Practical laboratory class to assess gene silencing using CRISPR interference (CRISPRi) technology in the archaeon Haloferax volcanii.

Perturbation of gene expression using RNA interference (RNAi) or CRISPR interference (CRISPRi) is a useful strategy to explore the function of essential genes. In the archaeon Haloferax volcanii, the CRISPR-Cas system has been adapted as a CRISPRi tool to silence the expression of specific genes. We developed a laboratory class (LC) to conceptualize gene silencing through inactivation of the H.

Single dose ivermectin for scabies pre-emptive therapy among healthcare workers in Careggi University Hospital, Florence, Italy.

Introduction: Scabies is a neglected disease that cause outbreaks in facilities such as hospitals and prisons. In Europe, treatment with 2 doses of ivermectin 200 mcg/kg, 7 days apart, is authorised and recommended especially in population mass treatment. We describe the management of a mass pre-emptive therapy of primary contacts of a confirmed case of classic scabies among health care workers.

Impact of rapid-antiretroviral therapy in a cohort of treatment-naïve migrants living with HIV in a high income setting.

Background: We evaluated the effect of rapid ART (RA) compared to delayed ART (DA) on viral load suppression (viral load <50 cp/mL) and loss to follow-up (LTFU) in a cohort of migrants living with HIV (MLWHs) in Italy.

Methods: Data were retrospectively gathered from MLWHs who began care at the Infectious and Tropical Diseases Unit of the Careggi University Hospital from January 2014 to December 2022. RA was defined as antiretrovirals prescribed within 7 days of HIV diagnosis.

Prospective observational pilot study of the T2Resistance panel in the T2Dx system for detection of resistance genes in bacterial bloodstream infections.

Unlabelled: Early initiation of antimicrobial therapy targeting resistant bacterial pathogens causing sepsis and bloodstream infections (BSIs) is critical for a successful outcome. The T2Resistance Panel (T2R) detects the following resistance genes within organisms that commonly cause BSIs directly from patient blood samples: , , , , , , , and A/C. We conducted a prospective study in two major medical centers for the detection of circulating resistance genes by T2R in patients with BSIs.

Latent Tuberculosis Infection and COVID-19: Analysis of a Cohort of Patients from Careggi University Hospital (Florence, Italy).

Data regarding the relationship between coronavirus disease (COVID-19) and active or latent tuberculosis (TB) are discordant. We conducted a retrospective study examining the impact of latent tuberculosis infection (LTBI) on the clinical progression of COVID-19 patients. We selected 213 patients admitted with COVID-19 in a tertiary-level Italian hospital (February-December 2020), who underwent a QuantiFERON-TB test (QFT) and/or chest radiological exam.

Orbital Infiltration in a Patient with Waldenström Macroglobulinemia: Need for Multidisciplinary Approach and Comparison with the Literature.

The use of specific inhibitory drugs of intracellular signalling pathways (such as Bruton-Kinase inhibitors) for the treatment of Waldenström's macroglobulinaemia (WM) is a recognised risk factor for . infections. The overlapping clinical manifestations of the two diseases may require the involvement of different medical specialities.

Characteristics of COVID-19 vaccinated and unvaccinated patients admitted to Careggi University Hospital, Florence, Italy.

More than 11.5 billion COVID-19 vaccine doses have been administered around the world. Although vaccine effectiveness for severe infections is reported to be 89.

Safety and Efficacy of Outpatient Treatments for COVID-19: Real-Life Data from a Regionwide Cohort of High-Risk Patients in Tuscany, Italy (the FEDERATE Cohort).

Early COVID-19 treatments can prevent progression to severe disease. However, real-life data are still limited, and studies are warranted to monitor the efficacy and tolerability of these drugs. We retrospectively enrolled outpatients receiving early treatment for COVID-19 in 11 infectious diseases units in the Tuscany region of Italy between 1 January and 31 March 2022, when Omicron sublineages BA.

The C-terminal region of phytoene synthase is a key element to control carotenoid biosynthesis in the haloarchaeon Haloferax volcanii.

Phytoene synthase (PSY) converts two molecules of geranyl-geranyl diphosphate to phytoene, the key regulatory step in carotenogenesis. However, post-translational mechanisms that control PSY expression are scarcely understood. Carotenoid biosynthesis (mainly bacterioruberin) is a distinctive feature of haloarchaea thriving in hypersaline environments.

Proteolytic Activity Assays in Haloarchaea.

Extreme halophilic archaea (haloarchaea) have adapted their physiology and biomolecules to thrive in saline environments (>2 M NaCl). Many haloarchaea produce extracellular hydrolases (including proteases) with potential biotechnological applications, which require unusual high salt concentrations to attain their function and maintain their stability. These conditions restrict many of the standard methods used to study these enzymes such as activity determination and/or protein purification.

