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Next generation sequencing (NGS) is becoming the new gold standard in public health microbiology. Like any disruptive technology, its growing popularity inevitably attracts cyber security actors, for whom the health sector is attractive because it combines mission-critical infrastructure and high-value data with cybersecurity vulnerabilities. In this Perspective, we explore cyber security aspects of microbial NGS. We discuss the motivations and objectives for such attack, its feasibility and implications, and highlight policy considerations aimed at threat mitigation. Particular focus is placed on the attack vectors, where the entire process of NGS, from sample to result, could be vulnerable, and a risk assessment based on probability and impact for representative attack vectors is presented. Cyber attacks on microbial NGS could result in loss of confidentiality (leakage of personal or institutional data), integrity (misdetection of pathogens) and availability (denial of sequencing services). NGS platforms are also at risk of being used as propagation vectors, compromising an entire system or network. Owing to the rapid evolution of microbial NGS and its applications, and in light of the dynamics of the cyber security domain, frequent risk assessments should be carried out in order to identify new threats and underpin constantly updated public health policies.


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