Abstracts

Oral Presentation Abstracts
laboratories in the states and internationally to
build applications to extract information about
genus, species, lineage, serotype, pathotype,
virulence profile and antimicrobial resistance
markers and subtyping using gene by gene approaches
(whole genome multi-locus sequence
typing, wgMLST) from the genome sequences.
The PulseNet foodborne disease surveillance
network infrastructure and analytical platform
(BioNumerics, Applied Maths) and database
will be used because of its versatility and
because the public health laboratories have
worked with it for > 15 years. Additionally,
the use of this analytic software does not require
extensive bioinformatics skills or local
high performance computing capacity. The
method will also be validated and will replace
conventional CLIA related reference identification
activities in the branch and public health
laboratories. Results: WGS has successfully
been tested for the US national surveillance
of listeriosis since September 2013 and the
wgMLST analysis has been implemented in
the daily routine. The technology has proven
its power supplementing traditional methods in
outbreak investigations by adding phylogenetic
relevance and increased resolution compared
with current methods thereby enhancing case
definitions and source tracking. The wgMLST
method is currently being piloted in-house
for surveillance of Campylobacteraceae,
Shiga toxin-producing E. coli, and Salmonella
with the remainder of foodborne bacteria to
be added over the next three years. A betatesting
pilot with the PulseNet public health
laboratory partners will start in summer 2015.
Conclusion: WGS will revolutionize the surveillance
of both sporadic and outbreak related
foodborne infections by replacing and enhancing
current laboratory methods in use in public
health laboratories.
n S4:4
SALMONELLA SEROTYPE DETERMINATION
UTILIZING HIGH-THROUGHPUT GENOME
SEQUENCING DATA
S. Zhang 1 , Y. Yin 2 , M. Jones 3 , Z. Zhang 4 , B.
Deatherage Kaiser 5 , B. Dinsmore 6 , C. Fitzgerald
6 , P. Fields 6 , X. Deng 1 ;
1
University of Georgia, Griffin, GA, 2 Illinois
Institute of Technology, Chicago, IL, 3 J. Craig
Venter Institute, Rockville, MD, 4 University of
Michigan, Ann Arbor, MI, 5 Pacific Northwest
National Laboratory, Richard, WA, 6 Centers
for Disease Control and Prevention, Atlanta,
GA.
Serotyping forms the basis of national and
international surveillance networks for Salmonella,
one of the most prevalent foodborne
pathogens worldwide. Public health microbiology
is currently being transformed by whole
genome sequencing (WGS) which opens the
door to serotype determination using WGS
data. SeqSero (www.denglab.info/SeqSero)
is a novel web-based tool for determining
Salmonella serotypes using high-throughput
genome sequencing data. SeqSero is based
on curated databases of Salmonella serotype
determinants (rfb gene cluster, fliC and fljB
alleles) and is predicted to determine serotype
rapidly and accurately for nearly the full spectrum
of Salmonella serotypes (more than 2,300
serotypes), from both raw sequencing reads
and genome assemblies. The performance of
SeqSero was evaluated by testing: 1) raw reads
from genomes of 308 Salmonella isolates of
known serotype; 2) raw reads from genomes
of 3,306 Salmonella isolates sequenced and
made publicly available by GenomeTrakr, a
U.S. national monitoring network operated
by the Food and Drug Administration; and 3)
354 other publicly available draft or complete
Salmonella genomes. We also demonstrated
Salmonella serotype determination from raw
sequencing reads of fecal metagenomes from
mice orally infected with this pathogen. Seq-
Sero can help to maintain the well-established
ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic
Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens
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