SARS-CoV-2 Infection is Associated with Age- and Gender-Specific Changes in the Nasopharyngeal Microbiome.

BACKGROUND: The recent Coronavirus Disease 2019 (COVID-19) pandemic has dramatically exposed our gap in understanding the pathogenesis of airborne infections. Within such a context, it is increasingly clear that the nasal cavity represents a critical checkpoint not only in the initial colonization phase but also in shaping any infectious sequelae. This is particularly relevant to COVID-19 in that the nasal cavity is characterized by high-level expression of the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) receptor, Angiotensin-Converting Enzyme 2 (ACE2), all along the respiratory tract. As part of the nasal mucosa, commensal microbes harbored by the nasal cavity likely are far more than just innocent bystanders in the interaction between SARS-CoV-2 and the local microenvironment. Yet the role of the qualitative composition of the nasal microbiome is unclear, as is its function, whether protective or not. METHODS: In this study, individuals undergoing SARS-CoV-2 molecular testing at the Hospital of Perugia (Italy) were recruited, with their residual material from the nasopharyngeal swabs being collected for microbiome composition analysis and short-chain fatty acid (SCFA) measurements (by 16S rRNA sequencing and gas chromatography-mass spectrometry), respectively. RESULTS: After stratification by age, gender, and viral load, the composition of the nasopharyngeal microbiome appeared to be influenced by age and gender, and SARS-CoV-2 infection further determined compositional changes. Notwithstanding this variability, a restricted analysis of female subjects-once SARS-CoV-2-infected-unraveled a shared expansion of Lachnospirales-Lachnospiraceae, irrespective of the viral load and age. This was associated with a reduction in the branched SCFA isobutanoic acid, as well as in the SCFAs with longer chains. CONCLUSIONS: Our results indicate that the nasopharyngeal microbiome is influenced by age, gender, and viral load, with consistent patterns of microbiome changes being present across specific groups. This may help in designing a personalized medicine approach in COVID-19 patients with specific patterns of nasal microbial communities.

A model-independent redundancy measure for human versus ChatGPT authorship discrimination using a Bayesian probabilistic approach.

The academic and scientific world in general is increasingly concerned about their inability to determine and ascertain the identity of the writer of a text. More and more often the question arises as to whether a scientific article or work handed in by a student was actually produced by the alleged author of the questioned text. The role of artificial intelligence (AI) is increasingly debated due to its dangers of undeclared use. A current example is undoubtedly the undeclared use of ChatGPT to write a scientific text. The article promotes an AI model-independent redundancy measure to support discrimination between hypotheses on authorship of various multilingual texts written by humans or produced by intelligence media such as ChatGPT. The syntax of texts written by humans tends to differ from that of texts produced by AIs. This difference can be grasped and quantified even with short texts (i.e. 1800 characters). This aspect of length is extremely important, because short texts imply a greater difficulty of analysis to characterize authorship. To meet the efficiency criteria required for the evaluation of forensic evidence, a probabilistic approach is implemented. In particular, to assess the value of the redundancy measure and to offer a consistent classification criterion, a metric called Bayes factor is implemented. The proposed Bayesian probabilistic method represents an original approach in stylometry. Analyses performed over multilingual texts (English and French) covering different scientific and human areas of interest (forensic science and socio-psycho-artistic topics) reveal the feasibility of a successful authorship discrimination with limited misclassification rates. Model performance is satisfactory even with small sample sizes.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike Protein S1 Induces Methylglyoxal-Derived Hydroimidazolone/Receptor for Advanced Glycation End Products (MG-H1/RAGE) Activation to Promote Inflammation in Human Bronchial BEAS-2B Cells.

