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Illumina introduces new research test to address one of the most common infections in US

San Diego
Thursday, November 3, 2022, 14:00 Hrs  [IST]

Illumina, Inc., a global leader in DNA sequencing and array-based technologies, announced a new research test for genitourinary pathogen and antimicrobial resistance (AMR) identification.

The Illumina Urinary Pathogen Infectious Disease/Antimicrobial Resistance (ID/AMR) Panel (UPIP) applies precision metagenomics to detect and quantify pathogens, including those that are drug resistant that cause complicated and recurrent urinary tract infections (UTIs).

Genitourinary tract infections are among the most common community and healthcare-associated infections, and rising drug resistance causes increasing morbidity and mortality. This announcement comes after the October launch of two research tests enabling high-risk virus surveillance, as part of Illumina's steadfast commitment to supporting global preparedness for epidemic and pandemic outbreaks.

In less than 48 hours, UPIP, a next-generation sequencing (NGS) based panel, 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.  

"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.

In the United States, UTIs are one of the most common infections in the community and in hospitalized patients; they account for an average of 10 million office visits and 1 million hospitalizations per year. The prevalence of drug resistance in disease-causing microorganisms (uropathogens) is increasing, and antibiotic treatment for acute infection or prophylaxis often does not prevent recurrent infections.

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

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 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. 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.

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. It provides a universal, culture-free method for infectious disease characterization and surveillance.

Illumina is committed to supporting preparedness for and response to future large-scale outbreaks and preventing pandemics. In October, it launched the Viral Surveillance Panel (VSP), offering whole-genome sequencing and characterization of 66 viruses, including SARS-CoV-2, influenza, RSV, monkeypox, and poliovirus, which represent a high risk to public health. VSP's design allows researchers and public health scientists to monitor multiple high-risk viruses (both DNA and RNA) proactively, using a variety of sample types, including wastewater, environmental, and post-clinical.

"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 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 is improving human health by unlocking the power of the genome. The company focus on innovation has established us as a global leader in DNA sequencing and array-based technologies, serving customers in the research, clinical, and applied markets.


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