Comparative genomics study of multi-drug-resistance mechanisms in the antibiotic-resistant Streptococcus suis R61 strain

PLoS ONE

Volumn 6, Issue 9, 2011, Pages

  Hu, Pan ^a   Yang, Ming ^b,c   Zhang, Anding ^a   Wu, Jiayan ^b   Chen, Bo ^a   Hua, Yafeng ^a   Yu, Jun ^b   Chen, Huanchun ^a   Xiao, Jingfa ^b   Jin, Meilin ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b Chinese Academy of Sciences   (China)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMOXICILLIN; AMPICILLIN; ANTIBIOTIC AGENT; AZITHROMYCIN; CEFACLOR; CEFEPIME; CEFOTAXIME; CEFTRIAXONE; CEFUROXIME; CHLORAMPHENICOL; CLAVULANATE POTASSIUM; CLINDAMYCIN; ERYTHROMYCIN; GATIFLOXACIN; LEVOFLOXACIN; LIDAPRIM; MEROPENEM; PENICILLIN G; TETRACYCLINE; TRIMETHOPRIM; VANCOMYCIN; ANTIINFECTIVE AGENT;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENOME; COMPARATIVE GENOMIC ANALYSIS; CONTROLLED STUDY; GENE LOSS; GENE MUTATION; GENE SEQUENCE; GENE TRANSFER; GENETIC ANALYSIS; GENOMICS; MULTIDRUG RESISTANCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; PLASTICITY; STRAIN DIFFERENCE; STREPTOCOCCUS SUIS; SWINE; AMINO ACID SEQUENCE; ANIMAL; CHEMICAL STRUCTURE; CHINA; COMPARATIVE STUDY; GENETIC VARIABILITY; GENETICS; HUMAN; METABOLISM; MICROBIOLOGICAL EXAMINATION; MOLECULAR GENETICS; MUTATION; SEQUENCE HOMOLOGY;

STREPTOCOCCUS SUIS; SUIDAE;

AMINO ACID SEQUENCE; ANIMALS; ANTI-BACTERIAL AGENTS; CHINA; DRUG RESISTANCE, BACTERIAL; DRUG RESISTANCE, MULTIPLE; GENETIC VARIATION; GENOME, BACTERIAL; GENOMICS; HUMANS; MICROBIAL SENSITIVITY TESTS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PHYLOGENY; SEQUENCE HOMOLOGY, AMINO ACID; STREPTOCOCCUS SUIS; SWINE;

EID: 80053150577     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0024988     Document Type: Article

References (61)

