Abstracts

Poster Abstracts
evolution. Determining which lineages are
present throughout Italy is crucial to understanding
brucellosis epidemiology as well as to
place Italian samples into a global evolutionary
context. The aim of this study was to evaluate
an NGS approach using different analyses
to investigate B. melitensis diversity in Italy.
Previous genetic assessment using variable
number tandem repeats (VNTRs) revealed the
presence of the west Mediterranean lineage
structured in several clades that were sometimes
geographically constrained. We selected
16 B. melitensis isolates for whole genome
sequencing representing maximum genetic and
geographic diversity. Libraries were sequenced
with both paired-end Illumina and Ion Torrent
sequencing, and our analyses included 59
publicly available B. melitensis genomes. We
performed SNP analysis in read alignments
and whole genomes using NASP pipeline, and
in parallel we applied a gene-based approach
using MLST+. Approximately 22,000 putative
SNPs were identified among the B. melitensis
samples. The MLST+ revealed 1,748 targets
for the first chromosome and 876 targets for
the second chromosome totaling 2,624 loci.
Both approaches found that the Italian isolates
formed 3 sub-clades as part of the B. melitensis
strain Ether lineage, a strain that was isolated
in Italy fifty years ago, suggesting that this
lineage has been well established and successful
for at least over half century in the Italian
peninsula. Finally, we compared our results to
a recently published shotgun metagenomic B.
melitensis sequence from bones from a medieval
grave in Sardinia (Italy) and confirm that
this same lineage has been present in the region
for centuries. This study is a step forward
in understanding of Brucella evolution in the
Mediterranean area, and demonstrates the utility
of WGS SNP analysis, and the feasibility
of MLST+ as a fast and reliable typing system
for analyzing the epidemiology of Brucella in
endemic regions.
n 41
GENOMIC EPIDEMIOLOGY AND
TRANSMISSION OF SALMONELLA
CHOLERAESUIS VAR. KUNZENDORF IN
EUROPEAN PIGS AND WILD BOAR
P. Leekitcharoenphon, F. M. Aarestrup, R. S.
Hendriksen;
Technical University of Denmark, Kgs. Lyngby,
DENMARK.
Salmonella Choleraesuis is a relative infrequent
serovar adapted to pigs but also have a
propensity to cause extraintestinal infections
in humans. S. Choleraesuis var. Kunzendorf
are responsible for the majority of outbreaks
among pigs. The global transmission was
believed to be a result of imported breeding
pigs from Canada and the USA into Taiwan.
In Europe, S. Choleraesuis is a relatively rare
serovar, both in slaughter pigs and in breeding
herds. In Denmark, only a few outbreaks have
been reported among pig herds within the last
decade; 1999 - 2000 and 2012 - 2013 and in
both cases it has been impossible to identify
the route of transmission and source of infection.
In order to understand transmission and
epidemiology of S. Choleraesuis, we have
sequenced 108 S. Choleraesuis isolates from
pig and wild boar from 12 European countries
and USA. We applied SNP-based phylogenetic
methods based on whole genome sequences to
identify the population structure. We used Baysian
phylogeny to estimate dates of divergence
and phylogeographic analyses of lineages by
using BEAST with Bayesian Skyline model of
population size change and relaxed uncorrelated
lognormal clock as the molecular clock.
The S. Choleraesuis isolates yielded 2,428
SNPs. We estimated that the ancestral emergence
of S. Choleraesuis was in 1946. The
mean evolutionary rates were approximated to
be 1.58 x 10-6 SNPs/site/year corresponding
to 7.5 SNPs/year. The isolates were divided
into two complex clusters and they resided
in sub-clusters according to countries and
neighbour countries of isolation. According to
the source of isolation, the wild boar isolates
ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic
Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens
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