The primary purpose of an enzyme surgical instrument cleaner is to remove all inorganic and organic bioburden material from the internal and external surfaces of surgical instruments and endoscopes. The secondary purpose of cleaning surgical instruments and scopes is to maintain and improve the passive Layer of stainless steel. 

The passive layer is provided by the manufacturer of surgical stainless steel to resist (prevent) corrosion. Proper cleaning of surgical instruments will maintain and improve this passive layer

If the manual cleaning of surgical instruments, brushing and rinsing steps are not properly carried out, protein debris can harden and lead to formation of biofilm on the biopsy channel of the endoscope. The optimal cleaning surgical instrument protocol will break down bioburden and clean the surface. Inadequate cleaning surgical of instruments can thus result in material remaining on the endoscope surfaces which prevents disinfection and sterilization fluids or gases reaching all parts of potentially contaminated surfaces. Inadequate sterilization or disinfection may in turn result in transmission of infectious organisms when the endoscope is reused. The intricate design, delicate materials and susceptibility to damage of flexible endoscopes further complicates their decontamination. 

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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 and recommend using a neutral ph detergent. 

Enzyme Surgical Instrument Cleaners function more effectively at temperatures above room temperature. The optimal range begins as > 22C - 72°F with performance reaching it's peak at 58.3C - 137F. This is often referred to as the optimal temperature for the performance or activity of enzymatic action. The activity of Surgical Instrument Cleaners enzymes does not stop at higher temperatures but the level of performance does begin to decrease. Enzyme cleaning concentrates enzyme-detergents and all-in-one Surgical Instrument Cleaners, which include enzymes, should be used in accordance with the manufacturer's recommendations and the recommendations of the medical devices being cleaned.

The use of combination enzymatic detergent Surgical Instrument Cleaners has offered the highest level of cleaning outcomes. Sterilization of an inadequately cleaned instrument is not possible. Cleaning is the prerequisite for sterilization. All disinfection processes, whether done manually or done automatically in a surgical instrument washer can only be effective if prior cleaning is adequate.