Discrimination of contagious and environmental strains of Streptococcus uberis in dairy herds by means of mass spectrometry and machine-learning.
Discrimination of contagious and environmental strains of Streptococcus uberis in dairy herds by means of mass spectrometry and machine-learning.
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通过质谱和机器学习的乳制群中，乳球链球菌的传染性和环境菌株的歧视。
DOI：
10.1038/s41598-018-35867-6
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发表时间：
2018-11-30
影响因子：
4.6
通讯作者：
Dottorini T
中科院分区：
文献类型：
--
作者：
Esener N;Green MJ;Emes RD;Jowett B;Davies PL;Bradley AJ;Dottorini T
Uberis链球菌是乳品行业临床乳房炎最常见的病原菌之一。病原体传播途径的知识对于选择最合适的干预措施是至关重要的。在这里，我们展示了使用基质辅助激光解吸电离/飞行时间(MALDI-TOF)从临床分离株获得的光谱特征可以用于实现基于机器学习的诊断分类器，以成功区分环境和传染性的Uberis菌株。当使用遗传算法时，专门用于单个农场的分类器在交叉验证时获得了高达97.81%的准确率，科恩的卡帕系数为0.94。这表明所提出的方法有可能成功地支持在群体水平上进行筛查。使用来自19个农场的合并数据开发的全局分类器在交叉验证(kappa 0.93)和外部验证(kappa 0.34)时获得了95.88%的准确率和70.67%的准确率(kappa 0.34)。这表明需要做更多的工作来制定在人口层面上成功的筛查解决方案。从训练好的分类器中提取了显著的MALDI-TOF谱峰。这些峰值对应于细菌素和核糖体蛋白，这表明免疫、生长和对营养的竞争可能与不同的传播途径有关。
Streptococcus uberis is one of the most common pathogens of clinical mastitis in the dairy industry. Knowledge of pathogen transmission route is essential for the selection of the most suitable intervention. Here we show that spectral profiles acquired from clinical isolates using matrix-assisted laser desorption ionization/time of flight (MALDI-TOF) can be used to implement diagnostic classifiers based on machine learning for the successful discrimination of environmental and contagious S. uberis strains. Classifiers dedicated to individual farms achieved up to 97.81% accuracy at cross-validation when using a genetic algorithm, with Cohen’s kappa coefficient of 0.94. This indicates the potential of the proposed methodology to successfully support screening at the herd level. A global classifier developed on merged data from 19 farms achieved 95.88% accuracy at cross-validation (kappa 0.93) and 70.67% accuracy at external validation (kappa 0.34), using data from another 10 farms left as holdout. This indicates that more work is needed to develop a screening solution successful at the population level. Significant MALDI-TOF spectral peaks were extracted from the trained classifiers. The peaks were found to correspond to bacteriocin and ribosomal proteins, suggesting that immunity, growth and competition over nutrients may be correlated to the different transmission routes.
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影响因子：
3.3
作者：
Baseggio, N;Mansell, PD;Browning, GF
通讯作者：
Browning, GF
影响因子：
2.4
作者：
LEIGH, JA;FIELD, TR;WILLIAMS, MR
通讯作者：
WILLIAMS, MR
影响因子：
2.4
作者：
Grant, RG;Finch, JM
通讯作者：
Finch, JM
影响因子：
56.9
作者：
Falush, D;Wirth, T;Suerbaum, S
通讯作者：
Suerbaum, S
影响因子：
14.8
作者：
Koul, Anil;Dendouga, Najoua;Andries, Koen
通讯作者：
Andries, Koen