Longitudinal evaluation of two different COVID-19 vaccination strategies in individuals with and without previous SARS-CoV-2 infection.

Background: We tested the antibody response to SARS-CoV-2 vaccination in individuals with and without previous infection that received different vaccination strategies. Methods: We recruited 203 volunteers. Individuals who have had SARS-CoV-2 infection during the six months preceding vaccination received one dose (group 1), the others received two (group 2). After 3 months, 98 subjects received a booster dose. Anti-SARS-CoV-2 Spike RBD IgG were tested in all subjects before vaccination (T0), and at 15 (T15), 90 (T90), 180 (T180) and 360 (T360) days after second or single dose; additionally, in group 2, IgG were tested 10 days after the vaccination (T10). Results: The difference of IgG concentration between the groups was statistically significant (p<0.05) at T0, T15 and T90, but not at T180 (p=0.713) and T360 (p=0.069). At T0 and T90 the antibody titre was higher in group 1, but it dropped in all volunteers 90 days after vaccination. Most of infections after vaccination occurred between T90 and T180. Conclusions: Antibody titre is significantly associated with a previous SARS-CoV-2 infection. Probability of contracting the infection increases after three months from primary vaccination, even among who had a previous infection, confirming the efficacy of vaccination as a preventive measure against SARS-CoV-2 infections and the need of booster administrations.

Cefiderocol use for the treatment of infections by carbapenem-resistant Gram-negative bacteria: an Italian multicentre real-life experience.

BACKGROUND: Cefiderocol is a novel siderophore cephalosporin with promising activity against most carbapenem-resistant Gram-negative bacteria (CRGNB). However, extensive postmarketing experiences are lacking. This study aimed to analyse the early experience on cefiderocol postmarketing use at three tertiary care hospitals in Italy. METHODS: We retrospectively included patients with infections caused by CRGNB treated with cefiderocol at three Italian tertiary care hospitals from 1 March 2021 to 30 June 2022. A multivariate Cox model was used to identify predictors of 30 day mortality. A propensity score (PS) analysis with inverse probability weighting (IPW) was also performed to compare the treatment effect of cefiderocol monotherapy (CM) versus combination regimens (CCRs). RESULTS: The cohort included 142 patients (72% male, median age 67 years, with 89 cases of Acinetobacter baumannii infection, 22 cases of Klebsiella pneumoniae, 27 cases of Pseudomonas aeruginosa and 4 of other pathogens). The 30 day all-cause mortality was 37% (52/142). We found no association between bacterial species and mortality. In multivariate analysis, a Charlson Comorbidity Index >3 was an independent predictor of mortality (HR 5.02, 95% CI 2.37-10.66, P < 0.001). In contrast, polymicrobial infection (HR 0.41, 95% CI 0.21-0.82, P < 0.05) was associated with lower mortality. There was no significant difference in mortality between patients receiving CM (n = 70) and those receiving a CCR (n = 72) (33% versus 40%, respectively), even when adjusted for IPW-PS (HR 1.11, 95% CI 0.63-1.96, P = 0.71). CONCLUSIONS: Real-life data confirm that cefiderocol is a promising option against carbapenem-resistant Gram-negative infections, even as monotherapy.

M100 ExaData: a data collection campaign on the CINECA's Marconi100 Tier-0 supercomputer.

Supercomputers are the most powerful computing machines available to society. They play a central role in economic, industrial, and societal development. While they are used by scientists, engineers, decision-makers, and data-analyst to computationally solve complex problems, supercomputers and their hosting datacenters are themselves complex power-hungry systems. Improving their efficiency, availability, and resiliency is vital and the subject of many research and engineering efforts. Still, a major roadblock hinders researchers: dearth of reliable data describing the behavior of production supercomputers. In this paper, we present the result of a ten-year-long project to design a monitoring framework (EXAMON) deployed at the Italian supercomputers at CINECA datacenter. We disclose the first holistic dataset of a tier-0 Top10 supercomputer. It includes the management, workload, facility, and infrastructure data of the Marconi100 supercomputer for two and half years of operation. The dataset (published via Zenodo) is the largest ever made public, with a size of 49.9TB before compression. We also provide open-source software modules to simplify access to the data and provide direct usage examples.

