Abstracts

Poster Abstracts
diversity. The diversity and evolution of toxinotype
V, NAP7 strains are especially important
because these strains are commonly found
in both food animals and humans and many
questions still remain about the potential role
of food animals in CA-CDI. Understanding the
true diversity within C. difficile toxinotypes
and North American Pulsed-field types is also
essential for discussions regarding appropriate
and standardized typing methods.
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A PATHOGENOMICS APPROACH TO
IMPROVE THE ACCURACY OF VETERINARY
CLINICAL DIAGNOSTICS
S. Das 1 , M. Thomas 1 , A. Pillatzki 1 , L. Holler 1 ,
M. Keena 1 , A. Foley 1 , E. Nelson 1 , J. Christopher-Hennings
1 , H. Suzuki 2 , J. Scaria 1 ;
1
South Dakota State University, Brookings, SD,
2
Yamaguchi University, Yamaguchi, JAPAN.
The recent advances in Next Generation Sequencing
(NGS) technology promise cheap
and fast whole genomic data and offer the
possibility to revolutionize veterinary clinical
diagnostics. It is now possible to improve the
accuracy of clinical diagnostics when pathology
data is combined with NGS based clinical
specimen sequencing. This approach offers
faster results and avoids the need for many
different tests to obtain the final interpretation.
We test such an approach in the clinical
evaluation of Salmonellosis cases in Animal
Disease Research and Diagnostic Laboratory
(ADRDL), South Dakota. All bovine
and swine salmonellosis cases submitted to
ADRDL from September 2014 till date was
included in this study. Salmonella isolates were
identified using standard microbiological protocols.
Further characterization of Salmonella
strains were then performed using NGS. Sequencing
libraries for NGS was prepared using
Illumina Nextera XT kit and the sequencing
was performed using Illumina 2 x 250 base
paired end sequencing chemistry. Genome
assembly of the strains was performed using
Spades Assembler v 3.5.0 and annotated
using Prokka v1.11. Comparative genomic
analysis of the isolates was performed using
ITEP tool kit. Antibiotic resistance gene profile
and virulence gene profile of the isolates was
determined using a custom PERL script. These
results were then combined with pathological
data. This combined approach revealed that in
most cases Salmonella infection was accompanied
by presence of other enteric pathogens
such as rotavirus, Clostridium perfringens,
hemolytic Escherichia coli and porcine epidemic
diarrhea virus. Salmonella enterica serotype
Dublin was found to be associated with
septicemia and colitis in the absence of other
pathogens. Antibiotic resistance gene profile
obtained based NGS data provided further
insights into the possible antibiotic susceptibility/resistance
pattern of the strains.
n 53
QUALITY ASSESSMENT OF SINGLE
NUCLEOTIDE POLYMORPHISM IN THE
HIGHLY CLONAL SALMONELLA ENTERITIDIS
D. Ogunremi;
Canadian Food Inspection Agency, Ottawa,
ON, CANADA.
Single nucleotide polymorphism (SNPs) has
emerged as the most informative genetic
variation for the characterization of the highly
clonal Salmonella Enteritidis (SE) to meet
the goals of epidemiological and evolutionary
investigations. Raw reads, contigs, draft
or polished genomes are used to identify SNP
variants typically by aligning the nucleotide
reads of an isolate to a reference genome.
Two relatively well-assembled genomes can
be compared to determine the number of SNP
variants between them. In addition, referencefree
SNP detection from raw reads has also
been proposed and used. There are limitations
to detecting SNPs from the currently available
software and bioinformatics pipelines
and these include the use of a significantly
disparate reference genome to align raw reads,
sequencing errors, mis-assembly and repeats.
To that end, large scale studies investigating
ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic
Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens
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