Division of Infection and Immunity


Illumina funded project

Precision AMR has partnered with Illumina a Biotechnology Company to offer a funded call.

Closed for applications

We are offering one funded project access to the UCL Pathogen Genomics Unit (PGU) for the comprehensive and rapid detection of respiratory pathogens and associated resistance genes.

Product highlights

The Respiratory Pathogen ID/AMR Enrichment Kit (RPIP) is a next-generation sequencing based, targeted enrichment workflow that delivers highly sensitive, comprehensive pathogen detection and antimicrobial resistance (AMR) insights for 1200+ AMR alleles, 180+ bacteria, 50+ fungi, and 40+ viruses, including SARS-CoV-2. Powered by the IDbyDNA Explify Analysis Software, the flexible and scalable end-to-end workflow, coupled with broad identification of respiratory pathogens and antimicrobial resistance markers in <24 hours, delivers a rapid and cost-effective solution for detection of respiratory tract infections in clinical research settings.

Features of this workflow

Universal detection of respiratory pathogens

Simultaneous detection of RNA and DNA for 180+ bacteria, 50+ fungi, and 40+ viruses, including SARS-CoV-2. The RPIP target enrichment workflow delivers comprehensive detection of critical respiratory pathogens

Detection of antimicrobial resistance genes

Detects 1200+ AMR alleles and provides insights for 16 classes of antibiotics

Strain typing of critical pathogens

Delivers whole-genome information for SARS-CoV-2 and Flu A/B viruses to support public health surveillance and epidemiology

Quality control

Includes probes targeting 10 commercially available spike-in control options


Comprehensive panel design enables cost-effective detection of RNA and DNA respiratory pathogens and antimicrobial resistance alleles all at the same time, from the same assay


Delivers simultaneous detection of bacteria, viruses, fungi, and AMR alleles in <24 hours using the MiniSeq Rapid Reagent Kit.

Sample types

The successful applicant will need to provide nucleic acid extracts to the PGU. Primary samples cannot be accepted.


Costs included

Reagents and the sequencing kits will be provided and costs for these will be included in this call. The kit details are shown below:

Combo SKUProducts included in Respiratory Pathogen ID/AMR Target Enrichment Kit (RUO)Units in Combo SKU

Respiratory Pathogen ID/AMR Target Enrichment Kit A (RUO)


Illumina® RNA Prep with Enrichment (L) Tagmentation, 96 Samples1
Respiratory Pathogen ID-AMR panel + IDbyDNA; 32 enrichments in 3-plex format, 96 samples1
IDT® for Illumina® DNA/RNA UD Indexes Set A, Tagmentation, 96 Indexes1
Explify software, 96 no charge analysis1

Costs not included

General lab wear, any reagents not included in the Illumina library preparation kit and QC reagents. A reduced facility fee will be charged for the sequencing runs. You are strongly advised to speak to the PGU first to understand what these costs are, and if you will be able to cover these costs. These costs will vary from project-to-project, therefore an indicative cost cannot be provided at this stage. These costs will be kept as low as possible as this is a Precision AMR badged project.

Please contact Dr Rachel Williams (PGU Manager) for further information and costs, or visit the PGU website.

Powerful, simple data analysis with the IDbyDNA Explify platform

You will receive 96 samples worth of analysis free of charge from IDbyDNA Explify Platform.

The Explify Respiratory ID/AMR Analysis App offers a paired and tailored data analysis solution for the Illumina Respiratory Pathogen ID/AMR Enrichment Kit. The app provides information on sample composition, including host and microbial abundance, and proportion of targeted vs. untargeted sequences.

This app is available in BaseSpace Sequence Hub. Users can select up to 35 individual samples or project folders containing any number of samples for analysis. Reports include a detailed text-based (JSON) and PDF file format.

Call details

All applications will need to submit a completed (with signatures). Completed application forms should be submitted to: precision.amr@ucl.ac.uk. This call is open to all UCL member of staff and students.


    • Call opens: Tuesday 24 November 2020
    • Call closes: Friday 18 December 2020
    • Projects will be reviewed and awarded over the Christmas period
    • Project start date: January 2021