Population analysis of D6-like plasmid prophage variants associated with specific IncC plasmid types in the emerging Salmonella Typhimurium ST213 genotype

Autoři: Claudia Silva aff001;  Edmundo Calva aff001;  Marcos Fernández-Mora aff001;  José L. Puente aff001;  Pablo Vinuesa aff002
Působiště autorů: Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico aff001;  Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico aff002
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0223975


The Salmonella enterica serovar Typhimurium sequence type 213 (ST213) emerged as a predominant genotype in Mexico. It is characterized by harboring multidrug resistance (MDR) IncC plasmids (previously IncA/C) and the lack of the Salmonella virulence plasmid (pSTV). Here we show that the D6-like plasmid prophage is present in most of the ST213 strains. We used the reported nucleotide sequence of YU39 plasmid (pYU39_89) to design a PCR typing scheme for the D6-like plasmid prophages, and determined the complete nucleotide sequences for the D6-like prophages of three additional ST213 strains (YU07-18, SL26 and SO21). Two prophage variants were described: i) a complete prophage, containing homologous sequences for most of the genetic modules described in P1 and D6 phages, which most likely allow for the lytic and lysogenic lifestyles; and ii) an incomplete prophage, lacking a 15 kb region containing morphogenesis genes, suggesting that it is defective. The tail fiber gene inversion region was the most divergent one between D6 and pYU39_89 genomes, suggesting the production of a distinct set of tail fibers, which could be involved in host range preferences. A glutaminyl-tRNA synthetase gene (glnS), which could be involved in providing host cell increased fitness or plasmid maintenance functions, was found in all D6-like genomes. Population level analysis revealed a biogeographic pattern of distribution of these plasmid-phages and specific associations with variants of MDR IncC plasmids. Statistically significant associations were found between the two prophage variants (p75 or p89), the type of IncC plasmids (I or II) and geographic isolation regions (Sonora, San Luis Potosí, Michoacán and Yucatán). This work integrates results from molecular typing, genomics and epidemiology to provide a broad overview for the evolution of an emergent Salmonella genotype.

Klíčová slova:

Bacteriophages – Comparative genomics – Genome evolution – Genomics – Mexican people – Polymerase chain reaction – Salmonella – Salmonella typhimurium


1. Wiesner M, Zaidi MB, Calva E, Fernandez-Mora M, Calva JJ, Silva C. Association of virulence plasmid and antibiotic resistance determinants with chromosomal multilocus genotypes in Mexican Salmonella enterica serovar Typhimurium strains. BMC Microbiol. 2009;9:131. doi: 10.1186/1471-2180-9-131 19573249.

2. Wiesner M, Calva E, Fernandez-Mora M, Cevallos MA, Campos F, Zaidi MB, et al. Salmonella Typhimurium ST213 is associated with two types of IncA/C plasmids carrying multiple resistance determinants. BMC Microbiol. 2011;11(1):9. Epub 2011/01/13. doi: 1471-2180-11-9 [pii] doi: 10.1186/1471-2180-11-9 21223599.

3. Ambrose SJ, Harmer CJ, Hall RM. Compatibility and entry exclusion of IncA and IncC plasmids revisited: IncA and IncC plasmids are compatible. Plasmid. 2018;96–97:7–12. doi: 10.1016/j.plasmid.2018.02.002 29486211.

4. Achtman M, Wain J, Weill FX, Nair S, Zhou Z, Sangal V, et al. Multilocus sequence typing as a replacement for serotyping in Salmonella enterica. PLoS Pathog. 2012;8(6):e1002776. doi: 10.1371/journal.ppat.1002776 22737074; PubMed Central PMCID: PMC3380943.

5. Zaidi MB, Leon V, Canche C, Perez C, Zhao S, Hubert SK, et al. Rapid and widespread dissemination of multidrug-resistant blaCMY-2 Salmonella Typhimurium in Mexico. J Antimicrob Chemother. 2007;60(2):398–401. doi: 10.1093/jac/dkm168 17526503.

