531 research outputs found

    Exploiting phages‚Äďbacteria co-evolution to overcome phage resistance and to ease the selection of new phage particles

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    Antibiotic resistance is one of the major threats of modern medicine. The limited conventional treatment options against multi-drug resistant bacteria, as well as the paucity of new effective antibiotics, is leading to the need of developing novel strategies, such as the therapeutic use of bacteriophages. However, it is necessary to combine a variety of phages to avoid the therapeutic inefficacy due to the possible resistance emergence to single particles. Here, we describe a novel bacteriophage, named GP-7, which was isolated from hospital wastewaters collected in Tuscany following standard methods. GP-7 was obtained using the K. pneumoniae BO-FR-1 strain, a member of sequence type 258 resistant to the infection of the previously characterized phage phiBO1E. Host spectrum was determined by spot-test and efficiency of plating techniques. Physiological features, including stability to pH and temperature changes was assessed. The kinetic of infection was defined by the one-step growth curve method. Phage genome was characterized by a next generation sequencing approach and bioinformatics analysis. GP-7 is myovirus with a strictly lytic cycle and exhibiting a narrow host spectrum restricted to its indicator strain and other K. pneumoniae phage-resistant mutants. The phage maintains its full infectivity between pH 4 and 11, and it is also stable after 1 h at 60¬į C. The infective cycle is characterized by a latency period of 25 min and a burst size of 45 particles. Results from this study could be of interest for the rationale design of phage cocktails to be used for therapeutic applications

    Ten golden rules for optimal antibiotic use in hospital settings: the WARNING call to action

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    Antibiotics are recognized widely for their benefits when used appropriately. However, they are often used inappropriately despite the importance of responsible use within good clinical practice. Effective antibiotic treatment is an essential component of universal healthcare, and it is a global responsibility to ensure appropriate use. Currently, pharmaceutical companies have little incentive to develop new antibiotics due to scientific, regulatory, and financial barriers, further emphasizing the importance of appropriate antibiotic use. To address this issue, the Global Alliance for Infections in Surgery established an international multidisciplinary task force of 295 experts from 115 countries with different backgrounds. The task force developed a position statement called WARNING (Worldwide Antimicrobial Resistance National/International Network Group) aimed at raising awareness of antimicrobial resistance and improving antibiotic prescribing practices worldwide. The statement outlined is 10 axioms, or ‚Äúgolden rules,‚ÄĚ for the appropriate use of antibiotics that all healthcare workers should consistently adhere in clinical practice

    Ten golden rules for optimal antibiotic use in hospital settings : the WARNING call to action

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    Abstract: Antibiotics are recognized widely for their benefits when used appropriately. However, they are often used inappropriately despite the importance of responsible use within good clinical practice. Effective antibiotic treatment is an essential component of universal healthcare, and it is a global responsibility to ensure appropriate use. Currently, pharmaceutical companies have little incentive to develop new antibiotics due to scientific, regulatory, and financial barriers, further emphasizing the importance of appropriate antibiotic use. To address this issue, the Global Alliance for Infections in Surgery established an international multidisciplinary task force of 295 experts from 115 countries with different backgrounds. The task force developed a position statement called WARNING (Worldwide Antimicrobial Resistance National/International Network Group) aimed at raising awareness of antimicrobial resistance and improving antibiotic prescribing practices worldwide. The statement outlined is 10 axioms, or "golden rules," for the appropriate use of antibiotics that all healthcare workers should consistently adhere in clinical practice

    Bacterial Species from Vaginal Microbiota Differently Affect the Production of the E6 and E7 Oncoproteins and of p53 and p-Rb Oncosuppressors in HPV16-Infected Cells

