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. 2022 Jan 4;14(1):1.
doi: 10.1186/s13099-021-00476-8.

Genomic characteristics and comparative genomics of Salmonella enterica subsp. enterica serovar Schwarzengrund strain S16 isolated from chicken feces

Seung-Min Yang  1 , Eiseul Kim  1 , Woojung Lee  1 , Hae-Yeong Kim  2
Affiliations

Genomic characteristics and comparative genomics of Salmonella enterica subsp. enterica serovar Schwarzengrund strain S16 isolated from chicken feces

Seung-Min Yang et al. Gut Pathog. .

Abstract

Background: Salmonella enterica subsp. enterica serovar Schwarzengrund (S. Schwarzengrund) is most frequently isolated from commensals humans or poultry. Here we report S. Schwarzengrund strain S16, the first sequenced genome in the Republic of Korea. Additionally, genome sequencing for strain S16 was performed and compared with other S. Schwarzengrund genomes obtained from public database.

Results: Strain S16 was isolated from chicken feces. The complete genome consists of one chromosome and one plasmid. The genome size is 4,822,755 bp with 4852 coding sequences. Strain S16 was determined as serovar Schwarzengrund by in silico serotyping and typed as sequence type (ST) 96. Forty-six S. Schwarzengrund genomes yielded a pangenome of 7112 genes, core-genome of 3374 genes, accessory-genome of 2906 genes, and unique-genome of 835 genes. Eighty-one genes were unique to strain S16, including hypothetical proteins and transcriptional regulators. Genotypic analysis of antibiotic resistance of strain S16 confirmed resistance to amikacin, ciprofloxacin, sulfamethoxazole, streptomycin, and tetracycline. Unlike other S. Schwarzengrund genomes, strain S16 had a mutation of gyrB. Moreover, similar to other S. Schwarzengrund genomes reported in other countries, strain S16 was harbored for 153 virulence genes including Saf operon and cdtB gene. All the antibiotic resistance genes and virulence genes were present in the core- or accessory-genomes.

Conclusions: Complete genome of strain S16 was sequenced. Comparative genomic analysis revealed several genes responsible for antibiotic resistance and specific genomic features of strain S16 and identified virulence factors that might contribute to the human and animal pathogenicity of other S. Schwarzengrund genomes.

Keywords: Antibiotic resistance gene; Comparative genomics; Salmonella; Schwarzengrund; Virulence gene; Whole-genome sequencing.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Circular genome mapping of the S. Schwarzengrund strain S16. From inner to outer rings, each ring indicates GC skew, GC content, drug target gene, transporter gene, virulence genes, antibiotic resistance genes, non-CDS, reverse CDS, and forward CDS
Fig. 2
Fig. 2
Phylogenetic tree based on concatenated core genes for 46 S. Schwarzengrund genomes. The geographical origin and isolation source of strains are color coded. The scale bar is depicted in millions of years (MYA)
Fig. 3
Fig. 3
Heatmap of antibiotic resistance genes identified in the 46 S. Schwarzengrund genomes. Resistance genes are indicated as present (orange) or absent (gray). Row and columns represent resistance genes and each genome, respectively
See this image and copyright information in PMC

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References

    1. Ashton PM, Nair S, Peters TM, Bale JA, Powell DG, Painset A, et al. Identification of Salmonella for public health surveillance using whole genome sequencing. PeerJ. 2016;4:e1752. doi: 10.7717/peerj.1752. - DOI - PMC - PubMed
    1. Duc VM, Shin J, Nagamatsu Y, Fuhiwara A, Toyofuku H, Obi T, et al. Increased Salmonella Schwarzengrund prevalence and antimicrobial susceptibility of Salmonella enterica isolated from broiler chickens in Kagoshima prefecture in Japan between 2013 and 2016. J Vet Med Sci. 2020;82:585–589. doi: 10.1292/jvms.20-0096. - DOI - PMC - PubMed
    1. Aarestrup FM, Hendriksen RS, Lockett J, Gay K, Teates K, McDermott PF, et al. International spread of multidrug-resistant Salmonella Schwarzengrund in food products. Emerg Infect Dis. 2007;13:726–731. doi: 10.3201/eid1305.061489. - DOI - PMC - PubMed
    1. Chen MH, Wang SW, Hwang WZ, Tsai SJ, Hsih YC, Chiou CS, et al. Contamination of Salmonella Schwarzengrund cells in chicken meat from traditional marketplaces in Taiwan and comparison of their antibiograms with those of the human isolates. Poult Sci. 2010;89:359–365. doi: 10.3382/ps.2009-00001. - DOI - PubMed
    1. Yun YS, Lee DY, Chung GT. Prevalence and characteristics of Salmonella spp. isolated in Korea, 2015. Public Health Weekly Report, KCDC. 2016. https://www.kdca.go.kr/board/board.es?mid=a20602010000&bid=0034&list_no=....

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