1932

Abstract

Bacteria occur ubiquitously in nature and are broadly relevant throughout the food supply chain, with diverse and variable tolerance levels depending on their origin, biological role, and impact on the quality and safety of the product as well as on the health of the consumer. With increasing knowledge of and accessibility to the microbial composition of our environments, food supply, and host-associated microbiota, our understanding of and appreciation for the ratio of beneficial to undesirable bacteria are rapidly evolving. Therefore, there is a need for tools and technologies that allow definite, accurate, and high-resolution identification and typing of various groups of bacteria that include beneficial microbes such as starter cultures and probiotics, innocuous commensals, and undesirable pathogens and spoilage organisms. During the transition from the current molecular biology–based PFGE (pulsed-field gel electrophoresis) gold standard to the increasingly accessible omics-level whole-genome sequencing (WGS) N-gen standard, high-resolution technologies such as CRISPR-based genotyping constitute practical and powerful alternatives that provide valuable insights into genome microevolution and evolutionary trajectories. Indeed, several studies have shown potential for CRISPR-based typing of industrial starter cultures, health-promoting probiotic strains, animal commensal species, and problematic pathogens. Emerging CRISPR-based typing methods open new avenues for high-resolution typing of a broad range of bacteria and constitute a practical means for rapid tracking of a diversity of food-associated microbes.

Keyword(s): casCRISPRepidemiologytyping
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2016-02-28
2024-06-13
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Literature Cited

  1. Abadia E, Zhang J, dos Vultos T, Ritacco V, Kremer K. et al. 2010. Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method. Infect. Genet. Evol. 10:1066–74 [Google Scholar]
  2. Abadia E, Zhang J, Ritacco V, Kremer K, Tuimy R. et al. 2011. The use of microbead-based spoligotyping for Mycobacterium tuberculosis complex to evaluate the quality of the conventional method: providing guidelines for quality assurance when working on membranes. BMC Infect. Dis. 11:110 [Google Scholar]
  3. Anderson RE, Brazelton WJ, Baross JA. 2011. Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage. FEMS Microbiol. Ecol. 77:120–33 [Google Scholar]
  4. Andersson AF, Banfield JF. 2008. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320:1047–50 [Google Scholar]
  5. Barrangou R. 2013. CRISPR-Cas systems and RNA-guided interference. Wiley Interdiscip. Rev. RNA 4:267–78 [Google Scholar]
  6. Barrangou R. 2015. The roles of CRISPR-Cas systems in adaptive immunity and beyond. Curr. Opin. Immunol. 32:36–41 [Google Scholar]
  7. Barrangou R, Briczinski EP, Traeger LL, Loquasto JR, Richards M. et al. 2009. Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04. J. Bacteriol. 191:4144–51 [Google Scholar]
  8. Barrangou R, Coûté-Monvoisin AC, Stahl B, Chavichvily I, Damange F. et al. 2013. Genomic impact of CRISPR immunization against bacteriophages. Biochem. Soc. Trans. 41:1383–91 [Google Scholar]
  9. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P. et al. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709–12 [Google Scholar]
  10. Barrangou R, Horvath P. 2012. CRISPR: new horizons in phage resistance and strain identification. Annu. Rev. Food Sci. Technol. 3:143–62 [Google Scholar]
  11. Barrangou R, Marraffini LA. 2014. CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol. Cell 54:234–44 [Google Scholar]
  12. Barrangou R, May AP. 2015. Unraveling the potential of CRISPR-Cas9 for gene therapy. Expert Opin. Biol. Ther. 15:311–14 [Google Scholar]
