak. Using metabarcoding and shotgun metagenomics, we demonstrate that hemolymph can be considered as an ecological niche hosting bacterial, protist and viral communities, each of them shaped by different factors and distinct from the corresponding communities in the surrounding seawater. Overall, we found that hemolymph microbiota is more strongly shaped by the environment than by host genetic background. Co-occurrence network analyses suggest a disruption of the microbial network after transplantation into natural environment during both non-infectious and infectious periods. Whereas we could not identify a common microbial community signature for healthy animals, OsHV-1 μVar virus dominated the hemolymph virome during the disease outbreak, without significant modifications of other microbiota components. Conclusion Our study shows that oyster hemolymph is a complex ecosystem containing diverse bacteria, protists and viruses, whose composition and dynamics are primarily determined by the environment. However, all of these are also shaped by oyster genetic backgrounds, indicating they indeed interact with the oyster host and are therefore not only of transient character. Although it seems that the three microbiome components respond independently to environmental conditions, better characterization of hemolymph-associated viruses could change this picture.

Abstract Background Nontuberculous mycobacteria (NTM) are pathogens that commonly affect the paediatric population and its most frequent manifestation is a cervicofacial lymphadenopathy. With the improvement of technologies, new species have been recently identified. Case presentation We report the first case of NMT lymphadenitis in a child caused by Mycobacterium marseillense, a newly described species belonging to Mycobacterium avium complex. Conclusions Improving the identification of these newly discovered mycobacteria, further information will be available about their clinical involvement and their best treatment.

The Pacific oyster Crassostrea gigas lives in microbe-rich marine coastal systems subjected to rapid environmental changes. It harbours a diversified and fluctuating microbiota that cohabits with immune cells expressing a diversified immune gene repertoire. In the early stages of oyster development, just after fertilization, the microbiota plays a key role in educating the immune system. Exposure to a rich microbial environment at the larval stage leads to an increase in immune competence throughout the life of the oyster, conferring a better protection against pathogenic infections at later juvenile/adult stages. This beneficial effect, which is intergenerational, is associated with epigenetic remodelling. At juvenile stages, the educated immune system participates in the control of the homeostasis. In particular, the microbiota is fine-tuned by oyster antimicrobial peptides acting through specific and synergistic effects. However, this balance is fragile, as illustrated by the Pacific Oyster Mortality Syndrome, a disease causing mass mortalities in oysters worldwide. In this disease, the weakening of oyster immune defences by OsHV-1 µVar virus induces a dysbiosis leading to fatal sepsis. This review illustrates the continuous interaction between the highly diversified oyster immune system and its dynamic microbiota throughout its life, and the importance of this cross-talk for oyster health. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

A severe outbreak of influenza A(H1N1pdm09) infection in seven children (median age: 52 months) occurred between December 2023 and January 2024 in Tuscany, Italy. Clinical presentation ranged from milder encephalopathy to acute necrotizing encephalopathy (ANE) with coma and multiorgan failure; one child died. This report raises awareness for clinicians to identify and treat early acute encephalopathy caused by H1N1 influenza and serves as a reminder of severe presentations of influenza in young children and the importance of vaccination.

Background: COVID-19 is generally milder in children than in adults, however severe infection has been described in some patients. Few data are available on use of Remdesivir (RDV) in children, as most clinical trials focused on adult patients. We report a multicenter study conducted in 10 Italian Hospitals to investigate the safety of RDV in children affected by COVID-19., Methods: We collected the clinical data of children with COVID-19 treated with RDV between March 2020 and February 2022 in 10 Italian hospitals. Clinical data were compared according to a duration of RDV therapy more or less than 5 days. Linear regression model was used to determine the association of significant variables from the bivariate analysis to the duration of RDV therapy., Results: A total of 50 patients were included, with a median age of 12.8 years. Many patients had at least one comorbidity (78%), mostly obesity. Symptoms were fever (88%), cough (74%) and dyspnea (68%). Most patients were diagnosed with pneumonia of either viral and/or bacterial etiology. Blood test showed leukopenia in 66% and increased C-reactive protein (CRP) levels in 63% of cases. Thirty-six patients received RDV for 5 days, nine patients up to 10 days. Most children who received RDV longer were admitted to the PICU (67%). Treatment with RDV was well tolerated with rare side effects: bradycardia was recorded in 6% of cases, solved in less than 24 h after discontinuation. A mild elevation of transaminases was observed in 26% of cases, however for the 8%, it was still detected before the RDV administration. Therefore, in these cases, we could not establish if it was caused by COVID-19, RDV o both. Patients who received RDV for more than 5 days waited longer for its administration after pneumonia diagnosis. The presence of comorbidities and the duration of O2 administration significantly correlated with the duration of RDV therapy at the linear regression analysis., Conclusion: Our experience indicates that RDV against SARS-CoV-2 is safe and well-tolerated in pediatric populations at high risk of developing severe COVID-19. Our data suggest that delaying RDV therapy after diagnosis of pneumonia may be associated with a longer duration of antiviral therapy, especially in patients with comorbidities., (© 2024. The Author(s).)

