Submitted to: BMC Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/1/2008
Publication Date: 3/10/2008
Citation: Dowd, S.E., Sun, Y., Secor, P.R., Rhoads, D.D., Wolcott, B.M., James, G.A., Wolcott, R.D. 2008. Survey of bacterial diversity in chronic wounds using Pyrosequencing, DGGE, and full ribosome shotgun sequencing. BMC Microbiology. 8:article 43. Interpretive Summary: Biofilms are the natural state in which bacteria reside in the environment. The study and development of methods to characterize the microbial diversity in pathogenic biofilms is vital to address the needs of public health and science. ARS scientists in Lubbock, TX, assisted leading world experts in biofilms to develop pyrosequencing as a method to characterize the diversity of pathogenic biofilms using chronic wound biofilms as a model. The use of pyrosequencing for determining microbial diversity in biofilms has advanced this area of research into a new paradigm. These next generation genetic methods and analyses tools being developed as part of this research can now be adapted to the study and monitoring of microbial diversity in many different environments.
Technical Abstract: Background: Chronic wound pathogenic biofilms are host-pathogen environments that colonize and exist as a cohabitation of many bacterial species that cooperate to promote their own survival and the chronic nature of the infection. Few studies have performed extensive surveys of the different populations that occur within different types of chronic wounds. Information on those bacterial species that occur as part of pathogenic biofilms is needed to aid in the design of better diagnostic tools. The use of 16S molecular amplification techniques followed by pyrosequencing, shotgun Sanger sequencing, and denaturing gradient gel electrophoresis were utilized to survey the major populations of bacteria that occur in the pathogenic biofilms of three types of chronic wound types: diabetic foot ulcers, venous leg ulcers, and pressure ulcers. Results: There are specific major populations of bacteria that are evident in all chronic wound biofilms, including Staphylococcus, Pseudomonas, Peptoniphilus, Enterobacter, Stenotrophomonas, Finegoldia, and Serratia spp. Each of the wound types reveals marked differences in bacterial populations, such as pressure ulcers in which 62% of the populations were identified as obligate anaerobes. There were also populations of bacteria that were identified but not widely recognized as wound pathogens, such as Abiotrophia para-adiacens and Rhodopseudomonas spp. Results of molecular analyses were compared to those obtained using traditional culture-based diagnostics. Only in one wound type did culture methods correctly identify the primary bacterial population indicating the need for improved diagnostic methods. Conclusions: If clinicians can gain a better understanding of the wound’s microbiota, it will give them a greater understanding of the wound’s ecology and will allow them to better manage healing of the wound improving the prognosis of patients. This research highlights the necessity to begin evaluating, studying, and treating chronic wound pathogenic biofilms as multi-species entities in order to improve the outcomes of patients. This survey will also foster the pioneering and development of molecular diagnostic tools that could be used to identify the community compositions of chronic wound pathogenic biofilms and other medical biofilm infections.