Evaluation of laboratory parameters in 1587 COVID-19 patients admitted to metropolitan hospital area of Bologna, Italy.

Since the outbreak of the 2019 pandemic coronavirus disease (COVID-19), great attention has been given to identifying the main clinical features of the disease. Identification of laboratory parameters able to classify patients based on their risk is mandatory to improve their clinical management. We retrospectively evaluated twenty-six laboratory tests measured in COVID-19 positive patients admitted to the hospital in March and April 2020 to find any correlation between their changes and the risk of death. We divided them into surviving and non-surviving patients. A total of 1587 patients were recruited, 854 males with median age of 71 (IQR 56-81) and 733 females with median age of 77 (IQR 61-87). On admission, death was found to be positively correlated with age (p=0.001), but not with sex (p=0.640) or with hospitalization in days (p=0.827). Brain natriuretic peptide (BNP), creatinine, C-reactive protein (CRP), INR, leukocyte count, lymphocyte count, neutrophil count, and procalcitonin (PCT) demonstrated a statistically significant difference between the two groups (p<0.001), suggesting their role as markers of disease severity; only lymphocyte count resulted as an independent risk factor for death.

Nosocomial outbreak by NDM-1-producing Klebsiella pneumoniae highly resistant to cefiderocol, Florence, Italy, August 2021 to June 2022.

A nosocomial outbreak by cefiderocol (FDC)-resistant NDM-1-producing Klebsiella pneumoniae (NDM-Kp) occurred in a large tertiary care hospital from August 2021-June 2022 in Florence, Italy, an area where NDM-Kp strains have become endemic. Retrospective analysis of NDM-Kp from cases observed in January 2021-June 2022 revealed that 21/52 were FDC-resistant. The outbreak was mostly sustained by clonal expansion of a mutant with inactivated cirA siderophore receptor gene, which exhibited high-level resistance to FDC (MIC ≥ 32 mg/L) and spread independently of FDC exposure.

Multicentric evaluation of the variability of digital morphology performances also respect to the reference methods by optical microscopy.

INTRODUCTION: Despite the important diagnostic role of peripheral blood morphology, cell classification is subjective. Automated image-processing systems (AIS) provide more accurate and objective morphological evaluation. The aims of this multicenter study were the evaluation of the intra and inter-laboratory variation between different AIS in cell pre-classification and after reclassification, compared with manual optical microscopy, the reference method. METHODS: Six peripheral blood samples were included in this study, for each sample, 70 May-Grunwald and Giemsa stained PB smears were prepared from each specimen and 10 slides were delivered to the seven laboratories involved. Smears were processed by both optical microscopy (OM) and AIS. In addition, the assessment times of both methods were recorded. RESULTS: Within-laboratory Reproducibility ranged between 4.76% and 153.78%; between-laboratory Precision ranged between 2.10% and 82.2%, while Total Imprecision ranged between 5.21% and 20.60%. The relative Bland Altman bias ranged between -0.01% and 20.60%. The mean of assessment times were 326 ± 110 s and 191 ± 68 s for AIS post reclassification and OM, respectively. CONCLUSIONS: AIS can be helpful when the number of cell counted are low and can give advantages in terms of efficiency, objectivity and time saving in the morphological analysis of blood cells. They can also help in the interpretation of some morphological features and can serve as learning and investigation tools.

Detection of a characteristic melting profile of a SARS-CoV-2 Kappa variant in Italy using the SARS-CoV-2 Variants ELITe MGB® Kit.

