Comparative genome analysis and characterization of the Salmonella Typhimurium strain CCRJ_26 isolated from swine carcasses using whole-genome sequencing approach

Letters in Applied Microbiology

Volumn 66, Issue 4, 2018, Pages 352-359

  Panzenhagen, P H N ^a,b   Cabral, C C ^b,c   Suffys, P N ^d   Franco, R M ^b   Rodrigues, D P ^d   Conte Junior, C A ^a,b,e  

^a FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^b FLUMINENSE FEDERAL UNIVERSITY   (Brazil)

^c UNIVERSIDADE SEVERINO SOMBRA   (Brazil)

^d INSTITUTO OSWALDO CRUZ   (Brazil)

^e National Institute for Quality Control in Health   (Brazil)

Author keywords

multiple drug resistance; PFGE; plasmids; Salmonella pathogenicity islands; whole genome sequencing

Indexed keywords

GENES;

ANALYSIS AND CHARACTERIZATION; GENOME ANALYSIS; MULTIPLE DRUG RESISTANCE; PFGE; PLASMID; PROPHAGES; S. TYPHIMURIUM; SALMONELLA PATHOGENICITY ISLANDS; SALMONELLA TYPHIMURIUM; WHOLE GENOME SEQUENCING;

SALMONELLA;

VIRULENCE FACTOR; ANTIINFECTIVE AGENT;

ANTIBIOTIC RESISTANCE; BACTERIUM; COMPARATIVE STUDY; GENE; GENOME; MICROBIOLOGY; PATHOGENICITY; PHENOTYPE; PLASMID; VIRULENCE;

ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BACTERIUM ISOLATION; CARCASS; DNA POLYMORPHISM; GENETIC VARIABILITY; GENOME ANALYSIS; NONHUMAN; PATHOGENICITY ISLAND; PHYLOGENY; PIG; SALMONELLA ENTERICA SEROVAR TYPHIMURIUM; WHOLE GENOME SEQUENCING; ANIMAL; ANIMAL SALMONELLOSIS; BRAZIL; CLASSIFICATION; GENETICS; GENOMIC ISLAND; HUMAN; ISOLATION AND PURIFICATION; MICROBIAL SENSITIVITY TEST; MICROBIOLOGY; PLASMID; PROPHAGE; RED MEAT; VIRULENCE;

BRAZIL; RIO DE JANEIRO [BRAZIL];

BACTERIA (MICROORGANISMS); SALMONELLA; SALMONELLA TYPHIMURIUM; SUIDAE;

ANIMALS; ANTI-BACTERIAL AGENTS; BRAZIL; DRUG RESISTANCE, BACTERIAL; GENOME, BACTERIAL; GENOMIC ISLANDS; HUMANS; MICROBIAL SENSITIVITY TESTS; PLASMIDS; PROPHAGES; RED MEAT; SALMONELLA INFECTIONS, ANIMAL; SALMONELLA TYPHIMURIUM; SWINE; VIRULENCE;

EID: 85043597979     PISSN: 02668254     EISSN: 1472765X     Source Type: Journal    
DOI: 10.1111/lam.12859     Document Type: Article

References (36)

