Pathogen_Persistance_AgWater

This depository contains collected data and statistical analyses associated with the study on the persistence of enteric pathogens in preharvest agricultural water. This work is licensed under the Creative Commons CC BY 4.0 license.

📁 Code and Output

• Obj1_modeling_NM110725.pdf: Rendered R scripts and statistical outputs supporting this research.

📊 Data Files

• obj1_dat.RDS: Microbial counts collected from the experiments.
• obj1_ph.RDS: Agricultural water pH measured at each sampling interval.
• 87205_2021_1_1_2024: Average daily weather data.

All the files are archived on Zenodo: https://doi.org/10.5281/zenodo.15374156.

📊 Data Structure

Column Name	Type	Description
day	Numerical	Sampling intervals in days
assay	Categorical	The assays used for the quantification of each microbial target
matrix	Categorical	Microbe-suspended matrix to be studied
microbe	Categorical	Microbial groups
pH	Numerical	pH of water samples
replicate	Numerical	Number of each biological replicate
survival	Numerical	Microbial survival
temp	Categorical	Temperature at which the water samples were incubated (set to 12ºC)
week	Numerical	Sampling intervals in weeks
week_fac	Categorical	Sampling intervals in weeks
MONTH	Numerical	Month
YEAR	Numerical	Year
meanTemp	Numerical	Average daily temperature (ºF)
mean_Temp_c	Numerical	Average daily temperature (ºC)
sd	Numerical	Standard deviation
se	Numerical	Standard error

🧾 Categorical Variables Levels

Category	Levels	Description	Unit
assay	plate	Total plate count	log10 Colony-Forming Units (CFU)/ml
	tcid50	50% Tissue Culture Infectious Dose (TCID50)	log10 TCID50/ml
	pcr	RNase RT-qPCR	log10 Genome Copies (GC)/ml
matrix	ag3	Preharvest agricultural water, served as treatment	-
	pbdw	Phosphate Buffer Dilution Water (PBDW), served as control	-
microbe	ec	Enteric bacteria: Escherichia coli TVS 353	-
	nv	Enteric virus: Human norovirus GII (HuNoV GII)	-
	tv	Enteric virus: Tulane virus (a surrogate for human norovirus)	-