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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

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

Gene # positive isolates (%) Distribution of non-syn SNVs w.r.t. reference seq. Latest trials ClinicalTrials identifier Ref.
0 < 1% < 2% < 5% ≥ 5% indels
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]