Abstracts

Poster Abstracts
comparable to a recent study which reported
mutation rates for different clades of a phylogenetic
tree constructed from 73 enterococci
isolates. The rate was 49 ± 3 SMY for a clade
belonging to clonal complex CC17, and was
3.6 ± 0.6 SMY and 13 ± 2 SMY for two
clades with mixed STs. We have developed
a method for mutation rate inference using
SNPs obtained from NGS data. Standardizing
the filtering process will allow expanding this
approach to other species. With studies reporting
variation in mutation rates within species
such procedural methodology becomes all the
more important. This bioinformatics approach
to identify disease transmission paths can help
recognize, control, and diagnose bacterial
clinical outbreaks.
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COMPARISON OF RNA AND DNA
EXTRACTION KITS FOR VIRUS DETECTION
BY NEXT GENERATION SEQUENCING (NGS)
J. Klenner, C. Kohl, P. Dabrowski, A. Nitsche;
Robert Koch Institute, Berlin, GERMANY.
A crucial step in the molecular detection of
viruses in clinical specimens is the efficient
extraction of viral nucleic acids. The total yield
of viral nucleic acid from a clinical specimen
is dependent on the specimens’ volume, the
initial virus concentration and the effectiveness
provided by the extraction method. Recent
Next Generation Sequencing (NGS)-based
diagnostic approaches provide a molecular
‘open view’ into the sample, as they generate
sequence reads of any nucleic acid present
in a specimen in a statistically representative
manner. However, since a higher virus-related
read output promises better sensitivity in the
subsequent bioinformatic analysis, the extraction
method selected determines the reliability
of diagnostic NGS. In this study four commercially
available nucleic acid extraction
kits (QIAGEN, Hilden, Germany: QIAamp
Viral RNA Mini Kit, QIAamp DNA Blood
Mini Kit, QIAamp cador Pathogen Mini Kit
and QIAamp MinElute Virus Spin Kit) were
evaluated by NGS. The nucleic acid yields
and sequence read output were compared for
four different model viruses comprising Reovirus,
Orthomyxovirus, Orthopoxvirus and
Paramyxovirus, each at defined but varying
concentrations in the same sample. The total
nucleic acid extracted was divided into two
aliquots; one was subjected to RNA and the
other to DNA processing for NGS. The yield
of nucleic acids was determined by Qubit and
virus-specific quantitative real-time PCR. NGS
libraries were prepared for sequencing on
the Illumina HiSeq 1500 system. Finally, the
percentage of reads which could be assigned
to each virus after extraction with the different
kits was determined via mapping. As presented
here, evaluation of the different commercial
nucleic acid extraction kits indicates little
deviation in the numbers for RNA and DNA
reads, depending on the kit used.
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TRANSMISSION OF HIGH RISK K.
PNEUMONIAE CLONES IN HEALTH CARE
NETWORKS LARGELY CHALLENGES THE
CURRENT INFECTION PREVENTION AND
CONTROL SYSTEM
K. Zhou, M. Lokate, R. H. Deurenberg, G. C.
Raangs, H. Grundmann, A. W. Friedrich, J. W.
Rossen;
University of Groningen, University Medical
Center Groningen, Groningen, NETHER-
LANDS.
Controlling dissemination of multidrugresistant
pathogens remains one of the major
challenges in hospitals and public health. Here
we describe an inter-institutional transmission
of an ESBL-producing ST15 Klebsiella pneumoniae
between patients caused by patient
referral. An epidemiological link between
the patient isolates was supported by patient
contact tracing and phylogenetic analysis of
the isolates obtained from May to November
2012 using next generation sequencing (NGS).
By May 2013, a patient treated in two institutions
in two cities was involved in expanding
ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic
Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens
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