Email Alerts
RSS
Volume 38 Issue 2
Feb.  2022
Turn off MathJax
Article Contents
Article Navigation >  CHINESE JOURNAL OF BURNS AND WOUNDS  > 2022  >  38(2): 137-146
Zhang J,Yan RS,Yang ZC,et al.Analysis of genomic information and biological characteristics of a bacteriophage against methicillin-resistant Staphylococcus aureus in patients with median sternal incision infection[J].Chin J Burns Wounds,2022,38(2):137-146.DOI: 10.3760/cma.j.cn501120-20211130-00400.
Citation: Zhang J,Yan RS,Yang ZC,et al.Analysis of genomic information and biological characteristics of a bacteriophage against methicillin-resistant Staphylococcus aureus in patients with median sternal incision infection[J].Chin J Burns Wounds,2022,38(2):137-146.DOI: 10.3760/cma.j.cn501120-20211130-00400.
shu

Analysis of genomic information and biological characteristics of a bacteriophage against methicillin-resistant Staphylococcus aureus in patients with median sternal incision infection

doi: 10.3760/cma.j.cn501120-20211130-00400

  • Department of Plastic and Cosmetic Surgery, the Second Affiliated Hospital of Army Medical University (the Third Military Medical University), Chongqing 400037, China

Funds:

Youth Science Foundation Project of National Natural Science Foundation of China 82002051

General Program of Natural Science Foundation of Chongqing of China cstc2021jcyj-msxm0655

More Information
  • Corresponding author: Zhang Yiming, Email: zhangyiming@tmmu.edu.cn
  • Received Date: 2021-11-30
    Abstract
  •   Objective  To isolate and purify a bacteriophage against methicillin-resistant Staphylococcus aureus (MRSA), and to analyze its genomic information and biological characteristics.  Methods  The experimental research methods were adopted. MRSA (hereinafter referred to as host bacteria) solution was collected from the wound of a 63-year-old female patient with the median sternum incision infection admitted to the Second Affiliated Hospital of Army Medical University (the Third Military Medical University). The bacteriophage, named bacteriophage SAP23 was isolated and purified from the sewage of the Hospital by sewage co-culture method and double-layer agar plate method, and the plaque morphology was observed. The morphology of bacteriophage SAP23 was observed by transmission electron microscope after phosphotungstic acid negative staining. The whole genome of bacteriophage SAP23 was sequenced with NovaSeq PE15 platform after its DNA was prepared by sodium dodecyl sulfonate/protease cleavage scheme, and genomic analysis including sequence assembly, annotation, and phylogenetic tree were completed. The bacteriophage SAP23 solution was co-incubated with the host bacterial solution for 4 h at the multiplicity of infection (MOI) of 10.000 0, 1.000 0, 0.100 0, 0.010 0, 0.001 0, and 0.000 1, respectively, and then the bacteriophage titer was measured by the drip plate method to select the optimal MOI, with here and the following sample numbers of 3. The bacteriophage SAP23 solution was co-incubated with the host bacterial solution at the optimal MOI for 5, 10, and 15 min, respectively, and the bacteriophage titer was measured by the same method as mentioned above to select the optimal adsorption time. After the bacteriophage SAP23 solution was co-incubated with the host bacterial solution at the optimal MOI for the optimal adsorption time, the bacteriophage titers were measured by the same method as mentioned above at 0 (immediately), 5, 10, 15, 20, 30, 40, 50, 60, 80, 100, and 120 min after culture, respectively, and a one-step growth curve was drawn. The bacteriophage SAP23 solution was incubated at 4, 37, 50, 60, 70, and 80 ℃ and pH 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12 for 1 h, respectively, to determine its stability. A total of 41 MRSA strains stored in the Department of Microbiology of Army Medical University (the Third Military Medical University) were used to determine the host spectrum of bacteriophage SAP23.  Results  The bacteriophage SAP23 could form a transparent plaque on the host bacteria double-layer agar plate. The bacteriophage SAP23 has a polyhedral head with (88±4) nm in diameter and a tail with (279±21) nm in length and (22.6±2.6) nm in width. The bacteriophage SAP23 has a linear, double-stranded DNA with a full length of 151 618 bp and 11 681 bp long terminal repeats sequence in the sequence ends. There were 220 open reading frames predicted and the bacteriophage could encode 4 transfer RNAs, while no resistance genes or virulence factors were found. The annotation function of bacteriophage SAP23 genes could be divided into 5 groups. The GenBank accession number was MZ427930. According to the genomic collinearity analysis, there were 5 local collinear blocks in the whole genome between the bacteriophage SAP23 and the chosen 6 Staphylococcus bacteriophages, while within or outside the local collinear region, there were still some differences. The bacteriophage SAP23 belonged to the Herelleviridae family, Twortvirinae subfamily, and Kayvirus genus. The optimal MOI of bacteriophage SAP23 was 0.010 0, and the optimal adsorption time was 10 min. The bacteriophage SAP23 had a latent period of 20 min, and a growth phase of 80 min. The bacteriophage SAP23 was able to remain stable at the temperature between 4 and 37 ℃ and at the pH values between 4 and 9. The bacteriophage SAP23 could lyse 3 of the 41 tested MRSA strains.  Conclusions  The bacteriophage SAP23 is a member of the Herelleviridae family, Twortvirinae subfamily, and Kayvirus genus. The bacteriophage SAP23 has a good tolerance for temperature and acid-base and a short latent period, and can lyse MRSA effectively. The bacteriophage SAP23 is a new type of potent narrow-spectrum bacteriophage without virulence factors and resistance genes.

