Complete genome sequence of a serotype 11A, ST62 Streptococcus pneumoniae invasive isolate

BMC Microbiology

Volumn 11, Issue , 2011, Pages

  Camilli, Romina ^a   Bonnal, Raoul J P ^b   Del Grosso, Maria ^a   Iacono, Michele ^b   Corti, Giorgio ^b   Rizzi, Ermanno ^b   Marchetti, Magda ^a   Mulas, Laura ^c   Iannelli, Francesco ^c   Superti, Fabiana ^a   Oggioni, Marco R ^c   De Bellis, Gianluca ^b   Pantosti, Annalisa ^a  

^a ISTITUTO SUPERIORE DI SANITÀ   (Italy)

^b INSTITUTE OF BIOMEDICAL TECHNOLOGIES   (Italy)

^c UNIVERSITY OF SIENA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ERYTHROMYCIN; RIBOSOME RNA; TRANSFER RNA; BACTERIAL DNA;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIOPHAGE; BACTERIUM ISOLATE; BACTERIUM PILUS; BASE PAIRING; CHROMOSOME REARRANGEMENT; CHROMOSOME REPLICATION; CLOSTRIDIUM DIFFICILE; COMPARATIVE STUDY; CONTROLLED STUDY; DNA REPLICATION ORIGIN; DNA SEQUENCE; GENE LOCUS; GENETIC CODE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOME SIZE; HORIZONTAL GENE TRANSFER; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PROPHAGE; SEROTYPE; STREPTOCOCCUS PNEUMONIAE; STREPTOCOCCUS PYOGENES; BACTERIAL CHROMOSOME; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; TRANSPOSON;

ANAEROCOCCUS PREVOTII; BACTERIA (MICROORGANISMS); CLOSTRIDIUM DIFFICILE; FINEGOLDIA MAGNA; SIPHOVIRIDAE; STREPTOCOCCUS PNEUMONIAE; STREPTOCOCCUS PYOGENES;

CHROMOSOMES, BACTERIAL; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; GENOME, BACTERIAL; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; PROPHAGES; SEQUENCE ANALYSIS, DNA; STREPTOCOCCUS PNEUMONIAE;

EID: 79351470168     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-11-25     Document Type: Article

References (70)

