Molecular Serotyping of Salmonella enterica by Complete rpoB Gene Sequencing

다국어 초록 (Multilingual Abstract)

Serotyping has been the gold standard for identifying Salmonella, but it requires large amounts of standard antisera. Multilocus sequence typing (MLST) has been applied to identify Salmonella serovars, but the recombination of 4–7 housekeeping genes and multiple analytic steps diminish its applicability. In the present study, we determined the complete sequences of the RNA polymerase beta subunit gene (rpoB) and 7 housekeeping genes (aroC, dnaN, hemD, hisD, purE, sucA, and thrA) for 76 strains of 33 Salmonella enterica serovars and conducted phylogenetic analyses together with the corresponding gene sequences of 24 reference strains registered in the GenBank database. Based on the phylogenetic analyses, 100 strains from 40 serovars and 91 strains from 37 serovars were classified into 60 rpoB (RST) and 49 multilocus sequence types (ST), respectively. The nucleotide similarities were 98.8–100% and 96.9–100% for the complete rpoB gene and the seven concatenated housekeeping genes, respectively. The strains of 35 and 30 serovars formed serovar-specific branches or clusters in the rpoB and housekeeping gene phylogenetic trees, respectively. Therefore, complete rpoB gene sequencing and phylogenetic analysis may be a useful method for identifying Salmonella serovars that is a simpler, more cost-effective, and less time-consuming alternative or complementary method to MLST and conventional serotyping.

참고문헌 (Reference)

1 Mollet, C., "rpoB sequence analysis as a novel basis for bacterial identification" 26 : 1005-1011, 1997

2 Kim, K. S., "Use of rpoB sequences for phylogenetic study of Mycoplasma species" 226 : 299-305, 2003

3 Adékambi, T., "The rpoB gene as a tool for clinical microbiologists" 17 : 37-45, 2009

4 Saitou, N., "The neighbor-joining method: a new method for reconstructing phylogenetic trees" 4 : 406-425, 1987

5 Hendriksen, R. S., "The External Quality Assurance System of the WHO Global Salm-Surv Year 2008, 2nded" The National Food Institute, Technical University of Denmark 2009

6 La Scola, B., "Sequencing of the rpoB gene and flanking spacers for molecular identification of Acinetobacter species" 44 : 827-832, 2006

7 Kidgell, C., "Salmonella typhi, the causative agent of typhoid fever, is approximately 50,000 years old" 2 : 39-45, 2002

8 Herikstad, H., "Salmonella surveillance: a global survey of public health serotyping" 129 : 1-8, 2002

9 Hopper, S.A., "Salmonella enteritidis in a commercial layer flock" 123 : 351-, 1988

10 Dauga, C., "Restriction fragment length polymorphism analysis of some flagellin genes of Salmonella enterica" 36 : 2835-2843, 1998

11 Korczak, B., "Phylogeny of the family Pasteurellaceae based on rpoB sequences" 54 : 1393-1399, 2004

12 Christensen, H., "Phylogenetic relationships of Salmonella based on DNA sequence comparison of atpD encoding the beta subunit of ATP synthase" 161 : 89-96, 1998

13 Suzuki, S., "Pathogenicity of Salmonella enteritidis in poultry" 21 : 89-105, 1994

14 Maiden, M. C., "Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl" 95 : 3140-3145, 1998

15 Fakhr, M. K., "Multilocus sequence typing lacks the discriminatory ability of pulsed-field gel electrophoresis for typing Salmonella enterica serovar Typhimurium" 43 : 2215-2219, 2005

16 Kotetishvili, M., "Multilocus sequence typing for characterization of clinical and environmental Salmonella strains" 40 : 1626-1635, 2002

17 Achtman, M., "Multilocus sequence typing as a replacement for serotyping in Salmonella enterica" 8 : e1002776-, 2012

18 Enright, M.C., "Multilocus sequence typing" 7 : 482-487, 1999

19 Marianelli, C., "Molecular characterization of the rpoB gene in Brucella species: new potential molecular markers for genotyping" 8 : 860-865, 2006

20 Falush, D., "Mismatch induced speciation in Salmonella: model and data" 361 : 2045-2053, 2006

21 Tankouo-Sandjong, B., "MLST-v, multilocus sequence typing based on virulence genes, for molecular typing of Salmonella enterica subsp. enterica serovars" 69 : 23-36, 2007

22 Tamura, K., "MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods" 28 : 2731-2739, 2011

23 Kim, B. J., "Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB)" 37 : 1714-1720, 1999

24 Oscar, T. P., "Identification and characterization of Salmonella isolates by automated ribotyping" 61 : 519-524, 1998

25 Torpdahl, M., "Genotypic characterization of Salmonella by multilocus sequence typing, pulsed-field gel electrophoresis and amplified fragment length polymorphism" 63 : 173-184, 2005

26 Benson, D. A., "GenBank" 39 : D32-D37, 2011

27 Sukhnanand, S., "DNA sequence-based subtyping and evolutionary analysis of selected Salmonella enterica serotypes" 43 : 3688-3698, 2005

28 Adékambi, T., "Complete rpoB gene sequencing as a suitable supplement to DNA-DNA hybridization for bacterial species and genus delineation" 58 : 1807-1814, 2008

29 Harbottle, H., "Comparison of multilocus sequence typing, pulsedfield gel electrophoresis, and antimicrobial susceptibility typing for characterization of Salmonella enterica serotype Newport isolates" 44 : 2449-2457, 2006

30 McClelland, M., "Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid" 36 : 1268-1274, 2004

31 Reeves, M. W., "Clonal nature of Salmonella typhi and its genetic relatedness to other salmonellae as shown by multilocus enzyme electrophoresis, and proposal of Salmonella bongori comb. nov" 27 : 313-320, 1989

32 Herrera-Leon, S., "Blind comparison of traditional serotyping with three multiplex PCRs for the identification of Salmonella serotypes" 158 : 122-127, 2007

33 Hall, T. A., "BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT" 41 : 95-98, 1999

34 Kwon, H. J., "Application of nucleotide sequence of RNA polymerase beta-subunit gene (rpoB) to molecular differentiation of serovars of Salmonella enterica subsp. enterica" 82 : 121-129, 2001

35 Grimont, P.A.D., "Antigenic formulae of the Salmonella serovars. WHO Collaborating Centre for Reference and Research on Salmonella" Institut Pasteur 2007

36 Christensen, H., "16S to 23S rRNA spacer fragment length polymorphism of Salmonella enterica at subspecies and serotype levels" 89 : 130-136, 2000