     

    • FullText(HTML)
  • loading
    • References(63)
  • [1]
    WangPH, HuangBS, HorngHC, et al.Wound healing[J].J Chin Med Assoc,2018, 81(2):94-101. DOI: 10.1016/j.jcma.2017.11.002.
    [2]
    WilkinsonHN, HardmanMJ.Wound healing: cellular mechanisms and pathological outcomes[J].Open Biol,2020, 10(9):200223. DOI: 10.1098/rsob.200223.
    [3]
    SarhanWA, AzzazyHME, El-SherbinyIM.Honey/chitosan nanofiber wound dressing enriched with allium sativum and cleome droserifolia: enhanced antimicrobial and wound healing activity[J].ACS Appl Mater Interfaces,2016, 8(10):6379-6390. DOI: 10.1021/acsami.6b00739.
    [4]
    HanG, CeilleyR.Chronic wound healing: a review of current management and treatments[J].Adv Ther,2017, 34(3):599-610. DOI: 10.1007/s12325-017-0478-y.
    [5]
    SiddiquiAR,BernsteinJM.Chronic wound infection: facts and controversies[J].Clin Dermatol,2010,28(5):519-526.DOI: 10.1016/j.clindermatol.2010.03.009.
    [6]
    LakhundiS, ZhangKY. Methicillin-resistant Staphylococcus aureus: molecular characterization, evolution, and epidemiology[J].Clin Microbiol Rev,2018,31(4):e0020-18.DOI: 10.1128/CMR.00020-18.
    [7]
    SongRh,YuB,FriedrichD,et al.Naphthoquinone-derivative as a synthetic compound to overcome the antibiotic resistance of methicillin-resistant S. aureus[J].Commun Biol,2020,3(1):529.DOI: 10.1038/s42003-020-01261-0.
    [8]
    Hernández-AristizábalI, Ocampo-IbáñezID.Antimicrobial peptides with antibacterial activity against vancomycin-resistant Staphylococcus aureus strains: classification, structures, and mechanisms of action[J].Int J Mol Sci,2021, 22(15):7927. DOI: 10.3390/ijms22157927.
    [9]
    CrockerTF, BrownL, LamN, et al. Information provision for stroke survivors and their carers[J].Cochrane Database Syst Rev,2021,11(11):CD001919.DOI: 10.1002/14651858.CD001919.pub4.
    [10]
    CisekAA, DąbrowskaI, GregorczykKP, et al.Phage therapy in bacterial infections treatment: one hundred years after the discovery of bacteriophages[J].Curr Microbiol,2017, 74(2):277-283. DOI: 10.1007/s00284-016-1166-x.
    [11]
    KortrightKE, ChanBK, KoffJL, et al.Phage therapy: a renewed approach to combat antibiotic-resistant bacteria[J].Cell Host Microbe,2019, 25(2):219-232. DOI: 10.1016/j.chom.2019.01.014.
    [12]
    SummersWC.The strange history of phage therapy[J].Bacteriophage,2012, 2(2):130-133. DOI: 10.4161/bact.20757.
    [13]
    SarkerSA,SultanaS,ReutelerG,et al. Oral phage therapy of acute bacterial diarrhea with two coliphage preparations: a randomized trial in children from Bangladesh[J].EBioMedicine,2016,4:124-137.DOI: 10.1016/j.ebiom.2015.12.023.
    [14]
    FurfaroLL, PayneMS, ChangBJ.Bacteriophage therapy: clinical trials and regulatory hurdles[J].Front Cell Infect Microbiol,2018, 8:376. DOI: 10.3389/fcimb.2018.00376.
    [15]
    JaultP,LeclercT,JennesS,et al.Efficacy and tolerability of a cocktail of bacteriophages to treat burn wounds infected by Pseudomonas aeruginosa (PhagoBurn): a randomised, controlled, double-blind phase 1/2 trial[J].Lancet Infect Dis,2019,19(1):35-45.DOI: 10.1016/S1473-3099(18)30482-1.
    [16]
    LeitnerL, UjmajuridzeA, ChanishviliN, et al.Intravesical bacteriophages for treating urinary tract infections in patients undergoing transurethral resection of the prostate: a randomised, placebo-controlled, double-blind clinical trial[J].Lancet Infect Dis,2021,21(3):427-436.DOI: 10.1016/S1473-3099(20)30330-3.
