Abstracts

Poster Abstracts
that resolved clinical strains of K. pneumoniae
prior to whole genome sequencing. Clinical
isolates with distinct Resistome Test results
were shown to be distinct strains by whole
genome sequencing while isolates with identical
Resistome Test results were often identical
strains by whole genome sequencing. The Resistome
Test was able to resolve 40% of the 65
isolates as distinct strains, thereby identifying
two potential groups of strain types for higher
resolution by whole genome sequencing. We
concluded that Acuitas ® Resistome Test is useful
for detecting carbapenem and cephalosporin
resistance in Gram-negative bacilli and as
a triage tool to select culture isolates for strain
typing by WGS.
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PATHOGEN DISCOVERY IN TRAVELERS’
DIARRHEA OF UNKNOWN ETIOLOGY BY
METAGENOMIC SEQUENCING
Q. Zhu, M. Jones, S. Highlander;
J. Craig Venter Institute, La Jolla, CA.
Infectious diarrhea is responsible for about
million deaths each year. We are studying
travelers’ diarrhea (TD) where the known
causative agents are members of Enterobacteriaceae,
such as enterotoxigenic Escherichia
coli, Shigella and Salmonella, viruses such
as norovirus, and parasites such as Giardia.
Nevertheless, in over 40% of cases, a known
pathogen cannot be identified by traditional
clinical tests. “Pathogen negative” diarrhea is
enigmatic, although this due, in part to a lack
of appropriate cultivation and screening tests
and poor sensitivity of the tests. DNA sequencing
is increasingly being applied in attempts to
characterize agents of infectious disease. We
hypothesize that unrecognized pathogens are
responsible for a significant proportion of TD.
These may be known organisms with unrecognized
pathogenic potential or may be completely
new species with new mechanisms of
virulence. We have performed deep NextSeq
paired-end sequencing of DNAs from stools of
eight pathogen-negative and two healthy traveler
controls in an attempt to identify pathogens.
A total of 132.8 Gb (ca. 12-20 Gb raw
data/sample) of sequencing data were retained
after quality filtering. Reads were mapped to
the NCBI RefSeq genomic database, resulting
in an average mapping rate of 72.4% (min:
33.1%, max: 93.8%). In the samples where
mapping was low, we believe that many of
the unmapped reads likely represent new uncharacterized
organisms. Taxonomic profiles
were generated based on the mapping results,
and revealed significantly uneven distribution
of microbial groups among samples. The low
complexity samples appear to be dominated by
a single pathogen, while the high complexity
samples may be the result of a mixed etiology.
Three TD samples are enriched for E. coli sequences,
despite the fact that enterotoxins were
not detected in clinical screens. Two of these
carry genes for the Shiga toxin. Additional
TD samples had, for example, high abundance
of Akkermansia muciniphila, Streptococcus
spp., Campylobacter jejuni, or Alistipes shahii
reads, while the two healthy traveler controls
had high abundance of reads that mapped to
several Bifidobacterium species, which were
not present in the diarrheal samples. De novo
assembly was performed for each sample
(average N50 statistic: 6516.4), followed by
contig binning and scaffolding. Near complete
draft genomes were successfully recovered
from the metagenomes. Some represent known
species (such as E. coli and Campylobacter),
while others could not be taxonomically placed
in proximity to any known bacterial groups.
Our results provide a glimpse into the microbiome
diversity composition and potential etiological
sources in “no pathogen identified” TD
samples, and demonstrate the power of highthroughput
DNA sequencing in the discovery
of pathogens in infectious disease.
ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic
Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens
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