林麝源屎肠球菌LS170308株多重耐药基因岛PRI1分析
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摘要
屎肠球菌作为条件致病菌在临床上报道的越来越多,主要引起宿主心内膜炎、败血症等,目前关于屎肠球菌的耐药性研究已日益突出,其原因主要在于该菌对β-内酰胺类药物天然耐药及对万古霉素等糖肽类抗生素耐药性不断增强,但该菌耐药性传播机制仍在进一步研究中。本研究拟描述1株林麝源屎肠球菌多重耐药基因岛的特征,显示出该基因岛在不同属细菌中的传播。采用单分子测序技术对这株林麝心源屎肠球菌进行从头测序,同时采用分子生物学工具对该基因岛进行分析。结果显示:这株屎肠球菌染色体上携带多个耐药基因,其中携带ANT(9)、ErmA的Tn554转座酶和携带AAC(6′)-le-APH(2″)-la的一对插入元件IS256共同构成的一个多重耐药基因岛来自金黄色葡萄球菌,该基因岛对大环内酯类、林可酰胺类及氨基糖苷类抗生素具有抗性。结果表明从死亡林麝内脏组织中分离得到1株屎肠球菌,该菌株携带有一个多重耐药基因组岛PRI1,该类型基因岛目前在屎肠球菌中并未有相关报道,同时这株菌来自野生动物,可为野生动物源细菌耐药性传播提供数据支持。
Enterococcus faecium has been reported as a conditional pathogen in clinical practice, mainly causing endocarditis and sepsis in the host. At present, the research on drug resistance of E. faecium has become increasingly prominent, mainly because the bacteria are natural resistant to β-lactam and its resistant ability to glycopeptide antibiotics(such as vancomycin) are increasing, but the drug resistance transmission mechanism of this strain is still under study. The purpose of this study was to describe the characteristics of a multidrug resistance genomic island from E. faecium. Highlight the spread of the genomic island in different genera of bacteria. At the same time, it provides data that support for the spread of bacterial resistance in wild animals. Single-molecule sequencing technology(de nove) was used in this E. faecium, and the genomic island was analyzed using all kinds of molecular biology tools. Results were as follows: This strain of E. faecium carries multiple resistance genes on its chromosome; The Tn554 transposase carrying ANT(9) and ErmA and the pair of intercalating elements IS256 carrying AAC(6′)-le-APH(2″)-la together constitute a multidrug resistance genomic island from Staphylococcus aureus. The genomic island is resistant to macrolides, lincosamides and aminoglycoside antibiotics. In conclusion, a strain of E. faecium was isolated from the visceral tissue of dead forest carp, which carries a multi-drug resistant genomic island PRI1. This genomic island is currently not reported in E. faecium. At the same time, this strain is derived from wild animals, so the resistance of wild animals has become more and more serious.
Enterococcus faecium has been reported as a conditional pathogen in clinical practice, mainly causing endocarditis and sepsis in the host. At present, the research on drug resistance of E. faecium has become increasingly prominent, mainly because the bacteria are natural resistant to β-lactam and its resistant ability to glycopeptide antibiotics(such as vancomycin) are increasing, but the drug resistance transmission mechanism of this strain is still under study. The purpose of this study was to describe the characteristics of a multidrug resistance genomic island from E. faecium. Highlight the spread of the genomic island in different genera of bacteria. At the same time, it provides data that support for the spread of bacterial resistance in wild animals. Single-molecule sequencing technology(de nove) was used in this E. faecium, and the genomic island was analyzed using all kinds of molecular biology tools. Results were as follows: This strain of E. faecium carries multiple resistance genes on its chromosome; The Tn554 transposase carrying ANT(9) and ErmA and the pair of intercalating elements IS256 carrying AAC(6′)-le-APH(2″)-la together constitute a multidrug resistance genomic island from Staphylococcus aureus. The genomic island is resistant to macrolides, lincosamides and aminoglycoside antibiotics. In conclusion, a strain of E. faecium was isolated from the visceral tissue of dead forest carp, which carries a multi-drug resistant genomic island PRI1. This genomic island is currently not reported in E. faecium. At the same time, this strain is derived from wild animals, so the resistance of wild animals has become more and more serious.
引文
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[15] 周纯葆.基因岛预测与隔离迁移模型并行化[D].长春:吉林大学,2012.ZHOU C B.Detection of genomic islands and parallelization of isolation with migration model[D].Changchun:Jilin University,2012.(in Chinese)
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[17] ORIESKOVA M,KAJSIK M,SZEMES T,et al.Contribution of the thermotolerance genomic island to increased thermal tolerance in Cronobacter strains[J].Antonie van Leeuwenhoek,2016,109(3):405-414.
[18] BERTELLI C,LAIRD M R,WILLIAMS K P,et al.IslandViewer 4:expanded prediction of genomic islands for larger-scale datasets[J].Nucleic Acids Res,2017,45(W1):W30-W35.
