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Open Access 01-12-2017 | Research

CRISPR-like sequences in Helicobacter pylori and application in genotyping

Authors: Khotchawan Bangpanwimon, Jaksin Sottisuporn, Pimonsri Mittraparp-arthorn, Warattaya Ueaphatthanaphanich, Attapon Rattanasupar, Christine Pourcel, Varaporn Vuddhakul

Published in: Gut Pathogens | Issue 1/2017

Abstract

Background

Many bacteria and archaea possess a defense system called clustered regularly interspaced short palindromic repeats (CRISPR) associated proteins (CRISPR-Cas system) against invaders such as phages or plasmids. This system has not been demonstrated in Helicobacter pylori. The numbers of spacer in CRISPR array differ among bacterial strains and can be used as a genetic marker for bacterial typing.

Results

A total of 36 H. pylori isolates were collected from patients in three hospitals located in the central (PBH) and southern (SKH) regions of Thailand. It is of interest that CRISPR-like sequences of this bacterium were detected in vlpC encoded for VacA-like protein C. Virulence genes were investigated and the most pathogenic genotype (cagA vacA s1m1) was detected in 17 out of 29 (58.6%) isolates from PBH and 5 out of 7 (71.4%) from SKH. vapD gene was identified in each one isolate from PBH and SKH. CRISPR-like sequences and virulence genes of 20 isolates of H. pylori obtained in this study were analyzed and CRISPR-virulence typing was constructed and compared to profiles obtained by the random amplification of polymorphic DNA (RAPD) technique. The discriminatory power (DI) of CRISPR-virulence typing was not different from RAPD typing.

Conclusion

CRISPR-virulence typing in H. pylori is easy and reliable for epidemiology and can be used for inter-laboratory interpretation.

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Kunin V, Sorek R, Hugenholtz P. Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol. 2007;8:R61.CrossRefPubMedPubMedCentral

Marraffini LA, Sontheimer EJ. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet. 2010;11:181–90.CrossRefPubMedPubMedCentral

Rahmatabadi SS, Nezafat N, Negahdaripour M, Hajighahramani N, Morowvat MH, Ghasemi Y. Studying the features of 57 confirmed CRISPR loci in 29 strains of Escherichia coli. J Basic Microbiol. 2016;56:645–53.CrossRefPubMed

Pourcel C, Salvignol G, Vergnaud G. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology. 2005;151:653–63.CrossRefPubMed

Almeida F, Medeiros MIC, dos Prazeres Rodrigues D, Allard MW, Falcão JP. Molecular characterization of Salmonella Typhimurium isolated in Brazil by CRISPR-MVLST. J Microbiol Methods. 2017;133:55–61.CrossRefPubMed

Yang S, Liu J, Shao F, Wang P, Duan G, Yang H. Analysis of the features of 45 identified CRISPR loci in 32 Staphylococcus aureus. Biochem Biophys Res Commun. 2015;464:894–900.CrossRefPubMed

Barrangou R, Horvath P. CRISPR: new horizons in phage resistance and strain identification. Annu Rev Food Sci Technol. 2012;3:143–62.CrossRefPubMed

Shariat N, Dudley EG. CRISPRs: molecular signatures used for pathogen subtyping. Appl Environ Microbiol. 2014;80:430–9.CrossRefPubMedPubMedCentral

Kusters JG, van Vliet AH, Kuipers EJ. Pathogenesis of Helicobacter pylori infection. Clin Microbiol Rev. 2006;19:449–90.CrossRefPubMedPubMedCentral

10.

Wroblewski LE, Peek RM, Wilson KT. Helicobacter pylori and gastric cancer: factors that modulate disease risk. Clin Microbiol Rev. 2010;23:713–39.CrossRefPubMedPubMedCentral

11.

Katz ME, Howarth PM, Yong WK, Riffkin GG, Depiazzi LJ, Rood JI. Identification of three gene regions associated with virulence in Dichelobacter nodosus, the causative agent of ovine footrot. J Gen Microbiol. 1991;137:2117–24.CrossRefPubMed

12.

Cao P, Cover TL. High-level genetic diversity in the vapD chromosomal region of Helicobacter pylori. J Bacteriol. 1997;179:2852–6.CrossRefPubMedPubMedCentral

13.

Cheetham BF, Katz ME. A role for bacteriophages in the evolution and transfer of bacterial virulence determinants. Mol Microbiol. 1995;1:201–8.CrossRef

14.

