QuickFISH beats MALDI-TOF in the Clinical Microbiology Laboratory

In recent years, MALDI-TOF has become an increasingly popular means of pathogen identification in the clinical microbiology laboratory. Although this technique has proven to be robust and reliable in many cases, there are occasions where MALDI-TOF may not provide a clear species identification.

Situations that MALDI-TOF can find challenging include:

  • gram positive bacteraemia
  • fungaemia
  • presence of charcoal or resin in culture
  • polymicrobial bacteraemia


Thankfully, the QuickFISH™ system from AdvanDX (based on patented PNA-FISH® technology) is often able to identify pathogens directly from blood cultures in those situations where a MALDI-TOF system may encounter issues. Interest in this capability is high and multiple studies are now appearing in the scientific and medical literature comparing the performance of QuickFISH/ PNA-FISH to MALDI-TOF.

“The PNA-FISH assays allowed identification of bacteria and yeasts 1.3 days before MALDI-TOF and 2 days earlier in the case of polymicrobial infections”

The most recent was undertaken by Calderaro et. al.1 who evaluated PNA-FISH assays in comparison to MALDI-TOF for the identification of Staphylococci, Enterococci, Gram negative rods and yeasts from positive blood and cerebrospinal fluid cultures. A total of 956 cultures were tested, with the data indicating that

“The PNA-FISH assays allowed identification of bacteria and yeasts 1.3 days before MALDI-TOF and 2 days earlier in the case of polymicrobial infections”.

These encouraging results led these authors to observe that the use of PNAFISH would improve laboratory diagnosis of sepsis by providing species identification in a shorter time than culture-based MALDI-TOF identification. It should also be noted that this study employed the first generation PNAFISH: use of the QuickFISH technique would be expected to further enhance the observed effects.

QuickFISH provides results 1 day earlier than MALDI-TOF performed on an isolate”

The most recent publication discussing the application of the QuickFISH system concerns the use of QuickFISH to detect and identify Enterococcus species directly from positive blood cultures.2 In this study, the QuickFISH system maintained the high sensitivity and specificity of the PNA-FISH system, with the additional benefit of further time savings. Interestingly it was also observed that QuickFISH offered the shortest turnaround time of any comparable test, including biochemical assays, amplified assays and MALDI-TOF. More specifically, the authors observed that:

QuickFISH provides results 1 day earlier than MALDI-TOF performed on an isolate”.

Other studies into the potential clinical impact of PNA-FISH have also yielded positive results on the treatment of bacteraemia3 and on the treatment of fungaemia.4 These studies were each conducted in UK hospitals. In both, the data indicated that in a number of cases antimicrobial treatment could have been implemented more effectively had PNA-FISH data been available to clinicians. In addition, Parcell and Orange3 concur with Calderaro et al1 in their assessment that PNA-FISH would be an effective economical alternative to tests such as MALDI-TOF and PCR based methods. Once again, it would be expected that the use of the new QuickFISH methodology would further magnify the positive effects delivered by the use of PNAFISH technology.

In conclusion, there is a growing body of evidence that the PNA-FISH technology can deliver tangible benefits in a clinical setting and that these are especially pronounced when the QuickFISH protocol is used. The technology matches or betters other techniques in terms of sensitivity and specificity but needs no complex instrumentation and is easy to perform in the laboratory. In this way, the use of the QuickFISH technique can offer tangible benefits to patients, clinicians, pharmacists and medical laboratory professionals.



1. Calderaro A. et al. Comparison of PNAFISH assays with culture based MALDI-TOF for the identification of bacteria and yeasts from blood cultures and yeasts from blood cultures and cerebrospinal fluid cultures. Clin Microbiol Infect 2014. Article in Press DOI: 10.1111/1469-0691.12490

2. Deck MK. et al. Rapid detection of Enterococcus spp. Direct from blood cultures using Enterococcus QuickFISH method: a multicentre investigation – in press in Diagnostic Microbiology and Infectious Disease. Diagn Microbiol Infect Dis 2014;78:338-42.

3. Parcell BJ, Orange GV. PNA-FISH Assays for early targeted bacteraemia treatment J Microbiol Methods 2013;95:253-5.

4. Stone NR, et al. Evaluation of PNA-FISH yeast traffic light for rapid identification of yeast directly from positive blood cultures and assessment of clinical impact. J Clin Microbiol 2013;51:1301-2.

This article was published previously in Alpha Laboratories’ Leading Edge Newsletter – Summer 2014.

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