Can sequencing improve the diagnosis and management of clostridioides difficile infection?
Expert Review of Molecular Diagnostics
Taylor & Francis
School of Medical and Health Sciences
Clostridioides difficile is a bacterium of great public health importance, responsible for half of the hospital-acquired gastrointestinal infections in Europe , as well as approximately 13,000 deaths and losses of one billion dollars in healthcare-related costs annually in the United States . Genome sequencing and the rapidly growing field of genomics are transforming clinical medicine . Although genomics has greatly enhanced our understanding of the epidemiology of C. difficile infection (CDI) and transmission pathways of C. difficile [4–6], widespread implementation of sequencing in the diagnosis and management of CDI remains limited, perhaps due to the logistical requirements for diagnostic laboratories to generate and analyze sequence data , as well as the relatively slow turnaround time compared to current diagnostic tests: toxin enzyme immunoassays (EIAs) and real-time toxin gene PCRs . However, the availability of newer high-throughput benchtop platforms, the development of user-friendly long-read technologies (such as Oxford Nanopore Technology, ONT) and open access semi-automated bioinformatics pipelines, including pipelines for metagenomic analysis , have made sequencing faster, cheaper and more accessible than ever. Clinician access to C. difficile sequence data should start to impact the efficacy of CDI management, as has been shown for other infections .