The pathogenesis of coronavirus disease 2019 (COVID-19) is associated with a hyperinflammatory response. The mechanisms of SARS-CoV-2-induced inflammation are scantly known. Methylglyoxal (MG) is a glycolysis-derived byproduct endowed with a potent glycating action, leading to the formation of advanced glycation end products (AGEs), the main one being MG-H1. MG-H1 exerts strong pro-inflammatory effects, frequently mediated by the receptor for AGEs (RAGE). Here, we investigated the involvement of the MG-H1/RAGE axis as a potential novel mechanism in SARS-CoV-2-induced inflammation by resorting to human bronchial BEAS-2B and alveolar A549 epithelial cells, expressing different levels of the ACE2 receptor (R), exposed to SARS-CoV-2 spike protein 1 (S1). Interestingly, we found in BEAS-2B cells that do not express ACE2-R that S1 exerted a pro-inflammatory action through a novel MG-H1/RAGE-based pathway. MG-H1 levels, RAGE and IL-1ß expression levels in nasopharyngeal swabs from SARS-CoV-2-positive and -negative individuals, as well as glyoxalase 1 expression, the major scavenging enzyme of MG, seem to support the results obtained in vitro. Altogether, our findings reveal a novel mechanism involved in the inflammation triggered by S1, paving the way for the study of the MG-H1/RAGE inflammatory axis in SARS-CoV-2 infection as a potential therapeutic target to mitigate COVID-19-associated pathogenic inflammation.

Case report: Coxiella burnetii endocarditis in the absence of evident exposure.

Q fever is a worldwide zoonotic disease caused by Coxiella burnetii. In humans, it can manifest clinically as an acute or chronic disease and endocarditis, the most frequent complication of chronic Q fever is associated with the greatest morbidity and mortality. We report a severe case of endocarditis in a 55-year-old man with a history of aortic valve replacement affected by monoclonal gammopathy of undetermined significance (MGUS), and living in a non-endemic area for C. burnetii. After two episodes of fever of unknown origin (FUO), occurring 2 years apart and characterized by negative blood cultures, a serological diagnosis of Q fever endocarditis was performed even though the patient did not refer to possible past exposure to C. burnetii. Since people with preexisting valvular heart disease, when infected with C. burnetii, have reported a 40% risk of Q fever endocarditis, clinicians should maintain a high index of suspicion for infective endocarditis in all patients with FUO even when the exposure to C. burnetii appears to be unlikely.

Immune correlates of protection by vaccine against SARS-CoV-2 in patients with chronic lymphocytic leukaemia.

In chronic lymphocytic leukaemia (CLL) the efficacy of SARS-CoV-2 vaccination remains unclear as most studies have focused on humoral responses. Here we comprehensively examined humoral and cellular responses to vaccine in CLL patients. Seroconversion was observed in 55.2% of CLL with lower rate and antibody titres in treated patients. T-cell responses were detected in a significant fraction of patients. CD4+ and CD8+ frequencies were significantly increased independent of serology with higher levels of CD4+ cells in patients under a Bruton tyrosine kinase (BTK) or a B-cell lymphoma 2 (BCL-2) inhibitor. Vaccination skewed CD8+ cells towards a highly cytotoxic phenotype, more pronounced in seroconverted patients. A high proportion of patients showed spike-specific CD4+ and CD8+ cells producing interferon gamma (IFNγ) and tumour necrosis factor alpha (TNFα). Patients under a BTK inhibitor showed increased production of IFNγ and TNFα by CD4+ cells. Vaccination induced a Th1 polarization reverting the Th2 CLL T-cell profile in the majority of patients with lower IL-4 production in untreated and BTK-inhibitor-treated patients. Such robust T-cell responses may have contributed to remarkable protection against hospitalization and death in a cohort of 540 patients. Combining T-cell metrics with seroprevalence may yield a more accurate measure of population immunity in CLL, providing consequential insights for public health.

Evidence, probability and relative plausibility.

A comparison is made between probability and relative plausibility as approaches for the interpretation of evidence. It is argued that a probabilistic approach is capable of answering the criticisms of the proponents of relative plausibility. It is also shown that a probabilistic approach can answer the problem of overlapping where there is evidence that each side claims supports its theory of what happened.

A High-Risk Profile for Invasive Fungal Infections Is Associated with Altered Nasal Microbiota and Niche Determinants.

