Article Search
닫기

Microbiology and Biotechnology Letters

보문(Article)

View PDF

Molecular and Cellular Microbiology / Biomedical Sciences  |  Molecular Genetics, Omics, and Systems Biology

Microbiol. Biotechnol. Lett. 2018; 46(2): 162-170

https://doi.org/10.4014/mbl.1802.02008

Received: February 8, 2018; Accepted: March 24, 2018

High Resolution Whole Genome Multilocus Sequence Typing (wgMLST) Schemes for Salmonella enterica Weltevreden Epidemiologic Investigations

Pakpoom Tadee 1, Phacharaporn Boonkhot 2, Matthew Hitchings 3, Ben Pascoe 4, 5, Samuel Sheppard 4, 5 and Prapas Patchanee 1*

1Integrative Research Center for Veterinary Preventive Medicine, Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand, 2Graduate School, Maejo University, Chiang Mai, 50290, Thailand, 3Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, United Kingdom, 4The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, BA2 7BA, United Kingdom, 5Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand

Non-typhoidal Salmonella is one of the main pathogens causing food-borne illness in humans, with up to 20% of cases resulting from consumption of pork products. Over the gastroenteritis signs, multidrug resistant Salmonella has arisen. In this study, pan-susceptible phenotypic strains of Salmonella enterica serotype Weltevreden recovered from pig production chain in Chiang Mai, Thailand during 2012−2014 were chosen for analysis. The aim of this study was to use whole genome sequencing (WGS) data with an emphasis on antimicrobial resistance gene investigation to assess their pathogenic potential and genetic diversity determination based on whole genome Multilocus Sequence Typing (wgMLST) to expand epidemiological knowledge and to provide additional guidance for disease control. Analyis using ResFinder 3.0 for WGS database tracing found that one of pan-susceptible phenotypic strain carried five classes of resistance genes: aminoglycoside, beta-lactam, phenicol, sulfonamide, and tetracycline associated genes. Twenty four and 36 loci differences were detected by core genome Multilocus Sequence Typing (cgMLST) and pan genome Multilocus Sequence Typing (pgMLST), respectively, in two matching strains (44/13 vs A543057 and A543056 vs 204/13) initially assigned by conventional MLST and Pulsed-field Gel Electrophoresis (PFGE). One hundread percent discriminant ability can be achieved using the wgMLST technique. WGS is currently the ultimate molecular technique for various in-depth studies. As the findings stated above, a new of “gold standard typing method era” for routine works in genome study is being set.

Keywords: Salmonella Weltevreden, pork, Thailand, pan-susceptible, whole gemone MLST

