Genomics of Streptococcus pneumoniae and Streptococcus mitis

Transcription

1 Genomics of Streptococcus pneumoniae and Streptococcus mitis Regine Hakenbeck Department of Microbiology and Nano+Bio Center University of Kaiserslautern

2

3 Meningitis patho-genomics Otitis Sinusitis Pneumonia Colonizer of the Nasopharynx antibiotic resistance Sepsis

4 90 capsular types rough (cps + ) The Transforming Principle colonies smooth ( cps)

5 Intra- and interspecies gene transfer mutation 'bottleneck' gene transfer spread of new clones

6 S. mitis? S. oralis?

7 Genetic Evidence of Gene Transfer of Virulence

8 The success of one major class of mosaic pbp2x genes S. pneumoniae resistant CZ 14 SP 6B Fi 6B F 6B TW 23F SA 19A SP 14 TW 19F USA 23F SP 23F F 9V SV18 SV10 M3 614 B6 B Uo S. mitis sensitive S. mitis resistant

9 Penicillin resistance is mediated by highly diverse mosaic genes Sm s Sp s GB 19 F 14 G 23F Fi 23F F 23F GB Sm s Hu Sm s Sp Sm r SA 19A SA 6A Hu 19A Hu 19A Hu 19A Hu 19A PNG 6

10 Mosaic Genes - Mosaic Chromosomes?

11 Genomes Streptococcus pneumoniae R Mb Streptococcus pneumoniae TIGR Mb Pathogens Commensals Streptococcus mitis B Mb

12 Gene transfer commensal S. mitis gene pool commensal S. oralis virulence factors Streptococcus pneumoniae pathogen antibiotic resistance determinants

13 Comparative Genomic Analysis clones 2 2 sensitive 23F SP (SA) 1985 (19F) resistant S. pneumoniae 6B strains S. mitis GB G SA SP HU species HU HU S. oralis HU HU

14 Genomic Comparison of Streptococcus pneumoniae Hu15 Hu9 Hu ATCC F D219 Fi2306 D39 R6 Fi2303R SA B232C2 * * % difference between clones mobile elements * 2000 genes 12 within clones * * % different genes Hakenbeck et al Infect Immun.69:

15 TIGR specific clusters versus R6 zmpc efflux 157 kb 1 2 cps ABC 3 (SSA) LPXTG c b a 4 5 LPXTG bacteriocin PTS rm/xerc2 V-type ATPase; nanc xerc4 ABC Brückner et al. (2004) IJMM 294:

16 Comparison of 20 S. pneumoniae strains (TIGR array) R6 clusters vs TIGR 69 kb R6 TIGR TIGR clusters vs R6 157 kb TIGR clusters vs alle anderen 90 kb 316 kb "floating material" in 20 S. pneumoniae pili bacteriocins cell surface proteins V-ATPase antibiotic resistance transporter 16 (partial) genomes: kb core genome (Hiller et. al., J. Bacteriol.)

17 B5 M3B6 Hu-o8 NTCC10712 Hu11 SA D39 Hu-o2 Hu-o12 Hu-o5 Hu-o16 % difference pneumoniae mitis 85 oralis oralis mitis pneumoniae

18 S714 HK386 S. pneumoniae R6 MLST analysis of Streptococcus sp. B6 S. mitis RSA31 HUO8 HUO4 HK816 NCTC12261 RSA38 HK TW17 S691 RSA37 B5 SV16 RSA60 NCTC10712 M3 SV10 RSA13 HK SV1 HKP1 PN93/872B MS22 HKP46 HKP CS111 S492 HK470 Sp264 HKP S S614 HKO17 R6 GM17 HK648 HUO14 B6 HUN RSA24 SV18 SV5 TL7/1993 HK RSA23 HKP7 HKP140 HKO10 HUO1 HKP15 HUO10 HKP26 HK553 TW31 HK666 RSA42 S578 HK651 S697 S661 RSA4 S47 0 HK575 S510 SV12 RSA20 HK S711 S739 S699 HK188 S476 S621 HK323 S532 HK62 HK579 HK680 HK122 S527 S586 S694 HK123 HK677 S. oralis RSA40 HUO2 HUO11 HK49 HK417 HK496 HK RSA11 HK754 HK51 HUO3 HUO17 HK263 HK299 HK312 HUO5 HK581 HK587 S698 S560 S197 S566 HK524 HK574 HK619 RSA18 S Chi et al., IJMM 279:

