Bioinformatic Analyses of Whole-

Genome Sequence Data in a Public

Health

Laboratory

InFORM 2017

Garden Grove, CA

Dr. Kelly F. Oakeson Ph.D.

UPHL Bioinformatic Workflow

Computational Requirements & Throughput

Oakeson KF, Wagner JM, Mendenhall M, Rohrwasser A, Atkinson-Dunn R.

Bioinformatic Analyses of Whole-Genome Sequence Data in a Public Health

Laboratory. Emerging Infect Dis. 2017 Sep;23(9):1441–5.

Analysis Workflow

Sequence QC

High Quality

Sequence

De novo Genome

AssemblyDraft Genome

Sequence

Annotation

Draft Genome

Annotation

Phylogenetic

Relationships

Phylogenetic Tree

Construction

Analysis Workflow

Sequence QC

High Quality

Sequence

Sequence QC with SeqyClean

lya Y. Zhbannikov, Samuel S. Hunter, James A. Foster, and Matthew L. Settles. 2017. SeqyClean: A Pipeline for High-throughput Sequence Data Preprocessing.

In Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB '17). ACM, New York,

NY, USA, 407-416. DOI: https://doi.org/10.1145/3107411.3107446

Analysis Workflow

Sequence QC

High Quality

Sequence

De novo Genome

AssemblyDraft Genome

Sequence

De novo Genome Assembly with SPAdes

Determine Sequence Overlap

————— —————

Assembled Overlapping Sequence

Assembled Draft Genome Sequence

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell

Sequencing. J Comput Biol. 2012 May;19(5):455–77.

Analysis Workflow

Sequence QC

High Quality

Sequence

De novo Genome

AssemblyDraft Genome

Sequence

Annotation

Draft Genome

Annotation

Draft Genome Annotation with Prokka

Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. Oxford University Press; 2014 Jul 15;30(14):2068–9.

De novo Genome Assembly & Annotation

Analysis Workflow

Sequence QC

High Quality

Sequence

De novo Genome

AssemblyDraft Genome

Sequence

Annotation

Draft Genome

Annotation

Phylogenetic

Relationships

Phylogenetic Tree

Construction

Phylogenetic Analysis with Roary

Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG, et al. Roary: rapid large-scale prokaryote pan genome analysis.

Bioinformatics. Oxford University Press; 2015 Nov 15;31(22):3691–3.

Phylogenetic Analysis with RAxML

RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22: 2688–2690. BMC Bioinformatics; 2009.

Phylogenetic Analysis

Campylobacter

jejuni

• May 2014, three confirmed

cases of C. jejuni infections

• Identical PFGE patterns

• All patients reported raw milk

consumption from dairy “A”

• Additional cases identified

during May and June

• Outbreak investigation initiated

June 10, 2014

• Total of 99 cases

Davis KR, Dunn AC, Burnett C, McCullough L, Dimond M, Wagner J,

et al. Campylobacter jejuni Infections Associated with Raw Milk

Consumption--Utah, 2014. MMWR Morb Mortal Wkly Rep. 2016 Apr

1;65(12):301–5.

Campylobacter jejuni

PFGE

• PFGE performed on 79 isolates

• 61 patient derived isolates

• 18 isolates derived from bulk milk

storage tanks

• 76 of 79 isolates have indistinguishable

SmaI PFGE patterns

Salmonella enterica

• Complex Multi-state Outbreak

• Associated with Rotisserie

Chicken

• Five Distinct PFGE Patterns

• 88 Isolates in Total

• 80 Patient Derived Isolates

• 8 Environmental Isolates

• Sequence Data Obtained From

SRA

Analysis Pipeline

Sequence QC

High Quality

Sequence

De novo Genome

AssemblyDraft Genome

Sequence

Annotation

Draft Genome

Annotation

Phylogenetic

Relationships

Signatures of

Selection

Phylogenetic Tree

Construction

Phylogenetic

Analysis

Molecular Evolutionary Analysis

Thank You

Utah Public Health Laboratory

Robyn Atkinson-Dunn

Andy Rohrwasser

Jenni Wagner

Erik Poole