Molecular Strain Typing and Characterisation of Toxigenic Clostridium difficile

At the turn of the century, a shift in incidence of Clostridium difficile infection occurred with the emergence of a novel, more virulent strain of C. difficile . It became apparent that strain typing was critical to our understanding of the epidemiology and transmission of the disease. Over the past 25 years, C. difficile strain typing methods have developed from phenotypic to genotypic techniques, each with their own advantages and disadvantages. Unfortunately, with the advent of polymerase chain reaction for C. difficile diagnosis, many clinical laboratories no longer perform anaerobic culture of the organism, and therefore routine strain typing for surveillance or detection of hospital outbreaks is rarely performed. Even among reference laboratories that do perform strain typing of C. difficile , standardisation of methods and inter-laboratory exchange of data continues to be problematic. Herein, an overview of molecular strain typing methods for C. difficile is provided, along with specific applications and limitations of each technique. In addition, current efforts to standardise laboratory protocols and a review of recent studies are discussed.