19 S. oralis S. pneumoniae S. mitis One pbp2x gene family in three 'species' TW17 PN93/872B MS22 HKP46 HKP CS111 TW31 HKP26 HKP7 HKP140 HKP15 HKO SV18 TL7/ HUN663 HUO GM R HKP68 HKO17 Sp264 HK470 HKP1 SV1 HUO4 B5 HUO8 SV10 RSA37 RSA38 M3 S691 HK29 NCTC12261 NCTC10712 HK HK816 RSA31 RSA60 SV16 RSA13 S614 S492 S658 HK648 B6 HK339 RSA24 SV5 RSA23 HUO1 HUO10 HK553 HK666 RSA42 S578 HK651 S697 S661 RSA4 S714 HK575 S47 S510 SV12 RSA20 HK HK188 HK323 HK62 HK579 HK122 S527 RSA40 HUO2 HUO11 RSA11 HK417 HUO5 HK754 HUO3 HUO17 S767 HK51 S698 S560 S197 S566 HK386 HK581 HK587 HK524 HK574 HK619 HK263 HK299 HK312 RSA18 HK496 HK49 HK S586 S694 HK123 HK677 HK680 S532 S476 S621 S739 S699 S B6

20 S.pseudopneumoniae S.pneumoniae S.mitis tree based on ddl, gdh, rpob, and soda S.oralis S.infantis Kilian et al., PLoS ONE 3: July 2008

21 Streptococcus mitis B6: A high level beta-lactam and multiple antibiotic resistant strain In vitro antibiotic susceptibilities of Streptococcus mitis B6 MIC (µg/ml) Penicillin G >32 Erythromycin 0.19 Cefotaxime >32 Clindamycin Piperacillin >256 Gentamicin >1024 Cephalothin >256 Tobramycin >256 Cefepime >32 Cepodoxime >256 RP Cefpirome 64 Sparfloxacin 0.75 Cefuroxime >256 Ceftazidime >256 Tetracyclin r Imipenem 2.0 Chloramphenicol s Meropenem 2 König, A., et al Microb. Drug Res. 4: 45-49

22 163 kb in six clusters Streptococcus mitis B6 GC skew (G-C)/G+C) aminoglycoside resistance 25,4 kb GC% prophage ΦB6 44,2 kb ser-rich cell surface protein cluster 34,4 kb GC V-type ATPase 15,5 kb tet(m) cluster 27,3 kb conserved / hypothetical 16,2 kb

23 Streptococcus pneumoniae virulence factors Phase variation (blood versus mucosa) cell wall associated proteins CELL WALL POLYSACCHARIDES capsule peptidoglycan choline containing WTA, LTA CBPs LPXTG LXXC lipoproteins BACTERIOCINS PROTEINS RELEASED UPON AUTOLYSIS pneumolysin autolysin SECRETED PROTEINS neuraminidase hyaluronidase

24 Dept. of Microbiology Reinhold Brückner Dalia Denapaite Bernhard Henrich Patrick Maurer Yvonne Schähle Abderrahim Madhour Ilka Zerfaß Regine Hakenbeck Nano-Bio-Center KL Peter Reichmann Michael Nuhn Sonja Schröck BMBF DFG EU Helmholtz Stiftung Innovation Rh-Pf. Schwerpunkt TU KL communication is evolution is communication is evolution is communication is evolution is communicati