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Can a technological shift in clinical pathogen identification improve patient outcome?

23 January 2023

By Alexandria Kilvington, Molecular Biology Technical Sales Specialist at VH Bio


Our bodies are equipped to fight off many pathogens that enter our blood stream. But some microorganisms can take hold when our immune defences are overwhelmed or manage to evade entirely. One of the most important functions of the clinical microbiology laboratory is the detection and characterisation of organisms causing bloodstream infections. The ‘gold standard’ method used in clinical laboratories for the detection of bacterial and fungal pathogens is blood culture (1). Culture methods have evolved due to the ever-changing technological developments (2), but do culture methods run the risk of being out-competed by culture-independent molecular methods?

Routine pathogen detection – how does it work?

Blood culture does what it says on the tin, it is the culture of patient blood to determine microorganism presence. Blood is cultured in an environment which promotes the growth of potentially present microorganisms which can be detected by automated systems monitoring the samples. After this, gram staining is performed which tests for the presence of bacteria and differentiating between gram-positive and gram-negative organisms due to the physical properties of their cell wall. This gives the first indication in treatment direction and is followed by antibiotic susceptibility testing to identify an appropriate treatment. Blood cultures have progressed into commercial, fully automated, and continuous-monitoring blood culture systems which result in earlier detection and better identification of pathogens but there are still limitations.

What are the limitations of blood culturing methods?

Blood cultures rely on a variety of detection principles and cultural environments for the appropriate recovery of pathogens in the blood. Critical factors include adequate skin disinfection at the blood draw site, the volume of cultured blood, incubation time and if the patient has been taking any antibiotics prior to the blood sample being taken. These factors allow the prevention of contamination, inaccurate results, and the incorrect prescription of antibiotics. Blood culturing methods have a low level of sensitivity which can result is false negatives regardless of what the patients’ clinical symptoms may suggest. The low level of sensitivity may be a result of previous antibiotic use and the presence of slow growing or unculturable microorganisms. For example, approximately 30-60% of sepsis patients demonstrate negative blood cultures despite presenting the clinical symptoms (3). This could be detrimental to patients, as in cases of suspected septic shock, each hour in delayed treatment increases mortality risk by nearly 8 % (4). Finally, another critical limitation for patients is the time from blood sample to result and hence effective therapy for the patient. Currently, generating results from blood culturing can take 2-7 days depending on the microorganism. Delayed appropriate treatment may result in prolonged hospitalisation and the administration of broad-spectrum antibiotics which can increase drug resistance (5). These limitations represent a need for improvement in diagnostic methods for microbial detection and identification for the patients which are quicker and more accurate.

Could molecular methods aid in improving current clinical diagnostics?

Microorganisms can be detected and identified through non-culture based molecular methods. Molecular techniques such as nucleic acid probing and amplification to identify both DNA unique to the microorganism and DNA which is universal to the microorganism genus, can allow microbiologists to identify individual organisms or populations quickly at a high level of sensitivity. Methods such as polymerase chain reaction (PCR) enable the rapid identification of microorganisms including those which are slow growing or unculturable which is not achieved in blood culturing methods. Microbial DNA is detected using conserved PCR targets for the microorganism in question which are amplified to allow detection. Real-time multiplex PCR and next generation sequencing (NGS) are other molecular techniques which can identify multiple targets and hence multiple microorganisms within a sample followed by downstream bioinformatic analysis tools. With pathogen panels available for detection becoming increasingly better and the ability to detect select antimicrobial drug resistant markers, DNA-based identification provides a time advantage compared to culture and an increased sensitivity for low level microbial infection.

What are the downsides to molecular technologies?

Currently, the main limitations for molecular methods are the need for skilled microbiologists to perform the tests and that the majority are not validated as diagnostic methods. Due to this, they are unable to replace the current ‘gold standard’ blood cultures and require further clinical study. Molecular methods may however have the potential to be used alongside blood cultures to prevent false negatives.

How will advances in molecular based diagnosis change patient outcome?

100,000 blood stream infections are detected every year within the UK (1,2). According to NHS England, bacterial infections account for approximately 40% of emergency admissions with 66% of total hospital deaths being related to such infections (1). Could a shift in how pathogens are detected improve these figures? Although measures have been implicated to improve patient safety and reduce antimicrobial resistance using blood cultures for diagnosis, molecular based microbial detection methods are quickly improving. Although blood cultures remain the primary diagnostic test available to detect blood stream infection to direct the most appropriate treatment, molecular methods can provide timely and accurate results and aid in reducing false outcomes, hence improving clinical diagnosis. Quicker diagnosis may also play a part in preventing antibiotic resistance in microorganisms. All in all, microbial detection can only improve with advances in knowledge in the microbiology field which will in turn result in improving patient outcome.

How can VH Bio add to this development?

All-inclusive, clinically validated CE-IVD kits for culture-independent, rapid molecular testing of pathogens causing sepsis, endocarditis, joint infections, ascites, peritonitis, meningitis and other diseases are available from Molzym. The CE-IVD assays enable the precise identification of strains at the species level and can diagnose true infections by identifying pathogens in culture-negative patients. Both automated and manual CE-IVD kits are available.

 To further enhance the sensitivity and specificity of molecular methods, enrichment of microbial DNA is beneficial prior to analysis with these downstream applications. Molzym have developed their MolYsis technology which facilitates the extraction and enrichment of bacterial and fungal DNA from human and animal samples. The enriched pathogen DNA can then be used for molecular-based downstream outputs such as PCR and NGS. Commercial kits add degree of standardisation and ease for the introduction of molecular diagnostics into the clinical microbiology lab.


  1.  Public Health England UK Standards for Microbiology Investigations B37 Investigation of blood cultures (for organisms other than Mycobacterium species. Issue no. 8.2 Issue date: 05.09.19 1-55
  2. NHS England 2022 Improving the blood culture pathway – executive summary. A national review of blood culture pathway processes to support better antimicrobial stewardship and improved patient safety. B0686-improving-the-blood-culture-pathway–executive-summary.pdf (
  3. Sigakis, M., Jewell, E., Maile, M., Cinti, S., Bateman, B., Engoren, M. (2020) Culture negative and culture positive sepsis: a comparison of characteristics and outcomes. Anesthesia & Analgesia. 129(5) 1300-1309
  4. Kumar A., Roberts, D., Wood, K., Light, B., Parrillo, J., Sharma, S., Suppes, R., Feinstein, D., Zanotti, S., Taiberg, L., Gurka, D., Kumar, A., Cheang, M. (2006) Duration of hypotension before initiation of effective antimicrobial therapy is the critical determinant of survival in human septic shock. Critical Care Medicine. 34(6) 1589-96
  5. Seymour C., Gesten, F., Prescott, H., Friedrich, M., Iwashyna, T., Phillips, G., Lemeshow, S., Osborn, T., Terry, K., Levy, M. (2017) Time to Treatment and Mortaility during Mandated Emergency Care for Sepsis. The New England Journal of Medicine. 376(23) 2235-2244
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