Assessing the faecal source sensitivity and specificity of ruminant and human genetic microbial source tracking markers in the central Ethiopian highlands,Letters in Applied Microbiology

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Assessing the faecal source sensitivity and specificity of ruminant and human genetic microbial source tracking markers in the central Ethiopian highlands
Letters in Applied Microbiology ( IF 2.0 ) Pub Date : 2020-12-24 , DOI: 10.1111/lam.13436
R.B. Linke ₁ , G. Kebede _{2,

3} , D. Mushi ₄ , A. Lakew ₅ , D.S. Hayes _{3,

6} , W. Graf ₃ , A.H. Farnleitner _{1,

7}

Affiliation

This study tested genetic microbial source tracking (MST) methods for identifying ruminant- (BacR) and human-associated (HF183/BacR287, BacHum) bacterial faecal contaminants in Ethiopia in a newly created regional faecal sample bank (n=173). BacR performed well, and its marker abundance was high (100% sensitivity (Sens), 95% specificity (Spec), median log10 8.1 marker equivalents (ME) g-1 ruminant faeces). Human-associated markers tested were less abundant in individual human samples (median: log10 5.4 and 4.2 (ME+1) g-1 ) and were not continuously detected (81% Sens, 91% Spec for BacHum; 77% Sens, 91% Spec for HF183/BacR287). Furthermore, the pig-associated Pig2Bac assay was included and performed excellent (100% Sens, 100% Spec). To evaluate the presence of MST targets in the soil microbiome, representative soil samples were tested during a whole seasonal cycle (n=60). Only BacR could be detected, but was limited to the dry season and to sites of higher anthropogenic influence (log10 3.0 to 4.9 (ME+1) g-1 soil). In conclusion, the large differences in marker abundances between target and non-target faecal samples (median distances between distributions ≥log10 3 to ≥log10 7) and their absence in pristine soil indicate that all tested assays are suitable candidates for diverse MST applications in the Ethiopian area.

中文翻译：

评估埃塞俄比亚中部高地反刍动物和人类遗传微生物源追踪标记的粪便来源敏感性和特异性

本研究在新创建的区域粪便样本库 (n=173) 中测试了用于识别埃塞俄比亚反刍动物 (BacR) 和人类相关 (HF183/BacR287, BacHum) 细菌粪便污染物的遗传微生物源追踪 (MST) 方法。BacR 表现良好，其标记丰度高（100% 灵敏度 (Sens)，95% 特异性 (Spec)，中值 log10 8.1 标记当量 (ME) g-1 反刍动物粪便）。测试的人类相关标志物在个体人类样本中的丰度较低（中位数：log10 5.4 和 4.2 (ME+1) g-1）并且未连续检测到（81% Sens，91% Spec for BacHum；77% Sens，91% HF183/BacR287 的规范）。此外，还包括与猪相关的 Pig2Bac 检测并表现出色（100% Sens，100% Spec）。为了评估土壤微生物组中 MST 目标的存在，在整个季节周期（n = 60）中测试了代表性土壤样品。只能检测到 BacR，但仅限于旱季和人为影响较高的地点（log10 3.0 至 4.9 (ME+1) g-1 土壤）。总之，目标和非目标粪便样本之间标记丰度的巨大差异（分布之间的中值距离 ≥log10 3 到 ≥log10 7）以及它们在原始土壤中的缺失表明所有测试的检测方法都是适用于不同 MST 应用的候选者。埃塞俄比亚地区。

更新日期：2020-12-24

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