Application of the Random Forest Method to Analyse Epidemiological and Phenotypic Characteristics of Salmonella 4,[5],12: I:- and Salmonella Typhimurium Strains

Zoonoses and Public Health

Volumn 59, Issue 7, 2012, Pages 505-512

  Barco, L ^a   Mancin, M ^a   Ruffa, M ^a   Saccardin, C ^a   Minorello, C ^a   Zavagnin, P ^a   Lettini, A A ^a   Olsen, J E ^b   Ricci, A ^a  

^a ISTITUTO ZOOPROFILATTICO SPERIMENTALE DELLE VENEZIE   (Italy)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Phage typing; Random Forests; Salmonella 4, 5 ,12:i: ; Salmonella Typhimurium

Indexed keywords

AMPICILLIN; CEFOTAXIME; CHLORAMPHENICOL; CIPROFLOXACIN; GENTAMICIN; KANAMYCIN; NALIDIXIC ACID; STREPTOMYCIN; SULFONAMIDE;

ANIMAL EXPERIMENT; ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIOPHAGE; BACTERIUM ISOLATION; CONTROLLED STUDY; MULTIDRUG RESISTANCE; NONHUMAN; PHENOTYPE; PREVALENCE; PRIORITY JOURNAL; RANDOM FOREST; SALMONELLA ENTERICA; SALMONELLA ENTERICA 4,[5],12:I:; SALMONELLA TYPHIMURIUM; SEROTYPING;

ANIMALS; BACTERIOPHAGE TYPING; DRUG RESISTANCE, MULTIPLE, BACTERIAL; ENVIRONMENT; FOOD MICROBIOLOGY; HUMANS; ITALY; MICROBIAL SENSITIVITY TESTS; PHENOTYPE; PHYLOGENY; PREVALENCE; SALMONELLA ENTERICA; SALMONELLA INFECTIONS; SALMONELLA INFECTIONS, ANIMAL; SALMONELLA TYPHIMURIUM; SEROTYPING;

ANIMALIA; SALMONELLA; SALMONELLA ENTERICA; SALMONELLA TYPHIMURIUM;

EID: 84866750631     PISSN: 18631959     EISSN: 18632378     Source Type: Journal    
DOI: 10.1111/j.1863-2378.2012.01487.x     Document Type: Article

References (36)

