A genomic insight into evolution and virulence of Corynebacterium diphtheriae

Transcription

1 A genomic insight into evolution and virulence of Corynebacterium diphtheriae Vartul Sangal, Ph.D. Northumbria University, Newcastle University 8 th January 2016

2 Corynebacterium diphtheriae Features: Gram-positive, aerobic, non-motile actinobacterium Causes diphtheria, a toxin mediated disease of upper respiratory tract Biochemically divided into four biovars: gravis, intermedius, mitis and belfanti C. diphtheriae Largely been eradicated through the use of diphtheria vaccine Mortality: ~5000 people per year globally A recent increase in the number of infections by non-toxigenic C. diphtheriae strains with varying degree of pathogenesis

3 Biochemical variations between C. diphtheriae biovars Biovar Lipophilism Haemolysis a Nitrate Ability to utilize b Reduction Starch Glycogen gravis - ± intermedius ± ± mitis - ± + ± - belfanti -? a Biovar gravis is haemolytic but some strains may be weakly haemolytic. Biovar mitis is weakly haemolytic. We could not find haemolytic properties of biovar belfanti in the literature. b Strains of biovar intermedius may utilize glycogen and starch while mitis strains can rarely use starch but not glycogen.

4 DIPNET Quality Assurance Test Neal et al., 2009, J Clin. Microbiol.

5 Sharing of genes between different biovars Core genome = 1717 genes Accessory genome = 1413 genes mitis (NCTC03529) (Sangal et al., 2012a, J. Bacteriology) intermedius (NCTC05011) (Sangal et al., 2012b, J. Bacteriology) gravis (NCTC13129) (Cerdeno-Tarraga et al., 2003, NAR) belfanti INCA402 (Trost et al., 2012, J. Bacteriology) Function gravis intermedius mitis belfanti Restriction-modification system mobile genetic elements Phage-associated Hypothetical proteins Others Potential biovar specific genes: genes encoding transcription regulators, membrane proteins, fimbrial proteins or other metabolic enzymes were grouped as others.

6 Biovar specific genes: carbohydrate, lipid, iron and nitrogen metabolism Locus COG Category Function Biovars DIP1639 C Carbohydrates/Energy production dihydrolipoamide acetyltransferase belfanti, gravis, mitis DIP0660 I Carbohydrate/lipid propionyl-coa carboxylase complex B subunit belfanti, gravis, mitis DIP1011 G Carbohydrates putative aldose 1-epimerase belfanti, gravis, mitis DIP1302 G Carbohydrates transketolase belfanti, gravis, mitis DIP1611 E Amino acid/ 5,10-methylenetetrahydrofolate reductase gravis, intermedius, Lipid/carbohydrate mitis Biovar specific nonsense single nucleotide polymorphisms Gene Biovar Function Metabolism DIP0794 intermedius Na + /H + antiporter-like protein Inorganic ion DIP2352 intermedius anthranilate synthase component I Amino acid/coenzyme DIP0842 intermedius putative secreted protein - metf (DIP1611) intermedius 5,10-methylenetetrahydrofolate reductase Amino acid Sangal et al., 2014, Infection, Genetics and Evolution

7 Phylogenetic analyses Core genome phylogeny A ML tree from the binary data from the accessory genome Sangal et al., 2015, BMC Genomics

8 Genome-wide CDS blast map Tox phage D Afonseca et al., 2012

9 CRISPR-Cas systems in C. diphtheriae A. Type II-C B. Type I-E-a C. Type I-E-b cas genes genes ending hypothetical proteins mobile genetic elements conserved genes Sangal et al., Microbiology, 2013 putative septation inhibitor CRISPR arrays: direct repeats shown in colour and spacers are shown in white. Fineran & Charpentier, 2012, Virology

10 Spacer diversity in Type II CRISPR-Cas system csn2 cas4 (Type II-C) Type II-A II-B C. diphtheriae Total unique spacers: 93 Shared spacers: 18 Duplicated spacers: 2 CRISPR direct repeats that are common between different strains are shown in the same colour and spacers are shown in white. Shared and duplicated spacers are numbered. Sangal et al., Microbiology, 2013

11 Variants of Type I-E CRISPR-Cas system Type I-E-a Total unique spacers: 101 Shared spacers: 12 Duplicated spacers: 3 Type I-E-b Total unique spacers: 25 Shared spacers: 4 Duplicated spacers: 5 Sangal et al., Microbiology, 2013

12 CRISPR-Cas phylogeny A. NJ tree from the repeat sequences B. NJ tree from the cas1 gene alignment G+C content = 47.8% G+C content = 49.5% G+C content = 46% Average genomic G+C content = 53% Sangal et al., Microbiology, 2013

13 Unique evolutionary histories of C. diphtheriae strains I-E-a (15) II-C (7) II-C (28) II-C (6) II-C (7) & I-E-b (26) II-C (4) II-C (11) I-E-a (19) I-E-a (17) II-C (15) & I-E-b (4) II-C (15) & I-E-b (4) II-C (5) I-E-a (12) I-E-a (15) II-C (14)

14 Variation in the degree of pathogenicity of non-toxigenic C. diphtheriae ISS 3319 (mitis), ISS 4060 (gravis), ISS 4746 (gravis) and ISS 4749 (gravis) from patients with severe pharyngitis and tonsilitis in Italy. Adhesion to D562 cell lines Hunolstein et al., 2003, J Med. Microbiol. Pulti et al., 2006, J Med. Microbiol. Ott et al., 2012, BMC Microbiology

15 Variation in potentially virulence associated proteome ST26 ST5 Protein category ISS 3319 ISS 4060 ISS 4746 ISS 4749 Lipoproteins 2 1 Secreted proteins 2 5 Trans membrane non-classical Sec Cytoplasmic Ambiguous Trans membrane proteins include TM-Sec and LPXTG proteins ST32 ISS ISS Predicted proteome (20 genomes)

16 Variation in the pilus gene clusters Sangal et al., 2015, BMC Genomics

17 1. A lack of correlation between gene content and biochemical differentiation. Conclusions 3. Three novel configurations of CRISPR-Cas systems 2. Bio-typing is not suitable for epidemiological & evolutionary studies. Biochemical differentiation CRISPR-Cas Systems 4. Horizontally acquired in three independent events. Genomics 5. The variation in number and organization of pilus gene clusters is associated with the variation in adhesive properties. Variation in the degree of virulence Evolutionary insights 7. Distinctive phylogeny and unique spacers suggest that unique evolutionary events in different environments led to current genomic diversity. 6. Strain specific lipoproteins and secretory proteins are potentially responsible for the variation in the degree of pathogenesis. 8. Recombination and gain/loss of the gene function introduced variation, even within a clonal group.

18 Acknowledgements Paul Hoskisson University of Strathclyde, Glasgow, UK Peter Fineran University of Otago, New Zealand Iain C. Sutcliffe Northumbria University, Newcastle, UK Andreas Burkovski Friedrich-Alexander-Universität Erlangen-Nürnberg Erlangen, Germany Jochen Blom Justus-Liebig-University, Giessen, Germany Thank You.