The pollution of seawater by both biotic (bacteria, viruses) and abiotic contaminants (biocides, pharmaceutical residues) frequently leads to economic losses in aquaculture activities mostly mortality events caused by microbial infection. Advanced Oxidation Processes (AOPs) such as heterogeneous photocatalysis allow the removal of all organic contaminants present in water and therefore could reduce production losses in land-based farms. Oysters in land-based farms such as hatcheries and nurseries suffer from a large number of mortality events, resulting in significant losses. If photocatalysis has been widely studied for the decontamination, its application for disinfection is still overlooked, especially on seawater for viruses. We therefore studied seawater disinfection using the photocatalysis (UV 365 /TiO 2 ) method in the context of Pacific oyster mortality syndrome (POMS). POMS has been defined as a polymicrobial disease involving an initial viral infection with Ostreid Herpes Virus 1, accompanied by multiple bacterial infections. We investigated the impact of treatment on Vibrio harveyi, a unique opportunistic pathogenic bacterium, and on a complex microbial community reflecting a natural POMS event. Viral inactivation was monitored using experimental infections to determine whether viral particles were still infectious after. Changes in the total bacterial community in seawater were studied by comparing UV 365 /TiO 2 treatment with UV 365 -irradiated seawater and untreated seawater. In the case of OsHV-1, a 2-h photocatalytic treatment prevents POMS disease and oyster mortality. The same treatment also inactivates 80% of viable Vibrio harveyi culture (c.a. 1.5 log). Since OsHV-1 and Vibrio harveyi are effectively inactivated without long-term destabilization of the total bacterial microbiota in the seawater, photocatalysis appears to be a relevant alternative for disinfecting seawater in land-based oyster beds., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Ltd.)

This study aims to investigate the sensitivity of microscopy, culture and polymerase chain reaction on three gastric aspirates (GAs) in the microbiological confirmation of active pulmonary tuberculosis (TB) and to identify possible changes in sensitivity derived from the collection of a different number of aspirates. Children with clinical and radiological diagnoses of active pulmonary TB who underwent three GAs between March 2007 and June 2019 were retrospectively evaluated. Clinical, radiological, and microbiological data were collected. The sensitivity of microbiological tests on GAs was calculated. Moreover, differences in sensitivity according to age and radiological pattern were investigated. Overall, 156 children with active pulmonary TB were enrolled with a median age of 51.5 (IQR: 25.2-113.2) months. Microbiological investigations on the first GA showed a sensitivity of 34% (95%CI 26.7, 42), the cumulative sensitivity of first and second GAs was 40.4% (95%CI 32.7, 48.5) and of the three GAs was 47.4% (95%CI 39.8, 55.2). The collection of three GAs leads to an overall increase in sensitivity of the first GA by 13.4% (95%CI 2.8, 24.1%; p=0.014). Moreover, the increase in sensitivity was significantly higher in children ≤ 4 years of age and in those with uncomplicated TB (p=0.008).Conclusions: Performing a higher number of GAs increases the sensitivity of microbiological confirmation of active pulmonary TB, particularly in children ≤ 4 years and with an uncomplicated radiological pattern. What is known: • The diagnosis of paediatric tuberculosis is a challenge for paediatricians • Despite their low sensitivity gastric aspirates represent the standard sample for microbiological confirmation of active pulmonary tuberculosis in children • Most international guidelines recommend performing three sequential gastric aspirates on three consecutive days What is new: • A significant increase in global sensitivity by 13.4% was found by the collection of three gastric aspirates compared to the first one • Performing a higher number of gastric aspirates increases the sensitivity of microbiological confirmation, particularly in children ≤ 4 years and with an uncomplicated radiological pattern., (© 2023. The Author(s).)

