2016.03.08 immem talk salmonella outbreaks

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


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


Three interesting Salmonella outbreaks


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’


1.Salmonella Enteritidis PT8‘slow burn’

‘slow burn’

Salmonella Enteritidis PT8


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’


2. Salmonella Enteritidis PT59

‘Enteritidis can be complex’



14 WGS for Salmonella epidemiology ‘Enteritidis can be complex’



Travel relatedNon-travel related



Outbreak

196 SNPs

In the context of all PHE Enteritidis, the outbreak forms a tight cluster



2 SNPs



3. Salmonella Typhimurium (4, 5, 12:i:-, ST34)

‘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



Date of onset of symptoms by week, February – October 2015 (n=76)*

February – March April - June August - October


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



Red – cases sampled in weeks 49 and 50

Brown - environmental samples


BIO-AEROSOL CROSS-TRANSMISSION VIA THE BUILDING DRAINAGE SYSTEMGormley et al., 2014

Plumbing!


'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.


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


2016.03.08 immem talk salmonella outbreaks

Science