References
- Aanensen D.M., Spratt B.G.: The multilocus sequence typing network: mlst.net. Nucleic Acids Res.33, 728–733 (2005)
- Adzitey F., Huda N., Ali G.R.R.: Molecular techniques for detecting and typing of bacteria, advantages and application to food- borne pathogens isolated from ducks. 3 Biotech.3, 97–107 (2013)
- Applied Maths: Five more wgMLST schemes available, 19.05. 2017, http://www.applied-maths.com/news/five-more-wgmlst- schemes-available (10.10.2017)
- Applied Maths: Six more wgMLST schemes available, 30.11. 2016, http://www.applied-maths.com/news/six-more-wgmlst- schemes-available (10.10.2017)
- Baj J., Markiewicz Z. Biologia molekularna bakterii. Wyd. Nau- kowe PWN, Warszawa, 2015, s. 11.
- Belkum A.: Tracing isolates of bacterial species by multilocus variable numer of tandem repeat analysis (MLVA). FEMS Immunol. Med. Microbiol.49, 22–27 (2007)
- Brown T.A. Genomy. Wydawnictwo Naukowe PWN, Warszawa, 2012, s. 121.
- Brzostek A., Dziadek J.: Molekularne metody genotypowania prątków gruźlicy w dochodzeniach epidemiologicznych trans- misji zakażeń. Pneumonol. Alergol. Pol.80, 193–197 (2012)
- Canard B., Sarfati R.S.: DNA polymerase fluorescent substrates with reversible 3’-tags. Gene,148, 1–6 (1994)
- Centers for Disease Control and Prevention: Multiple locus variable-number tandem repeat analysis (MLVA), https://www. cdc.gov/pulsenet/pathogens/mlva.html (10.10.2017)
- Chen Y., Zhang W., Knabel S.J.: Multi-virulence-locus sequence typing clarifies epidemiology of recent listeriosis outbreaks in the United States. J. Clin. Microbiol.43, 5291–5294 (2005)
- Compare: About Compare, http://www.compare-europe.eu/ about (10.10.2017)
- 13.Databases hosted on PubMLST, https://pubmlst.org/databases/ (10.10.2017)
- Edwards A., Debbonaire A.R., Sattler B., Mur L.A.J., Hodson A.J.: Extreme metagenomics using Nanopore DNA sequencing: a field report from Svalbard, 78°N. BioRxiv, 073965 (2016)
- Edwards D.J., Holt K.E.: Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data. Microb. Inform. Exp. DOI: 10.1186/2042-5783-3-2 (2013)
- European Centre for Disease Prevention and Control: Expert Opinion on the introduction of next-generation typing methods for food- and waterborne diseases in the EU and EEA. Stockholm: ECDC, DOI: 10.2900/453641 (2015)
- European Centre for Disease Prevention and Control: Expert opinion on whole genome sequencing for public health surveillance. Stockholm: ECDC, DOI: 10.2900/12442 (2016)
- European Centre for Disease Prevention and Control: Laboratory standard operating procedure for MLVA of Salmonella enterica serotype Typhimurium. Stockholm: ECDC, DOI:10.2900/56328 (2011)
- Fleischmann R.D., Venter J.C. i wsp. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269, 496–512 (1995)
- Fraser C.M., Venter J.C. i wsp.: The minimal gene complement of Mycoplasma genitalium. Science, 270, 397–403 (1995)
- Frey K.G., Herrera-Galeano J.E., Redden C.L., Luu T.V., Ser- vetas S.L., Mateczun A.J., Mokashi V.P., Bishop-Lilly K.A.: Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood. BMC Genomics, DOI: 10.1186/1471-2164-15-96 (2014)
- Gierczyński R., Golubov A., Neubauer H., Pham J.N., Rakin A.: Development of multiple-locus variable-number tandem-repeatanalysis for Yersinia enterocolitica subsp. Palearctic and its application to bioserogroup 4/O3 subtyping. J. Clinic. Microbiol.45, 2508–2515 (2007)
- Illumina: An introduction to Illumina next-generation sequencing technology for microbiologists, https://www.illumina. com/content/dam/illumina-marketing/documents/products/ sequencing_introduction_microbiology.pdf (10.10.2017)
- Illumina: An introduction to next-generation sequencing technology, https://www.illumina.com/content/dam/illumina- marketing/documents/products/illumina_sequencing_intro- duction.pdf (10.10.2017)
- 25.Illumina: Nextera DNA library preparation kits, https://www. illumina.com/content/dam/illumina-marketing/documents/ products/datasheets/datasheet_nextera_dna_sample_prep.pdf (10.10.2017)
- Kotetishvili M., Stine O.C., Chen Y., Kreger A., Sulakvelidze A., Sozhamannan S., Morris Jr.J.G.: Multilocus sequence typing has better discriminatory ability for typing Vibrio cholerae than does pulsed-field gel electrophoresis and provides a measure of phylogenetic relatedness. J. Clinic. Microbiol.41, 2191–2196 (2003)
- Kotowska M., Zakrzewska-Czerwińska J.: Kurs szybkiego czyta- nia DNA – nowoczesne techniki sekwencjonowania. Biotechno- logia, 4, 24–38 (2010)
