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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety & Quality Research » Research » Publications at this Location » Publication #352021

Research Project: Genomic and Metagenomic Differences in Foodborne Pathogens and Determination of Ecological Niches and Reservoirs

Location: Meat Safety & Quality Research

Title: Closed genome and comparative phylogenetic analysis of the clinical multidrug resistant Shigella sonnei strain 866

Author
item ALLUE-GUARDIA, ANNA - University Of Texas At San Antonio
item KOENIG, SARAH - University Of Texas At San Antonio
item QUIROS-FERNANDEZ, PABLO - University Of Barcelona
item MUNIESA, MAITE - University Of Barcelona
item Bono, James - Jim
item EPPINGER, MARK - University Of Texas At San Antonio

Submitted to: Genome Biology and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/28/2018
Publication Date: 10/1/2018
Citation: Allue-Guardia, A., Koenig, S.S.K., Quiros, P., Muniesa, M., Bono, J.L., Eppinger, M. 2018. Closed genome and comparative phylogenetic analysis of the clinical multidrug resistant Shigella sonnei strain 866. Genome Biology and Evolution. 10(9):2241-2247. https://doi.org/10.1093/gbe/evy168.
DOI: https://doi.org/10.1093/gbe/evy168

Interpretive Summary: Bacteriophages are viruses that infect bacteria and can carry factors that increase the bacteria’s ability to cause disease in humans. One such bacteriophage carries Shiga toxin, an important factor for causing human disease, and are found in some Shigella and Escherichia coli isolates. Shigella isolate 866 is highly susceptible to infection by a range of bacteriophages including those that carry Shiga toxin and therefore are a potential source for the spread of bacteriophage carrying Shiga toxin. The genome of isolate 866 was sequenced to provide information about the genetic make up of this isolate. The availability of the closed high-quality genome for isolate 866 is foundational to further clarify genome characteristics correlated with its ability to cause disease and bacteriophage susceptibility.

Technical Abstract: Shigella sonnei is responsible for the majority of shigellosis infections in the US with over 500,000 cases reported annually. Here, we present the complete genome of the clinical multidrug resistant (MDR) strain 866, which is highly susceptible to bacteriophage infections. The strain has a circular chromosome of 4.85 Mb and carries a 113 kb MDR plasmid. This IncB/O/K/Z-type plasmid, termed p866, confers resistance to five different classes of antibiotics including ß-lactamase, sulfonamide, tetracycline, aminoglycoside, and trimethoprim. Comparative analysis of the plasmid architecture and gene inventory revealed that p866 shares its plasmid backbone with previously described IncB/O/K/Z-type Shigella spp. and Escherichia coli plasmids,but is differentiated by the insertion of antibiotic resistance cassettes, which we found associated with mobile genetic elements such as Tn3, Tn7, and Tn10. A whole genome-derived phylogenetic reconstruction showed the evolutionary relationships of S. sonnei strain 866 and the four established Shigella species, highlighting the clonal nature of S. sonnei.