Surgical Instrument Cleaning Protocols, Cleaning of Surgical Instruments Prior to Sterilization, Cleaning Surgical Instruments Process, and Cleaning and Disinfecting Surgical Instruments. Yellow-brown to dark-brown stains or spots on surgical stainless steel instruments are frequently mistaken for rust. These residue deposits stains or spots arranged in groups or along edges or in crevices are usually the instrument being exposed to result of high chloride content. They will lead to pitting of the surgical instrument surface if not removed. Excessively hard water can contain high levels of salt sufficient to cause stains or spots that appear as rust. Boilers used to generate the steam for steam sterilizers, if not cleaned properly, will produce contaminated steam which can deposit minerals onto instruments during the sterilization process. Neutral pH Cleaning Concentrates recommended by Device Manufacturers. Virtually all manufacturers of surgical instruments, rigid scopes, flexible scopes, and instrument containers recommend the use of neutral pH Cleaning Concentrates. Do not use high acidic (pH <4) or high alkaline (pH >10) products for disinfection or cleaning, since these can corrode metal, cause  discoloration or stress fractures. The high pH of bleach causes surface deposits of brown stains and might even corrode the instrument.  Even high quality stainless steel is not impervious to an acidic  bleach solution. 

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Tap or Source Water when Cleaning Surgical Instruments
Tap water can contain many minerals, which may discolor and stain surgical instruments.  It is recommended that de-ionized water be used for the final rinsing to prevent  spotting. all-in-one or combination cleaning concentrates can be effective in treating unacceptably hard source water and removing hard water encrustation from surgical  instruments and equipment.  If untreated tap water is used for final rinsing, then the instruments must be dried immediately to avoid staining.
Manufacturers of surgical instruments recommend the use of neutral pH enzyme detergent cleaners. Neutral pH all-in-one or combination enzyme surgical instrument cleaner detergent concentrates have  been shown to be effective in optimizing the efficacy of the passive oxide layer. This will provide a longer life for stainless steel surgery instruments. Cleaning concentrates with a high or low pH have been shown to erode the passive layer. The most common of these cleaning concentrates utilize an alkaline detergent with an acid neutralizer. Virtually all manufacturers of surgical instruments and surgical instrument containers recommend against using these detergents and recommend using a neutral ph detergent. To maintain moving parts and protect instruments from staining and rusting during sterilization and storage, they should be lubricated with a water-soluble, preserved  lubricant after each cleaning. Most automated washer decontaminators provide the option for lubrication at the end of the final rinse treatment. Staining and spotting may result if residual chemicals are not completely rinsed from surgery instruments that are subjected to steam sterilization. Following the manufacturer’s recommendations for the proper sequence of treatments (cold water pre-wash, enzyme-detergent wash, purified water rinse/lubrication, and drying) is critical to prevent stains and spots. A Cleaning Concentrates that will avoid spotting are free-rinsing.