Prevalence and determinants of resistance mutations in HIV-1-infected patients exposed to integrase inhibitors in a large Italian cohort.

OBJECTIVES: The aim of the study was to analyse the prevalence of integrase resistance mutations in integrase strand transfer inhibitor (INSTI)-experienced HIV-1-infected patients and its predictors. METHODS: We selected HIV-1 integrase sequences from the Antiviral Response Cohort Analysis (ARCA) database, derived from INSTI-experienced patients between 2008 and 2017. Differences in the prevalence of resistance to raltegravir (RAL), elvitegravir (EVG) and dolutegravir (DTG) were assessed by χ2 test and predictors of resistance were analysed by logistic regression. RESULTS: We included 462 genotypes from INSTI-exposed individuals: 356 'INSTI-failing' patients and 106 'previously INSTI-exposed' patients (obtained a median of 42 weeks after INSTI discontinuation [interquartile range (IQR) 17-110 weeks]). Overall, at least low-level resistance (LLR) to any INSTI (Stanford 8.5 algorithm) was detected in 198 (42.9%) cases. The most frequent INSTI resistance mutation was N155H, followed by Q148H/K/R, G140A/C/S, E138A/K/T and Y143C/H/R. Y143R and E138A were more prevalent in viral subtype B versus non-B [5.2 versus 1.5%, respectively (P = 0.04), and 3.1 versus 0%, respectively (P = 0.02)]. Overall, the Q148H/K/R plus G140A/C/S and/or E138A/K/T pattern, defining an intermediate level of resistance to DTG, was detected in 70 (15%) cases. Independent predictors of at least LLR to any INSTI were current use versus past use of INSTIs, a lower genotypic sensitivity score (GSS) for contemporary antiretroviral drugs used, and having an integrase sequence obtained in calendar year 2016 as compared to 2008-2009. CONCLUSIONS: The results support integrase resistance testing in INSTI-experienced patients. Emergence of INSTI resistance is facilitated by the reduced genetic barrier of the regimen as a consequence of resistance to companion drugs. However, INSTI resistance may become undetectable by standard population sequencing upon INSTI discontinuation.

Impact of transmitted HIV-1 drug resistance on the efficacy of first-line antiretroviral therapy with two nucleos(t)ide reverse transcriptase inhibitors plus an integrase inhibitor or a protease inhibitor.

Objectives: To examine the impact of transmitted drug resistance (TDR) on response to first-line regimens with integrase strand transfer inhibitors (INSTIs) or boosted protease inhibitors (bPIs). Methods: From an Italian observational database (ARCA) we selected HIV-1-infected drug-naive patients starting two NRTIs and either an INSTI or a bPI, with an available pre-ART resistance genotype. The endpoint was virological failure (VF; plasma HIV-1 RNA >200 copies/mL after week 24). WHO surveillance drug resistance mutations and the Stanford algorithm were used to classify patients into three resistance categories: no TDR (A), TDR but fully-active ART prescribed (B), TDR and at least low-level resistance to one or more prescribed drug (C). Results: We included 1365 patients with a median follow-up of 96 weeks (IQR 54-110): 1205 (88.3%) starting bPI and 160 (11.7%) INSTI. Prevalence of TDR was 6.1%, 12.5%, 2.6% and 0% for NRTI, NNRTI, bPI and INSTI, respectively. Cumulative Kaplan-Meier estimates for VF at 48 weeks were 11% (95% CI 10.1%-11.9%) for the bPI group and 7.7% (95% CI 5.4%-10%) for the INSTI group. In the INSTI group, cumulative estimates for VF at 48 weeks were 6% (95% CI 4%-8%) in resistance category A, 5% (95% CI 1%-10%) in B and 50% (95% CI 30%-70%) in C (P < 0.001). Resistance category C [versus A, adjusted hazard ratio (aHR) 12.6, 95% CI 3.2-49.8, P < 0.001] and nadir CD4 (+100 cells/mm3, aHR 0.6, 95% CI 0.4-0.9, P = 0.03) predicted VF. In the bPI group, VF rates were not influenced by baseline resistance. Conclusions: Our data support the need for NRTI resistance genotyping in patients starting an INSTI-based first-line ART.

Soft X-Ray Second Harmonic Generation as an Interfacial Probe.

