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-1β 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 probabilistic approach to evaluate salivary microbiome in forensic science when the Defense says: `It is my twin brother'

Salivary microbiota profiles may represent a valid contribution to forensic investigation when standard DNA genotyping methods fail. Starting from questioned and control materials in the form of saliva, the evidence can be expressed by means of a distance between those materials taking into account specific aspects of the microbiota composition. The value of the evidence for forensic discrimination purposes is quantified by means of a Bayes' factor, that allows one to overcome the major limitations and pitfalls of intuition connected to the use of cut-off values as a mean of decision.

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.

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.

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.

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.

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 β-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.

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.

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.

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 (β2GPI) were assayed using homemade ELISA, IgA aCL and anti-β2GPI 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-β2GPI 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-β2GPI was comparable to oARD (13.4% vs. 13.2% and 7.1% vs. 11%, respectively), while IgG anti-β2GPI and IgM aCL were lower (p<0.01). IgA aCL and IgA anti-β2GPI 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.

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.

Are Inconclusive Decisions in Forensic Science as Deficient as They Are Said to Be?

Many quarters of forensic science use reporting formats such as “identification,” “inconclusive,” and “exclusion.” These types of conclusions express opinions as to whether or not a particular person or object is the source of the material or traces of unknown source that is of interest in a given case. Rendering an “inconclusive” conclusion is sometimes criticized as being inadequate because—supposedly—it does not provide recipients of expert information with helpful directions. In this paper, we critically examine this claim using decision theory. We present and defend the viewpoint according to which deciding to render an “inconclusive” conclusion is, on a formal account, not as inadequate as may commonly be thought. Using elements of decision theory from existing accounts on the topic, we show that inconclusive conclusions can actually be viable alternatives with respect to other types of conclusions, such as “identification.”

Intravenous immunoglobulin protects from experimental allergic bronchopulmonary aspergillosis via a sialylation-dependent mechanism

Intravenous immunoglobuin (IVIG) exerts protective effects in experimental allergic bronchopulmonary aspergillosis (ABPA) via a sialylation-dependent mechanism. The protection was associated with reduced recruitment of eosinophils, diminished goblet cell hyperplasia, suppressed Th2 and Th17 responses and reciprocally enhanced regulatory T cells and IL-10, and decreased IgE levels in the circulation.

The meaning of justified subjectivism and its role in the reconciliation of recent disagreements over forensic probabilism

In this paper we reply to recent comments in this Special Issue according to which subjective probability is not considered to be a concept fit for use in forensic evaluation and expert reporting. We identify the source of these criticisms to lie in a misunderstanding of subjective probability as unconstrained subjective probability; a lack of constraint that neither corresponds to the way in which we referred to subjective probability in our previous contributions, nor to the way in which probability assignment is understood by current evaluative guidelines (e.g., of ENFSI). Specifically, we explain that we understand subjective probability as a justified assertion, i.e. a conditional assessment based on task-relevant data and information, that may be thought of as a constrained subjective probability. This leads us to emphasise again the general conclusion that there is no gap between justified (or, reasonable) subjective probability and other concepts of probability in terms of its ability to provide assessments that are soundly based on whatever relevant information available. We also note that the challenges an expert faces in reporting probabilities apply equally to all interpretations of probability, not only to subjective probability.

Reframing the debate: A question of probability, not of likelihood ratio

Evidential value is measured by a likelihood ratio. This ratio has two components, the probability, or probability density, of the evidence if the prosecution proposition is true and the probability (density) of the evidence if the defence proposition is true. It takes the form of a single value, even if these probabilities are subjective measures of belief of the reporting forensic scientist.