Polymicrobial infections threaten the health of humans and animals but remain understudied in natural systems. We recently described the Pacific Oyster Mortality Syndrome (POMS), a polymicrobial disease affecting oyster production worldwide. In the French Atlantic coast, the disease involves coinfection with ostreid herpesvirus 1 (OsHV-1) and virulent Vibrio . However, it is unknown whether consistent Vibrio populations are associated with POMS in different regions, how Vibrio contribute to POMS, and how they interact with OsHV-1 during pathogenesis. By connecting field-based approaches in a Mediterranean ecosystem, laboratory infection assays and functional genomics, we uncovered a web of interdependencies that shape the structure and function of the POMS pathobiota. We show that Vibrio harveyi and Vibrio rotiferianus are predominant in OsHV-1-diseased oysters and that OsHV-1 drives the partition of the Vibrio community observed in the field. However only V. harveyi synergizes with OsHV-1 by promoting mutual growth and accelerating oyster death. V. harveyi shows high-virulence potential and dampens oyster cellular defenses through a type 3 secretion system, making oysters a more favorable niche for microbe colonization. In addition, V. harveyi produces a key siderophore called vibrioferrin. This important resource promotes the growth of V. rotiferianus , which cooccurs with V. harveyi in diseased oysters, and behaves as a cheater by benefiting from V. harveyi metabolite sharing. Our data show that cooperative behaviors contribute to synergy between bacterial and viral coinfecting partners. Additional cheating behaviors further shape the polymicrobial consortium. Controlling cooperative behaviors or countering their effects opens avenues for mitigating polymicrobial diseases.

Disease emergence is accelerating with global changes. Understanding by which mechanisms host populations can rapidly adapt will be crucial for management practices. Pacific oyster mortality syndrome (POMS) imposes a substantial and recurrent selective pressure on oyster populations, and rapid adaptation may arise through genetics and epigenetics. In this study, we used (epi)genome-wide association mapping to show that oysters differentially exposed to POMS displayed genetic and epigenetic signatures of selection. Consistent with higher resistance to POMS, the genes targeted included many genes in several pathways related to immunity. By combining correlation, DNA methylation quantitative trait loci, and variance partitioning, we revealed that a third of phenotypic variation was explained by interactions between the genetic and epigenetic information, ~14% by the genome, and up to 25% by the epigenome alone. Similar to genetically based adaptation, epigenetic mechanisms notably governing immune responses can contribute substantially to the rapid adaptation of hosts to emerging infectious diseases.

Anthropic diesel-derived contamination of Mediterranean coastal waters is of great concern. Nature-based solutions such as phytoremediation are considered promising technologies to remove contaminants from marine environments. The aim of this work was to investigate the tolerance of the Mediterranean autochthonous seaweed Caulerpa prolifera (Forsskal) Lamouroux to diesel fuel and its hydrocarbon degradation potential. Changes in C. prolifera traits, including its associated bacterial community abundance and structure, were determined by fluorescence microscopy and next-generation sequencing techniques. Thalli of C. prolifera artificially exposed to increasing concentration of diesel fuel for 30 days and thalli collected from three natural sites with different levels of seawater diesel-derived hydrocarbons were analysed. Gas chromatography was applied to determine the seaweed hydrocarbon degradation potential. Overall, in controlled conditions the lower concentration of diesel (0.01%) did not affect C. prolifera survival and growth, whereas the higher concentration (1%) resulted in high mortality and blade damages. Similarly, only natural thalli, collected at the most polluted marine site (750 mg L -1 ), were damaged. A higher abundance of epiphytic bacteria, with a higher relative abundance of Vibrio bacteria, was positively correlated to the health status of the seaweed as well as to its diesel-degradation ability. In conclusion, C. prolifera tolerated and degraded moderate concentrations of seawater diesel-derived compounds, especially changing the abundance and community structure of its bacterial coating. The protection and exploitation of this autochthonous natural seaweed-bacteria symbiosis represents a useful strategy to mitigate the hydrocarbon contamination in moderate polluted Mediterranean costal environments.

