Evergreen Online:

A platform for identification of foodborne

bacterial outbreaks
Judit Szarvas
Overview
• Intro to genomic epidemiology

• The workflow of Evergreen Online

• Evergreen Online platform

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Genomic epidemiology
• Use of genomic data in epidemiological investigations to track infectious
diseases.

• Samples, that differ only in a few single nucleotide polymorphisms

(SNPs), could be related and have a common source.

• Phylogenetic trees are useful for visualizing the relationships between

samples, and clustering related samples.

• Evergreen Online aims to discover foodborne disease outbreaks and

connect clinical samples to sources of the infection.

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The pipeline behind Evergreen Online
• Downloads raw sequencing data from public repositories, uploaded by
public health and food-safety laboratories, etc.

• Divides the data by subtyping

• Calls high-quality SNPs by aligning to references, calculates genetic

distances

• Infers phylogenies

• Displays trees and putative clusters

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 Illumina or IonTorrent
raw sequencing reads

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 Subtyping to find the
closely matching reference

DB

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 A

DB
Aligning reads to
B references
(Z-score 1.96, most
C
common base > 90%)

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A

C
DB

B
DB DB DB
C

D
Pairwise distance
calculation
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A

A TCTAGGCGTNTATTGGTGATGAAATCCCACAGGAAATCC
B TCTCGGCGTTTATTGGTGATGAAATCCCACAGGATATCC
A
C TCTCGGCGTCTATTGGTGATGAAATCCCACAGGNAATCC
D TCTAGGCGTTTATTGGTGATGAAATCCCACAGGAAATCC
B

A B C D
C
DB
A 0 2 1 0
A TCTAGGCGTNTATTGGTGATGAAATCCCACAGGAAATCC
* B B 2 0 2 2
C TCTCGGCGTCTATTGGTGATGAAATCCCACAGGNAATCC
DB
C
DB DB C 1 2 0 2
D 0 2 2 0
D
Pairwise distance
calculation
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A
B
New template set Continued template set No clustered sequences

C A

C
DB
DB DB DB
B
DB DB DB
C
Clustering at 10 SNPs
D
D
Pairwise distance
calculation
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 DB DB DB
A

D Phylogenetic tree
inference A

B
E
C
Report DB

B
DB DB DB
C

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A
New template set Continued template set No clustered sequences

A DB DB DB

B D
C
DB

B
DB DB DB
C
E
Clustered isolates are placed back onto tree with an *
D
Phylogenetic tree
inference Report
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 DB DB DB
A

D
A

Next sequencing batch

B
E
C
Report DB

B
DB DB DB
C

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Evergreen Online platform
https://cge.cbs.dtu.dk/services/Evergreen/

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Evergreen Online platform

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Evergreen Online platform

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SRR5188978

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Evergreen Online platform

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 Thank you for watching

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