    [17]
    CarvalhoC, CostaAR, SilvaF, et al.Bacteriophages and their derivatives for the treatment and control of food-producing animal infections[J].Crit Rev Microbiol,2017,43(5):583-601.DOI: 10.1080/1040841X.2016.1271309.
    [18]
    MichelsonD, GrundmanM, MagnusonK, et al.Randomized, placebo controlled trial of NPT088, a phage-derived, amyloid-targeted treatment for Alzheimer's disease[J].J Prev Alzheimers Dis,2019, 6(4):228-231. DOI: 10.14283/jpad.2019.37.
    [19]
    YangZC, LiuXZ, ShiYL, et al.Characterization and genome annotation of a newly detected bacteriophage infecting multidrug-resistant Acinetobacter baumannii[J].Arch Virol,2019,164(6):1527-1533.DOI: 10.1007/s00705-019-04213-0.
    [20]
    LuSG, LeS,TanYL, et al.Genomic and proteomic analyses of the terminally redundant genome of the Pseudomonas aeruginosa phage PaP1: establishment of genus PaP1-like phages[J].PLoS One,2013,8(5):e62933.DOI: 10.1371/journal.pone.0062933.
    [21]
    GarneauJR, DepardieuF, FortierLC, et al.PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data[J].Sci Rep,2017,7(1):8292.DOI: 10.1038/s41598-017-07910-5.
    [22]
    BesemerJ,LomsadzeA,BorodovskyM.GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions[J].Nucleic Acids Res,2001,29(12):2607-2618.DOI: 10.1093/nar/29.12.2607.
    [23]
    BrettinT,DavisJJ,DiszT,et al.RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes[J].Sci Rep,2015,5:8365.DOI: 10.1038/srep08365.
    [24]
    AzizRK,BartelsD,BestAA,et al.The RAST Server: rapid annotations using subsystems technology[J].BMC Genomics,2008,9:75.DOI: 10.1186/1471-2164-9-75.
    [25]
    ArndtD,GrantJR,MarcuA,et al. PHASTER: a better, faster version of the PHAST phage search tool[J].Nucleic Acids Res,2016,44(W1):W16-21.DOI: 10.1093/nar/gkw387.
    [26]
    LoweTM, EddySR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence[J].Nucleic Acids Res,1997,25(5):955-964.DOI: 10.1093/nar/25.5.955.
    [27]
    LagesenK,HallinP,RødlandEA,et al.RNAmmer: consistent and rapid annotation of ribosomal RNA genes[J].Nucleic Acids Res,2007,35(9):3100-3108.DOI: 10.1093/nar/gkm160.
    [28]
    DarlingACE, MauB, BlattnerFR,et al. Mauve: multiple alignment of conserved genomic sequence with rearrangements[J].Genome Res,2004,14(7):1394-1403.DOI: 10.1101/gr.2289704.
    [29]
    AnisimovaM.Evolutionary genomics: statistical and computational methods[M]. New York: Springer New York,2019: 121-147.
    [30]
    El-ArabiTF,GriffithsMW,SheYM,et al.Genome sequence and analysis of a broad-host range lytic bacteriophage that infects the Bacillus cereus group[J].Virol J,2013,10:48.DOI: 10.1186/1743-422X-10-48.
    [31]
    吴丽飞,王兆飞,王中华,等.高效裂解多重耐药金黄色葡萄球菌的噬菌体分离及裂解酶的制备[J].中国动物传染病学报,2021,29(3):1-9. DOI: 10.19958/j.cnki.cn31-2031/s.2021.03.001.
    [32]
    YangS,YangY,CuiSX,et al.Chitosan-polyvinyl alcohol nanoscale liquid film-forming system facilitates MRSA-infected wound healing by enhancing antibacterial and antibiofilm properties[J].Int J Nanomedicine,2018,13:4987-5002.DOI: 10.2147/IJN.S161680.
    [33]
    DouJL, JiangYW, XieJQ, et al.New is old, and old is new: recent advances in antibiotic-based, antibiotic-free and ethnomedical treatments against methicillin-resistant Staphylococcus aureus wound infections[J].Int J Mol Sci,2016, 17(5):617. DOI: 10.3390/ijms17050617.
    [34]
