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

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.

[1]  M. Allard,et al.  Molecular characterization of Salmonella Typhimurium isolated in Brazil by CRISPR-MVLST. , 2017, Journal of microbiological methods.

[2]  Z. Pan,et al.  Subtyping Salmonella enterica serovar Derby with multilocus sequence typing (MLST) and clustered regularly interspaced short palindromic repeats (CRISPRs) , 2017 .

[3]  Chris M. Brown,et al.  CRISPRDetect: A flexible algorithm to define CRISPR arrays , 2016, BMC Genomics.

[4]  Philippe Horvath,et al.  Diversity, Activity, and Evolution of CRISPR Loci in Streptococcus thermophilus , 2007, Journal of bacteriology.

[5]  R. Barrangou,et al.  Diversity Short Palindromic Repeat ( CRISPR ) Locus Basis of Clustered Regularly Interspaced Lactobacillus buchneri Genotyping on the , 2014 .

[6]  Jianguo Xu,et al.  Reemergence of human plague in Yunnan, China in 2016 , 2018, PloS one.

[7]  N. Shariat,et al.  Prevalence of Group I Salmonella Kentucky in domestic food animals from Pennsylvania and overlap with human clinical CRISPR sequence types , 2018, Zoonoses and public health.

[8]  Philippe Horvath,et al.  Phage Response to CRISPR-Encoded Resistance in Streptococcus thermophilus , 2007, Journal of bacteriology.

[9]  P. Horvath,et al.  The CRISPR-Cas app goes viral. , 2017, Current opinion in microbiology.

[10]  Philippe Horvath,et al.  CRISPR: new horizons in phage resistance and strain identification. , 2012, Annual review of food science and technology.

[11]  R. Barrangou,et al.  Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum , 2017, Front. Microbiol..

[12]  Philippe Horvath,et al.  The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA , 2010, Nature.

[13]  R. Barrangou,et al.  CRISPR Diversity and Microevolution in Clostridium difficile , 2016, Genome biology and evolution.

[14]  P. Glaser,et al.  Analysis of the type II-A CRISPR-Cas system of Streptococcus agalactiae reveals distinctive features according to genetic lineages , 2015, Front. Genet..

[15]  M. Ugarte-Ruiz,et al.  Efficacy of a typing scheme for Campylobacter based on the combination of true and questionable CRISPR. , 2015, Journal of microbiological methods.

[16]  Konstantin Severinov,et al.  Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence , 2011, Proceedings of the National Academy of Sciences.

[17]  HuQinghua,et al.  Association of CRISPR/Cas Evolution with Vibrio parahaemolyticus Virulence Factors and Genotypes , 2015 .

[18]  Jennifer A. Doudna,et al.  Integrase-mediated spacer acquisition during CRISPR–Cas adaptive immunity , 2015, Nature.

[19]  Y. Kawamura,et al.  Diversity and microevolution of CRISPR loci in Helicobacter cinaedi , 2017, PloS one.

[20]  P. Tsai,et al.  Clustered Regularly Interspaced Short Palindromic Repeats Are emm Type-Specific in Highly Prevalent Group A Streptococci , 2015, PloS one.

[21]  P. Moodley,et al.  Molecular Characterization of Corynebacterium diphtheriae Outbreak Isolates, South Africa, March–June 2015 , 2017, Emerging infectious diseases.

[22]  R. Barrangou,et al.  CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.

[23]  R. Barrangou,et al.  CRISPR Visualizer: rapid identification and visualization of CRISPR loci via an automated high-throughput processing pipeline , 2018, RNA biology.

[24]  P. Lanotte,et al.  Group B Streptococcus Vaginal Carriage in Pregnant Women as Deciphered by Clustered Regularly Interspaced Short Palindromic Repeat Analysis , 2018, Journal of Clinical Microbiology.

[25]  R. Barrangou,et al.  Characterization and evolution of Salmonella CRISPR-Cas systems. , 2015, Microbiology.

[26]  Qun Sun,et al.  Association of CRISPR/Cas evolution with Vibrio parahaemolyticus virulence factors and genotypes. , 2015, Foodborne pathogens and disease.

[27]  K. Makino,et al.  Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product , 1987, Journal of bacteriology.

[28]  S. Forsythe,et al.  CRISPR-cas loci profiling of Cronobacter sakazakii pathovars. , 2016, Future microbiology.

[29]  H. Cadillo-Quiroz,et al.  CRISPR Associated Diversity within a Population of Sulfolobus islandicus , 2010, PloS one.

[30]  R. Barrangou,et al.  The combination of CRISPR-MVLST and PFGE provides increased discriminatory power for differentiating human clinical isolates of Salmonella enterica subsp. enterica serovar Enteritidis. , 2013, Food microbiology.

[31]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[32]  Philippe Horvath,et al.  The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli , 2011, Nucleic acids research.

[33]  Jean-Baptiste Veyrieras,et al.  Phylogenetic Distribution of CRISPR-Cas Systems in Antibiotic-Resistant Pseudomonas aeruginosa , 2015, mBio.

[34]  Z. Pan,et al.  Genetic analysis of Salmonella enterica serovar Gallinarum biovar Pullorum based on characterization and evolution of CRISPR sequence. , 2017, Veterinary microbiology.

[35]  S. Forsythe,et al.  DNA-Sequence Based Typing of the Cronobacter Genus Using MLST, CRISPR-cas Array and Capsular Profiling , 2017, Front. Microbiol..

[36]  K. Makino,et al.  Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome , 1989, Journal of bacteriology.

[37]  P. Mittraparp-arthorn,et al.  CRISPR-like sequences in Helicobacter pylori and application in genotyping , 2017, Gut Pathogens.