WGS used in ‘near real-time’ to investigate Salmonella outbreak
Multilocus variable-number tandem repeat analysis (MLVA) and Whole Genome Sequencing (WGS) were used to analyse an outbreak that affected Austria, France, Germany, Luxembourg and the UK.
The researchers said WGS was used for the first time in ‘near real-time’ to define a multi-country Salmonella outbreak and inform public health control measures.
In England and Wales, 287 cases met the definition and 69% (198) could be linked to chicken eggs supplied by an unnamed company which has three sites in Germany and one in the Czech Republic.
Investigations at one of the German sites found Salmonella in chicken faeces and dust and eggs with the MLVA outbreak profile; another German site also had eggs positive for the strain.
PHE investigation
Ages ranged from < 1 to 92 years, 151 (53%) were male. Symptom onset dates ranged from 25 May to 7 September 2014.
Seventy-eight cases were reported to have been hospitalised (61 were not thought to have acquired infection while in hospital).
The European Centre for Disease Prevention and Control (ECDC) and European Food Safety Authority (EFSA ) also analysed the incident last year.
In June 2014, Public Health England (PHE) was alerted to an outbreak of S. Enteritidis PT14b in a hospital in central England.
Outbreaks of S. Enteritidis PT14b cases were then detected in the North West and South of England.
PHE was also alerted through the Epidemic Intelligence Information System (EPIS) to six Salmonella outbreaks in France associated with eggs from a German producer and one in Austria.
The human isolates from France, Austria, Germany and Luxembourg had the outbreak MLVA profile.
Following detection of the number of S. Enteritidis PT14b cases in England and Wales, some of whom reported the same MLVA profile, PHE launched a national investigation to identify the source of infection and put in place control measures to prevent further cases.
Cases were interviewed using questionnaires to find out foods eaten in the five days before onset of symptoms. These questionnaires differed depending on where in the UK the case was interviewed.
Isolates were characterised by MLVA typing and WGS so sequencing was carried out using Nextera library preparation and the Illumina HiSeq 2500 in fast run mode.
Case analysis
Between 25 May and 18 June, 32 cases were linked to a single hospital in central England and 17 had spent the whole incubation period there.
Salmonella was considered to be a contributory factor in the death for one patient.
Ninety-nine cases were linked to a restaurant in southern England, 31 to a restaurant in North West England and 14 were linked to a restaurant in central England.
Salmonella was isolated from a catering trolley on a ward at the hospital.
It was also found in food samples (cooked chicken and pork) and an environmental sample (a cleaning cloth) at the restaurant in North West England.
In the restaurant in central England a dishcloth, a swab from a vegetable preparation sink and a sample of egg-containing vegetarian noodles all tested positive.
The researchers said being able to sequence isolates from German eggs made the genetic evidence linking it to the UK cases more compelling.
“We therefore recommend that EU Members States support measures to create a framework to ensure that public health control measures are enhanced by the exchange of pathogen sequencing information.”
Source: Eurosurveillance, Volume 20, Issue 16, 23 April 2015
“A multi-country Salmonella Enteritidis phage type 14b outbreak associated with eggs from a German producer: ‘near real-time’ application of whole genome sequencing and food chain investigations, UK, May to September 2014”
Authors: T Inns, C Lane, T Peters, T Dallman, C Chatt, N McFarland, P Crook, T Bishop, J Edge, J Hawker, R Elson, K Neal, G K Adak, P Cleary
