Table 1.

Average fold changes for gene classes cumulative abundance of untreated HWW over UWW (2012–2015; significant differences indicated by asterisk *; p values ≤ 0.004) and HWW over MWW (2015, significant differences indicated by asterisk *; p values ≤ 0.03) ± Standard Deviation. 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. NA indicates that gene classes were undetectable in either one or both of the sample groups.

Gene classes conferring resistance to:	Fold change untreated Hospital WW/Urban WW	Fold change untreated Hospital WW/Mixed WW
chloramphenicol	84 (±93)*	13 (±11)*
aminoglycosides	43 (±31)*	8 (±6)*
bacitracin	8 (±13)*	7 (±4)*
beta-lactams	26 (±22)*	9 (±6)*
macrolides	1 (±1)	0.6 (±0.3)
(multi-drug) Efflux	9 (±11)*	4 (±4)*
quinolones (qnr)	161 (±326)*	10 (±8)*
heavy metals	7 (±9)*	4 (±3)*
quaternary ammonium compounds(QACs)	18 (±14)*	7 (±4)*
vancomycin	12 (±35)*	18 (±20)*
tetracycline	4 (±3)*	3 (±2)*
polymixin	8 (±9)*	4 (±4)*
sulphonamides	19 (±12)*	7 (±4)*
methicillin	NA (undetectable in UWW)	NA (undetectable in all but one MWW sample)
streptogramin	0.2 (±0.2)*	0.2 ((±0.2)*
trimethoprim	8 (±6)*	5 (±3)*
Gene classes grouped according to function:
transposase genes (MGEs)	3 (±1)*	2 (±1)
integron integrase genes	16 (±9)*	6 (±3)*