TABLE 2.

Prevalence of genes over-represented in acid-resistant E. coli as affected by stage of processing and within phylogroup^a

Genes	Prevalence (%) in E. coli
	Hide-on wash		Chilling		Equipment sanitation		Fabrication	P value < 0.05	Phylogroups
	Before	After	Before	During 4 to 24 h	Before	After			A	B1	B2	C	D	E	P value < 0.05
ydjI	70.4	60	72.7	58.1	33.3	5.3	78.6	*	96.6	29.9	100	50	100	100	**
atoA	59.3	56.7	54.5	35.5	12.5	5.3	64.3	*	98.3	11.2	100	100	66.7	0	*
xapB	59.3	56.7	48.5	22.6	37.5	36.8	57.1		50.8	44.9	0	100	0	0	*
xapR	63	56.7	48.5	25.8	37.5	36.8	57.1		52.5	45.8	0	100	0	0	*
fecA	37	36.7	33.3	12.9	33.3	89.5	57.1	*	47.5	37.4	0	50	0	0
fecI	37	36.7	36.4	22.6	33.3	89.5	57.1	*	54.2	37.4	0	50	0	0	*
fecR	37	36.7	36.4	16.1	33.3	89.5	57.1	*	52.5	37.4	0	50	0	0	*
ymjC	70.4	70	54.5	29	41.7	68.4	64.3	*	89.8	41.1	100	50	0	0	*

^aDifferences of gene prevelance among different processing stages or phylogroups were indicated by a single or double asterisk(s), respectively.