The 16S rRNA sequencing data and metadata generated in this study have been submitted to the NCBI Sequence Read Archive (SRA: http://www.ncbi.nlm.nih.gov/bioproject/381931).

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The margin of safety for the 100% EtO, vaporized H2O2, and ion plasma sterilizers is less than that of the 12/88 sterilizer. The inability of all sterilizers, including the 12/88, to kill organisms in narrow lumens reliably when serum and salt were present raises concern about the current practice of gas sterilization of flexible endoscopes.