Re-evaluation of a 2014 multi-country European outbreak of Salmonella Enteritidis phage type 14b using recent epidemiological and molecular data

Abstract

A European multi-country outbreak of Salmonella Enteritidis phage type (PT) 14b occurred from March to November 2014 associated with the consumption of eggs. The outbreak involved more than 400 human cases from France, Luxembourg, Austria and the United Kingdom. In 2016–2017, it has been re-evaluated combining recent epidemiological results with latest molecular data. The outbreak was traced back to one large Bavarian egg producer with four distinct premises, three located in Bavaria, one in the Czech Republic. The outbreak isolates of S. Enteritidis PT 14b were grouped into three closely related clades by whole genome sequencing. Two of these clades could be referred to two Bavarian premises of the egg producer on the basis of epidemiological and molecular data, while epidemiological data presumably linked the third clade to another premises of the egg producer. Interestingly and in contrast to the situation in other European countries where several outbreaks were documented, all notified 91 laboratory-confirmed cases of S. Enteritidis PT 14b from Bavaria were sporadic, singular cases not belonging to any epidemiological outbreaks. In conclusion, as demonstrated here, the resolution of food-related outbreaks with such a high discriminatory power is rare in outbreak investigation.

Identification of Genetic Features for Attenuation of Two Salmonella Enteritidis Vaccine Strains and Differentiation of These From Wildtype Isolates Using Whole Genome Sequencing

“…Whole genome sequencing (WGS) has been applied as an epidemiological tool for outbreak investigations as it provides high resolution for comparing genomes (12). In the United Kingdom, where human isolates of Salmonella are routinely sequenced, WGS has been used successfully to identify and investigate Salmonella outbreaks (13)(14)(15). Typing of all Salmonella isolates with WGS is planned at Animal and Plant Health Agency (APHA) in a near future and will include differentiation of the vaccine from the field isolates, removing the need for phenotypic testing of vaccine types.…”

Elucidation of global and local genomic epidemiology ofSalmonella entericaserovar Enteritidis through multilevel genome typing

“…Thus, MGT4-CC13 is more likely to cause large scale outbreaks than MGT4-CC1. In the past few years, the reported large scale outbreaks in Europe, the majority of which were due to the contaminated eggs [18,19,22,26], belonged to MGT4-CC13.…”

“…Other studies used SNP address or cgMLST [18,19,26] with SNP cut-offs or HierCC clustering for outbreak detection. All three methods use the same single linkage clustering method for outbreak detection.…”

“…Such a pattern of birth and death of a ST may be related to outbreaks. For example, MGT5-ST156, which increased substantially during June and July in 2014 and became rare after 2015, was associated with a reported large scale outbreak[19]. Other STs persisted for long periods of time.…”

Genetic diversity and delineation of Salmonella Agona outbreak strains by next generation sequencing, Bavaria, Germany, 1993 to 2018

“…Serotyping is still serving as a gold-standard technique for routine typing. In combination with other typing techniques like phage typing, it may be suited for the investigation of small, geographically limited outbreaks [7]. However, many serovars are polyphyletic and serotyping sometimes confounds genetically unrelated isolates and thus does not recognise evolutionary groupings in some cases.…”