It is becoming increasingly clear that the communities of microorganisms that populate the surfaces exposed to the external environment, termed microbiota, are key players in the regulation of pathogen-host cross talk affecting the onset as well as the outcome of infectious diseases. We have performed a multicenter, prospective, observational study in which nasal and oropharyngeal swabs were collected for microbiota predicting the risk of invasive fungal infections (IFIs) in patients with hematological malignancies. Here, we demonstrate that the nasal and oropharyngeal microbiota are different, although similar characteristics differentiate high-risk from low-risk samples at both sites. Indeed, similar to previously published results on the oropharyngeal microbiota, high-risk samples in the nose were characterized by low diversity, a loss of beneficial bacteria, and an expansion of potentially pathogenic taxa, in the presence of reduced levels of tryptophan (Trp). At variance with oropharyngeal samples, however, low Trp levels were associated with defective host-derived kynurenine production, suggesting reduced tolerance mechanisms at the nasal mucosal surface. This was accompanied by reduced levels of the chemokine interleukin-8 (IL-8), likely associated with a reduced recruitment of neutrophils and impaired fungal clearance. Thus, the nasal and pharyngeal microbiomes of hematological patients provide complementary information that could improve predictive tools for the risk of IFI in hematological patients.

Use of the Er:YAG Laser in Conservative Dentistry: Evaluation of the Microbial Population in Carious Lesions.

The aim of this study is to investigate the Erbium:Yttrio-Aluminum-Granate (Er:YAG) laser photothermal and mechanical effects on cariogenic species concentration and on the microbial load composition of therapeutic cavities, in order to evaluate the possible micro-organisms reduction and make a comparison with manual and rotating conventional therapy (CT). A clinical trial was designed, including adults with active deep carious lesions on permanent teeth who were divided into two groups, i.e., control group and intervention group treated with CT and Er:YAG therapy, respectively. Before and after any conservative treatment, two oral samples were collected using a small sterile microbrush scrubbed within the base of the dentinal cavity tissue. The percentage of reduction and the colony-forming units (CFUs) count after Er:YAG and conventional treatments were compared for total microorganisms, including Candida spp., Streptococcus spp., and Lactobacillus spp. The microbial reduction varied from 90.2% to 100% and was significantly observed for total microorganisms and Streptococcus spp. (p < 0.05). The Er:YAG laser shows the potential for clinical applications, especially with paediatric and complicated patients, thanks to its minimally invasive properties and its effect on the reduction of microbial load.

QuantiFERON-TB and tuberculin skin test in patients with active tuberculosis: the experience of a single medium-sized Italian University Hospital.

Interferon-γ releasing assays (IGRAs) are currently widely employed in the initial work up of Mycobacterium tuberculosis infection, as well as in suspected tuberculosis (TB). These assays are commonly utilized over the Tuberculin Skin Test (TST) in high resource and low TB burden settings, despite the unclear benefits shown in such contexts. The debate on the use of TST and IGRAs is of current interest also in Italy due to the increasing presence of immigrants from countries with a high incidence of TB and the rising attention of health care institutions to economic costs. The aim of this study was to compare QuantiFERON-TB (QFT) and TST results in active TB. We evaluated QFT results and TST reactions from 245 consecutive patients having both tests, registered among 411 patients admitted for TB at the Infectious Disease Clinic, Department of Medicine of the University of Perugia (Italy). We compared the rates of positive QFT and TST tests and noted no statistically significant differences overall or in relation to age, gender, HIV status and TB localization. Among foreign-born patients with confirmed TB, we observed a lower rate of positive TST results. The results of our study indicated that both QFT and TST can be used in the work up of TB having special attention when evaluating foreign-born patients.

Small Molecule CCR4 Antagonists Protect Mice from Aspergillus Infection and Allergy.

