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ORIGINAL RESEARCH

Association of CRISPR-Cas System with the Antibiotic Resistance and Virulence Genes in Nosocomial Isolates of Enterococcus

ORCID Icon, , , , &
Pages 6939-6949 | Received 08 Sep 2022, Accepted 26 Oct 2022, Published online: 30 Nov 2022

References

  • Said MS, Tirthani E, Lesho E. Enterococcus infections. In: StatPearls. Treasure Island (FL): StatPearls Publishing Copyright © 2022, StatPearls Publishing LLC.; 2022.
  • Bhardwaj SB, Mehta M, Sood S, Sharma J. Isolation of a novel phage and targeting biofilms of drug-resistant oral enterococci. J Glob Infect Dis. 2020;12(1):11–15. doi:10.4103/jgid.jgid_110_19
  • Mull RW, Harrington A, Sanchez LA, Tal-Gan Y. Cyclic peptides that govern signal transduction pathways: from prokaryotes to multi-cellular organisms. Curr Top Med Chem. 2018;18(7):625–644. doi:10.2174/1568026618666180518090705
  • Gołaś-Prądzyńska M, Rola JG. Occurrence and antimicrobial resistance of enterococci isolated from goat’s milk. J Vet Res. 2021;65(4):449–455. doi:10.2478/jvetres-2021-0071
  • Shahini Shams Abadi M, Taji A, Salehi F, Kazemian H, Heidari H. High-level gentamicin resistance among clinical isolates of enterococci in Iran: a systematic review and meta-analysis. Folia Med (Plovdiv). 2021;63(1):15–23. doi:10.3897/folmed.63.e53506
  • McInnes RS, McCallum GE, Lamberte LE, van Schaik W. Horizontal transfer of antibiotic resistance genes in the human gut microbiome. Curr Opin Microbiol. 2020;53:35–43. doi:10.1016/j.mib.2020.02.002
  • Boccella M, Santella B, Pagliano P, et al. Prevalence and antimicrobial resistance of enterococcus species: a retrospective cohort study in Italy. Antibiotics. 2021;10(12):1552. doi:10.3390/antibiotics10121552
  • Chanda W, Manyepa M, Chikwanda E, et al. Evaluation of antibiotic susceptibility patterns of pathogens isolated from routine laboratory specimens at Ndola Teaching Hospital: a retrospective study. PLoS One. 2019;14(12):e0226676. doi:10.1371/journal.pone.0226676
  • Haider MZ, Shabbir MAB, Yaqub T, et al. CRISPR-Cas system: an adaptive immune system’s association with antibiotic resistance in Salmonella enterica serovar enteritidis. Biomed Res Int. 2022;2022:9080396. doi:10.1155/2022/9080396
  • Xu Y, Li Z. CRISPR-Cas systems: overview, innovations and applications in human disease research and gene therapy. Comput Struct Biotechnol J. 2020;18:2401–2415. doi:10.1016/j.csbj.2020.08.031
  • Gholizadeh P, Köse Ş, Dao S, et al. How CRISPR-Cas system could be used to combat antimicrobial resistance. Infect Drug Resist. 2020;13:1111–1121. doi:10.2147/IDR.S247271
  • Wheatley RM, MacLean RC. CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa. ISME J. 2021;15(5):1420–1433. doi:10.1038/s41396-020-00860-3
  • Cho S, Shin J, Cho BK. Applications of CRISPR/Cas system to bacterial metabolic engineering. Int J Mol Sci. 2018;19(4):1089. doi:10.3390/ijms19041089
  • Guo M, Chen H, Dong S, Zhang Z, Luo H. CRISPR-Cas gene editing technology and its application prospect in medicinal plants. Chin Med. 2022;17(1):33. doi:10.1186/s13020-022-00584-w
  • Koujah L, Shukla D, Naqvi AR. CRISPR-Cas based targeting of host and viral genes as an antiviral strategy. Semin Cell Dev Biol. 2019;96:53–64. doi:10.1016/j.semcdb.2019.04.004
  • Wright AV, Liu JJ, Knott GJ, Doxzen KW, Nogales E, Doudna JA. Structures of the CRISPR genome integration complex. Science. 2017;357(6356):1113–1118. doi:10.1126/science.aao0679
  • Nidhi S, Anand U, Oleksak P, et al. Novel CRISPR-Cas systems: an updated review of the current achievements, applications, and future research perspectives. Int J Mol Sci. 2021;22(7):3327. doi:10.3390/ijms22073327
  • Amitai G, Sorek R. CRISPR-Cas adaptation: insights into the mechanism of action. Nat Rev Microbiol. 2016;14(2):67–76. doi:10.1038/nrmicro.2015.14
  • Makarova KS, Wolf YI, Alkhnbashi OS, et al. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol. 2015;13(11):722–736. doi:10.1038/nrmicro3569
  • Charpentier E, Richter H, van der Oost J, White MF. Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. FEMS Microbiol Rev. 2015;39(3):428–441. doi:10.1093/femsre/fuv023
  • Hille F, Charpentier E. CRISPR-Cas: biology, mechanisms and relevance. Philos Trans R Soc Lond B Biol Sci. 2016;371:1707.
