Reports from grant recipients 2015

Title: “Detection of minor variants of hepatitis C virus containing preexisting resistance mutations towards direct acting antivirals using Next Generation Sequencing”, Christian Østergaard Andersen. Grant sum: 60 000 SEK

Summary: The grant was used to design a Next Generation Sequencing (NGS) method to sequence hepatitis C virus (HCV) in a clinical setting without prior information about the sample. We developed a RT-PCR amplicon assay, which amplifies a ~9 kilobase near full-length open reading frame of the most common subtypes from Northern Europe. During the validation 12 different subtypes were successfully amplified and sequenced, including two different recombinant strains.The method can be applied to samples with low viral load and provides a high coverage, which enables looking at Direct Acting Antiviral (DAA) resistance mutations at 1% frequency. All relevant resistance mutations towards DAAs for NS3, NS5A, and NS5B are within the obtained sequence. More than 150 patient samples have so far been sequenced and investigated for DAA resistance mutations.

Title: “Host Directed Therapy against Antimicrobial Resistant Bacteria: Development of a Cellular Infection Model”, Peter Bergman. Grant sum: 100 000 SEK
Summary: With the help of this SSAC-grant we have been able to establish a cellular infection model, which we have used to screen for compounds with the ability to boost the antimicrobial machinery of the cell. The bactericidal somponent of the cell includes antimicrobial peptides (AMPs), reactive oxygen species (ROS) and nitric oxide. In our screen we have identified Entinostat, a HDAC-inhibitor, as a potent compound that induce bactericidal components in the cell, including AMPs and ROS. This approach has been found to be efficient in reducing the intracellular growth of multidrug resistant bacteria, especially in combination with conventional antibiotics. We believe that this host directed therapy approach holds great promise for future and novel treatment strategies against multidrug resistant bacteria.

Title: “The Nordic HIV Latency and Cure Research Collaboration (nCURE) cohort”, Jesper Damsgaard Gunst. Grant sum: 150 000 SEK
Summary: The grant received by the SSAC Foundation was used to establish a transnational cohort (nCURE) for research on HIV-1 latency and cure across the Nordic countries.
As part of nCURE, leukaphresis was established on HIV-1 infected individuals for research practice at the nCURE site in Aarhus, Denmark. nCURE research is still ongoing, and establishing the nCURE database and biobank are in progress.

Title: “Antimicrobial resistance in Streptococcus pneumoniae, Streptococcus pyogenes and Escherichia coli from the Faroese population, correlation with antimicrobial use and comparison with Denmark and Iceland”, Marita Debess Magnussen. Grant sum: 100 000 SEK
Summary: The grant from SSAC has done it possible for me to write and published one paper and I got one almost accepted with minor comment. I was also able to do the final serotyping and susceptibility testing of pneumococci. In October 2017, I’ll submit my PhD thesis and this was also made possible with the grant from SSAC.

Title: “Phagocyte GPCR pepducins and bacterial deformylase inhibitor are novel classes of anti-infective drugs” Huamei Forsman. Grant sum: 100 000 SEK
Summary: Molecules that modulate innate immune system and directly kill bacteria should be potentially used as a new approach to antibacterial chemotherapy.

 Title: “Rapid susceptibility testing of extended-spectrum beta-lactamase- and carbapenemase-producing Enterobacteriaceae using disk diffusion in an automated setting”, Christian Giske. Grant sum: 60 000 SEK
Summary: Intestinal carriage of ESBL-producing Enterobacteriaceae is increasingly common. The project studied the duration of and factors influencing length of carriage.

Title: “Lipid metabolism as a novel antibiotic target in Chlamydia”, Åsa Gylfe. Grant sum: 60 000 SEK
Summary: We have identified a novel class of compounds that may inhibit fatty acid synthesis in Chlamydia, an interesting target for novel antibiotics.

Title: “Prospective multicenter study on antibiotic therapy for the treatment of urinary infections caused by ESBL-producing bacteria”, Anna Hallgren. Grant sum: 100 000
Summary: A prospective observational multicenter study was carried out at 20 hospitals in Sweden to assess current practices in the treatment of urinary tract infections caused by ESBL-producing Enterobacteriaceae and evaluate clinical and bacteriological outcome. In total, 250 patients were included during November 2014 to April 2017. The analysis of outcome in relation to antibiotic treatment as well as phenotypic and genetic characteristics of the isolated bacteria is ongoing and will be completed in 2018.