1. The pneumococcal problem. SK Obaro MA Monteil DC Henderson, Br Med J 1996 312 7045 1521 1525 (Pubitemid 26177158)
2. Streptococcus pneumoniae colonisation: the key to pneumococcal disease. D Bogaert R De Groot PW Hermans, Lancet Infect Dis 2004 4 3 144 154 10.1016/S1473-3099(04)00938-7 14998500 (Pubitemid 38293138)
3. The role of Streptococcus pneumoniae virulence factors in host respiratory colonization and disease. A Kadioglu JN Weiser JC Paton PW Andrew, Nat Rev Microbiol 2008 6 4 288 301 10.1038/nrmicro1871 18340341 (Pubitemid 351404773)
4. The immune response to pneumococcal proteins during experimental human carriage. TL McCool TR Cate G Moy JN Weiser, J Exp Med 2002 195 3 359 365 10.1084/jem.20011576 11828011 (Pubitemid 34461494)
5. New faces of an old pathogen: emergence and spread of multidrug-resistant Streptococcus pneumoniae. A Tomasz, Am J Med 1999 107 1A 55S 62S 10.1016/S0002-9343(99)00107-2 10451010 (Pubitemid 29372762)
6. Regional trends in beta-lactam, macrolide, fluoroquinolone and telithromycin resistance among Streptococcus pneumoniae isolates 2001-2004. D Felmingham R Canton SG Jenkins, J Infect 2007 55 2 111 118 10.1016/j.jinf.2007. 04.006 17568680 (Pubitemid 47033820)
7. Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes. SD Bentley DM Aanensen A Mavroidi D Saunders E Rabbinowitsch M Collins K Danohoe D Harris L Murphy PR Reeves, et al. PLoS Genet 2006 2 31 10.1371/journal.pgen.0020031 16532061
8. Discovery of a new capsular serotype (6C) within serogroup 6 of Streptococcus pneumoniae. IH Park DG Pritchard R Cartee A Brandao MC Brandileone MH Nahm, J Clin Microbiol 2007 45 4 1225 1233 10.1128/JCM.02199-06 17267625 (Pubitemid 46626489)
9. First report of putative Streptococcus pneumoniae serotype 6D among nasopharyngeal isolates from Fijian children. P Jin F Kong M Xiao S Oftadeh F Zhou C Liu F Russell GL Gilbert, J Infect Dis 2009 200 9 1375 1380 10.1086/606118 19803727
10. A new pneumococcal serotype, 11E, has a variably inactivated wcjE gene. JJ Calix MH Nahm, J Infect Dis 2010 202 1 29 38 10.1086/653123 20507232
11. Post-PCV7 changes in colonizing pneumococcal serotypes in 16 Massachusetts communities, 2001 and 2004. SS Huang R Platt SL Rifas-Shiman SI Pelton D Goldmann JA Finkelstein, Pediatrics 2005 116 3 408 413 10.1542/peds.2004-2338 16140686
12. Decline in invasive pneumococcal disease after the introduction of protein-polysaccharide conjugate vaccine. CG Whitney MM Farley J Hadler LH Harrison NM Bennett R Lynfield A Reingold PR Cieslak T Pilishvili D Jackson, et al. N Engl J Med 2003 348 18 1737 1746 10.1056/NEJMoa022823 12724479 (Pubitemid 36514704)
13. Incidence of pneumococcal disease due to non-pneumococcal conjugate vaccine (PCV7) serotypes in the United States during the era of widespread PCV7 vaccination, 1998-2004. LA Hicks LH Harrison B Flannery JL Hadler W Schaffner AS Craig D Jackson A Thomas B Beall R Lynfield, et al. J Infect Dis 2007 196 9 1346 1354 10.1086/521626 17922399 (Pubitemid 351412007)
14. Postvaccine genetic structure of Streptococcus pneumoniae serotype 19A from children in the United States. R Pai MR Moore T Pilishvili RE Gertz CG Whitney B Beall, J Infect Dis 2005 192 11 1988 1995 10.1086/498043 16267772 (Pubitemid 41681898)
15. Increased penicillin nonsusceptibility of nonvaccine-serotype invasive pneumococci other than serotypes 19A and 6A in post-7-valent conjugate vaccine era. RE Gertz Jr Z Li FC Pimenta D Jackson BA Juni R Lynfield JH Jorgensen G Carvalho Mda BW Beall, J Infect Dis 2010 201 5 770 775 20178139
16. Effects of routine infant vaccination with the 7-valent pneumococcal conjugate vaccine on nasopharyngeal colonization with Streptococcus pneumoniae in children in Calgary, Canada. JD Kellner D Scheifele OG Vanderkooi J Macdonald DL Church GJ Tyrrell, Pediatr Infect Dis J 2008 27 6 526 532 10.1097/INF.0b013e3181658c5c 18458650
17. Continued impact of pneumococcal conjugate vaccine on carriage in young children. SS Huang VL Hinrichsen AE Stevenson SL Rifas-Shiman K Kleinman SI Pelton M Lipsitch WP Hanage GM Lee JA Finkelstein, Pediatrics 2009 124 1 1 11 10.1542/peds.2008-3099 19564254
