PathoQuest, a biotechnology company spun out from Institut Pasteur, announced today the on-line publication of results from the PATHOQUEST-1 study. The full manuscript, titled “Untargeted next-generation sequencing-based first-line diagnosis of infection in immunocompromised adults: a multicentre, blinded, prospective study“, is available in Clinical Microbiology and Infection. PATHOQUEST-1 (NCT02007642) is an observational, proof-of-concept study conducted in 2 reference hospitals; Necker-Enfants Malades and Européen-Georges Pompidou Hospitals (Paris, France). It enrolled 101 immunocompromised patients suspected of infection, and compared the performance of PathoQuest’s NGS-based metagenomics test and the conventional diagnostic pipeline to identify pathogens.
The results demonstrated two key findings:
- on samples collected at inclusion in the trial, a clinically relevant pathogen -virus or bacteria- was identified in 3 times more patients with the metagenomics test than with the conventional tests
- the statistically significant higher performance of PathoQuest’s test was maintained when comparing the metagenomics results obtained at inclusion to those cumulatively obtained with the conventional pipeline over 30 days (resp. 36% patients with a clinically relevant pathogen versus 19%)
PATHOQUEST-1 was run with a prototype version of the CE-IVD iDTECT Blood™ test. The 3 key components of the test (i.e. sample preparation, sequencing and data analysis) have been improved to reach the level of performance and validation required for CE marking. Specific steps of the test process have been patented or copyrighted and are proprietary.
“This study demonstrates that the metagenomic test identified a relevant pathogen in more patients in a difficult-to-diagnose population than the conventional pipeline,” said Marc Eloit, PhD, Pathogen Discovery Laboratory at Institut Pasteur, Paris, France, a study investigator and founder and scientific advisor for PathoQuest. “These data underscore the potential of NGS to improve detection and identification of pathogens in routine diagnostic testing of biological samples including blood which is technically challenging.”
“With the broader availability of sequencing platforms in clinical microbiology laboratories, metagenomics-based testing will increase our chances of identifying pathogens in infected patients and allow a better management of infectious diseases, especially in immunocompromised patients where the current diagnostic pipeline frequently fails to identify a responsible pathogen.” added Xavier Nassif, MD, PhD, Head of the Clinical Microbiology Laboratory, Necker-Enfants Malades Hospital, Paris, France, and a study investigator. “These study results should pave the way for such developments”.
About infections in immunocompromised patients
Immunocompromised patients have an impaired or weakened immune system resulting in an increased susceptibility to infection and reduced ability to efficiently respond to such situations. This inability to fight infections can be caused by a number of diseases (such as cancer or leukemia), or drugs (such as anti-cancer therapies or long term immune-suppressants used to prevent organ rejection). Prevalence of these conditions is increasing. Identifying the causative pathogen(s) in immunocompromised patients suspected of infection can be challenging. For instance, only 20 to 30% of blood cultures, the conventional diagnostic test in this clinical situation, are positive for a pathogen in patients developing febrile neutropenia following chemotherapy or stem cell transplantation (1-3). In most other cases, the infection remains of unknown origin, leading to the systematic use of broad spectrum instead of targeted antibiotics. Moreover, these patients are more susceptible to viruses or other microorganisms which have limited or no pathogenicity for non-immunocompromised subjects. Many also receive prophylactic or recurrent courses of antibiotics, making their pathogens difficult to grow in the lab.
1. Gyamarti et al, Scientific Reports, 2016
2. Freifeld et al, CID 2011
3. Gea-Banacloche, Hematology Am Soc Hematol Educ Program. 2013
PathoQuest, a spin out of Institut Pasteur, is a biotechnology company offering a game changing metagenomics approach to improving pathogen detection in biological samples that overcomes the current limitation associated with pathogen detection.
PathoQuest’s technology combines a Next-Generation Sequencing (NGS) platform and a proprietary sample preparation process which is applicable to several types of samples with a proprietary pathogen genome sequence database and automated analysis pipeline. The company’s solution provides microbiologists and clinicians with a comprehensive analysis covering all known clinically relevant human pathogens.
PathoQuest has developed iDTECT™ Blood Test, the first and only clinical CE IVD metagenomic test in infectious disease. Using a single blood sample, the test provides clinicians and microbiologists with an improved method for detecting pathogens, particularly for immunocompromised patients with suspected infections. This new molecular diagnostic test should improve antibiotic stewardship and lead to better patient care through precision medicine.
Based on the company’s technological platform, PathoQuest also offers biopharmaceutical companies a disruptive approach to secure production of biologics like vaccines and recombinant proteins. PathoQuest’s solution is currently being utilized by several major biopharma companies for this purpose.