[19] HUANG L,YUAN H,LIU M F,et al.Type B chloramphenicol acetyltransferases are responsible for chloramphenicol resistance in Riemerella anatipestifer,China[J].Front Microbiol,2017,8:297.
[20] MONTEALEGRE M C,ROH J H,RAE M,et al.Differential penicillin-binding protein 5 (PBP5) levels in the Enterococcus faecium clades with different levels of ampicillin resistance[J].Antimicrob Agents Chemother,2017,61(1):e02034-16.
[21] 李聪然,游雪甫,蒋建东.氨基糖苷类双功能修饰酶AAC(6′)-APH(2″)的研究进展[J].中国感染与化疗杂志,2007,7(6):468-471.LI C R,YOU X F,JIANG J D.Research update of aminoglycoside bifunctional modifying enzyme AAC(6′)-APH(2″)[J].Chinese Journal of Infection and Chemotherapy,2007,7(6):468-471.(in Chinese)
[22] DE FREITAS A D A R,FARIA A R,DE CASTRO ABREU PINTO T,et al.Distribution of species and antimicrobial resistance among enterococci isolated from the fecal microbiota of captive blue-fronted parrot (Amazona aestiva) in Rio de Janeiro,Brazil[J].Sci Total Environ,2018,615:1428-1437.
[23] MURPHY E.Nucleotide sequence of ermA,a macrolide-lincosamide-streptogramin B determinant in Staphylococcus aureus[J].J Bacteriol,1985,162(2):633-640.
[24] BASTOS M C,MURPHY E.Transposon Tn554 encodes three products required for transposition[J].EMBO J,1988,7(9):2935-2941.
[25] MURPHY E,HUWYLER L,DE FREIRE BASTOS M D C.Transposon Tn554:complete nucleotide sequence and isolation of transposition-defective and antibiotic-sensitive mutants[J].EMBO J,1985,4(12):3357-3365.
[26] SCHREIBER F,SZEKAT C,JOSTEN M,et al.Antibiotic-induced autoactivation of IS256 in Staphylococcus aureus[J].Antimicrob Agents Chemother,2013,57(12):6381-6384.
[27] PRUDHOMME M,TURLAN C,CLAVERYS J P,et al.Diversity of Tn4001 transposition products:the flanking IS256 elements can form tandem dimers and IS circles[J].J Bacteriol,2002,184(2):433-443.
[28] MURUGESAN S,MANI S,KUPPUSAMY I,et al.Role of insertion sequence element is256 as a virulence marker and its association with biofilm formation among methicillin-resistant Staphylococcus epidermidis from hospital and community settings in Chennai,South India[J].Indian J Med Microbiol,2018,36(1):124-126.
[2] CATTOIR V,GIARD J C.Antibiotic resistance in Enterococcus faecium clinical isolates[J].Expert Rev Anti-infect Ther,2014,12(2):239-248.
[3] MELEGH S,NYUL A,KOV?CS K,et al.Dissemination of VanA-type Enterococcus faecium isolates in hungary[J].Microb Drug Resist,2018,24(9):1376-1390.
[4] GUZEK A,RYBICKI Z,TOMASZEWSKI D.Changes in bacterial flora and antibiotic resistance in clinical samples isolated from patients hospitalized in the Military Institute of Medicine in Warsaw,Poland,between 2005 and 2012[J].Przegl Epidemiol,2017,71(2):165-176.
[5] COTTON M J,PACKER C D.Vancomycin-resistant Enterococcus faecium empyema in an asplenic patient[J].Cureus,2018,10(8):e3227.
[6] 方志华,余素飞.2011—2013临床分离屎肠球菌和粪肠球菌耐药情况[J].现代预防医学,2015,42(4):766-768.FANG Z H,YU S F.Drug resistance of Enterococcus faecium and Enterococcus faecalis clinically isolated between 2011 and 2013[J].Modern Preventive Medicine,2015,42(4):766-768.(in Chinese)
[7] SARROU S,MALLI E,TSILIPOUNIDAKI K,et al.MLSB-resistant Staphylococcus aureus in central greece:rate of resistance and molecular characterization[J].Microb Drug Resist,2018,doi:10.1089/mdr.2018.0259.
[8] AJANTHA G S,KULKARNI R D,SHETTY J,et al.Phenotypic detection of inducible clindamycin resistance among Staphylococcus aureus isolates by using the lower limit of recommended inter-disk distance[J].Indian J Pathol Microbiol,2008,51(3):376-378.
[9] ZEHRA A,GULZAR M,SINGH R,et al.Prevalence,multidrug resistance and molecular typing of methicillin-resistant Staphylococcus aureus (MRSA) in retail meat from punjab,India[J].J Glob Antimicrob Resist,2019,16:152-158.
