Advances in the Microbiome: Applications to Clostridium difficile Infection

Abstract

Clostridium difficile is a major cause of morbidity and mortality worldwide, causing over 400,000 infections and approximately 29,000 deaths in the United States alone each year. C. difficile is the most common cause of nosocomial diarrhoea in the developed world, and, in recent years, the emergence of hyper-virulent (mainly ribotypes 027 and 078, sometimes characterised by increased toxin production), epidemic strains and an increase in the number of community-acquired infections has caused further concern. Antibiotic therapy with metronidazole, vancomycin or fidaxomicin is the primary treatment for C. difficile infection (CDI). However, CDI is unique, in that, antibiotic use is also a major risk factor for acquiring CDI or recurrent CDI due to disruption of the normal gut microbiota. Therefore, there is an urgent need for alternative, non-antibiotic therapeutics to treat or prevent CDI. Here, we review a number of such potential treatments which have emerged from advances in the field of microbiome research.

Keywords: Clostridium difficile; antibiotic resistance; bacteriocin; faecal microbiota transplantation (FMT); genome sequencing; gut microbiota; human gut microbiome; nanopore sequencing; probiotics; synthetic biology.

Figure 1

(A) Overview of C. difficile infection (CDI). CDI results from ingestion of C. difficile spores, which germinate to vegetative cells in the gastrointestinal tract. C. difficile produces potent toxins, which cause enterotoxic, cytotoxic and inflammatory damage to intestinal epithelial cells. Primary treatment of CDI with antibiotics (e.g., metronidazole, vancomycin or fidaxomicin) can lead to clinical resolution of infection, but in some cases, relapse can occur causing recurrent CDI; (B) Overview of potential non-antibiotic therapeutic alternatives for CDI. (I) Faecal microbiota transplantation (FMT) involves the transfer of a whole stool preparation from a healthy donor to a patient with CDI. Cure rates of ~90% have been reported from numerous trials of patients with CDI, making FMT one of the most promising non-antibiotic therapeutics; (II) Use of defined mixtures of bacterial strains or spore preparations have also been trialled for treatment of CDI; (III) Antimicrobial compounds produced by bacteria, such as bacteriocins and small molecule metabolites have been identified, some with potent anti-C. difficile activity (e.g., thuricin CD); (IV) Probiotic strains of bacteria and yeast may hold some promise for the prevention of CDI, when administered as adjunct therapies with antibiotics; (V) Integrating developments in synthetic biology and genetic engineering may enable the development of bioengineered probiotics, which target specific pathogens and toxins; (C) (I) Whole genome sequencing (WGS) has the potential to revolutionise pathogen diagnostics. Ultra-fine resolution single nucleotide polymorphism (SNP) analysis and phylogenetic reconstructions can help improve the identification of the source of an infectious disease outbreak, as well as potential transmission events. Improvements to DNA sequencing technologies, such as Oxford Nanopore’s MinION, could also dramatically reduce the time from sample isolation to pathogen identification; (II) Similarly, microbiome-wide association studies (MWAS) have the potential to improve our understanding of disease dynamics and the complex interactions between pathogen and the host microbiota during infection, by integrating approaches such as metagenomics, metaproteomics, metatranscriptomics and metabolomics.