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    Vaginal dysbiosis is characterized by a decrease in the relative abundance of Lactobacillus species in favor of other species. This condition facilitates infections by sexually transmitted pathogens including high risk (HR)-human papilloma viruses (HPVs) involved in the development of cervical cancer. Some vaginal dysbiosis bacteria contribute to the neoplastic progression by inducing chronic inflammation and directly activating molecular pathways involved in carcinogenesis. In this study, SiHa cells, an HPV-16-transformed epithelial cell line, were exposed to different representative vaginal microbial communities. The expression of the HPV oncogenes E6 and E7 and the production of relative oncoproteins was evaluated. The results showed that Lactobacillus crispatus and Lactobacillus gasseri modulated the basal expression of the E6 and E7 genes of SiHa cells and the production of the E6 and E7 oncoproteins. Vaginal dysbiosis bacteria had contrasting effects on E6/E7 gene expression and protein production. The expression of the E6 and E7 genes and the production of the relative oncoproteins was increased by strains of Gardnerella vaginalis and, to a lesser extent, by Megasphaera micronuciformis. In contrast, Prevotella bivia decreased the expression of oncogenes and the production of the E7 protein. A decreased amount of p53 and pRb was found in the cultures of SiHa cells with M. micronuciformis, and accordingly, in the same cultures, a higher percentage of cells progressed to the S-phase of the cell cycle compared to the untreated or Lactobacillus-stimulated cultures. These data confirm that L. crispatus represents the most protective component of the vaginal microbiota against neoplastic progression of HR-HPV infected cells, while M. micronuciformis and, to a lesser extent, G. vaginalis may directly interfere in the oncogenic process, inducing or maintaining the production of viral oncoproteins

    Wastewater surveillance of SARS-CoV-2 variants in October‚ÄďNovember 2022 in Italy: detection of XBB.1, BA.2.75 and rapid spread of the BQ.1 lineage

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    This study adds insight regarding the occurrence and spread of SARS-CoV-2 Variants of Concern (VOCs) and Variants of Interest (VOIs) in Italy in October and November 2022, by testing urban wastewater collected throughout the country. A total of 332 wastewater samples were collected from 20 Italian Regions/Autonomous Provinces (APs) within the framework of national SARS-CoV-2 environmental surveillance. Of these, 164 were collected in the first week of October and 168 in the first week of November. A ‚ąľ1600 bp fragment of the spike protein was sequenced by Sanger (for individual samples) and long-read nanopore sequencing (for pooled Region/AP samples). In October, mutations characteristic of Omicron BA.4/BA.5 were detected in the vast majority (91 %) of the samples amplified by Sanger sequencing. A fraction of these sequences (9 %) also displayed the R346T mutation. Despite the low prevalence documented in clinical cases at the time of sampling, amino acid substitutions characteristic of sublineages BQ.1 or BQ.1.1 were detected in 5 % of sequenced samples from four Regions/APs. A significantly higher variability of sequences and variants was documented in November 2022, when the rate of sequences harbouring mutations of lineages BQ.1 and BQ1.1 increased to 43 %, and the number of Regions/APs positive for the new Omicron subvariant more than tripled (n = 13) compared to October. Moreover, an increase in the number of sequences with the mutation package BA.4/BA.5 + R346T (18 %), as well as the detection of variants never observed before in wastewater in Italy, such as BA.2.75 and XBB.1 (the latter in a Region where no clinical cases associated with this variant had ever been documented) was recorded. The results suggest that, as predicted by the ECDC, BQ.1/BQ.1.1 is rapidly becoming dominant in late 2022. Environmental surveillance proves to be a powerful tool for tracking the spread of SARS-CoV-2 variants/subvariants in the population

    Validation of Two Commercial Multiplex Real-Time PCR Assays for Detection of SARS-CoV-2 in Stool Donors for Fecal Microbiota Transplantation

