Abstracts

Poster Abstracts
n 72
TRANSFORMING PUBLIC HEALTH
MICROBIOLOGY FOR CAMPYLOBACTER
WITH WHOLE GENOME SEQUENCING:
PULSENET AND BEYOND
J. Pruckler 1 , D. Wagner 1 , G. Williams 1 , H.
Carleton 1 , C. Bennett 1 , L. Joseph 1 , E. Trees 1 ,
A. Huang 1 , L. S. Katz 1 , L. Gladney 1 , M. C.
Maiden 2 , W. Miller 3 , Y. Chen 4 , S. Zhao 4 , P.
McDermott 4 , J. Whichard 1 , H. Pouseele 5 , E. M.
Ribot 1 , C. Fitzgerald 1 , P. Gerner-Smidt 1 ;
1
Centers for Disease Control and Prevention,
Atlanta, GA, 2 University of Oxford, Oxford,
UNITED KINGDOM, 3 United States Department
of Agriculture, Albany, CA, 4 United States
Food and Drug Administration, Laurel, MD,
5
Applied Maths, Inc., Sint-Martens-Latem,
BELGIUM.
Background: Conventional phenotypic and
genotypic methods employed for identification
and subtyping of Campylobacter are labor
intensive, expensive, and imprecise. We have
begun development of Enteric Reference Identification
and Campylobacter subtype characterization
whole genome sequence (WGS)
databases. The PulseNet infrastructure (BioNumerics)
will be used in conjunction with the
existing BIGSdb platform to build the databases,
with the goal of characterizing Campylobacter
in a single workflow using WGS.
Methods: Reference genomes (n=103) provided
by FDA and USDA and strains (n=100)
sequenced at CDC were used to develop the
database. Assemblies and annotations were
performed using the Computational Genomics
Pipeline v0.4. These genomes cover the known
members of the species and genera within
Campylobacteraceae and the known genetic
diversity of C. jejuni. The data will be used
to set criteria for the current PubMLST.org/
campylobacter locus definitions. Multiple subschema
are being set up within the databases to
perform identification and scalable, hierarchical
subtyping that will include seven locus,
ribosomal, core genome and whole genome
(MLST, rMLST, cgMLST and wgMLST).
Results: To date 203 reference genomes
have been sequenced, annotated and used for
development of the BioNumerics databases
including an additional 600 isolates that are
being used to validate the prototype databases.
Conclusions: These WGS BioNumerics
databases will provide a single, unified, costeffective
approach for accurate species identification
and subtyping to aid the surveillance of
sporadic and outbreak related Campylobacter
infections. Through continued collaboration
with domestic and international partners, we
will test and refine the nomenclature, databases
and CLIA validate the reference identification
subschema within the next year.
n 73
METAGENOMIC PATHOGEN DETECTION AND
GUT MICROBIOME RESPONSE TO ACUTE
SALMONELLA INFECTION
A. D. Huang 1 , M. R. Weigand 1 , A. Pena-Gonzalez
2 , K. T. Konstantinidis 2 , C. L. Tarr 1 ;
1
Centers for Disease Control and Prevention,
Atlanta, GA, 2 Georgia Institute of Technology,
Atlanta, GA.
Background: Current diagnostic testing
for bacterial foodborne pathogens relies on
culture-based techniques even though many
microorganisms, including known pathogens,
cannot be cultured. Powerful sequence-based
approaches such as metagenomics have potential
to derive epidemiologically-relevant
information directly from complex samples,
bypassing the need to isolate individual organisms.
However, such methods have not been
systematically applied to foodborne pathogen
detection because standardized bioinformatics
techniques for analysis have not been established.
Methods: We applied shotgun metagenomics
to anonymized residual stool samples
collected from foodborne outbreaks attributed
88
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