6. Zaidi MB, McDermott PF, Fedorka-Cray P, Leon V, Canche C, Hubert SK, et al. Nontyphoidal Salmonella from human clinical cases, asymptomatic children, and raw retail meats in Yucatan, Mexico. Clin Infect Dis. 2006;42(1):21–8. doi: 10.1086/498508 16323087.

7. Calva E, Silva C, Zaidi MB, Sanchez-Flores A, Estrada K, Silva GG, et al. Complete Genome Sequencing of a Multidrug-Resistant and Human-Invasive Salmonella enterica Serovar Typhimurium Strain of the Emerging Sequence Type 213 Genotype. Genome Announc. 2015;3(3). doi: 10.1128/genomeA.00663-15 26089426; PubMed Central PMCID: PMC4472903.

8. Gilcrease EB, Casjens SR. The genome sequence of Escherichia coli tailed phage D6 and the diversity of Enterobacteriales circular plasmid prophages. Virology. 2018;515:203–14. doi: 10.1016/j.virol.2017.12.019 29304472.

9. Lobocka MB, Rose DJ, Plunkett G 3rd, Rusin M, Samojedny A, Lehnherr H, et al. Genome of bacteriophage P1. J Bacteriol. 2004;186(21):7032–68. Epub 2004/10/19. doi: 186/21/7032 [pii] doi: 10.1128/JB.186.21.7032-7068.2004 15489417.

10. Zaidi MB, Calva JJ, Estrada-Garcia MT, Leon V, Vazquez G, Figueroa G, et al. Integrated food chain surveillance system for Salmonella spp. in Mexico. Emerg Infect Dis. 2008;14(3):429–35. doi: 10.3201/eid1403.071057 18325258.

11. Miller SA, Dykes DD, Polesky HF. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 1988;16(3):1215. doi: 10.1093/nar/16.3.1215 3344216; PubMed Central PMCID: PMC334765.

12. Silva C, Betancor L, Garcia C, Astocondor L, Hinostroza N, Bisio J, et al. Characterization of Salmonella enterica isolates causing bacteremia in Lima, Peru, using multiple typing methods. PLoS One. 2017;12(12):e0189946. doi: 10.1371/journal.pone.0189946 29267322.

13. Kieser T. Factors affecting the isolation of CCC DNA from Streptomyces lividans and Escherichia coli. Plasmid. 1984;12(1):19–36. 6387733.

14. Sambrook J, Russell DW. Molecular cloning. A laboratory manual. Third ed. New York: Cold Spring Harbor Laboratory Press; 2001.

15. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017;13(6):e1005595. doi: 10.1371/journal.pcbi.1005595 28594827; PubMed Central PMCID: PMC5481147.

16. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20. doi: 10.1093/bioinformatics/btu170 24695404; PubMed Central PMCID: PMC4103590.

17. Wick RR, Schultz MB, Zobel J, Holt KE. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 2015;31(20):3350–2. doi: 10.1093/bioinformatics/btv383 26099265; PubMed Central PMCID: PMC4595904.

18. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068–9. doi: 10.1093/bioinformatics/btu153 24642063.

19. Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011;27(7):1009–10. doi: 10.1093/bioinformatics/btr039 21278367; PubMed Central PMCID: PMC3065679.

20. Sengupta M, Austin S. Prevalence and significance of plasmid maintenance functions in the virulence plasmids of pathogenic bacteria. Infect Immun. 2011;79(7):2502–9. doi: 10.1128/IAI.00127-11 21555398; PubMed Central PMCID: PMC3191983.

21. Casjens SR, Grose JH. Contributions of P2- and P22-like prophages to understanding the enormous diversity and abundance of tailed bacteriophages. Virology. 2016;496:255–76. doi: 10.1016/j.virol.2016.05.022 27372181; PubMed Central PMCID: PMC4969182.

22. Grose JH, Casjens SR. Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae. Virology. 2014;468–470:421–43. doi: 10.1016/j.virol.2014.08.024 25240328; PubMed Central PMCID: PMC4301999.

