Abstracts

Poster Abstracts
to Salmonella to evaluate metagenomics as
a diagnostic and disease surveillance tool, as
well as to gain insight into the gut microbial
community responses to foodborne bacterial
infection. These outbreaks were geographically
isolated and the etiologic agents were
identified by culture methods as distinct strains
of Salmonella enterica serovar Heidelberg.
We performed shotgun sequencing on these
samples using the Illumina MiSeq platform.
Community and taxonomic analysis were
performed using Parallel-META, Metaphlan,
and GOTTCHA. Subspecies analysis was
performed using BLAST recruitment analysis.
Further phylogenetic analysis was performed
on metagenomic assemblies of samples and
resulting contigs matching S. enterica. Results:
Sample consistency and human DNA
sequence abundance varied greatly, often
reducing the sequencing depth of the targeted
microbial communities, yet referenced-based
detection of Salmonella serovar Heidelberg
was possible by metagenomic read recruitment
as well as metagenomic assembly, even in
samples with high human DNA content (90-
96%). Taxonomic profiling revealed similar
microbial community structures between individual
patients from each localized outbreak;
samples from different outbreaks clustered
separately and were distinct from a subset of
‘healthy’ references selected from the Human
Microbiome Project. Microbial gut communities
consistently showed reduced species
diversity in each foodborne outbreak compared
to ‘healthy’ references. Conclusions: These
results highlight the potential utility of metagenomic-based
diagnostic tools for foodborne
pathogen identification and epidemiologically
relevant clustering, even in samples with high
human DNA abundance. Furthermore, shotgun
metagenomic approaches offer additional insight
into gut microbial community responses
to foodborne illness that may hold clues to
pathogen ecology.
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INTEGRATING WHOLE GENOME
SEQUENCING OF SALMONELLA ENTERICA
SEROVAR ENTERITIDIS INTO THE PUBLIC
HEALTH LABORATORY FOR SURVEILLANCE
AND OUTBREAK INVESTIGATIONS
K. J. Levinson 1 , M. Dickinson 2 , S. Wirth 2 , M.
Anand 3 , D. J. Baker 2 , D. Bopp 2 , L. Thompson 2 ,
K. A. Musser 2 , P. Lapierre 2 , W. J. Wolfgang 2 ;
1
School of Public Health, SUNY Albany,
Albany, NY, 2 Wadsworth Center/NYSDOH,
Albany, NY, 3 Bureau of Communicable Disease
Control/NYSDOH, Albany, NY.
Salmonella enterica serovar Enteritidis is
a leading cause of foodborne illness in the
United States. Pulsed-field gel electrophoresis
(PFGE) is the gold standard for outbreak detection
of enteric pathogens. However, the low
genetic diversity of S. Enteritidis and frequent
exchanges of mobile genetic elements limits
how well PFGE can discriminate between
isolates and identify clusters that may be
epidemiologically linked. Two-thirds of all S.
Enteritidis isolates received at the Wadsworth
Center have PFGE patterns that are considered
“endemic” and over half of these are pattern
JEGX01.0004. Consequently, these cases
are not routinely investigated by epidemiologists.
To improve discrimination between
sporadic and outbreak associated isolates, the
Wadsworth Center began performing whole
genome sequencing (WGS) single nucleotide
polymorphism (SNP) based phylogenetic typing
on all S. Enteritidis isolates in addition to
PFGE typing. The goal of this project was to
explore the utility of incorporating WGS-based
typing into routine public health laboratory
surveillance and to establish a standard for reporting
WGS data in a manner that was useful
for both laboratorians and epidemiologists. Using
a pipeline developed in-house, we created
cumulative SNP based phylogenetic trees from
514 S. Enteritidis isolates in real time over a
period of 20 months. Based on retrospective
studies, we used a SNP diversity of 0-5 to de-
ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic
Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens
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