Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315(5819):1709–1712. https://doi.org/10.1126/science.1138140
Article PubMed CAS Google Scholar
Bisht H, Kumar N (2023) Characterization and evaluation of the nickel-removal capacity of Kluyvera cryocrescens m7 isolated from industrial wastes. Pollution 9(3):1059–1073. https://doi.org/10.22059/poll.2023.347580.1586
Biswas A, Gagnon JN, Brouns SJJ, Fineran PC, Brown CM (2013) CRISPRTarget. Bioinformatic prediction and analysis of CrRNA targets. RNA Biol 10:817–827. https://doi.org/10.4161/rna.24046
Article PubMed PubMed Central CAS Google Scholar
Biswas A, Staals RHJ, Morales SE, Fineran PC, Brown CM (2016) CRISPRDetect: a flexible algorithm to define CRISPR arrays. BMC Genomics 17:1–14. https://doi.org/10.1186/s12864-016-2627-0
Boechat CL, Quadros PDD, Giovanella P, Brito ACC, Carlos FS, Sá ELSD, Camargo FADO (2018) Metal-resistant rhizobacteria change soluble-exchangeable fraction in multi-metal-contaminated soil samples. Rev Bras Ciênc Solo 42. https://doi.org/10.1590/18069657rbcs20170266
Bonomo ME, Deem MW (2017) How the other half lives: CRISPR-Cas’s influence on bacteriophages. In: Pontarotti P (ed) Evolutionary biology: Self/Nonself Evolution, species and complex traits Evolution, methods and concepts. Springer, Cham. https://doi.org/10.1007/978-3-319-61569-1_4
Burd GI, Dixon DG, Glick BR (2000) Plant growth-promoting bacteria that decrease heavy metal toxicity in plants. Can J Microbiol 46(3):237–245. https://doi.org/10.1139/w99-143
Article PubMed CAS Google Scholar
Cao L, Gao CH, Zhu J, Zhao L, Wu Q, Li M, Sun B (2016) Identification and functional study of type III-A CRISPR-Cas systems in clinical isolates of Staphylococcus aureus. Int J Med Microbiol 306(8):686–696. https://doi.org/10.1016/j.ijmm.2016.08.005
Article PubMed CAS Google Scholar
Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, Rocha EPC, Vergnaud G, Gautheret D, Pourcel C (2018) CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res 46(W1):W246–W251. https://doi.org/10.1093/nar/gky425
Article PubMed PubMed Central CAS Google Scholar
Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14:1188–1190. https://doi.org/10.1101/gr.849004
Article PubMed PubMed Central CAS Google Scholar
Erbin A, Gozdas HT, Guler Y, Canat HL (2020) Urosepsis caused by Kluyvera Ascorbata in a pregnant woman. J Coll Physicians Surg Pak 30:324–326. https://doi.org/10.29271/jcpsp.2020.03.324
Fallah T, Shafiei M (2024) Comprehensive analysis of CRISPR-Cas systems and their influence on antibiotic resistance in Salmonella enterica strains. Bioinform Biol Insights 18:11779322241307984. https://doi.org/10.1177/11779322241307984
Article PubMed PubMed Central Google Scholar
Goh YX, Wang M, Hou XP, He Y, Ou HY (2023) Analysis of CRISPR-Cas loci and their targets in Levilactobacillus brevis. Interdiscip Sci Comput Life Sci 15:349–359. https://doi.org/10.1007/s12539-023-00555-1
Hu T, Cui Y, Qu X (2020) Characterization and comparison of CRISPR loci in Streptococcus thermophilus. Arch Microbiol 202:695–710. https://doi.org/10.1007/s00203-019-01780-3
Article PubMed CAS Google Scholar
Jackson RN, Golden SM, van Erp PBG, Carter J, Westra ER, Brouns SJJ, van der Oost J, Terwilliger TC, Read RJ, Wiedenheft B (2015) Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli. Science 345(6203):1473–1479. https://doi.org/10.1126/science.1256328
Kahraman Ilıkkan Ö (2022) Analysis of probiotic bacteria genomes: comparison of CRISPR/Cas systems and spacer acquisition diversity. Indian J Microbiol 62:40–46. https://doi.org/10.1007/s12088-021-00971-1
