title: Comparison of typing methods with a new procedure based on sequence characterization for Salmonella serovar prediction.
abstract: As the development of molecular serotyping approaches is critical for Salmonella spp., which include >2,600 serovars, we performed an initial evaluation of the ability to identify Salmonella serovars using (i) different molecular subtyping methods and (ii) a newly implemented combined PCR- and sequencing-based approach that directly targets O- and H-antigen-encoding genes. Initial testing was performed using 46 isolates that represent the top 40 Salmonella serovars isolated from human and nonhuman sources, as reported by the U.S. Centers for Disease Control and Prevention and the World Health Organization. Multilocus sequence typing (MLST) was able to accurately predict the serovars for 42/46 isolates and showed the best ability to predict serovars among the subtyping methods tested. Pulsed-field gel electrophoresis (PFGE), ribotyping, and repetitive extragenic palindromic sequence-based PCR (rep-PCR) were able to accurately predict the serovars for 35/46, 34/46, and 30/46 isolates, respectively. Among the methods, S. enterica subsp. enterica serovars 4,5,12:i:-, Typhimurium, and Typhimurium var. 5- were frequently not classified correctly, which is consistent with their close phylogenetic relationship. To develop a PCR- and sequence-based serotyping approach, we integrated available data sources to implement a combination PCR-based O-antigen screening and sequencing of internal fliC and fljB fragments. This approach correctly identified the serovars for 42/46 isolates in the initial set representing the most common Salmonella serovars, as well as for 54/63 isolates representing less common Salmonella serovars. Our study not only indicates that different molecular approaches show the potential to allow for rapid serovar classification of Salmonella isolates, but it also provides data that can help with the selection of molecular serotyping methods to be used by different laboratories.
authors.affiliation: Cornell University, Department of Food Science, Ithaca, New York, USA.
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Ranieri
authors.forename: Chunlei
authors.initials: C
authors.lastname: Shi
authors.forename: Andrea I
authors.initials: AI
authors.lastname: Moreno Switt
authors.forename: Henk C
authors.initials: HC
authors.lastname: den Bakker
authors.forename: Martin
authors.initials: M
authors.lastname: Wiedmann
mesh_terms: D000942:Antigens, Bacterial / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D006801:Humans; D058889:Molecular Typing / Q000379:methods*; D019081:O Antigens / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods; D019779:Salmonella enterica / Q000145:classification* / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D012703:Serotyping / Q000379:methods
chemical_list: D000942:Antigens, Bacterial; D004269:DNA, Bacterial; C022863:H antigen; D019081:O Antigens
references.citation: J Food Prot. 2002 Jun;65(6):1005-7
references.pmid: 12092713
references.citation: Appl Environ Microbiol. 2011 Dec;77(24):8648-55
references.pmid: 22003026
references.citation: Int J Food Microbiol. 2008 Apr 30;123(3):293-8
references.pmid: 18258323
references.citation: J Clin Microbiol. 2002 Mar;40(3):1127-8
references.pmid: 11880463
references.citation: Foodborne Pathog Dis. 2010 Jun;7(6):707-17
references.pmid: 20180633
references.citation: J Clin Microbiol. 2002 May;40(5):1626-35
references.pmid: 11980932
references.citation: Ann Inst Pasteur Microbiol (1985). 1985 Sep-Oct;136B(2):169-79
references.pmid: 2417542
references.citation: Poult Sci. 2013 Feb;92(2):562-72
references.pmid: 23300324
references.citation: Bioinformatics. 2006 Nov 1;22(21):2688-90
references.pmid: 16928733
references.citation: J Clin Microbiol. 2004 May;42(5):1923-32
references.pmid: 15131150