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    Recurrent infection by Clostridioides difficile has recently been treated by fecal microbiota transplantation (FMT). As viable SARS-CoV-2 was recovered from stool of asymptomatic individuals, the FMT procedure could be a potential risk of SARS-CoV-2 transmission, thus underlying the need to reliably detect SARS-CoV-2 in stool. Here, we performed a multicentric study to explore performances of two commercially available assays for detection of SARS-CoV-2 RNA in stool of potential FMT donors. In three hospitals, 180 stool samples were spiked with serial 10-fold dilutions of a SARS-CoV-2 inactivated lysate to evaluate the Seegene Allplex‚ĄĘ SARS-CoV-2 (SC2) and SARS-CoV-2/FluA/FluB/RSV (SC2FABR) Assays for the detection of viral RNA in stool of FMT donors. The results revealed that both assays detected down to 2 TCID50/mL with comparable limit of detection values, SC2 showing more consistent target positivity rate than SC2FABR. Beyond high amplification efficiency, correlation between CT values and log concentrations of inactivated viral lysates showed R2 values ranging from 0.88 to 0.90 and from 0.87 to 0.91 for the SC2 and SC2FABR assay, respectively. The present results demonstrate that both methods are highly reproducible, sensitive, and accurate for SARS-CoV-2 RNA detection in stool, suggesting a potential use in FMT-donor screening

    Co-circulation of SARS-CoV-2 Alpha and Gamma variants in Italy, February and March 2021

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    97Background: Several SARS-CoV-2 variants of concern (VOC) have emerged through 2020 and 2021. There is need for tools to estimate the relative transmissibility of emerging variants of SARS-CoV-2 with respect to circulating strains. Aim: We aimed to assess the prevalence of co-circulating VOC in Italy and estimate their relative transmissibility. Methods: We conducted two genomic surveillance surveys on 18 February and 18 March 2021 across the whole Italian territory covering 3,243 clinical samples and developed a mathematical model that describes the dynamics of co-circulating strains. Results: The Alpha variant was already dominant on 18 February in a majority of regions/autonomous provinces (national prevalence: 54%) and almost completely replaced historical lineages by 18 March (dominant across Italy, national prevalence: 86%). We found a substantial proportion of the Gamma variant on 18 February, almost exclusively in central Italy (prevalence: 19%), which remained similar on 18 March. Nationally, the mean relative transmissibility of Alpha ranged at 1.55‚Äď1.57 times the level of historical lineages (95% CrI: 1.45‚Äď1.66). The relative transmissibility of Gamma varied according to the assumed degree of cross-protection from infection with other lineages and ranged from 1.12 (95% CrI: 1.03‚Äď1.23) with complete immune evasion to 1.39 (95% CrI: 1.26‚Äď1.56) for complete cross-protection. Conclusion: We assessed the relative advantage of competing viral strains, using a mathematical model assuming different degrees of cross-protection. We found substantial co-circulation of Alpha and Gamma in Italy. Gamma was not able to outcompete Alpha, probably because of its lower transmissibility.nonenoneStefanelli P.; Trentini F.; Guzzetta G.; Marziano V.; Mammone A.; Schepisi M.S.; Poletti P.; Grane C.M.; Manica M.; del Manso M.; Andrianou X.; Ajelli M.; Rezza G.; Brusaferro S.; Merler S.; Di Martino A.; Ambrosio L.; Lo Presti A.; Fiore S.; Fabiani C.; Benedetti E.; Di Mario G.; Facchini M.; Puzelli S.; Calzoletti L.; Fontana S.; Venturi G.; Fortuna C.; Marsili G.; Amendola A.; Stuppia L.; Savini G.; Picerno A.; Lopizzo T.; Dell'Edera D.; Minchella P.; Greco F.; Viglietto G.; Atripaldi L.; Limone A.; D'Agaro P.; Licastro D.; Pongolini S.; Sambri V.; Dirani G.; Zannoli S.; Affanni P.; Colucci M.E.; Capobianchi M.R.; Icardi G.; Bruzzone B.; Lillo F.; Orsi A.; Pariani E.; Baldanti F.; Molecolare U.V.; Gismondo M.R.; Maggi F.; Caruso A.; Ceriotti F.; Boniotti M.B.; Barbieri I.; Bagnarelli P.; Menzo S.; Garofalo S.; Scutella M.; Pagani E.; Collini L.; Ghisetti V.; Brossa S.; Ru G.; Bozzetta E.; Chironna M.; Parisi A.; Rubino S.; Serra C.; Piras G.; Coghe F.; Vitale F.; Tramuto F.; Scalia G.; Palermo C.I.; Mancuso G.; Pollicino T.; Di Gaudio F.; Vullo S.; Reale S.; Cusi M.G.; Rossolini G.M.; Pistello M.; Mencacci A.; Camilloni B.; Severini S.; Di Benedetto M.; Terregino C.; Monne I.; Biscaro V.Stefanelli, P.; Trentini, F.; Guzzetta, G.; Marziano, V.; Mammone, A.; Schepisi, M. S.; Poletti, P.; Grane, C. M.; Manica, M.; del Manso, M.; Andrianou, X.; Ajelli, M.; Rezza, G.; Brusaferro, S.; Merler, S.; Di Martino, A.; Ambrosio, L.; Lo Presti, A.; Fiore, S.; Fabiani, C.; Benedetti, E.; Di Mario, G.; Facchini, M.; Puzelli, S.; Calzoletti, L.; Fontana, S.; Venturi, G.; Fortuna, C.; Marsili, G.; Amendola, A.; Stuppia, L.; Savini, G.; Picerno, A.; Lopizzo, T.; Dell'Edera, D.; Minchella, P.; Greco, F.; Viglietto, G.; Atripaldi, L.; Limone, A.; D'Agaro, P.; Licastro, D.; Pongolini, S.; Sambri, V.; Dirani, G.; Zannoli, S.; Affanni, P.; Colucci, M. E.; Capobianchi, M. R.; Icardi, G.; Bruzzone, B.; Lillo, F.; Orsi, A.; Pariani, E.; Baldanti, F.; Molecolare, U. V.; Gismondo, M. R.; Maggi, F.; Caruso, A.; Ceriotti, F.; Boniotti, M. B.; Barbieri, I.; Bagnarelli, P.; Menzo, S.; Garofalo, S.; Scutella, M.; Pagani, E.; Collini, L.; Ghisetti, V.; Brossa, S.; Ru, G.; Bozzetta, E.; Chironna, M.; Parisi, A.; Rubino, S.; Serra, C.; Piras, G.; Coghe, F.; Vitale, F.; Tramuto, F.; Scalia, G.; Palermo, C. I.; Mancuso, G.; Pollicino, T.; Di Gaudio, F.; Vullo, S.; Reale, S.; Cusi, M. G.; Rossolini, G. M.; Pistello, M.; Mencacci, A.; Camilloni, B.; Severini, S.; Di Benedetto, M.; Terregino, C.; Monne, I.; Biscaro, V