Molecular sensitivity threshold of wet mount and an immunochromatographic assay evaluated by quantitative real-time PCR for diagnosis of Trichomonas vaginalis infection in a low-risk population of childbearing women

Vaginal trichomoniasis is a sexually transmitted infection caused by Trichomonas vaginalis, a flagellated protozoan. Diagnosis of T. vaginalis infection is mainly performed by wet mount microscopy, with a sensitivity ranging from 38% to 82%, compared to culture, still considered the gold standard. Commercial immunochromatographic tests for monoclonal-antibody-based detection have been introduced as alternative methods for diagnosis of T. vaginalis infection and have been reported in some studies to be more sensitive than wet mount. Real-time PCR methods have been recently developed, with optimal sensitivity and specificity. The aim of this study was to evaluate whether there is a molecular sensitivity threshold for both wet mount and imunochromatographic assays. To this aim, a total of 1487 low-risk childbearing women (median age 32 years, interquartile range 27-37) were included in the study, and underwent vaginal swab for T. vaginalis detection by means of a quantitative real-time PCR assay, wet mount and an immunochromatographic test. Upon comparing the results, prevalence values observed were 1.3% for real-time PCR, 0.5% for microscopic examination, and 0.8% for the immunochromatographic test. Compared to real-time PCR, wet mount sensitivity was 40% (95% confidence interval 19.1% to 63.9%) and specificity was 100% (95% CI 99.7% to 100%). The sensitivity and specificity of the immunochromatographic assay were 57.9% (95% CI 33.5% to 79.8%) and 99.9% (95% CI 99.6% to 100%), respectively. Evaluation of the wet mount results and those of immunochromatographic assay detection in relation to the number of T. vaginalis DNA copies detected in vaginal samples showed that the lower identification threshold for both wet mount (chi-square 6.1; P = 0.016) and the immunochromatographic assay (chi-square 10.7; P = 0.002) was ≥100 copies of T. vaginalis DNA/5 mcl of eluted DNA.

Diagnostic accuracy of presepsin (sCD14-ST) and procalcitonin for prediction of bacteraemia and bacterial DNAaemia in patients with suspected sepsis

Early diagnosis and prompt targeted therapy are essential for septic patients' outcome. Procalcitonin (PCT) has been shown to predict bacteraemia and bacterial DNAaemia. Presepsin, the circulating soluble form of CD14 subtype, increases in response to bacterial infections, and is considered a new, emerging, early marker for sepsis. We evaluated the diagnostic accuracy of presepsin in predicting bacteraemia and bacterial DNAaemia in 92 patients with suspected sepsis, and we compared it with that of PCT and C-reactive protein (CRP). Presepsin median values were significantly higher in bacteraemic vs non-bacteraemic patients [1290 pg ml-1, interquartile range (IQR) 1005-2041 vs 659 pg ml-1, IQR 381-979; P<0.001] and in patients with vs patients without bacterial DNAaemia (1297 pg ml-1, IQR 1001-2046 vs 665 pg ml-1, IQR 381-940; P<0.001). Receiver operating characteristics analysis showed an area under the curve (AUC) for presepsin of 0.788 [95 % confidence interval (CI): 0.687-0.889; P<0.001] in predicting bacteraemia and of 0.777 (95 % CI: 0.676-0.878; P<0.001) in predicting bacterial DNAaemia, lower, but not significantly different, than those of PCT (0.876, P=0.12 and 0.880, P=0.07, respectively). Both biomarkers performed significantly better than CRP, which had an AUC for bacteraemia of 0.602 and for DNAaemia of 0.632 (all P values <0.05). In conclusion, in patients with suspected sepsis, presepsin and PCT showed a good diagnostic accuracy in predicting both bacteraemia and bacterial DNAaemia, superior to CRP.

Statistical hypothesis testing and common misinterpretations: Should we abandon p-value in forensic science applications?