  13. Bolotin A, Quinquis B, Sorokin A, Ehrlich SD. 2005. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151:2551–61 [Google Scholar]
  14. Borile C, Labarre M, Franz S, Sola C, Refregier G. 2011. Using affinity propagation for identifying subspecies among clonal organisms: lessons from M. tuberculosis. BCM Bioinform. 12:224 [Google Scholar]
  15. Bourdichon F, Casaregola S, Farrokh C, Frisvad JC, Gerds ML. et al. 2012. Food fermentations: microorganisms with technological beneficial use. Int. J. Food Microbiol. 154:87–97 [Google Scholar]
  16. Briner AE, Barrangou R. 2014. Lactobacillus buchneri genotyping on the basis of clustered regularly interspaced short palindromic repeat (CRISPR) locus diversity. Appl. Environ. Microbiol. 80:994–1001 [Google Scholar]
  17. Briner AE, Lugli GA, Milani C, Duranti S, Turroni F. et al. 2015. Occurrence and diversity of CRISPR-Cas systems in the genus Bifidobacterium. PLOS ONE 10:e0133661 [Google Scholar]
  18. Broadbent JR, Neeno-Eckwall EC, Stahl B, Tandee K, Cai H. et al. 2012. Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. BMC Genomics 13:533 [Google Scholar]
  19. Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ. et al. 2008. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321:960–64 [Google Scholar]
  20. Brudey K, Driscoll JR, Rigouts L, Prodinger WM, Gori A. et al. 2006. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol. 6:23 [Google Scholar]
  21. Brüggemann H, Lomholt HB, Tettelin H, Kilian M. 2012. CRISPR/Cas loci of type II Propionibacterium acnes confer immunity against acquisition of mobile elements present in type I P. acnes. PLOS ONE 7:e34171 [Google Scholar]
  22. Cady KC, White AS, Hammond JH, Abendroth MD, Karthikeyan RS. et al. 2011. Prevalence, conservation and functional analysis of Yersinia and Escherichia CRISPR regions in clinical Pseudomonas aeruginosa isolates. Microbiology 157:430–37 [Google Scholar]
  23. Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W. et al. 2013. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155:1479–91 [Google Scholar]
  24. Cong L, Ran FA, Cox D, Lin S, Barretto R. et al. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–23 [Google Scholar]
  25. Cui Y, Li Y, Gorge O, Platonov ME, Yan Y. et al. 2008. Insight into microevolution of Yersinia pestis by clustered regularly interspaced short palindromic repeats. PLOS ONE 3:e2652 [Google Scholar]
  26. D'Auria G, Jimenez-Hernandez N, Peris-Bondia F, Moya A, Latorre A. 2010. Legionella pneumophila pangenome reveals strain-specific virulence factors. BMC Genomics 11:181 [Google Scholar]
  27. Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y. et al. 2011. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471:602–7 [Google Scholar]
  28. Deveau H, Barrangou R, Garneau JE, Labonté J, Fremaux C. et al. 2008. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J. Bacteriol. 190:1390–400 [Google Scholar]
  29. Diez-Villasenor C, Almendros C, Garcia-Martinez J, Mojica FJ. 2010. Diversity of CRISPR loci in Escherichia coli. Microbiology 156:1351–61 [Google Scholar]
  30. DiMarzio M, Shariat N, Kariyawasam S, Barrangou R, Dudley EG. 2013. Antibiotic resistance in Salmonella Typhimurium associates with CRISPR sequence type. Antimicrob. Agents Chemother. 9:4282–89 [Google Scholar]
  31. Doudna JA, Charpentier E. 2014. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346:6213 [Google Scholar]
  32. Fabre L, Zhang J, Guigon G, Le Hello S, Guibert V. et al. 2012. CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections. PLOS ONE 7:e36995 [Google Scholar]
  33. Fraser-Liggett CM. 2005. Insights on biology and evolution from microbial genome sequencing. Genome Res. 15:1603–10 [Google Scholar]
