Division of Infection and Immunity


Pathogen Genomics Unit

The UCL Pathogen Genomics Unit (PGU) is an initiative established by grants from the Medical Research Council (Professor Judith Breuer, Dr Mahdad Noursadeghi) and the UCL/UCLH Biomedical Research Centre.

Pathogen Genomics Unit logo

What is the PGU able to do?

The UCL-PGU can carry out the following:

  • Library preparation ± NGS of whole pathogen genomes, amplicons and host exomes
  • Library preparation for enrichment of pathogen genomes or host exomes including from clinical samples or FFPE ± NGS
  • RNASeq for transcriptome analysis or pathogen discovery
  • Amplification of viral resistance genes and amplicon sequencing
  • Sequence analysis and bioinformatics.

We use the Agilent Bravo workstation, which enables us to automate library preparation. This platform can generate libraries from amplicons and isolates. The UCL-PGU has optimised the use of Agilent's SureSelectXT target enrichment protocol for enrichment of pathogen nucleic acid directly from clinical samples and paraffin embedded material for whole pathogen genome sequencing.

The UCL-PGU is also able to undertake genome sequencing for any bacterial isolate, sub-genomic amplicon sequencing including viral resistance genes, and RNASeq including for transcriptome analysis or pathogen detection. In addition, the UCL-PGU is also able to offer sequencing of non-pathogen- related material including human exomes. The UCL-PGU is equipped with an Illumina MiSeq machine, and a BRC-funded Illumina NextSeq.

Next Generation Sequencing for research and clinical applications

Targeted Enrichment

Suitable for whole genome sequencing of pathogens directly from clinical samples. There are three options available for this service: 

1. Customers use bait sets that have already been optimised by the PGU. Pathogens that can currently be sequenced using the targeted enrichment protocol are shown in the table below:

PathogenWGS     GenotypingResistance
Adenovirus (ADV) 
Cytomegalovirus (CMV)
Epstein-Barr virus (EBV) 
Hepatitis B virus (HBV)
Hepatitis C virus (HCV)
Herpes simplex virus (HSV)
Human herpesvirus 6 (HHV6) 
Human Immunodeficiency virus 1 (HIV-1) 
Human papillomavirus (HPV)  
Influenza A (FluA)
Varicella zoster virus (VZV) 
Mycobacterium tuberculosis (Mtb) 
Chlamydia trachomatis (Ct)  
Neisseria meningitidis

In addition, we have listed those pathogens for which we are able to provide antimicrobial or antiviral resistance testing either from amplicons or whole genomes.

2. Customers design, optimize, order and supply their own baits. Per sample charges will be lowered accordingly.

3. Customers collaborate with the UCL-PGU to design and optimize a new bait set. This option is available if customers wish to develop a new bait set for a pathogen that is not already held by the PGU. For further details please e-mail Dr Rachel Williams.

WGS of Bacterial Isolates and Amplicons

The UCL-PGU can sequence whole genomes from bacterial isolates and PCR fragments, including 16S rRNA.

Specialised and Standard RNASeq

The UCL-PGU uses targeted enrichment technology during library preparation for pathogen transcriptome analysis or detection of RNA viruses in clinical samples. In addition, standard RNASeq can be used to analyse pathogen and host transcription simultaneously.

Bioinformatic Analysis

The UCL-PGU can carry out reference and de novo based sequence assemblies for whole pathogen genome sequencing, and RNASeq analysis. Please contact either Professor Judith Breuer or Dr José Afonso Guerra-Assunção to discuss your requirements and to obtain a quote.

How do I arrange for my samples to be sequenced?

To use the UCL-PGU service please e-mail Dr Rachel Williams, who will contact you to:

  • Discuss your exact requirements including, importantly, your starting material, library preparation and sequencing requirements
  • Generate a quote based on your request
  • Send you the sample submission protocol and form
  • Arrange with you when and how to submit samples.