We apply for a SNAC small UPPMAX 2017 project, including transfer of the data from the current project file on Milou to the new project file. All data that is left on the /proj/b2017045 is considered as “active”.
We will apply for UPPMAX Storage 2017.
In our application for the UPPNEX-project we have had, we mentioned three different projects. We have finalized the first project, which involved a proteomic and genetic analysis of a pathogen called Aerococcus urinae. This work is currently being prepared for submission to an international biomedical journal. The two other projects (described in detail below) have not been finalized yet, although some progress has been made.
We have studied the molecular epidemiology of severe infections with Streptococcus dysgalactiae, which is an emerging human pathogen. We have shown that bacteremia with S. dysgalactiae has a tendency to recur. We have bacteria isolated from blood of the same patient from different episodes and these isolates have been typed by sequencing of the emm gene encoding the M protein. A type denoted StG643 was found to be a common cause of bacteremia both in patients with a single and with multiple episodes. We have whole genome sequenced 24 bacteremia-isolates of S. dysgalactiae type StG643 (Illumina HiSeq 2500, paired-end 125 bp reads) from patients with two episodes and also from patients with single episodes. This enables us to determine if the isolates from the same patient are clonally related despite that the two episodes sometimes were separated more than one year apart. This analysis will also allow us to study the effect on pathogen evolution over time during colonization and dissemination of a given human host.
A clinically important group of anaerobic bacteria is the Gram-positive anaerobic cocci (GPAC), which comprise several different species. Many of the GPAC bacteria are included in the intestinal microbiome. They cause, for instance, wound infections and in some cases also bacteremia (blood stream infections). The mechanisms through which GPAC cause disease are not well described, although some work has previously been done on one species, Finegoldia magna, and its surface proteins. We have prepared samples from 20 bacterial isolates belonging to six different bacterial genera in the GPAC group (Peptoniphilus, Parvimonas, Anaerococcus, Finegoldia, Ruminococcus and Atopobium) and will soon generate whole genome sequences with NGS-technique (Illumina sequencing).
We will analyze the genomes in search for potential virulence factors, such as genes encoding surface proteins with a so-called LPXTG motif. Other potential virulence genes will also be searched for. Also, the antibiotic susceptibility of the GPAC remains poorly studied. The slow growth of GPAC bacteria and their requirement for anaerobic cultivation conditions makes antimicrobial susceptibility testing (AST) difficult. Recently, WGS-based AST have been evaluated with promising results for some bacterial species. Our second aim with this study is to investigate if GPAC bacteria possess resistance genes and if whole genome sequences predict AST results.