Health-care professionals need to collect wound samples to identify potential pathogens that contribute to wound infection. Obtaining appropriate samples from diabetic foot ulcers (DFUs) where there is a suspicion of infection is of high importance. Paired swabs and tissue biopsies were collected from DFUs and both sampling techniques were compared using 16S rRNA gene sequencing. Mean bacterial abundance determined using quantitative polymerase chain reaction (qPCR) was significantly lower in tissue biopsies (p = 0.03). The mean number of reads across all samples was significantly higher in wound swabs $$ \Big(\overline{X} $$ = 32,014) compared to tissue ($$ \overline{X} $$ = 15,256, p = 0.001). Tissue biopsies exhibited greater overall diversity of bacteria relative to swabs (Shannon’s H diversity p = 0.009). However, based on a presence/absence analysis of all paired samples, the frequency of occurrence of bacteria from genera of known and potential pathogens was generally higher in wound swabs than tissue biopsies. Multivariate analysis identified significantly different bacterial communities in swabs compared to tissue (p = 0.001). There was minimal correlation between paired wound swabs and tissue biopsies in the number and types of microorganisms. RELATE analysis revealed low concordance between paired DFU swab and tissue biopsy samples (Rho = 0.043, p = 0.34). Using 16S rRNA gene sequencing this study identifies the potential for using less invasive swabs to recover high relative abundances of known and potential pathogen genera from DFUs when compared to the gold standard collection method of tissue biopsy.

中文翻译：

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糖尿病足溃疡的微生物组：使用16S rRNA基因测序的拭子和组织活检伤口采样技术的比较。

卫生保健专业人员需要收集伤口样本，以识别导致伤口感染的潜在病原体。从怀疑有感染的糖尿病足溃疡（DFU）中获取适当的样品非常重要。从DFU中收集成对的拭子和组织活检样品，并使用16S rRNA基因测序比较两种采样技术。在组织活检中，使用定量聚合酶链反应（qPCR）测定的平均细菌丰度显着降低（p = 0.03）。与组织（$$ \ overline {X} $$ = 15,256，p = 0.001）相比，伤口拭子$$ \ Big（\ overline {X} $$ = 32,014）中所有样本的平均读取次数显着更高。相对于拭子，组织活检显示细菌总体多样性更高（Shannon H多样性p = 0.009）。然而，根据所有成对样品的存在/不存在分析，伤口拭子中来自已知和潜在病原体属的细菌的发生频率通常高于组织活检。与组织相比，多变量分析确定了拭子中的细菌群落显着不同（p = 0.001）。配对的拭子与组织活检之间的微生物数量和类型之间的相关性最小。相关分析显示，成对的DFU拭子和组织活检样本之间的一致性较低（Rho = 0.043，p = 0.34）。与组织活检的金标准收集方法相比，使用16S rRNA基因测序可以确定使用侵入性较小的药签从DFU中回收相对较高的已知病原体和潜在病原体属的潜力。在伤口拭子中，来自已知和潜在病原体属的细菌的发生频率通常高于组织活检。与组织相比，多变量分析确定了拭子中细菌的显着不同（p = 0.001）。配对的拭子与组织活检之间的微生物数量和类型之间的相关性最小。相关分析显示，成对的DFU拭子和组织活检样本之间的一致性较低（Rho = 0.043，p = 0.34）。与组织活检的金标准收集方法相比，使用16S rRNA基因测序可以确定使用侵入性较小的药签从DFU中回收相对较高的已知病原体和潜在病原体属的潜力。通常，伤口拭子中来自已知和潜在病原体属的细菌的发生频率高于组织活检。与组织相比，多变量分析确定了拭子中的细菌群落显着不同（p = 0.001）。配对的拭子与组织活检之间的微生物数量和类型之间的相关性最小。相关分析显示，成对的DFU拭子和组织活检样本之间的一致性较低（Rho = 0.043，p = 0.34）。与组织活检的金标准收集方法相比，使用16S rRNA基因测序可以确定使用侵入性较小的药签从DFU中回收相对较高的已知病原体和潜在病原体属的潜力。