"Pathogen" in this instance means "living/viable entity." Toxins those entities produce & leave behind are something else . http://www.cdc.gov/healthywater/pdf/drinking/Backcountry_Water_Treatment.pdf
If you read this PDF again, you will see they are not saying the water is safe to drink, just that the pathogens are dead.
It is Fact Sheet for Healthy Drinking Water
I presume this means these process produce drinkable water