Tick-borne Encephalitis Identified in Ireland: Diagnosis and Outcome.

Presentation Tick borne encephalitis (TBE) is not endemic in Ireland and diagnostic tests are seldom requested. We describe the first notified case in Ireland. A 50-year-old female returned from Lithuania and presented with fever and new neurologic signs. Diagnosis TBE was diagnosed by detection of TBE virus specific antibodies in serum and cerebrospinal fluid (CSF). Treatment The patient was managed with observation and supportive care consisting of intravenous fluids and analgesia. Discussion The case highlights the importance of awareness of TBE among physicians and travellers to guide appropriate testing and vaccination. TBE is being recognised in non-endemic countries posing an emerging risk to public health.

Changing demographics and immunity to vaccine preventable diseases in people with HIV in Ireland.

BACKGROUND: HIV infection is associated with an increased risk of morbidity and mortality from vaccine preventable infections. This research describes, in the context of changing patient demographics, the seroprevalence of vaccine preventable viral infections among attendees of the largest centre for HIV positive patients in Ireland. METHODS: Baseline serum IgG results for measles, mumps, rubella, varicella zoster virus (VZV) & hepatitis A, as well as hepatitis B sAg, cAb and sAb results, were retrieved for 2534 clinic attendees attending in 2018. Results were available for between 990 and 2363 attendees (39-93%), depending on the test, and were compared with 2013 clinic data. RESULTS: There was a 35% increase in attendees in 2018 when compared to 2013. The largest increase was in attendees of South American origin. In 2018, males accounted for 73% of the entire cohort and the HIV acquisition risk for 48% of attendees was MSM. 47% of attendees were originally from Ireland. Among those tested, 33% were susceptible to at least one component of the MMR vaccine. 5% were VZV non-immune (significantly associated with younger age and the acquisition risk status of injection drug use). 21% were hepatitis A non-immune (significantly associated with younger age and being of European or South American origin). 32% were hepatitis B cAb seropositive (significantly associated with older age, injection drug use status and being originally from Africa). 3% demonstrated hepatitis B sAg positivity. 64% had hepatitis B sAb ≥ 10mIU. CONCLUSION: In a cohort of attendees to an HIV clinic in a large urban setting, the susceptibility to several common vaccine preventable viral infections, in particular MMR and hepatitis A and B, was high. These results highlight the importance of proactive screening and immunisation to help protect this high risk patient group against vaccine preventable diseases.

A Comparison of the Performance of SARS-CoV-2 Antibody Assays in Healthcare Workers with COVID-19.

Aims Since its emergence, significant interest surrounds the use of SARS-CoV-2 serological tests as an alternative or as an adjunct to molecular testing. However, given the speed of this pandemic, paralleled with the pressure to develop and provide serological tests in an expediated manner, not every assay has undergone the rigorous evaluation that is usually associated with medical diagnostic assays. We aimed to examine the performance of several commercially available SARS-CoV-2 IgG antibody assays among participants with confirmed COVID-19 disease and negative controls. Methods Serum taken between day 17 and day 40 post onset of symptoms from 41 healthcare workers with RT-PCR confirmed COVID-19 disease, and pre-pandemic serum from 20 negative controls, were tested for the presence of SARS-CoV-2 IgG using 7 different assays including point-of-care (POC) and laboratory-based assays. Results Assay performance varied. The lab-based Abbott diagnostics SARS-CoV-2 IgG assay proved to be the assay with the best positive and negative predictive value, and overall accuracy. The POC Nal von Minden GmbH and Biozek assays also performed well. Conclusion Our research demonstrates the variations in performance of several commercially available SARS-CoV-2 antibody assays. These findings identify the limitations of some serological tests for SARS-CoV-2. This information will help inform test selection and may have particular relevance to providers operating beyond accredited laboratories.

Antimicrobial resistance and molecular epidemiology using whole-genome sequencing of Neisseria gonorrhoeae in Ireland, 2014-2016: focus on extended-spectrum cephalosporins and azithromycin.