[10] KHASHEI R,MALEKZADEGAN Y,SEDIGH EBRAHIM-SARAIE H,et al.Phenotypic and genotypic characterization of macrolide,lincosamide and streptogramin B resistance among clinical isolates of staphylococci in southwest of Iran[J].BMC Res Notes,2018,11:711.
[11] SZEMRAJ M,KWASZEWSKA A,SZEWCZYK E M.New gene responsible for resistance of clinical corynebacteria to macrolide,lincosamide and streptogramin B[J].Pol J Microbiol,2018,67(2):237-240.
[12] TOKA ?ZER T.The rate of inducible MLSB resistance in the methicillin-resistant staphylococci isolated from clinical samples[J].J Clin Lab Anal,2016,30(5):490-493.
[13] CAI J,SCHWARZ S,CHI D,et al.Faecal carriage of optrA-positive enterococci in asymptomatic healthy humans in Hangzhou,China[J].Clin Microbiol Infect,2018,doi:10.1016/j.cmi.2018.07.025.
[14] ISOGAI N,URUSHIBARA N,KAWAGUCHIYA M,et al.Characterization of Enterococcus faecium with macrolide resistance and reduced susceptibility to quinupristin/dalfopristin in a Japanese hospital:detection of extensive diversity in erm(B)-regulator regions[J].Microb Drug Resist,2013,19(4):298-307.
[15] 周纯葆.基因岛预测与隔离迁移模型并行化[D].长春:吉林大学,2012.ZHOU C B.Detection of genomic islands and parallelization of isolation with migration model[D].Changchun:Jilin University,2012.(in Chinese)
[16] SOLIMAN A M,SHIMAMOTO T,NARIYA H,et al.Emergence of Salmonella genomic island 1 variant SGI1-W in a clinical isolate of Providencia stuartii from Egypt[J].Antimicrob Agents Chemother,2019,63(1),doi:10.1128/AAC.01793-18.
[17] ORIESKOVA M,KAJSIK M,SZEMES T,et al.Contribution of the thermotolerance genomic island to increased thermal tolerance in Cronobacter strains[J].Antonie van Leeuwenhoek,2016,109(3):405-414.
[18] BERTELLI C,LAIRD M R,WILLIAMS K P,et al.IslandViewer 4:expanded prediction of genomic islands for larger-scale datasets[J].Nucleic Acids Res,2017,45(W1):W30-W35.
[19] HUANG L,YUAN H,LIU M F,et al.Type B chloramphenicol acetyltransferases are responsible for chloramphenicol resistance in Riemerella anatipestifer,China[J].Front Microbiol,2017,8:297.
[20] MONTEALEGRE M C,ROH J H,RAE M,et al.Differential penicillin-binding protein 5 (PBP5) levels in the Enterococcus faecium clades with different levels of ampicillin resistance[J].Antimicrob Agents Chemother,2017,61(1):e02034-16.
[21] 李聪然,游雪甫,蒋建东.氨基糖苷类双功能修饰酶AAC(6′)-APH(2″)的研究进展[J].中国感染与化疗杂志,2007,7(6):468-471.LI C R,YOU X F,JIANG J D.Research update of aminoglycoside bifunctional modifying enzyme AAC(6′)-APH(2″)[J].Chinese Journal of Infection and Chemotherapy,2007,7(6):468-471.(in Chinese)
[22] DE FREITAS A D A R,FARIA A R,DE CASTRO ABREU PINTO T,et al.Distribution of species and antimicrobial resistance among enterococci isolated from the fecal microbiota of captive blue-fronted parrot (Amazona aestiva) in Rio de Janeiro,Brazil[J].Sci Total Environ,2018,615:1428-1437.
[23] MURPHY E.Nucleotide sequence of ermA,a macrolide-lincosamide-streptogramin B determinant in Staphylococcus aureus[J].J Bacteriol,1985,162(2):633-640.
[24] BASTOS M C,MURPHY E.Transposon Tn554 encodes three products required for transposition[J].EMBO J,1988,7(9):2935-2941.
[25] MURPHY E,HUWYLER L,DE FREIRE BASTOS M D C.Transposon Tn554:complete nucleotide sequence and isolation of transposition-defective and antibiotic-sensitive mutants[J].EMBO J,1985,4(12):3357-3365.
[26] SCHREIBER F,SZEKAT C,JOSTEN M,et al.Antibiotic-induced autoactivation of IS256 in Staphylococcus aureus[J].Antimicrob Agents Chemother,2013,57(12):6381-6384.
[27] PRUDHOMME M,TURLAN C,CLAVERYS J P,et al.Diversity of Tn4001 transposition products:the flanking IS256 elements can form tandem dimers and IS circles[J].J Bacteriol,2002,184(2):433-443.
[28] MURUGESAN S,MANI S,KUPPUSAMY I,et al.Role of insertion sequence element is256 as a virulence marker and its association with biofilm formation among methicillin-resistant Staphylococcus epidermidis from hospital and community settings in Chennai,South India[J].Indian J Med Microbiol,2018,36(1):124-126.