BACKGROUND: Although more than a year has passed since the start of the pandemic, SARS-CoV-2 infection still represents a major challenge for public health all over the world due to viral genome capability of gaining rapid mutations. Whole-genome sequencing (WGS) is the gold standard for variant identification, but it is time consuming and relatively expensive. For this reason, assays targeting multiple regions of the SARS-CoV-2 genome may be useful for a rapid traceability of either known or new variants, anyway, not all the manufacturers are able to sustain the rapid development of variants. OBJECTIVE: We tested forty nasopharyngeal swabs, resulted positive for the presence of SARS-CoV-2 RNA at low cycle threshold (CT < 25), with SARS-CoV-2 Variants ELITe MGB® Kit, which was designed to identify Nigerian variant, possible UK variant and South African or Brazilian variant. RESULTS: During the analysis, we noted an atypical melting curve, different from the other variants recognizable by the kit. The subsequent WGS reported this variant as Kappa, so we assess the possibility of "suspecting" the presence of a Kappa variant using SARS-CoV-2 Variants ELITe MGB® Kit. CONCLUSIONS: Rapid variant screening followed by WGS offers the opportunity to study mutation dynamics and quickly identify possible variants of interest (VOI) and/or variants of concern (VOC), which is crucial in virus spreading control. Furthermore, an accurate analysis of the melting peak could be useful to suspect the presence of new variants.

Interleukin-6 and Serum/Fecal Calprotectin as Useful Specific Markers for Monitoring Rheumatic Diseases: A Pilot Study.

OBJECTIVE: Some conventional laboratory tests are routinely used for the prediction of systemic autoimmune disease activity, such as the erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP); however, they can give false-negative results, pointing out the need to identify more specific markers. METHODS: We evaluated biomarkers in 21 Italian patients naïve to treatment with a diagnosis of autoimmune rheumatic disease according to the 2010 American College of Rheumatology/European League Against Rheumatism Classification Criteria for Rheumatoid Arthritis during 6 months of therapeutic treatments. RESULTS: We found a significant difference in interleukin-6 (IL-6), CRP, ESR, platelet count, and fecal calprotectin in diagnosed patients compared with healthy participants and a significant decrease in these values during follow-up, except for IL-6 and platelet count. CONCLUSION: We found that CRP, ESR, and fecal calprotectin seemed to be related to autoimmune rheumatic disorders and to be associated with therapy, whereas serum calprotectin and IL-6 did not seem to be associated with disease improvement after the start of treatment, along with leukocyte count and platelet count.

The role of laboratory medicine in managing biological risk: proposal for a simple and easy-to-follow protocol for occupational accidents at risk of bloodborne infection.

Bloodborne pathogens represent a major hazard for healthcare workers (HCWs) and exposure prevention still represents the primary strategy to reduce the risk of occupational bloodborne pathogen infections, such as hepatitis B (HBV), hepatitis C virus (HCV) and human immunodeficiency virus (HIV). Each healthcare organization should have simple and easy-to-apply operating procedures (OPs), quickly accessible to their personnel, including educational programmes, written protocols for prompt reporting and procedures for correct evaluation, counselling, treatment and follow-up of occupational exposure. From a careful review of literature data and international recommendations, in this study we summarize the recommendations to follow in the event of occupational exposure to HIV, HBV and HCV, also providing tables and a flowchart, that are simple to apply and could be a guide, especially in moments of apprehension caused by the occurrence of an occupational accident due to biohazard, in which important decisions must be taken and appropriate assessments carried out in the shortest possible time. Obviously, for this purpose, the people to be involved in the various processes must appear clearly in each OP, and the forms to be filled in must be easily and promptly accessible at all times.

Multicentric evaluation of analytical performances digital morphology with respect to the reference methods by manual optical microscopy.