Proteome Turnover Analysis in Haloferax volcanii by a Heavy Isotope Multilabeling Approach.

The cellular protein repertoire is highly dynamic and responsive to internal or external stimuli. Its changes are largely the consequence of the combination of protein synthesis and degradation, referred collectively as protein turnover. Different proteomics techniques have been developed to determine the whole proteome turnover of a cell, but very few have been applied to archaea.

Accuracy and Impact on Patient Management of New Tools for Diagnosis of Sepsis: Experience with the T2 Magnetic Resonance Bacteria Panel.

The rapid and accurate identification of pathogens responsible for sepsis is essential for prompt and effective antimicrobial therapy. Molecular technologies have been developed to detect the most common causative agents, with high sensitivity and short time to result (TTR). T2 Bacteria Panel (T2), based on a combination of PCR and T2 magnetic resonance, can identify directly in blood samples , , , , , and pathogens.

Direct Testing for KPC-Mediated Carbapenem Resistance from Blood Samples Using a T2 Magnetic Resonance Based Assay.

Molecular-based carbapenem resistance testing in Gram-negative bacterial bloodstream infections (BSIs) is currently limited because of the reliance on positive blood culture (BC) samples. The T2Resistance™ panel may now allow the detection of carbapenemase- and other β-lactamase encoding genes directly from blood samples. We detected carbapenem resistance genes in 11 (84.

Evaluation of Lumipulse® G SARS-CoV-2 antigen assay automated test for detecting SARS-CoV-2 nucleocapsid protein (NP) in nasopharyngeal swabs for community and population screening.

Objectives: To compare the Lumipulse® SARS-CoV-2 antigen test with the gold standard real-time reverse transcription-polymerase chain reaction (RT-PCR) for diagnosis of SARS-CoV-2 infection and to evaluate its role in screening programs.

Methods: Lumipulse® SARS-CoV-2 antigen assay was compared with the gold standard RT-PCR test in a selected cohort of 226 subjects with suspected SARS-CoV-2 infection, and its accuracy was evaluated. Subsequently, the test was administered to a real-life screening cohort of 1738 cases.

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%.

Accelerate Pheno™ system in sepsis by Gram-negative pathogens: four months of hospital experience.

This study reports our experience with the Accelerate PhenoTM system (ACC) to guide management of patients with sepsis by Gram-negative pathogens. A diagnostic workflow, based on pathogen and resistance genes detection or ACC testing, was applied to 33 patients. Clinical and microbiological data were recorded, and analysis of broad-spectrum agents sparing was performed.

Measurement and prediction of antimicrobial resistance in bloodstream infections by ESKAPE pathogens and Escherichia coli.

Objectives: This study aimed to evaluate a cumulative antimicrobial resistance index (ARI) as a possible key outcome measure of antimicrobial stewardship programmes (ASPs) and a tool to predict the antimicrobial resistance (AMR) trend.

Methods: Antimicrobial susceptibility for Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Escherichia coli (ESKAPEEc) pathogens recovered from blood cultures during a 5-year period (2014-2018) was analysed to obtain a cumulative ARI.

Laboratory automation reduces time to report of positive blood cultures and improves management of patients with bloodstream infection.

The impact on time to results (TTR) and clinical decisions was evaluated for mono-microbial positive blood cultures (BC) processed using the BD Kiestra Work Cell Automation (WCA) system. Positive BC were processed by the WCA system by full-automatic subculture on solid media and digital imaging after 8 h of incubation (8-h method) followed by identification (ID) and antimicrobial susceptibility testing (AST). To evaluate the accuracy of the 8-h method, ID and AST from 8-h and overnight incubated colonies were compared for the same organisms.

Proteomic Study of the Exponential-Stationary Growth Phase Transition in the Haloarchaea Natrialba magadii and Haloferax volcanii.

The dynamic changes that take place along the phases of microbial growth (lag, exponential, stationary, and death) have been widely studied in bacteria at the molecular and cellular levels, but little is known for archaea. In this study, a high-throughput approach was used to analyze and compare the proteomes of two haloarchaea during exponential and stationary growth: the neutrophilic Haloferax volcanii and the alkaliphilic Natrialba magadii. Almost 2000 proteins were identified in each species (≈50% of the predicted proteome).

Functional roles of C-terminal extension (CTE) of salt-dependent peptidase activity of the Natrialba magadii extracellular protease (NEP).

Nep (Natrialba magadii extracellular protease) is a halolysin-like peptidase secreted by the haloalkaliphilic archaeon Natrialba magadii. Many extracellular proteases have been characterized from archaea to bacteria as adapted to hypersaline environments retaining function and stability until 4.0M NaCl.