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


RESULTS
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.


CONCLUSIONS
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.
Price
Lance B
LB
Translational Genomics Research Institute, Flagstaff, Arizona, United States of America. lprice@tgen.org
Liu
Cindy M
CM
Melendez
Johan H
JH
Frankel
Yelena M
YM
Engelthaler
David
D
Aziz
Maliha
M
Bowers
Jolene
J
Rattray
Rogan
R
Ravel
Jacques
J
Kingsley
Chris
C
Keim
Paul S
PS
Lazarus
Gerald S
GS
Zenilman
Jonathan M
JM
D000328:Adult; D000368:Aged; D000900:Anti-Bacterial Agents / Q000494:pharmacology* / Q000627:therapeutic use; D001419:Bacteria / Q000145:classification* / Q000187:drug effects / Q000235:genetics; D001424:Bacterial Infections / Q000188:drug therapy; D002908:Chronic Disease; D015331:Cohort Studies; D003920:Diabetes Mellitus / Q000382:microbiology*; D005260:Female; D006801:Humans; D008297:Male; D008826:Microbial Sensitivity Tests; D008875:Middle Aged; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D014947:Wounds and Injuries / Q000382:microbiology*
D000900:Anti-Bacterial Agents; D012336:RNA, Ribosomal, 16S