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Respiratory Pathogen ID/AMR Enrichment Kit

Respiratory Pathogen ID/AMR Enrichment Panel Kit

Library prep and enrichment kit that delivers highly sensitive, comprehensive respiratory pathogen identification and antimicrobial resistance insights.

< 9 hr library prep time

Assay time

< 2 hr library prep time

Hands-on time

Based on volume (not concentration dependent)

Input quantity

See full details in the specifications table

Overview

The Respiratory Pathogen ID/AMR Enrichment Panel (RPIP) Kit is a next-generation sequencing (NGS)-based respiratory pathogen panel and library prep and enrichment kit that targets > 280 respiratory pathogens and > 2000 antimicrobial resistance (AMR) markers in a single assay, providing both pathogen identification and associated AMR information.

Streamlined, sample-to-results workflow

Together with an Illumina sequencing system and Explify RPIP Data Analysis App, the flexible and scalable sample-to-results workflow delivers a rapid, cost-effective solution for identifying pathogens associated with respiratory tract infections in clinical research settings.

View the Explify RPIP Analysis App

Features of this workflow:

  • Comprehensive targeting of DNA and RNA respiratory pathogens and associated AMR markers/alleles that provide known predicted resistance to antimicrobial agents

  • Robust and sensitive detection of low-abundance respiratory pathogen and antimicrobial resistance alleles using various sequencing read lengths and depths

  • Sensitive detection of single or multiple targeted pathogens in low or high complexity samples 

  • Powerful pathogen quantitation using 10 commercially available spike-in controls

Specifications

Assay time < 9 hr library prep time
Automation capability Liquid handling robots
Automation details Explore available automation methods
Content specifications Detects respiratory pathogen DNA and RNA simultaneously and profiles antimicrobial resistance (AMR) gene expression concurrently.
Description Identify respiratory infections and co-infections, detect antimicrobial resistance markers, and perform strain typing of critical pathogens (SARS-CoV-2 and Flu A/B viruses) to study viral evolution and transmission.
Hands-on time < 2 hr library prep time
Input quantity Based on volume (not concentration dependent)
Instruments MiSeq System, NextSeq 550 System, MiniSeq System
Mechanism of action On-bead tagmentation followed by a single hybridization step
Method Targeted DNA sequencing, Targeted RNA sequencing, Target enrichment
Multiplexing Up to 384 samples in a single run with unique dual indexes
Nucleic acid type DNA, RNA
Species category Fungal, Virus, Bacteria
Species details Detects respiratory pathogens (180+ bacteria, 50+ fungi, and 40+ viruses, including SARS-CoV-2) and antimicrobial resistance alleles (1200+).
Technology Sequencing

Required products

In addition to the Respiratory Pathogen ID/AMR Enrichment Panel Kit, you'll need a sequencing instrument, compatible sequencing reagents, and additional products listed in the user guide in the Documentation section. 

/ Results

Applications

The Respiratory Pathogen ID/AMR Enrichment Panel Kit is used for the identification of > 280 respiratory pathogens (including Influenza and SARS-CoV-2) and > 2000 antimicrobial resistance markers in clinical research samples or general surveillance of respiratory pathogens/AMR in samples such as wastewater.

Example workflow

1
Prep

Respiratory Pathogen ID/AMR Enrichment Panel Kit

2
Sequence
3
Analyze

Project recommendations

Instrument Recommended number of samples Read length
MiniSeq System

MiniSeq Rapid Kit: 20 samples per run based on 1M single reads per sample. MiniSeq High-Output Kit: 25 samples per run based on 1M single reads per sample. 

Rapid Kit: 1 × 100 bp.   High-Output Kit: 1 × 75 bp 
MiSeq System

MiSeq v3 Kit: 25 samples per run based on 2M paired-end reads per sample.    MiSeq v2 Kit: 15 samples per run based on 2M paired-end reads per sample. 

MiSeq v3 Kit: 2 × 75 bp   MiSeq v2 Kit: 2 × 150 bp 
NextSeq 550 System

NextSeq 550 High-Output Kit: 384 (available indexes) samples per run based on 2M paired-end reads per sample.  NextSeq 550 Mid-Output Kit: 15 samples per run based on 2M paired-end reads per sample.  

NextSeq 550 High-Output Kit: 2 × 75 bp. NextSeq 550 High-Output Kit: 2 × 150 bp. NextSeq 550 Mid-Output Kit: 2 × 75 bp. NextSeq 550 Mid-Output Kit: 2 × 150 bp. 

