Table 1.

Comprehensive ranking of persister genes and pathways according to scores^∗.

	Mutated persister genes	Persistence pathways	KEGG pathways	Score
1	oxyR	Antioxidant defense		10
2	dnaK	Global regulator	RNA degradation	9
3	sucB	Energy production	Lysine degradation| Citrate cycle (TCA cycle)| Carbon metabolism	8
	relA	Stringent response	Purine metabolism	8
4	rpoS	Global regulator		7
5	clpB	Global regulator		6
	mqsR	TA module		6
	recA	SOS response	Homologous recombination	6
6	lon	TA module/protease		5
7	phoU	Global regulator		4
	smpB	Trans-translation		4
	glpD	Energy production	Glycerophospholipid metabolism	4
	relE	TA module		4
8	ssrA	Trans-translation		3
	uvrA	SOS response	Nucleotide excision repair	3
	tisAB	TA module		3
9	tnaA	Signaling pathway	Tryptophan metabolism	1
	umuD	SOS response		1
	hipA	TA module		1
10	pspF	Signaling pathway		0
	dinJ	TA module		0

^∗Persister genes were ranked according to cell survival under exposure to four different antibiotics at different times. The persisters genes whose mutants show significant difference compared to the parent strain were scored as “1” point, whereas those mutants that did show significant difference were scored as “0”. All scores for a given mutant are calculated from the sum of different antibiotic exposures to obtain the ranking order of the 21 persister genes.