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http://dx.doi.org/10.4014/mbl.1802.02008

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

Tadee, Pakpoom (Integrative Research Center for Veterinary Preventive Medicine, Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University)
Tadee, Phacharaporn (Faculty of Animal Science and Technology, Maejo University)
Hitchings, Matthew D. (Swansea University Medical School, Swansea University)
Pascoe, Ben (The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath)
Sheppard, Samuel K. (The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath)
Patchanee, Prapas (Integrative Research Center for Veterinary Preventive Medicine, Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University)
Publication Information
Microbiology and Biotechnology Letters / v.46, no.2, 2018 , pp. 162-170 More about this Journal
Abstract
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;
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1 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.   DOI
2 Kolar M, Urbanek K, Latal T. 2001. Antibiotic selective pressure and development of bacterial resistance. Int. J. Antimicrob. Agents. 17: 357-363.   DOI
3 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.   DOI
4 Richard JF, Yitzhak T. 2014. Antibiotics and bacterial resistance in the 21st century. Perspect. Medicin. Chem. 6: 25-64.
5 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.   DOI
6 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: 1778-1782.   DOI
7 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.   DOI
8 Foxman B. 2012. Molecular Tools and Infectious Disease Epidemiology, pp. 23-40. 1st Ed. Academic Press, Massachusetts.
9 Almeida F, Pitondo-Silva A, Oliveira MA, Falcao JP. 2013. Molecular epidemiology and virulence markers of Salmonella Infantis isolated over 25 years in Sao Paulo State, Brazil. Infect. Genet. Evol. 19: 145-151.   DOI
10 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: 455-477.   DOI
11 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.
12 Guardabassi L, Jensen BL, Kruse H. 2008. Guide to antimicrobial use in animals, pp. 13-26. 1st Ed. Blackwell Publishing, New Jersey.
13 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 extendedspectrum-beta-lactamase-producing enterobacteriaceae. J. Clin. Microbiol. 54: 2919-2927.   DOI
14 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.   DOI
15 Gilchrist CA, Turner SD, Riley MF, Petri WA, Hewlett EL. 2015. Whole-genome sequencing in outbreak analysis. Clin. Microbiol. Rev. 28: 541-563.   DOI
16 Rychlik I, Gregorova D, Hradecka H. 2006. Distribution and function of plasmids in Salmonella enterica. Vet. Microbiol. 112: 1-10.   DOI
17 Foley SL, Lynne AM. 2008. Food animal-associated Salmonella challenges: pathogenicity and antimicrobial resistance. J. Anim. Sci. 86: 173-187.   DOI
18 Giguere S, Prescott JF, Dowling PM. 2013. Antimicrobial therapy in veterinary medicine, pp. 21-40. 5th Ed. Blackwell Publishing, New Jersey.
19 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.   DOI
20 Padungtod P, Kaneene JB. 2006. Salmonella in food animals and humans in northern Thailand. Int. J. Food Microbiol. 108: 346-354.
21 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.   DOI
22 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.   DOI
23 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.   DOI
24 Kovanen S, Kivisto R, Llarena AK, Zhang J, Karkkainen 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.   DOI
25 Center for Genome Epidemiology. 2017. ResFinder 3.0. Available from https://cge.cbs.dtu.dk/services/ResFinder/. Accessed Nov. 18, 2017.
26 Center for Genome Epidemiology. 2017. MLST 1.8 (MultiLocus Sequence Typing). Available from https://cge.cbs.dtu.dk/services/MLST/. Accessed Nov. 17, 2017.
27 Instituto de Medicina Molecular. 2011. Diversity and partition congruence coefficients calculation. Available from http://www.comparingpartitions.info/?link=Tool. Accessed Nov. 17, 2017.
28 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.
29 Hubert L, Arabie P. 1985. Comparing partitions. J. Classification. 2: 193-218.   DOI
30 Fowlkes EB, Mallows CL. 1983. A method for comparing two hierarchical clusterings. J. Am. Stat. Assoc. 78: 553-569.   DOI
31 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.   DOI
32 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.   DOI
33 Campioni F, Bergamini AMM, Falcao 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.   DOI
34 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.
35 Carraminana JJ, Rota C, Agustin 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.
36 Rostagno MH, Callaway TR. 2012. Pre-harvest risk factors for Salmonella enterica in pork production. Food Res. Int. 45: 634-640.   DOI
37 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.
38 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.   DOI
39 Jawetz E, Melnick JL, Adelberg EA. 1984. Review of Medical Microbiology, pp. 224-248. 1st Ed. McGraw-Hill Education, Pennsylvania.