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Genomic Epidemiology Analysis
- De-novo assemble and annotate genomes
- Screen for the presence of virulence, resistance and mycotoxin genes
- Type multiple bacterial strains simultaneously (e.g. cgMLST analysis)
- Determine composition of meta-communities
- Detect genetic variations and study the resulting consequences
Considerations before starting a genomic epidemiology analysis project:
- Is there a reference genome?
- Is there a MLST profile?
- Are larger modifications expected?
- May a substantial DNA contamination occur – metacommunity expected?
- Are there already known resistance, virulence, mycotoxin genes specific for the strain to be analyzed?
Let us guide you – from design to analysis
Example projects using genomic epidemiology analysis:
- Determine the pathogenicity of bacterial DNA isolates by MLST
- Detect SNVs and InDels
- Check for molecular epidemiology of putative carrier strains for virulence, mycotoxicity factors and drug resistance
Applications related to genomic epidemiology analysis:
- Amplicon/shotgun metagenomics
- De novo sequencing
- Microbial resequencing
- Shotgun Transcriptomics
Generally in genomic epidemiology studies a bacterial strain is sequenced and analyzed for its pathogenicity in various ways. Our genomic epidemiology analysis module helps you to answer the following questions, for instance:
- How does the sequenced strain relate to the already known phylogenetic tree of the analyzed microbe? (see Table 1)
- Which resistance, virulence and mycotoxin genes are present in the analyzed sample?
- Are there any variations as single nucleotide variations (SNVs) or small insertions and deletions (InDels) present in relation to a reference genome or reference genes and what is their consequence ? (see Table 2)
- What is the composition of the meta-community if any present? (see Table 3)
- Are there novel genes that show significant homology to known protein families? (see Table 4)
- Delivery of data within 20 working days upon sample receipt (includes library preparation and sequencing)
- Additional 5 working days for data analysis (bioinformatics)
- Express service possible on request