: What parasites are problematic in sous vide? Obviously, one should use only clean ingredients. However, especially with game and river/lake fish that's rather difficult. What are parasites that should be taken into account

All information that gives safe cooking temperatures without reference to time at that temperature is wrong. The FDA guidelines, and state and local health dept. guidelines not only confict with each other, they are flat out wrong!

They all represent efforts to simplify molecular biology to two or three mindless rules. In the process, they guarantee that you will either overcook your food, or (if you care about good food) ignore the rules. Or possibly both.

For a summary of the actual bacteriocidal data, take a look at Douglas Baldwin's site: www.douglasbaldwin.com/sous-vide.html#Safety He has compiled information based on the actual growth and death curves for the pathogens that concern us most in the kitchen: salmonella, e.coli, lysteria, clostridium perfringes. Taking care of these will also get you out of the woods with protists, parasitic worms, norovirus, and everything else besides bacterial spores (another subject ... more relevant to canning).

For an even more thorough examination of the issue, take a look at the Microbiology for Cooks chapter in Vol. 1 of the Modernist Cuisine series. Both Baldwin and Myhrvold have arrived at the same conclusion by consulting the actual science. The official guidelines are irrelevant.

The original question is "what is the shortest temperature and time to kill all parasites." By "parasite" I'm assuming the OP means pathogen, since parasites are technically just one type, and not usually the most important.

There's no good answer if we take this question literally, because killing all of anything is almost impossible. Autoclaving in a pressure cooker at 250°F / 121°C for 30 minutes still leaves about one in a trillion botulinum spores alive. Pasteurization leaves about 1 in 300 million pathogens alive (by definition, actually).

Cooking guidelines aren't about trying to kill everything; we just try to bring pathogens down to a safe level. A safe level is one where if you eat the food that's been refrigerated properly, in a reasonable amount of time, and you have a reasonably good immune system, it will be very unlikely that you'll get sick. I know that's a lot of disclaimers, but it's a messy world.

Here are some basic guidelines. You'll get much more thorough versions looking at the above (or similar) sources. This stuff is best expressed as a graph. I'm padding it a bit for simplicity and safety:

126°F / 52°C for 6 hours

130°F / 54.5°C for 2 hours

135°F / 57°C for 40 minutes

140°F / 60°C for 12 minutes

150°F / 65.5°C for for 1 minute 15 seconds

160°F / 71°C for 8 seconds

This is the time for killing salmonella (the most heat resistant of the pathogens we care about) to pasteurization standards.

Please note that these are not cooking times: these are times the food needs to be held at the temperature after reaching it. Normal minimum cooking times just reflect how long it will take for the center of the food to reach a given temperature. The above times are additional.

You may have noticed that the first three temperatures above are well within the FDA's "danger zone." It's curious that the official guidelines consider your food in danger when it's actually in the process of being pasteurized.

But it's not necessarily that complicated. We don't really have to pasteurize food most of the time. If you eat conventionally cooked medium-rare steak, fish that doesn't taste like rubber, or chicken that still has some juice left in it, then you eat un-pasteurized food. It's not a problem, because with the exception of ground meat, virtually all pathogens reside on the outer surfaces of the food. And they get more than hot enough when you sear the food, whether the main part of the cooking was sous-vide or some other way.

Pasteurization is mostly an issue with cook-chill sous-vide, which is where you prepare food for reheating many days (even weeks) later.

Botulism is not a concern unless you're doing cook-chill and trying to keep the food for way, way too long (or in a much too warm fridge). The bacteria does indeed like the airtight bag, but it doesn't like the cold.

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Edited for clarity. USDA Recommendations do not fully apply to this technique

Additional Source

The biggest risk with sous-vide is botulism. The lack of oxygen with this particular technique allows the botulism bacteria to thrive. The general recommendation is that the meat must reach an internal temperature of at least 131F/55C within 4 hours. This should properly "pasteurize" the meat.

USDA Recommendations:

Pork, beaf, veal, and lamb STEAKS are now considered safe at 145F.

Fish is safe at 145F (sushi anyone?)

Poultry is safe at 165F

All GROUND meats should be cooked to a minimum of 160F.

You'll notice that by these guidelines, a medium-rare burger is considered dangerous. So you'll have to use your best judgement. For context, E. coli is killed at around 155F, so there is logic to these numbers.