AIMS: Optical microscopic (OM) evaluation of peripheral blood (PB) cells is still a crucial step of the laboratory haematological workflow. The morphological cell analysis is time-consuming and expensive and it requires skilled operator. To address these challenges, automated image-processing systems, as digital morphology (DM), were developed in the last few years. The aim of this multicentre study, performed according to international guidelines, is to verify the analytical performance of DM compared with manual OM, the reference method. METHODS: Four hundred and ninety PB samples were evaluated. For each sample, two May Grunwald-stained and Giemsa-stained smears were performed and the morphological evaluation of cells was analysed with both DM and OM. In addition, the assessment times of both methods were recorded. RESULTS: Comparison of DM versus OM methods was assessed with Passing-Bablok and Deming fit regression analysis: slopes ranged between 0.17 for atypical, reactive lymphocytes and plasma cells (LY(AT)) and 1.24 for basophils, and the intercepts ranged between -0.09 for blasts and 0.40 for LY(AT). The Bland-Altman bias ranged between -6.5% for eosinophils and 21.8% for meta-myemielocytes. The diagnostic agreement between the two methods was 0.98. The mean of assessment times were 150 s and 250 s for DM and OM, respectively. CONCLUSION: DM shows excellent performance. Approximately only 1.6% of PB smears need the OM revision, giving advantages in terms of efficiency, standardisation and assessment time of morphological analysis of the cells. The findings of this study may provide useful information regarding the use of DM to improve the haematological workflow.

Comparison between a novel molecular tool and conventional methods for diagnostic classification of bacterial vaginosis: is integration of the two approaches necessary for a better evaluation?

The etiological cause of bacterial vaginosis (BV) is the change of the vaginal ecosystem characterized by a decrease of lactobacilli and an increase of other germs, such as Gardnerella vaginalis and Atopobium vaginae. Molecular tools have revolutionized the diagnosis of these conditions. The aim of this paper was to compare results obtained from 158 vaginal swabs collected from women aged between 18 and 59 years old and subjected to microscopic evaluation (Nugent Score), culture and to the multiparametric molecular assay Vaginitis and Vaginosis Multiplex-Tandem (MT) PCR (AU27117) - Nuclear Laser Medicine. In 50 samples we also used matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for bacterial microbiome identification. Our results showed a moderate concordance between traditional and molecular methods for diagnosis of candidiasis and a lower concordance for BV and normal flora. MALDI TOF MS allowed us to discriminate more than 10 species of lactobacilli with a greater abundance of Lactobacillus gasseri, Lactobacillus paracasei spp. paracasei, Lactobacillus pentosus and Lactobacillus crispatus in BV and altered flora. This work underlined how the integration of different assays and metagenomics studies can greatly expand our current understanding of vaginal microbial diversity, providing more reliable diagnostic criteria for BV and its intermediate condition diagnosis.

A case of necrotizing fasciitis caused by Finegoldia magna in a patient with type 2 diabetes mellitus.

Diabetes mellitus is one of the serious conditions associated with necrotizing fasciitis, a severe bacterial skin infection that spreads quickly and is characterized by extensive necrosis of the deep and superficial fascia resulting in devascularization and necrosis of the associated tissues. In addition to debridement and aggressive surgery procedures, the effectiveness of therapy depends on choosing the appropriate antibacterial agents. Hence the key to successful management is an early and accurate diagnosis. We report a case of necrotizing fasciitis caused by Finegoldia magna in a patient with type 2 diabetes mellitus.

Phenotypic typing and epidemiological survey of antifungal resistance of Candida species detected in clinical samples of Italian patients in a 17 months' period.

INTRODUCTION: Yeast pathogens are emerging agents of nosocomial as well as community-acquired infections and their rapid and accurate identification is crucial for a better management of high-risk patients and for an adequate treatment. METHODS: We performed a retrospective review of 156 yeast isolates collected during a 17 months' period of regular clinical practice at the Microbiology Department of San Camillo Hospital in Treviso, Italy and analyzed by the traditional culture-based method combined with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). RESULTS: Out of all the samples collected MALDI-TOF MS was able to characterize with a MT score ≥1.7 (accurate result at species level) 12 different yeast and yeast-like species from 140 samples: Candida albicans (63.7%), Candida glabrata (13.6%), Saccharomyces cerevisiae (6.5%), Candida parapsilosis (5.7%), Candida tropicalis (2.1%), Candida pararugosa (2.1%), Candida guilliermondii (2.1%), Candida kefyr (1.4%), Candida lusitaniae (0.7%), Candida palmioleophila (0.7%), Geotrichum silvicola (0.7%), Rhodotorula mucilaginosa (0.7%). Susceptibility testing toward seven common antifungal agents showed a characteristic MIC distribution of C. albicans isolates for echinocandins: particularly we noticed that 72% and 46% of C. albicans showed an MIC value close to clinical breakpoint as defined by EUCAST, respectively for anidulafungin and micafungin. CONCLUSION: Accurate identification of microorganisms and the study of their antifungal susceptibility allow to understand the epidemiology of a particular area, permitting the choice of the most appropriate early antifungal treatment.

