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Background and Importance Internal audits play a key role in ensuring compliance and continuous improvement within the hospital pharmacy compounding unit. Risk-based internal audits (RBIA) focus on high risk areas to improve efficiency and resource allocation.Aim and Objectives We aimed to determine whether an RBIA program is at least as effective as a compliance-based system audit (SA) program in identifying both total and severe (major or critical) nonconformities of the hospital pharmacy compounding unit.Material and Methods Compounding processes subject to RBIA were selected through risk analysis using an algorithm validated by the Belgian pharmaceutical association (Algemene Pharmaceutische Bond (APB)). This was followed by a prospective comparison of multiple audits by independent assessors using either the RBIA or SA approach. A multicentre expert Delphi panel classified the nonconform findings by severity, which served as a proxy of audit effectiveness.Results In total, eight audits were conducted by four RBIA and four SA auditors. Both groups audited a median of 75% out of the total 222 standard. RBIA auditors identified significantly more nonconformities than SA auditors, especially those scored critical (p= .049) and major (p= .021).Conclusion and Relevance This pioneering study demonstrates that risk-based auditing, guided by algorithm-driven risk analysis, is more effective at identifying severe nonconformities within the same timeframe. This results in an increase in regulatory compliance and may improve the quality of the compounding operations and its products.Conflict of Interest No conflict of interest