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

Daniel D Rhoads,Eric J Rees,Randall D Wolcott,Yan Sun,Stephen B Cox

doi:10.1186/1471-2334-12-321

Daniel D Rhoads, Eric J Rees + Show 3 more

Open Access

https://doi.org/10.1186/1471-2334-12-321

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Abstract

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.

Highlights

Chronic wounds affect millions of people and cost billions of dollars in the United States each year
Results & discussion Like previous studies, this study demonstrates that culture testing and molecular testing of wound bacteria produce differing and often conflicting results because molecular methods are more sensitive than culture methods [7,8,9,10]
These findings are different from what has been previously reported in a study using a different molecular method of analysis, which reported, “the absence of a correlation between the bacterial species [Staphylococcus aureus and Pseudomonas aeruginosa] detected in wound by culture and what is present” [5]

Summary

Introduction

Chronic 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. Chronic wounds impact the health of over 8 million people in the United States each year, and the direct healthcare associated cost of these wounds is over 25 billion of dollars each year [1]. These chronic wounds include venous stasis ulcers, diabetic foot ulcers, decubitus ulcers, and non-healing surgical wounds. The molecular test used in this study produces a relative abundance score, and we describe the relevance of this score and the correlation it has to culture results

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Conclusion