Many people regard the concept of hypothesis testing as fundamental to inferential statistics. Various schools of thought, in particular frequentist and Bayesian, have promoted radically different solutions for taking a decision about the plausibility of competing hypotheses. Comprehensive philosophical comparisons about their advantages and drawbacks are widely available and continue to span over large debates in the literature. More recently, controversial discussion was initiated by an editorial decision of a scientific journal [1] to refuse any paper submitted for publication containing null hypothesis testing procedures. Since the large majority of papers published in forensic journals propose the evaluation of statistical evidence based on the so called p-values, it is of interest to expose the discussion of this journal's decision within the forensic science community. This paper aims to provide forensic science researchers with a primer on the main concepts and their implications for making informed methodological choices.

Deletion of the α-(1,3)-glucan synthase genes induces a restructuring of the conidial cell wall responsible for the avirulence of Aspergillus fumigatus

α-(1,3)-Glucan is a major component of the cell wall of Aspergillus fumigatus, an opportunistic human fungal pathogen. There are three genes (AGS1, AGS2 and AGS3) controlling the biosynthesis of α-(1,3)-glucan in this fungal species. Deletion of all the three AGS genes resulted in a triple mutant that was devoid of α-(1,3)-glucan in its cell wall; however, its growth and germination was identical to that of the parental strain in vitro. In the experimental murine aspergillosis model, this mutant was less pathogenic than the parental strain. The AGS deletion resulted in an extensive structural modification of the conidial cell wall, especially conidial surface where the rodlet layer was covered by an amorphous glycoprotein matrix. This surface modification was responsible for viability reduction of conidia in vivo, which explains decrease in the virulence of triple agsΔ mutant.

Aspergillus fumigatus is the predominant mold pathogen of humans, responsible for life-threatening systemic infections in patients with depressed immunity. Because of its external localization and specific composition, the fungal cell wall represents a target for recognition by and interaction with the host immune cells. In A. fumigatus, α-(1,3)-glucan is a key component of the extracellular matrix, which encloses the cell wall β-(1,3)-glucan-chitin fibrillar core. Interestingly, the deletion of the genes responsible for α-(1,3)-glucan synthesis resulted in a mutant that exhibited wild type phenotype in vitro; while the altered cell wall organization resulted in this fungus being avirulent in vivo. This study confirms that any modification in the cell wall components is associated with compensatory reactions developed by the fungus to counteract stress on the cell wall that may result in unexpected fungal response when challenged with the host immune system.

Immunity and tolerance to fungi in hematopoietic transplantation: principles and perspectives

Resistance and tolerance are two complementary host defense mechanisms that increase fitness in response to low-virulence fungi. Resistance is meant to reduce pathogen burden during infection through innate and adaptive immune mechanisms, whereas tolerance mitigates the substantial cost of resistance to host fitness through a multitude of anti-inflammatory mechanisms, including immunological tolerance. In experimental fungal infections, both defense mechanisms are activated through the delicate equilibrium between Th1/Th17 cells, which provide antifungal resistance, and regulatory T cells limiting the consequences of the ensuing inflammatory pathology. Indoleamine 2,3-dioxygenase (IDO), a rate-limiting enzyme in the tryptophan catabolism, plays a key role in induction of tolerance against fungi. Both hematopoietic and non-hematopoietic compartments contribute to the resistance/tolerance balance against Aspergillus fumigatus via the involvement of selected innate receptors converging on IDO. Several genetic polymorphisms in pattern recognition receptors influence resistance and tolerance to fungal infections in human hematopoietic transplantation. Thus, tolerance mechanisms may be exploited for novel diagnostics and therapeutics against fungal infections and diseases.