1. Ahmer, B.M.M., Tran, M. and Heffron, F. (1999) The virulence plasmid of Salmonella Typhimurium is self-transmissible. J Bacteriol 181, 1364–1368.
2. Almeida, F., Medeiros, M.I., Rodrigues, D.P., Payne, J., Timme, R.E., Allard, M.W. and Falcão, J.P. (2016) Draft genome sequences of 40 Salmonella enterica serovar Typhimurium strains isolated from humans and food in Brazil. Genome Announc [Online] 4, pii: e00892-16. Available at: http://typhimurium.ncbi.nlm.nih.gov/pmc/articles/PMC5034119/ [Accessed: 16 November 2016].
3. Arndt, D., Grant, J.R., Marcu, A., Sajed, T., Pon, A., Liang, Y. and Wishart, D.S. (2016) PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 44, W16–W21.
4. Bishop, A.L., Baker, S., Jenks, S., Fookes, M., Ó Gaora, P., Pickard, D., Anjum, M., Farrar, J. et al. (2005) Analysis of the Hypervariable Region of the Salmonella enterica Genome Associated with tRNAleuX. J Bacteriol 187, 2469–2482.
5. Cabral, C.C., Panzenhagen, P.H.N., Delgado, K.F., Silva, G.R.A., Rodrigues, D.D.P., Franco, R.M. and Conte-Junior, C.A. (2017) Contamination of carcasses and utensils in small swine slaughterhouses by Salmonella in the northwestern region of the state of Rio de Janeiro, Brazil. J Food Prot 80, 1128–1132.
6. Carattoli, A., Zankari, E., García-Fernández, A., Voldby Larsen, M., Lund, O., Villa, L., Møller Aarestrup, F. and Hasman, H. (2014) In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58, 3895–3903.
7. Chiu, C.H., Tang, P., Chu, C., Hu, S., Bao, Q., Yu, J., Chou, Y.Y., Wang, H.S. et al. (2005) The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen. Nucleic Acids Res 33, 1690–1698.
8. Choi, Y. and Chan, A.P. (2015) PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics 31, 2745–2747.
9. CLSI (2010) Perfomance Standards for Antimicrobial Susceptibility Testing – Twentieth Informational Supplement CLSI Document M100–S20. Wayne, PA: Clinical and Laboratory Standards Institute.
10. Deng, W., Liou, S.-R., Plunkett III, G., Mayhew, G.F., Rose, D.J., Burland, V., Kodoyianni, V., Schwatz, D.C. et al. (2003) Comparative Genomics of Salmonella enterica Serovar Typhi Strains Ty2 and CT18. J. Bacteriol 185, 2330–2337.
11. Figueroa-Bossi, N., Uzzau, S., Maloriol, D. and Bossi, L. (2001) Variable assortment of prophages provides a transferable repertoire of pathogenic determinants in Salmonella. Mol Microbiol 39, 260–271.
12. Folkesson, A., Löfdahl, S. and Normark, S. (2002) The Salmonella enterica subspecies I specific centisome 7 genomic island encodes novel protein families present in bacteria living in close contact with eukaryotic cells. Res Microbiol 153, 537–545.
13. Galanis, E., Lo Fo Wong, D.M., Patrick, M.E., Binsztein, N., Cieslik, A., Chalermchikit, T., Aidara-Kane, A., Ellis, A. et al., World Health Organization Global Salm-Surv. (2006) Web-based surveillance and global Salmonella distribution, 2000–2002. Emerg Infect Dis 12, 381–388.
14. Gerlach, R.G. and Hensel, M. (2007) Protein secretion systems and adhesins: the molecular armory of Gram-negative pathogens. Int J Med Microbiol 297, 401–415.
15. Haneda, T., Ishii, Y., Danbara, H. and Okada, N. (2009) Genome-wide identification of novel genomic islands that contribute to Salmonella virulence in mouse systemic infection. FEMS Microbiol Lett 297, 241–249.
16. Issenhuth-Jeanjean, S., Roggentin, P., Mikoleit, M., Guibourdenche, M., de Pinna, E., Nair, S., Fields, P.I. and Weill, F.X. (2014) Supplement 2008–2010 (no. 48) to the White–Kauffmann–Le Minor scheme. Res Microbiol 165, 526–530.
17. Jarvik, T., Smillie, C., Groisman, E.A. and Ochman, H. (2010) Short-term signatures of evolutionary change in the Salmonella enterica serovar Typhimurium 14028 genome. J Bacteriol 192, 560–567.