Invasive alien species are among the main global drivers of biodiversity loss posing major challenges to nature conservation and to managers of protected areas. The present study applied a methodological framework that combined invasive Species Distribution Models, based on propagule pressure, abiotic and biotic factors for 14 invasive alien plants of Union concern in Italy, with the local interpretable model-agnostic explanation analysis aiming to map, evaluate and analyse the risk of plant invasions across the country, inside and outside the network of protected areas. Using a hierarchical invasive Species Distribution Model, we explored the combined effect of propagule pressure, abiotic and biotic factors on shaping invasive alien plant occurrence across three biogeographic regions (Alpine, Continental, and Mediterranean) and realms (terrestrial and aquatic) in Italy. We disentangled the role of propagule pressure, abiotic and biotic factors on invasive alien plant distribution and projected invasion risk maps. We compared the risk posed by invasive alien plants inside and outside protected areas. Invasive alien plant distribution varied across biogeographic regions and realms and unevenly threatens protected areas. As an alien's occurrence and risk on a national scale are linked with abiotic factors followed by propagule pressure, their local distribution in protected areas is shaped by propagule pressure and biotic filters. The proposed modelling framework for the assessment of the risk posed by invasive alien plants across spatial scales and under different protection regimes represents an attempt to fill the gap between theory and practice in conservation planning helping to identify scale, site, and species-specific priorities of management, monitoring and control actions. Based on solid theory and on free geographic information, it has great potential for application to wider networks of protected areas in the world and to any invasive alien plant, aiding improved management strategies claimed by the environmental legislation and national and global strategies., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Globally Ambrosia species (Asteraceae), commonly called ragweed, are recognized to be one of the most problematic groups of invasive weeds and one of the main allergenic genus. Climate and land-use change and air pollution are expected to promote ragweed spread, increase airborne ragweed pollen concentrations (the source of allergens), extend the pollen season, and promote longdistance transport of pollen or sub-pollen particles containing allergens. The allergenicity of pollen itself is going to increase. Likely, all these factors will have meaningful effects in the exacerbation of the sensitization to ragweed pollen and the severity of allergy symptoms. Globally the major health concern regards A. artemisiifolia, because of its very wide global distribution and highly invasive behavior. Together with A. artemisiifolia, also A. trifida and A. psilostachya are species of health concern distributed across different continents, widespread and invasive in several regions. The present review summarizes the characteristics of these species and gives an overview of factors contributing to their allergenicity., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Big defensins are two-domain antimicrobial peptides (AMPs) that have highly diversified in mollusks. Cg -BigDefs are expressed by immune cells in the oyster Crassostrea gigas , and their expression is dampened during the Pacific Oyster Mortality Syndrome (POMS), which evolves toward fatal bacteremia. We evaluated whether Cg -BigDefs contribute to the control of oyster-associated microbial communities. Two Cg -BigDefs that are representative of molecular diversity within the peptide family, namely Cg -BigDef1 and Cg -BigDef5, were characterized by gene cloning and synthesized by solid-phase peptide synthesis and native chemical ligation. Synthetic peptides were tested for antibacterial activity against a collection of culturable bacteria belonging to the oyster microbiota, characterized by 16S sequencing and MALDI Biotyping. We first tested the potential of Cg -BigDefs to control the oyster microbiota by injecting synthetic Cg -BigDef1 into oyster tissues and analyzing microbiota dynamics over 24 h by 16S metabarcoding. Cg -BigDef1 induced a significant shift in oyster microbiota β-diversity after 6 h and 24 h, prompting us to investigate antimicrobial activities in vitro against members of the oyster microbiota. Both Cg -BigDef1 and Cg -BigDef5 were active at a high salt concentration (400 mM NaCl) and showed broad spectra of activity against bacteria associated with C. gigas pathologies. Antimicrobial specificity was observed for both molecules at an intra- and inter-genera level. Remarkably, antimicrobial spectra of Cg -BigDef1 and Cg -BigDef5 were complementary, and peptides acted synergistically. Overall, we found that primary sequence diversification of Cg -BigDefs has generated specificity and synergy and extended the spectrum of activity of this peptide family.

