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

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

doi:10.1371/journal.pone.0145223

Cited by 5 publications

(3 citation statements)

References 33 publications

(43 reference statements)

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“…All emm1, emm12, and emm28 strains possess two CRISPR loci and emm3 strains have no CRISPR2 locus. Analyzing the composition of CRISPR loci, has enabled to show relations between spacer content and emm-types (Zheng et al, 2015). Indeed, they have highlighted that most spacers are emm-type specific and so, they propose CRISPR sequencing as a new typing method.…”

Section: Streptococcus Pyogenesmentioning

confidence: 99%

Distribution, Diversity and Roles of CRISPR-Cas Systems in Human and Animal Pathogenic Streptococci

et al. 2022

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Streptococci form a wide group of bacteria and are involved in both human and animal pathologies. Among pathogenic isolates, differences have been highlighted especially concerning their adaptation and virulence profiles. CRISPR-Cas systems have been identified in bacteria and many streptococci harbor one or more systems, particularly subtypes I-C, II-A, and III-A. Since the demonstration that CRISPR-Cas act as an adaptive immune system in Streptococcus thermophilus, a lactic bacteria, the diversity and role of CRISPR-Cas were extended to many germs and functions were enlarged. Among those, the genome editing tool based on the properties of Cas endonucleases is used worldwide, and the recent attribution of the Nobel Prize illustrates the importance of this tool in the scientific world. Another application is CRISPR loci analysis, which allows to easily characterize isolates in order to understand the interactions of bacteria with their environment and visualize species evolution. In this review, we focused on the distribution, diversity and roles of CRISPR-Cas systems in the main pathogenic streptococci.

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Section: Streptococcus Pyogenesmentioning

confidence: 99%

Distribution, Diversity and Roles of CRISPR-Cas Systems in Human and Animal Pathogenic Streptococci

et al. 2022

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“…Globally, there are about 616 million cases of GAS pharyngitis every year, among which, 17,800 cases are new infections, and about 517,000 patients with severe GAS are deceased every year [2]. Recently, the positive rate of GAS was estimated at 21.2% in the pharyngeal culture of patients diagnosed as "streptococcal infection/tonsillitis/angina" [3]. Moreover, the incidence of streptococcal pharyngitis is common in children aged 0-14 years.…”

Section: Introductionmentioning

confidence: 99%

Molecular epidemiology and antimicrobial resistance of group a streptococcus recovered from patients in Beijing, China

Zhou

Zhao

et al. 2020

BMC Infect Dis

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Background: Group A streptococcus (GAS) is an important human pathogen responsible for a broad range of infections. Epidemiological surveillance has been crucial to detect changes in the geographical and temporal variation of the disease pattern. The objective of this study was to investigate the molecular epidemiological characteristics and antimicrobial resistance of GAS isolates from patients in Children's Hospital in Beijing. Methods: From 2016 to 2017, pharyngeal swab samples were collected from the outpatients in Children's Hospital, Capital Institute of Pediatrics, who were diagnosed with scarlet fever. Antimicrobial susceptibility test was performed according to the distribution of conventional antibiotics and Clinical and Laboratory Standards Institute (CLSI) recommendations. The distribution of the macrolide-resistance genes (ermB, ermA, mefA), emm (M proteincoding gene) typing, and superantigens (SAg) gene profiling were examined by polymerase chain reaction (PCR). Results: A total of 297 GAS isolates were collected. The susceptibility of the isolates to penicillin, ceftriaxone, and levofloxacin was 100%. The resistance rate to erythromycin and clindamycin was 98.3 and 96.6%, respectively. The dominant emm types were emm12 (65.32%), emm1 (27.61%), emm75 (2.69%), and emm89 (1.35%). Of the 297 isolates, 290 (97.64%) carried the ermB gene, and 5 (1.68%) carried the mefA gene, while none carried the ermA gene. The most common superantigen genes identified from GAS isolates were smeZ (96.97%), speC (92.59%), speG (91.58%), ssa (85.52%), speI (54.55%), speH (52.19%), and speA (34.34%). Isolates with the genotype emm1 possessed speA, speC, speG, speJ, speM, ssa, and smeZ, while emm12 possessed speC, speG, speH, speI, speM, ssa, and smeZ superantigens. Conclusions: The prevalent strain of GAS isolates in Beijing has a high resistance rate to macrolides; however, penicillin can still be the preferred antibiotic for treatment. Erythromycin resistance was predominantly mediated by ermB. The common emm types were emm12 and emm1. There was a correlation between emm and the superantigen gene. Thus, long-term monitoring and investigation of the emm types and superantigen genes of GAS prevalence are imperative.

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“…This feature, combined with the evolving structure of the CRISPR locus, results in a hypervariable DNA region that provides information on strain origin, evolutionary path and even phage resistance/sensitivity profiles. Thus, CRISPR typing has been used to identify and greatly improve strain typing resolution for a variety of bacterial species in clinical, epidemiological, environmental and industrial settings [ 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 ].…”

Section: Introductionmentioning

confidence: 99%

CRISPRStudio: A User-Friendly Software for Rapid CRISPR Array Visualization

Dion

Labrie²,

Shah

et al. 2018

Viruses

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The CRISPR-Cas system biologically serves as an adaptive defense mechanism against phages. However, there is growing interest in exploiting the hypervariable nature of the CRISPR locus, often of viral origin, for microbial typing and tracking. Moreover, the spacer content of any given strain provides a phage resistance profile. Large-scale CRISPR typing studies require an efficient method for showcasing CRISPR array similarities across multiple isolates. Historically, CRISPR arrays found in microbes have been represented by colored shapes based on nucleotide sequence identity and, while this approach is now routinely used, only scarce computational resources are available to automate the process, making it very time-consuming for large datasets. To alleviate this tedious task, we introduce CRISPRStudio, a command-line tool developed to accelerate CRISPR analysis and standardize the preparation of CRISPR array figures. It first compares nucleotide spacer sequences present in a dataset and then clusters them based on sequence similarity to assign a meaningful representative color. CRISPRStudio offers versatility to suit different biological contexts by including options such as automatic sorting of CRISPR loci and highlighting of shared spacers, while remaining fast and user-friendly.

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

Cited by 5 publications

References 33 publications

Distribution, Diversity and Roles of CRISPR-Cas Systems in Human and Animal Pathogenic Streptococci

Distribution, Diversity and Roles of CRISPR-Cas Systems in Human and Animal Pathogenic Streptococci

Molecular epidemiology and antimicrobial resistance of group a streptococcus recovered from patients in Beijing, China

CRISPRStudio: A User-Friendly Software for Rapid CRISPR Array Visualization

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