The canine skin and ear microbiome: A comprehensive survey of pathogens implicated in canine skin and ear infections using a novel next-generation-sequencing-based assay
The canine skin and ear microbiome: A comprehensive survey of pathogens implicated in canine skin and ear infections using a novel next-generation-sequencing-based assay
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DOI：
10.1016/j.vetmic.2020.108764
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发表时间：
2020-08-01
影响因子：
3.3
通讯作者：
Krumbeck, Janina A.
中科院分区：
文献类型：
--
作者：
Tang, Shuiquan;Prem, Aishani;Krumbeck, Janina A.
这项研究分析了健康和临床受影响的犬耳和皮肤样本中复杂的细菌和真菌微生物群。总共包括 589 份犬样本：使用下一代测序 (NGS) 分析 257 份耳拭子样本（128 份健康对照 129 份临床受影响）和 332 份皮肤拭子样本（172 份健康对照 160 份临床受影响），以确定样本中存在的细菌和真菌的相对和绝对丰度。这项研究强调了临床受影响病例的犬类微生物群的特点是微生物多样性总体丧失、微生物生物量高，并且微生物群的某些成员过度生长。这些样品观察到的表型最好通过相对和绝对微生物丰度的组合来描述。与健康样本相比，78.3% 的临床受影响耳朵样本存在微生物过度生长； 69.8% 存在细菌过度生长，16.3% 存在真菌过度生长，7.0% 存在细菌和真菌过度生长。临床受影响的耳朵中富集的最重要的微生物类群是厚皮马拉色菌、伪中间葡萄球菌、施莱弗氏葡萄球菌和一些厌氧菌，例如大菲尼戈尔德菌、犬消化链球菌和牙龈卟啉单胞菌。这里鉴定出的厌氧微生物以前并不被普遍认为是犬耳感染的病原体。在皮肤样本中也发现了类似的观察结果，但与临床受影响的病例相比，酵母菌和厌氧菌的丰度较低。本文强调的结果表明，基于 NGS 的方法在诊断犬皮肤和耳朵感染时准确定量和鉴定细菌和真菌种群的潜力，并强调了传统基于培养的测试的局限性。
This study analyzed the complex bacterial and fungal microbiota of healthy and clinically affected canine ear and skin samples. A total of 589 canine samples were included: 257 ear swab samples (128 healthy vs. 129 clinically affected) and 332 skin swab samples (172 healthy vs. 160 clinically affected) were analyzed using next-generation sequencing (NGS) to determine both relative and absolute abundances of bacteria and fungi present in the samples. This study highlighted the canine microbiota of clinically affected cases was characterized by an overall loss of microbial diversity, high microbial biomass, with overgrowth of certain members of the microbiota. The observed phenotype of these samples was best described by the combination of both relative and absolute microbial abundances. Compared to healthy samples, 78.3% of the clinically affected ear samples had microbial overgrowth; 69.8% bacterial overgrowth, 16.3% fungal overgrowth, and 7.0% had both bacterial and fungal overgrowth. The most important microbial taxa enriched in clinically affected ears were Malassezia pachydermatis, Staphylococcus pseudintermedius, Staphylococcus schleiferi, and a few anaerobic bacteria such as Finegoldia magna, Peptostreptococcus canis, and Porphyromonas cangingivalis. The anaerobic microbes identified here were previously not commonly recognized as pathogens in canine ear infections. Similar observations were found for skin samples, but yeasts and anaerobes were less abundant when compared to clinically affected cases.Results highlighted herein, signify the potential of NGS-based methods for the accurate quantification and identification of bacterial and fungal populations in diagnosing canine skin and ear infections, and highlight the limitations of traditional culture-based testing.