Abstracts

Poster Abstracts
contiguity information in short-read sequencing.
This limitation also impedes metagenome
assembly, since one cannot tell which sequences
originate from the same species within
a population. We have overcome these bottlenecks
by adapting a chromosome conformation
capture technique (Hi-C) for the deconvolution
of metagenomes and the scaffolding of de novo
assemblies of individual genomes. In modeling
the 3D structure of a genome, chromosome
conformation capture techniques such as Hi-C
are used to measure long-range interactions of
DNA molecules in physical space. These tools
employ crosslinking of chromatin in intact
cells followed by intra-molecular ligation,
joining DNA fragments that were physically
nearby at the time of crosslink. Subsequent
deep sequencing of these DNA junctions generates
a genome-wide contact probability map
that allows the 3D modeling of genomic conformation
within a cell. The strong enrichment
in Hi-C signal between genetically neighboring
loci allows the scaffolding of entire chromosomes
from fragmented draft assemblies.
Hi-C signal also preserves the cellular origin
of each DNA fragment and its interacting partner,
allowing for deconvolution and assembly
of multi-chromosome genomes from a mixed
population of organisms. We have used Hi-C
to scaffold whole genomes of animals, plants,
fungi, as well as prokaryotes and archaea. We
have also been able to use this data to annotate
functional features of microbial genomes, such
as centromeres in many fungal species. Additionally,
we have applied our technology to
diverse metagenomic populations such as craft
beer, bacterial vaginosis infections, soil, and
tree endophyte samples to discover and assemble
the genomes of novel strains of known
species as well as novel prokaryotes and
eukaryotes. The high quality of Hi-C-based
assemblies allows the simultaneous closing of
numerous unculturable genomes, placement of
plasmids within host genomes, and microbial
strain deconvolution in a way not possible
with other methods. Reference: Burton JN*,
Liachko I*, Dunham MJ, Shendure J. Specieslevel
deconvolution of metagenome assemblies
with Hi-C-based contact probability maps. G3.
2014, May 22;4(7):1339-46.
n 101
AN AUTOMATED WGS PIPELINE FOR
ANALYSIS OF BACTERIAL GENOMES
M. Thomsen 1 , H. Hasman 2,3 , A. Petersen 3 , R.
Skov 3 , O. Lund 1 , A.R. Larsen 3 and F.M. Aarestrup
2 ;
1
Danish Technical University – Systems Biology,
CBS, Lyngby, Denmark, 2 , Danish Technical
University – National Food Institute,
Lyngby, Denmark, 3 Statens Serum Institut,
Copenhagen, Denmark.
Background New approaches within diagnostics
and surveillance for species identification,
clonal clustering, and identification
of resistance genes are based whole genome
sequencing (WGS). The Centre for Genomic
Epidemiology (CGE) has been developing
stand-alone web-tools for handling WGS information
for outbreak investigation, epidemiological
surveillance and diagnostics.
Material and methods Based on previously
published web-based CGE tools we developed
a pipeline for automatic analysis of WGS data
from bacterial isolate samples https://cge.cbs.
dtu.dk/services/CGEpipeline-2.0/). The bacterium
analysis pipeline (BAP) automatically
identifies the bacterial species and identify
the multilocus sequence type (MLST), spa
type (S. aureus only), serotype (E. coli only)
and antimicrobial resistance genes. To test the
BAP, a set of 101 S. aureus strains originating
from bacterial infections at Danish hospitals
submitted to Statens Serum Institute (SSI) for
genotypic by traditional Sanger sequencing
were subjected to WGS on an Illumina HiSeq
to a minimum coverage of 30x and assembled
by Velvet prior to being uploaded to the
BAP. Draft genomes including a mandatory
metadata spread sheet containing sequenc-
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