  • Wan F, Draz MS, Gu M, Yu W, Ruan Z, Luo Q. Novel strategy to combat antibiotic resistance: a sight into the combination of CRISPR/Cas9 and nanoparticles. Pharmaceutics. 2021;13(3):352. doi:10.3390/pharmaceutics13030352
  • Lerminiaux NA, Cameron ADS. Horizontal transfer of antibiotic resistance genes in clinical environments. Can J Microbiol. 2019;65(1):34–44. doi:10.1139/cjm-2018-0275
  • Arnold BJ, Huang IT, Hanage WP. Horizontal gene transfer and adaptive evolution in bacteria. Nat Rev Microbiol. 2022;20(4):206–218. doi:10.1038/s41579-021-00650-4
  • Pinilla-Redondo R, Russel J, Mayo-Muñoz D, et al. CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids. Nucleic Acids Res. 2022;50(8):4315–4328. doi:10.1093/nar/gkab859
  • Mulkerrins KB, Lyons C, Shiaris MP. Draft genome sequence of Enterococcus faecalis AS003, a strain possessing all three type II-a CRISPR loci. Microbiol Resource Announcements. 2021;10(11). doi:10.1128/MRA.01449-20
  • Gophna U, Kristensen DM, Wolf YI, Popa O, Drevet C, Koonin EV. No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales. ISME J. 2015;9(9):2021–2027. doi:10.1038/ismej.2015.20
  • Alduhaidhawi AHM, AlHuchaimi SN, Al-Mayah TA, et al. Prevalence of CRISPR-Cas systems and their possible association with antibiotic resistance in Enterococcus faecalis and Enterococcus faecium collected from hospital wastewater. Infect Drug Resist. 2022;15:1143–1154. doi:10.2147/IDR.S358248
  • Huescas CGY, Pereira RI, Prichula J, Azevedo PA, Frazzon J, Frazzon APG. Frequency of clustered regularly interspaced short palindromic repeats (CRISPRs) in non-clinical Enterococcus faecalis and Enterococcus faecium strains. Braz J Biol. 2019;79(3):460–465. doi:10.1590/1519-6984.183375
  • Palmer KL, Gilmore MS. Multidrug-resistant enterococci lack CRISPR-cas. mBio. 2010;1(4). doi:10.1128/mBio.00227-10
  • Dos Santos BA, de Oliveira JDS, Parmanhani-da-Silva BM, Ribeiro RL, Teixeira LM, Neves FPG. CRISPR elements and their association with antimicrobial resistance and virulence genes among vancomycin-resistant and vancomycin-susceptible enterococci recovered from human and food sources. Infect Genet Evol. 2020;80:104183. doi:10.1016/j.meegid.2020.104183
  • Lindenstrauss AG, Pavlovic M, Bringmann A, Behr J, Ehrmann MA, Vogel RF. 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. 2011;34(8):553–560. doi:10.1016/j.syapm.2011.05.002
  • Gholizadeh P, Aghazadeh M, Ghotaslou R, et al. CRISPR-cas system in the acquisition of virulence genes in dental-root canal and hospital-acquired isolates of Enterococcus faecalis. Virulence. 2020;11(1):1257–1267. doi:10.1080/21505594.2020.1809329
  • Burley KM, Sedgley CM. CRISPR-Cas, a prokaryotic adaptive immune system, in endodontic, oral, and multidrug-resistant hospital-acquired Enterococcus faecalis. J Endod. 2012;38(11):1511–1515. doi:10.1016/j.joen.2012.07.004
  • Price VJ, Huo W, Sharifi A, Palmer KL. CRISPR-Cas and restriction-modification act additively against conjugative antibiotic resistance plasmid transfer in Enterococcus faecalis. mSphere. 2016;1(3). doi:10.1128/mSphere.00064-16