The ability to regulate the recruitment of immune cells makes chemokines and their receptors attractive drug targets in many inflammatory diseases. Based on its preferential expression on T helper type 2 (Th2) cells, C-C chemokine receptor type 4 (CCR4) has been widely studied in the context of allergic diseases, but recent evidence on the expression of CCR4 in other cell types has considerably expanded the potential applications of CCR4 antagonism. However, the current number of approved indications, as well as the portfolio of CCR4-targeting drugs, are still limited. In the present study, we have assessed the potential therapeutic efficacy of a CCR4 small molecule antagonist, SP50, discovered via an in silico-based approach, against a variety of pre-clinical settings of infection with the fungus Aspergillus fumigatus. We show that SP50 efficiently worked as prophylactic vaccine adjuvant in immunocompetent mice, protected against invasive aspergillosis in immunosuppressed mice. Further, the CCR4 antagonist prevented allergic bronchopulmonary aspergillosis in susceptible mice, and in a murine model of cystic fibrosis, a genetic disorder characterized by chronic pulmonary inflammation and recurrent infections. In conclusion, our results extend the potential applications of CCR4 antagonism and prompt for the development of novel compounds with the potential to progress to clinical trials.

Minor or adult? Introducing decision analysis in forensic age estimation.

Nowadays, forensic age estimation takes an important role in worldwide forensic and medico-legal institutes that are solicited by judicial or administrative authorities for providing an expert report on the age of individuals. The authorities' ultimate issue of interest is often the probability that the person is younger or older than a given age threshold, which is usually the age of majority. Such information is fundamental for deciding whether a person being judged falls under the legal category of an adult. This is a decision that may have important consequences for the individual, depending on the legal framework in which the decision is made. The aim of this paper is to introduce a normative approach for assisting the authority in the decision-making process given knowledge from available findings reported by means of probabilities. The normative approach proposed here has been acknowledged in the forensic framework, and represents a promising structure for reasoning that can support the decision-making process in forensic age estimation. The paper introduces the fundamental elements of decision theory applied to the specific case of age estimation, and provides some examples to illustrate its practical application.

Bayesian multivariate models for case assessment in dynamic signature cases.

Dynamic signatures are recordings of signatures made on digitizing devices such as tablet PCs. These handwritten signatures contain both dynamic and spatial information on every data point collected during the signature movement and can therefore be described in the form of multivariate data. The management of dynamic signatures represents a challenge for the forensic science community through its novelty and the volume of data available. Much as for static signatures, the authenticity of dynamic signatures may be doubted, which leads to a forensic examination of the unknown source signature. The Bayes' factor, as measure of evidential support, can be assigned with statistical models to discriminate between competing propositions. In this respect, the limitations of existing probabilistic solutions to deal with dynamic signature evidence is pointed out and explained in detail. In particular, the necessity to remove the independence assumption between questioned and reference material is emphasized.

Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature.

Can a patient diagnosed with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) be infected again? This question is still unsolved. We tried to analyze local and literature cases with a positive respiratory swab after recovery. We collected data from symptomatic patients diagnosed with SARS-CoV-2 infection in the Italian Umbria Region that, after recovery, were again positive for SARS-CoV-2 in respiratory tract specimens. Samples were also assessed for infectivity in vitro. A systematic review of similar cases reported in the literature was performed. The study population was composed of 9 patients during a 4-month study period. Among the new positive samples, six were inoculated in Vero-E6 cells and showed no growth and negative molecular test in culture supernatants. All patients were positive for IgG against SARS-CoV-2 nucleoprotein and/or S protein. Conducting a review of the literature, 1350 similar cases have been found. The presumptive reactivation occurred in 34.5 days on average (standard deviation, SD, 18.7 days) after COVID-19 onset, when the 5.6% of patients presented fever and the 27.6% symptoms. The outcome was favorable in 96.7% of patients, while the 1.1% of them were still hospitalized at the time of data collection and the 2.1% died. Several hypotheses have been formulated to explain new positive respiratory samples after confirmed negativity. According to this study, the phenomenon seems to be due to the prolonged detection of SARS-CoV-2 RNA traces in respiratory samples of recovered patients. The failure of the virus to replicate in vitro suggests its inability to replicate in vivo.

Hijacking SARS-CoV-2/ACE2 Receptor Interaction by Natural and Semi-synthetic Steroidal Agents Acting on Functional Pockets on the Receptor Binding Domain.

