Programmpunkt

14:00

Titel: Comparison of Fourier-Transform-Infrared (FTIR) Spectroscopy, Whole Genome Sequencing and PFGE for Strain Typing in an Outbreak Investigation
ID: 14/DKMV
Art: Abstractautor
Session: Workshop 03
Diagnostic Microbiology (StAG DV)

Referent: Arthur B. Pranada (Dortmund)


Abstract - Text

Introduction:

Pulsed-field gel electrophoresis (PFGE) is one of the well-established methods for subtyping of bacterial strains in investigations of (possible) outbreaks but often performed only in specialised reference laboratories.

With decreasing costs, more general approaches like whole genome sequencing (WGS) become accessible. Further, Fourier-Transform-Infrared (FTIR) spectroscopy has recently been presented as an easy-to-apply method for strain typing in microbiology routine settings.

 

Objectives:

We have evaluated the applicability of FTIR spectroscopy and WGS for strain typing with a number of strains from an outbreak to assess the handling, complexity and discriminatory power of these technologies.

 

Materials and Methods:

N=17 strains collected between May 2016 and October 2017 from an outbreak with OXA-48-positive K. pneumoniae were analysed by FTIR and WGS.

FTIR spectroscopy was performed with at least 3 technical replicates after overnight culture on an IR Biotyper system (Bruker Daltonik, Germany).

For WGS, DNA of the strains was prepared using the Nextera XT DNA Library Prep Kit followed by sequencing on a MiSeq-Instrument (Illumina, San Diego, USA).

IR Biotyper software and ASA3P (Universität Gießen, Germany) were used for data analysis. PFGE typing had been conducted before at the National Reference Laboratory for multidrug-resistant gram-negative bacteria (Director: Prof. S. Gatermann).

 

Results:

From the N=17 strains, PFGE had found n=13 being related to the outbreak and n=4 individual strains.

This clustering could also be seen in the WGS data.

FTIR grouped 11 of the 13 strains from the outbreak cluster together. The 2 remaining strains were seen as individual strains as well as the 4 other individual strains.

 

Summary:

PFGE and WGS showed 13 strains as being related to the outbreak. FTIR showed similar results with standard algorithms but classified two more strains as being individual.

FTIR results could be obtained after one overnight culture while WGS analysis was available after about 1-2 weeks.