  34. Fricke WF, Mammel MK, McDermott PF, Tartera C, White DG. et al. 2011. Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution. J. Bacteriol. 193:3556–68 [Google Scholar]
  35. Garneau JE, Dupuis ME, Villion M, Romero DA, Barrangou R. et al. 2010. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468:67–71 [Google Scholar]
  36. Gasiunas G, Barrangou R, Horvath P, Siksnys V. 2012. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. PNAS 109:E2579–86 [Google Scholar]
  37. Godde JS, Bickerton A. 2006. The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes. J. Mol. Evol. 62:718–29 [Google Scholar]
  38. Gomaa AA, Klumpe HE, Luo ML, Selle K, Barrangou R, Beisel CL. 2014. Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems. mBio 5:e00928–13 [Google Scholar]
  39. Grissa I, Vergnaud G, Pourcel C. 2007. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinform. 23:172 [Google Scholar]
  40. Groenen PM, Bunschoten AE, van Soolingen D, van Embden JD. 1993. Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method. Mol. Microbiol. 10:1057–65 [Google Scholar]
  41. Guinane C, Kent RM, Norberg S, Hill C, Fitzgerald GF. et al. 2011. Host specific diversity in Lactobacillus johnsonii as evidenced by a major chromosomal inversion and phage resistance mechanisms. PLOS ONE 6:e18740 [Google Scholar]
  42. Haft DH, Selengut J, Mongodin EF, Nelson KE. 2005. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLOS Comput. Biol. 1:e60 [Google Scholar]
  43. Hale CR, Zhao P, Olson S, Duff MO, Graveley BR. et al. 2009. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139:945–56 [Google Scholar]
  44. Hargreaves KR, Flores CO, Lawley TD, Clokie MR. 2014. Abundant and diverse clustered regularly interspaced short palindromic repeat spacers in Clostridium difficile strains and prophages target multiple phage types within this pathogen. mBio 5:e01045–13 [Google Scholar]
  45. He J, Deem MW. 2010. Heterogeneous diversity of spacers within CRISPR (clustered regularly interspaced short palindromic repeats). Phys. Rev. Lett. 105:128102 [Google Scholar]
  46. Heidelberg JF, Nelson WC, Schoenfeld T, Bhaya D. 2009. Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes. PLOS ONE 4:e4169 [Google Scholar]
  47. Held NL, Herrera A, Cadillo-Quiroz H, Whitaker RJ. 2010. CRISPR associated diversity within a population of Sulfolobus islandicus. PLOS ONE 5:e12988 [Google Scholar]
  48. Held NL, Whitaker RJ. 2009. Viral biogeography revealed by signatures in Sulfolobus islandicus genomes. Environ. Microbiol. 11:457–66 [Google Scholar]
  49. Hilton IB, D'Ippolito AM, Vockley CM, Thakore PI, Crawford GE. et al. 2015. Epigenome editing by a CRISPR-Cas9–based acetyltransferase activates genes from promoters and enhancers. Nat. Biotechnol. 33:510–17 [Google Scholar]
  50. Horvath P, Barrangou R. 2010. CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167–70 [Google Scholar]
  51. Horvath P, Coûté-Monvoisin AC, Romero DA, Boyaval P, Fremaux C, Barrangou R. 2009. Comparative analysis of CRISPR loci in lactic acid bacteria genomes. Int. J. Food Microbiol. 131:62–70 [Google Scholar]
  52. Horvath P, Romero DA, Coûté-Monvoisin AC, Richards M, Deveau H. et al. 2008. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J. Bacteriol. 190:1401–12 [Google Scholar]
  53. Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. 1987. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J. Bacteriol. 169:5429–33 [Google Scholar]
  54. Jansen R, Embden JD, Gaastra W, Schouls LM. 2002a. Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol. 43:1565–75 [Google Scholar]
  55. Jansen R, van Embden JD, Gaastra W, Schouls LM. 2002b. Identification of a novel family of sequence repeats among prokaryotes. OMICS 6:23–33 [Google Scholar]