Background: Intravenous administration of zidovudine (ZDV) during labour is a key step for vertical HIV transmission (VT) prevention, but there is no evidence of benefit when maternal HIV-RNA at delivery is <50 copies/mL. The aim of this study is evaluating the appropriateness of intrapartum ZDV use in Italy., Methods: Observational study including mother-infant pairs with perinatal HIV exposure during 2002-2019, enrolled in the Italian Register for HIV Infection in Children. Univariable and multivariable logistic regression were used to evaluate factors associated with VT., Results: A total of 3,861 infants, born from 3,791 pregnancies were included. The frequency of ZDV use was 79.9%, 92.1%, 93.7% and 92.8% when HIV-RNA was not available, ≥400 copies, between 50 and 399 copies, and <50 copies/mL. Thirty-three out of 3861 (0.85%) infants were subsequently diagnosed with HIV, 25/3861 (0.6%) of them born to mothers receiving intrapartum ZDV, and 31 (93.9%) to mothers with HIV-RNA ≥50 copies/mL or not available. In women with HIV-RNA < 50 copies/mL, ART discontinuation during pregnancy was the strongest risk factor for VT (odds ratio, OR, 23.1, 95%CI 2.4-219.3), while a higher gestational age (OR 0.6, 95%CI 0.4-0.8) and PEP administration to the newborn (aOR 0.004, 95%CI <0.0001-0.4) were protective factors. Intrapartum ZDV administration did not influence the final outcome in this group., Conclusions: In ART era, more transmission events may occur in utero, limiting value of intrapartum ZDV, particularly for women with suppressed HIV-RNA load. More attention to the HIV-RNA testing of mothers before delivery may avoid unnecessary ZDV use., Competing Interests: Declaration of Competing Interest None of the authors declare conflicts of interest relevant to the present study., (Copyright © 2022. Published by Elsevier Ltd.)

Compared to adults, severe or fatal COVID-19 disease is much less common in children. However, a higher risk for progression has been reported in infants. Different pediatric COVID-19 severity scores are reported in the literature. Methods: Subjects under 90 days of age admitted to 35 Italian institutions for COVID-19 were included. The severity of COVID-19 was scored as mild/moderate or severe/critical following the classification reported in the literature by Venturini, Dong, Kanburoglu, and Gale. To assess the diagnostic accuracy of each classification system, we stratified all enrolled patients developing a posteriori severity score based on clinical presentation and outcomes and then compared all different scores analyzed. Results: We included 216 infants below 90 days of age. The most common symptom was fever, followed by coryza, poor feeding, cough, and gastrointestinal manifestations. According to Venturini, Dong, Kanburoglu, and Gale’s severity scores, 18%, 6%, 4.2%, and 29.6% of infants presented with severe/critical disease, respectively. A correlation analysis between these four scores and the a posteriori severity score assigned to all enrolled subjects was performed, and a crescent strength of correlation from Gale (R = 0.355, p < 0.001) to Venturini (R = 0.425, p < 0.001), Dong (R = 0.734, p < 0.001), and Kanburoglu (R = 0.859, p < 0.001) was observed. Conclusions: The percentage of infants with severe COVID-19 varies widely according to the score systems. A unique clinical score should be designed for neonates and infants with COVID-19.

Introduction: Chronic osteomyelitis in children is a rare condition. Debridement surgery, along with appropriate antibiotic therapy, is widely agreed to represent the best procedure in the treatment of chronic osteomyelitis but can result in an extensive dead space formation. In this study, we evaluated the use of bioactive glass to address dead space management., Methods: Four consecutive cases of chronic osteomyelitis treated with antibiotic therapy, one stage- surgical debridement and bioglass implantation between September 2016 and February 2017 were prospectively followed for a minimum of three years. Two cases followed acute hematogenous osteomyelitis, two cases followed fracture fixation. Clinical, histology, laboratory and radiographic findings were recorded. Primary endpoint was eradication of infection. Possible complication related to bioglass application were investigated., Results: All patients achieved healing at the latest follow-up of minimum three years. No successive surgical treatments were required at any time. No complications related to the bioglass were detected. Radiographic reconstruction of normal anatomy progressed through the years., Conclusions: Bioglass for the treatment of dead space after surgical debridement appears a viable option in the treatment of chronic osteomyelitis in children., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Immune response to tuberculosis (TB) has been extensively studied in the past decades and classically involves cellular immunity. However, evidence suggests that humoral immunity may play a relevant role. Past studies regarding serum immunoglobulin (Ig) levels in TB are dated and only involve adult subjects. In this study, we retrospectively studied a cohort of 256 children with TB disease and analyzed 111 patients screened for total serum Ig at diagnosis. According to the severity and extent of organ involvement, subjects were divided into four groups, namely, uncomplicated pulmonary TB (UCPTB, 56.3% of patients), complicated pulmonary TB (CPTB, 22.5%), lymph node extrapulmonary TB (LN-EPTB, 7.2%), and extra-nodal extrapulmonary TB (EN-EPTB, 13.5%). Serum IgG and IgA levels were significantly higher in more severe and extended TB disease. Median IgG levels progressively increased from uncomplicated to complicated pulmonary and nodal forms, reaching their highest values in diffuse extra-pulmonary TB. In parallel, UCPTB showed significantly lower frequencies of patients presenting a substantial increase in IgG levels when compared with the other three groups. No relevant differences in IgM levels were detected. Ig screening at follow-up showed a significant reduction in IgG and IgA levels. Finally, we unveiled three cases of selective IgA and one case of selective IgM deficiencies (SIgMD), the latter with a severe clinical course. Serum IgG and IgA may be a useful clinical tool to assess the severity and monitor the treatment response in pediatric TB disease. Moreover, immunological workup in children with TB disease may unmask primary defects of humoral immunity., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Consonni, Chiti, Ricci, Venturini, Canessa, Bianchi, Lippi, Montagnani, Giovannini, Chiappini, Galli, Azzari and Lodi.)