18. Kingsley, R.A., Msefula, C.L., Thomson, N.R., Kariuki, S., Holt, K.E., Gordon, M.A., Harris, D., Clarke, L. et al. (2009) Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Res 19, 2279–2287.
19. Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359.
20. Luo, Y., Kong, Q., Yang, J., Mitra, A., Golden, G., Wanda, S.Y., Roland, K.L., Jensen, R.V. et al. (2012) Comparative genome analysis of the high pathogenicity Salmonella Typhimurium strain UK-1. PLoS ONE 7, e40645.
21. Marcus, S.L., Brumell, J.H., Pfeifer, C.G. and Finlay, B.B. (2000) Salmonella pathogenicity islands: big virulence in small packages. Microbes Infect 2, 145–156.
22. McClelland, M., Sanderson, K.E., Spieth, J., Clifton, S.W., Latreille, P., Courtney, L., Porwollik, S., Ali, J. et al. (2001) Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413, 852–856.
23. Okoro, C.K., Kingsley, R.A., Connor, T.R., Harris, S.R., Parry, C.M., Al-Mashhadani, M.N., Kariuki, S., Msefula, C.L. et al. (2012) Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat Genet 44, 1215–1221.
24. Panzenhagen, P.H.N., Cabral, C.C., Suffys, P.N., Aquino, M.H.C., Franco, R.M., Pereira, V.L.A., Rodrigues, D.P. and Conte-Junior, C.A. (2017) Draft genome sequences of Salmonella enterica subsp. enterica Serovar Typhimurium strains isolated from chicken and swine carcasses in two distinct geographical regions from Rio de Janeiro State, Brazil. Genome Announc 5, e00197–17.
25. Parkhill, J., Dougan, G., James, K.D., Thomson, N.R., Pickard, D., Wain, J., Churcher, C., Mungall, K.L. et al. (2001) Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413, 848–852.
26. Parsons, D.A. and Heffron, F. (2005) sciS, an icmF homolog in Salmonella enterica Serovar Typhimurium, limits intracellular replication and decreases virulence. Infect Immun 73, 4338–4345.
27. Price-Carter, M., Roy-Chowdhury, P., Pope, C.E., Paine, S., de Lisle, G.W., Collins, D.M., Nicol, C. and Carter, P.E. (2011) The evolution and distribution of phage ST160 within Salmonella enterica serotype Typhimurium. Epidemiol Infect 139, 1262–1271.
28. Rotger, R. and Casadesus, J. (1999) The virulence plasmids of Salmonella. Int Microbiol 2, 177–184.
29. Saroj, S.D., Shashidhar, R., Karani, M. and Bandekar, J.R. (2008) Distribution of Salmonella pathogenicity island (SPI)-8 and SPI-10 among different serotypes of Salmonella. J Med Microbiol 57, 424–427.
30. Shah, D.H., Lee, M.J., Park, J.H., Lee, J.H., Eo, S.K., Kwon, J.T. and Chae, J.S. (2005) Identification of Salmonella Gallinarum virulence genes in a chicken infection model using PCR-based signature-tagged mutagenesis. Microbiology 151, 3957–3968.
31. Soto, S.M., Rodríguez, I., Rodicio, M.R., Vila, J. and Mendoza, M.C. (2006) Detection of virulence determinants in clinical strains of Salmonella enterica serovar Enteritidis and mapping on macrorestriction profiles. J Med Microbiol 55, 365–373.
32. Stamatakis, A. (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313.
33. Vernikos, G.S. and Parkhill, J. (2006) Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22, 2196–2203.
34. Wagner, P.L. and Waldor, M.K. (2002) Bacteriophage control of bacterial virulence. Infect Immun 70, 3985–3993.
35. Wong, K.K., McClelland, M., Stillwell, L.C., Sisk, E.C., Thurston, S.J. and Saffer, J.D. (1998) Identification and sequence analysis of a 27-kilobase chromosomal fragment containing a Salmonella pathogenicity island located at 92 minutes on the chromosome map of Salmonella enterica serovar Typhimurium LT2. Infect Immun 66, 3365–3371.
36. Zankari, E., Hasman, H., Cosentino, S., Vestergaard, M., Rasmussen, S., Lund, O., Aarestrup, F.M. and Larsen, M.V. (2012) Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67, 2640–2644.