Article PubMed CAS Google Scholar
Kerber-Diaz JC, Leos-Ramírez MA, Flores-Ceron AA, Ponce-Mendoza A, Estrada-de los Santos P, Ibarra JA (2022) Distribution of CRISPR-Cas systems in the Burkholderiaceae family and its biological implications. Arch Microbiol 204:703. https://doi.org/10.1007/s00203-022-03312-y
Article PubMed CAS Google Scholar
Koonin EV, Gootenberg JS, Abudayyeh OO (2023) Discovery of diverse CRISPR-Cas systems and expansion of the genome engineering toolbox. Biochemistry 62(24):3465–3487. https://doi.org/10.1021/acs.biochem.3c00159
Article PubMed CAS Google Scholar
Kumar S, Stecher G, Suleski M, Sanderford M, Sharma S, Tamura K (2024) MEGA12: molecular evolutionary genetic analysis version 12 for adaptive and green computing. Mol Biol Evol 41(12):msae263. https://doi.org/10.1093/molbev/msae263
Article PubMed PubMed Central CAS Google Scholar
Kushwaha SK, Kumar AA, Gupta H, Marathe SA (2023) The phylogenetic study of the CRISPR-Cas system in Enterobacteriaceae. Curr Microbiol 80:196. https://doi.org/10.1007/s00284-023-03298-w
Article PubMed CAS Google Scholar
Long J, Zhang J, Xi Y, Zhao J, Jin Y, Yang H, Chen S, Duan G (2023) Genomic insights into CRISPR-harboring plasmids in the Klebsiella genus: distribution, backbone structures, antibiotic resistance, and virulence determinant profiles. Antimicrob Agents Chemother 67(3):e01189–e01122. https://doi.org/10.1128/aac.01189-22
Article PubMed PubMed Central CAS Google Scholar
Mackow NA, Shen J, Adnan M, Khan AS, Fries BC, Diago-Navarro E (2019) CRISPR-Cas influences the acquisition of antibiotic resistance in Klebsiella pneumoniae. PLoS ONE 14(11):e0225131. https://doi.org/10.1371/journal.pone.0225131
Article PubMed PubMed Central CAS Google Scholar
Makarova K, Haft D, Barrangou R, Brouns SJJ, Charpentier E, Horvath P, Moineau S, Mojica FJM, Wolf YI, Yakunin AF, van der Oost J, Koonin EV (2011) Evolution and classification of the CRISPR–Cas systems. Nat Rev Microbiol 9:467–477. https://doi.org/10.1038/nrmicro2577
Article PubMed CAS Google Scholar
Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJ, Charpentier E, Haft DH, Horvath P (2015) An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol 13:722–736. https://doi.org/10.1038/nrmicro3569
Article PubMed PubMed Central CAS Google Scholar
Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, Charpentier E, Cheng D, Haft DH, Horvath P, Moineau S, Mojica FJM, Scott D, Shah SA, Siksnys V, Terns MP, Venclovas Č, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV (2020) Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol 18(2):67–83. https://doi.org/10.1038/s41579-019-0299-x
Article PubMed CAS Google Scholar
Marraffini LA, Sontheimer EJ (2008) CRISPR interference limits horizontal gene transfer in Staphylococci by targeting DNA. Science 322(5909):1843–1845. https://doi.org/10.1126/science.1165771
Article PubMed PubMed Central CAS Google Scholar
Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Nat Acad Sci USA 101:7287–7292. https://doi.org/10.1073/pnas.0401799101
Article PubMed PubMed Central CAS Google Scholar
McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, De Pascale G, Ejim L, Kalan L, King AM, Koteva K, Morar M, Mulvey MR, O’Brien JS, Pawlowski AC, Piddock LJV, Spanogiannopoulos P, Sutherland AD, Tang I, Taylor PL, Thaker M, Wang W, Yan M, Yu T, Wright GD (2013) The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57:3348–3357. https://doi.org/10.1128/AAC.00419-13
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