Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale

Table 6 Summary of microbial GWAS. Microbial GWAS developed until now are listed comparing their workflows, mutations of interest, studied phenotypes and genome dataset

Workflow	Explicative mutations	Population structure correction	Trait	Species	Sample	Reference ^a
bespoke	Phenotype + kmer	YES	Preferential host	Campylobacter jejuni	192	[30]
PhyC	Phenotype + SNP	YES	Antibiotic resistance	Mycobacterium tuberculosis	123	[33]
N/A	Phenotype + SNP	NO	Virulence	Staphylococcus aureus	90	[32]
Scoary	Gene	YES	Antibiotic resistance	Streptococcus pneumoniae	3085	[38]
Gemma	SNP	YES	Antimicrobial resistance	M. tuberculosis, S. aureus, E coli, K. pneumoniae	3144	[40]
Treewas	SNP + Gene + kmer	YES	Antimicrobial resistance	Neisseria meningitidis	ND	[41]
PLINK	SNP	NO	Drug resistance	Mycobacterium tuberculosis	123	[36]
PhyC	SNP	ND	Drug resistance	Mycobacterium tuberculosis	498	[39]
RoadTrips	SNP	NO	Drug Resistance	Staphylococcus aureus	75	[34]
PLINK	SNP	NO	Drug resistance	Streptococcus pneumoniae	3701	[35]
Scoary	Gene	YES	Geographical origin	Salmonella enterica	1327	[28]
DBGWAS	kmer	YES	Antibiotic resistance	M. tuberculosis, S. aureus, P. aeruginosa	1302, 992, 282	[42]
Scoary + GEMMA	Gene + SNPs	YES	Cold persistence	Listeria monocytogenes	51	[29]
PLINK	SNP	NO	Drug resistance	HIV	343	[140]
PLINK	SNP	NO	Viral load	HIV	1071	[31]
FaST-LMM	SNP	YES	Drug resistance	Plasmodium falciparum	1063	[37]

ISSN: 1471-2164