1. Agasan, A., J. Kornblum, G. Williams, C. C. Pratt, P. Fleckenstein, M. Wong, and A. Ramon, 2002: Profile of Salmonella enterica subsp. enterica (subspecies I) serotype 4, 5, 12:i:- strains causing food-borne infections in New York City. J. Clin. Microbiol. 40, 1924-1929.
2. Anderson, E. S., L. R. Ward, M. J. Saxe, and J. D. de Sa, 1977: Bacteriophage-typing designations of Salmonella Typhimurium. J. Hyg. (Lond). 78, 297-300.
3. Baggesen, D. L., G. Sørensen, E. M. Nielsen, and H. C. Wegener, 2010: Phage typing of Salmonella Typhimurium - is it still a useful tool for surveillance and outbreak investigation? Euro. Surveill. 15, 19471.
4. Barco, L., A. A. Lettini, E. Ramon, A. Longo, C. Saccardin, M. C. Dalla Pozza, and A. Ricci, 2011: A rapid and sensitive method to identify and differentiate Salmonella enterica serotype Typhimurium and Salmonella enterica serotype 4, [5], 12:i:- by combining traditional serotyping and multiplex polymerase chain reaction. Foodborne Pathog. Dis. 8, 741-743.
5. Barone, L., V. A. Dal, N. Pellissier, A. Viganò, C. Romani, and M. Pontello, 2008: Emergence of Salmonella Typhimurium monophasic serovar: determinants of antimicrobial resistance in porcine and human strains. Ann. Ig. 20, 199-209.
6. Bone, A., H. Noel, S. Le Hello, N. Pihier, C. Danan, M. E. Raguenaud, S. Salah, H. Bellali, V. Vaillant, F. X. Weill, and N. Jourdan-da Silva, 2010: Nationwide outbreak of Salmonella enterica serotype 4, 12:i:- infections in France, linked to dried pork sausage. Euro. Surveill. 15, 19592.
7. CLSI, 2008: M100-S18. Performance Standards for Antimicrobial Susceptibility Testing, 18. Informational Supplement. Clinical and Laboratory Standards Institute, Wayne, PA.
8. Cortiñas Abrahantes, J., K. Bollaerts, M. Aerts, V. Ogunsanya, and Y. Van der Stede, 2009: Salmonella serosurveillance: different statistical methods to categorise pig herds based on serological data. Prev. Vet. Med. 89, 59-66.
9. Cutler, D. R., T. C. Edwards Jr, K. H. Beard, A. Cutler, K. T. Hess, J. Gibson, and J. J. Lawler, 2007: Random forests for classification in ecology. Ecology 88, 2783-2792.
10. Denwood, M. J., A. E. Mather, D. T. Haydon, L. Matthews, D. J. Mellor, and S. W. J. Reid, 2011: From phenotype to genotype: a Bayesian solution. Biol. Sci. 278, 1434-1440.
11. Didelot, X., R. Bowden, T. Street, T. Golubchik, C. Spencer, G. McVean, V. Sangal, M. F. Anjum, M. Achtman, D. Falush, and P. Donnelly, 2011: Recombination and population structure in Salmonella enterica. PLoS Genet. 7, e1002191. doi:10.1371/journal.pgen.1002191
12. Dionisi, A. M., C. Graziani, C. Lucarelli, E. Filetici, L. Villa, S. Owczarek, A. Caprioli, and I. Luzzi, 2009: Molecular characterization of multidrug-resistant strains of Salmonella enterica serotype Typhimurium and monophasic variant (S. 4, [5], 12:i:-) isolated from human infections in Italy. Foodborne Pathog. Dis. 6, 711-717.
13. Echeita, M. A., A. Aladueña, S. Cruchaga, and M. A. Usera, 1999: Emergence and spread of an atypical Salmonella enterica subsp. enterica serotype 4, 5, 12:i:- strain in Spain. J. Clin. Microbiol. 37, 3425.
14. Echeita, M. A., S. Herrera, and M. A. Usera, 2001: Atypical, fljB-negative Salmonella enterica subsp. enterica strain of serovar 4, 5, 12:i:- appears to be a monophasic variant of serovar Typhimurium. J. Clin. Microbiol. 39, 2981-2983.
15. European Food Safety Authority (EFSA), European Centre for Disease Prevention and Control, 2011: The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2009. EFSA Journal, 9, 2090.
16. European Food Safety Authority (EFSA) Panel on Biological Hazards (BIOHAZ), 2010: Scientific Opinion on monitoring and assessment of the public health risk of "Salmonella Typhimurium-like" strains. EFSA Journal, 8, 1826.
17. Garaizar, J., S. Porwollik, A. Echeita, A. Rementeria, S. Herrera, R. M. Wong, J. Frye, M. A. Usera, and M. McClelland, 2002: DNA microarray-based typing of an atypical monophasic Salmonella enterica serovar. J. Clin. Microbiol. 40, 2074-2078.
18. García, P., B. Guerra, M. Bances, M. C. Mendoza, and M. R. Rodicio, 2011: IncA/C plasmids mediate antimicrobial resistance linked to virulence genes in the Spanish clone of the emerging Salmonella enterica serotype 4, [5], 12:i:- J. Antimicrob. Chemother. 66, 543-549.