    MaciejewskaB,OlszakT,Drulis-KawaZ.Applications of bacteriophages versus phage enzymes to combat and cure bacterial infections: an ambitious and also a realistic application?[J].Appl Microbiol Biotechnol,2018,102(6):2563-2581.DOI: 10.1007/s00253-018-8811-1.
    [35]
    MorozovaVV, VlassovVV, TikunovaNV.Applications of bacteriophages in the treatment of localized infections in humans[J].Front Microbiol,2018, 9:1696. DOI: 10.3389/fmicb.2018.01696.
    [36]
    OoiML, DrillingAJ, MoralesS, et al.Safety and tolerability of bacteriophage therapy for chronic rhinosinusitis due to Staphylococcus aureus[J].JAMA Otolaryngol Head Neck Surg,2019, 145(8):723-729. DOI: 10.1001/jamaoto.2019.1191.
    [37]
    FishR, KutterE, BryanD, et al.Resolving digital staphylococcal osteomyelitis using bacteriophage-a case report[J].Antibiotics (Basel),2018, 7(4):87. DOI: 10.3390/antibiotics7040087.
    [38]
    胡福泉.噬菌体的过去、现在与未来[J].西南医科大学学报,2021,44(5):417-424.DOI: 10.3969/j.issn.2096-3351.2021.05.001.
    [39]
    RegeimbalJM, JacobsAC, CoreyBW, et al.Personalized therapeutic cocktail of wild environmental phages rescues mice from Acinetobacter baumannii wound infections[J].Antimicrob Agents Chemother,2016, 60(10):5806-5816. DOI: 10.1128/aac.02877-15.
    [40]
    GillJJ, HymanP.Phage choice, isolation, and preparation for phage therapy[J].Curr Pharm Biotechnol,2010, 11(1):2-14. DOI: 10.2174/138920110790725311.
    [41]
    KrupovicM,DutilhBE,AdriaenssensEM,et al.Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee[J].Arch Virol,2016,161(4):1095-1099.DOI: 10.1007/s00705-015-2728-0.
    [42]
    ŁobockaM,HejnowiczMS,DąbrowskiK,et al.Genomics of staphylococcal Twort-like phages--potential therapeutics of the post-antibiotic era[J].Adv Virus Res,2012,83:143-216.DOI: 10.1016/B978-0-12-394438-2.00005-0.
    [43]
    AzamAH, TanjiY.Peculiarities of Staphylococcus aureus phages and their possible application in phage therapy[J].Appl Microbiol Biotechnol,2019, 103(11):4279-4289. DOI: 10.1007/s00253-019-09810-2.
    [44]
    Głowacka-RutkowskaA, UlatowskaM, EmpelJ, et al.A Kayvirus distant homolog of staphylococcal virulence determinants and VISA biomarker is a phage lytic enzyme[J].Viruses,2020, 12(3):292. DOI: 10.3390/v12030292.
    [45]
    DonovanDM,LardeoM,Foster-FreyJ.Lysis of staphylococcal mastitis pathogens by bacteriophage phi11 endolysin[J].FEMS Microbiol Lett,2006,265(1):133-139.DOI: 10.1111/j.1574-6968.2006.00483.x.
    [46]
    PaulVD,RajagopalanSS,SundarrajanS,et al.A novel bacteriophage tail-associated muralytic enzyme (TAME) from Phage K and its development into a potent antistaphylococcal protein[J].BMC Microbiol,2011,11:226.DOI: 10.1186/1471-2180-11-226.
    [47]
    GuJM,XuW,LeiLC,et al.LysGH15, a novel bacteriophage lysin, protects a murine bacteremia model efficiently against lethal methicillin-resistant Staphylococcus aureus infection[J].J Clin Microbiol,2011,49(1):111-117.DOI: 10.1128/JCM.01144-10.
    [48]
    KaurJ, SinghP, SharmaD, et al. A potent enzybiotic against methicillin-resistant Staphylococcus aureus[J].Virus Genes,2020, 56(4):480-497. DOI: 10.1007/s11262-020-01762-4.
    [49]
    CahillJ, YoungR.Phage lysis: multiple genes for multiple barriers[J].Adv Virus Res,2019, 103:33-70. DOI: 10.1016/bs.aivir.2018.09.003.
    [50]
    LindenSB,ZhangH,HeselpothRD,et al.Biochemical and biophysical characterization of PlyGRCS, a bacteriophage endolysin active against methicillin-resistant Staphylococcus aureus[J].Appl Microbiol Biotechnol,2015,99(2):741-752.DOI: 10.1007/s00253-014-5930-1.
