Prediction of antibiotic susceptibility profiles from whole-genome sequencing
In order to limit the spread of pathogenic drug-resistant bacteria and to maintain treatment options the analysis of clinical samples and their AMR profiles are essential. Particularly, in low-resource settings a timely analysis of AMR profiles is often impaired due to lengthy culturing procedures for antibiotic susceptibility testing or lack of laboratory capacity. Because of the relatively low costs, the possibility for real-time data analyses, and portability, the Oxford Nanopore Technologies MinION sequencing platform — especially in light of an upcoming less error-prone technology for the platform — appears to be well suited for pathogen genomic analyses. We developed the pipeline CholerAegon for the in silico prediction of AMR profiles of Vibrio cholerae genomes assembled from long and/or short sequencing reads. We aim to adapt our pipeline to other pathogenic microorganisms.
People involved: Sebastian Krautwurst
Collaborations: Kathrin Schuldt, Valeria Fuesslin
In: Front Microbiol, vol. 13, pp. 909692, 2022.
Workflow development for HTS data
High-throughput sequencing (HTS) of DNA and RNA has become a standard procedure in molecular biology. Widely used methods include next-generation sequencing (NGS) of short reads, offered primarily by Illumina, and third-generation sequencing (TGS) of long reads e.g. using Nanopore ONT. With decreasing costs, technological improvements, and wider use, there are more and more HTS datasets. The amount and size of the data can make the analysis difficult. We are developing reproducible, scalable, and portable workflows for processing and analyzing HTS data by deploying workflow management frameworks such as Nextflow. The goal is to provide easy-to-use workflows with state-of-the-art tools for different HTS types and applications.
Molecular serology for rapid determination of vaccination titers
The Permanent Vaccination Commission (STIKO) annually publishes a list of recommended vaccinations. A high vaccination rate in a population is the best requirement to prevent the spread of vaccine-preventable diseases. However, the present system is being challenged by massive migration of people from crisis areas. Therefore, we want to develop a novel diagnostic tool to determine, in a single test run, the antibody status against all vaccinations recommended by the STIKO. For this purpose, new bioinformatic tools for in silico identification of diagnostically relevant epitopes will be developed. This will render the diagnosis faster, less expensive and less time consuming and, at the same time, considerably more informative.
Grants: Zwanzig20 – InfectControl 2020: Molekulare Serologie zur schnellen Bestimmung der Impftiter gegen impf-präventable Infektionskrankheiten (STIKO-Liste) bei Migranten und anderen Patientengruppen; Subproject: STIKO-Serologie
Towards solving the puzzle of aging
Aging is still an enigma, which has challenged scientists and philosophers for centuries. For example, individuals within one species or population show a divers range of life spans (most humans die around 80 years of age, whereas some reach the age of 100 or even more). Which genes are responsible for this variance in lifespan and how exactly is aging caused? We try to help answer these questions by the means of transcriptomic data analysis, including the identification of genes and biological processes that are differentially regulated through time, in different species and tissues.
Grants: RegenerAging — Analyzing the regulation of aging
In: Aging, vol. 13, no. 24, pp. 25694-25716, 2021.
In: Genomics Proteomics Bioinformatics, vol. 18, no. 4, pp. 430–442, 2020.
In: Aging, vol. 11, no. 19, pp. 8556—8572, 2019.
Finding mitogenomes in fungi using short-read NGS data
Mitochondria are essential energy producing cell organelles in eukaryotes. Their genomes are common objects for phylogenetic studies. For fungi, mitochondria play also a key role for pathogenicity and drug resistance. The structure and evolution of the mitogenomes differs between plants, animals and fungi, whereby fungal mitogenomes have been less studied than in plants or animals. The loss of tRNAs and ribosomal proteins has been reported in fungal mitogenome, as well as recombination and variable gene distribution. Hence de novo tools for reconstructing the mitogenome in silico should work with as few information from related species as possible. We will develop a pipeline to find and annotate mitogenomes of fungal short-read NGS data automatically.
People involved: Marie Lataretu
Collaborations: Matthias Bernt
Multiplex-sequencing for different kingdoms
The concept of the German Centre for Integrative Biodiversity Research (iDiv) encompasses the detection of biodiversity, understanding its emergence, exploring its consequences for ecosystem functions and services, and developing strategies to safeguard biodiversity under global change.
To record biological diversity is fundamental but faces many challenges. To analyse genomes and transcriptomes from all organisms e.g. in soil or gut of insects, we usually use different (wet-lab) extraction protocols for bacteria, fungi and viruses. Sometimes also a common host needs to be sequenced. Instead of sequencing about 10 times the same sample from different extraction protocols to obtain the complete biodiversity, we aim to develop a method to multiplex organisms from different kingdoms into one sequencing approach.
People involved: Franziska Hufsky
Grants: DFG iDiv: All-in-one Multiplex-Sequencing