Title: “The efficacy of pivmecillinam 3 days respectively 5 days t.i.d against community acquired uncomplicated urinary tract infections”, Filip Jansåker. Grant sum: 60 000 SEK

Summary: We have presently included 240 patients and we will include at least 300 before the study terminates in may 2017. We firmly believe it will help fill the gaps concerning pivmecillinam to uncomplicated urinary tract infections, among other findings. The inclusion was slower than expected, why we expanded the study period. The follow-up is good (app. 75%), and as expected app. 70% of the cases have significant bacteriuria. The cure rate in this population seems high, but we do not yet know whether or not there are differences between the regimens, as the study is still blinded. The study protocol is published on an open access journal:

Title: “Targeting fibrinolysis for prevention and treatment of Biofilm-associated Staphylococcus aureus infections”, Tao Jin. Grant sum: 60 000
Summary: My research group demonstrated that staphylokinase plays an important role in S. aureus skin infections by activating plasminogen. Intriguingly, bacteria utilize the host proteins e.g. fibrin/fibrinogen to build up the biofilm architectures. Importantly, fibrinolysis activated by both bacterial and host plasminogen activators prevent biofilm formation and promote detachment of biofilms. Our finding on anti-biofilm coatings was chosen for press release by the American Society for Microbiology and was subsequently reported in newspapers and blogs in USA, France, Germany, Denmark and Sweden. We will continue with the development of new therapeutic approaches based on these findings. Institution of Medicine/Sahlgrenska Academy supports this project by financing 70% of a PhD student salary. This part of work generated 5 publications in JID, Appl Environ Microbiol, BMC Microbio, and Curr Microbiol.

Summary: Every fifth traveller to (sub)tropical regions contracted resistant intestinal bacteria. Diarrhea and antibiotic use were found to predispose to colonization.

Title: “Study of resistance in Hepatitis C virus prior to treatment with new directly acting antivirals. A Nordic Multicenter Study”, Johan Lennerstrand. Grant sum: 100 000 SEK
Summary: Treatment of HCV infection is since a few years undergoing a paradigm shift with direct-acting agents (DAAs), resulting in a treatment effect of > 90% cure. However, the cost of the new treatment is 0.15 – 0.5 MSEK per patient, depending on the drug combination, duration of treatment and other factors such as genotype (GT), fibrosis stage etc.
Development of resistance occurs when NS5A and NS3-protease inhibitors are used sub-optimal. Even treatment-naïve patients could have resistance associated variants (RAVs) at baseline. Thus, the baseline RAVs, especially NS5A, could contribute to treatment failure, depending on the frequency within HCV quasispecies and the level of resistance to DAA.
At Clinical Microbiology, Uppsala, as the first laboratory in the Nordic countries, we have developed assays for NS3 and NS5A resistance, which are used as routine since 2014. We have started a real-life Nordic multi-center studies, at sites in Uppsala, Gävle, Falun, Örebro, Tromsö and Bodö, where we are studying specific baseline RAVs (Q80K RAV in NS3 GT 1a and Y93H in GT 3a NS5A) to predict treatment outcome together with other negative factors. We expect these two projects to be completed at the beginning of 2018.
It is important to find the most cost-effective treatment combinations/duration, both in a perspective of evidence based healthcare delivery, and in the case of the individual patient to avoid relapse and reducing the retreatment options.

Title: Toll-like receptor 9 enhancement of antiviral immunity in chronic HIV-1 infection: a phase 1b/2a trial", Rasmus Offersen. Grant sum: 100 000 SEK

Summary: We demonstrate that MGN1703 (a TLR9 agonist currently undergoing phase 3 testing for the treatment of metastatic colorectal cancer) induces potent antiviral responses in immune effector cells from HIV-1-infected individuals on suppressive antiretroviral therapy. The significantly improved safety and tolerability profiles of MGN1703 versus TLR-9 agonists of the CpG-oligodeoxynucleotide (CpG-ODN) family are due to its novel "dumbbell-shape" structure made of covalently closed, natural DNA. In our study, we found that incubation of peripheral blood mononuclear cells with MGN1703 results in natural killer cell activation and increased natural killer cell function, which significantly inhibited the spread of HIV in a culture of autologous CD4(+) T cells. Furthermore, we discovered that MGN1703-mediated activation can enhance HIV-1 transcription in CD4(+) T cells, suggesting that this molecule may serve a dual purpose in HIV-1 eradication therapy: enhanced immune function and latency reversal. These findings provide a strong preclinical basis for the inclusion of MGN1703 in an HIV eradication clinical trial.

