Source attribution in Campylobacter jejuni
Daniel Wilson
Nuffield Department of Clinical Medicine
www.danielwilson.me.uk
JR Microbiology Seminar 16th November 2010
QuickTime™ and a decompressorare needed to see this picture.
QuickTime™ and a decompressorare needed to see this picture.
Paul FearnheadLancaster University
Andrew FoxHealth Protection Agency
QuickTime™ and a decompressor
are needed to see this picture.
Edith GabrielUniversite d’Avignon
QuickTime™ and a decompressor
are needed to see this picture.
Peter DiggleLancaster University
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressorare needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
Petra MullnerMassey University
Nigel FrenchMassey University
QuickTime™ and a decompressor
are needed to see this picture.Martin MaidenUniversity of Oxford
Sam SheppardUniversity of Oxford
Funded byHEFCE, DEFRA, EPSRCWellcome TrustFood Standards Agency ScotlandNew Zealand Food Safety Authority
Evolutionary genetics as a framework for understanding genetic diversity
GeneticsRelatedness
Contact tracing
Population structure
Transmission
Source attribution
Epidemiology
Population dynamics
R0
Resistance genesHost
susceptibilityVaccination
Diagnosis
Evolution
Adaptation
Emergence
Control + prevention
Inferring host-host transmission: zoonotic transmission of Campylobacter jejuni
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
Foodborne illness in the UKFood Standards Agency figures for 2000
Salmonella 16,987 20.9%
Campylobacter 62,867 77.3%
E.coli O157 1,147 1.4%
Clostridium perf. 166 0.2%
Listeria 113 0.1%
Total 81,280
$8bnAnnual cost to US economy
Buzby et al. JID (1997)
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
Cases and controls RiskSignificance
Poisson point process
QuickTime™ and a decompressor
are needed to see this picture.
Seasonal patterns
Harmonic regression
25.4% reduction year-on-year
Multi-locus sequence typing (MLST)
tkt 459bp
glyA 507bp489bp uncA
498bp pgm
402bp gltA
477bp glnA
477bp aspA
1.6 million bp genome
MLST: 3300 bp in total(0.2%)
QuickTime™ and a decompressor
are needed to see this picture.
0
20
40
60
80
100
120
140
21 257 48 104 45 53 50 19 61 574
Sequence Type
Abundance
21
257
48104
4553
50
1961
574
Multi-locus sequence typing (MLST)
ST 21: 2 1 1 3 2 1 5
ST 104: 2 1 1 3 7 1 5
ST 50: 2 1 12 3 2 1 5
ST 21: 2 1 1 3 2 1 5
CATTLE cattle 212beef offal or meat 47calf 12cows milk 11calf faeces 1cattle faeces 1 284
CHICKEN chicken 222chicken offal or meat 153chick 17 392
BIRD wild bird 172starling 71goose faeces 25turkey 22goose 12duck 7starling faeces 4 313
ENVIRONMENT sand (bathing beach) 52environmental waters 28soil 3potable/drinking water 2 85
SHEEP sheep 84lamb offal or meat 74lamb 10sheep faeces 2 170
PIG pig 35pork offal or meat 10piglet 1 46
broiler environment 17cat 3dog 5farm slurry 10gazelle 1giraffe 1goat 5horse 1human blood culture 57human stool 1684human unspecified 102marmoset 2ostrich 1other animal 25rabbit 3unspecified 144
BIRD
CATTLE
CHICKEN
ENVIRONMENT
PIG
SHEEP
Haplotype structure in sequences of known originfrom pubMLST
origin
BIRD
CATTLE
CHICKEN
ENVIRONMENT
PIG
SHEEP
Haplotype structure in human isolates
key
NOVEL
BIRD
CATTLE
CHICKEN
ENVIRONMENT
PIG
SHEEP
Haplotype structure in human isolates
key
NOVEL
Attributing novel genotypes ST 574: 7 53 2 10 11 3 3 Human-specific, but similar to...
ST 305: 9 53 2 10 11 3 3 ST 713: 12 53 2 10 11 3 3 ST 728: 4 53 2 10 10 3 3 ST 2585: 7 2 3 10 11 3 3
All these found in chicken, so the likely source is chicken
QuickTime™ and a decompressor
are needed to see this picture.
Zoonotic transmission in Campylobacter jejuni
Zoonotic transmission in Campylobacter jejuni
QuickTime™ and a decompressor
are needed to see this picture.
Zoonotic transmission in Campylobacter jejuni
QuickTime™ and a decompressor
are needed to see this picture.
CATTLE
SHEEP
CHICKEN
PIG
BIRD
ENVIRONMENT
CATTLE
SHEEP
CHICKEN
PIG
BIRD
ENVIRONT
HUMAN
Does it work?Empirical cross-validation
Split sequences of known origin into two groups. Treat one group as having unknown origin (pseudo-human cases)
Infer the proportion of pseudo-human cases drawn from each source population
Repeat 100 times to study the performance of the method
Simulation and empirical cross-validationResults: Linked model
Unlinked model Linked modelPredicted Correct 0.86 0.66Actual Correct 0.56 0.58Coverage CATTLE 22 100
CHICKEN 85 82BIRD 81 100
ENVIRONMENT 63 99SHEEP 16 98
PIG 89 94Combined 18 95
Bias CATTLE -0.13 0.00CHICKEN -0.01 -0.05
BIRD -0.02 -0.02ENVIRONMENT -0.01 0.00
SHEEP 0.16 0.06PIG 0.01 0.00
RMSE CATTLE 0.14 0.08CHICKEN 0.03 0.05
BIRD 0.03 0.04ENVIRONMENT 0.03 0.04
SHEEP 0.17 0.09PIG 0.01 0.01
Gene flow between source populations
Case-by-casesourceprobability
CATTLE
SHEEP
CHICKEN
PIG WILD BIRDENVIRONMENT
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
The evidence provided by our approach has supported national policy making by providing an important contribution to the New Zealand Food Safety Authority (NZFSA) Campylobacter Risk Management Strategy (2007), which has subsequently included mandatory targets for limiting contamination with Campylobacter spp. of chilled poultry carcasses. The introduction of these interventions has coincided with a dramatic decrease in human campylobacteriosis notifications to a 16-year low. In 2008 some 6689 human cases were reported in New Zealand compared to 15,873 cases in 2006; the year before the announcement and implementation of control measures.
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
Conclusions Incidence is spatially heterogeneous at broad scales and clustered at fine
scales.
Urban areas suffer greater incidence of campylobacteriosis in general, and poultry-associated infections in particular.
Incidence is periodic, peaking in summer.
The primary source of Campylobacter jejuni infectious to humans is meat, in particular poultry.
The further observation that environmental sources appear unimportant strongly suggests a food-borne transmission route.
These patterns are consistent in England, Scotland and New Zealand.
Measures to limit Campylobacter infection in poultry appear to have reduced human disease in New Zealand.
www.danielwilson.me.uk
Top Related