Food & Nutrition Analysis:

Is there a ‘best’ method for the identification of micro- organisms? MALDI-TOF or DNA methods?

MALDI-TOF (Matrix Assisted Laser Desorption/Ionisation Time Of Flight) allows the identification of micro-organisms by profiling proteins (chemo-taxonomy) in a reliable and extremely cost-effective procedure.

Because of its speed, simple protocol and “ready to read” results, it has become the  routine method of choice for pathogen confirmations in the UK food industry.

Additional modules in the application now allow the results to be viewed in greater detail, which opens the prospect of MALDI-TOF being used for typing organisms (Listeria species) and potentially beyond species, to strain level,  which moves the technology into the realms of emulating more complicated DNA based methods such as Multi Locus Sequence Typing (MLST).

With the obvious cost and time benefits associated with MALDI-TOF this capability, on the face of things, seems a very attractive prospect. Especially as current DNA based methods have a reputation for being slightly slower and reliant on a higher level of technical expertise to understand, and interpret, several bioinformatics software packages rarely used in routine testing. However, before deciding on any specific method there are some aspects, which should be taken into consideration.

MALDI- TOF – How  it works?

MALDI investigates microorganism by protein profiling and creates digital representation of “Western Blots” which provide the basis for isolates comparison. By matching these representative images to the reference strains in the MALDI database, the technology indirectly assumes relatedness between isolates and allows differentiation/grouping of “un-disguisable” isolates. The methodology is much the same as that used in  Ribotyping and therefore, in some cases, can have the same inherent limitations.

Limitations of MALDI-TOF

In theory, using MALDI to replace MLST typing seems like a technological breakthrough. However, as MALDI relies on optical comparison it does still face the arguments of reproducibility, reliability and subjectivity even when images have been optimised.  

MALDI typing is mainly focussed on ribosomal proteins to identify bacteria; therefore, further characterisation to strain level implies looking at other protein subsets, highly susceptible to metabolic pathway changes and many variable culturing/environmental factors even for a same organism.

The clear risk is the creation of a  false association between isolates due to external factors rather than true comparison as delivered through the DNA approach.

Conclusions:

Undeniably, MALDI TOF is an excellent tool to deliver accurate, cost effective pathogen confirmations. However, in some applications the technology does have limitations, which reside in the fact that the quality and accuracy of the identification is expressed as a score dictated by proprietary algorithms: It is therefore currently impossible to verify or compare scores between identifications performed on different machines.

This limitation represents real disadvantages for the technology in comparison to DNA sequencing when optimum accuracy and repeatability, necessary for more detailed and sensitive analysis, is critical.

The main driver, which made DNA sequencing such a powerful tool, resides in the access to open resources, not only for the technology but also for data generated, shared and curated by a whole scientific community.

MALDI-TOF is an excellent tool in certain applications and having the expertise to understand its capabilities and limitations, in combination with the ability to deliver DNA solutions beyond those capabilities, is of crucial importance in situations where crisis management and critical path analysis are paramount.

As a leading laboratory in investigative analysis, SYNLAB Food UK have both MALDI-TOF and DNA sequencing as part of our investigative toolbox. More importantly we have the technical expertise, depth of knowledge and industry experience within our team to advise which technique will provide the  most robust and cost effective solutions in any specific scenario. It is this all-round capability, which makes Synlab UK the investigative laboratory of choice for much of the UK food production industry and leading retailers.

 Technical Summary:

MALDI TOF:

  • Proteins profiling analysis, (mainly ribosomal proteins)
  • Proprietary databases
  • Fast
  • Cost effective Reliable for genus/species levels

Subtyping: Approximate to less than Ribotyping level

  • Grouping by indirect comparison/matching to reference organisms of database (limitation by database size and possible lack of representation)
  • Potential interferences due to external factors such as environmental stress/culturing etc… impacting on reliability and reproducibly.

MLST:

  • DNA Sequencing, fully scalable to customer needs.
  • Open resources not only for the technology but also for data, shared and curated by a whole of the scientific community. International schemes
  • Relatively Fast  
  • Reliable for genus/species

Subtyping: Best option in term of reliability/effectiveness

  • Adaptable to any species of bacteria for strain differentiation.
  • The Gold standard as DNA approach for Governmental Institution, especially for characterization of type strain.
  • Offer maximum accuracy, reproducibility, method transparence and traceability.
  • Adaptable and compatible to Next Generation Sequencing.
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