Raw genome sequence data for 13 isogenic Aspergillus fumigatus strains isolated over a 2 year period from a patient with chronic granulomatous disease

EB, AB and AW are supported by the Wellcome Trust Strategic Award (grant 097377), and the MRC Centre for Medical Mycology at the University of Aberdeen (grant MR/N006364/1). AB was also supported by the Biotechnology and Biological Research Council (BB/K017365/1) and the Medical Research Council (MR/M026663/1). The work in this paper is funded by a BBSRC EASTBIO grant (BB/M010996/1) awarded to AW. The funders had no role in study design, data interpretation, or the decision to submit the work for publication.Peer reviewedPublisher PD

still a concern in patients with haematological malignancies and stem cell transplant recipients-authors' response

publishersversionpublishe

Azole resistance in Aspergillus fumigatus

Invasive aspergillosis remains an important complication of immunosuppressive treatment regimens in humans. Triazoles are increasingly used in the prevention and management of invasive aspergillosis. Voriconazole is first choice for the primary therapy of invasive aspergillosis, and posaconazole was shown to be highly effective in preventing invasive aspergillus disease when given to high-risk groups prophylactically. Resistance in moulds is uncommon in clinical medicine, but might occur in specific patient groups. It appears that azole resistance might evolve in patients that harbor a high number of reproducing Aspergillus and are treated with azoles for long period of time. These conditions are present in patients with aspergilloma or other cavitary lung diseases caused by Aspergillus species. Azole resistance has been described to emerge in this patient group. Recently azole resistance was also reported in patients with acute invasive aspergillosis, where the conditions for resistance development appear to be less that optimal: fungal proliferation through hyphal elongation and relative short treatment episodes. This might suggest that azole resistance is caused by exposure outside the patient, for instance in the environment. Molecular studies have shown that triazole resistance in A. fumigatus is associated with amino acid substitutions in the cyp51A protein. Alterations might result in different patterns of azole resistance, primarily of itraconazole, with varying reduced activity of other triazoles such as voriconazole and posaconazole. Azole resistance in A. fumigatus has been associated with treatment failure. At present clinical microbiology laboratories do not routinely perform in vitro susceptibility testing, but it appears to be appropriate to test A. fumigatus isolates at least in those isolates recovered from patients that fail to azole therapy

Next-Generation Sequencing in the Mycology Lab

New state-of-the-art techniques in sequencing offer valuable tools in both detection of mycobiota and in understanding of the molecular mechanisms of resistance against antifungal compounds and virulence. Introduction of new sequencing platform with enhanced capacity and a reduction in costs for sequence analysis provides a potential powerful tool in mycological diagnosis and research. In this review, we summarize the applications of next-generation sequencing techniques in mycology

Trends in Azole resistance in Aspergillus fumigatus, The Netherlands, 1994–2016

We investigated azole resistance in Aspergillus fumigatus in a tertiary reference hospital in the Netherlands during 1994–2016. The 5-year patient-adjusted proportion of resistance increased from 0.79% for 1996–2001 to 4.25% for 2002–2006, 7.17% for 2007–2011, and 7.04% for 2012–2016. However, we observed substantial variation between years.</p

Breaking pseudo-twofold symmetry in the poliovirus 3′-UTR Y-stem by restoring Watson–Crick base pairs

The previously described NMR structure of a 5′-CU-3′/5′-UU-3′ motif, which is highly conserved within the 3′-UTR Y-stem of poliovirus-like enteroviruses, revealed striking regularities of the local helix geometry, thus retaining the pseudo-twofold symmetry of the RNA helix. A mutant virus with both pyrimidine base pairs changed into Watson–Crick replicated as wild type, indicating the functional importance of this symmetry relation in viral RNA replication. Here we investigated the effect of changing only one of the two pyrimidine base pairs to Watson–Crick. We determined the NMR structures of two Y-stem variants: one containing the 5′-CU-3′/5′-AU-3′ motif, which has been found in wild-type virus isolates as well, and the other containing a 5′-CU-3′/5′-UG-3′ motif, which is not present in any enterovirus sequenced to date. Both structures show single pyrimidine mismatches with intercalated bases. In the 5′-CU-3′/5′-AU-3′ motif a C–U Watson–Crick-type base pair is formed that retains the pseudo-twofold symmetry, while in the 5′-CU-3′/5′-UG-3′ motif a single asymmetric U–U mismatch breaks the twofold symmetry. Surprisingly, for the nonnatural variant no effect of the single base-pair replacement was observed on polioviral RNA replication using an in vitro replicon assay

Longitudinal analysis on the ecological dynamics of the cervicovaginal microbiome in hrHPV infection

The cervicovaginal microbiome (CVM) is a dynamic continuous microenvironment that can be clustered in microbial community state types (CSTs) and is associated with women’s cervical health. Lactobacillus-depleted communities particularly associate with an increased susceptibility for persistence of high-risk human papillomavirus (hrHPV) infections and progression of disease, but the long-term ecological dynamics of CSTs after hrHPV infection diagnosis remain poorly understood. To determine such dynamics, we examined the CVM of our longitudinal cohort of 141 women diagnosed with hrHPV infection at baseline with collected cervical smears at two timepoints six-months apart. Here we describe that the long-term microbiome dissimilarity has a positive correlation with microbial diversity at both visits and that women with high abundance and dominance for Lactobacillus iners at baseline exhibit more similar microbiome composition at second visit than women with Lactobacillus-depleted communities at baseline. We further show that the species Lactobacillus acidophilus and Megasphaera genomosp type 1 associate with CST changes between both visits. Lastly, we also observe that Gardnerella vaginalis is associated with the stability of Lactobacillus-depleted communities while L. iners is associated with the instability of Megasphaera genomosp type 1-dominated communities. Our data suggest dynamic patterns of cervicovaginal CSTs during hrHPV infection, which could be potentially used to develop microbiome-based therapies against infection progression towards disease