  1. Carramiñana JJ, Rota C, Agustín I, Herrera A. 2002. High prevalence of multiple resistance to antibiotics in Salmonella serovars isolated from a poultry slaughterhouse in Spain. Vet Microbiol. 104: 133-139.
    Pubmed CrossRef
  2. Rostagno MH, Callaway TR. 2012. Pre-harvest risk factors for Salmonella enterica in pork production. Food Res. Int. 45: 634-640.
    CrossRef
  3. Kuang X, Hao H, Dai M, Wang Y, Ahmad I, Liu Z, et al. 2015. Serotypes and antimicrobial susceptibility of Salmonella spp. isolated from farm animals in China. Front. Microbiol. 6: 602.
    Pubmed KoreaMed CrossRef
  4. Majowicz SE, Musto J, Scallan E, Angulo FJ, Kirk M, O'Brien SJ, et al. 2010. The global burden of nontyphoidal Salmonella gastroenteritis. Clin. Infect. Dis. 50: 882-889.
    Pubmed CrossRef
  5. Campioni F, Bergamini AMM, Falcão JP. 2012. Genetic diversity, virulence genes and antimicrobial resistance of Salmonella Enteritidis isolated from food and humans over a 24-year period in Brazil. Food Microbiol. 32: 254-264.
    Pubmed CrossRef
  6. Jawetz E, Melnick JL, Adelberg EA. 1984. Review of Medical Microbiology, pp. 224-248. 1st Ed. McGraw-Hill Education, Pennsylvania.
  7. Rychlik I, Gregorova D, Hradecka H. 2006. Distribution and function of plasmids in Salmonella enterica. Vet. Microbiol. 112: 1-10.
    Pubmed CrossRef
  8. Foley SL, Lynne AM. 2008. Food animal-associated Salmonella challenges: pathogenicity and antimicrobial resistance. J. Anim. Sci. 86: 173-187.
    Pubmed CrossRef
  9. Guardabassi L, Jensen BL, Kruse H. 2008. Guide to antimicrobial use in animals, pp. 13-26. 1st Ed. Blackwell Publishing, New Jersey.
    CrossRef
  10. Giguère S, Prescott JF, Dowling PM. 2013. Antimicrobial therapy in veterinary medicine, pp. 21-40. 5th Ed. Blackwell Publishing, New Jersey.
    CrossRef
  11. Mürmann L, Dos Santos MC, Cardoso M. 2009. Prevalence, genetic characterization and antimicrobial resistance of Salmonella isolated from fresh pork sausages in Porto Alegre, Brazil. Food Control. 20: 191-195.
    CrossRef
  12. Padungtod P, Kaneene JB. 2006. Salmonella in food animals and humans in northern Thailand. Int. J. Food Microbiol. 108: 346-354.
    CrossRef
  13. Sanguankiat A, Pinthong R, Padungtod P, Baumann MPO, Zessin KH, Srikitjakarn L, et al. 2010. A cross-sectional study of Salmonella in Pork products in Chiang Mai, Thailand. Foodborne Pathog. Dis. 7: 873-878.
    Pubmed CrossRef
  14. Tadee P, Boonkhot P, Pornruangwong S, Patchanee P. 2015. Comparative phenotypic and genotypic characterization of Salmonella spp. in pig farms and slaughterhouses in two provinces in Northern Thailand. PLoS One 10: e0116581.
    Pubmed KoreaMed CrossRef
  15. Patchanee P, Tansiricharoenkul K, Buawiratlert T, Wiratsudakul A, Angchokchatchawal K, Yamsakul P, et al. 2016. Salmonella in pork retail outlets and dissemination of its pulsotypes through pig production chain in Chiang Mai and surrounding areas, Thailand. Prev. Vet. Med. 130: 99-105.
    CrossRef
  16. Kolár M, Urbánek K, Látal T. 2001. Antibiotic selective pressure and development of bacterial resistance. Int. J. Antimicrob. Agents. 17: 357-363.
    CrossRef
  17. Torpdahl M, Skov MN, Sandvang D, Baggesen DL. 2005. Genotypic characterization of Salmonella by multilocus sequence typing, pulsed-field gel electrophoresis and amplified fragment length polymorphism. J. Microbiol. Methods 63: 173-184.
    Pubmed CrossRef
  18. Foxman B. 2012. Molecular Tools and Infectious Disease Epidemiology, pp. 23-40. 1st Ed. Academic Press, Massachusetts.
    CrossRef
  19. Almeida F, Pitondo-Silva A, Oliveira MA, Falcão JP. 2013. Molecular epidemiology and virulence markers of Salmonella Infantis isolated over 25 years in São Paulo State, Brazil. Infect. Genet. Evol. 19: 145-151.
    Pubmed CrossRef
  20. Kaur J, Sharma A, Lee S, Park YS. 2017. DNA profiling of Leuconostoc citreum strains in fermented foods by repetitive element Polymerase Chain Reaction. J. Microbiol. Biotechnol. 27: 17781782.
    Pubmed CrossRef
