Biomaterial-related infection represents a significant public health issue and financial burden on the governments around the world. The situation is likely to get worse in the future with the prevalence of antibiotic-resistant bacteria and increasing adoption of biomedical implants and devices. It is estimated that by 2050 drug-resistant bacteria will kill 10 million people a year worldwide. The most common nosocomial complications associated with biomaterials are catheter-associated urinary tract infections (CAUTIs), which account for over 1 million cases annually and represent over 40% of all nosocomial infections in hospitals and aged care homes and community facilities and 80% of all nosocomial UTIs. The annual hospital costs associated with CAUTIs were estimated to be $390 to $450 million in 2009 in the USA. CAUT is of particular risk to those patients who are continuously catheterised. These issues are particularly exacerbated by the rise of drug resistant pathogens, limiting treatment options and highlights the need for new strategies to monitor and treat infections. In this study, we have performed whole community sequencing and molecular finger-printing of catheter associated biofilms to monitor changes in the communities with a view to define community changes that are associated with or predictive of infections. In addition, patients who participated in a probiotic treatment study were included and sequence data demonstrates changes in the host microflora associated with inclusion in the probiotic groups. The results show congruence of fingerprinting and sequencing methods and suggest that fingerprinting methods can be used to develop early intervention strategies to minimise infection risk.