Effect of CRISPR/Cas system on drug resistance and virulence genes of <i>Staphylococcus aureus</i>

XIE Longfei; XIAO Danyu; CHANG Yi; ZHANG Xucai; LI Xiaoshen; XIONG Wenguang

doi:10.7671/j.issn.1001-411X.202111024

Journal of South China Agricultural University > 2023 > 44(2): 179-186. > DOI: 10.7671/j.issn.1001-411X.202111024

XIE Longfei, XIAO Danyu, CHANG Yi, et al. Effect of CRISPR/Cas system on drug resistance and virulence genes of Staphylococcus aureus[J]. Journal of South China Agricultural University, 2023, 44(2): 179-186. DOI: 10.7671/j.issn.1001-411X.202111024

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Effect of CRISPR/Cas system on drug resistance and virulence genes of Staphylococcus aureus

Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation/National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs/National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria/College of Veterinary Medicine, South China Agricultural University/ Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China

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Received Date: November 20, 2021
Available Online: May 17, 2023

Graphical Abstract

Abstract

Abstract

Objective
To understand the distribution of clustered regularly interspaced short palindromic repeats (CRISPR) in Staphylococcus aureus and analyze their effects on the horizontal transfer of antibiotic resistance gene and virulence gene.

Method
Total 575 complete S. aureus genomes were obtained from public databases, and bioinformatics methods were used to count the CRISPR carriage, multi-locus sequence typing (MLST) types distribution of strains and the distribution of strain drug resistance genes and virulence genes. The significance analysis of the difference in the number of drug resistance genes and virulence genes was carried out between CRISPR structure-positive (CRISPR+) and CRISPR structure-negative (CRISPR−)S. aureus. The data of 60 strains of S. aureus were also analyzed by second-generation sequencing to verify the results of public database analysis. We also counted the carriage of prophages and conjugative plasmids in 60 strains of S. aureus in the laboratory, and discussed the effect of CRISPR structure on the prophages and conjugative plasmids of the strains.

Result
Among the 575 strains with complete genome assembly, there were 62 strains with CRISPR structure (CRISPR+) and 513 strains without (CRISPR−). The number of drug resistance genes and virulence genes of CRISPR+S. aureus was less than that of CRISPR−S. aureus, and the difference was significant. Among 60 strains of S. aureus in the laboratory, there were 14 strains of CRISPR+ and 46 strains of CRISPR−. CRISPR+S. aureus carried fewer drug resistance genes and virulence genes, which was consistent with the results of the public database analysis. Analysis of prophages and conjugative plasmids showed that CRISPR− strains carried more prophage sequences, which were significantly different from CRISPR+ strains (P<0.05). For conjugative plasmids, CRISPR− and CRISPR+ strains were largely consistent with no significant difference.

Conclusion
CRISPR structure may limit the horizontal transfer of drug resistance and virulence genes in S. aureus, and CRISPR− strains are more susceptible to be interfered by phage and removable plasmids. This study provides a reference for further research on transmission of drug resistance and virulence genes inS. aureus.
- Staphylococcus aureus,
- CRISPR/Cas system,
- Drug resistance gene,
- Virulence gene

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References (27)

