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Illumina Debuts ‘Metagenomics’ Research Test Kit

BIOTECH: Strengthening Global High-Risk Virus Surveillance

San Diego-based Illumina has unveiled a new, next-generation test to help researchers identify one of the most common infections in the U.S.

Last month, the global leader in DNA sequencing and array-based technologies announced that its new test targeting genitourinary pathogen and antimicrobial resistance (AMR) applies precision “metagenomics” to detect and quantify pathogens, including those that are drug resistant and cause complicated and recurrent urinary tract infections (UTIs).

Metagenomics is the study of genetic material recovered directly from environmental or clinical samples. The broad field is also sometimes referred to as environmental genomics, ecogenomics or microbiomics.

Illumina’s newest metagenomics test kit follows the recent launch of panel testing for 66 viral pathogens that pose persistent threats to global public health.

UTIs are among the most common infections in the U.S., both in the community at large and in hospitalized patients – accounting for an average of 10 million office visits and 1 million hospitalizations per year.

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Genitourinary tract infections are among the most common community and healthcare-associated infections, and rising drug resistance causes increasing morbidity and mortality, health officials say.

Illumina’s new test – called the Urinary Pathogen Infectious Disease/Antimicrobial Resistance (ID/AMR) Panel (UPIP) — comes on the heels of the October launch of two new research tests enabling high-risk virus surveillance.

Company officials say UPIP also identifies more than 20 sexually transmitted pathogens and their respective antimicrobial profile.

The new tests are part of Illumina’s commitment to supporting global preparedness for epidemic and pandemic outbreaks. In less than 48 hours, UPIP detects and quantifies over 170 organisms that can cause genitourinary infections – and more than 3,700 AMR markers associated with 18 different drug classes.

Combined with the use of Explify, a fully automated data analysis platform, this workflow provides a comprehensive infection profile across bacterial, fungal, viral and parasitic microbes.

Dr. Phil Febbo
Chief Medical Officer
Illumina

“The growing threat of infections by common and uncommon microbes with growing antimicrobial drug resistance is alarming; public health and private laboratories require new tools to fight emerging threats. Our UPIP test represents a unique opportunity for microbiologists and clinical researchers to rapidly identify pathogens and potential drug resistance for complicated or recurrent urinary infections,” said Dr. Phil Febbo, chief medical officer of Illumina.

Current testing methods require culture of the urinary sample as the first line of detection for UTIs and STIs, but many organisms do not grow in culture and remain undetected. UPIP detects and quantifies common and underrecognized but crucial uropathogens with no need for culture. UPIP can also identify slow-growing and anaerobic bacteria linked to UTIs that are typically missed in traditional detection methods.

Precision Metagenomics

Illumina says precision metagenomics can reduce the time to learn critical information about microbes from weeks to hours. UPIP is the second precision metagenomics panel on the Illumina Explify platform. It follows the NGS-based Respiratory Pathogen ID/AMR Panel (RPIP) launched in June 2020 in partnership with IDbyDNA, a Salt Lake City-based firm that Illumina acquired in June of this year.

RPIP targets over 280 respiratory pathogens, including SARS-CoV-2, influenza, respiratory syncytial virus, bacteria, fungi, and more than 2000 AMR markers. Both pathogen panels offer culture-free, flexible and scalable workflow in less than 48 hours, comprising a rapid, cost-effective solution for detecting respiratory and urinary tract infections in clinical research settings.

Beyond the clinical research utilization, both RPIP and UPIP can also bring valuable insights to public health and surveillance, being used to monitor respiratory, genitourinary pathogens, and AMR markers in wastewater and environmental samples.

Global High-Risk Virus Surveillance

Public health professionals are more often using genomics for surveillance of epidemics and pandemics. NGS has proven to be a more flexible, rapid and comprehensive approach compared to traditional methods of assessing pathogenic agents – providing a universal, culture-free method for infectious disease characterization and surveillance.

“We believe that a long-term, consistent, proactive genomic surveillance solution focused on high-risk viruses and deployed globally is necessary to help ensure better protection against future outbreaks,” said Dr. Febbo.

In parallel with VSP, Illumina launched the Pan-Coronavirus Panel (Pan-CoV), which allows for the detection and whole-genome sequencing of 203 known coronaviruses and over 370 strains of animal and closely related novel coronaviruses. With this panel, public health and zoonotic researchers can detect and characterize viruses that have the potential to move from wildlife and domestic animals to human populations.

Illumina

FOUNDED: 1998
CEO: Francis deSouza
HEADQUARTERS: San Diego
EMPLOYEES: 7,825
STOCK: ILMN (NASDAQ)
REVENUE: $4.5 billion (2021)
WEBSITE: illumina.com
NOTABLE: Illumina is the world’s leading genomics sequencing company.

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