Genome analysis and CRISPR typing of Salmonella enterica serovar Virchow

Bachmann, Nathan L., Petty, Nicola K., Ben Zakour, Nouri L., Szubert, Jan M., Savill, John and Beatson, Scott A. (2014) Genome analysis and CRISPR typing of Salmonella enterica serovar Virchow. BMC Genomics, 15 1: . doi:10.1186/1471-2164-15-389


Author Bachmann, Nathan L.
Petty, Nicola K.
Ben Zakour, Nouri L.
Szubert, Jan M.
Savill, John
Beatson, Scott A.
Title Genome analysis and CRISPR typing of Salmonella enterica serovar Virchow
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2014-05-21
Year available 2014
Sub-type Article (original research)
DOI 10.1186/1471-2164-15-389
Open Access Status DOI
Volume 15
Issue 1
Total pages 14
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2015
Language eng
Abstract Background: Salmonella enterica subsp. enterica serovar Virchow has been recognized as a significant health burden in Asia, Australia and Europe. In addition to its global distribution, S. Virchow is clinically significant due to the frequency at which it causes invasive infections and its association with outbreaks arising from food-borne transmission. Here, we examine the genome of an invasive isolate of S. Virchow SVQ1 (phage type 8) from an outbreak in southeast Queensland, Australia. In addition to identifying new potential genotyping targets that could be used for discriminating between S. Virchow strains in outbreak scenarios, we also aimed to carry out a comprehensive comparative analysis of the S. Virchow genomes.Results: Genome comparisons between S. Virchow SVQ1 and S. Virchow SL491, a previously published strain, identified a high degree of genomic similarity between the two strains with fewer than 200 single nucleotide differences. Clustered Regularly Interspaced Palindromic Repeats (CRISPR) regions were identified as a highly variable region that could be used to discriminate between S. Virchow isolates. We amplified and sequenced the CRISPR regions of fifteen S. Virchow isolates collected from seven different outbreaks across Australia. We observed three allelic types of the CRISPR region from these isolates based on the presence/absence of the spacers and were able to discriminate S. Virchow phage type 8 isolates originating from different outbreaks. A comparison with 27 published Salmonella genomes found that the S. Virchow SVQ1 genome encodes 11 previously described Salmonella Pathogenicity Islands (SPI), as well as additional genomic islands including a remnant integrative conjugative element that is distinct from SPI-7. In addition, the S. Virchow genome possesses a novel prophage that encodes the Type III secretion system effector protein SopE, a key Salmonella virulence factor. The prophage shares very little similarity to the SopE prophages found in other Salmonella serovars suggesting an independent acquisition of sopE.Conclusions: The availability of this genome will serve as a genome template and facilitate further studies on understanding the virulence and global distribution of the S. Virchow serovar, as well as the development of genotyping methods for outbreak investigations.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2015 Collection
School of Chemistry and Molecular Biosciences
 
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