Table 2.

Average fold changes for gene classes of untreated WW over treated WW for H, U and M WW (p values ≤ 0.03) ± Standard Deviation. * = significantly lower; + = significantly higher. Significant differences were calculated by comparing the normalized cumulative abundance values of individual gene classes for all samples belonging to each sample group using the non-parametric Mann-Whitney test. Fold changes were calculated for individually paired samples for each gene class/sample group. Average fold change ± Standard Deviation are depicted in the table for comparison. NA indicates that gene classes were undetectable in either one or both of the sample groups.

Gene classes conferring resistance to:	Fold change H untreated WW/H treated WW	Fold change U untreated WW/U treated WW	Fold change M untreated WW/M treated WW
chloramphenicol	34 (±47)*	5 (±12)*	16 (±27)*
aminoglycosides	15 (±14)*	3 (±5) *	7 (±10)*
bacitracin	12 (±30)*	1 (±2)	1 (±1)
beta-lactams	30 (±42) *	4 (±14)	10 (±21)
erythromycin (macrolides)	48 (±68)*	27 (±55)*	23 (+17)*
(multi-drug) efflux	29 (±43)*	9 (±27)*	13 (±17)*
quinolones	78 (±123)*	3 (±5)	19 (±29)*
heavy metals	15 (±32) *	3 (±3)	2 (±2)
quaternary ammonium compounds(QACs)	5 (±5) *	1 (±2)	2 (±2)
vancomycin	NA (undetectable in all but one sample for treated HWW)	NA (undetectable in all but one sample for treated UWW)	NA (undetectable in all samples for treated MWW)
tetracycline	51 (±77)*	13 (±40)*	6 (±5)
polymixin	29 (±52)*	5 (±12) *	7 (±7)*
sulphonamides	5 (±6)*	1 (±1)+	2 (±1)
Streptogramin	17 (±43)*	43 (±77)*	41 (±20)*
methicillin	NA (undetectable in all treated HWW samples)	NA (undetectable in all treated UWW samples)	NA (undetectable in all but one treated MWW sample)
trimethoprim	66 (±101)*	9 (±28)*	6 (±7)*
Gene classes grouped according to function:
transposase genes (MGEs)	5 (±5)*	6 (±7)*	5 (±3)*
integron integrase genes	7 (±6)*	1 (±1)	3 (±4)*