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WGS evaluated in Salmonella outbreak

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By Joe Whitworth+

Last updated on 08-Aug-2014 at 14:57 GMT

Watermelons from Brazil were found to be the source of the outbreak
Watermelons from Brazil were found to be the source of the outbreak

An outbreak of Salmonella Newport from watermelon across six countries has been used as an opportunity to evaluate whole genome sequencing (WGS) by researchers.

During the outbreak, 63 confirmed cases of Salmonella Newport were reported across six countries with isolates indistinguishable by pulsed-field gel electrophoresis (PFGE) from the watermelon isolate.

Onset dates ranged from 5 November 2011 to 19 January 2012, with almost half of these between the 28 November and 11 December 2011.

In total, 14 cases were hospitalised: three in England, two in Wales, one in Ireland and eight in Germany.

There were three fatalities: one in England and two in Germany - all three had underlying health conditions.

Greater clarity with WGS data

Researchers found that by using WGS data, they were able to describe with greater clarity the relatedness of strains isolated from cases and watermelons and demonstrate the scale of difference between these organisms and other S. Newport strains concurrently circulating in Europe.

“While it could be deduced from the traceback investigations that the outbreak strain was not European in origin, the WGS data provided objective evidence to confirm the scale of genetic difference between imported and indigenous strains,” said the researchers.

“Understanding these effects should help inform future food-borne outbreak investigations where WGS data analyses could be used to provide important clues as to the geographic origins of implicated food vehicles, which in turn could feed back into hypothesis generation.”

In November 2011, the presence of S. Newport in a ready-to-eat watermelon slice was confirmed as part of a local food survey in England.

In December 2011, cases were reported in England, Wales, Northern Ireland, Scotland, Ireland and Germany.

Germany reported through the Epidemic Intelligence Information System (EPIS) at the European Centre of Disease Prevention and Control (ECDC) fourteen S. Newport isolates that were indistinguishable from the PFGE profile of the sliced watermelon isolate in January 2012.

Four cases with this profile were also reported in Ireland in the same month.

In total, 46 confirmed cases were interviewed of which 27 reported watermelon consumption.

Investigations confirmed the outbreak was linked to the watermelon imported from Brazil.

PFGE using the PulseNet-Europe/Salm-gene protocol was performed on S. Newport isolates from patients with an onset of illness date reported during the outbreak period (31 October 2011 to 31 January 2012).

A subset of isolates from UK cases were selected for WGS, including 24 of 37 outbreak isolates from UK cases and the isolate from the watermelon slice. An additional 11 non-outbreak isolates were selected for comparison.  

WGS to replace conventional typing?

The researchers said as costs decline, and the speed and fidelity of sequencing improve, WGS is becoming an increasingly accessible element of public health microbiology.

“WGS can provide a level of evidence of linkage between specific sources of infection and human cases that is close to irrefutable.

“In view of the sensitivity of reputation for food business operators and food-producing countries, this level of evidence is important in gaining support for intervention measures to protect public health.”

As genome databases expand it is reasonable to expect detection of previously unrecognised links between cases of infection and complex food chains, said the team.

“The challenge for public health microbiology laboratories is to achieve the capacity for rapid sequence determination, data storage and analysis that will allow full exploitation of this powerful new approach.”

Source: Eurosurveillance, Volume 19, Issue 31, 7 August 2014

“A multi-country outbreak of Salmonella Newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by Whole Genome Sequencing: October 2011 to January 2012”

Authors: L Byrne, I Fisher, T Peters, A Mather, N Thomson, B Rosner, H Bernard, P McKeown, M Cormican, J Cowden, V Aiyedun, C Lane, on behalf of the International Outbreak Control Team 

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