Advancing West Nile virus monitoring through whole genome sequencing: Insights from a One Health genomic surveillance study in Romagna (Italy).

In the last 6 years, Italy accounted for 36 % of the total autochthonous European West Nile virus (WNV) cases reported to ECDC. Since 2001, the country put in place a multi-species national surveillance plan. The plan was enhanced in 2020 by adopting a fully integrated "One Health" approach, including human, wild bird, equine, and mosquito surveillance for the early detection of WNV.

Sanitary Waters: Is It Worth Looking for Mycobacteria?

The freshwater environment is suitable for nontuberculous mycobacteria (NTMs) growth. Their high adaptability represents a considerable risk for sanitary water systems, which are a potential vector for NTMs transmission. This study investigated the occurrence of NTMs, such as , in hospital water systems to support the surveillance and control of potentially pathogenic NTMs.

Isolation and Genomic Analysis of a Case of ST2250 Related to Sepsis in Italy.

, identified in 2006, represents a challenging case of bacterial taxonomic identification because of its high similarity to . In this context, neither mass spectrometry (MS) nor 16S gene analysis cannot precisely reveal the difference between the two species. In our study, the sensitivity to antibiotics of isolated from blood culture was tested, and the investigation of the bacterial genome was performed by Multi-Locus Sequence Typing (MLST) and Whole-Genome Next-Generation Sequencing (WG-NGS).

Evaluation of a rapid Loop Mediated Isothermal Amplification (LAMP) test for the laboratory diagnosis of sexually transmitted infections.

Sexually transmitted infections (STIs) have seen a considerable increase in the last years and given the health burden they may represent from both a personal and community perspective, they require surveillance and prevention programmes based on a timely and decentralized diagnosis. In this context, user-friendly rapid molecular tests may represent a good trade-off between diagnostic accuracy, accessibility and affordability. In this study we evaluated the diagnostic performance of a new real-time LAMP (Loop Mediated Isothermal Amplification) method for the rapid detection and differentiation of 7 major sexually transmissible pathogens by analysing real clinical samples (genital and extra-genital matrices) from individuals with suspected STIs.

Evaluation of Biofilm Production and Antifungal Susceptibility to Fluconazole in Clinical Isolates of spp. in Both Planktonic and Biofilm Form.

spp. are an important opportunistic pathogen that can represent a possible cause of severe infections, especially in immunocompromised individuals. The clinical impact of spp.

Genomic and Temporal Analysis of Deletions Correlated to qRT-PCR Dropout in N Gene in Alpha, Delta and Omicron Variants.

Since the first SARS-CoV-2 outbreak, mutations such as single nucleotide polymorphisms (SNPs) and insertion/deletions (INDELs) have changed and characterized the viral genome sequence, structure and protein folding leading to the onset of new variants. The presence of those alterations challenges not only the clinical field but also the diagnostic demand due to failures in gene detection or incompleteness of polymerase chain reaction (PCR) results. In particular, the analysis of understudied genes such as and the investigation through whole-genome next generation sequencing (WG-NGS) of regions more prone to mutate can help in the identification of new or reacquired mutations, with the aim of designing robust and long-lasting primers.

An Enhanced Dissolving Cyclosporin-A Inhalable Powder Efficiently Reduces SARS-CoV-2 Infection In Vitro.

This work illustrates the development of a dry inhalation powder of cyclosporine-A for the prevention of rejection after lung transplantation and for the treatment of COVID-19. The influence of excipients on the spray-dried powder's critical quality attributes was explored. The best-performing powder in terms of dissolution time and respirability was obtained starting from a concentration of ethanol of 45% (/) in the feedstock solution and 20% (/ of mannitol.

Kinetics of dried blood spot-measured anti-SARS-CoV2 Spike IgG in mRNA-vaccinated healthcare workers.

Introduction: One of the major criticisms facing the research community during SARS-CoV2 pandemic was the lack of large-scale, longitudinal data on the efficacy of the SARS-CoV2 mRNA vaccines. Currently, even if COVID-19 antiviral treatments have been authorized by European Medicine Agency, prevention through approved specific vaccines is the best approach available in order to contain the ongoing pandemic.

Objectives: Here, we studied the antibody kinetic over a one-year period from vaccination with the Pfizer-BioNTech (Pfizer) vaccines and subsequent boosting with either the BioNTech or Moderna (Spikevax) vaccines in a large cohort of 8,071 healthcare workers (HCW).