Nonlinear optical processes at soft x-ray wavelengths have remained largely unexplored due to the lack of available light sources with the requisite intensity and coherence. Here we report the observation of soft x-ray second harmonic generation near the carbon K edge (∼284 eV) in graphite thin films generated by high intensity, coherent soft x-ray pulses at the FERMI free electron laser. Our experimental results and accompanying first-principles theoretical analysis highlight the effect of resonant enhancement above the carbon K edge and show the technique to be interfacially sensitive in a centrosymmetric sample with second harmonic intensity arising primarily from the first atomic layer at the open surface. This technique and the associated theoretical framework demonstrate the ability to selectively probe interfaces, including those that are buried, with elemental specificity, providing a new tool for a range of scientific problems.

Passive Linearization of the Magnetic Bunch Compression Using Self-Induced Fields.

In linac-driven free-electron lasers, colliders, and energy recovery linacs, a common way to compress the electron bunch to kiloampere level is based upon the implementation of a magnetic dispersive element that converts particle energy deviation into a path-length difference. Nonlinearities of such a process are usually compensated by enabling a high harmonic rf structure properly tuned in amplitude and phase. This approach is however not straightforward, e.g., in C-band and X-band linacs. In this Letter we demonstrate that the longitudinal self-induced field excited by the electron beam itself is able to linearize the compression process without any use of high harmonic rf structure. The method is implemented at the FERMI linac, with the resulting high quality beam used to drive the seeded free-electron laser during user experiments.

Time-Resolved Measurement of Interatomic Coulombic Decay Induced by Two-Photon Double Excitation of Ne_{2}.

The hitherto unexplored two-photon doubly excited states [Ne^{*}(2p^{-1}3s)]_{2} were experimentally identified using the seeded, fully coherent, intense extreme ultraviolet free-electron laser FERMI. These states undergo ultrafast interatomic Coulombic decay (ICD), which predominantly produces singly ionized dimers. In order to obtain the rate of ICD, the resulting yield of Ne_{2}^{+} ions was recorded as a function of delay between the extreme ultraviolet pump and UV probe laser pulses. The extracted lifetimes of the long-lived doubly excited states, 390(-130/+450) fs, and of the short-lived ones, less than 150 fs, are in good agreement with ab initio quantum mechanical calculations.

Slow Interatomic Coulombic Decay of Multiply Excited Neon Clusters.

Ne clusters (∼5000 atoms) were resonantly excited (2p→3s) by intense free electron laser (FEL) radiation at FERMI. Such multiply excited clusters can decay nonradiatively via energy exchange between at least two neighboring excited atoms. Benefiting from the precise tunability and narrow bandwidth of seeded FEL radiation, specific sites of the Ne clusters were probed. We found that the relaxation of cluster surface atoms proceeds via a sequence of interatomic or intermolecular Coulombic decay (ICD) processes while ICD of bulk atoms is additionally affected by the surrounding excited medium via inelastic electron scattering. For both cases, cluster excitations relax to atomic states prior to ICD, showing that this kind of ICD is rather slow (picosecond range). Controlling the average number of excitations per cluster via the FEL intensity allows a coarse tuning of the ICD rate.

The FERMI free-electron lasers.

FERMI is a seeded free-electron laser (FEL) facility located at the Elettra laboratory in Trieste, Italy, and is now in user operation with its first FEL line, FEL-1, covering the wavelength range between 100 and 20 nm. The second FEL line, FEL-2, a high-gain harmonic generation double-stage cascade covering the wavelength range 20-4 nm, has also completed commissioning and the first user call has been recently opened. An overview of the typical operating modes of the facility is presented.

Experimental demonstration of enhanced self-amplified spontaneous emission by an optical klystron.

We report the first experimental evidence of enhancement of self-amplified spontaneous emission, due to the use of an optical klystron. In this free-electron laser scheme, a relativistic electron beam passes through two undulators, separated by a dispersive section. The latter converts the electron-beam energy modulation produced in the first undulator in density modulation, thus enhancing the free-electron laser gain. The experiment has been carried out at the FERMI facility in Trieste. Powerful radiation has been produced in the extreme ultraviolet range, with an intensity a few orders of magnitude larger than in pure self-amplified spontaneous emission mode. Data have been benchmarked with an existing theoretical model.

