Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota

• Published in: PloS one 2009-07, Vol.4 (7), p.e6462-e6462
• Main Authors: Price, Lance B, Liu, Cindy M, Melendez, Johan H, Frankel, Yelena M, Engelthaler, David, Aziz, Maliha, Bowers, Jolene, Rattray, Rogan, Ravel, Jacques, Kingsley, Chris, Keim, Paul S, Lazarus, Gerald S, Zenilman, Jonathan M
• Format: Article
• Language: English
• Subjects: Acids; Adult; Aged; Agroforestry; Anaerobic bacteria; Anaerobic conditions; Analysis; Anti-Bacterial Agents - pharmacology; Anti-Bacterial Agents - therapeutic use; Antibiotics; Bacteria; Bacteria - classification; Bacteria - drug effects; Bacteria - genetics; Bacterial Infections - drug therapy; Biodiversity; Chronic Disease; Chronic illnesses; Cohort Studies; Colonization; Community ecology; Community structure; Comparative analysis; Dermatology/Skin Infections; Diabetes; Diabetes and Endocrinology; Diabetes mellitus; Diabetes Mellitus - microbiology; DNA sequencing; Drug resistance; Ecology/Community Ecology and Biodiversity; Female; Genes; Genetic research; Genomics; Healing; Humans; Infectious Diseases; Infectious Diseases/Antimicrobials and Drug Resistance; Infectious Diseases/Bacterial Infections; Infectious Diseases/Skin Infections; Male; Medical research; Microbial Sensitivity Tests; Microbiology; Microbiology/Medical Microbiology; Microbiota (Symbiotic organisms); Middle Aged; Molecular Biology; Multivariate analysis; Patients; RNA; RNA, Ribosomal, 16S - genetics; rRNA 16S; Staphylococcus infections; Statistical methods; Studies; Taxonomy; Ulcers; Wound healing; Wounds and Injuries - microbiology
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0006462

Bacterial colonization is hypothesized to play a pathogenic role in the non-healing state of chronic wounds. We characterized wound bacteria from a cohort of chronic wound patients using a 16S rRNA gene-based pyrosequencing approach and assessed the impact of diabetes and antibiotics on chronic wound microbiota. We prospectively enrolled 24 patients at a referral wound center in Baltimore, MD; sampled patients' wounds by curette; cultured samples under aerobic and anaerobic conditions; and pyrosequenced the 16S rRNA V3 hypervariable region. The 16S rRNA gene-based analyses revealed an average of 10 different bacterial families in wounds--approximately 4 times more than estimated by culture-based analyses. Fastidious anaerobic bacteria belonging to the Clostridiales family XI were among the most prevalent bacteria identified exclusively by 16S rRNA gene-based analyses. Community-scale analyses showed that wound microbiota from antibiotic treated patients were significantly different from untreated patients (p = 0.007) and were characterized by increased Pseudomonadaceae abundance. These analyses also revealed that antibiotic use was associated with decreased Streptococcaceae among diabetics and that Streptococcaceae was more abundant among diabetics as compared to non-diabetics. The 16S rRNA gene-based analyses revealed complex bacterial communities including anaerobic bacteria that may play causative roles in the non-healing state of some chronic wounds. Our data suggest that antimicrobial therapy alters community structure--reducing some bacteria while selecting for others.