1. Willenburg KS, Sentochnik DE, Zadoks RN, (2006) Human Streptococcus suis meningitis in the United States. N Engl J Med 354: 1325-1325.
2. Wangkaew S, Chaiwarith R, Tharavichitkul P, Supparatpinyo K, (2006) Streptococcus suis infection: a series of 41 cases from Chiang Mai University Hospital. J Infect 52: 455-460.
3. Tang J, Wang C, Feng Y, Yang W, Song H, et al. (2006) Streptococcal toxic shock syndrome caused by Streptococcus suis serotype 2. PLoS Med 3: e151.
4. Martel A, Baele M, Devriese LA, Goossens H, Wisselink HJ, et al. (2001) Prevalence and mechanism of resistance against macrolides and lincosamides in Streptococcus suis isolates. Vet Microbiol 83: 287-297.
5. Princivalli MS, Palmieri C, Magi G, Vignaroli C, Manzin A, et al. (2009) Genetic diversity of Streptococcus suis clinical isolates from pigs and humans in Italy (2003-2007). Euro Surveill 14: 15-21.
6. Zhang C, Ning Y, Zhang Z, Song L, Qiu H, et al. (2008) In vitro antimicrobial susceptibility of Streptococcus suis strains isolated from clinically healthy sows in China. Vet Microbiol 131: 386-392.
7. Cantin M, Harel J, Higgins R, Gottschalk M, (1992) Antimicrobial resistance patterns and plasmid profiles of Streptococcus suis isolates. J Vet Diagn Invest 4: 170-174.
8. Takamatsu D, Osaki M, Sekizaki T, (2003) Chloramphenicol resistance transposable element TnSs1 of Streptococcus suis, a transposon flanked by IS6-family elements. Plasmid 49: 143-151.
9. Wasteson Y, Hoie S, Roberts MC, (1994) Characterization of antibiotic resistance in Streptococcus suis. Vet Microbiol 41: 41-49.
10. Escudero JA, San Millan A, Catalan A, de la Campa AG, Rivero E, et al. (2007) First characterization of fluoroquinolone resistance in Streptococcus suis. Antimicrob Agents Chemother 51: 777-782.
11. Donadio S, Maffioli S, Monciardini P, Sosio M, Jabes D, (2010) Antibiotic discovery in the twenty-first century: current trends and future perspectives. The Journal of Antibiotics 63: 423-430.
12. Aarestrup FM, Rasmussen SR, Artursson K, Jensen NE, (1998) Trends in the resistance to antimicrobial agents of Streptococcus suis isolates from Denmark and Sweden. Vet Microbiol 63: 71-80.
13. Wisselink HJ, Veldman KT, Van den Eede C, Salmon SA, Mevius DJ, (2006) Quantitative susceptibility of Streptococcus suis strains isolated from diseased pigs in seven European countries to antimicrobial agents licensed in veterinary medicine. Vet Microbiol 113: 73-82.
14. Woodford N, Ellington MJ, (2007) The emergence of antibiotic resistance by mutation. Clin Microbiol Infect 13: 5-18.
15. Shendure J, Ji H, (2008) Next-generation DNA sequencing. Nat Biotechnol 26: 1135-1145.
16. Holden M, Hauser H, Sanders M, Ngo T, Cherevach I, et al. (2009) Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis. PLoS ONE 4: 29-45.
17. Ye C, Bai X, Zhang J, Jing H, Zheng H, et al. (2008) Spread of Streptococcus suis sequence type 7, China. Emerg Infect Dis 14: 787-791.
18. Mahillon J, Leonard C, Chandler M, (1999) IS elements as constituents of bacterial genomes. Research in microbiology 150: 675-687.
19. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12.
20. Liu B, Pop M, (2008) ARDB-antibiotic resistance genes database. Nucleic Acids Research 37: D443-D447.
21. Wilke M, Lovering A, Strynadka N, (2005) [beta]-Lactam antibiotic resistance: a current structural perspective. Current opinion in microbiology 8: 525-533.
22. Pernot L, Chesnel L, Le Gouellec A, Croize J, Vernet T, et al. (2004) A PBP2x from a clinical isolate of Streptococcus pneumoniae exhibits an alternative mechanism for reduction of susceptibility to beta-lactam antibiotics. J Biol Chem 279: 16463-16470.
23. Mouz N, Gordon E, Di Guilmi AM, Petit I, Petillot Y, et al. (1998) Identification of a structural determinant for resistance to beta-lactam antibiotics in Gram-positive bacteria. Proc Natl Acad Sci U S A 95: 13403-13406.
24. Gordon E, Mouz N, Duee E, Dideberg O, (2000) The crystal structure of the penicillin-binding protein 2x from Streptococcus pneumoniae and its acyl-enzyme form: implication in drug resistance1. Journal of Molecular Biology 299: 477-485.
25. Wang D, Zhang Y, Zhang Z, Zhu J, Yu J, (2010) KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics 8: 77-80.
26. Contreras-Martel C, Dahout-Gonzalez C, Martins A, Kotnik M, Dessen A, (2009) PBP Active Site Flexibility as the Key Mechanism for [beta]-Lactam Resistance in Pneumococci. Journal of Molecular Biology 387: 899-909.
27. Jones ME, Sahm DF, Martin N, Scheuring S, Heisig P, et al. (2000) Prevalence of gyrA, gyrB, parC, and parE mutations in clinical isolates of Streptococcus pneumoniae with decreased susceptibilities to different fluoroquinolones and originating from Worldwide Surveillance Studies during the 1997-1998 respiratory season. Antimicrob Agents Chemother 44: 462-466.