    Clinical consequences of very major errors with semi-automated testing systems for antimicrobial susceptibility of carbapenem-resistant Enterobacterales

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    none21noObjectives: In this study we investigated the rate of susceptibility testing discrepancies between semi-automated and reference systems with carbapenem-resistant Enterobacterales (CRE) and the impact of alleged errors by semi-automated systems on guiding targeted therapy for CRE bloodstream infection (BSI). Methods: This was a multicentre, retrospective study enrolling patients with monomicrobial BSI caused by CRE from January 2013 to December 2016. Nonduplicate isolates from index blood cultures tested locally with semi-automated systems were centralized at a referral laboratory and retested with a reference broth microdilution or agar dilution method. Results: We enrolled 366 patients with CRE-BSI; 220 (60%) were male, and the median age was 67 years (interquartile range, 54‚Äď76 years). When compared with the results of the reference methods, those of the semi-automated systems exhibited variable rates of very major errors (VMEs; i.e. false susceptibilities) and major errors (MEs; i.e. false resistances). The highest rates of VMEs were observed with fosfomycin (14%) and colistin (13.9%), and the highest rates of MEs were observed with gentamicin (21%), fosfomycin (7.7%), and tigecycline (34%). Overall, VMEs and MEs led clinicians to prescribe or confirm ineffective therapy in 25 of 341 patients (7%). Receipt of ineffective therapy supported by a misleading susceptibility test was associated with higher 30-day mortality rates by Kaplan‚ÄďMeier survival curves rates compared with receipt of active therapy (56% vs. 26%; p = 0.002), and the difference was confirmed after adjustment for confounders in a Cox regression model (adjusted hazard ratio: 2.91; 95% CI, 1.62‚Äď5.22; p < 0.001). Discussion: MEs and VMEs were relatively common with semi-automated susceptibility testing systems. VMEs were associated with inappropriate use of antibiotics and poorer outcomes.openBartoletti M.; Antonelli A.; Bussini L.; Corcione S.; Giacobbe D.R.; Marconi L.; Pascale R.; Dettori S.; Shbaklo N.; Ambretti S.; Gaibani P.; Giani T.; Coppi M.; Bassetti M.; De Rosa F.G.; Marchese A.; Cavallo R.; Lewis R.; Rossolini G.M.; Viale P.; Giannella M.Bartoletti M.; Antonelli A.; Bussini L.; Corcione S.; Giacobbe D.R.; Marconi L.; Pascale R.; Dettori S.; Shbaklo N.; Ambretti S.; Gaibani P.; Giani T.; Coppi M.; Bassetti M.; De Rosa F.G.; Marchese A.; Cavallo R.; Lewis R.; Rossolini G.M.; Viale P.; Giannella M

