Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Genome-wide networks reveal emergence of epidemic strains of Salmonella
  Enteritidis   Objectives: To enhance monitoring of high-burden foodborne pathogens, there
is opportunity to combine pangenome data with network analysis.
  Methods: Salmonella enterica subspecies Enterica serovar Enteritidis isolates
were referred to the New South Wales (NSW) Enteric Reference Laboratory between
August 2015 and December 2019 (1033 isolates in total), inclusive of a
confirmed outbreak. All isolates underwent whole genome sequencing. Distances
between genomes were quantified by in silico MLVA as well as core SNPs, which
informed construction of undirected networks. Prevalence-centrality spaces were
generated from the undirected networks. Components on the undirected SNP
network were considered alongside a phylogenetic tree representation.
  Results: Outbreak isolates were identifiable as distinct components on the
MLVA and SNP networks. The MLVA network based centrality/prevalence space did
not delineate the outbreak, whereas the outbreak was clearly delineated in the
SNP network based centrality/prevalence space. Components on the undirected SNP
network showed a high concordance to the SNP clusters based on phylogenetic
analysis.
  Conclusions: Bacterial whole genome data in network based analysis can
improve the resolution of population analysis. High concordance of network
components and SNP clusters is promising for rapid population analyses of
foodborne Salmonella spp. due to the low overhead of network analysis.

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The categories of this paper are: comp-gas
21
The categories of this paper are: adap-org
5
The categories of this paper are: gr-qc
28
The categories of this paper are: alg-geom
6
The categories of this paper are: astro-ph
16
The categories of this paper are: stat
23
The categories of this paper are: solv-int
11
The categories of this paper are: hep-lat
2
The categories of this paper are: math
4
The categories of this paper are: cond-mat
33
The categories of this paper are: plasm-ph
13
The categories of this paper are: quant-ph
31
The categories of this paper are: ao-sci
0
The categories of this paper are: hep-ph
7
The categories of this paper are: hep-th
24
The categories of this paper are: dg-ga