  56. Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA. 2013. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 31:233–39 [Google Scholar]
  57. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–21 [Google Scholar]
  58. Kinnevey PM, Shore AC, Brennan GI, Sullivan DJ, Ehricht R. et al. 2013. Emergence of sequence type 779 methicillin-resistant Staphylococcus aureus harboring a novel pseudo staphylococcal cassette chromosome mec (SCCmec)-SCC-SCCCRISPR composite element in Irish hospitals. Antimicrob. Agents Chemother. 57:524–31 [Google Scholar]
  59. Kovanen SM, Kivistö RI, Rossi M, Hänninen ML. 2014. A combination of MLST and CRISPR typing reveals dominant Campylobacter jejuni types in organically farmed laying hens. J. Appl. Microbiol. 117:249–57 [Google Scholar]
  60. Kunin V, Sorek R, Hugenholtz P. 2007. Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol. 8:R61 [Google Scholar]
  61. Kuno S, Yoshida T, Kaneko T, Sako Y. 2012. Intricate interactions between the bloom-forming cyanobacterium Microcystis aeruginosa and foreign genetic elements, revealed by diversified clustered regularly interspaced short palindromic repeat (CRISPR) signatures. Appl. Environ. Microbiol. 78:5353–60 [Google Scholar]
  62. Kyrpides NC. 2009. Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream. Nat. Biotechnol. 27:627–32 [Google Scholar]
  63. Ledford H. 2015. CRISPR, the disruptor. Nature 522:20–24 [Google Scholar]
  64. Levin BR, Moineau S, Bushman M, Barrangou R. 2013. The population and evolutionary dynamics of phage and bacteria with CRISPR-mediated immunity. PLOS Genet. 9:e1003312 [Google Scholar]
  65. Lier C, Baticle E, Horvath P, Haguenoer E, Valentin AS. et al. 2015. Analysis of the type II-A CRISPR-Cas system of Streptococcus agalactiae reveals distinctive features according to genetic lineages. Front. Genet. 6:214 [Google Scholar]
  66. Lindenstrauss AG, Pavlovic M, Bringmann A, Behr J, Ehrmann MA, Vogel RF. 2011. Comparison of genotypic and phenotypic cluster analyses of virulence determinants and possible role of CRISPR elements towards their incidence in Enterococcus faecalis and Enterococcus faecium. Syst. Appl. Microbiol. 34:553–60 [Google Scholar]
  67. Liu F, Barrangou R, Gerner-Smidt P, Ribot EM, Knabel SJ. et al. 2011a. 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. 77:1946–56 [Google Scholar]
  68. Liu F, Kariyawasam S, Jayarao B, Barrangou R, Gerner-Smidt P. et al. 2011b. Subtyping Salmonella serovar Enteritidis isolates from different sources using sequence typing based on virulence genes and CRISPRs. App. Environ. Microbiol. 77:4520–26 [Google Scholar]
  69. Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B. et al. 2006a. Comparative genomics of the lactic acid bacteria. PNAS 103:15611–16 [Google Scholar]
  70. Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV. 2006b. A putative RNA-interference–based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct 1:7 [Google Scholar]
  71. Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E. et al. 2011. Evolution and classification of the CRISPR/Cas systems. Nat. Rev. Microbiol. 9:467–77 [Google Scholar]
  72. Makarova KS, Wolf YI, Alkhnbashi O, Costa F, Shah S. et al. 2015. An updated evolutionary classification scheme for CRISPR-Cas systems. Nat. Rev. Microbiol. 13:722–36 [Google Scholar]
  73. Mali P, Yang L, Esvelt KM, Aach J, Guell M. et al. 2013. RNA-guided human genome engineering via Cas9. Science 339:823–26 [Google Scholar]
  74. Marraffini LA, Sontheimer EJ. 2008. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322:1843–45 [Google Scholar]
