Table 2. Streptococcus pneumoniae genetic determinants involved in colonization, competition, disease, antibiotic resistance and natural transformation.

		Non-PCV7 clones
Pneumococcal genetic determinants	Main role	6A	15A	19A
		ST2191	ST63	ST276
Colonization
Capsule	Prevents entrapment in the nasal mucus, thereby allowing access to epithelial surfaces. Also inhibits effective opsonophagocytosis.	P (6A)	P (15A)	P (19A)
Choline binding protein (pspC)	Binds to human secretory component on a polymeric Ig receptor during the first stage of translocation across the epithelium.	P	P	P
Choline binding protein (pcpA)	Role in pneumococcal adhesion and biofilm formation.	P	P	P
nanA, bgaA and strH	Act sequentially to cleave terminal sugars from human glycoconjugates, which might reveal receptors for adherence.	P	P	P
hyl	Breaks down hyaluronan-containing extracellular matrix components.	P	P	P
pavA	Binds to fibronectin.	P	P	P
eno	Binds to plasminogen.	P	P	P
rlrA pathogenicity islet	The rlrA islet encodes pili-like structures contributing to adherence.	M	M	M
Competition in upper airway
Bacteriocin Locus (blpC and βlpH)	Small antimicrobial peptide that targets members of the same species.	P	P	P
Disease
ply	Cytolytic toxin that also activates complement. An important determinant of virulence in in vivo models of disease. Wide range of effects on host immune components at sub-lytic concentrations.	P	P	P
pspA	Prevents binding of C3 onto pneumococcal surface. Also binds lactoferrin.	P	P	P*
lytA	Digests the cell wall, which results in the release of ply.	P	P	P
psaA	Component of the ABC transport system, which is involved in resistance to oxidative stress.	P	P	P
piaA and piuA	Component of the ABC transport system.	P	P	P
nanA and nanB	Aid colonization by revealing receptors for adherence, modifying the surfaces of competing bacteria that are within the same niche and/or modifying the function of host clearance glycoproteins.	P	P	P
igA	Cleaves human IgA1.	P	P	P
srtA	Responsible for anchoring most LXPTG-containing proteins.	P	P	P

P=present; M=missing. * small coverage over multiple contigs. Likely to be present in the contig gaps [32-36].