Related applications and methods

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Coronavirus software

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Documentation

Product literature
Support documentation

Compare

Respiratory Pathogen ID/AMR Enrichment Panel Kit Illumina Respiratory Virus Enrichment Kit
Assay time < 9 hr library prep time < 9 hr library prep time
Automation capability Liquid handling robots Liquid handling robots
Automation details Explore available automation methods Explore available automation methods
Content specifications Detects respiratory pathogen DNA and RNA simultaneously and profiles antimicrobial resistance (AMR) gene expression concurrently. Targets and characterizes ~40 common respiratory viruses, including SARS-CoV-2, influenza A and B viruses, adenovirus, rhinovirus, respiratory syncytial virus, and other common respiratory viruses.
Description Identify respiratory infections and co-infections, detect antimicrobial resistance markers, and perform strain typing of critical pathogens (SARS-CoV-2 and Flu A/B viruses) to study viral evolution and transmission. A streamlined workflow for detecting and analyzing SARS-CoV-2 and other common respiratory viruses. The agnostic design allows for widespread identification of pathogenic viruses across multiple sample types of interest.
Hands-on time < 2 hr library prep time < 2 hr library prep time
Input quantity Based on volume (not concentration dependent) 10-100 ng
Instruments MiSeq System, NextSeq 550 System, MiniSeq System MiSeq System, NextSeq 550 System, NextSeq 2000 System, MiniSeq System
Mechanism of action On-bead tagmentation followed by a single hybridization step On-bead tagmentation followed by a single hybridization step
Method Targeted DNA sequencing, Targeted RNA sequencing, Target enrichment Targeted DNA sequencing, Targeted RNA sequencing, Target enrichment
Multiplexing Up to 384 samples in a single run with unique dual indexes Up to 384 samples in a single run with unique dual indexes
Nucleic acid type DNA, RNA DNA, RNA
Species category Fungal, Virus, Bacteria Human, Virus
Species details Detects respiratory pathogens (180+ bacteria, 50+ fungi, and 40+ viruses, including SARS-CoV-2) and antimicrobial resistance alleles (1200+). Detects common respiratory viruses, including recent influenza virus strains and SARS-CoV-2. The panel includes probes to human targets as a quality feature, and therefore detects those human targets in every sample assayed.
Technology Sequencing Sequencing

Figures

graph of comprehensive coverage

Comprehensive genomic coverage of critical viral pathogens

Target enrichment probes and the Respiratory Pathogen ID/AMR Panel Kit workflow provide uniform coverage of the two viruses in the panel that are tiled completely with probes.

table of improved detection for panel

Sensitive detection of four different pathogens

Using the Respiratory Pathogen ID/AMR Panel Kit, pathogens were detectable down to 100 genome copies except for A. fumigatus. Detection of Influenza A was more sensitive and detected to 10 genome copies.

table of targets on the panel

Strong correlation between NGS and qPCR quantitation of viral loads.

The Respiratory Pathogen ID/AMR Panel Kit enables quantitation of pathogen levels using a spiked-in control followed by analysis using the Explify RPIP Data Analysis App. This figure shows a comparison of SARS-CoV-2 viral loads in clinical research samples determined by qPCR and NGS. The two methods show significant correlation, Spearman r = 0.87, and importantly, this NGS approach does not require generation of a standard curve like qPCR.

Respiratory Pathogen ID/AMR Enrichment Kit Set A (RUO) (96 indexes, 96 samples)

20047050

Includes all reagents necessary for library prep and enrichment including Illumina RNA Prep with Enrichment kit reagents, IDT for Illumina DNA/RNA UD Indexes Set A, and Respiratory Pathogen ID/AMR Panel to prepare libraries from 96 samples followed by 32, 3-plex enrichment reactions.

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Respiratory Pathogen ID/AMR Enrichment Kit Set B (RUO) (96 indexes, 96 samples)

20046969

Includes all reagents necessary for library prep and enrichment including Illumina RNA Prep with Enrichment kit reagents, IDT for Illumina DNA/RNA UD Indexes Set B, and Respiratory Pathogen ID/AMR Panel to prepare libraries from 96 samples followed by 32, 3-plex enrichment reactions.

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Respiratory Pathogen ID/AMR Enrichment Kit Set C (RUO) (96 indexes, 96 Samples)

20047051

Includes all reagents necessary for library prep and enrichment including Illumina RNA Prep with Enrichment kit reagents, IDT for Illumina DNA/RNA UD Indexes Set C, and Respiratory Pathogen ID/AMR Panel to prepare libraries from 96 samples followed by 32, 3-plex enrichment reactions.

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Respiratory Pathogen ID/AMR Enrichment Kit Set D (RUO) (96 indexes, 96 Samples)

20047052

Includes all reagents necessary for library prep and enrichment including Illumina RNA Prep with Enrichment kit reagents, IDT for Illumina DNA/RNA UD Indexes Set D, and Respiratory Pathogen ID/AMR Panel to prepare libraries from 96 samples followed by 32, 3-plex enrichment reactions.

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FAQs

Results list targeted respiratory pathogens that have at least the minimum level of support that indicates they may be present in the sample. This decision is based on the pathogen sequence data generated and interpreted based on the number of supporting reads and machine learning.

AMR genes are listed together with the associated bacteria and antibiotics against which they can confer resistance. 

Whole genome information is provided for SARS-CoV-2 and Influenza A and B viruses only. Other targeted pathogens are identified based on small, highly informative targeted regions of each genome.

The panel in this kit includes probes that will recognize 10 different commercially available controls. Those controls, however, are not provided as part of this kit and must be purchased separately and then spiked into samples prior to DNA and RNA extraction.  Only one spike-in control is necessary for each experiment/sample. Please contact your Illumina Sales Rep or Tech Support for further information.

We generally recommend starting with 1M single reads, or 2M paired-end reads per sample using a minimum of 1 × 100 bp or 2 × 100 bp sequencing chemistries. These numbers are a starting point and should be optimized based on sample types and target abundance.

Yes. If your experiments can leverage the content and analysis provided by this kit and software, then you can use DNA and RNA extracted from a variety of sample types. Wastewater samples are often tested using this kit for surveillance of respiratory pathogens and their associated AMR. For wasterwater samples, we generally recommend increasing the number of reads to 10M single reads or 20M paired-end reads.
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