- Larsson J.T., Torpdahl M., Petersen R.F., Sorensen G., Lind- stedt B.A., Nielsen E.M.: Development of a new nomenclature for Salmonella Typhimurium multilocus variable numer of tandem repeats analysis (MLVA). Euro Surveill. DOI: https://doi. org/10.2807/ese.14.15.19174-en (2009)
- Leekitcharoenphon P., Nielsen E.M., Kaas R.S., Lund O., Aare- strup F.M.: Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica. PLoS ONE9, e87991, (2014)
- Li W., Raoult D., Fournier P.E.: Bacterial strain typing in the genomic era. FEMS Microbiol. Rev.33, 892–916 (2009)
- Lienemann T., Kyyhkynen A., Halkilahti J., Haukka K., Siito- nen A.: Characterization of Salmonella Typhimurium isolates from domestically acquired infections in Finland by phage typing, antimicrobial susceptibility testing, PFGE and MLVA. BMC Microbiol. DOI: 10.1186/s12866-015-0467-8 (2015)
- Lindstedt B.A., Åkerström S. i wsp.: Use of multilocus variablenumber tandem repeat analysis (MLVA) in eight European countries, 2012. Euro Surveill. DOI: 10.2807/ese.18.04.20385- en (2013)
- MacCannell D.: Bacterial strain typing. Clin. Lab. Med.33, 629–650 (2013)
- Madoui M., Engelen S., Cruaud C., Belser C., Bertrand L., Alberti A., Lemainque A., Wincker P., Aury J.M.: Genome assembly using Nanopore-guided long and error-free DNA reads. BMC Genomics, DOI: 10.1186/s12864-015-1519-z (2015)
- Maiden M.C.J., Spratt B.G. i wsp.: Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA, 95, 3140–3145 (1998)
- Małek W., Wdowiak-Wróbel S., Kalita M., Szlachetka M.: Dyle- maty z koncepcją i definicją gatunku bakteryjnego. Post. Mikro- biol.47, 177–182 (2008)
- Margulies M., Rothberg J.M. i wsp.: Genome sequencing in open microfabricated high density picoliter reactors. Nature,437, 376–380 (2005)
- Maxam A.M., Gilbert W.: A new method for sequencing DNA. Proc. Natl. Acad. Sci. USA74, 560–564 (1977)
- MLST, http://www.mlst.net/ (10.10.2017)
- Nadon C., Walle I.V., FWD-NEXT Expert Panel i wsp.: PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance. Euro Surveill., DOI: http://dx.doi.org/10.2807/1560-7917. ES.2017.22.23.30544 (2017)
- 41.NASA: Sequencing the station: investigation aims to identify unknown microbes in space, 25.04.2017, https://www.nasa. gov/mission_pages/station/research/news/genes_in_space3
(10.10.2017)
- NCBI: Genome, https://www.ncbi.nlm.nih.gov/genome (10.10.2017)
- Oxford Nanopore Technologies: How it works, https://nanopo- retech.com/how-it-works (10.10.2017)
- Oxford Nanopore Technologies: Portable, real-time biological analyses, https://nanoporetech.com/products/minion (10.10.2017)
- Oxford Nanopore Technologies: VolTRAX, https://nanoporetech.com/products/voltrax (10.10.2107)
- Pareek C.S., Smoczynski R., Tretyn A.: Sequencing technologies and genome sequencing. J. Appl. Genetics,52, 413–435 (2011)
- Pareek C.S.: An overview of next-generation genome sequencing platforms (w) Next-generation Sequencing: Current Technologies and Applications. red. Xu J., Caister Academic Press, 2014, s. 1–24
- Prober J.M., Trainor G.L., Dam R.J., Hobbs F.W., Robertson C.W., Zagursky R.J., Cocuzza A.J., Jensen M.A., Baumeister K.: A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science,238, 336–341 (1987)
- Ronaghi M., Uhlén M., Nyrén P.: A sequencing method based on real-time pyrophosphate. Science, 281, 363–365 (1998)
- 50.Sabat A.J., Budimir A., Nashev D., Sá-Leão R., van Dijl J.M., Laurent F., Grundmann H., Friedrich A.W.: Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Euro Surveill.
DOI: https://doi.org/10.2807/ese.18.04.20380-en (2013)
- Salipante S.J., SenGupta D.J., Cummings L.A., Land T.A., Hoogestraat D.R., Cookson B.T.: Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology. J. Clin. Microbiol.53, 1072–1079 (2015)
- Sanger F., Nicklen S., Coulson A.R.: DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA, 74, 5463–5467 (1977)
- Singh A., Goering R.V., Simjee S., Foley S.L., Zervos M.J.: Application of molecular techniques to the study of hospital infection. Clin. Microbiol. Rev.19, 512–530 (2006)
- Struelens M.J. and the Members ESGEM, ESCMID: Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems. Clin. Microbiol. Infect.2, 2–11 (1996)
- Tenover F.C., Arbeit R.D., Goering R.V., Mickelsen P.A., Murray B.E., Persing D.H., Swaminathan B.: Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J. Clin. Microbiol.33, 2233–2239 (1995)
- Urwin R., Maiden M.C.J.: Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol.11, 479–487 (2003)