CD4(+) T cell vaccination overcomes defective cross-presentation of fungal antigens in a mouse model of chronic granulomatous disease

Aspergillus fumigatus is a model fungal pathogen and a common cause of infection in individuals with the primary immunodeficiency chronic granulomatous disease (CGD). Although primarily considered a deficiency of innate immunity, CGD is also linked to dysfunctional T cell reactivity. Both CD4(+) and CD8(+) T cells mediate vaccine-induced protection from experimental aspergillosis, but the molecular mechanisms leading to the generation of protective immunity and whether these mechanisms are dysregulated in individuals with CGD have not been determined. Here, we show that activation of either T cell subset in a mouse model of CGD is contingent upon the nature of the fungal vaccine, the involvement of distinct innate receptor signaling pathways, and the mode of antigen routing and presentation in DCs. Aspergillus conidia activated CD8(+) T cells upon sorting to the Rab14(+) endosomal compartment required for alternative MHC class I presentation. Cross-priming of CD8(+) T cells failed to occur in mice with CGD due to defective DC endosomal alkalinization and autophagy. However, long-lasting antifungal protection and disease control were successfully achieved upon vaccination with purified fungal antigens that activated CD4(+) T cells through the endosome/lysosome pathway. Our study thus indicates that distinct intracellular pathways are exploited for the priming of CD4(+) and CD8(+) T cells to A. fumigatus and suggests that CD4(+) T cell vaccination may be able to overcome defective antifungal CD8(+) T cell memory in individuals with CGD.

Galactosaminogalactan, a new immunosuppressive polysaccharide of Aspergillus fumigatus

A new polysaccharide secreted by the human opportunistic fungal pathogen Aspergillus fumigatus has been characterized. Carbohydrate analysis using specific chemical degradations, mass spectrometry, ¹H and ¹³C nuclear magnetic resonance showed that this polysaccharide is a linear heterogeneous galactosaminogalactan composed of α1-4 linked galactose and α1-4 linked N-acetylgalactosamine residues where both monosacharides are randomly distributed and where the percentage of galactose per chain varied from 15 to 60%. This polysaccharide is antigenic and is recognized by a majority of the human population irrespectively of the occurrence of an Aspergillus infection. GalNAc oligosaccharides are an essential epitope of the galactosaminogalactan that explains the universal antibody reaction due to cross reactivity with other antigenic molecules containing GalNAc stretches such as the N-glycans of Campylobacter jejuni. The galactosaminogalactan has no protective effect during Aspergillus infections. Most importantly, the polysaccharide promotes fungal development in immunocompetent mice due to its immunosuppressive activity associated with disminished neutrophil infiltrates.

Aspergillus fumigatus is an opportunistic human fungal pathogen that causes a wide range of diseases including allergic reactions and local or systemic infections such as invasive pulmonary aspergillosis that has emerged in the recent years as a leading cause of infection related mortality among immunocompromised patients. Polysaccharides from the fungal cell wall play essential biological functions in the fungal cell biology and in host-pathogen interactions. Indeed, it has been shown that polysaccharides can modulate the human immune response; some of them (β-glucan and α-glucans) having a protective effect against Aspergillus infection. We report here the purification and chemical characterization of a new antigenic polysaccharide (galactosaminogalactan) produced by A. fumigatus. This polymer is secreted during infection. In murine models of aspergillosis, this galactosaminogalactan is not protective but it is immunosuppressive and favors A. fumigatus infection. Particularly it induces the apoptotic death of neutrophils that are the phagocytes playing an essential role in the killing of fungal pathogens.

Non-hematopoietic cells contribute to protective tolerance to Aspergillus fumigatus via a TRIF pathway converging on IDO

Innate responses combine with adaptive immunity to generate the most effective form of anti-Aspergillus immune resistance. Whereas the pivotal role of dendritic cells in determining the balance between immunopathology and protective immunity to the fungus is well established, we determined that epithelial cells (ECs) also contributes to this balance. Mechanistically, EC-mediated protection occurred through a Toll-like receptor 3/Toll/IL-1 receptor domain-containing adaptor-inducing interferon (TLR3/TRIF)-dependent pathway converging on indoleamine 2,3-dioxygenase (IDO) via non-canonical nuclear factor-κB activation. Consistent with the high susceptibility of TRIF-deficient mice to pulmonary aspergillosis, bone marrow chimeric mice with TRIF unresponsive ECs exhibited higher fungal burdens and inflammatory pathology than control mice, underexpressed the IDO-dependent T helper 1/regulatory T cell (Th1/Treg) pathway and overexpressed the Th17 pathway with massive neutrophilic inflammation in the lungs. Further studies with interferon (IFN)-γ, IDO or IL-17R unresponsive cells confirmed the dependency of immune tolerance to the fungus on the IFN-γ/IDO/Treg pathway and of immune resistance on the MyD88 pathway controlling the fungal growth. Thus, distinct immune pathways contribute to resistance and tolerance to the fungus, to which the hematopoietic/non-hematopoietic compartments contribute through distinct, yet complementary, roles.