Personal recommendation: All meat should be cooked to a minimum of an internal temperature of 140 degrees, and kept there for at least 90 minutes. The meat must reach 131F within 4 hours to prevent the risk of botulism.

Poultry should always be cooked to at least 160, according to USDA recommendations, but Salmonella will die if cooked at 131F for at least 90 minutes. This should be sufficient.

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Modernist Cuisine, Vol 1, p122 (includes my bold):

A separate family of parasitic worms, known as nematodes or anisakids,
includes species such as Anisakis simplex and Pseudoterranova
decipiens (which is also listed under the genus Terranova or
Phocanema). These worms follow a life cycle that resembles that of trichinae but in a marine environment.
Raw fish poses the biggest risk
of infection because cooking fish to an internal temperature of 60 °C
/ 140 °F or more for at least one minute kills the worms. Several food
safety guides assert that 15 seconds at an interior temperature of 63
°C / 145 °F will also do the trick. Those temperatures, however, are
high enough to overcook the fish, at least to many people’s taste.
Not
surprisingly, sushi-loving Japan is the epicenter of foodborne
anisakid infections, also known as anisakiasis. Tokyo alone tallies
about 1,000 cases annually, most of which are from home-prepared sushi
and sashimi. Only rarely are sushi bars with professional sushi chefs
implicated. The U.S. reports fewer than 10 cases a year.
Anisakid
infection occurs more frequently in certain fish species that
fishermen catch near the shore, such as salmon, mackerel, squid,
herring, anchovies, and rockfish, than it does in other species.
Coastal fish are more likely to eat infected copepods that regenerate
in seals and other marine mammals. Farmed salmon do not eat copepods
and are therefore generally anisakid-free, as are wild tuna and other
deep-ocean species.
Wild salmon, however, are especially prone to
infection. In 1994, for instance, an FDA study found anisakids in 10%
of raw salmon samples that were obtained from 32 sushi bars in the
Seattle area. Despite this alarming statistic, human anisakiasis cases
are still relatively rare because most ingested larvae die or pass
harmlessly through the intestinal tract.
The technique traditionally
used by chefs to detect worms requires them to hold fish fillets up to
a light and inspect them visually, a procedure called candling. Master
sushi chefs say they can feel the worms with their fingers. And
although some chefs can indeed find a few worms through candling or
handling, studies suggest that others may be easily missed, especially
in salmon or mackerel. No matter how experienced the sushi master,
then, neither method is fully reliable.
Freezing kills anisakids, and
in this way the food industry ensures that worms pose no health risk
in fish that is served raw. For commercial retailers, the FDA
recommends freezing and storing the fish in a blast freezer for seven
days at ?20°C/?4°F, or for 15hours at ?35°C/?31°F. Most sushi is, in
fact, frozen before it is served; the 1994 FDA study found that all
but one of the anisakid worms spotted in the Seattle sushi were dead
or dying—casualties of the freezing process. If done improperly,
however, freezing can negatively affect the taste and texture of the
fish.

Modernist Cuisine, Vol 1, p123-124 (moreso Asia, but for posterity it is worth mentioning):

[ … ] species of liver fluke are endemic to Asia and Eastern Europe,
where researchers have linked them to eating raw or undercooked
freshwater fish.
Researchers have tied many infections, mostly in Asia, to eating raw,
pickled, or poorly cooked freshwater crabs and crawfish (especially
Chinese “drunken crabs”) that are contaminated with lung flukes,
another major fluke group comprising eight known species. These
animals produce a serious human disease called paragonimiasis, in
which immature worms infect the lungs and encapsulate themselves in
protective cysts, where they can remain for decades.

A table on freezing times by FDA:

So, to kill parasites, a blast freezer is the way to go.
Afterwards, we need to cook sous vide to get rid of nasty bacteria.
This is my sous vide bible: www.douglasbaldwin.com/sous-vide.html Cook-hold sous vide (hold the temperature and serve):

For cook-hold sous vide, the main pathogens of interest are the Salmonella species and the pathogenic strains of Escherichia coli. There are, of course, many other food pathogens but these two species are relatively heat resistant and require very few active bacteria (measured in colony forming units, CFU, per gram) to make you sick. Since you’re unlikely to know how contaminated your food is or how many of these bacteria your (or your guests) immune system can handle, most experts recommend a 6.5 to 7 decimal reductions of all Salmonella species and a 5 decimal reduction of pathogenic E. coli.