  75. McShan WM, Ferretti JJ, Karasawa T, Suvorov AN, Lin S. et al. 2008. Genome sequence of a nephritogenic and highly transformable M49 strain of Streptococcus pyogenes. J. Bacteriol 190:7773–85 [Google Scholar]
  76. Mojica FJ, Díez-Villaseñor C, García-Martínez J, Almendros C. 2009. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155:733–40 [Google Scholar]
  77. Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E. 2005. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60:174–82 [Google Scholar]
  78. Mokrousov I, Limeschenko E, Vyazovaya A, Narvskaya O. 2007. Corynebacterium diphtheriae spoligotyping based on combined use of two CRISPR loci. Biotechnol. J. 2:901–6 [Google Scholar]
  79. Mokrousov I, Vyazovaya A, Kolodkina V, Limeschenko E, Titov L, Narvskaya O. 2009. Novel macroarray-based method of Corynebacterium diphtheriae genotyping: evaluation in a field study in Belarus. Eur. J. Clin. Microbiol. Infect. Dis. 28:701–3 [Google Scholar]
  80. Nuñez JK, Lee AS, Engelman A, Doudna JA. 2015. Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity. Nature 519:193–98 [Google Scholar]
  81. Oh JH, van Pijkeren JP. 2014. CRISPR-Cas9-assisted recombineering in Lactobacillus reuteri. Nucleic Acids Res. 42:e131 [Google Scholar]
  82. Paez-Espino D, Morovic W, Sun CL, Thomas BC, Ueda K. et al. 2013. Strong bias in the bacterial CRISPR elements that confer immunity to phage. Nat. Commun. 4:1430 [Google Scholar]
  83. Pennisi E. 2013. The CRISPR craze. Science 341:833–36 [Google Scholar]
  84. Pettengill JB, Timme RE, Barrangou R, Toro M, Allard MW. et al. 2014. The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica. Peer J. 2:e340 [Google Scholar]
  85. Pourcel C, Salvignol G, Vergnaud G. 2005. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 151:653–63 [Google Scholar]
  86. Pride DT, Sun CL, Salzman J, Rao N, Loomer P. et al. 2011. Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time. Genome Res. 21:126–36 [Google Scholar]
  87. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS. et al. 2013. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152:1173–83 [Google Scholar]
  88. Relman DA. 2011. Microbial genomics and infectious diseases. N. Engl. J. Med. 365:347–57 [Google Scholar]
  89. Rezzonico F, Smits THM, Duffy B. 2011. Diversity, evolution and functionality of clustered regularly interspaced short palindromic repeat (CRISPR) regions in the fire blight pathogen Erwinia amylovora. Appl. Environ. Microbiol. 77:3819–29 [Google Scholar]
  90. Riehm JM, Vergnaud G, Kiefer D, Damdindorj T, Dashdavaa O. et al. 2012. Yersinia pestis lineages in Mongolia. PLOS ONE 7:e30624 [Google Scholar]
  91. Selle K, Barrangou R. 2015. Harnessing CRISPR-Cas systems for bacterial genome editing. Trends Microbiol. 23:225–32 [Google Scholar]
  92. Selle K, Klaenhammer TR, Barrangou R. 2015. CRISPR-based screening of genomic island excision events in bacteria. PNAS 112:8076–81 [Google Scholar]
  93. Semenova E, Nagornykh M, Pyatnitskiy M, Artamonova II, Severinov K. 2009. Analysis of CRISPR system function in plant pathogen Xanthomonas oryzae. FEMS Microbiol. Lett. 296:110–16 [Google Scholar]
  94. Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA. et al. 2014. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343:84–87 [Google Scholar]
  95. Shariat N, DiMarzio MJ, Yin S, Dettinger L, Sandt CH. et al. 2013a. 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. 34:164–73 [Google Scholar]
  96. Shariat N, Dudley EG. 2014. CRISPRs: molecular signatures used for pathogen subtyping. Appl. Environ. Microbiol. 80:430–39 [Google Scholar]
  97. Shariat N, Kirchner MK, Sandt CH, Trees E, Barrangou R, Dudley EG. 2013b. Subtyping of Salmonella enterica serovar Newport outbreak isolates by CRISPR-MVLST and determination of the relationship between CRISPR-MVLST and PFGE results. J. Clin. Microbiol. 51:2328–36 [Google Scholar]
