From molecular detection to clinical decision: Integrating microbiology BCID testing

• Identifying the cause of bloodstream infections is critical to ensure appropriate treatment is prescribed, but traditional testing methods can take several days
• Molecular detection for blood culture identification  provides rapid results for pathogens along with a genetic profile for antimicrobial resistance
• Implementation of templated comments alongside a BCID test on a molecular testing platform can facilitate more guided treatment, faster

Bloodstream infections caused by bacteria, fungi, or viruses can be extremely dangerous. In some cases, the body’s response to infection can lead to sepsis, which is the number one cause of hospital deaths, readmissions, and costs in the healthcare industry.¹ Early identification of the cause of infection is critical to allow appropriate treatment to be given. In the case of sepsis, studies have shown that every hour that treatment is delayed, the risk of death increases by 8%.² Identification of specific pathogens to guide treatment also contributes to reducing inappropriate or broad-spectrum antibiotic prescribing, which is essential for preventing the emergence of drug-resistant bacteria.³

At the 36th Congress of the European Society of Clinical Microbiology & Infectious Diseases 2026, Mateu Espasa, MD from Hospital Clínic de Barcelona, Spain, discussed the challenges of accurately and rapidly diagnosing infections, and how integrating advanced diagnostics in the lab can improve clinical outcomes.

The “gold standard” for identification of pathogens is blood culture.⁴ In Dr. Espasa’s lab, first the blood sample is incubated, before moving on to solid culture incubation, and finally identification and antimicrobial susceptibility testing to determine if the pathogen is susceptible or resistant to specific treatments. He explains that this process takes several days to obtain a result, which is not optimal when time to results matters.

A study from his center analyzed time to positivity and found that real-time reporting of rapidly growing pathogens made a significant difference to 30-day mortality rates.⁵ “There is a need to inform clinicians of results as fast as possible,” he concludes. He also recommends that continuous 24/7 workflows within microbiology would reduce delays, enabling faster diagnosis and improved outcomes. Along with the time taken for identification, the traditional process can lack sensitivity and specificity for some pathogens, increasing the risk of broad-spectrum prescribing.³

Alternatives to traditional methods for diagnosing bloodstream infections are available that can shorten time to results. Molecular testing platforms offer a rapid time to detection, reducing turnaround times from days to hours.⁶ Along with improvement in time, Dr. Espasa notes that molecular testing platforms are useful due to their broad range of detection for bacteria, fungi, and also resistant determinants. Unlike traditional methods, he notes they are also very sensitive and specific for detection of bloodstream infection agents. He notes a French study that found using a molecular testing platform vs standard of care resulted in a 22% increase in patients with an optimized treatment.⁶

Another way in which molecular testing platforms can help within the lab is by freeing up staff time. Dr. Espasa explains that preparing for traditional blood cultures can take over an hour, but preparing for the molecular testing platform is much quicker. “It takes five minutes, and then you wait an hour, maybe an hour and a half, and you get the results,” he says. This ease of preparation and performing the test is an important consideration for optimizing staff time. “Sometimes you only have one lab tech, so by simplifying techniques you save them time and they can get on with other tasks,” says Dr. Espasa. As the platforms provide clear results, they also save time in interpretation.

Although there can be a high upfront cost for molecular testing platforms, Dr. Espasa explains this is balanced out by the savings elsewhere. Along with staff time and resources saved in the lab setting, he sees cost savings in the clinical setting through fewer days staying in the hospital and fewer complications due to early, appropriate treatment. 

Dr. Espasa’s lab has the functionality to provide customized templated comments to clinicians. Specific comments will populate on the molecular testing platform with individual test results. For example, when Staphylococcus aureus and a mec. A gene are detected in a gram-positive blood culture, the customized comment will read as follows: “MRSA detected. Resistant to beta-lactams. Review therapy.”

Or when a carbapenemase resistance gene is detected in a gram-negative blood culture, a templated comment will populate automatically with the result on the molecular platform to say: “Carbapenemase-producing strain. Apply contact isolation. Review therapy. Consult infectious diseases specialist.”

He explains that whether a resistant determinant is found or not, it is important to get these results to clinicians as soon as possible to help guide treatment decisions. Initially Dr. Espasa was concerned about how the clinicians would perceive these comments, admitting, “The first issue that came to my head is that the clinicians are going to say, ‘No way. This is our work.'"

Changing clinician perceptions was therefore important to implementing the change: “In some places the lab is a kind of black box. Samples go in there, and there is a result, and no one knows what is happening in there,” says Dr. Espasa. “We need to become open and clear as to how our work is useful for clinicians. We need to convince them to come to the lab to understand what we are doing, and that our results are of relevance for them.” By working together with clinicians and explaining how the comments can aid them in their role, he has found they are more receptive to them.

Dr. Espasa also sees the comments as a tool for improved antimicrobial stewardship. He explains, “If you have done your work well, then this will impact your stewardship because the clinicians believe in these comments. For example, the microbiologist might say, ‘You don’t have this resistant determinant so you should move to this antibiotic.’ If we have done the work together beforehand, they will realize that these results are good, and that they can follow the stewardship or guidelines.” 

Further evaluation is needed to assess how clinicians are using these comments in the real world, but overall Dr. Espasa thinks they are a really useful tool that can be adapted to suit the work of individual labs. He reiterates the importance of labs working with clinicians on this, noting, “My experience is that if you work together it will improve our work, their work and at last patient outcomes.”

To achieve the best clinical outcomes, Dr. Espasa believes there is not one perfect option. Traditional testing methods and molecular detection methods each have limitations and should therefore be seen as complementary. “We need to diversify our options, to try to do our best,” notes Dr. Espasa. “We’ll have to select which patients, and which samples will profit from molecular technology, and that really depends on the work of your lab.”

Ultimately, he concludes that diagnostic stewardship is about doing what is best for the patient by choosing “the right test, for the right patient, at the right time.”