Cook-chill sous vide (chill after cooking for later re-heating and serving):

For cook-chill sous vide, Listeria monocytogenes and the spore forming pathogenic bacteria are our pathogens of interest. That’s because Listeria is the most heat resistant non-spore forming pathogen and can grow at refrigerator temperatures (Nyati, 2000b; Rybka-Rodgers, 2001), but appears to require more bacteria to make you sick than Salmonella or E. coli. Most experts recommend a 6 decimal reduction in Listeria if you don’t know the contamination level of your food.
While keeping your food sealed in plastic pouches prevents recontamination after cooking, spores of Clostridium botulinum, C. perfringens, and B. cereus can all survive the mild heat treatment of pasteurization. Therefore, after rapid chilling, the food must either be frozen or held at

below 36.5°F (2.5°C) for up to 90 days,
below 38°F (3.3°C) for less than 31 days,
below 41°F (5°C) for less than 10 days,
or below 44.5°F (7°C) for less than 5 days

to prevent spores of non-proteolytic C. botulinum from outgrowing and producing deadly neurotoxin (Gould, 1999; Peck, 1997).

We all consume small amounts of harmful bacteria that passes through our system unbeknownst to us, so we're talking about cooking to safe levels.
There is an easy table of data for this, and it is based upon the thickness of the items you are cooking sous vide. Please keep in mind, cylindrical items will cook faster in sous vide than their relatively box-shaped counterparts (a roulade, for instance, vs. a 1" thick steak.)
Also, depending on the meat, you will want to cook it to a different temperature to cull those particular bacteria (fish vs. chicken vs. beef)
There are several tables of data: www.douglasbaldwin.com/sous-vide.html#Fish_and_Shellfish Pasteurization Time for Lean Fish
(starting at 41°F / 5°C and put in a 131–140°F / 55–60°C water bath)
55°C 56°C 57°C 58°C 59°C 60°C
Thickness 131°F 133°F 134.5°F 136.5°F 138°F 140°F
5 mm 2½ hr 1¾ hr 1¼ hr 50 min 35 min 30 min
10 mm 2¾ hr 2 hr 1½ hr 60 min 45 min 35 min
15 mm 2¾ hr 2 hr 1½ hr 1¼ hr 55 min 50 min
20 mm 3 hr 2¼ hr 1¾ hr 1½ hr 1¼ hr 60 min
25 mm 3¼ hr 2½ hr 2 hr 1¾ hr 1½ hr 1¼ hr
30 mm 3¾ hr 3 hr 2½ hr 2 hr 1¾ hr 1¾ hr
35 mm 4 hr 3¼ hr 2¾ hr 2½ hr 2¼ hr 2 hr
40 mm 4½ hr 3¾ hr 3 hr 2¾ hr 2½ hr 2¼ hr
45 mm 4¾ hr 4 hr 3½ hr 3¼ hr 2¾ hr 2½ hr
50 mm 5¼ hr 4½ hr 4 hr 3½ hr 3¼ hr 3 hr
55 mm 5¾ hr 5 hr 4½ hr 4 hr 3¾ hr 3½ hr
60 mm 6¼ hr 5½ hr 5 hr 4½ hr 4 hr 3¾ hr
65 mm 7 hr 6 hr 5½ hr 5 hr 4½ hr 4¼ hr
70 mm 7½ hr 6¾ hr 6 hr 5½ hr 5 hr 4¾ hr

Pasteurization Time for Fatty Fish
(starting at 41°F / 5°C and put in a 131–140°F / 55–60°C water bath)
55°C 56°C 57°C 58°C 59°C 60°C
Thickness 131°F 133°F 134.5°F 136.5°F 138°F 140°F
5 mm 4¼ hr 3 hr 2 hr 1½ hr 60 min 40 min
10 mm 4¼ hr 3 hr 2 hr 1½ hr 1¼ hr 50 min
15 mm 4½ hr 3¼ hr 2¼ hr 1¾ hr 1¼ hr 60 min
20 mm 4¾ hr 3½ hr 2½ hr 2 hr 1½ hr 1¼ hr
25 mm 5 hr 3¾ hr 2¾ hr 2¼ hr 1¾ hr 1½ hr
30 mm 5¼ hr 4 hr 3¼ hr 2½ hr 2¼ hr 2 hr
35 mm 5½ hr 4¼ hr 3½ hr 3 hr 2½ hr 2¼ hr
40 mm 6 hr 4¾ hr 4 hr 3¼ hr 3 hr 2½ hr
45 mm 6½ hr 5¼ hr 4¼ hr 3¾ hr 3¼ hr 3 hr
50 mm 7 hr 5¾ hr 4¾ hr 4¼ hr 3¾ hr 3¼ hr
55 mm 7½ hr 6¼ hr 5¼ hr 4¾ hr 4¼ hr 3¾ hr
60 mm 8 hr 6¾ hr 5¾ hr 5¼ hr 4¾ hr 4¼ hr
65 mm 8½ hr 7¼ hr 6¼ hr 5¾ hr 5¼ hr 4¾ hr
70 mm 9¼ hr 8 hr 7 hr 6¼ hr 5¾ hr 5¼ hr