SARS-CoV-2 coinfection in immunocompromised host leads to the generation of recombinant strain.

Objectives: Recombination related to coinfection is a huge driving force in determining the virus genetic variability, particularly in conditions of partial immune control, leading to prolonged infection. Here, we characterized a distinctive mutational pattern, highly suggestive of Delta-Omicron double infection, in a lymphoma patient.

Methods: The specimen was characterized through a combined approach, analyzing the results of deep sequencing in primary sample, viral culture, and plaque assay.

Viral Population Heterogeneity and Fluctuating Mutational Pattern during a Persistent SARS-CoV-2 Infection in an Immunocompromised Patient.

Literature offers plenty of cases of immunocompromised patients, who develop chronic and severe SARS-CoV-2 infections. The aim of this study is to provide further insight into SARS-CoV-2 evolutionary dynamic taking into exam a subject suffering from follicular lymphoma, who developed a persistent infection for over 7 months. Eight nasopharyngeal swabs were obtained, and were analyses by qRT-PCR for diagnostic purposes.

Omicron Sub-Lineage BA.5 and Recombinant XBB Evasion from Antibody Neutralisation in BNT162b2 Vaccine Recipients.

The recent emergence of a number of new SARS-CoV-2 variants resulting from recombination between two distinct parental lineages or sub-lineages within the same lineage has sparked the debate regarding potential enhanced viral infectivity and immune escape. Among these, XBB, recombinant of BA.2.

Molecular Approach for the Laboratory Diagnosis of Periprosthetic Joint Infections.

The incidence of total joint arthroplasty is increasing over time since the last decade and expected to be more than 4 million by 2030. As a consequence, the detection of infections associated with surgical interventions is increasing and prosthetic joint infections are representing both a clinically and economically challenging problem. Many pathogens, from bacteria to fungi, elicit the immune system response and produce a polymeric matrix, the biofilm, that serves as their protection.

Mutational induction in SARS-CoV-2 major lineages by experimental exposure to neutralising sera.

The ongoing evolution of SARS-CoV-2 and the emergence of new viral variants bearing specific escape mutations responsible for immune evasion from antibody neutralisation has required a more accurate characterisation of the immune response as one of the evolutive forces behind viral adaptation to a largely immunised human population. In this work, culturing in the presence of neutralising sera vigorously promoted mutagenesis leading to the acquisition of known escape mutations on the spike as well as new presumptive escape mutations on structural proteins whose role as target of the neutralizing antibody response might have been thus far widely neglected. From this perspective, this study, in addition to tracing the past evolution of the species back to interactions with neutralising antibody immune response, also offers a glimpse into future evolutive scenarios.

Importance of external quality assessment for SARS-CoV-2 antigen detection during the COVID-19 pandemic.

Background: Antigen testing has become an essential part of fighting the ongoing COVID-19 pandemic. With the continual increase in available tests, independent and extensive comparative evaluations using data from external quality assessment (EQA) studies to evaluate test performance between different users are required.

Objectives: An EQA scheme was established to assess the sensitivity of antigen tests and the potential impact of circulating SARS-CoV-2 strains on their performance.

Organic Electrochemical Transistors as Versatile Tool for Real-Time and Automatized Viral Cytopathic Effect Evaluation.

In-vitro viral studies are still fundamental for biomedical research since studying the virus kinetics on cells is crucial for the determination of the biological properties of viruses and for screening the inhibitors of infections. Moreover, testing potential viral contaminants is often mandatory for safety evaluation. Nowadays, viral cytopathic effects are mainly evaluated through end-point assays requiring dye-staining combined with optical evaluation.

Modelling RT-qPCR cycle-threshold using digital PCR data for implementing SARS-CoV-2 viral load studies.

Objectives: To exploit the features of digital PCR for implementing SARS-CoV-2 observational studies by reliably including the viral load factor expressed as copies/μL.

Methods: A small cohort of 51 Covid-19 positive samples was assessed by both RT-qPCR and digital PCR assays. A linear regression model was built using a training subset, and its accuracy was assessed in the remaining evaluation subset.

A deletion in the N gene may cause diagnostic escape in SARS-CoV-2 samples.

Five SARS-CoV-2-positive samples showed N-gene drop-out with a RT-PCR multiplex test. WGS found all samples to harbor a deletion in the same region of the N gene, which is likely to impair the efficiency of amplification. This highlights the need for a continued surveillance of viral evolution and diagnostic test performance.

