Identification of a Novel Hepatitis E Virus Genotype 3 Strain Isolated from a Chronic Hepatitis E Virus Infection in a Kidney Transplant Recipient in Switzerland

Hepatitis E virus genotype 3 (HEV-3) is the causal pathogen of chronic hepatitis E. We report here the full-length genome sequence of an HEV-3 strain, isolated from a kidney transplant recipient in Switzerland (SW/16-0282). This HEV-3 strain showed less than 88% homology compared to known strains, suggesting a new HEV-3 strain

GeneXpert Captures Unstable Methicillin-Resistant Staphylococcus aureus Prone to Rapidly Losing the mecA Gene ▿

A cefoxitin-susceptible Staphylococcus aureus strain was identified by the Cepheid GeneXpert as methicillin-resistant S. aureus (MRSA). This strain was highly unstable and rapidly lost SCCmec upon subculturing in vitro, indicating that unstable MRSA is best detected by gene amplification-based methods

Systematic Internal Transcribed Spacer Sequence Analysis for Identification of Clinical Mold Isolates in Diagnostic Mycology: a 5-Year Study▿ †

The implementation of internal transcribed spacer (ITS) sequencing for routine identification of molds in the diagnostic mycology laboratory was analyzed in a 5-year study. All mold isolates (n = 6,900) recovered in our laboratory from 2005 to 2009 were included in this study. According to a defined work flow, which in addition to troublesome phenotypic identification takes clinical relevance into account, 233 isolates were subjected to ITS sequence analysis. Sequencing resulted in successful identification for 78.6% of the analyzed isolates (57.1% at species level, 21.5% at genus level). In comparison, extended in-depth phenotypic characterization of the isolates subjected to sequencing achieved taxonomic assignment for 47.6% of these, with a mere 13.3% at species level. Optimization of DNA extraction further improved the efficacy of molecular identification. This study is the first of its kind to testify to the systematic implementation of sequence-based identification procedures in the routine workup of mold isolates in the diagnostic mycology laboratory

Decreasing Proportion of Recent Infections among Newly Diagnosed HIV-1 Cases in Switzerland, 2008 to 2013 Based on Line-Immunoassay-Based Algorithms.

BACKGROUND: HIV surveillance requires monitoring of new HIV diagnoses and differentiation of incident and older infections. In 2008, Switzerland implemented a system for monitoring incident HIV infections based on the results of a line immunoassay (Inno-Lia) mandatorily conducted for HIV confirmation and type differentiation (HIV-1, HIV-2) of all newly diagnosed patients. Based on this system, we assessed the proportion of incident HIV infection among newly diagnosed cases in Switzerland during 2008-2013. METHODS AND RESULTS: Inno-Lia antibody reaction patterns recorded in anonymous HIV notifications to the federal health authority were classified by 10 published algorithms into incident (up to 12 months) or older infections. Utilizing these data, annual incident infection estimates were obtained in two ways, (i) based on the diagnostic performance of the algorithms and utilizing the relationship 'incident = true incident + false incident', (ii) based on the window-periods of the algorithms and utilizing the relationship 'Prevalence = Incidence x Duration'. From 2008-2013, 3'851 HIV notifications were received. Adult HIV-1 infections amounted to 3'809 cases, and 3'636 of them (95.5%) contained Inno-Lia data. Incident infection totals calculated were similar for the performance- and window-based methods, amounting on average to 1'755 (95% confidence interval, 1588-1923) and 1'790 cases (95% CI, 1679-1900), respectively. More than half of these were among men who had sex with men. Both methods showed a continuous decline of annual incident infections 2008-2013, totaling -59.5% and -50.2%, respectively. The decline of incident infections continued even in 2012, when a 15% increase in HIV notifications had been observed. This increase was entirely due to older infections. Overall declines 2008-2013 were of similar extent among the major transmission groups. CONCLUSIONS: Inno-Lia based incident HIV-1 infection surveillance proved useful and reliable. It represents a free, additional public health benefit of the use of this relatively costly test for HIV confirmation and type differentiation

Incident infection estimates based on models adjusting for possible selection bias.

<p>S₁, no adjustment; S₂, model with adjustment for selection bias exerted by seeking early testing after a suspected exposure; S₃, model with adjustment for seeking medical attention due to symptoms of acute HIV infection. Refer to Methods for further explanations. The blue curve without symbols on top in each panel shows the number of HIV notifications.</p

HIV-1 infections ruled incident by the 10 best-performing Inno-Lia algorithms.

<p>Analysis restricted to notifications that contained Inno-Lia results.</p><p>HIV-1 infections ruled incident by the 10 best-performing Inno-Lia algorithms.</p

Number of HIV notifications and incident HIV infections over time, as obtained by performance-based and window-based incident infection estimates.

<p>Panels on top labeled “All” show the data for all patients, lower panels show the data per risk category (MSM, men who have sex with men; HET, heterosexual transmission; IDU, intravenous drug use; UNK, unknown transmission pathway). In all panels, the blue curve with the circle symbols denotes the annual number of HIV notifications, and the black curve without symbols shows the estimated number of incident infections (means and their 95% confidence intervals). The top panels also show the results obtained with the 10 individual algorithms (grey lines in the background).</p

Incident infection estimates based on models adjusting for possible selection bias.

<p>S₁, no adjustment; S₂, model with adjustment for selection bias exerted by seeking early testing after a suspected exposure; S₃, model with adjustment for seeking medical attention due to symptoms of acute HIV infection. Refer to Methods for further explanations. The blue curve without symbols on top in each panel shows the number of HIV notifications.</p

Incident HIV-1 infection estimates utilizing the performance-based method.

<p>Incident HIV-1 infection estimates utilizing the performance-based method.</p

Characteristics of the 3’851 HIV notifications received 2008–2013.

<p>IQR, interquartile range;</p><p>* all infected abroad;</p><p>** predominantly infected abroad</p><p>Characteristics of the 3’851 HIV notifications received 2008–2013.</p