Table 1.

Summary of all BRD and culture and susceptibility (C/S) outcomes and BRD onset times considered when examining associations with C/S results for deep nasopharyngeal (DNP) samples collected at 1DOF and 13DOF for individual animal-level and pen-level analysis.

Outcome of interest		Unit of analysis
		Individual	Pen
1st BRD treatment	Timing of BRD treatment:	Outcome:	Outcome:
		Individual calf treatment for BRD (Yes/No)	Number calves treated per pen/ Number calves at risk per pen
		Risk factor:	Risk factor:
		Matched to calf DNP results from C/S at:	Proportion of pen DNP positive for C/S at:
	Day 1 to 13	1DOF	1DOF
	Day 1 to 45	1DOF	1DOF
	Day 14 to 45	13DOF	13DOF
Culture and susceptibility results at the time of BRD treatment	Timing of 1st BRD treatment and BRD sample collection:	Outcome:	Outcome:
		DNP C/S—Calf status at BRD treatment (positive/negative)	DNP C/S positive at BRD treatment per pen/BRD calves treated per pen
		Risk factor:	Risk factor:
		Matched to calf DNP results from C/S at:	Proportion of pen DNP positive for C/S at:
	Day 1 to 13	1DOF	1DOF
	Day 1 to 45	1DOF	1DOF
	Day 14 to 45	13DOF	13DOF

Culture and susceptibility (C/S) results considered: • recovery of M. haemolytica, P. multocida, or H. somni, • recovery of any BRD bacteria with any AMR, macrolide resistance, or tetracycline resistance.