18. Changing epidemiology of antimicrobial-resistant Streptococcus pneumoniae in the United States, 2004-2005. SS Richter KP Heilmann CL Dohrn F Riahi SE Beekmann GV Doern, Clin Infect Dis 2009 48 3 23 33 10.1086/595857 19115971
19. Clonal relationships between invasive and carriage Streptococcus pneumoniae and serotype- and clone-specific differences in invasive disease potential. AB Brueggemann DT Griffiths E Meats T Peto DW Crook BG Spratt, J Infect Dis 2003 187 9 1424 1432 10.1086/374624 12717624 (Pubitemid 36549688)
20. Clonal and capsular types decide whether pneumococci will act as a primary or opportunistic pathogen. K Sjostrom C Spindler A Ortqvist M Kalin A Sandgren S Kuhlmann-Berenzon B Henriques-Normark, Clin Infect Dis 2006 42 4 451 459 10.1086/499242 16421787 (Pubitemid 43202515)
21. Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. NL Hiller B Janto JS Hogg R Boissy S Yu E Powell R Keefe NE Ehrlich K Shen J Hayes, et al. J Bacteriol 2007 189 22 8186 8195 10.1128/JB.00690-07 17675389 (Pubitemid 350178930)
22. New genetic element carrying the erythromycin resistance determinant erm(TR) in Streptococcus pneumoniae. R Camilli M Del Grosso F Iannelli A Pantosti, Antimicrob Agents Chemother 2008 52 2 619 625 10.1128/AAC.01081-07 18070957 (Pubitemid 351170836)
23. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. H Tettelin KE Nelson IT Paulsen JA Eisen TD Read S Peterson J Heidelberg RT DeBoy DH Haft RJ Dodson, et al. Science 2001 20 293 498 506 10.1126/science.1061217 (Pubitemid 32679078)
24. A second pilus type in Streptococcus pneumoniae is prevalent in emerging serotypes and mediates adhesion to host cells. F Bagnoli M Moschioni C Donati V Dimitrovska I Ferlenghi C Facciotti A Muzzi F Giusti C Emolo A Sinisi, et al. J Bacteriol 2008 190 15 5480 5492 10.1128/JB.00384-08 18515415
25. Mosaic genes and mosaic chromosomes-genomic variation in Streptococcus pneumoniae. R Brückner M Nuhn P Reichmann B Weber R Hakenbeck, Int J Med Microbiol 2004 294 2-3 157 168 15493826 (Pubitemid 39281046)
26. Comparative genomics of Streptococcus pneumoniae: intra-strain diversity and genome plasticity. H Tettelin SK Hollingshead, Washington, DC, USA: ASM Press 2004
27. Identification and characterization of a novel family of pneumococcal proteins that are protective against sepsis. JE Adamou JH Heinrichs AL Erwin W Walsh T Gayle M Dormitzer R Dagan YA Brewah P Barren R Lathigra, et al. Infect Immun 2001 69 2 949 958 10.1128/IAI.69.2.949-958.2001 11159990 (Pubitemid 32109561)
28. Genome evolution driven by host adaptations results in a more virulent and antimicrobial-resistant Streptococcus pneumoniae serotype 14. F Ding P Tang MH Hsu P Cui S Hu J Yu CH Chiu, BMC Genomics 2009 10 158 19361343
29. Genome of the bacterium Streptococcus pneumoniae strain R6. J Hoskins WEJ Alborn J Arnold LC Blaszczak S Burgett BS DeHoff ST Estrem L Fritz DJ Fu W Fuller, et al. J Bacteriol 2001 183 19 5709 5717 10.1128/JB.183.19.5709-5717. 2001 11544234 (Pubitemid 32898618)
30. Streptococcus pneumoniae: virulence factors and variation. AM Mitchell TJ Mitchell, Clin Microbiol Infect Dis 2010 16 5 411 418 10.1111/j.1469-0691.2010. 03183.x
31. Validation of serotyping of Streptococcus pneumoniae in Europe. HB Konradsen, Vaccine 2005 23 11 1368 1373 10.1016/j.vaccine.2004.09.011 15661385 (Pubitemid 40127329)
32. Elucidation and comparison of the chemical structures of the specific capsular polysaccharides of Streptococcus pneumoniae groups 11 (11F, 11B, 11C, and 11A). JC Richards MB Perry M Moreau, Adv Exp Med Biol 1988 228 595 596
33. Pneumococcal diversity: considerations for new vaccine strategies with emphasis on pneumococcal surface protein A (PspA). DE Briles RC Tart E Swiatlo JP Dillard P Smith KA Benton BA Ralph A Brooks-Walter MJ Crain SK Hollingshead, et al. Clin Microbiol Rev 1998 11 4 645 657 9767061 (Pubitemid 28497567)
34. Contribution of novel choline-binding proteins to adherence, colonization and immunogenicity of Streptococcus pneumoniae. C Rosenow P Ryan JN Weiser S Johnson P Fontan A Ortqvist HR Masure, Mol Microbiol 1997 25 5 819 829 10.1111/j.1365-2958.1997.mmi494.x 9364908 (Pubitemid 27397511)
