Bacterial keratitis and bacterial endophthalmitis are two of the most devastating sight threatening eye infections. It is currently unclear whether the organisms isolated from these infections represent specialised members of these species or whether all strains are equally likely to cause infection. One method of differentiating strains genotypically is by a typing technique known as multilocus sequence typing (MLST). Using this technique, a better understanding of the molecular epidemiology of eye infections can be achieved.\ud Propionibacterium acnes (P. acnes) is an important anaerobic organism causing several types of eye infections. Although it is now beginning to be recognised as a serious opportunistic pathogen, few studies have been done to investigate the population biology of P. acnes at the molecular level. Our continuing inability to distinguish between strains of P. acnes means that we still do not fully understand how antibiotic-resistant strains spread, nor whether certain strains, or clonal complexes, of P. acnes are associated with certain infections. These are key issues that can now be understood with our development of an MLST system for P. acnes. A diverse culture collection of 125 P. acnes isolates have been analysed using the MLST scheme developed. Sequence analysis shows that there are phylogenetically distinct groups within P. acnes and identified a novel cluster not previously described. Analysis of recombination using several methods suggests that frequent recombination occurs within these subgroups. There appears to be no association between these subgroups and clinical manifestation of P. acnes infection or geographical location. The P. acnes MLST scheme was validated against 16S rRNA gene and complete recA gene typing as well as immunofluorescence microscopy (IFM) and random amplification of polymorphic DNA (RAPD) analysis.\ud P. acnes is a slow growing organism and is difficult to culture from ocular samples. A real-time PCR assay was developed in order to overcome the low culture positive rate and delay associated with conventional culture methods. Primers targeting one of the seven housekeeping genes used in the MLST scheme (gmk), specific for P. acnes were selected. The real-time PCR assay was both specific to P. acnes and highly sensitive.\ud Pseudomonas aeruginosa (P. aeruginosa) is another important organism in the development of serious eye infections, and is the commonest cause of contact lens related microbial keratitis. Infections with this organism can lead to rapid deterioration of vision and possible blindness. A previously developed MLST scheme has been applied to 117 eye isolates from around the UK and China. This typing data was compared to 166 P. aeruginosa isolates from other clinical and environmental sources. Overall, MLST data supports previous findings that P. aeruginosa has a nonclonal population with epidemic clones. Sequence analysis showed that eye isolates do not cluster away from isolates from other clinical infection sites
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