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Genomic Epidemiology Analysis

Genomic Epidemiology Analysis
Use Microsynths Genomic Epidemiology Analysis service to:
  • 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


A typical workflow for a genomic epidemiology analysis project is shown in the graphic below. Please note that our highly-modular processes allow you various entry and exit options. You may outsource your entire NGS project or only parts of it to Microsynth.
For further reading and a detailed technical description, please download our Application Note Genomic Epidemiology Analysis (see related downloads).



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:

  1. How does the sequenced strain relate to the already known phylogenetic tree of the analyzed microbe? (see Table 1)
  2. Which resistance, virulence and mycotoxin genes are present in the analyzed sample?
  3. 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)
  4. What is the composition of the meta-community if any present? (see Table 3)
  5. Are there novel genes that show significant homology to known protein families? (see Table 4)
Table 1. Result of Multi Locus Sequence Typing (MLST) showing the sequence type of the species found in the sample. In this case, the scheme used for typing included 7 genes (arcC, aroE, glpF, gmk, pta, tpi and yqiL) to identify the respective Sequence Type (ST) and Clonal Complex.
Table 2: Summary table of the number of observed SNVs and small InDels in the analyzed sample including the type of mutation (silent and non-silent).
Table 3. This cutout of a result of a shotgun metagenomics taxonomy assignment, shows the composition of the bacterial community found in the analyzed sample. In this case, the sample contains 96 % of the Staphylococcus genus (Tax Level: G) and 92% are identified as Staphylococcus aureus species (Tax Level: S).
Table 4. Detail of a table showing the homologous protein domains and their significance found for the predicted genes of the analyzed sample.

Turnaround Time

  • 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