Abstracts

Poster Abstracts
tive comparator for contextualizing isolates
regardless of the molecular typing method
used. Two isolates occurred in clades with
bootstraps of 65 and 100%, which otherwise
contained single PCR RTs. Repeat sequencing
and PCR ribotyping of these two isolates confirmed
the unusual placement of a single RT
014 isolate within the RT 020 clade, and vice
versa. Fluoroquinolone resistance determinants
were common (82%) among the hypervirulent
epidemic RT 027 genomes; only one non-027
isolate (RT 017) harbored a Thr82Ile mutation
in GyrA, which confers fluoroquinolone resistance
in other species. These molecular and
epidemiological data will be publicly available
through NCBI, and isolates have been deposited
for distribution with BEI Resources.
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IMPLEMENTATION OF WHOLE GENOME
SEQUENCING (WGS) FOR SURVEILLANCE
AND OUTBREAK DETECTION OF SHIGA
TOXIN-PRODUCING ESCHERICHIA COLI
(STEC) IN THE UNITED STATES
R. L. Lindsey 1 , H. Carleton 1 , K. Joensen 2 , F.
Scheutz 3 , L. Garcia-Toledo 1 , D. Stripling 1 , H.
Martin 1 , N. Strockbine 1 , L. S. Katz 1 , L. Gladney
1 , T. Griswold 1 , S. Im 1 , E. M. Ribot 1 , E.
Trees 1 , H. Pouseele 4 , P. Gerner-Smidt 1 ;
1
Centers for Disease Control and Prevention,
Atlanta, GA, 2 Technical University of Denmark,
Lyngby, DENMARK, 3 Statens Serum
Institut, Copenhagen, DENMARK, 4 Applied
Maths, Sint-Martens-Latem, BELGIUM.
Introduction: Shiga toxin-producing Escherichia
coli (STEC) is an important foodborne
pathogen capable of causing severe disease in
humans. Current methods for characterization
of STEC are expensive and time-consuming.
Work has begun to replace traditional methods
with those using whole genome sequence
(WGS) data by developing an allele database
of individual Escherichia genes in BioNumerics
7.5, (Applied Maths, Austin, TX). This
will allow characterization of Escherichia
in a single workflow using a multi-locus sequence
typing (MLST) approach. Materials
and Methods: The Escherichia allele database
was built with 314 annotated reference
genomes from a geographically diverse collection
of human, animal and environmental
strains as well as genes encoding virulence
factors, antimicrobial resistance and O and
H antigens from databases at the Center for
Genomic Epidemiology (DTU, Lyngby, Denmark).
The reference genomes represent 50
E. coli serogroups, four Shigella species and
four additional Escherichia species. Multiple
subschema will be built within the database
to perform identification, characterization and
subtyping, including classical, extended, core
and whole genome MLST. To test the ability of
the BioNumerics-based whole genome MLST
approach to correctly identify, characterize and
cluster strains, we analyzed 500 Escherichia
isolates from sporadic and outbreak-related
infections and compared the findings to those
obtained previously with phenotypic and
molecular subtyping methods. Results and
Discussion: The Escherichia allele database
contains 18,883 loci. For the 500 Escherichia
isolates analyzed, there was 95% concordance
in the results generated by the traditional and
wgMLST approaches. Conclusions: The
BioNumerics-based wgMLST approach provides
a single, cost effective strategy to identify
and characterize isolates for surveillance
and outbreak investigations. The analysis tools
in BioNumerics will enable end-users in public
health laboratories to analyze WGS data they
generate with little bioinformatics expertise,
making the system equally efficient for local
and central investigations. The system will be
refined through continued collaboration with
domestic and international partners.
ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic
Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens
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