Multicolor High-Gain Free-Electron Laser Driven by Seeded Microbunching Instability.

Laser-heater systems are essential tools to control and optimize high-gain free-electron lasers (FELs) working in the x-ray wavelength range. Indeed, these systems induce a controllable increase of the energy spread of the electron bunch. The heating suppresses longitudinal microbunching instability which otherwise would limit the FEL performance. Here, we demonstrate that, through the action of the microbunching instability, a long-wavelength modulation of the electron beam induced by the laser heater at low energy can persist until the beam entrance into the undulators. This coherent longitudinal modulation is exploited to control the FEL spectral properties, in particular, multicolor extreme-ultraviolet FEL pulses can be generated through a frequency mixing of the modulations produced by the laser heater and the seed laser in the electron beam. We present an experimental demonstration of this novel configuration carried out at the FERMI FEL.

Impact of non-Gaussian electron energy heating upon the performance of a seeded free-electron laser.

Laser-heater systems have been demonstrated to be an important component for the accelerators that drive high gain free electron laser (FEL) facilities. These heater systems suppress longitudinal microbunching instabilities by inducing a small and controllable slice energy spread to the electron beam. For transversely uniform heating, the energy spread augmentation is characterized by a non-Gaussian distribution. In this Letter, we demonstrate experimentally that in addition to suppression of the microbunching instability, the laser heater-induced energy distribution can be preserved to the FEL undulator entrance, significantly impacting the performance of high-gain harmonic generation (HGHG) FELs, especially at soft x-ray wavelengths. In particular, we show that the FEL intensity has several local maxima as a function of the induced heating caused by the non-Gaussian energy distribution together with a strong enhancement of the power at high harmonics relative to that expected for an electron beam with an equivalent Gaussian energy spread at an undulator entrance. These results suggest that a single stage HGHG FEL can produce scientifically interesting power levels at harmonic numbers m ≥ 25 and with current seed laser technology could reach output photon energies above 100 eV or greater.

Experimental demonstration of electron longitudinal-phase-space linearization by shaping the photoinjector laser pulse.

Control of the electron-beam longitudinal-phase-space distribution is of crucial importance in a number of accelerator applications, such as linac-driven free-electron lasers, colliders and energy recovery linacs. Some longitudinal-phase-space features produced by nonlinear electron beam self- fields, such as a quadratic energy chirp introduced by geometric longitudinal wakefields in radio-frequency (rf) accelerator structures, cannot be compensated by ordinary tuning of the linac rf phases nor corrected by a single high harmonic accelerating cavity. In this Letter we report an experimental demonstration of the removal of the quadratic energy chirp by properly shaping the electron beam current at the photoinjector. Specifically, a longitudinal ramp in the current distribution at the cathode linearizes the longitudinal wakefields in the downstream linac, resulting in a flat electron current and energy distribution. We present longitudinal-phase-space measurements in this novel configuration compared to those typically obtained without longitudinal current shaping at the FERMI linac.

Efficacy and safety of boosted and unboosted atazanavir-containing antiretroviral regimens in real life: results from a multicentre cohort study.

BACKGROUND: Atazanavir (ATV) has demonstrated high efficacy and safety in both treatment-naïve and treatment-experienced patients. Some comparative data are available on the durability of ritonavir-boosted (ATV/r) and unboosted formulations, but there are no data on clinicians' motivations for choosing one or another in everyday practice. The aim of this study was to evaluate the long-term efficacy of boosted and unboosted ATV in a cohort of treatment-experienced patients. METHODS: All patients included in the study were enrolled in an observational cohort within the Surveillance Cohort Long-Term Toxicity Antiretrovirals (SCOLTA) Project. Data on CD4 cell count, HIV viral load, metabolic parameters and adverse events of grade 3-4 are collected through an on-line system every six months. The duration of treatment with ATV was evaluated using the Kaplan-Meier curve and boosted and unboosted regimens were compared using the log-rank test. RESULTS: A total of 509 patients starting ATV as a component of their antiretroviral therapy were enrolled in the SCOLTA Project at the time of the study. Boosted ATV was received by 379 patients (74.5%) while 130 (25.5%) were treated with the unboosted formulation. The last therapeutic regimen did not influence the choice of ATV formulation. The mean observational time was 23.9 months. At the end of follow-up, 58.5% of patients on unboosted ATV and 58.1% of patients on ATV/r continued the treatment and no statistically significant differences were observed for ATV durability between the formulations or among the single causes of therapy interruption. CONCLUSIONS: Our results suggest that, in unselected clinical settings, ATV-containing antiretroviral therapy is durable and safe in both its formulations.

