Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology

Table 1 Early bacterial genome-wide association studies based on whole-genome shotgun data

Organism	Sample size	Phenotype	Finding	Genome-wide association study program used	Reference
Organism	(isolates)	Phenotype	Finding	Genome-wide association study program used	Reference
Campylobacter jejuni and C. coli	192	Host adaptation	Vitamin B5 biosynthesis is important	30 bp `word’ searching [17]	[17]
Mycobacterium tuberculosis	123	Antibiotic resistance	39 novel resistance-associated loci	PhyC [18]	[18]
Staphylococcus aureus	75	Antibiotic resistance	Novel associated single nucleotide polymorphism in rpoB gene	ROADTRIPS [50]	[20]
S. aureus	90	Virulence	121 novel associated loci	PLINK [49]	[19]
Streptococcus pneumoniae	3,701	Antibiotic resistance	Multiple novel associated loci	PLINK [49]	[21]

ISSN: 1756-994X