Most people probably don't think too much about how they're preparing their carrots: you peel 'em, slice 'em, eat 'em. In an industrial setting, however, the method of preparation can affect how safe they product is for consumers. If pathogens are given the opportunity to penetrate beyond the surface of the product, a food product that is eaten raw can be tough to make safe. This is why most public health legislation requires cut fruits and vegetables to be maintained at fridge temperatures: if there has been an introduction of bacteria, it won't have the opportunity to multiple / produce toxins.
A study by Irish food scientists published in volume 40 of Food Control looks at the effect of different means of slicing, peeling, and storage of carrots to identify if any controls could be put in place to reduce the risk of E. coli O157:H7 contamination. They took a bunch of carrots, dunked them in a solution of E. coli for 30 minutes, and then washed them twice for a minute with distilled water before packaging them. The packaging and storage in plastic allowed the researchers to replicate the type of environment in which industrially-produced carrots would be found. The carrots were stored in the plastic for five days, at either 4'C (recommended) or 10'C (abused).
After the storage period ended, the researchers peeled, sliced, and stored the carrots in various ways to identify differences in E. coli penetration and resilience. The carrots were peeled either by hand or using an industrial abrasion peeler. They were sliced by hand using a razor blade, or mechanically with either a dull or sharp blade on a vegetable processing machine. Storage of the cut carrots was at either 4'C or 10'C, as with the pre-cut, inoculated carrots. They also looked at the effect of gas atmosphere on the growth and survival of the bacteria, but that's not something that's easily controlled in a home or restaurant environment, so I won't go too deeply into it.
While the original analysis of the carrots showed similar surface levels of E. coli, more bacteria was able to penetrate deep into the tissue when the cutting was performed with the dull blade. As time progressed, bacterial counts were higher throughout the carrot with the dull blade vs. the razor cutting. For the peeling methods, there was originally no difference between the methods on E. coli levels throughout the carrot, though as time progressed, the industrial peeler led to higher counts throughout. It is worth noting that overall levels of E. coli, for both methods of peeling, decreased over time. In results that should surprise nobody, there was less bacterial growth at 4'C vs. 10'C, and surface bacteria grew more significantly than bacteria within the carrots.
The researchers were looking at the results of this study to guide industrial operations: how to keep produce safe between the field and the table. However, the results also have implications for the home cook or the restaurant operator. If you're planning to pre-process fruits and vegetables, it's better to cut them with a sharp knife, and keep them stored at or below 4'C. How you peel them is entirely up to you, because it doesn't seem to matter from a food safety perspective.
Source: O'Beirne, D., Gleeson, E., Auty, M., & Jordan, K. (2014). Effects of processing and storage variables on penetration and survival of Escherichia coli O157:H7 in fresh-cut packaged carrots. Food Control, (40), 71-77.