Abstracts

Poster Abstracts
bacteria. However, resistance genes are widely
distributed and present in zoonotic agents as
well as commensal bacteria that can exchange
them by horizontal gene transfer. By directly
sequencing animal fecal DNA, the entire intestinal
resistome can be characterized at once.
In this study, we aimed to develop a workflow
appropriate for quantifying agricultural resistance
and use it to characterize the Danish
swine herd resistome. Ten Danish swine herds
with diverse antimicrobial usage were enrolled
in the study. In each herd, a fecal floor
sample was obtained from 30 random pens.
Those random samples were pooled for each
herd and DNA was extracted using a modified
QIAamp stool mini kit protocol. DNA was
fragmented to 300 bp and prepared with the
NEXTflex PCR-Free DNA Library Prep kit.
Libraries were sequenced on a HiSeq2500 (PE,
2x100 bp), producing roughly 7 billion bp/
sample. MGmapper, a BWA-based pipeline
for metagenomics, was used to map qualitytrimmed
reads to the ResFinder database (2130
resistance genes). To ensure high specificity,
we only counted read pairs where both reads
aligned with 50+ bp to the same reference
gene. To minimize unspecific read mapping
without excluding ambiguous alignments, read
counts from gene variants were aggregated to
gene and drug levels. The relationship between
resistance gene abundances and herd-level
antimicrobial consumption of more than seven
drug classes was analyzed using correlation
analysis. A total of 123 resistance genes were
observed and 64 were detected in at least half
of the samples. In all samples, tet(Q), mefA
and tet(W) comprised over half the detected
resistance genes. Besides tetracycline and
macrolide resistance genes, beta-lactam and
lincosamide resistance genes were also very
prevalent. Positive correlations between drug
use and gene abundances were frequently significant
(p < 0.05). This was not the case for
negative correlations, suggesting antimicrobial
use in Danish swine herds is associated with
an increase in resistance gene abundances.
In conclusion, our metagenomic approach
facilitates herd-level resistance monitoring in
swine. The resolution is sufficient to observe
antimicrobial-induced effects on the swine
resistome and quantify more than 100 resistance
genes. The data may furthermore be well
suited to study other functional sequences like
virulence genes and transposable elements,
making metagenomics an attractive option for
routine environmental monitoring.
n 47
MOLECULAR AND GENOMIC TYPING OF
POULTRY ASSOCIATED SALMONELLA
ENTERICA STRAINS FROM NIGERIA
N. Useh 1 , H. Suzuki 2 , N. Akange 1 , M. Thomas 3 ,
A. Foley 3 , M. Keena 3 , E. Nelson 3 , J. Christopher-Hennings
3 , J. Scaria 3 ;
1
University of Agriculture, Makurdi, NIGERIA,
2
Yamguchi University, Yamaguchi, JAPAN,
3
South Dakota State University, Brookings, SD.
Non-typhoidal Salmonellosis is one of the
common cause of bacterial diarrhea worldwide.
Globally 94 million cases of gastroenteritis
and 115,000 deaths each year is estimated
to be caused as a result of non-typhoidal
Salmonellosis. Transmission of pathogenic
Salmonella strains between different countries
has increased due to global travel and food
import. While North America and Europe have
constituted active Salmonella surveillance
programs, very limited epidemiologic data is
available in developing countries, particularly
in sub-Saharan Africa. Therefore, we have
conducted an epidemiologic investigation of
Salmonella prevalence in poultry samples from
Nigeria. Salmonella was isolated by enrichment
culture in tetrathionate broth followed by
growth on XLT4 agar. Identify of the strains
were further confirmed by Matrix Assisted
Laser Desorption Ionization Time-of-Flight
(MALDI-TOF). After positive identification,
virulence of each strain was estimated using
Human Colo-rectal cell (Caco-2) invasion
assay. Total of 40 isolates were typed using
Caco-2 invasion assay. These isolates were further
typed using Next Generation Sequencing
(NGS). Sequencing libraries were prepared us-
ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic
Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens
71