Akopyanz N, Bukanov NO, Westblom TU, Kresovich S, Berg DE. DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting. Nucleic Acids Res. 1992;20:5137–42.CrossRefPubMedPubMedCentral

15.

Park C-Y, Kwak M, Gutierrez O, Graham DY, Yamaoka Y. Comparison of genotyping Helicobacter pylori directly from biopsy specimens and genotyping from bacterial cultures. J Clin Microbiol. 2003;41:3336–8.CrossRefPubMedPubMedCentral

16.

Akopyanz N, Bukanov NO, Westblom TU, Berg DE. PCR-based RFLP analysis of DNA sequence diversity in the gastric pathogen Helicobacter pylori. Nucleic Acids Res. 1992;20:6221–5.CrossRefPubMedPubMedCentral

17.

Kwon DH, El-Zaatari FA, Woo JS, Perng CL, Graham DY, Go MF. REP-PCR fragments as biomarkers for differentiating gastroduodenal disease-specific Helicobacter pylori strains. Dig Dis Sci. 1998;43:980–7.CrossRefPubMed

18.

Colding H, Hartzen SH, Roshanisefat H, Andersen LP, Krogfelt KA. Molecular methods for typing of Helicobacter pylori and their applications. FEMS Immunol Med Microbiol. 1999;24:193–9.CrossRefPubMed

19.

Burucoa C, Lhomme V, Fauchere JL. Performance criteria of DNA fingerprinting methods for typing of Helicobacter pylori isolates: experimental results and meta-analysis. J Clin Microbiol. 1999;37:4071–80.PubMedPubMedCentral

20.

Calleros L, Betancor L, Iraola G, Méndez A, Morsella C, Paolicchi F, Silveyra S, Velilla A, Pérez R. Assessing the intra-species genetic variability in the clonal pathogen Campylobacter fetus: CRISPRs are highly polymorphic DNA markers. J Microbiol Methods. 2017;132:86–94.CrossRefPubMed

21.

Lage AP, Godfroid E, Fauconnier A, Burette A, Butzler JP, Bollen A, Glupczynski Y. Diagnosis of Helicobacter pylori infection by PCR: comparison with other invasive techniques and detection of cagA gene in gastric biopsy specimens. J Clin Microbiol. 1995;33:2752–6.PubMedPubMedCentral

22.

Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007;35:W52–7.CrossRefPubMedPubMedCentral

23.

Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870–4.CrossRefPubMed

24.

Chattopadhyay S, Patra R, Ramamurthy T, Chowdhury A, Santra A, Dhali G, Bhattacharya S, Berg DE, Nair GB, Mukhopadhyay AK. Multiplex PCR assay for rapid detection and genotyping of Helicobacter pylori directly from biopsy specimens. J Clin Microbiol. 2004;42:2821–4.CrossRefPubMedPubMedCentral

25.

Morales-Espinosa R, González-Valencia G, Delgado G, Méndez JL, Torres J, Cravioto A. Frequency and characterization of vapD gene in Helicobacter pylori strains of different vacA and cag-PAI genotype. Bioquimia. 2008;33:43–50.

26.

Berg DE, Lelwala-Guruge J, Incecik ET, Srivastava K, Akopyants NS. H. pylori DNA fingerprinting using the arbitrarily primed PCR (AP-PCR) or random amplified polymorphic DNA (RAPD) method. Methods Mol Med. 1997;8:117–32.PubMed

27.

Hunter PR, Gaston MA. Numerical index of the discriminatory ability of typing systems: an application of Simpson’s index of diversity. J Clin Microbiol. 1988;26:2465–6.PubMedPubMedCentral

28.

Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Banfield JF. New CRISPR–Cas systems from uncultivated microbes. Nature. 2017;542:237–41.CrossRefPubMed

29.

Foegeding NJ, Caston RR, McClain MS, Ohi MD, Cover TL. An overview of Helicobacter pylori VacA toxin biology. Toxins. 2016;8:173. https://doi.org/10.3390/toxins8060173.CrossRefPubMedCentral

30.

Albert TJ, Dailidiene D, Dailide G, Norton JE, Kalia A, Richmond TA, Molla M, Singh J, Green RD, Berg DE. Mutation discovery in bacterial genomes: metronidazole resistance in Helicobacter pylori. Nat Methods. 2005;2:951–3.CrossRefPubMed

31.

Conrad MD, Gorman AW, Schillinger JA, Fiori PL, Arroyo R, Malla N, Dubey ML, Gonzalez J, Blank S, Secor WE, et al. Extensive genetic diversity, unique population structure and evidence of genetic exchange in the sexually transmitted parasite Trichomonas vaginalis. PLoS Negl Trop Dis. 2012;6:e1573. https://doi.org/10.1371/journal.pntd.0001573.CrossRefPubMedPubMedCentral

32.