35. Diversity of PspA: mosaic genes and evidence for past recombination in Streptococcus pneumoniae. SK Hollingshead R Becker DE Briles, Infect Immun 2000 68 10 5889 5900 10.1128/IAI.68.10.5889-5900.2000 10992499
36. Allelic variation in the highly polymorphic locus pspC of Streptococcus pneumoniae. F Iannelli MR Oggioni G Pozzi, Gene 2002 284 1-2 63 71 10.1016/S0378-1119(01)00896-4 11891047 (Pubitemid 34219401)
37. A pneumococcal pilus influences virulence and host inflammatory responses. MA Barocchi J Ries X Zogaj C Hemsley B Albiger A Kanth S Dahlberg J Fernebro M Moschioni V Masignani, et al. Proc Natl Acad Sci USA 2006 103 8 2857 2862 10.1073/pnas.0511017103 16481624
38. Increase in pilus islet 2-encoded pili among Streptococcus pneumoniae isolates, Atlanta, Georgia, USA. D Zahner A Gudlavalleti DS Stephens, Emerg Infect Dis 2010 16 6 955 962 20507746
39. Characterization of the Streptococcus pneumoniae immunoglobulin A1 protease gene (iga) and its translation product. K Poulsen J Reinholdt M Kilian, Infect Immun 1996 64 10 3957 3966 8926055 (Pubitemid 26318109)
40. Pneumococcal zinc metalloproteinase ZmpC cleaves human matrix metalloproteinase 9 and is a virulence factor in experimental pneumonia. MR Oggioni G Memmi T Maggi D Chiavolini F Iannelli G Pozzi, Mol Microbiol 2003 49 3 795 805 10.1046/j.1365-2958.2003.03596.x 12864860 (Pubitemid 36918697)
41. Zinc metalloproteinase genes in clinical isolates of Streptococcus pneumoniae: association of the full array with a clonal cluster comprising serotypes 8 and 11A. R Camilli E Pettini M Del Grosso G Pozzi A Pantosti MR Oggioni, Microbiology 2006 152 2 313 321 10.1099/mic.0.28417-0 16436419 (Pubitemid 43210662)
42. The three extra-cellular zinc metalloproteinases of Streptococcus pneumoniae have a different impact on virulence in mice. D Chiavolini G Memmi T Maggi F Iannelli G Pozzi, BMC Microbiology 2003 3 14 10.1186/1471-2180-3-14 12841855
43. Genomewide screening for novel genetic variations associated with ciprofloxacin resistance in Bacillus anthracis. M Serizawa T Sekizuka A Okutani S Banno T Sata S Inoue M Kuroda, Antimicrob Agents Chemother 54 7 2787 2792 10.1128/AAC.01405-09 20385868
44. The TetR family of transcriptional repressors. JL Ramos M Martinez-Bueno AJ Molina-Henares W Teran K Watanabe X Zhang MT Gallegos R Brennan R Tobes, Microbiol Mol Biol Rev 2005 69 2 326 356 10.1128/MMBR.69.2.326-356.2005 15944459 (Pubitemid 40847943)
45. Contribution of exogenous genetic elements to the Group A Streptococcus metagenome. SB Beres JM Musser, PLoS One 2007 2 8 800 10.1371/journal.pone. 0000800 17726530
46. Conjugative transposons: the tip of the iceberg. V Burrus G Pavlovic B Decaris G Guédon, Mol Microbiol 2002 46 3 601 610 10.1046/j.1365-2958. 2002.03191.x 12410819 (Pubitemid 35365597)
47. Genome sequence of a serotype M28 strain of group A Streptococcus: potential new insights into puerperal sepsis and bacterial disease specificity. NM Green S Zhang SF Porcella MJ Nagiec KD Barbian SB Beres RB Lefebvre JM Musser, J Infect Dis 2005 192 5 760 770 10.1086/430618 16088825 (Pubitemid 41193073)
48. Genetic elements responsible for erythromycin resistance in streptococci. PE Varaldo MP Montanari E Giovanetti, Antimicrob Agents Chemother 2009 53 2 343 353 10.1128/AAC.00781-08 19001115
49. Complete genome sequence of Finegoldia magna, an anaerobic opportunistic pathogen. G Takatsugu Y Atsushi H Hideki M Minenosuke T Kozo O Kenshiro T Hidehiro M Kazuaki K Satoru H Masahira, et al. DNA Research 2008 15 39 47 10.1093/dnares/dsm030 18263572
50. Similarly organized lysogeny modules in temperate Siphoviridae from low GC content Gram-positive bacteria. S Lucchini F Desiere H Brussow, Virology 1999 263 2 427 435 10.1006/viro.1999.9959 10544115 (Pubitemid 29521534)
51. Proteins PblA and PblB of Streptococcus mitis, which promote binding to human platelets, are encoded within a lysogenic bacteriophage. BA Bensing IR Siboo PM Sullam, Infect Immun 2001 69 10 6186 6192 10.1128/IAI.69.10.6186-6192. 2001 11553559 (Pubitemid 32885181)
52. Mechanism of cell surface expression of the Streptococcus mitis platelet binding proteins PblA and PblB. J Mitchell IR Siboo D Takamatsu HF Chambers PM Sullam, Mol Microbiol 2007 64 3 844 857 10.1111/j.1365-2958.2007.05703.x 17462028 (Pubitemid 46653223)
