Implementation of whole genome sequencing for bacteria genotyping

1.Aanensen D.M., Spratt B.G.: The multilocus sequence typing network: mlst.net. Nucleic Acids Res.33, 728–733 (2005)10.1093/nar/gki415Search in Google Scholar

2.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)10.1007/s13205-012-0074-4Search in Google Scholar

3.Applied Maths: Five more wgMLST schemes available, 19.05. 2017, http://www.applied-maths.com/news/five-more-wgmlst- schemes-available (10.10.2017)Search in Google Scholar

4.Applied Maths: Six more wgMLST schemes available, 30.11. 2016, http://www.applied-maths.com/news/six-more-wgmlst- schemes-available (10.10.2017)Search in Google Scholar

5.Baj J., Markiewicz Z. Biologia molekularna bakterii. Wyd. Nau- kowe PWN, Warszawa, 2015, s. 11.Search in Google Scholar

6.Belkum A.: Tracing isolates of bacterial species by multilocus variable numer of tandem repeat analysis (MLVA). FEMS Immunol. Med. Microbiol.49, 22–27 (2007)10.1111/j.1574-695X.2006.00173.xSearch in Google Scholar

7.Brown T.A. Genomy. Wydawnictwo Naukowe PWN, Warszawa, 2012, s. 121.Search in Google Scholar

8.Brzostek A., Dziadek J.: Molekularne metody genotypowania prątków gruźlicy w dochodzeniach epidemiologicznych trans- misji zakażeń. Pneumonol. Alergol. Pol.80, 193–197 (2012)10.5603/ARM.27583Search in Google Scholar

9.Canard B., Sarfati R.S.: DNA polymerase fluorescent substrates with reversible 3’-tags. Gene,148, 1–6 (1994)10.1016/0378-1119(94)90226-7Search in Google Scholar

10.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)10.5210/ojphi.v10i1.8902Search in Google Scholar

11.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)10.1128/JCM.43.10.5291-5294.2005124851516208000Search in Google Scholar

12.Compare: About Compare, http://www.compare-europe.eu/ about (10.10.2017)Search in Google Scholar

13.Databases hosted on PubMLST, https://pubmlst.org/databases/ (10.10.2017)Search in Google Scholar

14.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)Search in Google Scholar

15.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)10.1186/2042-5783-3-2363001323575213Search in Google Scholar

16.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)Search in Google Scholar

17.European Centre for Disease Prevention and Control: Expert opinion on whole genome sequencing for public health surveillance. Stockholm: ECDC, DOI: 10.2900/12442 (2016)Search in Google Scholar

18.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)Search in Google Scholar

19.Fleischmann R.D., Venter J.C. i wsp. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269, 496–512 (1995)10.1126/science.75428007542800Search in Google Scholar

20.Fraser C.M., Venter J.C. i wsp.: The minimal gene complement of Mycoplasma genitalium. Science, 270, 397–403 (1995)10.1126/science.270.5235.3977569993Search in Google Scholar

21.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)10.1186/1471-2164-15-96392254224495417Search in Google Scholar

22.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)10.1128/JCM.02252-06Search in Google Scholar

23.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)Search in Google Scholar

24.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)Search in Google Scholar

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)Search in Google Scholar

26.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)10.1128/JCM.41.5.2191-2196.2003Search in Google Scholar

27.Kotowska M., Zakrzewska-Czerwińska J.: Kurs szybkiego czyta- nia DNA – nowoczesne techniki sekwencjonowania. Biotechno- logia, 4, 24–38 (2010)Search in Google Scholar

28.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)10.2807/ese.14.15.19174-enSearch in Google Scholar

29.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)10.1371/journal.pone.0087991Search in Google Scholar

30.Li W., Raoult D., Fournier P.E.: Bacterial strain typing in the genomic era. FEMS Microbiol. Rev.33, 892–916 (2009)10.1111/j.1574-6976.2009.00182.xSearch in Google Scholar

31.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)10.1186/s12866-015-0467-8Search in Google Scholar

32.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)Search in Google Scholar

33.MacCannell D.: Bacterial strain typing. Clin. Lab. Med.33, 629–650 (2013)Search in Google Scholar

34.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)10.1186/s12864-015-1519-zSearch in Google Scholar

35.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)10.1073/pnas.95.6.3140Search in Google Scholar

36.Małek W., Wdowiak-Wróbel S., Kalita M., Szlachetka M.: Dyle- maty z koncepcją i definicją gatunku bakteryjnego. Post. Mikro- biol.47, 177–182 (2008)Search in Google Scholar

37.Margulies M., Rothberg J.M. i wsp.: Genome sequencing in open microfabricated high density picoliter reactors. Nature,437, 376–380 (2005)Search in Google Scholar

38.Maxam A.M., Gilbert W.: A new method for sequencing DNA. Proc. Natl. Acad. Sci. USA74, 560–564 (1977)10.1073/pnas.74.2.560Search in Google Scholar

39.MLST, http://www.mlst.net/ (10.10.2017)Search in Google Scholar

40.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)Search in Google Scholar

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)10.1016/S1464-2859(17)30300-0Search in Google Scholar

42.NCBI: Genome, https://www.ncbi.nlm.nih.gov/genome (10.10.2017)Search in Google Scholar

43.Oxford Nanopore Technologies: How it works, https://nanopo- retech.com/how-it-works (10.10.2017)Search in Google Scholar

44.Oxford Nanopore Technologies: Portable, real-time biological analyses, https://nanoporetech.com/products/minion (10.10.2017)Search in Google Scholar

45.Oxford Nanopore Technologies: VolTRAX, https://nanoporetech.com/products/voltrax (10.10.2107)Search in Google Scholar

46.Pareek C.S., Smoczynski R., Tretyn A.: Sequencing technologies and genome sequencing. J. Appl. Genetics,52, 413–435 (2011)10.1007/s13353-011-0057-x318934021698376Search in Google Scholar

47.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. 1–24Search in Google Scholar

48.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)10.1126/science.24439752443975Search in Google Scholar

49.Ronaghi M., Uhlén M., Nyrén P.: A sequencing method based on real-time pyrophosphate. Science, 281, 363–365 (1998)10.1126/science.281.5375.3639705713Search in Google Scholar

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)10.2807/ese.18.04.20380-en23369389Search in Google Scholar

51.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)10.1128/JCM.03385-14436520925631811Search in Google Scholar

52.Sanger F., Nicklen S., Coulson A.R.: DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA, 74, 5463–5467 (1977)10.1073/pnas.74.12.5463431765271968Search in Google Scholar

53.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)10.1128/CMR.00025-05153910716847083Search in Google Scholar

54.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)10.1111/j.1469-0691.1996.tb00193.x11866804Search in Google Scholar

55.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)10.1128/jcm.33.9.2233-2239.19952283857494007Search in Google Scholar

56.Urwin R., Maiden M.C.J.: Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol.11, 479–487 (2003)10.1016/j.tim.2003.08.00614557031Search in Google Scholar