28. Davies TA, Evangelista A, Pfleger S, Bush K, Sahm DF, et al. (2002) Prevalence of single mutations in topoisomerase type II genes among levofloxacin-susceptible clinical strains of Streptococcus pneumoniae isolated in the United States in 1992 to 1996 and 1999 to 2000. Antimicrob Agents Chemother 46: 119-124.
29. Speer BS, Shoemaker NB, Salyers AA, (1992) Bacterial resistance to tetracycline: mechanisms, transfer, and clinical significance. Clin Microbiol Rev 5: 387-399.
30. Roberts MC, (1994) Epidemiology of tetracycline-resistance determinants. Trends Microbiol 2: 353-357.
31. Chopra I, Roberts M, (2001) Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiol Mol Biol Rev 65: 232-260.
32. Manzin A, Palmieri C, Serra C, Saddi B, Princivalli MS, et al. (2008) Streptococcus suis Meningitis without History of Animal Contact, Italy. Emerging Infectious Diseases 14: 1946-1948.
33. Roberts M, (2005) Update on acquired tetracycline resistance genes. FEMS microbiology letters 245: 195-203.
34. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, et al. (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39: D225-229.
35. Del Grosso M, Iannelli F, Messina C, Santagati M, Petrosillo N, et al. (2002) Macrolide efflux genes mef(A) and mef(E) are carried by different genetic elements in Streptococcus pneumoniae. J Clin Microbiol 40: 774-778.
36. Tait-Kamradt A, Clancy J, Cronan M, Dib-Hajj F, Wondrack L, et al. (1997) mefE is necessary for the erythromycin-resistant M phenotype in Streptococcus pneumoniae. Antimicrobial Agents and Chemotherapy 41: 2251-2255.
37. Hoa NT, Chieu TT, Nghia HD, Mai NT, Anh PH, et al. (2011) The antimicrobial resistance patterns and associated determinants in Streptococcus suis isolated from humans in southern Vietnam, 1997-2008. BMC Infect Dis 11: 6 doi:10.1186/1471-2334-1111-1186.
38. Bapteste E, Susko E, Leigh J, MacLeod D, Charlebois RL, et al. (2005) Do orthologous gene phylogenies really support tree-thinking? BMC Evolutionary Biology 5 doi:10.1186/1471-2148-1185-1133.
39. Mirkin BG, Fenner TI, Galperin MY, Koonin EV, (2003) Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol Biol 3 doi:10.1186/1471-2148-1183-1182.
40. Li H, Ruan J, Durbin R, (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
41. Ochman H, Lawrence JG, Groisman EA, (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304.
42. Pal C, Papp B, Lercher MJ, (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 37: 1372-1375.
43. Wirawan RE, Klesse NA, Jack RW, Tagg JR, (2006) Molecular and genetic characterization of a novel nisin variant produced by Streptococcus uberis. Appl Environ Microbiol 72: 1148-1156.
44. van Kraaij C, de Vos WM, Siezen RJ, Kuipers OP, (1999) Lantibiotics: biosynthesis, mode of action and applications. Nat Prod Rep 16: 575-587.
45. Aarestrup FM, (2005) Veterinary drug usage and antimicrobial resistance in bacteria of animal origin. Basic Clin Pharmacol Toxicol 96: 271-281.
46. Delcher A, Phillippy A, Carlton J, Salzberg S, (2002) Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Research 30: 2478.
47. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
48. Ewing B, Hillier L, Wendl MC, Green P, (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185.
49. Ewing B, Green P, (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
50. Gordon D, Abajian C, Green P, (1998) Consed: a graphical tool for sequence finishing. Genome Res 8: 195-202.
51. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL, (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27: 4636-4641.
52. Besemer J, Borodovsky M, (2005) GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33: W451-454.
53. Remm M, Storm CE, Sonnhammer EL, (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of Molecular Biology 314: 1041-1052.
54. O'Brien KP, Remm M, Sonnhammer EL, (2005) Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res 33: D476-480.
55. Alexeyenko A, Tamas I, Liu G, Sonnhammer EL, (2006) Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 22: e9-15.
56. Lowe TM, Eddy SR, (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
57. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, et al. (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35: 3100-3108.
58. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M, (2006) ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34: D32-36.
59. Huelsenbeck JP, Ronquist F, (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
60. Ronquist F, Huelsenbeck JP, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
61. Sali A, Blundell TL, (1993) Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology 234: 779-815.