The concept of sous vide is not the most intuitive, so like a lot of people, I had a lot of questions about safety. Rest assured, smarter people than you and me have decided it is safe. There's already a good chance that you have already eaten something cooked sous vide. Not only is it frequently used in high end restaurants, but also at Chipotle (carnitas, barbacoa) and Panera (steak, salmon, turkey).
In many ways, the exact temperature control of sous vide allows for safer cooking than conventional methods. But when comparing to oven temperatures, people are often wary of cooking chicken to 140 F. The important thing to keep in mind is that the longer times of sous vide compensate for the lower temperatures. For example, Salmonella is killed in 30 seconds at 150F, but it takes 15 minutes at 130F. With the exception of fish, most sous vide cooking is done at least at 130F, so as long as you follow the established minimum cooking times and temperatures, your food will be perfectly cooked and perfectly safe.
This is an important topic, so it is very understandable if you are still wary. For more context and information, I found this post on the question and answer site, stackexchange to be very helpful.
Simply put, any fears about plastic and sous vide cooking are misplaced. Firstly, the anxiety about BPA is unrelated to sous vide packaging, as BPA is only contained in rigid polycarbonate. Even then, it is still approved for food use and only becomes a real concern when the polycarbonate cracks.
The more relevant concern around plastic comes from plasticizers and the possibility that these chemicals might become absorbed into food. Fortunately, the FDA regulates that high-density polyethylene, low-density polyethylene, and polypropylene cannot be made with any plasticizers. As a result, all brand-name storage bags and even plastic wrap are made up of these food safe plastics and are totally safe to use in sous vide cooking.
Long associated with contaminated home canning, the toxin that causes botulism and some other forms of food poisoning can develop in oxygen-free environments. Luckily, it is easy to avoid this by adhering to basic safety guidelines. Unlike canning, sous vide does not allow for enough time most pathogens to develop. Although the USDA the danger zone for food holding food is 40F to 140F, this is overly simplified and created with conventional cooking methods in mind. With sous vide, it is possible to hold temperatures at an exact level and slowly pasteurize foods at lower temperatures.
The major possible pitfall is what happens after you cook. The general rule of thumb is that foods should not left out beyond two hours and for long term storage, you must properly chill your food in an ice bath. Creating a mixture of equal parts water and ice is vital in ensuring that food chills rapidly and pathogens do not have enough time to develop. Also, make sure that you are not chilling foods in ziploc bags as over long periods of time, trace amounts of air will enter the bag.
Do your best to make sure your food is fresh and properly cleaned.
Avoid cross contamination by using separate cutting boards and storage containers for vegetables, meat and fruit.
Make sure sink handles, cooking utensils, and kitchen towels are properly cleaned.
Follow proper guidelines for cook times and storage, especially for chilling and storage.