Characterisation of microbunching instability with 2D Fourier analysis.

The optimal performance of high-brightness free-electron lasers (FELs) is limited by the microbunching instability, which can cause variations in both the slice energy spread and longitudinal profile of electron beams. In this paper, we perform 2D Fourier analysis of the full bunch longitudinal phase space, such that modulations in both planes can be studied simultaneously. Unlike the standard 1D analysis, this method is able to reveal modulations in a folded phase space, which would otherwise remain uncovered. Additionally, the plasma oscillation between energy and density modulations is also revealed by this method. The damping of the microbunching instability, through the use of a laser heater, is also analysed with this technique. We confirm a mitigation of the amplitude of modulation and a red-shift of the microbunching frequency as the energy spread added increases. As an outcome of this work, a systematic experimental comparison of the development of the instability in the presence of different compression schemes is here presented for the first time.

Prevalence of transmitted HIV-1 drug resistance in HIV-1-infected patients in Italy: evolution over 12 years and predictors.

OBJECTIVES: Transmitted HIV-1 drug resistance (TDR) can reduce the efficacy of first-line antiretroviral therapy. PATIENTS AND METHODS: A retrospective analysis was performed to assess the prevalence and correlates of TDR in Italy over time. TDR was defined as the presence of at least one of the mutations present in the surveillance drug resistance mutation (SDRM) list. RESULTS: Among 1690 antiretroviral therapy-naive patients, the most frequent HIV subtypes were B (78.8%), CRF02_AG (5.6%) and C (3.6%). Overall, TDR was 15%. TDR was 17.3% in subtype B and 7.0% in non-B carriers (P < 0.001). TDR showed a slight, although not significant, decline (from 16.3% in 1996-2001 to 13.4% in 2006-07, P = 0.15); TDR declined for nucleoside reverse transcriptase inhibitors (from 13.1% to 8.2%, P = 0.003) but remained stable for protease inhibitors (from 3.7% to 2.5%, P = 0.12) and non-nucleoside reverse transcriptase inhibitors (from 3.7% to 5.8%). TDR to any drug was stable in B subtype and showed a decline trend in non-B. In multivariable analysis, F1 subtype or any non-B subtype, compared with B subtype, and higher HIV RNA were independent predictors of reduced odds of TDR. CONCLUSIONS: Prevalence of TDR to nucleoside reverse transcriptase inhibitors seems to have declined in Italy over time. Increased prevalence of non-B subtypes partially justifies this phenomenon.

Coherent THz Emission Enhanced by Coherent Synchrotron Radiation Wakefield.

We demonstrate that emission of coherent transition radiation by a ∼1 GeV energy-electron beam passing through an Al foil is enhanced in intensity and extended in frequency spectral range, by the energy correlation established along the beam by coherent synchrotron radiation wakefield, in the presence of a proper electron optics in the beam delivery system. Analytical and numerical models, based on experimental electron beam parameters collected at the FERMI free electron laser (FEL), predict transition radiation with two intensity peaks at ∼0.3 THz and ∼1.5 THz, and extending up to 8.5 THz with intensity above 20 dB w.r.t. the main peak. Up to 80-µJ pulse energy integrated over the full bandwidth is expected at the source, and in agreement with experimental pulse energy measurements. By virtue of its implementation in an FEL beam dump line, this work promises dissemination of user-oriented multi-THz beamlines parasitic and self-synchronized to EUV and x-ray FELs.

Single Shot Polarization Characterization of XUV FEL Pulses from Crossed Polarized Undulators.

Polarization control is a key feature of light generated by short-wavelength free-electron lasers. In this work, we report the first experimental characterization of the polarization properties of an extreme ultraviolet high gain free-electron laser operated with crossed polarized undulators. We investigate the average degree of polarization and the shot-to-shot stability and we analyze aspects such as existing possibilities for controlling and switching the polarization state of the emitted light. The results are in agreement with predictions based on Gaussian beams propagation.