Sorek R, Kunin V, Hugenholtz P. CRISPR—a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol. 2008;6:181–6.CrossRefPubMed

33.

Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJ, Charpentier E, Haft DH, et al. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol. 2015;13:722–36.CrossRefPubMedPubMedCentral

34.

Westra ER, Buckling A, Fineran PC. CRISPR-Cas systems: beyond adaptive immunity. Nat Rev Microbiol. 2014;12:317–26.CrossRefPubMed

35.

Radin JN, Gaddy JA, Gonzalez-Rivera C, Loh JT, Algood HM, Cover TL. Flagellar localization of a Helicobacter pylori autotransporter protein. MBio. 2013;4(2):e00613.CrossRefPubMedPubMedCentral

36.

Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, et al. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature. 1999;399:323–9.CrossRefPubMed

37.

Bridge DR, Merrell DS. Polymorphism in the Helicobacter pylori CagA and VacA toxins and disease. Gut Microbes. 2013;4:101–17.CrossRefPubMedPubMedCentral

38.

Sahara S, Sugimoto M, Vilaichone R-K, Mahachai V, Miyajima H, Furuta T, Yamaoka Y. Role of Helicobacter pylori cagA EPIYA motif and vacA genotypes for the development of gastrointestinal diseases in Southeast Asian countries: a meta-analysis. BMC Infect Dis. 2012;12:223.CrossRefPubMedPubMedCentral

39.

Kwon AR, Kim JH, Park SJ, Lee KY, Min YH, Im H, Lee I, Lee KY, Lee BJ. Structural and biochemical characterization of HP0315 from Helicobacter pylori as a VapD protein with an endoribonuclease activity. Nucleic Acids Res. 2012;40:4216–28.CrossRefPubMedPubMedCentral

40.

Louwen R, Staals RH, Endtz HP, van Baarlen P, van der Oost J. The role of CRISPR-Cas systems in virulence of pathogenic bacteria. Microbiol Mol Biol Rev. 2014;78:74–88.CrossRefPubMedPubMedCentral

41.

Sun H, Li Y, Shi X, Lin Y, Qiu Y, Zhang J, Liu Y, Jiang M, Zhang Z, Chen Q. Association of CRISPR/Cas evolution with Vibrio parahaemolyticus virulence factors and genotypes. Foodborne Pathog Dis. 2015;12:68–73.CrossRefPubMed

42.

Hullahalli K, Rodrigues M, Schmidt BD, Li X, Bhardwaj P, Palmer KL. Comparative analysis of the orphan CRISPR2 locus in 242 Enterococcus faecalis strains. PLoS ONE. 2015;10(9):e0138890.CrossRefPubMedPubMedCentral

43.

Liu F, Barrangou R, Gerner-Smidt P, Ribot EM, Knabel SJ, Dudley EG. Novel virulence gene and clustered regularly interspaced short palindromic repeat (CRISPR) multilocus sequence typing scheme for subtyping of the major serovars of Salmonella enterica subsp. enterica. Appl Environ Microbiol. 2011;77:1946–56.CrossRefPubMedPubMedCentral

44.

Shariat N, DiMarzio MJ, Yin S, Dettinger L, Sandt CH, Lute JR, Barrangou R, Dudley EG. The combination of CRISPR-MVLST and PFGE provides increased discriminatory power for differentiating human clinical isolates of Salmonella enterica subsp. enterica serovar Enteritidis. Food Microbiol. 2013;34:164–73.CrossRefPubMed

45.

Gherardi G, Creti R, Pompilio A, Di Bonaventura G. An overview of various typing methods for clinical epidemiology of the emerging pathogen Stenotrophomonas maltophilia. Diagn Microbiol Infect Dis. 2015;81:219–26.CrossRefPubMed

Title: CRISPR-like sequences in Helicobacter pylori and application in genotyping
Authors: Khotchawan Bangpanwimon
Jaksin Sottisuporn
Pimonsri Mittraparp-arthorn
Warattaya Ueaphatthanaphanich
Attapon Rattanasupar
Christine Pourcel
Varaporn Vuddhakul
Publication date: 01-12-2017
Publisher: BioMed Central
Published in: Gut Pathogens / Issue 1/2017
Electronic ISSN: 1757-4749
DOI: https://doi.org/10.1186/s13099-017-0215-8

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