INTRODUCTION: In April and May 2014, two suspected egg-related outbreaks of @entity10435 ( @entity10435 ) were investigated by the Belgian National Reference Laboratory of Foodborne Outbreaks. Both the suspected food and @entity1 isolates being available, and this for both outbreaks, made these the ideal case study for a retrospective @entity5555 ( @entity5555 ) analysis with the goal to investigate the feasibility of this technology for outbreak investigation by a National Reference Laboratory or National Reference Centre without thorough bioinformatics expertise. METHODS: The two outbreaks were originally investigated epidemiologically with a standard questionnaire and with serotyping, phage typing, multiple-locus variable-number of tandem repeats analysis (MLVA) and antimicrobial susceptibility testing as classical microbiological methods. Retrospectively, @entity5555 of six outbreak isolates was done on an Illumina HiSeq. Analysis of the @entity5555 data was performed with currently available, user-friendly software and tools, namely CLC Genomics Workbench, the tools available on the server of the Center for Genomic Epidemiology and BLAST Ring Image Generator (BRIG). RESULTS: To all collected @entity1 and food outbreak isolates, classical microbiological investigation assigned phage type PT4 (variant phage type PT4a for one @entity1 isolate) and MLVA profile 3-10-5-4-1, both of which are common for @entity1 isolates in Belgium. The @entity5555 analysis confirmed the link between food and @entity1 isolates for each of the outbreaks and clearly discriminated between the two outbreaks occurring in a same time period, thereby suggesting a non-common source of contamination. Also, an additional plasmid carrying an antibiotic resistance gene was discovered in the @entity1 isolate with the variant phage type PT4a. DISCUSSION: For the two investigated outbreaks occurring at geographically separated locations, the gold standard classical microbiological subtyping methods were not sufficiently discriminative to distinguish between or assign a common origin of contamination for the two outbreaks, while @entity5555 analysis could do so. This case study demonstrated the added value of @entity5555 for outbreak investigations by confirming and/or discriminating food and @entity1 isolates between and within outbreaks. It also proved the feasibility of @entity5555 as complementary or even future replacing (sub)typing method for the average routine laboratory.

Whole Genome Sequence Analysis of XXXX PT4 Outbreaks from a National Reference Laboratory's Viewpoint.

@entity1 :: ('9606', 'Species') :: ['human'] @entity5555 :: ('MESH:D042822', 'Disease') :: ['WGS', 'whole genome sequencing'] @entity10435 :: ('149539', 'Species') :: ['Salmonella enterica subsp. enterica serovar Enteritidis', 'S. Enteritidis']
@entity10435 :: (149539,Species) :: ['Salmonella Enteritidis']