Table 3.1: Pasteurization times for a one million to one reduction of Listeria in fin-fish. I used D605.59 = 2.88 minutes for lean fish (such as cod) and D605.68 = 5.13 minutes for fatty fish (such as salmon) from Embarek and Huss (1993). For my calculations I used a thermal diffusivity of 0.995×10-7 m2/s, a surface heat transfer coefficient of 95 W/m2-K, and took ? = 0.28 (to simulate the heating speed of a 2:3:5 box).
www.douglasbaldwin.com/sous-vide.html#Chicken_or_Turkey_Breast Pasteurization Time for Poultry
(starting at 41°F / 5°C and put in a 134.5–149°F / 57–65°C water bath)
134.5°F 136.5°F 138°F 140°F 142°F 143.5°F 145.5°F 147°F 149°F
Thickness 57°C 58°C 59°C 60°C 61°C 62°C 63°C 64°C 65°C
5 mm 2¼ hr 1¾ hr 1¼ hr 45 min 35 min 25 min 18 min 15 min 13 min
10 mm 2¼ hr 1¾ hr 1¼ hr 55 min 40 min 35 min 30 min 25 min 20 min
15 mm 2½ hr 1¾ hr 1½ hr 1¼ hr 50 min 45 min 40 min 35 min 30 min
20 mm 2¾ hr 2 hr 1¾ hr 1¼ hr 1¼ hr 55 min 50 min 45 min 40 min
25 mm 3 hr 2¼ hr 2 hr 1½ hr 1½ hr 1¼ hr 1¼ hr 60 min 55 min
30 mm 3¼ hr 2¾ hr 2¼ hr 2 hr 1¾ hr 1½ hr 1½ hr 1¼ hr 1¼ hr
35 mm 3¾ hr 3 hr 2½ hr 2¼ hr 2 hr 1¾ hr 1¾ hr 1½ hr 1½ hr
40 mm 4 hr 3¼ hr 2¾ hr 2½ hr 2¼ hr 2 hr 2 hr 1¾ hr 1¾ hr
45 mm 4½ hr 3¾ hr 3¼ hr 3 hr 2¾ hr 2½ hr 2¼ hr 2 hr 2 hr
50 mm 4¾ hr 4¼ hr 3¾ hr 3¼ hr 3 hr 2¾ hr 2½ hr 2½ hr 2¼ hr
55 mm 5¼ hr 4½ hr 4 hr 3¾ hr 3½ hr 3¼ hr 3 hr 2¾ hr 2¾ hr
60 mm 5¾ hr 5 hr 4½ hr 4¼ hr 3¾ hr 3½ hr 3¼ hr 3¼ hr 3 hr
65 mm 6¼ hr 5½ hr 5 hr 4½ hr 4¼ hr 4 hr 3¾ hr 3½ hr 3¼ hr
70 mm 7 hr 6 hr 5½ hr 5 hr 4¾ hr 4½ hr 4¼ hr 4 hr 3¾ hr

