SMBE Satellite Meeting on Pathogen Evolution and Transmission
-
Upload
jennifer-gardy -
Category
Science
-
view
491 -
download
0
Transcript of SMBE Satellite Meeting on Pathogen Evolution and Transmission
Genomics in the public health TB lab:what have we done, where are we
going, and why does evolution keep screwing everything up?
@JENNIFERGARDY
DATELINE: PORT ALBERNI, 2008-2010
DARWIN-O-METERWINNINGNESSGENOMES SEQUENCED
36BUREAUCRACY
• Sequenced 36 genomes - why did this outbreak happen? • Micro-evolution lets us deduce transmission
DATELINE: KELOWNA, 2011
• 40 (33) new genomes - local health authority wants to know, “is our outbreak control strategy appropriate?”, we want to know, “where did this outbreak come from”?
DATELINE: KELOWNA, 2011
DARWIN-O-METERWINNINGNESSGENOMES SEQUENCED40
BUREAUCRACY
• 40 (33) new genomes - local health authority wants to know, “is our outbreak control strategy appropriate?”, we want to know, “where did this outbreak come from”?
BUILD A TIME-LABELLED PHYLOGENY AND USE TRANSPHYLO TO IDENTIFY TRANSMISSION EVENTS.
Caroline Colijn & Xavier Didelot
BACK-CALCULATE THE SET OF TRANSMISSION EVENTS THAT COULD HAVE GIVEN RISE TO THE SUITE OF OBSERVED PHYLOGENIES.
DATELINE: VANCOUVER, 2012
DARWIN-O-METERWINNINGNESSGENOMES SEQUENCEDLOTS
BUREAUCRACY
• Can we figure out every interesting bit of TB epidemiology in BC with genomics?
Resurrect all culture-positive cases in our freezer
Extract dna from said cases
miru-vntr “everything” (2005-2014)
do some descriptive epidemiology
sequence everything in clusters
do some genomic epidemiology
figure out interesting trends
~4500
2350
1200
Resurrect all culture-positive cases in our freezer
Extract dna from said cases
miru-vntr “everything” (2005-2014)
do some descriptive epidemiology
sequence everything in clusters
do some genomic epidemiology
figure out interesting trends
~4500
2350
1200
Resurrect all culture-positive cases in our freezer
Extract dna from said cases
miru-vntr “everything” (2005-2014)
do some descriptive epidemiology
sequence everything in clusters
do some genomic epidemiology
figure out interesting trendsDATELINE: VANCOUVER, 2016
DARWIN-O-METERWINNINGNESSGENOMES SEQUENCED276+
BUREAUCRACY
by 2014, the outbreak had grown to 52 cases and 2310 screened clients.
COULD THE OUTBREAK BE DECLARED OVER?2008 2009 2010 2011 2012 2013
7 7
11 12
86
1
DATELINE: VANCOUVER, 2015
WINNINGNESSGENOMES SEQUENCED11
DARWIN-O-METER BUREAUCRACY
• 4x suspected lab contamination events • What happened? Can genomics confirm? • How can we detect this in future?
Of 345 Mycobacterial samples tested, 322
were correctly predicted from miseq
genomic data.
94% of the 168 resistance-typed mtb
isolates were correctly predicted.
WGS TURNAROUND WAS
FOR CONVENTIONAL LAB DIAGNOSIS AND TYPING.
5 DAYS VS 31
Of 345 Mycobacterial samples tested, 322
were correctly predicted from miseq
genomic data.
94% of the 168 resistance-typed mtb
isolates were correctly predicted.
WGS TURNAROUND WAS
FOR CONVENTIONAL LAB DIAGNOSIS AND TYPING.
5 DAYS VS 31
DATELINE: VANCOUVER, 2017
WINNINGNESS
750+GENOMES SEQUENCED DARWIN-O-METER BUREAUCRACY