S. aureus lives up your nose. You do not need to be ill to carry this opportunist pathogen around. However, if you have a habit of touching your nose, have a cold, cough or a fit of sneeezing you can contaminate a large area. If another person's immune system is down, S. aureus can make that person very ill.
If you happen to sneeze in the bottling plant, this could contaminate the water at that critical stage between filling and capping. It is essential, in preventing this, to have a positive air pressure either around the bottling machine or preferably throughout the bottling plant.
A high percentage of bacteria in the bottling plant are airborne. They float in through open doors. One flush of a toilet releases an aerosol of bacteria many of which remain airborne. Enterococcus faecalis is very common in indoor environments and represents a high percentage of airborne bacteria.
Check your airflow in the plant and make sure the flow is out rather than in. Ideally, the bottling plant should be sealed off from the rest of the building, although, for practical reasons, this is not always possible. Another point is that bacterial aerosols can be formed by spraying the floor too vigorously during clean up. Always use a foaming disinfectant before spraying the floor with water.