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Insight into Salmonella epidemiology from whole genome sequencing
Philip Ashton @flashton2003Gastrointestinal Bacteria Reference Unit
Colindale, London
2 Revolutionising Salmonella reference microbiology
> 38000 cases of Salmonella
gastroenteritis in the UK per year, of
which > 11000 report to their GP.
Tam et al, 2011, Gut gut.2011.238386
Typhoidal Salmonella as well.
77 deaths in UK 2008, FSA Foodborne
Disease Strategy
Introduction
Introduction
3 WGS for Salmonella epidemiology
Achtman et al., 2012 Satheesh Nair
Introduction
4 WGS for Salmonella epidemiology
PHE have been sequencing all Salmonella isolates received since April 2014.
Since April 2015 it has been the primary test for id and typing.
Platonic ideal of an outbreak
5 WGS for Salmonella epidemiology
Three interesting Salmonella outbreaks
6 WGS for Salmonella epidemiology
1.Salmonella Enteritidis PT8• ‘Slow-burn’ outbreak
2.Salmonella Enteritidis PT59• ‘Enteritidis is more complex than you
think’
3.Salmonella Typhimurium (4, 5, 12:i:-)• ‘Using WGS to assess interventions’
7 WGS for Salmonella epidemiology
1.Salmonella Enteritidis PT8‘slow burn’
‘slow burn’
Salmonella Enteritidis PT8
8 WGS for Salmonella epidemiology
Figure 1: S. Enteritidis PT8 cases from 2012 and 2015
Richard ElsonSanch Kanagarajah
‘slow burn’
9 WGS for Salmonella epidemiology ‘slow burn’
‘slow burn’
‘slow burn’
= isolate from mouse house
‘slow burn’
13 WGS for Salmonella epidemiology
2. Salmonella Enteritidis PT59
‘Enteritidis can be complex’
‘Enteritidis can be complex’
Salmonella Enteritidis PT59
14 WGS for Salmonella epidemiology ‘Enteritidis can be complex’
15 WGS for Salmonella epidemiology
Salmonella Enteritidis PT59
Travel relatedNon-travel related
‘Enteritidis can be complex’
16 WGS for Salmonella epidemiology
Outbreak
196 SNPs
In the context of all PHE Enteritidis, the outbreak forms a tight cluster
‘Enteritidis can be complex’
17 WGS for Salmonella epidemiology
2 SNPs
‘Enteritidis can be complex’
18 WGS for Salmonella epidemiology
3. Salmonella Typhimurium (4, 5, 12:i:-, ST34)
‘using WGS to assess interventions’
‘using WGS to assess interventions’
19
Restaurant
Danie van der Merwe Creative Commons Attribution 2.0 Generic license.
• National chain• Carvery buffet, a la
carte menu, take away• 20,000 covers per
month• Newly built and no
previous issues
‘using WGS to assess interventions’
20 WGS for Salmonella epidemiology
Date of onset of symptoms by week, February – October 2015 (n=76)*
February – March April - June August - October
‘using WGS to assess interventions’
21
Timeline of actionsActions: deep clean, staff training, changing and supervision of carvery staff
Actions: staff sampling
Actions: deep clean, change of management, training, new sinks
Actions: deep clean, staff sampling
‘using WGS to assess interventions’
22 WGS for Salmonella epidemiology
Red – cases sampled in weeks 49 and 50
Brown - environmental samples
23 WGS for Salmonella epidemiology
BIO-AEROSOL CROSS-TRANSMISSION VIA THE BUILDING DRAINAGE SYSTEMGormley et al., 2014
Plumbing!
‘using WGS to assess interventions’
'The mode of viral transmission was identified as airborne aerosolised particles from virus-laden excreta emanating from the drainage system through empty fixture trap seals. '
Summary• WGS allows identification of ‘slow-burn’ outbreaks
• WGS allows identification of international outbreaks
• WGS brings a high degree of certainty to outbreak investigation, allows confidence in oubtreak investigation.
• Context, context, context.
• Always have an open mind.
24 WGS for Salmonella epidemiology
AcknowledgmentsEnteritidis PT8 Outbreak Control Team – Richard Elson, Alison Waldram
Enteritidis PT59 Outbreak Control Team – Roberto Vivancos, Tom Inns
Typhimurium Outbreak Control Team – Philip Monk, Richard Puleston, John Mair Jenkins
Staff in Gastrointestinal Bacteria Reference Unit, Genome Sequencing and Development Unit & Infectious Disease Informatics – Tim Dallman, Kathie Grant
25 WGS for Salmonella epidemiology
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