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Suits are not pressure sealed suits -- look at your gloves, the wrists are just taped. Those bear slashes are cutting you up good but somehow your suit isn't giving some low pressure warning right? The helmets and suits we prospectors are using are roughly equivalent to SCUBA or fire-fighter's gear. Great for preventing toxic chemicals from harming your lungs (yes water counts) - not so great at stopping biological infections because bacteria can crawl right up the one-way valves used to keep the toxic chemicals out.
Yes, a normal infection could take hours or days infect a person and in that time the gear would normally but taken off and disinfected regularly in the real world but it'd also take weeks to recover. So to game-ify it it's sped up considerably along with an instant cure.
SCUBA (Self-Contained Underwater Breathing Apparatus) gear works with one-way valves. You've seen all the bubbles leaving a diver's mask when they breath out? That's the one-way valve - opens up to let air escape but closes to keep water out. Simple and effective.
One way valves are also cheap compared to a filtration system. Remember this is all low-cost bidder type government work on Icarus. Only thing they're required to give us is a working suit. One way valves work great against chemical. Not so much bacteria. The thing with airborne bacteria is that they don't stay in the air and they stick to things. Valve opens up air rushing out prevents any chemicals in the air from entering the helmet, but what about the bacteria growing and crawling along the inside of the hose? Which is why SCUBA and SAR (Supplied Air Respirator) gear are usually cleaned before and after every use.
Yes you can get an infection if you improperly care for your gear. (I recommend you clean any SCUBA gear you rent VERY thoroughly before you use it.) It takes a lot longer than the few seconds in a cave it's happening on Icarus, but like I said it has been game-ified.
Whatever conditions are required for the caveworm gut bacteria to survive outside of their hosts seem to be present in many of the caves found throughout Icarus. The bacteria spread like wildfire within the cave and become airborne. When we muck about in these caves, we are exposed. After a certain amount of time, the bacteria infests our breathing apparatus and ends up in our lungs. When the bacterial load reaches a tipping point, we get sick.
My current guess is that direct exposure to heat and sunlight, or light from UV lamps, very quickly fries (figuratively) caveworm gut bacteria, thus allowing us to recover once we exit an infected cave.
The animals imported from Earth do not catch cave pneumonia because the adaptations engineered into them by UDA, along with SWAG changes caused by Exotics, are providing inborn protection.
The weakest protection these systems offer is from nuclear. They will protect against Alpha and Beta radiation as well as fallout, however you are still susceptible to higher energy radiation such as xray or gamma. For those you need to be behind thick concrete or a special shielding, usually lead-lined.
Regardless of all this, protective masks (gasmasks) are not what is used in game as is evidenced by the fact the character can breathe underwater. Gasmasks don't work that way. It is obviously a respirator, likely pressure regulated, with a face shield/helmet combined with a basic protective overgarment (like Kevlar, Spectra/Dyneema or possibly even sturdy canvas, treated for protection against chemical threats) suitable for protecting you from the environment, but not aggressive fauna. We can reasonably assume that the mask has a good seal as according to lore, "Terraforming derailed catastrophically, lacing the oxygen atmosphere with toxins like cyanide". See https://icarus.fandom.com/wiki/Story
If that is true then a leaking mask would kill the player well before bacteria from a cave would cause pneumonia. This also supports the idea that the air system is pressurized, so that if a leak were to develop then the overpressure would stop any contaminates from getting in.
I say all this because:
I support the OP. While the suits are likely not sealed, the idea that you would develop a lung infection, caused by breathing in harmful bacteria, while wearing; a sealed pressure-regulated breathing apparatus, a protective helmet, and a protective overgarment, makes zero sense. I get that it's gamified, but it still makes no sense.
Living in a cave is EXTREMELY unhealthy. No one really does it. People work in caves (coal miners, chinese people harvesting stuff for birds nest soup, etc). But they don't permanently live in caves.
The closest thing I can think of is a group of jews who hid out in a series of caves during world war II. They spent several years in the caves. People in a nearby village snuck food out to them. They had a TON of health issues. The caves were freezing cold all the time, and that just sucks the body heat out of people. The broke out in rashes, got respiratory infections, and host of other health issues. Many of these conditions stayed with them for the rest of their lives.
Even in some caves today (like the ones that are tourist attractions), they'll bring in items from outside and a day later they will be covered in mold. Mold so thick and so fuzzy, that it looks like bright green shag carpet. Every square inch of the item covered in mold.
Also... it's an alien planet. So what if the infectious organisms are alien? and do things that earth organisms can't do?
While that is technically correct in the game you are walking around in a SEALED enviro-suit with, as other posters have pointed out, a seperate air-supply.
I get why the cave infection is there for game balance reasons but it doesn't make sense logically and is even immersion breaking once you think about it.
All that said I struggle to come up with an alternative to preserve the intended effect ... maybe make all caves arctic cold or desert hot ? it'll limit the time early-game players can spend in there and be just as easily overcome with later game equipment/meds as the cave illness.