Onlineumfrage zur Anwendung von molekularbiologischen Typisierungsverfahren und MALDI-TOF-MS in diagnostischen Laboren in Deutschland

[Assessment of available and currently applied typing methods including genome-based methods for zoonotic pathogens with a focus on Salmonella enterica]

BACKGROUND

In recent years, whole genome sequencing (WGS) in combination with bioinformatic analyses has become state of the art in evaluating the pathogenicity/resistance potential and relatedness of bacteria. WGS analysis thus represents a central tool in the investigation of the resistance and virulence potential of pathogens, as well as their dissemination via outbreak clusters and transmission chains within the framework of molecular epidemiology. In order to gain an overview of the available genotypic and phenotypic methods used for pathogen typing of Salmonella and Shiga toxin-producing and enterohemorrhagic Escherichia coli (STEC/EHEC) in Germany at state and federal level, along with the availability of WGS-based typing and corresponding analytical methods, a survey of laboratories was conducted.

METHODS

An electronic survey of laboratories working for public health protection and consumer health protection was conducted from February to June 2020.

RESULTS AND CONCLUSION

The results of the survey showed that many of the participating laboratories provide a wide range of phenotypic and molecular methods. Molecular typing is most commonly used for species identification of Salmonella. In many cases, WGS-based methods have already been established at federal and state institutions or are in the process of being established. The Illumina sequencing technology is the most widely used technology. The survey confirms the importance of molecular biology and whole genome typing technologies for laboratories in the diagnosis of bacterial zoonotic pathogens.

Aus der § 64 LFGB-Arbeitsgruppe MALDI-TOF: Leitlinien für die Validierung von Spezies-Identifizierungen mittels MALDI-TOF-MS

Matrix-assisted laser-desorption/ionization-time-of-flight-mass-spectrometry (MALDI-TOF-MS) is widely used to identify microorganisms. Recently, new applications such as identification of the animal species from meat, milk or fish are emerging. Standards for the validation of species identifications are still missing. Now, the § 64-LFGB working-group “MALDI-TOF”, established at the Federal Office of Consumer Protection and Food Safety, has compiled a guideline for the validation of species identifications. This guideline is intended for single laboratories as well as for lab networks and shows practical ways for validation of qualitative MALDI-TOF-MS methods. The special opportunities of the technology, in particular the use of extended reference databases and of collections of well-documented individual spectra for validation, have been taken into account in the guideline presented.