Thymosin alpha1: the regulator of regulators?

The peripheral immune system can promote either immunity or tolerance when presented with new antigens. Current knowledge withholds that populations of suppressor or regulatory T cells (T(reg) cells) constitute a pivotal mechanism of immunological tolerance. The potential role of malfunctioning T(reg) cells in chronic inflammatory immune and auto-immune diseases is well-documented. Learning how to successfully manipulate T(reg) responses could result in more effective vaccines and immunomodulators. We have already shown that Thymosin alpha1 (Talpha1), a naturally occurring thymic peptide first described and characterized by Allan Goldstein in 1972, by modulating signals delivered through innate immune receptors on dendritic cells, affects adaptive immune responses via modulation of Th cell effector and regulatory functions. We will discuss recent molecular mechanisms underlying the ability of Talpha1 to activate or inhibit immune responses.

How do airborne fungal spores avoid immune recognition? (40.1)

Every day we inhale thousands of tiny fungal spores (conidia), originating from many different fungal species such as Aspergillus, Cladosporium, Penicillium and Alternaria. Although these spores are packed with antigens and allergens, yet their inhalation does not continuously activate our innate immune cells or provoke inflammatory responses. By using several fungal inhabitants of the air-borne microflora including the human opportunistic fungal pathogen Aspergillus fumigatus, in vitro assays using human dendritic cells (DC) and alveolar macrophages (AM) and in vivo experiments using a murine model we show that a protein surface-layer called ‘rodlet’ on the dormant conidia masks their recognition by the immune system and hence prevents immune response to conidia. Interestingly, rodlet proteins are found to be immunologically inert and failed to activate either human or mouse DC and AM and did not induce adaptive T responses in vivo upon transfer of rodlet-pulsed DC. Furthermore, dormant conidia that lacked rodlet layer induced strong immune responses in vitro and in vivo despite being dormant in nature. All these results indicate that rodlet layer on dormant conidia masks the immunogenic molecules and prevent immune aggression against inhaled conidia.

Protection against Pseudomonas aeruginosa lung infection in mice by recombinant OprF-pulsed dendritic cell immunization

BACKGROUND

The Pseudomonas aeruginosa major constitutive outer membrane porin protein F (OprF) has been shown to be a protective antigen and was previously used to activate an immunological response in a mouse model of lung pneumonia. The purpose of our study was to demonstrate the ability of mouse dendritic cells pulsed with purified or recombinant OprF to protect mice against P. aeruginosa infection and inflammation.Both native (n-OprF), isolated and purified from PAO1 bacterial strain, and recombinant (histidin-conjugated) OprF (His-OprF), obtained by cloning of the oprF gene into the pET28a expression vector, were used to stimulate dendritic cells in vitro before adoptive transfer into prospective recipient mice with P. aeruginosa pulmonary infection.

RESULTS

Similar to n-OprF, His-OprF activated dendritic cells in vitro, inducing the costimulatory molecule expression as well as cytokine production. Upon adoptive transfer in vivo, porin-pulsed dendritic cells (DCs) induced Th1-mediated resistance to infection and associated inflammatory pathology caused by either the PAO1 strain or a clinically-isolated mucoid strain.

CONCLUSIONS

This study highlights the pivotal contribution of DCs to vaccine-induced protection against P. aeruginosa infection and associated inflammation.