High-level resistance and treatment failures with ceftriaxone and azithromycin, the first-line agents for gonorrhoea treatment are reported and antimicrobial-resistant Neisseria gonorrhoeae is an urgent public health threat. Our aims were to determine antimicrobial resistance rates, resistance determinants and phylogeny of N. gonorrhoeae in Ireland, 2014-2016. Overall, 609 isolates from four University Hospitals were tested for susceptibility to extended-spectrum cephalosporins (ESCs) and azithromycin by the MIC Test Strips. Forty-three isolates were whole-genome sequenced based on elevated MICs. The resistance rate to ceftriaxone, cefixime, cefotaxime and azithromycin was 0, 1, 2.1 and 19%, respectively. Seven high-level azithromycin-resistant (HLAzi-R) isolates were identified, all susceptible to ceftriaxone. Mosaic penA alleles XXXIV, X and non-mosaic XIII, and G120K plus A121N/D/G (PorB1b), H105Y (MtrR) and A deletion (mtrR promoter) mutations, were associated with elevated ESC MICs. A2059G and C2611T mutations in 23S rRNA were associated with HLAzi-R and azithromycin MICs of 4-32 mg/L, respectively. The 43 whole-genome sequenced isolates belonged to 31 NG-MAST STs. All HLAzi-R isolates belonged to MLST ST1580 and some clonal clustering was observed; however, the isolates differed significantly from the published HLAzi-R isolates from the ongoing UK outbreak. There is good correlation between previously described genetic antimicrobial resistance determinants and phenotypic susceptibility categories for ESCs and azithromycin in N. gonorrhoeae. This work highlights the advantages and potential of whole-genome sequencing to be applied at scale in the surveillance of antibiotic resistant strains of N. gonorrhoeae, both locally and internationally.

Late Cretaceous marine arthropods relied on terrestrial organic matter as a food source: Geochemical evidence from the Coon Creek Lagerstätte in the Mississippi Embayment.

The Upper Cretaceous Coon Creek Lagerstätte of Tennessee, USA, is known for its extremely well-preserved mollusks and decapod crustaceans. However, the depositional environment of this unit, particularly its distance to the shoreline, has long been equivocal. To better constrain the coastal proximity of the Coon Creek Formation, we carried out a multiproxy geochemical analysis of fossil decapod (crab, mud shrimp) cuticle and associated sediment from the type section. Elemental analysis and Raman spectroscopy confirmed the presence of kerogenized carbon in the crabs and mud shrimp; carbon isotope (δ13 C) analysis of bulk decapod cuticle yielded similar mean δ13 C values for both taxa (-25.1‰ and -26‰, respectively). Sedimentary biomarkers were composed of n-alkanes from C16 to C36 , with the short-chain n-alkanes dominating, as well as other biomarkers (pristane, phytane, hopanes). Raman spectra and biomarker thermal maturity indices suggest that the Coon Creek Formation sediments are immature, which supports retention of unaltered, biogenic isotopic signals in the fossil organic carbon remains. Using our isotopic results and published calcium carbonate δ13 C values, we modeled carbon isotope values of carbon sources in the Coon Creek Formation, including potential marine (phytoplankton) and terrestrial (plant) dietary sources. Coon Creek Formation decapod δ13 C values fall closer to those estimated for terrigenous plants than marine phytoplankton, indicating that these organisms were feeding primarily on terrigenous organic matter. From this model, we infer that the Coon Creek Formation experienced significant terrigenous organic matter input via a freshwater source and thus was deposited in a shallow, nearshore marine environment proximal to the shoreline. This study helps refine the paleoecology of nearshore settings in the Mississippi Embayment during the global climatic shift in the late Campanian-early Maastrichtian and demonstrates for the first time that organic δ13 C signatures in exceptionally preserved fossil marine arthropods are a viable proxy for use in paleoenvironmental reconstructions.

Theory of Thomson scattering in inhomogeneous media.

Thomson scattering of laser light is one of the most fundamental diagnostics of plasma density, temperature and magnetic fields. It relies on the assumption that the properties in the probed volume are homogeneous and constant during the probing time. On the other hand, laboratory plasmas are seldom uniform and homogeneous on the temporal and spatial dimensions over which data is collected. This is particularly true for laser-produced high-energy-density matter, which often exhibits steep gradients in temperature, density and pressure, on a scale determined by the laser focus. Here, we discuss the modification of the cross section for Thomson scattering in fully-ionized media exhibiting steep spatial inhomogeneities and/or fast temporal fluctuations. We show that the predicted Thomson scattering spectra are greatly altered compared to the uniform case, and may lead to violations of detailed balance. Therefore, careful interpretation of the spectra is necessary for spatially or temporally inhomogeneous systems.

Identification of emergent bla CMY-2 -carrying Proteus mirabilis lineages by whole-genome sequencing.