  • Tomida J, Morita Y, Shibayama K, et al. Diversity and microevolution of CRISPR loci in Helicobacter cinaedi. PLoS One. 2017;12(10):e0186241. doi:10.1371/journal.pone.0186241
  • Zheng Z, Zhang Y, Liu Z, et al. The CRISPR-Cas systems were selectively inactivated during evolution of Bacillus cereus group for adaptation to diverse environments. ISME J. 2020;14(6):1479–1493. doi:10.1038/s41396-020-0623-5
  • Wu Q, Cui L, Liu Y, et al. CRISPR-Cas systems target endogenous genes to impact bacterial physiology and alter mammalian immune responses. Mol Biomed. 2022;3(1):22. doi:10.1186/s43556-022-00084-1
  • Hullahalli K, Rodrigues M, Palmer KL. Exploiting CRISPR-Cas to manipulate Enterococcus faecalis populations. eLife. 2017;6. doi:10.7554/eLife.26664
  • Gholizadeh P, Aghazadeh M, Ghotaslou R, et al. Role of CRISPR-Cas system on antibiotic resistance patterns of Enterococcus faecalis. Ann Clin Microbiol Antimicrob. 2021;20(1):49. doi:10.1186/s12941-021-00455-6
  • Palmer KL, Godfrey P, Griggs A, et al. Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus. mBio. 2012;3(1):e00318–11. doi:10.1128/mBio.00318-11
  • McBride SM, Fischetti VA, Leblanc DJ, Moellering RC, Gilmore MS. Genetic diversity among Enterococcus faecalis. PLoS One. 2007;2(7):e582. doi:10.1371/journal.pone.0000582
  • Bourgogne A, Garsin DA, Qin X, et al. Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF. Genome Biol. 2008;9(7):R110. doi:10.1186/gb-2008-9-7-r110
  • Hullahalli K, Rodrigues M, Nguyen UT, Palmer K. An attenuated CRISPR-Cas system in Enterococcus faecalis permits DNA acquisition. mBio. 2018;9(3). doi:10.1128/mBio.00414-18
  • Pillay S, Zishiri OT, Adeleke MA. Prevalence of virulence genes in Enterococcus species isolated from companion animals and livestock. Onderstepoort J Vet Res. 2018;85(1):e1–e8. doi:10.4102/ojvr.v85i1.1583
  • Roy S, Naha S, Rao A, Basu S. CRISPR-Cas system, antibiotic resistance and virulence in bacteria: through a common lens. Prog Mol Biol Transl Sci. 2021;178:123–174.
  • Pursey E, Dimitriu T, Paganelli FL, Westra ER, van Houte S. CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens. Philos Trans R Soc Lond B Biol Sci. 2022;377(1842):20200464. doi:10.1098/rstb.2020.0464
  • Wang G, Song G, Xu Y. Association of CRISPR/Cas system with the drug resistance in Klebsiella pneumoniae. Infect Drug Resist. 2020;13:1929–1935. doi:10.2147/IDR.S253380
  • Ren L, Deng LH, Zhang RP, et al. Relationship between drug resistance and the clustered, regularly interspaced, short, palindromic repeat-associated protein genes cas1 and cas2 in Shigella from giant panda dung. Medicine. 2017;96(7):e5922. doi:10.1097/MD.0000000000005922
  • Toro M, Cao G, Ju W, et al. 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. 2014;80(4):1411–1420. doi:10.1128/AEM.03018-13
  • Touchon M, Charpentier S, Pognard D, et al. Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements. Microbiology. 2012;158(Pt 12):2997–3004. doi:10.1099/mic.0.060814-0
  • Shabbir MA, Wu Q, Shabbir MZ, et al. The CRISPR-cas system promotes antimicrobial resistance in Campylobacter jejuni. Future Microbiol. 2018;13:1757–1774. doi:10.2217/fmb-2018-0234