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

By Scot E. Dowd, Yan Sun, Patrick R. Secor, D. Rhoads, B. Wolcott, G. James, R. Wolcott. BMC Microbiology, 2008

809 citations recorded by the source corpus.

BackgroundChronic 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).ResultsThere 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.ConclusionIf 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.

Subfields: Endocrinology, Diabetes and Metabolism, Molecular Biology, Rehabilitation

View Paper: https://www.semanticscholar.org/paper/d3782a9bed29be76b622089ae5bde454213b2ed5

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In Endocrinology, Diabetes and Metabolism

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Citations in the corpus

Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) (2008, methodology): “The use of rapid sequencing technologies combined with molecular methods is becoming a gold standard for evaluating the microbiomes of animals [21-25].”
Microbial Biofilm: A Review on Formation, Infection, Antibiotic Resistance, Control Measures, and Innovative Treatment (2023, positive): “As aerobic bacteria create biofilms on the exterior of deep wounds, anaerobic bacteria invade the interior [68,69].”
The skin microbiome (2011, background): “However, molecular studies thus far have been unable to identify a unique organism that colonizes wounds of the same aetiology (for example, in diabetic foot ulcers or venous leg ulcers”
Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing (2008, background): “Other recent human health studies include microbes in breast milk [18], chronic wounds [19], human gut [20], dental caries [21], and childcare facilities [22].”
The wound microbiota: microbial mechanisms of impaired wound healing and infection (2024, positive): “B. fragilis is a predominant anaerobe found in bite wounds, surgical wounds from intestinal surgery and chronic wounds 88,98 .”
Targeting bacterial membrane function: an underexploited mechanism for treating persistent infections (2010, background): “Most approaches do not consider that medical biofilms often have a polymicrobial compositio”
Epithelialization in Wound Healing: A Comprehensive Review (2014, background): “Depending on the study and the type of chronic wounds evaluated, among the most prevalent genus in chronic wounds were Staphylococcus, Pseudomonas, and Corynobacterium, while obligate anaerobes Bacteroides, Peptoniphilus, Fingoldia, Anaerococcus, and Peptostreptococcus spp were identified as well.(1”
Culture-independent molecular tools for soil and rhizosphere microbiology (2013, background): “In addition, interpretation can be misleading as a single band may represent multiple species and same species may be represented by multiple bands [68,69].”
Pyrosequencing analysis of the Oral Microflora of healthy adults (2008, background): “Within the human body, vaginal microflora (Sundquist et al., 2007) and bacteria of chronic wounds (Dowd et al., 2008) have been assessed by this approach, but we are not aware of reports on the oral microbial population.”
Characterization of bacterial populations in Danish raw milk cheeses made with different starter cultures by denaturating gradient gel electrophoresis and pyrosequencing (2011, methodology): “…been used to monitor microbial communities in various ecosystems like sputum (Armougom et al., 2009), gut (Andersson et al., 2008; Larsen et al., 2010), soil (Acosta-Martinez, Dowd, Sun, & Allen, 2008), wounds (Dowd et al., 2008) and fermented foods (Humblot & Guyot, 2009; Roh et al., 2010).”