    [51]
    高明明,刘慧莹,李璞媛,等.金黄色葡萄球菌噬菌体vB_SauH_IME522的分离鉴定及全基因组分析[J].第三军医大学学报,2020,42(3):229-240.DOI: 10.16016/j.1000-5404.201909016.
    [52]
    ShimamoriY, PramonoAK, KitaoT, et al. Isolation and characterization of a novel phage SaGU1 that infects Staphylococcus aureus clinical isolates from patients with atopic dermatitis[J].Curr Microbiol,2021, 78(4):1267-1276. DOI: 10.1007/s00284-021-02395-y.
    [53]
    Bailly-BechetM, VergassolaM, RochaE. Causes for the intriguing presence of tRNAs in phages[J].Genome Res,2007,17(10):1486-1495.DOI: 10.1101/gr.6649807.
    [54]
    NunesA, RibeiroDR, MarquesM,et al.Emerging roles of tRNAs in RNA virus infections[J].Trends Biochem Sci,2020,45(9):794-805.DOI: 10.1016/j.tibs.2020.05.007.
    [55]
    McCallinS, SarkerSA, BarrettoC,et al.Safety analysis of a Russian phage cocktail: from metagenomic analysis to oral application in healthy human subjects[J].Virology,2013,443(2):187-196.DOI: 10.1016/j.virol.2013.05.022.
    [56]
    QuirósP,Colomer-LluchM,Martínez-CastilloA,et al.Antibiotic resistance genes in the bacteriophage DNA fraction of human fecal samples[J].Antimicrob Agents Chemother,2014,58(1):606-609.DOI: 10.1128/AAC.01684-13.
    [57]
    靳晓东,张聪慧,钟江.两株新的金黄色葡萄球菌烈性噬菌体的生物学特性和基因组学研究[J].微生物与感染,2018,13(6):335-341.DOI: 10.3969/j.issn.1673-6184.2018.06.003.
    [58]
    JiJW, LiuQ, WangR, et al. Identification of a novel phage targeting methicillin-resistant Staphylococcus aureus in vitro and in vivo[J].Microbial Pathogenesis,2020, 149:104317. DOI: https://doi.org/10.1016/j.micpath.2020.104317.
    [59]
    GutiérrezD, VandenheuvelD, MartínezB, et al.Two phages, phiIPLA-RODI and phiIPLA-C1C, lyse mono- and dual-species Staphylococcal biofilms[J].Appl Environ Microbiol,2015, 81(10):3336-3348. DOI: 10.1128/aem.03560-14.
    [60]
    FengTT, LeptihnS, DongK, et al. JD419, a Staphylococcus aureus phage with a unique morphology and broad host range[J].Front Microbiol,2021, 12:602902. DOI: 10.3389/fmicb.2021.602902.
    [61]
    DoubJB, NgVY, JohnsonAJ, et al.Salvage bacteriophage therapy for a chronic MRSA prosthetic joint infection[J].Antibiotics (Basel),2020, 9(5):241. DOI: 10.3390/antibiotics9050241.
    [62]
    JikiaD,ChkhaidzeN,ImedashviliE,et al.The use of a novel biodegradable preparation capable of the sustained release of bacteriophages and ciprofloxacin, in the complex treatment of multidrug-resistant Staphylococcus aureus-infected local radiation injuries caused by exposure to Sr90[J].Clin Exp Dermatol,2005,30(1):23-26.DOI: 10.1111/j.1365-2230.2004.01600.x.
    [63]
    LuongT, SalabarriaAC, RoachDR.Phage therapy in the resistance era: where do we stand and where are we going?[J].Clin Ther,2020, 42(9):1659-1680. DOI: 10.1016/j.clinthera.2020.07.014.
    • Relative Articles
    • Supplements(0)
    • Cited By
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Figures(6)  / Tables(1)

    Get Citation
    PDF
    XML

    Article Metrics

    Article views (842) PDF downloads(44) Cited by()
    Proportional views
    Related

    Copyright © Chinese Journal of Burns京ICP备07035254号-14

    E-mail：shaoshangzazhi@163.com

    Website：https://zhsszz.xml-journal.net/

    Supported by: Beijing Renhe Information Technology Co. Ltd    

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return