53. Comparative genomic analysis of ten Streptococcus pneumoniae temperate bacteriphages. P Romero NJ Croucher NL Hiller FZ Hu GD Ehrlich SD Bentley E Garcia TJ Mitchell, J Bacteriol 2009 191 15 4854 4862 10.1128/JB.01272-08 19502408
54. Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. H Tettelin V Masignani MJ Cieslewicz JA Eisen S Peterson MR Wessels IT Paulsen KE Nelson I Margarit TD Read, et al. Proc Natl Acad Sci USA 2002 99 19 12391 12396 10.1073/pnas. 182380799 12200547
55. Genome organization and molecular analysis of the temperate bacteriophages MM1 of Streptococcus pneumoniae. V Obregon JL Garcia E Garcia R Lopez P Garcia, J Bacteriol 2003 185 7 2362 2368 10.1128/JB.185.7.2362-2368.2003 12644508 (Pubitemid 36363198)
56. Genomic organization and molecular characterization of SM1, a temperate bacteriophage of Streptococcus mitis. IR Siboo BA Bensing PM Sullam, J Bacteriol 2003 185 23 6968 6975 10.1128/JB.185.23.6968-6975.2003 14617660 (Pubitemid 37444497)
57. Development of a Prophage Typing System and Analysis of Prophage Carriage in Streptococcus pneumoniae. P Romero E Garcia TJ Mitchell, Appl Environ Microbiol 2009 75 6 1642 1649 10.1128/AEM.02155-08 19168661
58. Molecular characterization of lactococcal bacteriophage Tuc2009 and identification and analysis of genes encoding lysin, a putative holin, and two structural proteins. EK Arendt GF Fitzgerald M van de Guchte, Appl Environ Microbiol 1994 60 6 1875 1883 8031083 (Pubitemid 24165832)
59. Construction of new unencapsulated (rough) strains of Streptococcus pneumoniae. BJ Pearce F Iannelli G Pozzi, Res Microbiol 2002 153 4 243 247 10.1016/S0923-2508(02)01312-8 12066896 (Pubitemid 34327898)
60. Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer. R Bordoni R Bonnal E Rizzi P Carrera S Benedetti L Cremonesi S Stenirri A Colombo C Montrasio S Bonalumi, et al. BMC Genomics 2008 9 464 10.1186/1471-2164-9-464 18842124
61. Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group. M Iacono L Villa D Fortini R Bordoni F Imperi RJP Bonnal T Sicheritz-Ponten G De Bellis P Visca A Cassone, et al. Antimicrob Agents Chemother 2008 52 7 2616 2625 10.1128/AAC.01643-07 18411315 (Pubitemid 351915695)
62. Serotype specific invasive capacity and persistent reduction in invasive pneumococcal disease. I Yildirim WP Hanage M Lipsitch KM Shea A Stevenson J Finkelstein SS Huang GM Lee K Kleinman SI Pelton, Vaccine 2011 29 2 283 288 10.1016/j.vaccine.2010.10.032
63. Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution. I Nakagawa K Kurokawa A Yamashita M Nakata Y Tomiyasu N Okahashi S Kawabata K Yamazaki T Shiba T Yasunaga, et al. Genome Res 2003 13 6A 1042 1055 10.1101/gr.1096703 12799345 (Pubitemid 36764186)
64. Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content. F Maruyama M Kobata K Kurokawa K Nishida A Sakurai K Nakano R Nomura S Kawabata T Ooshima K Nakai, et al. BMC Genomics 2009 10 358 10.1186/1471-2164-10-358 19656368
65. The genome of Streptococcus mitis B6 - what is a commensal? D Denapaite R Bruckner M Nuhn P Reichmann B Henrich P Maurer Y Schahle P Selbmann W Zimmermann R Wambutt, et al. PLoS One 2010 5 2 9426 10.1371/journal.pone.0009426 20195536
66. Genome sequencing in microfabricated high-density picolitre reactors. M Margulies M Egholm WE Altman S Attiya JS Bader LA Bemben J Berka MS Braverman YJ Chen Z Chen, et al. Nature 2005 437 7057 376 380 16056220 (Pubitemid 41613494)
67. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. J Besemer M Borodovsky, Nucleic Acids Res 2005 33 Web Server 451 454 10.1093/nar/gki487 15980510
68. Improved microbial gene identification with GLIMMER. AL Delcher D Harmon S Kasif O White SL Salzberg, Nucleic Acids Res 1999 27 23 4636 4641 10.1093/nar/27.23.4636 10556321
69. Artemis: sequence visualization and annotation. K Rutherford J Parkhill J Crook T Horsnell P Rice MA Rajandream B Barrell, Bioinformatics 2000 16 10 944 945 10.1093/bioinformatics/16.10.944 11120685
70. Characterization of some pneumococcal bacteriophages. RD Porter WR Guild, J Virol 1976 19 2 659 667 8652