references.citation: Appl Environ Microbiol. 2006 Dec;72(12):7575-85
references.pmid: 17028236
references.citation: Res Microbiol. 2010 Jan-Feb;161(1):26-9
references.pmid: 19840847
references.citation: J Microbiol Methods. 2007 Aug;70(2):261-71
references.pmid: 17555834
references.citation: J Clin Microbiol. 2005 Mar;43(3):1045-50
references.pmid: 15750058
references.citation: J Clin Microbiol. 2007 Feb;45(2):472-6
references.pmid: 17166969
references.citation: Trends Microbiol. 1996 Dec;4(12):495-503
references.pmid: 9004408
references.citation: FEMS Microbiol Lett. 2012 Dec;337(1):61-72
references.pmid: 22998607
references.citation: BMC Microbiol. 2004 Aug 06;4:31
references.pmid: 15298703
references.citation: Vet Microbiol. 2004 Jun 3;100(3-4):205-17
references.pmid: 15145499
references.citation: Carbohydr Res. 2003 Nov 14;338(23):2503-19
references.pmid: 14670712
references.citation: J Biol Chem. 1985 Dec 15;260(29):15758-61
references.pmid: 2999134
references.citation: Foodborne Pathog Dis. 2007 Fall;4(3):293-303
references.pmid: 17883313
references.citation: Epidemiol Infect. 2011 Aug;139(8):1272-80
references.pmid: 20950515
references.citation: J Clin Microbiol. 1993 Feb;31(2):233-7
references.pmid: 8432808
references.citation: J Clin Microbiol. 2011 Feb;49(2):565-73
references.pmid: 21159932
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: J Microbiol Methods. 2009 Jan;76(1):18-24
references.pmid: 18835303
references.citation: BMC Genomics. 2012 Jan 19;13:32
references.pmid: 22260654
references.citation: J Clin Microbiol. 2010 Sep;48(9):3122-6
references.pmid: 20631109
references.citation: J Clin Microbiol. 2007 Oct;45(10):3323-34
references.pmid: 17634307
references.citation: J Clin Microbiol. 2011 Aug;49(8):2954-65
references.pmid: 21697324
references.citation: Proc Natl Acad Sci U S A. 1979 Jan;76(1):391-5
references.pmid: 370828
references.citation: Clin Infect Dis. 2010 Mar 15;50(6):882-9
references.pmid: 20158401
references.citation: Acta Vet Hung. 2005;53(2):163-72
references.pmid: 15959975
references.citation: Appl Environ Microbiol. 2006 Dec;72(12):7949-53
references.pmid: 17056694
references.citation: Infect Genet Evol. 2002 Oct;2(1):39-45
references.pmid: 12797999
references.citation: J Clin Microbiol. 2008 Dec;46(12):4037-40
references.pmid: 18842945
references.citation: Foodborne Pathog Dis. 2006 Spring;3(1):59-67
references.pmid: 16602980
references.citation: J Clin Microbiol. 2006 Oct;44(10):3608-15
references.pmid: 16943358
references.citation: Appl Environ Microbiol. 2003 Oct;69(10):6099-105
references.pmid: 14532067
references.citation: Res Microbiol. 2007 Mar;158(2):122-7
references.pmid: 17258433
references.citation: J Clin Microbiol. 2012 May;50(5):1524-32
references.pmid: 22378901
references.citation: PLoS Pathog. 2012;8(6):e1002776
references.pmid: 22737074
references.citation: Foodborne Pathog Dis. 2009 May;6(4):407-15
references.pmid: 19292687
references.citation: J Clin Microbiol. 2008 Aug;46(8):2581-9
references.pmid: 18524964
references.citation: Int J Food Microbiol. 2009 Aug 31;134(1-2):83-8
references.pmid: 19237218
references.citation: Emerg Infect Dis. 2006 Mar;12(3):381-8
references.pmid: 16704773
references.citation: BMC Genomics. 2011 Aug 22;12:425
references.pmid: 21859443
references.citation: J Clin Microbiol. 1993 Aug;31(8):2118-23
references.pmid: 8370740
references.citation: J Appl Microbiol. 2012 Jan;112(1):185-96
references.pmid: 21981579
references.citation: BMC Infect Dis. 2005 Feb 03;5:7
references.pmid: 15691371
references.citation: J Clin Microbiol. 2009 May;47(5):1290-9
references.pmid: 19261787
references.citation: Brief Bioinform. 2008 Jul;9(4):286-98
references.pmid: 18372315
references.citation: J Food Prot. 2013 Feb;76(2):283-94
references.pmid: 23433376
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: J Clin Microbiol. 2009 Nov;47(11):3546-56
references.pmid: 19741087