Title: “Genetic relatedness of vanA vancomycin resistant E. faecium and contemporary ampicillin resistant E. faecium and characterisation of the vanA gene cluster (Tn1546) by whole genome sequencing”, Mette Pinholt. Grant sum: 60 000 SEK
Summary: Genomic epidemiology of vancomycin resistant Enterococcus faecium and dissemination of the vanA transposon (Tn1546) in Copenhagen 2012-14.
Vancomycin resistant Enterococcus faecium (VREfm) is an emergent nosocomial problem. From 2012 - 2014 a ten-fold increase of vanA VREfm isolates was observed in Copenhagen, Denmark. The objective of this study was to determine the clonal structure of the vanA VREfm isolates in Copenhagen. Furthermore, all vanA transposons were characterised to assess their similarity.
Four hundred and ninety five vanA VREfm isolates identified in Copenhagen from January 2012 through December 2014 were whole genome sequenced. The SNP-tree revealed a picture of genetic diversity where the isolates were divided into 19 distinct groups and 25 singletons. Using a similarity threshold of ≤4 SNPs demonstrated that many VREfm isolates were genetically closely related. A total of 318 (64%) isolates differed by ≤4 SNPs to at least five VREfm isolates.
Four different transposon structures were identified. The dominant Tn1546-like transposon (81%) had a deletion of orf1 and an insertion of a transposase IS1251 in the intergenic region between vanS and vanH. Eleven percent had a similar structure including a deletion of orf2. The original Tn1546 structure was present in 4% of the isolates and another 4% had a deletion of orf1 and orf2. Multiple alignments demonstrated that the transposon elements were highly conserved.
Genomic epidemiology has revealed a polyclonal structure of the VREfm isolates. However, within the groups the isolates are genetically closely related. The majority of the isolates contain an identical Tn1546-like transposon. This suggests that dissemination of the Tn1546-like transposon by horizontal transfer into ampicillin resistant, vancomycin susceptible E. faecium, followed by clonal spread of VREfm in the hospitals have contributed to the increase and diversity of VREfm in Copenhagen.

Title: “Chemokines as Antimicrobial Peptides in a Macrophage Infection Model with Leishmania spp”, Sara Søbirk. Grant sum: 60 000 SEK

Summary: Our studies on Leishmaniasis have recently focused on epidemiologcal data, retrieved through retrospective studies of Medical journals, National Health Care Registers and information from the databases of Clinical Microbiology Departments, maínly the one at Public Health Agency of Sweden.
Research data that the SSAC-grant facilitated have been presented at one international Conference (WorldLeish6, Toledo, Spain May 2017, oral presentation), and at the largest national Swedish Conference on Infection Medicine and Clinical Microbiology (Infektionsveckan och Mikrobiologiskt vårmöte, Karlskrona maj 2017, poster).
Two manuscripts are in progress, one already subitted for publication, and one to be submitted within shortly.

Title: “In-vitro activity of solithromycin against anaerobic bacteria in the normal intestinal microbiota of healthy human volunteers”, Andrej Weintraub. Grant sum: 60 000 SEK
Summary: Solithromycin is a novel fluoroketolide with high activity against bacteria associated with community-acquired respiratory tract infections as well as gonorrhea. However, data on the activity of solithromycin against anaerobic bacteria from the normal intestinal microbiota are scarce. In this study, 1,024 Gram-positive and Gram-negative anaerobic isolates from the normal intestinal microbiota were analyzed for in-vitro susceptibility against solithromycin and compared to azithromycin, amoxicillin/clavulanic acid, ceftriaxone, metronidazole and levofloxacin by determining the minimum inhibitory concentration (MIC). Solithromycin was active against Bifidobacteria (MIC50, 0.008 mg/L) and Lactobacilli (MIC50, 0.008 mg/L). The MIC50 for Clostridia, Bacteroides, Prevotella and Veillonella were 0.5, 0.5, 0.125 and 0.016 mg/L, respectively. Gram-positive anaerobes were more susceptible to solithromycin as compared to the other antimicrobials tested. The activity of solithromycin against Gram-negative anaerobes was equal or higher as compared to other tested agents.

Title: “Impact on the intestinal microbiome caused by prophylactic treatment with dicloxacillin and cefuroxime”, Frederik Hertz. Grant sum: 60 000 SEK

Summary: Pending

Title: “Serious cardiac side-effects of fluoroquinolone and macrolide antibiotics”, Malin Inghammar. Grant sum: 100 000 SEK

Summary: Pending