19. Graziani, C., L. Busani, A. M. Dionisi, C. Lucarelli, S. Owczarek, A. Ricci, M. Mancin, A. Caprioli, and I. Luzzi, 2008: Antimicrobial resistance in Salmonella enterica serovar Typhimurium from human and animal sources in Italy. Vet. Microbiol. 128, 414-418.
20. Guerra, B., I. Laconcha, S. M. Soto, M. A. González-Hevia, and M. C. Mendoza, 2000: Molecular characterisation of emergent multiresistant Salmonella enterica serotype [4, 5, 12:i:-] organisms causing human salmonellosis. FEMS Microbiol. Lett. 190, 341-347.
21. Hauser, E., E. Tietze, R. Helmuth, E. Junker, K. Blank, R. Prager, W. Rabsch, B. Appel, A. Fruth, and B. Malorny, 2010: Pork contaminated with Salmonella enterica serovar 4, [5], 12:i:-, an emerging health risk for humans. Appl. Environ. Microbiol. 76, 4601-4610.
22. Hopkins, K. L., M. Kirchner, B. Guerra, S. A. Granier, C. Lucarelli, M. C. Porrero, A. Jakubczak, E. J. Threlfall, and D. J. Mevius, 2010: Multiresistant Salmonella enterica serovar 4, [5], 12:i:- in Europe: a new pandemic strain? Euro. Surveill. 15, 2-10.
23. Kim, Y., and H. Kim, 2007: Application of random forests to association studies using mitochondrial single nucleotide polymorphisms. Genome Inform 5, 168-173.
24. Lan, R., P. R. Reeves, and S. Octavia, 2009: Population structure, origins and evolution of major Salmonella enterica clones. Infect. Genet. Evol. 9, 996-1005.
25. Lin, X., L. Sun, Y. Li, Z. Guo, Y. Li, K. Zhong, Q. Wang, X. Lu, Y. Yang, and G. Xu, 2010: A random forest of combined features in the classification of cut tobacco based on gas chromatography fingerprinting. Talanta 82, 1571-1575.
26. Mossong, J., P. Marques, C. Ragimbeau, P. Huberty-Krau, S. Losch, G. Meyer, G. Moris, C. Strottner, W. Rabsch, and F. Schneider, 2007: Outbreaks of monophasic Salmonella enterica serovar 4, [5], 12:i:- in Luxembourg, 2006. Euro. Surveill. 12, E11-E12.
27. Paine, S. W., P. Barton, J. Bird, R. Denton, K. Menochet, A. Smith, N. P. Tomkinson, and K. K. Chohan, 2010: A rapid computational filter for predicting the rate of human renal clearance. J. Mol. Graph. Model. 29, 529-537.
28. Shi, T., D. Seligson, A. S. Belldegrun, A. Palotie, and S. Horvath, 2005: Tumor classification by tissue microarray profiling: random forest clustering applied to renal cell carcinoma. Mod. Pathol. 18, 547-557.
29. Smith, A., B. Sterba-Boatwright, and J. Mott, 2010: Novel application of a statistical technique, Random Forests, in a bacterial source tracking study. Water Res. 44, 4067-4076.
30. Soyer, Y., A. Moreno Switt, M. A. Davis, J. Maurer, P. L. McDonough, D. J. Schoonmaker-Bopp, N. B. Dumas, T. Root, L. D. Warnick, Y. T. Gröhn, and M. Wiedmann, 2009: Salmonella enterica serotype 4, 5, 12:i:-, an emerging Salmonella serotype that represents multiple distinct clones. J. Clin. Microbiol. 47, 3546-3556.
31. Switt, A. I., Y. Soyer, L. D. Warnick, and M. Wiedmann, 2009: Emergence, distribution, and molecular and phenotypic characteristics of Salmonella enterica serotype 4, 5, 12:i:- Foodborne Pathog. Dis. 6, 407-415.
32. Tavechio, A. T., A. C. Ghilardi, and S. A. Fernandes, 2004: "Multiplex PCR" identification of the atypical and monophasic Salmonella enterica subsp. enterica serotype 1, 4, [5], 12:i:- in São Paulo State, Brazil: frequency and antibiotic resistance patterns. Rev. Inst. Med. Trop. Sao Paulo 46, 115-117.
33. Tavechio, A. T., S. A. Fernandes, A. C. Ghilardi, G. Soule, R. Ahmed, and C. E. Melles, 2009: Tracing lineage by phenotypic and genotypic markers in Salmonella enterica subsp. enterica serovar 1, 4, [5], 12:i:- and Salmonella Typhimurium isolated in state of Sao Paulo, Brazil. Mem. Inst. Oswaldo Cruz 104, 1042-1046.
34. Xu, M., K. G. Tantisira, A. Wu, A. A. Litonjua, J. H. Chu, B. E. Himes, A. Damask, and S. T. Weiss, 2011: Genome Wide Association Study to predict severe asthma exacerbations in children using random forests classifiers. BMC Med. Genet. 12, 90-98.
35. Zamperini, K., V. Soni, D. Waltman, S. Sanchez, E. C. Theriault, J. Bray, and J. J. Maurer, 2007: Molecular characterization reveals Salmonella enterica serovar 4, [5], 12:i:- from poultry is a variant Typhimurium serovar. Avian Dis. 51, 958-964.
36. Zou, W., W. J. Lin, S. L. Foley, C. H. Chen, R. Nayak, and J. J. Chen, 2010: Evaluation of pulsed-field gel electrophoresis profiles for identification of Salmonella serotypes. J. Clin. Microbiol. 48, 3122-3126.