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Whole-Genome Analysis of Salmonella Enterica subsp. Enterica serovar Gallinarum biovar Gallinarum Strain IJES3-1 Isolated from a Retail Chicken Shell Egg in Korea

  • 투고 : 2024.08.19
  • 심사 : 2024.08.26
  • 발행 : 2024.08.30

초록

Salmonella enterica subsp. enterica serovar Gallinarum biovar Gallinarum causes fowl typhoid in poultry. In this study, we isolated Salmonella from a Korean retail chicken shell egg and performed whole-genome sequencing, from which we identified one chromosome (4,659,977-bp) and two plasmids (plasmid_1: 87,506 bp and plasmid_2: 2,331 bp). The isolate serotype was confirmed to be Gallinarum, with a biovar type of Gallinarum, which was finally identified as Salmonella enterica subsp. enterica serovar Gallinarum biovar Gallinarum. Multilocus sequence typing confirmed that the isolate was that of sequence type 78. The antimicrobial resistance gene, aac(6')-laa, was identified on the chromosome, and 166 virulence genes were detected on the chromosome and plasmid_1.

키워드

과제정보

This study was supported by a grant from the Ministry of Food and Drug Safety (22192MFDS021) of the Republic of Korea.

참고문헌

  1. Farhat, M., Khayi, S., Berrada, J., Mouahid, M., Ameur, N., El-Adawy, H., Fellahi, S., Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum in poultry: review of pathogenesis, antibiotic resistance, diagnosis and control in the genomic era. Antibiotics, 13, 23 (2023).
  2. Lozica, L., Faraguna, S., Artukovic, B., Gottstein, Z., Fowl typhoid outbreak on a commercial turkey farm in Croatia. Microorganisms, 12, 165 (2024).
  3. Zhou, X., Kang, X., Zhou, K., Yue, M., A global dataset for prevalence of Salmonella Gallinarum between 1945 and 2021. Sci. Data, 9, 495 (2022).
  4. Beylefeld, A., Abolnik, C., Salmonella Gallinarum strains from outbreaks of fowl typhoid fever in Southern Africa closely related to SG9R vaccines. Front. Vet. Sci., 10, 1191497 (2023).
  5. Tatusova, T., DiCuccio, M., Badretdin, A., Chetvernin, V., Nawrocki, E.P., Zaslavsky, L., Lomsadze, A., Pruitt, K.D., Borodovsky, M., Ostell, J., NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res., 44, 6614-6624 (2016). https://doi.org/10.1093/nar/gkw569
  6. Larsen, M.V., Cosentino, S., Rasmussen, S., Friis, C., Hasman, H., Marvig, R.L., Jelsbak, L., Sicheritz-Ponten, T., Ussery, D.W., Aarestrup, F.M., Lund, O., Multilocus sequence typing of total-genome-sequenced bacteria. J. Clin. Microbiol., 50, 1355-1361 (2012). https://doi.org/10.1128/JCM.06094-11
  7. Hasman, H., Saputra, D., Sicheritz-Ponten, T., Lund, O., Svendsen, C.A., Frimodt-Moller, N., Aarestrup, F.M., Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J. Clin. Microbiol., 52, 139-146 (2014). https://doi.org/10.1128/JCM.02452-13
  8. Zhang, S., Yin, Y., Jones, M.B., Zhang, Z., Deatherage Kaiser, B.L., Dinsmore, B.A., Fitzgerald, C., Fields, P.I., Deng, X., Salmonella serotype determination utilizing high-throughput genome sequencing data. J. Clin. Microbiol., 53, 1685-1692 (2015). https://doi.org/10.1128/JCM.00323-15
  9. Okonechnikov, K., Golosova, O., Fursov, M., The UGENE team, Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics, 28, 1166-1167 (2012). https://doi.org/10.1093/bioinformatics/bts091
  10. Bortolaia, V., Kaas, R.S., Ruppe, E., Roberts, M.C., Schwarz, S., Cattoir, V., Philippon, A., Allesoe, R.L., Rebelo, A.R., Florensa, A.F., Fagelhauer, L., Chakraborty, T., Neumann, B., Werner, G., Bender, J.K., Stingl, K., Nguyen, M., Coppens, J., Xavier, B.B., Malhotra-Kumar, S., Westh, H., Pinholt, M., Anjum, M.F., Duggett, N.A., Kempf, I., Nykasenoja, S., Olkkola, S., Wieczorek, K., Amaro, A., Clemente, L., Mossong, J., Losch, S., Ragimbeau, C., Lund, O., Aarestrup, F.M., ResFinder 4.0 for predictions of phenotypes from genotypes. J. Antimicrob. Chemother., 75, 3491-3500 (2020). https://doi.org/10.1093/jac/dkaa345
  11. Feldgarden, M., Brover, V., Gonzalez-Escalona, N., Frye, J.G., Haendiges, J., Haft, D.H., Hoffmann, M., Pettengill, J.B., Prasad, A.B., Tillman, G.E., Tyson, G.H., Klimke, W., AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci. Rep., 11, 12728 (2021).
  12. Srednik, M.E., Morningstar-Shaw, B.R., Hicks, J.A., Mackie, T.A., Schlater, L.K., Antimicrobial resistance and genomic characterization of Salmonella enterica serovar Senftenberg isolates in production animals from the United States. Front. Microbiol., 13, 979790 (2022).
  13. Liu, B., Zheng, D., Zhou, S., Chen, L., Yang, J., VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res., 50, D912-D917 (2022). https://doi.org/10.1093/nar/gkab1107
  14. Xiong, D., Song, L., Pan, Z., Jiao, X., Identification and discrimination of Salmonella enterica serovar gallinarum biovars pullorum and gallinarum based on a one-step multiplex PCR assay. Front. Microbiol., 9, 1718 (2018).