Appendix 1—table 1. Number and proportion of sample types collected in each arm at each phase.

	Baseline		12 month		24 month
	Control	Intervention	Control	Intervention	Control	Intervention
Whole stool	377 (96%)	351 (97%)	361 (91%)	380 (93%)	307 (67%)	333 (72%)
Diarrheal diaper	15 (3.8%)	10 (2.8%)	4 (1.0%)	4 (0.98%)	32 (7.0%)	20 (4.3%)
Rectal swab*	0 (0%)	0 (0%)	30 (7.6%)	24 (5.9%)	120 (26%)	109 (24%)

*Mean concentration of double-stranded DNA recovered from whole stool was 40.8 ng/μL (SD = 16.5, n = 33 with 57 samples excluded as their concentrations exceeded the upper detection limit of the assay), diaper samples was 28.7 ng/μL (SD = 16.9, n = 61 with 16 samples excluded as concentrations exceeded upper detection limit of assay), and rectal swabs was 26.3 ng/μL (SD = 15.5, n = 195 with 25 samples excluded as concentrations exceeded upper detection limit of assay). Only a subset of each sample type assayed for dsDNA concentration.