CRISPR-like sequences in Helicobacter pylori and application in genotyping

Abstract

BackgroundMany 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.ResultsA 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.ConclusionCRISPR-virulence typing in H. pylori is easy and reliable for epidemiology and can be used for inter-laboratory interpretation.Electronic supplementary materialThe online version of this article (10.1186/s13099-017-0215-8) contains supplementary material, which is available to authorized users.

Analysis of the structures of confirmed and questionable CRISPR loci in 325 Staphylococcus genomes

“…This element also forms a secondary structure and can affect the toxicity of Listeria, which depends on the polynucleotide phosphorylase (PNPase) when acting. It has been reported that CRISPR like elements was found in the vlpC gene of Helicobacter pylori and can be used for virulence typing of Helicobacter pylori . Further research remains to be done whether these independent CRISPR elements of Staphylococcus have an effect on their virulence, or whether they have other undiscovered effects.…”

Correction to: CRISPR-like sequences in Helicobacter pylori and application in genotyping

“…In the original version of this article [ 1 ], published on 17 November 2017, Table 2 contains an error: the first “T” in the first sequence in the column ‘Consensus direct repeats (CDRs) sequences’ has been incorrectly underlined. In Table 2, the underlining indicates the Consensus sequence.…”

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“…CRISPRFinder revealed the existence of additional loci to the CRISPR-like locus inserted into the VlpC gene described by Bangpanwimon et al, 2017 15 (Fig. S2, S5, S7, and S9).…”

“…The lack of this system in some prokaryotes has been related to the increase in the capacity to integrate exogenous DNA in the genome of these bacteria and, resulting in the acquisition of new functions, which can confer an adaptive advantage to these strains, particularly during their transition to pathogenesis . But recently, Bangpanwimon et al, 2017 15 reported the presence of CRISPR-type sequences inserted into the VlpC gene of H pylori. In that study, the detection was performed by PCR in partial regions of the genome of Thailand isolates 15 .…”

“…But recently, Bangpanwimon et al, 2017 15 reported the presence of CRISPR-type sequences inserted into the VlpC gene of H pylori. In that study, the detection was performed by PCR in partial regions of the genome of Thailand isolates 15 . Each isolated strain showed a CRISPR-like locus with similar DRs sequences.…”