Quite a lot of information in this thread, some of it good, some of it bad; hopefully I can help to shed a bit of light. To preface, I’m a molecular microbiologist, with particular focus on infectious and emerging disease - in simple terms, I perform the type of research those CDC reports are based on. Some quick notes I typed up, hopefully someone finds this of use or interest.
There are two basic categories, and several subcategories, of contaminants you should be concerned with when it comes to drinking water:
1.1) Viral - Viral contamination is extremely prevalent in nature. Thankfully, most of these viruses are known as bacteriophage, and infect only prokaryotic (bacterial) cells. These cannot infect eukaryotic organisms (for reasons I can specific if anyone is interested), and as such, pose little threat to human life. Little does not mean none however. As humans, we are inhabited by thousands to millions of different bacterial species, many of which, while symbiotic in nature, are only a handful of genes away from virulence. The perhaps best known example of this is one of the most common soil bacterias, present in almost all human gut micro biomes, Bacillus subtilis. With the addition of a few very well known and studied genes, it quickly goes from a harmless organism, to something called B. anthracis, which many of you will recognize as the infamous bioterrorism agent. While unlikely the necessary genes could be transferred via bacteriophage (called horizontal transfer) for this kind of change to occur, it isn’t impossible. Some caution should be taken against viral contamination to prevent mutation of human flora and microbiome mutations resulting in increased virulence.
Depending on the nature of the viral strain, boiling can be insufficient to destroy. DNA damage (due to UV light or other method), chemical reagents (bleach), biological reagents (proteolysis), and in some cases autoclaving (pressurized super heated water) are the only options for sterility. As viruses are smaller than the filter pore size of 0.2uM, these devises are ineffective against viral particles. Your best defense against these in the field would be a UV pen or chemical agent.
1.2) Bacterial / Protozoa - It is a commonly held standard that a pore size of 0.2uM is sufficient to filter out biological contamination from liquid samples. When preparing chemical solutions in a research lab, a filtration device with this pore size will be used to sterilize material sufficient to achieve reaction grade biologicals. While there do exist both bacterial cells (known as ultramicrobacteria) as well as bacterial spores smaller than 0.2uM, though not Protozoa to the best of my knowledge. These are generally uncommon however, and to the best of my knowledge, none of yet to be identified with mammalian pathogenicity.
Heat is often enough to kill most biological samples, though boiling (as defined for this purpose to be at 100C though does change with pressure) can be insufficient in some cases. One of the most important bacterial species in science, Thermus aquaticus, part of a group of organisms known as thermophiles, thrive in high temperatures, often in excess of 80C. Other species of this group have been observed to tolerate up to 122C for extended periods. As someone previously mentioned, it is not only the temperature, but the duration of time as well that determines survivability for organisms. Any good molecular gastronomy cookbook (Modernist Cuisine being my favorite) will have kill curves showing time plotted against temperature to determine the correct conditions to adequately decontaminate (not sterilize) material. Chemical agents will have a similar effect as heat, with most being easily effected, but some having limited efficacy. Bleach is the most common compound used in laboratory settings, though some species can survive for prolonged periods in high concentrations of chlorine. Those are again rare, but highly pathogenetic when encountered.
Typically speaking, 30 minutes at 121C is considered sterile for liquid samples. For common drinking water contaminants, contaminants should be killed fairly quickly at 100C; exact times and temperature are of course entirely dependent on what you're trying to kill though. Keep in mind however, bacteria that posses the ability to infect a mammalian host, which an internal body temperature somewhere around 36C, are optimized to grow at that temperature (which is why they choice the human as a host), and are unlikely to be able to survive a wide enough range of temperatures to including 100C for any amount of time.
1.3) Protein based - These are the deadliest of all, and least common. Formally known as “prions,” these are mis-folded proteins, that upon contact with normal state proteins, auto-induce their transition to disease state. Prions are virtually impossible to remove by filtration, due to their small size, unaffected by heat, due to their hyper-stable state, and often cannot be dissolved by chemical means. There are reports of one of the more famous prions, bovine spongiform encephalopathy (otherwise known as Mad Cow), infecting a farm with farmers reacting by killing the cows, burning the property, and abandoning it for decades, only to come back and find the prion still exists. There is no cure, no test for contamination, and no real way to remove them via field or even lab setting. Current protocols call for several treatments of gaseous solvent to be passed over the contaminant, along with a number of other measures, and even then, many have proven ineffective.
I won’t go into great detail here, but this category includes everything from toxins produced by biological threats (such as the toxin produced by Clostridium botulinum), to nerve agents, poisons, etc. These can typically be filtered out by activated charcoal, or other distillation methods.
Now, all this said, the best thing to do is just practice common sense. How likely are you to encounter a prion from a clear moving spring along the cost of Maine? How safe is that water just outside the cattle farm to drink? What are the contaminants most common in that area, and where are they typically found? I personally rely on three purification techniques, in this order: a 0.1uM filter (Sawyer Squeeze, not mini), UV SteriPen, and chlorine dioxide (Aquamira). Between the three of them, they can neutralize almost any pathogenic biological contaminant, and certainly all of the more common ones. If a water supply looks clean and unpolluted, I simply use the filter. If I’m unsure, or want extra protection, I treat with UV for a bit, or chlorine dioxide if the volume is larger. Be safe, use common sense, and you should go home happy and healthy.