The coronavirus disease 2019 (COVID-19) is a respiratory tract infection caused by the severe acute respiratory syndrome coronavirus (SARS)-CoV-2. In light of the urgent need to identify novel approaches to be used in the emergency phase, we have embarked on an exploratory campaign aimed at repurposing natural substances and clinically available drugs as potential anti-SARS-CoV2-2 agents by targeting viral proteins. Here we report on a strategy based on the virtual screening of druggable pockets located in the central ß-sheet core of the SARS-CoV-2 Spike's protein receptor binding domain (RBD). By combining an in silico approach and molecular in vitro testing we have been able to identify several triterpenoid/steroidal agents that inhibit interaction of the Spike RBD with the carboxypeptidase domain of the Angiotensin Converting Enzyme (ACE2). In detail, we provide evidence that potential binding sites exist in the RBD of the SARS CoV-2 Spike protein and that occupancy of these pockets reduces the ability of the RBD to bind to the ACE2 consensus in vitro. Naturally occurring and clinically available triterpenoids such as glycyrrhetinic and oleanolic acids, as well as primary and secondary bile acids and their amidated derivatives such as glyco-ursodeoxycholic acid and semi-synthetic derivatives such as obeticholic acid reduces the RBD/ACE2 binding. In aggregate, these results might help to define novel approaches to COVID-19 based on SARS-CoV-2 entry inhibitors.

Accelerate Pheno™ blood culture detection system: a literature review.

Accelerate Pheno™ (ACC) is a fully automated system providing rapid identification of a panel of bacteria and yeasts, and antimicrobial susceptibility testing of common bacterial pathogens responsible for bloodstream infections and sepsis. Diagnostic accuracy for identification ranges from 87.9 to 100%, and antimicrobial susceptibility testing categorical agreement is higher than 91%. The present review includes peer-reviewed studies on ACC published to date. Both interventional and hypothetical studies evidenced the potential positive clinical role of ACC in the management and therapy of patients with bloodstream infections and sepsis, due to the important reduction in time to report, suggesting a crucial impact on the therapeutic management of these patients, provided the presence of a hospital antimicrobial stewardship program, a 24/7 laboratory operating time and a strict collaboration between clinical microbiologist and clinician. Further prospective multicenter studies are necessary to explore the impact of this system on mortality, length of stay and spread of multidrug-resistant organisms.

Anti-Biofilm Properties of Saccharomyces cerevisiae CNCM I-3856 and Lacticaseibacillus rhamnosus ATCC 53103 Probiotics against G. vaginalis.

Bacterial vaginosis (BV) is characterized by the presence of a polymicrobial biofilm where Gardnerella vaginalis plays a key role. Previously, we demonstrated that Saccharomyces cerevisiae CNCM (French National Collection of Cultures of Microorganisms) I-3856 is helpful in resolving experimental simulated BV in mice. In this study, we analyzed its capacity to affect G. vaginalis biofilms and to potentiate the activity of standard antimicrobial agents. We also investigated the anti-biofilm activity of Lacticaseibacillus rhamnosus GG (ATCC 53103), a well-known strain for its intestinal healthy benefits. Biofilm biomass was assessed by crystal violet staining, and G. vaginalis viability was assessed by a colony forming unit (CFU) assay. Here, for the first time, we demonstrated that S. cerevisiae CNCM I-3856 as well as L. rhamnosus GG were able (i) to significantly inhibit G. vaginalis biofilm formation, (ii) to markedly reduce G. vaginalis viability among the biomass constituting the biofilm, (iii) to induce disaggregation of preformed biofilm, and (iv) to kill a consistent amount of bacterial cells in a G. vaginalis preformed biofilm. Furthermore, S. cerevisiae CNCM I-3856 strongly potentiates the metronidazole effect on G. vaginalis biofilm viability. These results suggest that S. cerevisiae CNCM I-3856 as well as L. rhamnosus GG could be potential novel therapeutic agents against bacterial vaginosis.

Frequency and clinical correlates of antiphospholipid antibodies arising in patients with SARS-CoV-2 infection: findings from a multicentre study on 122 cases.

