TABLE 2.

Prophage-borne virulence genes overrepresented among isolates from HA SNP clusters

Gene	Prophage	Odds ratioa	P valueb	Gene product and associated functions	Reference(s)
sodCI	Gifsy-2	10.64	<0.001	Periplasmic Cu-Zn superoxide dismutase; reacts with phagocytic superoxide radicals	24, 25
gtgE	Gifsy-2	Inf	<0.001	T3SS effector GtgE; inactivates Rab32 subfamily, leading to inhibition of the phagosomal fusion with lysosome	26, 27
sseI	Gifsy-2	Inf	<0.001	T3SS effector sseI; deamidates Gαi family G proteins, affecting the migration of macrophages and dendritic cells	30 – 32
gtgA	Gifsy-1/Gifsy-2c	72	<0.001	T3SS effector GtgA; cleaves NF-κB transcription factors RelA and RelB, suppressing proinflammatory responses	33
sspH1	Gifsy-1	Inf	0.015	E3 ubiquitin ligase; ubiquitinates protein kinase N1, leading to inhibition of the phagosomal fusion with lysosome	28, 29

^aThe odds ratio refers to the ratio of the odds that the gene is present in the HA isolates to the odds that the gene is present in the NHA isolates.

^bBH-corrected P value of the Fisher’s exact tests.

^cHomologs of gtgA are found in both Gifsy-1 and Gifsy-2 prophages.