BIOHAZ said that molecular typing methods should provide appropriate discriminatory power, reproducibility, capability for international harmonisation and reduced handling of and exposure to pathogens in laboratories.
Several methods are used in combination to obtain the resolution needed and they depend on the pathogen and the application sought.
The European Food Safety Authority (EFSA) asked the Panel on Biological Hazards (BIOHAZ) to deliver the scientific opinion.
Evaluation of molecular typing methods applied to Salmonella, Campylobacter, Shiga toxin-producing E. coli and Listeria monocytogenes formed part one of the scientific opinion.
It evaluated the effectiveness of the methods for detecting and identifying foodborne outbreaks, estimating contribution of various sources to illnesses and predicting which strains may cause epidemics.
Assessment criteria
Molecular typing methods were assessed on discriminatory capacity, reproducibility, repeatability and current or potential suitability for international harmonisation.
They were evaluated for their appropriateness in different public health-related applications.
Applications include outbreak detection and investigation, attribution modelling, potential for early identification of foodborne strains with epidemic potential and integration of the resulting data in risk assessment.
The BIOHAZ panel said that in the future, bacterial identification and molecular typing may be combined in a single procedure and included in a culture-independent diagnostic process.
Available methods
Current methods include molecular serotyping, restriction fragment length polymorphism (RFLP) analysis, pulsed-field gel electrophoresis (PFGE) analysis, specific gene characterisation and multiple-locus variable number tandem repeat analysis (MLVA).
Sequence-based typing methods such as single locus sequences typing (SLST) and multi locus sequence typing (MLST) were studied.
Novel and prospective technologies, whole genome mapping (WGM) analysis and whole genome sequence (WGS) analysis.
The panel said that even with high-resolution molecular approaches it is not possible to establish how closely two isolates are related without an appreciation of the structure and diversity of the bacterial population in question.
The clear advantage of molecular methods compared to phenotypic methods is that the former have a much higher discriminatory level.
If reliable genetic markers for identifying virulence-associated characteristics of hazardous strains could be identified, then their appearance could raise alerts at an early stage, so control measures could be put in place to prevent or reduce the impact of an epidemic.
Molecular typing methods are laboratory techniques, such as whole genome sequencing, that enable the classification and comparison of strains of disease-causing bacteria.
The panel will produce a scientific opinion covering evaluating requirements for the design of surveillance activities for foodborne pathogens and reviewing the requirements for harmonised data collection, management and analysis by July 2014.
Source: EFSA Journal 2013;11(12):3502, 84 pp
“Scientific Opinion on the evaluation of molecular typing methods for major foodborne microbiological hazards and their use for attribution modelling, outbreak investigation and scanning surveillance: Part 1 (evaluation of methods and applications)”