  98. Shariat N, Sandt CH, DiMarzio MJ, Barrangou R, Dudley EG. 2013c. CRISPR-MVLST subtyping of Salmonella enterica subsp. enterica serovars Typhimurium and Heidelberg and application in identifying outbreak isolates. BMC Microbiol. 13:254 [Google Scholar]
  99. Shariat N, Timme RE, Pettengill JB, Barrangou R, Dudley E. 2014. Characterization and evolution of Salmonella CRISPR-Cas systems. Microbiology 161:374–86 [Google Scholar]
  100. Sontheimer E, Barrangou R. 2015. The bacterial origins of the CRISPR genome editing revolution. Hum. Gene Ther. 26:413–24 [Google Scholar]
  101. Sun CL, Barrangou R, Thomas BC, Horvath P, Fremaux C, Banfield JF. 2013. Phage mutations in response to CRISPR diversification in a bacterial population. Environ. Microbiol. 15:463–70 [Google Scholar]
  102. Sun H, Li Y, Shi X, Lin Y, Qiu Y. et al. 2015. Association of CRISPR/Cas evolution with Vibrio parahaemolyticus virulence factors and genotypes. Foodborne Pathog. Dis. 12:68–73 [Google Scholar]
  103. Timme RE, Pettengill JB, Allard MW, Strain E, Barrangou R. et al. 2013. Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters. Genome Biol. Evol. 5:2109–23 [Google Scholar]
  104. Toro M, Cao G, Ju W, Allard M, Barrangou R. et al. 2014. Association of clustered regularly interspaced short palindromic repeat (CRISPR) elements with specific serotypes and virulence potential of shiga toxin–producing Escherichia coli. Appl. Environ. Microbiol. 80:1411–20 [Google Scholar]
  105. Touchon M, Charpentier S, Clermont O, Rocha EPC, Denamur E, Branger C. 2011. CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection. J. Bacteriol. 193:2460–67 [Google Scholar]
  106. Touchon M, Rocha EP. 2010. The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLOS ONE 5:e11126 [Google Scholar]
  107. Tremblay CL, Charlebois A, Masson L, Archambault M. 2013. Characterization of hospital-associated lineages of ampicillin-resistant Enterococcus faecium from clinical cases in dogs and humans. Front. Microbiol. 4:245 [Google Scholar]
  108. Tyson GW, Banfield JF. 2008. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ. Microbiol. 10:200–7 [Google Scholar]
  109. Ventura M, Turroni F, Lima-Mendez G, Foroni E, Zomer A. et al. 2009. Comparative analyses of prophage-like elements present in bifidobacterial genomes. Appl. Environ. Microbiol. 75:6929–36 [Google Scholar]
  110. Very KJ, Kirchner MF, Shariat N, Cottrell W, Sandt CH. et al. 2015. Prevalence and spacial distribution of Salmonella infections in the Pennsylvania common raccoon (Procyon lotor). Zoonoses Pub. Health doi: 10.1111/zph.12222 [Google Scholar]
  111. Wehnes CA, Rehberger TG, Barrangou R, Smith AH. 2014. Determination of Salmonella clustered regularly interspaced short palindromic repeats (CRISPR) diversity on dairy farms in Wisconsin and Minnesota. J. Dairy Sci. 97:6370–77 [Google Scholar]
  112. Weinberger AD, Sun CL, Pluciński MM, Denef VJ, Thomas BC. et al. 2012. Persisting viral sequences shape microbial CRISPR-based immunity. PLOS Comput. Biol. 8:e1002475 [Google Scholar]
  113. Yin S, Jensen MA, Bai J, Debroy C, Barrangou R, Dudley EG. 2013. The evolutionary divergence of shiga toxin–producing Escherichia coli is reflected in clustered regularly interspaced short palindromic repeat (CRISPR) spacer composition. Appl. Environ. Microbiol. 79:5710–20 [Google Scholar]
  114. Zhang J, Abadia E, Refregier G, Tafaj S, Boschiroli ML. et al. 2010. Mycobacterium tuberculosis complex CRISPR genotyping: improving efficiency, throughput and discriminative power of “spoligotyping” with new spacers and a microbead-based hybridization assay. J. Med. Microbiol. 59:285–94 [Google Scholar]
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