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. 2024 Jan 20;11(1):46.
doi: 10.3390/vetsci11010046.

Genomic Characterization of a Plasmid-Free and Highly Drug-Resistant Salmonella enterica Serovar Indiana Isolate in China

Jiansen Gong  1   2 , Ximin Zeng  3 , Jingxiao Xu  4 , Di Zhang  1 , Xinhong Dou  1   2 , Jun Lin  3 , Chengming Wang  5
Affiliations

Genomic Characterization of a Plasmid-Free and Highly Drug-Resistant Salmonella enterica Serovar Indiana Isolate in China

Jiansen Gong et al. Vet Sci. .

Abstract

The emergence of multi-drug resistant (MDR) Salmonella enterica serovar Indiana (S. Indiana) strains in China is commonly associated with the presence of one or more resistance plasmids harboring integrons pivotal in acquiring antimicrobial resistance (AMR). This study aims to elucidate the genetic makeup of this plasmid-free, highly drug-resistant S. Indiana S1467 strain. Genomic sequencing was performed using Illumina HiSeq 2500 sequencer and PacBio RS II System. Prodigal software predicted putative protein-coding sequences while BLASTP analysis was conducted. The S1467 genome comprises a circular 4,998,300 bp chromosome with an average GC content of 51.81%, encompassing 4709 open reading frames (ORFs). Fifty-four AMR genes were identified, conferring resistance across 16 AMR categories, aligning closely with the strain's antibiotic susceptibility profile. Genomic island prediction unveiled an approximately 51 kb genomic island housing a unique YeeVU toxin-antitoxin system (TAS), a rarity in Salmonella species. This suggests that the AMR gene cluster on the S1467 genomic island may stem from the integration of plasmids originating from other Enterobacteriaceae. This study contributes not only to the understanding of the genomic characteristics of a plasmid-free, highly drug-resistant S. Indiana strain but also sheds light on the intricate mechanisms underlying antimicrobial resistance. The implications of our findings extend to the broader context of horizontal gene transfer between bacterial species, emphasizing the need for continued surveillance and research to address the evolving challenges posed by drug-resistant pathogens.

Keywords: ST17; YeeVU toxin–antitoxin system; genomic island; highly drug-resistant Salmonella enterica serovar Indiana; resistance mechanism.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Circular visualization of the completed chromosome of S. Indiana S1467. The rings show (from inside to outside) the scale in mb, GC skew, GC content, CDS; position of CDS, tRNA, and rRNA.
Figure 2
Figure 2
Gene orthology analysis of S. Indiana S1467 (text in red) and related Enterobacteriaceae strains. Venn diagram represents the numbers of unique and shared orthologous clusters between S. Indiana S1467 (text in red) and related Enterobacteriaceae strains.
Figure 3
Figure 3
Concatenated core genome tree highlights the phylogenetic relationship between S. Indiana S1467 (shown in red) and other Enterobacteriaceae strains. The tree was constructed using 2583 core genes and is represented as a cladogram. The corresponding Genbank accession numbers are displayed in parentheses.
Figure 4
Figure 4
Concatenated core genome tree highlights the position of the S. Indiana S1467 (shown in red) AMR genomic island, relative to other Enterobacteriaceae strains. The corresponding Genbank accession numbers are displayed in parentheses.
Figure 5
Figure 5
Major structural features of the S1467 AMR genomic island (shown in red), when compared with the corresponding chromosomal regions of other Enterobacteriaceae strains from the NCBI database. The arrows indicate the extent and direction of transcription of the genes. The open reading frames (ORFs) with different functions are presented in various colors (red: AMR genes, yellow: ORFs). The corresponding Genbank accession numbers are displayed in parentheses.
See this image and copyright information in PMC

References

    1. Havelaar A.H., Kirk M.D., Torgerson P.R., Gibb H.J., Hald T., Lake R.J., Praet N., Bellinger D.C., de Silva N.R., Gargouri N., et al. World Health Organization Global Estimates and Regional Comparisons of the Burden of Foodborne Disease in 2010. PLoS Med. 2015;12:e1001923. doi: 10.1371/journal.pmed.1001923. - DOI - PMC - PubMed
    1. Feasey N.A., Dougan G., Kingsley R.A., Heyderman R.S., Gordon M.A. Invasive non-typhoidal salmonella disease: An emerging and neglected tropical disease in Africa. Lancet. 2012;379:2489–2499. doi: 10.1016/S0140-6736(11)61752-2. - DOI - PMC - PubMed
    1. Fernández J., Guerra B., Rodicio M.R. Resistance to Carbapenems in Non-Typhoidal Salmonella enterica Serovars from Humans, Animals and Food. Vet. Sci. 2018;5:40. doi: 10.3390/vetsci5020040. - DOI - PMC - PubMed
    1. Aarestrup F.M., Hendriksen R.S., Lockett J., Gay K., Teates K., McDermott P.F., White D.G., Hasman H., Sørensen G., Bangtrakulnonth A., 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. Hendriksen R.S., Vieira A.R., Karlsmose S., Lo Fo Wong D.M.A., Jensen A.B., Wegener H.C., Aarestrup F.M. Global Monitoring of Salmonella Serovar Distribution from the World Health Organization Global Foodborne Infections Network Country Data Bank: Results of Quality Assured Laboratories from 2001 to 2007. Foodborne Pathog. Dis. 2011;8:887–900. doi: 10.1089/fpd.2010.0787. - DOI - PubMed

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