A case of invasive infection caused by a highly virulent strain of Klebsiella pneumoniae displaying hypermucoviscosity in a patient with hepatic involvement without liver abscess.

Klebsiella pneumoniae is an opportunistic nosocomial pathogen belonging to the Enterobacteriaceae family that is associated with a wide range of infections. In the 1980s a new hypervirulent (hypermucoviscous) variant of Klebsiella pneumoniae (hvKP) emerged in southeast Asia and is now increasingly spreading to Western countries due to an invasive syndrome. hvKP isolates can cause serious, life-threatening community-acquired infections in younger healthy hosts, including liver abscess, pneumonia, meningitis and endophthalmitis. We present a case of an 83-year-old man who was examined in the Medicine Department of San Camillo Hospital in Treviso for dehydration in gastroenteritis. Since he presented fever on admission, microbiological investigations were performed and empiric antibiotic therapy with cefotaxime was started. Blood analysis showed a high level of cholestasis indexes and transaminases. Blood cultures were found positive for K. pneumoniae that showed hypermucoviscosity. The hypermucoviscous phenotype of this K. pneumoniae isolate was easily identified by the "string test". Abdominal computed tomography and ultrasonography did not show presence of liver abscesses. After a few days of antibiotic therapy the patient's clinical condition improved. Correct microbiology identification of this kind of strain was essential for appropriate clinical management.

Identification of twenty-nine novel germline unclassified variants of BRCA1 and BRCA2 genes in 1400 Italian individuals.

OBJECTIVES: Breast and/or ovarian cancers are complex multifactorial diseases caused by interaction of both genetic and non-genetic factors and characterized by predisposition to inheritance. BRCA1 and BRCA2 genes are the most clinically involved with these kinds of cancer and the spectrum of variants affecting these genes is very wide. In fact, point variants, large or small insertions/deletions, genomic rearrangements can be found in these patients, although a large number of variants with uncertain biological and clinical significance continues to be identified. Next-generation sequencing (NGS) technology is actually the most powerful tool for the discovering of causative mutations and novel disease genes, moreover it allows to make a rapid diagnosis of genetic variants giving fast, inexpensive and detailed genetic information. MATERIAL AND METHODS: In this study, we report the screening of BRCA1 and BRCA2 genes on 1400 consecutive Caucasian patients with breast and/or ovarian cancer history or family risk, attending the oncogenetic ambulatory at the Foundation Policlinico Agostino Gemelli in Rome. RESULTS: We describe twenty-nine novel BRCA1 and BRCA2 variants detected in Italian individuals suffering from hereditary breast and ovarian cancer syndrome (HBOC). CONCLUSION: Data regarding novel variants can provide useful information not only at epidemiological but also at clinical level, allowing for the better managing of breast and ovarian cancer patients and their family members.

Energy Analysis of Decoders for Rakeness-Based Compressed Sensing of ECG Signals.

In recent years, compressed sensing (CS) has proved to be effective in lowering the power consumption of sensing nodes in biomedical signal processing devices. This is due to the fact the CS is capable of reducing the amount of data to be transmitted to ensure correct reconstruction of the acquired waveforms. Rakeness-based CS has been introduced to further reduce the amount of transmitted data by exploiting the uneven distribution to the sensed signal energy. Yet, so far no thorough analysis exists on the impact of its adoption on CS decoder performance. The latter point is of great importance, since body-area sensor network architectures may include intermediate gateway nodes that receive and reconstruct signals to provide local services before relaying data to a remote server. In this paper, we fill this gap by showing that rakeness-based design also improves reconstruction performance. We quantify these findings in the case of ECG signals and when a variety of reconstruction algorithms are used either in a low-power microcontroller or a heterogeneous mobile computing platform.