References

[1]	CHEN L, TANG Z Y, CUI S Y, et al. Biofilm production ability, virulence and antimicrobial resistance genes in Staphylococcus aureus from various veterinary hospitals[J]. Pathogens, 2020, 9(4): 264. doi: 10.3390/pathogens9040264.
[2]	SHOPSIN B, KREISWIRTH B N. Molecular epidemiology of methicillin-resistant Staphylococcus aureus[J]. Emerging Infectious Diseases, 2001, 7(2): 323-326. doi: 10.3201/eid0702.010236
[3]	KRISHNA S, MILLER L S. Host-pathogen interactions between the skin and Staphylococcus aureus[J]. Current Opinion Microbiology, 2012, 15(1): 28-35. doi: 10.1016/j.mib.2011.11.003
[4]	毛婷婷. 金黄色葡萄球菌CRISPR结构及耐药毒力分子特征[D]. 郑州: 郑州大学, 2019.
[5]	LINDSAY J A. Staphylococcus aureus genomics and the impact of horizontal gene transfer[J]. International Journal of Medical Microbiology, 2014, 304(2): 103-109. doi: 10.1016/j.ijmm.2013.11.010
[6]	ANITHA P, ANBARASU A, RAMAIAH S. Gene network analysis reveals the association of important functional partners involved in anti-biotic resistance: A report on an important pathogenic bacterium Staphylococcus aureus[J]. Gene, 2016, 575(2): 253-263. doi: 10.1016/j.gene.2015.08.068
[7]	左祥, 查艳景, 王征. 金黄色葡萄球菌的临床分布及耐药基因研究[J]. 中国病原生物学杂志, 2017, 12(6): 566-569.
[8]	ITO T, OKUMA K, MA X X, et al. Insights on antibiotic resistance of Staphylococcus aureus from its whole genome: Genomic island SCC[J]. Drug Resistance Updates, 2003, 6(1): 41-52. doi: 10.1016/S1368-7646(03)00003-7
[9]	ITO T, KATAYAMA Y, HIRAMATSU K. Cloning and nucleotide sequence determination of the entire mec DNA of pre-methicillin-resistant Staphylococcus aureus N315[J]. Antimicrobial Agents and Chemotherapy, 1999, 43(6): 1449-1458. doi: 10.1128/AAC.43.6.1449
[10]	KATAYAMA Y, ITO T, HIRAMATSU K. A new class of genetic element, staphylococcus cassette chromosome mec, encodes methicillin resistance in Staphylococcus aureus[J]. Antimicrobial Agents and Chemotherapy, 2000, 44(6): 1549-1555. doi: 10.1128/AAC.44.6.1549-1555.2000
[11]	LIU J, CHEN D, PETERS B M. Staphylococcal chromosomal cassettes mec (SCCmec): A mobile genetic element in methicillin-resistant Staphylococcus aureus[J]. Microbial Pathogenesis, 2016, 101: 56-67. doi: 10.1016/j.micpath.2016.10.028
[12]	SZCZEPANIK A, KOZIOL-MONTEWKA M, Al-DOORI Z, et al. Spread of a single multiresistant methicillin-resistant Staphylococcus aureus clone carrying a variant of staphylococcal cassette chromosome mec type III isolated in a university hospital[J]. European Journal of Clinical Microbiology & Infectious Diseases, 2007, 26(1): 29-35.
[13]	BARRANGOU R, FREMAUX C, DEVEAU H, et al. CRISPR provides acquired resistance against viruses in prokaryotes[J]. Science, 2007, 315(5819): 1709-1712. doi: 10.1126/science.1138140
[14]	SOREK R, KUNIN V, HUGENHOLTZ P. CRISPR: A widespread system that provides acquired resistance against phages in bacteria and archaea[J]. Nature Reviews Microbiology, 2008, 6(3): 181-186. doi: 10.1038/nrmicro1793
[15]	MARRAFFINI L A, SONTHEIMER E J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA[J]. Science, 2008, 322(5909): 1843-1845. doi: 10.1126/science.1165771
[16]	张蒙蒙, 毕春霞, 王梦圆, 等. 葡萄球菌CRISPR-Cas系统的基因结构及其与耐药基因的关系[J]. 中国病原生物学杂志, 2019, 14(5): 553-559.
[17]	ISHINO Y, SHINAGAWA H, MAKINO K, et al. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product[J]. Journal of Bacteriology, 1987, 169(12): 5429-5433. doi: 10.1128/jb.169.12.5429-5433.1987
[18]	LUO K, SHAO F, KAMARA K N, et al. Molecular characteristics of antimicrobial resistance and virulence determinants of Staphylococcus aureus isolates derived from clinical infection and food[J]. Journal of Clinical Laboratory Analysis, 2018, 32(7): e22456. doi: 10.1002/jcla.22456
[19]	GOPHNA U, KRISTENSEN D M, WOLF Y I, et al. No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales[J]. ISME Journal, 2015, 9(9): 2021-2027. doi: 10.1038/ismej.2015.20
[20]	BOLOTIN A, QUINQUIS B, SOROKIN A, et al. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin[J]. Microbiology-SGM, 2005, 151(8): 2551-2561. doi: 10.1099/mic.0.28048-0
[21]	PALMER K L, GILMORE M S. Multidrug-resistant enterococci lack CRISPR-cas[J]. mBio, 2010, 1(4): e00227-10.
[22]	BURSTEIN D, SUN C L, BROWN C T, et al. Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems[J]. Nature Communications, 2016, 7: 10613. doi: 10.1038/ncomms10613.
[23]	JIANG W, MANIV I, ARAIN F, et al. Dealing with the evolutionary downside of CRISPR immunity: Bacteria and beneficial plasmids[J]. PLoS Genetics, 2013, 9(9): e1003844. doi: 10.1371/journal.pgen.1003844
[24]	TOUCHON M, CHARPENTIER S, POGNARD D, et al. Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements[J]. Microbiology, 2012, 158(Pt 12): 2997-3004.
[25]	洪丽娟, 张冰, 段广才, 等. CRISPR/Cas系统与志贺菌毒力和耐药的关系及插入序列IS600对cse2表达水平的影响[J]. 微生物学报, 2016, 56(12): 1912-1923.
[26]	WATSON B N J, STAALS R H J, FINERAN P C. CRISPR-Cas-mediated phage resistance enhances horizontal gene transfer by transduction[J]. mBio, 2018, 9(1): e02406-17.
[27]	WIEDENHEFT B, BONDY-DENOMY J. CRISPR control of virulence in Pseudomonas aeruginosa[J]. Cell Research, 2017, 27(2): 163-164. doi: 10.1038/cr.2017.6

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Effect of CRISPR/Cas system on drug resistance and virulence genes of Staphylococcus aureus

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