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Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing.

Dowd SE, Sun Y, Secor PR, Rhoads DD, Wolcott BM, James GA, Wolcott RD - BMC Microbiol. (2008)

Bottom Line: Results of molecular analyses were also 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: United States Department of Agriculture ARS Livestock Issues Research Unit, Lubbock, TX, USA. sdowd@lbk.ars.usda.gov

ABSTRACT

Background: Chronic wound pathogenic biofilms are host-pathogen environments that colonize and exist as a cohabitation of many bacterial species. These bacterial populations cooperate to promote their own survival and the chronic nature of the infection. Few studies have performed extensive surveys of the bacterial populations that occur within different types of chronic wound biofilms. The use of 3 separate16S-based molecular amplifications 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 (D), venous leg ulcers (V), and pressure ulcers (P).

Results: There are specific major populations of bacteria that were evident in the biofilms of all chronic wound types, 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 recognized as wound pathogens, such as Abiotrophia para-adiacens and Rhodopseudomonas spp. Results of molecular analyses were also 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.

Conclusion: 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 new molecular diagnostic tools, which can be used to identify the community compositions of chronic wound pathogenic biofilms and other medical biofilm infections.

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Distribution of Bacterial Populations in Chronic Wounds in Relation to Aerotolerance. Diabetic, venous, or pressure ulcer types were analyzed separately using pyrosequencing and the resulting populations grouped into 3 catagories based upon their suggested aerotolerance. This figure graphically illustrates the relative distribution of these functional catagories among the wound types.
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Figure 1: Distribution of Bacterial Populations in Chronic Wounds in Relation to Aerotolerance. Diabetic, venous, or pressure ulcer types were analyzed separately using pyrosequencing and the resulting populations grouped into 3 catagories based upon their suggested aerotolerance. This figure graphically illustrates the relative distribution of these functional catagories among the wound types.

Mentions: It should be noted that this paper is not intended to contrast each of the molecular methods, or to purposefully compare wound types, but rather to detail the results of each individually in the hopes of gaining an understanding of the microbial diversity within pathogenic biofilms. Although this study could be used to compare or contrast the three molecular methods, we sought instead to use these relatively different strategies to better survey and report the diversity in the different types of wounds. A portion of the bias of one molecular method (e.g. due to primer specificity and universality) we intended to be somewhat compensated by the other methods, each of which utilize different "universal" 16S primers. Another important note is that these analyses do not represent the diversity within a given wound from a single patient; instead these data represented diversity among a given chronic wound type. In-depth comparison of the populations between each wound type as part of this study would also have been outside the scope of the methodologies and experimental design employed. The primary observations that could be logically employed when comparing wound types are two-fold. Each wound type demonstrated populations and diversity that were markedly more prevalent than those seen in other wound types as discussed below. Each wound group also demonstrated a different level of oxygen tolerance among its bacterial populations (Figure 1). This second observation indicates there may be a common pathophysiology among wound types that likely affects the ecology of the wound environment and may play an important role in determining the bacterial genera that can become integrated as part of a wound biofilm. These observations obviously cannot be fully addressed within the scope of this survey yet they do provide important directions for future research.


Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing.

Dowd SE, Sun Y, Secor PR, Rhoads DD, Wolcott BM, James GA, Wolcott RD - BMC Microbiol. (2008)

Distribution of Bacterial Populations in Chronic Wounds in Relation to Aerotolerance. Diabetic, venous, or pressure ulcer types were analyzed separately using pyrosequencing and the resulting populations grouped into 3 catagories based upon their suggested aerotolerance. This figure graphically illustrates the relative distribution of these functional catagories among the wound types.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2289825&req=5

Figure 1: Distribution of Bacterial Populations in Chronic Wounds in Relation to Aerotolerance. Diabetic, venous, or pressure ulcer types were analyzed separately using pyrosequencing and the resulting populations grouped into 3 catagories based upon their suggested aerotolerance. This figure graphically illustrates the relative distribution of these functional catagories among the wound types.
Mentions: It should be noted that this paper is not intended to contrast each of the molecular methods, or to purposefully compare wound types, but rather to detail the results of each individually in the hopes of gaining an understanding of the microbial diversity within pathogenic biofilms. Although this study could be used to compare or contrast the three molecular methods, we sought instead to use these relatively different strategies to better survey and report the diversity in the different types of wounds. A portion of the bias of one molecular method (e.g. due to primer specificity and universality) we intended to be somewhat compensated by the other methods, each of which utilize different "universal" 16S primers. Another important note is that these analyses do not represent the diversity within a given wound from a single patient; instead these data represented diversity among a given chronic wound type. In-depth comparison of the populations between each wound type as part of this study would also have been outside the scope of the methodologies and experimental design employed. The primary observations that could be logically employed when comparing wound types are two-fold. Each wound type demonstrated populations and diversity that were markedly more prevalent than those seen in other wound types as discussed below. Each wound group also demonstrated a different level of oxygen tolerance among its bacterial populations (Figure 1). This second observation indicates there may be a common pathophysiology among wound types that likely affects the ecology of the wound environment and may play an important role in determining the bacterial genera that can become integrated as part of a wound biofilm. These observations obviously cannot be fully addressed within the scope of this survey yet they do provide important directions for future research.

Bottom Line: Results of molecular analyses were also 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: United States Department of Agriculture ARS Livestock Issues Research Unit, Lubbock, TX, USA. sdowd@lbk.ars.usda.gov

ABSTRACT

Background: Chronic wound pathogenic biofilms are host-pathogen environments that colonize and exist as a cohabitation of many bacterial species. These bacterial populations cooperate to promote their own survival and the chronic nature of the infection. Few studies have performed extensive surveys of the bacterial populations that occur within different types of chronic wound biofilms. The use of 3 separate16S-based molecular amplifications 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 (D), venous leg ulcers (V), and pressure ulcers (P).

Results: There are specific major populations of bacteria that were evident in the biofilms of all chronic wound types, 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 recognized as wound pathogens, such as Abiotrophia para-adiacens and Rhodopseudomonas spp. Results of molecular analyses were also 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.

Conclusion: 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 new molecular diagnostic tools, which can be used to identify the community compositions of chronic wound pathogenic biofilms and other medical biofilm infections.

Show MeSH
Related in: MedlinePlus