  21. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. 2012. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19: 455477.
    Pubmed KoreaMed CrossRef
  22. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, et al. 2010. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67: 2640-2644.
    Pubmed KoreaMed CrossRef
  23. Kluytmans-van den Bergh MF, Rossen JW, Bruijning-Verhagen PC, Bonten MJ, Friedrich AW, Vandenbroucke-Grauls CM, et al. 2016. Whole-genome multilocus sequence typing of extendedspectrumbeta-lactamase-producing enterobacteriaceae. J. Clin. Microbiol. 54: 2919-2927.
    Pubmed KoreaMed CrossRef
  24. Sheppard KS, Jolley AK, Maiden CM. 2012. A gene-by-gene approach to bacterial population genomes: whole genome MLST of Campylobacter. Genes (Basel) 3: 261-277.
    Pubmed KoreaMed CrossRef
  25. Gilchrist CA, Turner SD, Riley MF, Petri WA, Hewlett EL. 2015. Whole-genome sequencing in outbreak analysis. Clin. Microbiol. Rev. 28: 541-563.
    Pubmed KoreaMed CrossRef
  26. Kovanen S, Kivistö R, Llarena AK, Zhang J, Kärkkäinen UM, Tuuminen T, et al. 2016. Tracing isolates from domestic human Campylobacter jejuni infections to chicken slaughter batches and swimming water using whole-genome multilocus sequence typing. Int. J. Food Microbiol. 226: 53-60.
    Pubmed CrossRef
  27. Center for Genome Epidemiology. 2017. ResFinder 3.0. Available from https://cge.cbs.dtu.dk/services/ResFinder/. Accessed Nov.18, 2017.
  28. Center for Genome Epidemiology. 2017. MLST 1.8 (MultiLocus Sequence Typing). Available from https://cge.cbs.dtu.dk/services/MLST/. Accessed Nov. 17, 2017.
  29. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, et al. 2012. Multilocus Sequence Typing of total genome sequenced bacteria. J. Clin. Micobiol. 50: 1355-1361.
    Pubmed KoreaMed CrossRef
  30. Hunter PR, Gaston MA. 1988. Numerical index of the discriminatory ability of typing system: an application of Simpson’s index of diversity. J. Clin. Microbiol. 26: 2465-2466.
    Pubmed KoreaMed
  31. Hubert L, Arabie P. 1985. Comparing partitions. J. Classification. 2:193-218.
    CrossRef
  32. Fowlkes EB, Mallows CL. 1983. A method for comparing two hierarchical clusterings. J. Am. Stat. Assoc. 78: 553-569.
    CrossRef
  33. Instituto de Medicina Molecular. 2011. Diversity and partition congruence coefficients calculation. Available from http://www.comparingpartitions.info/?link=Tool. Accessed Nov. 17,2017.
  34. Rowe TA, Leonard FC, Kelly G, Lynch PB, Egan J, Quirke AM, et al. 2003. Salmonella serotypes present on a sample of Irish pig farms. Vet. Rec. 153: 453-456.
    Pubmed CrossRef
  35. Lim SK, Byun JR, Nam HM, Lee HS, Jung SC. 2011. Phenotypic and genotypic characterization of Salmonella spp. Isolated from pigs and their farm environment in Korea. J. Microbiol. Biotechnol. 21:50-54.
    Pubmed CrossRef
  36. Schmidt WJ, Brichta-Harhay MD, Kalchayanand N, Bosilevac JM, Shackelford DS, Wheeler TL, et al. 2012. Prevalence, enumeration, serotypes, and antimicrobial resistance phenotypes of Salmonella enterica isolates from carcasses at two large United States pork processing plants. Appl. Environ. Microbiol. 78: 2716-2726.
    Pubmed KoreaMed CrossRef
  37. Richard JF, Yitzhak T. 2014. Antibiotics and bacterial resistance in the 21st century. Perspect. Medicin. Chem. 6: 25-64.
  38. Rosengren BL, Waldner LC, Reid-Smith JR. 2009. Associations between antimicrobial resistance phenotypes, antimicrobial resistance genes, and virulence genes of fecal Escherichia coli isolates from healthy grow-finish Pigs. Appl. Environ. Microbiol. 75:1373-1380.
    Pubmed KoreaMed CrossRef
  39. Zhou H, Liu W, Qin T, Liu C, Ren H. 2017. Defining and Evaluating a core genome Multilocuc Sequence Typing scheme for whole genome sequence-based typing of Klebsiella pneumoniae. Front. Microbiol. 8: 371.
    Pubmed KoreaMed

Starts of Metrics

Share this article on :

  • mail

Related articles in MBL

Most KeyWord ?

What is Most Keyword?

  • It is most registrated keyword in articles at this journal during for 2 years.