Raltegravir-based therapy in a cohort of HIV/HCV co-infected individuals.

The relationship between hepatic tolerance and hepatitis C virus (HCV) co-infection has not been extensively studied in clinical practice. We assessed the efficacy and safety of raltegravir-based therapy in an Italian cohort of HIV/HCV co-infected patients. One hundred and forty patients with HIV/HCV co-infection initiating raltegravir from SCOLTA project (Surveillance Cohort Long-Term Toxicity Antiretrovirals) were examined. Of them, 43 were women, with mean age of 45.4±6.4years; 65 (46%) had undetectable HIV-RNA<50copies/mL and 75 (54%) HIV-RNA≥50copies/mL. According to CDC classification, 49 (35%) were in stage C. Based on Fib4 score at the time of starting raltegravir, patients were classified in class I in 41 cases, class II in 68 and in class III in 31 cases. Globally, the Fib4 score slightly decreased during 24months follow-up, from 2.2 to a value of 1.8. Hepatic adverse events of any grade were observed in 67 patients, of which only 2 cases (3%) had severe liver toxicity (grade 3-4). Only one patient had to discontinue the therapy because of adverse events. According to univariate analysis, being in CDC stage C represented a risk for the development of liver toxicity, with a hazard ratio (HR) of 2.27 (95% CI 1.06-4.84, P=0.033). None of the other variables considered (age, sex, years since detection of HIV and HCV-RNA detectable, years of previous HIV therapy, concomitant therapy with PI or NRTI, CD4+ cell count, Fib4, and transaminases level at baseline) resulted statistically correlated to the outcome. In conclusion, raltegravir-based regimens can be safely used in HCV infected patients; in this study, the hepatic toxicity has been found to be more frequent in patients with an advanced HIV disease (CDC stage C), independently of HIV-RNA suppression at raltegravir initiation.

[Isoniazid therapy and monitoring plasma levels]. / Terapia con isoniazide e monitoraggio dei livelli plasmatici.

Plasma levels of isoniazid (INH) have been monitored in fifteen children, aged 1 to 13 years, who were under chronic therapy with INH plus rifampin for tuberculosis. The pharmacokinetic parameters of children were not significantly different from those found in adults by other authors. It is necessary to check two plasma concentrations at the 3rd h. versus different doses (5 mg/kg and 10 mg/kg) of INH, in order to determine the optimal dose to be given. In subjects with external ventricular drainage, the concentrations of INH in cerebro-spinal fluid are lower than in plasma. The latter finding should be stressed for its importance in the therapy of tuberculous meningitis.

Gender differences in HIV infection: is there a problem? Analysis from the SCOLTA cohorts.

OBJECTIVES: Evaluate gender differences with regard to baseline characteristics and outcome of therapy in cohorts of the SCOLTA (surveillance cohort long-term toxicity of antiretrovirals) project. METHODS: The SCOLTA project is an active pharmacovigilance system for new antiretroviral drugs. Since 2002, patients were enrolled in nine cohorts (lopinavir, tenofovir, atazanavir, fosamprenavir, enfuvirtide, tipranavir, darunavir, raltegravir and maraviroc). RESULTS: Two thousand one hundred and fifty-four patients were included in 5 PI cohorts; 607 (28.2%) were female. Women were younger and less frequently HCV-coinfected than men. At study entry, they were less frequently in CDC stage C, but CD4+ cells/mm(3) and detectable HIV-RNA were not different by gender. Women had triglycerides alterations less frequently than men, but showed a higher proportion of low HDL-cholesterol. Women were protected from incident grade 2-4 triglycerides increase (odds ratio=0.39, 95% confidence interval 0.18-0.88; P=0.02). Mean CD4+ cell count increased in both men and women; despite a non-significantly lower initial CD4+ level, women had a better immunological recovery. Women discontinued PI treatment for adverse events and their own will more frequently. CONCLUSIONS: In these cohorts, gender distribution mirrored the Italian HIV population. Women were younger than men when they started their first ARV therapy and when they entered our cohorts. On the same treatment, they had a better immune response, though no significant difference emerged on virologic control and treatment durability. As compared to men, women appeared at lower risk of hypertriglyceridaemia. They stopped PI-based treatment of their own will more frequently than men, suggesting the need for a focused effort on adherence.