Correlating qRT-PCR, dPCR and Viral Titration for the Identification and Quantification of SARS-CoV-2: A New Approach for Infection Management.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in Wuhan, China, in late 2019 and is the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) represents the gold standard for diagnostic assays even if it cannot precisely quantify viral RNA copies. Thus, we decided to compare qRT-PCR with digital polymerase chain reaction (dPCR), which is able to give an accurate number of RNA copies that can be found in a specimen.

COVID-19 Infection: Viral Clearance and Antibody Response in Dialysis Patients and Renal Transplant Recipients.

Background/aims: The coronavirus disease 2019 (CO-VID-19) pandemic is the major current health emergency worldwide, adding a significant burden also to the community of nephrologists for the management of their patients. Here, we analyzed the impact of COVID-19 infection in renal patients to assess the time to viral clearance, together with the production and persistence of IgG and IgM antibody response, in consideration of the altered immune capacity of this fragile population.

Methods: Viral clearance and antibody kinetics were investigated in 49 renal patients recovered from COVID-19 infection: 7 of them with chronic decompensated renal failure, 31 under dialysis treatment, and 11 kidney transplant recipients.

[Resilience in COVID-19 times: general considerations on the recovery of a 93-year-old patient on haemodialysis treatment].

We report the case of a 93-year-old woman on haemodialysis treatment for more than 30 months and with multiple comorbidities who recovered from a Covid-19 infection without any significant clinical problems. The patient has shown a delay in viral clearance with swab test negativization (confirmed) after 33 days; after testing positive again, she has resulted persistently negative, (confirmed after 49 days). After the first negative swab, IgG and IgM antibodies have been found; these have remained persistently positive after a month.

Diagnosing Clostridioides difficile infections with molecular diagnostics: multicenter evaluation of revogene C. difficile assay.

Clostridioides difficile infections are a significant threat to our healthcare system, and rapid and accurate diagnostics are crucial to implement the necessary infection prevention and control measurements. Nucleic acid amplification tests are such reliable diagnostic tools for the detection of toxigenic Clostridioides difficile strains directly from stool specimens. In this multicenter evaluation, we determined the performance of the revogene C.

Comparison of Four Commercial Screening Assays for the Detection of bla, bla, bla, bla and bla in Rectal Secretion Collected by Swabs.

The spread of carbapenem-resistant Enterobacteriaceae (CRE) has been enabled by the lack of control measures directed at carriers of multidrug-resistant organisms in healthcare settings. Screening patients for asymptomatic colonization on the one hand, and implementation of contact precautions on the other hand, reduces patient-to-patient transmission. Screening plates represents a relatively low-cost method for isolating CRE from rectal swabs; however, molecular assays have become widely available.

Easyscreen™ Enteric Protozoa Assay For the Detection of Intestinal Parasites: A Retrospective Bi-Center Study.

Gastroenteritis caused by single or multiple pathogens remains a major diagnostic challenge for the laboratory, as diagnosis is achieved using different techniques with variable sensitivity and specificity. The aim of this study was to evaluate the EasyScreen™ Enteric Protozoa Detection Kit, a multiplex PCR assay for the detection and identification of the 5 most common protozoan parasites in fecal samples. A total of 632 fecal samples, submitted for routine screening to 2 centers in north-eastern Italy, was included in the study.

Seroprevalence of West Nile virus-specific antibodies in a cohort of blood donors in northeastern Italy.

IgG and IgM levels against West Nile virus (WNV) were measured in 20,033 serum samples that were obtained between October 2008 to September 2009 from 9913 blood donors in the district of Ferrara, northeastern Italy. As confirmatory test, a microneutralization assay was used to detect the presence of neutralizing antibodies against WNV. Sixty-eight subjects (0.

Paraffin embedding allows effective analysis of proliferation, survival, and immunophenotyping of cells cultured on poly(l-lactic acid) electrospun nanofiber scaffolds.

Morphological and immunophenotypic characterization of cells grown on poly(l-lactic acid) (PLLA) electrospun scaffolds is usually performed using immunofluorescence and cryosections. However, these methods present practical limits; histological processing, on the other hand, is believed to lead to artifactual changes in the scaffold structure. Here the formalin-fixed paraffin-embedding (FFPE) procedure was tailored to process PLLA electrospun scaffolds grown with human umbilical vein endothelial cells.