Clinical Diagnostics

Identifying pathogens – the problem associated with the current clinical approach

Patients admitted to hospitals with a fever of unknown origin require rapid and precise identification of microbes which are the cause of their infection. The conventional approach to identifying bacteria and viruses is the use of blood cultures – a method which takes 48 to 72 hours to produce results, requires frequent repetition during the hospital stay, and does not always readily identify infectious agents, especially in immunocompromised patients.

Why are blood cultures not as reliable for identifying microbes in immunomcompromised patients?

  1. They are at increased risk of infection from low virulence (low infectivity) organism which are difficult to culture.
  2. The frequent prophylactic use of antimicrobials in this group of patients may interfere with blood cultures.
  3. Polymicrobial infections (more than one organism) are often missed with this method.

Alternative testing approaches (e.g. PCR-based testing) are available, but these methods are targeted, meaning that they require the doctor to predetermine the list of potential causal pathogens to be tested.

What are the consequences of the limitations of current pathogen identification approaches?

Because of the failure or delay in the identification of a responsible pathogen with the current testing methods, clinicians often empirically utilize broad spectrum antibiotics or combinations of antimicrobial agents which are intended to treat as many pathogens as possible. Unfortunately, the use of non-targeted antibiotics is associated with a number of problems which include:

  • Ineffective treatment, especially if the infection is caused by a virus since viruses are not treatable with antibiotics
  • Opportunistic bacterial or fungal infections (e.g. Clostridium difficile, Candida albicans) due to the broad spectrum antibiotic killing off natural bacterial flora in the body that keeps other pathogenic organisms in check.
  • Ineffective antibiotic stewardship, increasing the risk of development of antibiotic resistance

The above contribute to suboptimal patient outcomes, prolonged hospital stays, treatment related complications, and finally an increased cost of care. Ineffective identification of pathogens, the inappropriate use of antibiotics, and the progressive development of antimicrobial resistance also put patients at risk following commonly performed elective surgical procedures such as prosthetic orthopedic surgery and when receiving cancer treatment.

What is PathoQuest’s solution?

PathoQuest has developed an advanced new method to effectively  identify microorganisms causing infections. This new approach combines 3 key components: next generation sequencing (NGS) and metagenomics, a proprietary sample preparation process, and an curated database of genomic data. Unlike PCR testing, PathoQuest’s approach is non-targeted (unbiased), meaning that there is no need for the clinician to pre-select which pathogens should be looked for by the test.

Click here for more detailed information of PathoQuest’s NGS-based solution for identifying clinical pathogens.