Clustered Regularly Interspaced Short Palindromic Repeats Are emm Type-Specific in Highly Prevalent Group A Streptococci.

Po-Xing Zheng,Chuan Chiang-Ni,Woei-Jer Chuang,Pei-Jane Tsai,Chien-Shun Chiou,Yee-Shin Lin,Shu-Ying Wang,Jiunn-Jong Wu,Yuen-Chi Chan,Ching-Chuan Liu,Jose Melo-Cristino

doi:10.1371/journal.pone.0145223

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPR) are the bacterial adaptive immune system against foreign nucleic acids. Given the variable nature of CRISPR, it could be a good marker for molecular epidemiology. Group A streptococcus is one of the major human pathogens. It has two CRISPR loci, including CRISPR01 and CRISPR02. The aim of this study was to analyze the distribution of CRISPR-associated gene cassettes (cas) and CRISPR arrays in highly prevalent emm types. The cas cassette and CRISPR array in two CRISPR loci were analyzed in a total of 332 strains, including emm1, emm3, emm4, emm12, and emm28 strains. The CRISPR type was defined by the spacer content of each CRISPR array. All strains had at least one cas cassette or CRISPR array. More than 90% of the spacers were found in one emm type, specifically. Comparing the consistency between emm and CRISPR types by Simpson’s index of diversity and the adjusted Wallace coefficient, CRISPR01 type was concordant to emm type, and CRISPR02 showed unidirectional congruence to emm type, suggesting that at least for the majority of isolates causing infection in high income countries, the emm type can be inferred from CRISPR analysis, which can further discriminate isolates sharing the same emm type.

Highlights

Clustered regularly interspaced short palindromic repeats (CRISPR) are composed of serial spacer sequences flanked by repeats
We have demonstrated that highly prevalent emm types of GAS strains had at least one cas cassette or CRISPR array, and more than 90% of spacers were emm type-specific
Based on Simpson’s index of diversity and adjusted Wallace coefficient, CRISPR01 and emm types were associated, and CRISPR02 showed strong unidirectional congruence to emm type, suggesting that CRISPR typing can be used as an alternative way to infer the emm type of GAS, at least among the highly prevalent emm types included in this study

Summary

Introduction

Clustered regularly interspaced short palindromic repeats (CRISPR) are composed of serial spacer sequences flanked by repeats. CRISPR is considered to be the prokaryotic adaptive. CRISPR and emm Types in GAS immune system against foreign nucleic acid [1]. Prokaryotes can acquire small fragments from invading sequences, including phages or plasmids, to become new spacers in CRISPR. CRISPR can be transcribed from a leader promoter into a long RNA, and further processed into small RNAs containing one spacer and a partial repeat. Mature small RNAs, together with serial CRISPR-associated proteins (Cas), can recognize and degrade invading sequences complementary to spacer sequences. CRISPR is like molecular “vaccination cards”, recording bacteria-virus interactions in spacer-repeat units [2], and providing adaptive immunity against foreign nucleic acids

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