Abstracts

Poster Abstracts
gonococcal infections in a culture independent
manner. Ten AMR markers were examined,
here and with the complete genome information
provided by NGS there is the potential for
many more to be investigated and for novel
markers to be identified, highlighting the potential
of this technology to enable continued
AMR surveillance in areas where culture is no
longer performed.
n 76
SUBTYPING OF E. COLI STEC BY
TRADITIONAL LABORATORY METHODS AND
WGS, A COMPARISON!
E. Litrup, K. Kiil;
Statens Serum Institut, Copenhagen, DEN-
MARK.
The traditional subtyping of E. coli STEC
strains consists of many different and somewhat
laborious and slow methods. In Denmark,
we began whole genome sequencing of all E.
coli STEC strains isolated from humans in
January 2015. From January through June,
we received and typed more than 70 STEC
strains by both the traditional methods and
WGS. The methods performed in our laboratory
are serotyping, PCR assays and dot blot
hybridization among others. Whole Genome
Sequencing was performed in-house on an
Illumina MiSeq with the Nextera Library
Preparation kit and 250bp paired reads. For the
comparison of WGS and traditional subtyping,
we focused on the serotype, the stx1 and stx2
subtypes and the presence of several genes
e.g. the eae and ehxA gene. For detection of
the serotype and virulence genes, we used the
CGE finders (Serotype Finder and Virulence
Finder https://cge.cbs.dtu.dk/services/), but
we also used reference based mapping to the
databases behind the finders with srst2 (https://
github.com/katholt/srst2). The serotype was
the subtyping method with the most divergent
results as expected. The Serotype Finder was
able to detect all but one serovar detected by
the traditional serotyping. Additionally, almost
all the strains typed as rough or smooth
in the laboratory, were assigned an O-type
by the Serotype Finder tool. Further, all the
non-motile strains with no phenotypic H-type,
were assigned an H-type by the Serotype
Finder tool. Finally, there were some cross
reactions between different sera in the laboratory,
where the Serotype Finder was also able
to give a result regarding which H type was
more similar to the one sequenced. Regarding
the detection of the stx1 and stx2 variants, eae
and ehxA genes, we found an almost 100%
correlation to the laboratory results achieved
by PCR and dot blot hybridization. Only in a
few cases did the laboratory achieve different
results. We used the Virulence Finder on
contigs assembled denovo by CLC and also we
used reference based mapping to the databases
behind the finder using SRST2, and we saw
no differences in the performance of the two
approaches. It is believed that reference based
mapping is important for gene detection in E.
coli as it can be challenging to assemble the
reads into acceptable contigs, but in the case of
these four genes and their variants this was not
the case. This might be due to the location of
these genes; they are probably located in parts
of the genome that are easy to assemble.
n 77
DR. JEKYLL AND MR. HYDE: THE CASE
FOR MIXED NOCARDIA POPULATIONS
IN CLINICAL ISOLATES AS REVEALED BY
WHOLE GENOME SEQUENCE ANALYSIS
A. C. Lauer, B. Lasker, J. R. McQuiston;
Centers for Disease Control and Prevention,
Atlanta, GA.
Nocardia species are aerobic GC-rich,
partially-acid fast, opportunistic, pathogenic
actinomycetes. Every year, approximately 200
nocardiae isolates are received by the Special
Bacteriology Reference Laboratory (SBRL) at
CDC, however the true incidence of nocardiosis
in the U.S. remains unknown. Despite reports
of resistance to co-trimoxazole, the treatment
of choice for nocardiosis, the molecular
mechanisms of resistance in nocardiae are not
ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic
Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens
91