Download - 2016.03.08 immem talk salmonella outbreaks
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Insight into Salmonella epidemiology from whole genome sequencing
Philip Ashton @flashton2003Gastrointestinal Bacteria Reference Unit
Colindale, London
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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
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Introduction
3 WGS for Salmonella epidemiology
Achtman et al., 2012 Satheesh Nair
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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.
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Platonic ideal of an outbreak
5 WGS for Salmonella epidemiology
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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’
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7 WGS for Salmonella epidemiology
1.Salmonella Enteritidis PT8‘slow burn’
‘slow burn’
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Salmonella Enteritidis PT8
8 WGS for Salmonella epidemiology
Figure 1: S. Enteritidis PT8 cases from 2012 and 2015
Richard ElsonSanch Kanagarajah
‘slow burn’
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9 WGS for Salmonella epidemiology ‘slow burn’
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‘slow burn’
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‘slow burn’
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= isolate from mouse house
‘slow burn’
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13 WGS for Salmonella epidemiology
2. Salmonella Enteritidis PT59
‘Enteritidis can be complex’
‘Enteritidis can be complex’
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Salmonella Enteritidis PT59
14 WGS for Salmonella epidemiology ‘Enteritidis can be complex’
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15 WGS for Salmonella epidemiology
Salmonella Enteritidis PT59
Travel relatedNon-travel related
‘Enteritidis can be complex’
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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’
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17 WGS for Salmonella epidemiology
2 SNPs
‘Enteritidis can be complex’
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18 WGS for Salmonella epidemiology
3. Salmonella Typhimurium (4, 5, 12:i:-, ST34)
‘using WGS to assess interventions’
‘using WGS to assess interventions’
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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’
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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’
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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’
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22 WGS for Salmonella epidemiology
Red – cases sampled in weeks 49 and 50
Brown - environmental samples
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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. '
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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.
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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