Abstracts

Poster Abstracts
resources leading to more effective epidemiologic
field investigations and an improved
ability to identify where public health intervention
will have the greatest impact. This curated
data set can be used to evaluate bioinformatic
pipelines for variant detection using whole
genome SNP or multi-locus sequence typing
(wgMLST) platforms.
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RAPID WHOLE GENOME SEQUENCING
AND DE NOVO ASSEMBLY PIPELINE FOR
BORDETELLA PERTUSSIS USING MULTIPLE
PLATFORMS
Y. Peng, M. M. Williams, M. R. Weigand, K.
Bowden, M. L. Tondella;
Centers for Disease Control and Prevention,
Atlanta, GA.
In the U.S. and many other developed countries,
pertussis is currently the least well controlled
vaccine‐preventable bacterial disease
despite excellent vaccination coverage. Whole
genome sequences of Bordetella pertussis, the
causative agent of pertussis disease, will help
us better understand the epidemiologic and
clinical relevance of current circulating strains,
develop novel diagnostic assays, and elucidate
the possible reasons for the current increase
in pertussis in the U.S. and around the world.
However, with hundreds of insertion sequences,
repeat regions, and large rearrangements
in the B. pertussis genome, whole-genome
sequencing and assembly is challenging. There
are currently over 400 B. pertussis incomplete
genome assemblies publically available,
most of them are composed of over hundreds
contigs assembled from short read sequencing.
Our group has developed a rapid whole
genome sequencing and assembly pipeline for
B. pertussis by taking advantage of the latest
long read PacBio RSII sequencing platform;
highly accurate, high coverage and low cost
Illumina sequencing platforms; and the OpGen
genome optical mapping system. High quality
genomic DNA was isolated with the Qiagen
Puregene Yeast/Bact. Kit. Utilizing P6 PacBio
chemistry and 240 minutes movie recording,
one SMRT cell produced over 50 X coverage
subreads with N 50
as high as 13 kb, which was
able to assemble into one complete genome using
HGAP 3.0. After removing the end overlap
to close the circular genome, the structure of
de novo assemblies was further tested and confirmed
by optical mapping and finally polished
by mapping with high quality short Illumina
reads. So far, nearly 200 genomes have been
completed using this multi-platform pipeline
and sequencing of more than 200 additional
isolates is currently underway. Deep genome
variation analysis (SNPs, rearrangements and
IS-elements, etc.) will direct future work with
other ‘omics’ approaches, including RNASeq
and peptide profiling, to determine causes for
pertussis increase.
n 87
DEVELOPMENT OF A SUBTYPING ASSAY
FOR DIRECT DETECTION AND TARGETED
SEQUENCING OF SHIGA TOXIN-PRODUCING
ESCHERICHIA COLI (STEC) FROM CLINICAL
SAMPLES
L. M. Gladney 1 , D. Fasulo 2 , R. L. Lindsey 1 , A.
Huang 1 , E. Trees 1 , N. Strockbine 1 , E. R. Ribot 1 ,
H. A. Carleton 1 , J. Besser 1 ;
1
Centers for Disease Control, Atlanta, GA,
2
Pattern Genomics, LLC, Madison, CT.
Shiga toxin-producing Escherichia coli
(STEC) is an important foodborne pathogen
that causes approximately 265,000 infections
and nearly 30 outbreaks per year in the US.
STEC has been traditionally diagnosed by
culture and subtyped using a variety of methods
to help detect outbreaks. Recently, cultureindependent
diagnostic tests (CIDTs) have
been introduced in many clinical labs in place
of culture-based methods. These methods are
attractive because they are cost-effective, can
be performed at point-of-care, and do not require
culture of the pathogen. As a result, the
current laboratory-based surveillance system
in the US, PulseNet, is threatened because it
relies on pure cultures to perform subtyping by
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