Background: The interaction of organisms with their surrounding microbial communities influences many biological processes, a notable example of which is the shaping of the immune system in early life. In the Pacific oyster, Crassostrea gigas, the role of the environmental microbial community on immune system maturation - and, importantly, protection from infectious disease - is still an open question., Results: Here, we demonstrate that early life microbial exposure durably improves oyster survival when challenged with the pathogen causing Pacific oyster mortality syndrome (POMS), both in the exposed generation and in the subsequent one. Combining microbiota, transcriptomic, genetic, and epigenetic analyses, we show that the microbial exposure induced changes in epigenetic marks and a reprogramming of immune gene expression leading to long-term and intergenerational immune protection against POMS., Conclusions: We anticipate that this protection likely extends to additional pathogens and may prove to be an important new strategy for safeguarding oyster aquaculture efforts from infectious disease. tag the videobyte/videoabstract in this section Video Abstract., (© 2022. The Author(s).)

Ostreid herpesvirus-1 (OsHV-1) RNAs are enzymatically modified by A-to-I conversions during the infection of Crassostrea gigas . The increase of ADAR1 expression and hyper-editing activity parallel to OsHV-1 RNAs suggests a functional connection between dsRNA editing and antiviral responses. We analyzed 87 RNA-seq data sets from immuno-primed, resistant, and susceptible oysters exposed to OsHV-1 to compare the ADAR hyper-editing levels on host and viral transcripts and trace hyper-editing on the oyster genes. Host RNAs were more hyper-edited than viral RNAs, despite the increased editing of viral RNAs in late infection phases. A set of genes, representing ∼0.5% of the oyster transcriptome and including several tripartite motif-containing sequences, were constantly hyper-edited. Conversely, we identified genes involved in antiviral response, miRNA maturation, and epigenetic regulation that were hyper-edited in specific conditions only. Despite technical and biological bottlenecks that hamper the understanding of the bivalve "RNA editome," available tools and technologies can be adapted to bivalve mollusks. IMPORTANCE Ostreid herpesvirus-1 (OsHV-1) is a harmful pathogen of bivalve species, such as oysters. However, knowledge is lacking about host-virus interactions at the molecular level, hampering the possibility of a correct management of viral outbreaks and related massive mortalities. Notably, OsHV-1 transcripts are massively modified by host RNA editing enzyme during infection, resulting in multiple A-to-I variations along RNAs assuming double-strand conformations. The impact of these modifications on host transcripts is, however, not completely clear. Analyzing RNA-seq data of oysters infected with OsHV-1, we revealed that ∼0.5% of the oyster transcriptome is always enzymatically modified by ADAR, whereas genes involved in antiviral response, miRNA maturation, and epigenetic regulation were hyper-edited in specific conditions only. Despite our results, relevant technical bottlenecks impair an accurate quantification of RNA editing events, making necessary an approach specifically dedicated to the progressive understanding of oyster "RNA editome."