Whole-genome sequencing of 24 Proteus mirabilis isolates revealed the clonal expansion of two cefoxitin-resistant strains among patients with community-onset infection. These strains harboured bla CMY-2 within a chromosomally located integrative and conjugative element and exhibited multidrug resistance phenotypes. A predominant strain, identified in 18 patients, also harboured the PGI-1 genomic island and associated resistance genes, accounting for its broader antibiotic resistance profile. The identification of these novel multidrug-resistant strains among community-onset infections suggests that they are endemic to this region and represent emergent P. mirabilis lineages of clinical significance.

Electron and Ion Heating Characteristics during Magnetic Reconnection in the MAST Spherical Tokamak.

Electron and ion heating characteristics during merging reconnection start-up on the MAST spherical tokamak have been revealed in detail using a 130 channel yttrium aluminum garnet (YAG) and a 300 channel Ruby-Thomson scattering system and a new 32 chord ion Doppler tomography diagnostic. Detailed 2D profile measurements of electron and ion temperature together with electron density have been achieved for the first time and it is found that electron temperature forms a highly localized hot spot at the X point and ion temperature globally increases downstream. For the push merging experiment when the guide field is more than 3 times the reconnecting field, a thick layer of a closed flux surface form by the reconnected field sustains the temperature profile for longer than the electron and ion energy relaxation time ~4-10 ms, both characteristic profiles finally forming a triple peak structure at the X point and downstream. An increase in the toroidal guide field results in a more peaked electron temperature profile at the X point, and also produces higher ion temperatures at this point, but the ion temperature profile in the downstream region is unaffected.

High speed measurements of neutral beam turn-on and impact of beam modulation on measurements of ion density.

Modulation of neutral beams on tokamaks is performed routinely, enabling background rejection for active spectroscopic diagnostics, and control of injected power and torque. We find that there exists an anomalous initial transient in the beam neutrals delivered to the tokamak that is not accounted for by the accelerator voltage and power supply current. Measurements of the charge-exchange and beam photoemission on the DIII-D tokamak [J. L. Luxon, Nucl. Fusion 42, 614 (2002)] at high speed (200 µs) reveal that the energy of the beam neutrals is constant, but the density of beam neutrals displays dramatic variation in the first 2-3 ms following beam turn-on. The impact of this beam density variation on inferred ion densities and impurity transport is presented, with suggested means to correct for the anomalous transient.

Investigation of the first outbreak of OXA-48-producing Klebsiella pneumoniae in Ireland.

BACKGROUND: Carbapenemase-producing Enterobacteriaceae (CPE) strains are encountered with increasing frequency in Europe. In November 2010 the European Centre for Disease Control (ECDC) graded Ireland as only having sporadic occurrence of CPE. AIM: To describe the epidemiological and molecular typing analysis of the first outbreak of OXA-48-producing Klebsiella pneumoniae in an Irish tertiary care referral centre. METHODS: Sixteen OXA-48-producing K. pneumoniae isolates were detected, from both clinical and screening specimens, and analysed by pulsed-field gel electrophoresis and by multi-locus sequence typing. FINDINGS: Typing analysis revealed that two outbreak strains were circulating in the hospital, one among surgical patients and one among medical patients. The 'medical strain' ST13 had already been identified as an internationally disseminated clone, whereas the 'surgical strain' ST221 had not previously been reported as an OXA-48-carrying strain. CONCLUSION: Although the outbreak on surgical wards was successfully controlled by implementing strict infection control measures, intermittent detection of individual patients carrying the 'medical strain' of OXA-48 K. pneumoniae has persisted since then. The experience from this outbreak suggests that OXA-48 K. pneumoniae is endemic at low level in the healthcare setting in the Dublin region.

Electron-ion equilibration in ultrafast heated graphite.

We have employed fast electrons produced by intense laser illumination to isochorically heat thermal electrons in solid density carbon to temperatures of ∼10,000 K. Using time-resolved x-ray diffraction, the temperature evolution of the lattice ions is obtained through the Debye-Waller effect, and this directly relates to the electron-ion equilibration rate. This is shown to be considerably lower than predicted from ideal plasma models. We attribute this to strong ion coupling screening the electron-ion interaction.

Orbital-free density-functional theory simulations of the dynamic structure factor of warm dense aluminum.