Table 4.1: Time required for at least a one million to one reduction in Listeria and a ten million to one reduction in Salmonella in poultry starting at 41°F (5°C). I calculated the D- and z-values using linear regression from (O’Bryan et al., 2006): for Salmonella I used D606.45 = 4.68 minutes and for Listeria I used D605.66 = 5.94 minutes. For my calculations I used a thermal diffusivity of 1.08×10-7 m2/s, a surface heat transfer coefficient of 95 W/m2-K, and took ?=0.28 (to simulate the heating speed of a 2:3:5 box). For more information on calculating log reductions, see Appendix A.
www.douglasbaldwin.com/sous-vide.html#Beef Pasteurization Time for Meat (Beef, Pork, and Lamb)
(starting at 41°F / 5°C and put in a 131–151°F / 55–66°C water bath)
55°C 56°C 57°C 58°C 59°C 60°C
Thickness 131°F 133°F 134.5°F 136.5°F 138°F 140°F
5 mm 2 hr 1¼ hr 60 min 45 min 40 min 30 min
10 mm 2 hr 1½ hr 1¼ hr 55 min 45 min 40 min
15 mm 2¼ hr 1¾ hr 1½ hr 1¼ hr 60 min 55 min
20 mm 2½ hr 2 hr 1¾ hr 1½ hr 1¼ hr 1¼ hr
25 mm 2¾ hr 2¼ hr 2 hr 1¾ hr 1½ hr 1½ hr
30 mm 3 hr 2½ hr 2 hr 2 hr 1¾ hr 1½ hr
35 mm 3¼ hr 2¾ hr 2¼ hr 2 hr 2 hr 1¾ hr
40 mm 3½ hr 3 hr 2½ hr 2¼ hr 2¼ hr 2 hr
45 mm 4 hr 3¼ hr 3 hr 2¾ hr 2½ hr 2¼ hr
50 mm 4½ hr 3¾ hr 3¼ hr 3 hr 2¾ hr 2½ hr
55 mm 5 hr 4¼ hr 3¾ hr 3½ hr 3 hr 3 hr
60 mm 5¼ hr 4¾ hr 4¼ hr 3¾ hr 3½ hr 3¼ hr
65 mm 6 hr 5¼ hr 4¾ hr 4¼ hr 4 hr 3¾ hr
70 mm 6½ hr 5¾ hr 5¼ hr 4¾ hr 4¼ hr 4 hr
61°C 62°C 63°C 64°C 65°C 66°C
Thickness 142°F 143.5°F 145.5°F 147°F 149°F 151°F
5 mm 25 min 25 min 18 min 16 min 14 min 13 min
10 mm 35 min 30 min 30 min 25 min 25 min 25 min
15 mm 50 min 45 min 40 min 40 min 35 min 35 min
20 mm 60 min 55 min 55 min 50 min 45 min 45 min
25 mm 1¼ hr 1¼ hr 1¼ hr 60 min 55 min 55 min
30 mm 1½ hr 1½ hr 1¼ hr 1¼ hr 1¼ hr 1¼ hr
35 mm 1¾ hr 1½ hr 1½ hr 1½ hr 1¼ hr 1¼ hr
40 mm 1¾ hr 1¾ hr 1¾ hr 1½ hr 1½ hr 1½ hr
45 mm 2¼ hr 2 hr 2 hr 1¾ hr 1¾ hr 1¾ hr
50 mm 2½ hr 2¼ hr 2¼ hr 2 hr 2 hr 2 hr
55 mm 2¾ hr 2¾ hr 2½ hr 2½ hr 2¼ hr 2¼ hr
60 mm 3 hr 3 hr 2¾ hr 2¾ hr 2½ hr 2½ hr
65 mm 3½ hr 3¼ hr 3¼ hr 3 hr 3 hr 2¾ hr
70 mm 3¾ hr 3¾ hr 3½ hr 3¼ hr 3¼ hr 3¼ hr

Table 5.1: Time required to reduce Listeria by at least a million to one, Salmonella by at least three million to one, and E. coli by at least a hundred thousand to one in thawed meat starting at 41°F (5°C). I calculated the D- and z-values using linear regression from O’Bryan et al. (2006), Bolton et al. (2000), and Hansen and Knøchel (1996): for E. coli I use D554.87 = 19.35 min; for Salmonella I use D557.58 = 13.18 min; and for Listeria I use D559.22 = 12.66 min. For my calculations I used a thermal diffusivity of 1.11×10-7 m2/s, a surface heat transfer coefficient of 95 W/m2-K, and took ?=0 up to 30 mm and ?=0.28 above 30 mm (to simulate the heating speed of a 2:3:5 box). For more information on calculating log reductions, see Appendix A. [Note that if the beef is seasoned using a sauce or marinate which will acidify the beef, then the pasteurizing times may need to be doubled to accommodate the increased thermal tolerance of Listeria (Hansen and Knøchel, 1996).]

There's also a table for Government (I'm assuming US Government) pasturisation times: www.douglasbaldwin.com/sous-vide.html#Government_Pasteurization_Tables As well as a list of sources: www.douglasbaldwin.com/sous-vide.html#Bibliography

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