Clinical identification of bacteria in human chronic wound infections: culturing vs. 16S ribosomal DNA sequencing

BMC Infectious Diseases

Research Article

Daniel D Rhoads¹  Stephen B Cox²  Yan Sun²  Eric J Rees²  Randall D Wolcott³ 

[1] Department of Pathology, University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, USA;Research and Testing Laboratory (RTL), Lubbock, TX, USA;Research and Testing Laboratory (RTL), Lubbock, TX, USA;Southwest Regional Wound Care Center (WCC), Lubbock, TX, USA;PathoGenius Laboratories (PGL), Lubbock, TX, USA;

关键词: Pressure ulcer;    Diabetic foot;    Molecular diagnostic techniques;    Bacteria;    Microbiology;    16S;   

DOI  :  10.1186/1471-2334-12-321

 received in 2012-04-19, accepted in 2012-11-05,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundChronic wounds affect millions of people and cost billions of dollars in the United States each year. These wounds harbor polymicrobial biofilm communities, which can be difficult to elucidate using culturing methods. Clinical molecular microbiological methods are increasingly being employed to investigate the microbiota of chronic infections, including wounds, as part of standard patient care. However, molecular testing is more sensitive than culturing, which results in markedly different results being reported to clinicians. This study compares the results of aerobic culturing and molecular testing (culture-free 16S ribosomal DNA sequencing), and it examines the relative abundance score that is generated by the molecular test and the usefulness of the relative abundance score in predicting the likelihood that the same organism would be detected by culture.MethodsParallel samples from 51 chronic wounds were studied using aerobic culturing and 16S DNA sequencing for the identification of bacteria.ResultsOne hundred forty-five (145) unique genera were identified using molecular methods, and 68 of these genera were aerotolerant. Fourteen (14) unique genera were identified using aerobic culture methods. One-third (31/92) of the cultures were determined to be < 1% of the relative abundance of the wound microbiota using molecular testing. At the genus level, molecular testing identified 85% (78/92) of the bacteria that were identified by culture. Conversely, culturing detected 15.7% (78/497) of the aerotolerant bacteria and detected 54.9% of the collective aerotolerant relative abundance of the samples. Aerotolerant bacterial genera (and individual species including Staphylococcus aureus, Pseudomonas aeruginosa, and Enterococcus faecalis) with higher relative abundance scores were more likely to be detected by culture as demonstrated with regression modeling.ConclusionDiscordance between molecular and culture testing is often observed. However, culture-free 16S ribosomal DNA sequencing and its relative abundance score can provide clinicians with insight into which bacteria are most abundant in a sample and which are most likely to be detected by culture.

【 授权许可】

Unknown   
© Rhoads et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.