Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital

Table 2 Sequence variability of genes of interest for vaccine development. Number (and relative abundance) of isolates positive for the gene, followed by the percentage of positive isolates carrying 0 or less than 1%, 2%, 5%, or more/equal to 5% of non-synonymous SNVs or insertions-deletions (indels) with respect to reference gene. Both clinical trial IDs (ClinicalTrials.gov database identifiers, http://clinicaltrials.gov) and reference studies refer to the latest available trials

Gene	# positive isolates (%)	Distribution of non-syn SNVs w.r.t. reference seq.						Latest trials	ClinicalTrials identifier	Ref.
Gene	# positive isolates (%)	0	< 1%	< 2%	< 5%	≥ 5%	indels	Latest trials	ClinicalTrials identifier	Ref.
clfA	95 (70.4%)	0%	9.5%	0%	0%	0%	90.5%	Phases I–II	NCT01643941; NCT01364571	[159, 160, 171]
csa1a	70 (51.9%)	41.4%	4.3%	0%	0%	0%	54.3%	Preclinical		[168, 172]
csa1b	36 (26.7%)	19.4%	47.2%	0%	2.8%	0%	30.6%
esxA	134 (99.3%)	85.1%	14.9%	0%	0%	0%	0%	Preclinical		[168, 172]
esxB	89 (65.9%)	0%	98.9%	1.1%	0%	0%	0%	Preclinical		[168, 172]
esxC	89 (65.9%)	25.8%	40.4%	33.7%	0%	0%	0%
esxD	89 (65.9%)	58.4%	41.6%	0%	0%	0%	0%
fhuD2	135 (100%)	31.1%	68.9%	0%	0%	0%	0%	Preclinical		[168, 172]
hla	124 (91.9%)	6.5%	0%	9.7%	78.2%	2.4%	3.2%	Phase II	NCT02296320	[168, 172, 173]
hlgA	135 (100%)	65.2%	29.6%	2.2%	0%	0%	3%
hlgB	132 (97.8%)	11.4%	65.2%	22.7%	0%	0%	0.8%	Preclinical		[174]
hlgC	135 (100%)	61.5%	8.1%	28.1%	2.2%	0%	0%
isdB	134 (99.3%)	11.9%	21.6%	0%	0%	0%	66.4%	Phase III	NCT00518687	[152, 166]
lukF	37 (27.4%)	0%	97.3%	0%	0%	0%	2.7%
lukS	37 (27.4%)	56.8%	40.5%	0%	0%	0%	2.7%	Phases I–II	NCT01011335	[175]
mntC	135 (100%)	79.3%	20.7%	0%	0%	0%	0%	Phases I–II	NCT01643941; NCT01364571	[159, 160, 171]
tst	8 (5.9%)	0%	100%	0%	0%	0%	0%	Phase I	NCT02340338	[176]

ISSN: 1756-994X