infectious diseases 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 moleculartyping 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.
Identification of microorganisms
Identification denotes the assignment of a microorganism into a
Gorica Popova, Dean Jankuloski, Benjamin Felix, Katerina Boskovska, Biljana Stojanovska-Dimzovska, Velibor Tasic and Katerina Blagoevska
20. Caprioli, A., Maugliani, A., Michelacci, V., Morabito, S. (2014). Moleculartyping of Verocytotoxin -producing E. coli (VTEC) strains isolated from food, feed and animals : state of play and standard operating procedures for pulsed field gel electrophoresis (PFGE) typing, profiles interpretation and curation. EFSA journal EN704, 55.
21. Barrett, T.J., Gerner-Smidt, P., Swaminathan, B. (2006). Interpretation of pulsed-field gel electrophoresis patterns in foodborne disease investigations and surveillance. Foodborne Pathog Dis. 3(1): 20
Enterobiasis is a human intestinal parasitic disease caused by human pinworm, Enterobius vermicularis. Despite being the most prevalent nematode infection in Europe and North America, predominantly among in school aged children, the data concerning infection rate and knowledge of genetic variability of pinworms are incomplete. The aim of the study was the estimation of prevalence and molecular typing of Enterobius vermicularis among healthy children in north-eastern Poland. In 2013 – 2015, 296 individuals (aged 2 – 18 years) from 12 kindergartens, schools and orphanages were examined by the adhesive cellophane tape method. Data on socio-demographic status were collected using a questionnaire. Molecular analysis was performed using the DNA of adult female pinworms and primers targeting the region of cytochrome oxidase I gene. The overall prevalence of enterobiasis was 10.1 %. Enterobius vermicularis infection rates were 3.9 % in children living in families and 32.8 % among the orphans (OR=0.08; 95 % CI: 0.04 – 0.19; p<0.001). There were no associations between distribution of enterobiasis and gender, pets possession and the season of examination. In 43.3 % of the infected children enterobiasis was asymptomatic. Based on a molecular marker three different haplotypes of pinworm were identified. All sequences clustered within type B, together with human E. vermicularis isolates from Denmark, Germany, Greece, and Japan. This paper provides complementary data on the occurrence and intraspecific variability of E. vermicularis in human population in Europe.
11. Hamnes, I. S, Gjerde, B. K., Robertson, L. J. (2007b). A longitudinal study on the occurrence of Cryptosporidium and Giardia in dogs during their 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 moleculartyping 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
primers. PCR Meth Appl 1993, 3, 85-94.
4. Falcao J.P., Falcao D.P., Pitondo-Silva A., Malaspina A.C., Brocchi M.: Moleculartyping 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
Ewelina Pyzik, Agnieszka Marek and Tomasz Hauschild
.H., Byrne S.K., Zhang J.L., Chow A.W.: Moleculartyping of Staphylococcus aureus on the basis of coagulase gene polymorphism. J Clin Microbiol 1992, 30, 1642-1645.
11. Graham J.C., Murphy O.M., Stewart D., Kearns A.M., Galloway A., Freeman R.: Comparison of PCR detection of mecA with methicillin and oxacillin disc susceptibility testing in coagulase-negative staphylococci. J Antimicrob Chemother 2000, 45, 111-113.
12. Hussain Z., Stoakes L., Lannigan R., Longo S., Nancekivell B.: Evaluation of screening and commercial methods for detection
-borne Campylobacter jejuni isolates in California. J Clin Microbiol 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 moleculartyping 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
Monika Szymańska-Czerwińska, Krzysztof Niemczuk and Agata Mitura
infected herd. 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 moleculartyping of Coxiella burnetii in bulk tank milk in Belgian dairy goats, 20092013. Vet Microbiol 2014, 170, 117-124.
Ewelina Szacawa, Monika Szymańska-Czerwińska, Krzysztof Niemczuk, Katarzyna Dudek, Grzegorz Woźniakowski and Dariusz Bednarek
15. Manso-Silván L., Dupuy V., Lysnyansky I., Ozdemir U., Thiaucourt F.: Phylogeny and moleculartyping of Mycoplasma agalactiae and Mycoplasma bovis by multilocus sequencing. Vet Microbiol 2012, 161, 104-112, doi: 10.1016/j.vetmic.2012.07.015.
16. McAuliffe L., Ellis R.J., Lawes J.R., Ayling R.D., Nicholas R.A.J.: 16S rDNA PCR and denaturing gradient gel electrophoresis; a single generic test for detecting and differentiating Mycoplasma species. J Med Microbiol 2005, 54, 731-739.
17. McAuliffe L., Kokotovic B., Ayling R
Fei-Fei Chang, Chang-Chieh Chen, Shao-Hung Wang and Chiou-Lin Chen
.L., Wang S.T., Chu C., Wang S.H.: Comparison of four moleculartyping 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