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are a leading cause of morbidity worldwide ( Rowell et al., 2012 ; Palm et al., 2014). The aim of this outline is to review the value of strain typing in public health and in the food industry. Selected examples are used to give an overview on current molecular typing tools, discussing the potential as well as the shortcomings of diverse techniques in reference to our own work and to present an outlook on upcoming technologies based on WGS. 2 Identification of microorganisms Identification denotes the assignment of a microorganism into a classification scheme based

mechanisms and specific resistances of clinical and/or epidemiological importance.Version 1.0, 2013. http://www.eucast.org . 19. Ribot, E.M., Fair, M.A., Gautom, R., Cameron, D.N., Hunter, S.B., Swaminathan, B., Barrett, T.J. (2006). Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet. Foodborne Pathog Dis. 3(1): 59-67. https://doi.org/10.1089/fpd.2006.3.59 PMid:16602980 20. Caprioli, A., Maugliani, A., Michelacci, V., Morabito, S. (2014). Molecular typing of Verocytotoxin

first year of life. Acta Vet Scand. 49, 22. http://dx.doi.org/10.1186/1751-0147-49-22 PMid:17848186; PMCid:PMC2040143 12. Beck, R., Sprong, H., Bata, I., Lucinger, S., Pozio, E., Cacció, S. M. (2011b). Prevalence and molecular typing of Giardia spp. in captive mammals at the ZOO of Zagreb, Croatia. Vet Parasitol. 175, 40-46. http://dx.doi.org/10.1016/j.vetpar.2010.09.026 PMid:20970259

.P., Pitondo-Silva A., Malaspina A.C., Brocchi M.: Molecular typing and virulence markers of Yersinia enterocolitica strains from human, animal and food origins isolated between 1968 and 2000 in Brazil. J Med Microbiol 2006, 55, 1539-1548. 5. Garin-Bastuji B., Hummel N., Gerbier G., Cau C., Pouillot R., Da Costa M., Fontaine J.J.: Nonspecific serological reactions in the diagnosis of bovine brucellosis: experimental oral infection of cattle with repeated doses of Yersinia enterocolitica O:9. Vet Microbiol 1999, 66, 223-233. 6. Gerbier G., Garin-Bastuji B., Pouillot R

coagulase-negative staphylococci in toxic shock syndrome. J Clin Microbiol 1986, 23, 43-45. 8. Cunha M.L.R.S., Peresi E., Calsolari R.A.O., Junior J.P.A.: Detection of enterotoxins genes in coagulase-negative staphylococci isolated from foods. Brazil J Microbiol 2006, 37, 70-74. 9. Dinges M.M., Orwin P.M., Schlievert P.M.: Exotoxins of Staphylococcus aureus. Clin Microbiol Rev 2000, 13, 16-34. 10. Goh S.H., Byrne S.K., Zhang J.L., Chow A.W.: Molecular typing of Staphylococcus aureus on the basis of coagulase gene polymorphism. J Clin Microbiol 1992, 30, 1642-1645. 11

2013, 51, 195–201. 12. Kaakoush N.O., Castaño-Rodriguez N., Mitchell H.M., Man S.M.: Global epidemiology of Campylobacter infection. Clin Microbiol Rev 2015, 28, 687–720. 13. Lévesque S., Fournier E., Carrier N., Frost E., Arbeit R.D., Michaud S.: Campylobacteriosis in urban versus rural areas: A case-case study integrated with molecular typing to validate risk factors and to attribute sources of infection. PLoS ONE 2013, 8, e83731. 14. Müllner P., Spencer S.E.F., Wilson D.J., Jones G., Noble A.D., Midwinter A.C., Collins-Emerson J.M., Carter P., Hathaway S

-resistant Staphylococcus aureus isolated from bovine milk. Zoonoses Public Hlth 2010, 57, 197-203. 28. Wang D., Wang Z., Yan Z., Wu J., Ali T., Li J., Lv Y., Han B.: Bovine mastitis Staphylococcus aureus: Antibiotic susceptibility profile, resistant genes and molecular typing of methicillinresistant and methicillin-sensitive strains in China. Infect Genet Evol 2015, 31, 9-16. 29. Wasiński B., Różańska H., Osek J.: Occurrence of extended spectrum ß-lactamase and AmpC-producing Escherichia coli in meat samples. Bull Vet Inst Pulawy 2013, 57, 513-517. 30. Watson E., Jeckel S., Snow L

. Public Health Rep 1963, 78, 707-710. 4. Berri M., Rekiki A., Sidi Boumedine K., Rodolakis A.: Simultaneous differential detection of Chlamydophila abortus, Chlamydophila pecorum and Coxiella burnetii from aborted ruminant’s clinical samples using multiplex PCR. BMC Microbiol 2009, 9:130, doi:10.1186/1471-2180-9-130. 5. Boarbi S., Mori M., Rousset E., Sidi-Boumedine K., van Esbroeck M., Fretin D.: Prevalence and molecular typing of Coxiella burnetii in bulk tank milk in Belgian dairy goats, 20092013. Vet Microbiol 2014, 170, 117-124. 6. Böttcher J., Vossen A

., Wang S.H.: Comparison of four molecular typing methods for Riemerella anatipestifer . Taiwan Vet J 2015, 41, 177–185. 5. Chen Y.P., Lee S.H., Chou C.H., Tsai H.J.: Detection of florfenicol resistance genes in Riemerella anatipestifer isolated from ducks and geese. Vet Microbiol 2012, 154, 325–331. 6. Chen Y.P., Lee S.H., Tsai H.J.: Serotyping of Riemerellar anatipestifer isolates from waterfowl in Taiwan between 2008 and 2012. Exp Rep Taiwan AHRI 2013, 48, 21–28. 7. Chu C.Y., Liu C.H., Liou J.J., Lee J.W., Cheng L.T.: Development of a subunit vaccine containing

Microbiol 2009, 136, 1–2. 15. Harada K., Kijima-Tanaka M., Uchiyama M., Yamamoto T., Oishi K., Arao M., Takahashi T.: Molecular typing of Japanese field isolates and live commercial vaccine strain of Mycoplasma synoviae using improved pulsed-field gel electrophoresis and vlhA gene sequencing. Avian Dis 2009, 53, 538–543. 16. Hong Y., Garcia M., Leiting,V., Benčina D., Dufour-Zavala L., Zavala G., Kleven S.H.: Specific detection and typing of Mycoplasma synoviae strains in poultry with PCR and DNA sequence analysis targeting the hemagglutinin encoding gene vlhA. Avian