Here, we report orbital-free density-functional theory (OF DFT) molecular dynamics simulations of the dynamic ion structure factor of warm solid density aluminum at T=0.5 eV and T=5 eV. We validate the OF DFT method in the warm dense matter regime through comparison of the static and thermodynamic properties with the more complete Kohn-Sham DFT. This extension of OF DFT to dynamic properties indicates that previously used models based on classical molecular dynamics may be inadequate to capture fully the low frequency dynamics of the response function.

Stable isotopes document resource partitioning and effects of forest disturbance on sympatric cheirogaleid lemurs.

The future of Madagascar's forests and their resident lemurs is precarious. Determining how species respond to forest fragmentation is essential for management efforts. We use stable isotope biogeochemistry to investigate how disturbance affects resource partitioning between two genera of cheirogaleid lemurs (Cheirogaleus and Microcebus) from three humid forest sites: continuous and fragmented forest at Tsinjoarivo, and selectively logged forest at Ranomafana. We test three hypotheses: (H1) cheirogaleids are unaffected by forest fragmentation, (H2) species respond individually to disturbance and may exploit novel resources in fragmented habitat, and (H3) species alter their behavior to rely on the same key resource in disturbed forest. We find significant isotopic differences among species and localities. Carbon data suggest that Microcebus feed lower in the canopy than Cheirogaleus at all three localities and that sympatric Cheirogaleus crossleyi and C. sibreei feed at different canopy heights in the fragmented forest. Microcbus have higher nitrogen isotope values than Cheirogaleus at all localities, indicating more faunivory. After accounting for baseline isotope values in plants, our results provide the most support for H3. We find similar isotopic variations among localities for both genera. Small differences in carbon among localities may reflect shifts in diet or habitat use. Elevated nitrogen values for cheirogaleid lemurs in fragments may reflect increased arthropod consumption or nutritional stress. These results suggest that cheirogaleids are affected by forest disturbance in Eastern Madagascar and stress the importance of accounting for baseline isotopic differences in plants in any work comparing localities.

Comparison between x-ray scattering and velocity-interferometry measurements from shocked liquid deuterium.

The equation of state of light elements is essential to understand the structure of Jovian planets and inertial confinement fusion research. The Omega laser was used to drive a planar shock wave in the cryogenically cooled deuterium, creating warm dense matter conditions. X-ray scattering was used to determine the spectrum near the boundary of the collective and noncollective scattering regimes using a narrow band x-ray source in backscattering geometry. Our scattering spectra are thus sensitive to the individual electron motion as well as the collective plasma behavior and provide a measurement of the electron density, temperature, and ionization state. Our data are consistent with velocity-interferometry measurements previously taken on the same shocked deuterium conditions and presented by K. Falk et al. [High Energy Density Phys. 8, 76 (2012)]. This work presents a comparison of the two diagnostic systems and offers a detailed discussion of challenges encountered.

BK virus (BKV) plasma dynamics in patients with BKV-associated hemorrhagic cystitis following allogeneic stem cell transplantation.

INTRODUCTION: The use of real-time polymerase chain reaction testing in the investigation of BK virus (BKV)-associated disease has been widely studied in renal transplant recipients; however, far less research has been done in this area with respect to the plasma BK viral load dynamics of BKV hemorrhagic cystitis (BKV-HC) in hematopoietic stem cell transplant recipients. AIM: The aim of this study was to examine the BK viral load dynamics in plasma samples collected from patients post transplant who had laboratory-confirmed BKV-HC. METHODS: Patients who developed BK viremia were compared with patients who did not develop viremia, and a statistical comparison of risk factors for viremia was performed. Seventeen patients were included in this study. Urine samples from the day of BKV diagnosis were available in 13 of the 17 cases. In total, 154 archived plasma samples from around the time of the BKV-HC event were also included in the study from these 17 patients. RESULTS: The median time from transplantation to the onset of detectable viremia was 68 days. The median viral load in the 13 urine samples was 1.8 × 10(8) copies/mL, which was significantly higher than the median viral load in the 38 positive plasma samples of 6.6 × 10(2) copies/mL (Mann-Whitney test, U = 16, P < 0.001). CONCLUSION: The lymphocyte count on the day of the positive BKV test was significantly lower in patients with BKV viremia than in patients with no viremia (P = 0.02) and also the white cell and platelet counts were lower on the day of the first positive BKV test. Although there is not inter-patient consistency as regards correlation between urinary BK viral loads and severity of clinical BKV-HC, in individual patients the decline in viral load in plasma did correlate with clinical recovery.