The genetic diversity of viral populations is a key driver of the spatial and temporal diffusion of viruses; yet, studying the diversity of whole genomes from natural populations still remains a challenge. Phylodynamic approaches are commonly used for RNA viruses harboring small genomes but have only rarely been applied to DNA viruses with larger genomes. Here, we used the Pacific oyster mortality syndrome (a disease that affects oyster farms around the world) as a model to study the genetic diversity of its causative agent, the Ostreid herpesvirus 1 (OsHV-1) in the three main French oyster-farming areas. Using ultra-deep sequencing on individual moribund oysters and an innovative combination of bioinformatics tools, we de novo assembled twenty-one OsHV-1 new genomes. Combining quantification of major and minor genetic variations, phylogenetic analysis, and ancestral state reconstruction of discrete traits approaches, we assessed the connectivity of OsHV-1 viral populations between the three oyster-farming areas. Our results suggest that the Marennes-Oléron Bay represents the main source of OsHV-1 diversity, from where the virus has dispersed to other farming areas, a scenario consistent with current practices of oyster transfers in France. We demonstrate that phylodynamic approaches can be applied to aquatic DNA viruses to determine how epidemiological, immunological, and evolutionary processes act and potentially interact to shape their diversity patterns., (© The Author(s) 2022. Published by Oxford University Press.)

Surgical site infections (SSIs), which are a potential complications in surgical procedures, are associated with prolonged hospital stays and increased postoperative mortality rates, and they also have a significant economic impact on health systems. Data in literature regarding risk factors for SSIs in pediatric age are scarce, with consequent difficulties in the management of SSI prophylaxis and with antibiotic prescribing attitudes in the various surgical procedures that often tend to follow individual opinions. The lack of pediatric studies is even more evident when we consider surgeries performed in subjects with underlying conditions that may pose an increased risk of complications. In order to respond to this shortcoming, we developed a consensus document to define optimal surgical antimicrobial prophylaxis (SAP) in neonates and children with specific high-risk conditions. These included the following: (1) colonization by methicillin-resistant Staphylococcus aureus (MRSA) and by multidrug resistant (MDR) bacteria other than MRSA; (2) allergy to first-line antibiotics; (3) immunosuppression; (4) splenectomy; (5) comorbidity; (6) ongoing antibiotic therapy or prophylaxis; (7) coexisting infection at another site; (8) previous surgery in the last month; and (9) presurgery hospitalization lasting more than 2 weeks. This work, made possible by the multidisciplinary contribution of experts belonging to the most important Italian scientific societies, represents, in our opinion, the most up-to-date and comprehensive collection of recommendations relating to behaviors to be undertaken in a perioperative site in the presence of specific categories of patients at high-risk of complications during surgery. The application of uniform and shared protocols in these high-risk categories will improve surgical practice with a reduction in SSIs and consequent rationalization of resources and costs, as well as being able to limit the phenomenon of antimicrobial resistance.

Background: Retropharyngeal and parapharyngeal abscesses (RPAs, PPAs) usually affect young children. Surgical drainage and/or antibiotic therapy are treatment of choice, but no specific guidelines exist. In order to reduce the risk of severe complications, appropriate diagnosis and therapy are necessary. The aims of the study were to review diagnosis and management of children with RPAs/PPAs and to compare surgical versus medical approach., Methods: This is a multicenter retrospective study including all patients younger than 15 years admitted at 4 Italian pediatric hospitals of Florence, Padua, Rome, and Treviso, with International Classification of Diseases, Ninth Revision discharge diagnosis code of RPAs and PPAs, from January 1, 2008, to December 31, 2016., Results: One hundred fifty-three children were included. The median age was 4.4 years, with overall male predominance. Heterogeneous signs and symptoms (fever, neck cervical, lymphadenopathy, pain, and stiff neck most frequently) and a large mixture of bacteria from pus cultures were detected. Computer tomography (66.7%) and magnetic resonance imaging (27.5%) were performed to confirm the presence of abscess. Fifty-one percent of abscesses were greater than 3 cm. Eighty-seven patients (56.9%) underwent surgery, and 66 (43.1%) were treated with antibiotics alone (mostly ceftriaxone, metronidazole, amikacin, and clindamycin) with median days of therapy of 26.5 days and length of therapy of 16.0 days of median. Median length of stay was 11 days. None had severe complications. Multivariate analysis indicated as independent predictive factors of surgery abscess of 3 cm or greater, high white blood cell count, and-most of all-the hospital of admission., Conclusions: Deep neck abscesses mostly affect patients in early childhood, with a combination of nonspecific signs and symptoms, and it still emerges as a heterogeneous approach in diagnosis and management of these infections. Thus, common shared protocols represent an essential tool in order to standardize care and improve patients' outcomes., Competing Interests: Disclosure: The authors declare no conflict of interest., (Copyright © 2020 Wolters Kluwer Health, Inc. All rights reserved.)