OBJECTIVES: COVID-19 features include disseminated intravascular coagulation and thrombotic microangiopathy indicating a hypercoagulable state. We aimed to investigate antiphospholipid antibodies (aPL) prevalence and clinical relationships in a large cohort of COVID-19 patients. METHODS: We analysed the prevalence and titres of serum aPL in 122 patients with COVID-19 and 157 with primary antiphospholipid syndrome (PAPS) and 91 with other autoimmune rheumatic diseases (oARD) for comparison. IgG/IgM anticardiolipin (aCL) and IgG/IgM anti-beta2glycoprotein I (ß2GPI) were assayed using homemade ELISA, IgA aCL and anti-ß2GPI by commercial ELISA kits and lupus anticoagulant (LAC) by multiple coagulation tests following updated international guidelines. RESULTS: Prevalence of IgG and IgM aCL and of IgG and IgM anti-ß2GPI across COVID-19 patients were 13.4%, 2.7%, 6.3% and 7.1%, being significantly lower than in PAPS (p<0.0001 for all). Frequency of IgG aCL and IgM anti-ß2GPI was comparable to oARD (13.4% vs. 13.2% and 7.1% vs. 11%, respectively), while IgG anti-ß2GPI and IgM aCL were lower (p<0.01). IgA aCL and IgA anti-ß2GPI were retrieved in 1.7% and 3.3% of COVID-19 patients, respectively. Positive LAC was observed in 22.2% COVID-19 vs. 54.1% of PAPS (p<0.0001) and 14.6% of oARD (p=0.21). Venous or arterial thromboses occurred in 18/46 (39.1%) COVID-19 patients and were not associated with positive aPL (p=0.09). CONCLUSIONS: Thrombosis is a frequent manifestation during COVID-19 infection. However, prevalence and titres of aPL antibodies or LAC were neither consistently increased nor associated with thrombosis when measured at a single timepoint, therefore not representing a suitable screening tool in the acute stage of disease.

Measles immunity in healthcare workers of an Italian hospital.

BACKGROUND: In Italy, 4991 cases of measles were reported in 2017 and 322 involved healthcare workers (HCWs). These professionals are at high risk of infection and transmission of virus both to other hospital staff and importantly, to patients, some of whom may be at risk of severe illness and complications. According to the Italian National Immunization and Prevention Plan, all HCWs should have demonstrable evidence of immunity to measles and specific hospital surveillance is recommended. Given a recent measles outbreak recorded in Italy, which also involved HCWs, the aim of this study has been to assess the measles immunization status of the Perugia General Hospital's HCWs. METHODS: A survey on all hospital staff was carried out, using a questionnaire to obtain information on demographic characteristics, personal history of measles and self-reported vaccination status, and offering the serological testing to HCWs who did not know their immune status. RESULTS: Among the 1714 HCWs included in the study, 1207 (70%) were protected against measles (due to vaccination or natural infection), and 507 (30%) did not know their immune status. Of these, 461 subjects accepted a serological control, while 46 refused. Protective measles-specific IgG antibody titres were documented in 410/461 (89%) HCWs, and the percentage of immune subjects decreased with the age. CONCLUSIONS: Our study shows that in Perugia General Hospital, 26% of HCWs under the age of 30 were not protected against measles. In Italy, campaigns promoting vaccination of HCWs are needed to prevent transmission of this infection in hospital setting.

Improving the etiological diagnosis of osteoarticular infections with the commercial multiplex real-time polymerase chain reaction SeptiFast®.

Detection of etiological agents is pivotal for adequate therapy of osteoarticular bacterial infections. Culture often lacks sensitivity, especially in patients under antibiotic therapy. The present study investigates the potential clinical utility of the commercial multiplex real-time polymerase chain reaction SeptiFast® (SF) in the etiological diagnosis of osteoarticular infections. Results obtained from conventional culture and SF were compared in 86 osteoarticular specimens collected from patients with suspected infection. The number of specimens positive by SF (38/86, 44.18%) was significantly greater (P = 0.001) than that of specimens positive by culture (20/86, 23.25%). The sensitivity of SF was 48.71%, significantly higher than culture sensitivity (25.64%). Specificity was 100% for both tests. The overall diagnostic accuracy for SF was 53.48%, and that of culture was 32.55%. Even with the limitation of the low number of specimens, this study supports the usefulness of SF in the diagnosis of osteoarticular infections.