Efficient Sample Delay Calculation for 2-D and 3-D Ultrasound Imaging.

Ultrasound imaging is a reference medical diagnostic technique, thanks to its blend of versatility, effectiveness, and moderate cost. The core computation of all ultrasound imaging methods is based on simple formulae, except for those required to calculate acoustic propagation delays with high precision and throughput. Unfortunately, advanced three-dimensional (3-D) systems require the calculation or storage of billions of such delay values per frame, which is a challenge. In 2-D systems, this requirement can be four orders of magnitude lower, but efficient computation is still crucial in view of low-power implementations that can be battery-operated, enabling usage in numerous additional scenarios. In this paper, we explore two smart designs of the delay generation function. To quantify their hardware cost, we implement them on FPGA and study their footprint and performance. We evaluate how these architectures scale to different ultrasound applications, from a low-power 2-D system to a next-generation 3-D machine. When using numerical approximations, we demonstrate the ability to generate delay values with sufficient throughput to support 10 000-channel 3-D imaging at up to 30 fps while using 63% of a Virtex 7 FPGA, requiring 24 MB of external memory accessed at about 32 GB/s bandwidth. Alternatively, with similar FPGA occupation, we show an exact calculation method that reaches 24 fps on 1225-channel 3-D imaging and does not require external memory at all. Both designs can be scaled to use a negligible amount of resources for 2-D imaging in low-power applications and for ultrafast 2-D imaging at hundreds of frames per second.

Prevalence of intestinal parasitoses detected in Padua teaching hospital, Italy, March 2011 - February 2013.

The aim of this study was to evaluate the distribution of parasitic intestinal infections in patients attending Padua teaching hospital during a two-year period. Between 1st March 2011 and 28th February 2013, we examined stool specimens from 7341 patients (6127 Italians, 1214 non-Italians) for ova and parasites using microscopy, rapid enzyme immunoassays, culture techniques and molecular methods. Stools of 1080 patients (14.71%) were positive for parasites; a total of 1349 intestinal parasites were counted. Protozoa were detected in 1028/1080 patients (95.19%), while helminths were present in 80/1080 patients (7.41%). The protozoa most commonly detected were Blastocystis spp., Dientamoeba fragilis and Giardia duodenalis. Enterobius vermicularis was the helminth most frequently encountered. Of the 1080 infected patients, 227 (21.02%) had more than one parasite in their stool. To conclude, in Italy intestinal parasitoses must be unquestionably considered in differential diagnoses of gastrointestinal diseases. For this purpose, sound knowledge of epidemiology is essential.

Prevalence, molecular epidemiology and intra-hospital acquisition of Klebsiella pneumoniae strains producing carbapenemases in an Italian teaching hospital from January 2015 to September 2016.

OBJECTIVES: We described Klebsiella pneumoniae producing carbapenemase (CPKP) spread from 01/01/2015 to 13/09/16 in a tertiary level hospital. METHODS: The first positive surveillance rectal swab (SRS) or clinical sample (CS) collected in the medical department (MD), surgical department (SD) and intensive care department (ICD) were included in the study. A validated in-house Real-Time PCR method was used to detect carbapenemases; multilocus sequence typing (MLST) was used for further characterization of the strains. RESULTS: 21535 patients were included: 213 CPKP strains from surveillance rectal swab (SRS) and 98 from clinical samples (CS) were collected. The percentage of CPKP detected in SRS with respect to CS increased in the medical MD from 2015 to 2016 (p=0.01) and in ICD from 2012 to 2015 (p=0.0001), while it decreased in SD from 2014 to 2016 (p=0.003); 68.5% of the positive SRS had a previous negative SRS; CPKP was more frequently identified in CS than in SRS in MD. Twelve strains harboured more than one carbapenemase gene. Many other species harbouring a carbapenemase gene were collected. CONCLUSIONS: MDs need more inclusive surveillance criteria. The late detection of positive SRS underlined the risk of colonization during hospitalization.