23. Mise K, Suzuki K. New generalized transducing bacteriopahge in Echerichia coli. J Virol. 1970;6(2):253–5. 4100529; PubMed Central PMCID: PMC376115.

24. Lienau EK, Strain E, Wang C, Zheng J, Ottesen AR, Keys CE, et al. Identification of a salmonellosis outbreak by means of molecular sequencing. N Engl J Med. 2011;364(10):981–2. Epub 2011/02/25. doi: 10.1056/NEJMc1100443 21345093.

25. Allard MW, Luo Y, Strain E, Li C, Keys CE, Son I, et al. High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach. BMC Genomics. 2012;13:32. doi: 10.1186/1471-2164-13-32 22260654; PubMed Central PMCID: PMC3368722.

26. McDermott PF, Tyson GH, Kabera C, Chen Y, Li C, Folster JP, et al. Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella. Antimicrob Agents Chemother. 2016;60(9):5515–20. doi: 10.1128/AAC.01030-16 27381390; PubMed Central PMCID: PMC4997858.

27. Daniels JB, Call DR, Besser TE. Molecular epidemiology of blaCMY-2 plasmids carried by Salmonella enterica and Escherichia coli isolates from cattle in the Pacific Northwest. Appl Environ Microbiol. 2007;73(24):8005–11. doi: 10.1128/AEM.01325-07 17933916.

28. Wiesner M, Fernandez-Mora M, Cevallos MA, Zavala-Alvarado C, Zaidi MB, Calva E, et al. Conjugative transfer of an IncA/C plasmid-borne blaCMY-2 gene through genetic re-arrangements with an IncX1 plasmid. BMC Microbiol. 2013;13:264. Epub 2013/11/23. doi: 10.1186/1471-2180-13-264 [pii]. 24262067.

29. Wiesner M, Calva JJ, Bustamante VH, Perez-Morales D, Fernandez-Mora M, Calva E, et al. A multi-drug resistant Salmonella Typhimurium ST213 human-invasive strain (33676) containing the blaCMY-2 gene on an IncF plasmid is attenuated for virulence in BALB/c mice. BMC Microbiol. 2016;16(1):18. doi: 10.1186/s12866-016-0633-7 26862033; PubMed Central PMCID: PMC4748464.

30. Boyd EF, Brussow H. Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved. Trends Microbiol. 2002;10(11):521–9. doi: 10.1016/s0966-842x(02)02459-9 12419617.

31. Brussow H, Canchaya C, Hardt WD. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev. 2004;68(3):560–602. doi: 10.1128/MMBR.68.3.560-602.2004 15353570.

32. Whelan KF, Colleran E, Taylor DE. Phage inhibition, colicin resistance, and tellurite resistance are encoded by a single cluster of genes on the IncHI2 plasmid R478. J Bacteriol. 1995;177(17):5016–27. Epub 1995/09/01. doi: 10.1128/jb.177.17.5016-5027.1995 7665479.

33. Taylor DE. Bacterial tellurite resistance. Trends Microbiol. 1999;7(3):111–5. Epub 1999/04/21. doi: S0966-842X(99)01454-7 [pii]. doi: 10.1016/s0966-842x(99)01454-7 10203839.

34. Bobay LM, Touchon M, Rocha EP. Pervasive domestication of defective prophages by bacteria. Proc Natl Acad Sci USA. 2014;111(33):12127–32. doi: 10.1073/pnas.1405336111 25092302; PubMed Central PMCID: PMC4143005.

35. Hayes F. Toxins-antitoxins: plasmid maintenance, programmed cell death, and cell cycle arrest. Science. 2003;301(5639):1496–9. doi: 10.1126/science.1088157 12970556.

36. Canals R, Hammarlof DL, Kroger C, Owen SV, Fong WY, Lacharme-Lora L, et al. Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580. PLoS Biol. 2019;17(1):e3000059. doi: 10.1371/journal.pbio.3000059 30645593; PubMed Central PMCID: PMC6333337.

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2019 Číslo 10
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