    Effects of viremia and CD4 recovery on gut \u201cmicrobiome-immunity\u201d axis in treatment-na\uefve HIV-1-infected patients undergoing antiretroviral therapy

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    BACKGROUND Human immunodeficiency virus type 1 (HIV-1) infection is characterized by persistent systemic inflammation and immune activation, even in patients receiving effective antiretroviral therapy (ART). Converging data from many cross-sectional studies suggest that gut microbiota (GM) changes can occur throughout including human immunodeficiency virus (HIV) infection, treated by ART; however, the results are contrasting. For the first time, we compared the fecal microbial composition, serum and fecal microbial metabolites, and serum cytokine profile of treatment-na\uefve patients before starting ART and after reaching virological suppression, after 24 wk of ART therapy. In addition, we compared the microbiota composition, microbial metabolites, and cytokine profile of patients with CD4/CD8 ratio < 1 (immunological non-responders [INRs]) and CD4/CD8 > 1 (immunological responders [IRs]), after 24 wk of ART therapy. AIM To compare for the first time the fecal microbial composition, serum and fecal microbial metabolites, and serum cytokine profile of treatment-na\uefve patients before starting ART and after reaching virological suppression (HIV RNA < 50 copies/mL) after 24 wk of ART. METHODS We enrolled 12 treatment-na\uefve HIV-infected patients receiving ART (mainly based on integrase inhibitors). Fecal microbiota composition was assessed through next generation sequencing. In addition, a comprehensive analysis of a blood broad-spectrum cytokine panel was performed through a multiplex approach. At the same time, serum free fatty acid (FFA) and fecal short chain fatty acid levels were obtained through gas chromatography-mass spectrometry. RESULTS We first compared microbiota signatures, FFA levels, and cytokine profile before starting ART and after reaching virological suppression. Modest alterations were observed in microbiota composition, in particular in the viral suppression condition, we detected an increase of Ruminococcus and Succinivibrio and a decrease of Intestinibacter. Moreover, in the same condition, we also observed augmented levels of serum propionic and butyric acids. Contemporarily, a reduction of serum IP-10 and an increase of IL-8 levels were detected in the viral suppression condition. In addition, the same components were compared between IRs and INRs. Concerning the microflora population, we detected a reduction of Faecalibacterium and an increase of Alistipes in INRs. Simultaneously, fecal isobutyric, isovaleric, and 2-methylbutyric acids were also increased in INRs. CONCLUSION Our results provided an additional perspective about the impact of HIV infection, ART, and immune recovery on the \u201cmicrobiome-immunity axis\u201d at the metabolism level. These factors can act as indicators of the active processes occurring in the gastrointestinal tract. Individuals with HIV-1 infection, before ART and after reaching virological suppression with 24 wk of ART, displayed a microbiota with unchanged overall bacterial diversity; moreover, their systemic inflammatory status seems not to be completely restored. In addition, we confirmed the role of the GM metabolites in immune reconstitution
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