Weese J Scott, Slifierz Mackenzie, Jalali Mohammad, Friendship Robert
Department of Pathobiology and Centre for Public Health and Zoonoses, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G2W1, Canada.
BMC Vet Res. 2014 Mar 15;10:69. doi: 10.1186/1746-6148-10-69.
The nasal microbiota of pigs has been poorly assessed but could play a role in carriage of important microorganisms such as methicillin-resistant Staphylococcus aureus (MRSA). The objectives of this study were to describe the nasal microbiota in slaughter age pigs, to evaluate the impact of farm management on the nasal microbiota and to provide a preliminary assessment of the influence of the microbiota on MRSA carriage.
Nasal swabs were collected from five MRSA positive and eight MRSA negative pigs on one farm that used a liquid feeding system and routine tylosin treatment, and seven MRSA negative pigs from an antibiotic-free farm that used conventional feeding. A total of 946310 sequences passed all quality control filters. The number of sequences per sample ranged from 4307 to 165656 (mean 56092, SD 40007). CatchAll analysis of richness predicted a mean of 1749 OTUs (range 213-3736, SD 996). Overall, 6291 OTUs were identified, yet 5125 (81%) were identified less than 10 times and the 12 most abundant OTUs accounted for 80.7% of sequences. Proteobacteria predominated in all but two samples. Liquid-fed/tylosin-exposed pigs had significantly lower relative abundances of Verrucomicrobia (P = 0.004), Fibrobacteres (P = <0.0001) and sequences unclassified at the phylum level (P = 0.028). When comparing only liquid-fed pigs, MRSA carriers had significantly more Bacteroidetes (P = 0.037) than MRSA negative pigs. 124 genera were identified, with Moraxella accounting for 35.4% of sequences. In the Jaccard index tree, five of eight MRSA positive pigs clustered closely together, as did six of the seven conventionally-fed pigs. A significant difference was identified between conventional and liquid-fed pigs using parsimony test with the Jaccard (P < 0.001) but not the Yue&Clayton (P = 0.26) index. There were no significant differences between MRSA positive and negative pigs (P = 0.133 and 0.175). OTUs belonging to Firmicutes were the main indicators of MRSA negative pigs, including Lactobacillus and another Lactobacillaceae and Staphylococcus.
Farm management can influence the nasal microbiota in pigs, but no impact of the microbiota on MRSA carriage was identified. Studies that further define the impact of management on the microbiota, and the impact of the microbiota on pathogen carriage are indicated.
猪鼻腔微生物群的评估较少，但可能在耐甲氧西林金黄色葡萄球菌（MRSA）等重要微生物的携带中发挥作用。本研究的目的是描述屠宰年龄猪的鼻腔微生物群，评估农场管理对鼻腔微生物群的影响，并初步评估微生物群对MRSA携带的影响。
从一个使用液体饲喂系统和常规泰乐菌素治疗的农场的5头MRSA阳性猪和8头MRSA阴性猪，以及一个使用传统饲喂的无抗生素农场的7头MRSA阴性猪中采集鼻拭子。共有946310个序列通过了所有质量控制筛选。每个样本的序列数范围为4307至165656（平均56092，标准差40007）。丰富度的CatchAll分析预测平均有1749个操作分类单元（范围213 - 3736，标准差996）。总体而言，共鉴定出6291个操作分类单元，但其中5125个（81%）的鉴定次数少于10次，最丰富的12个操作分类单元占序列的80.7%。除两个样本外，变形菌门在所有样本中占主导地位。液体饲喂/接触泰乐菌素的猪的疣微菌门（P = 0.004）、纤维杆菌门（P = <0.0001）和门水平未分类序列的相对丰度显著较低（P = 0.028）。仅比较液体饲喂的猪时，MRSA携带者的拟杆菌门比MRSA阴性猪显著更多（P = 0.037）。鉴定出124个属，莫拉克斯氏菌属占序列的35.4%。在杰卡德指数树中，8头MRSA阳性猪中的5头紧密聚集在一起，7头传统饲喂猪中的6头也是如此。使用杰卡德简约检验（P < 0.001）时，传统饲喂猪和液体饲喂猪之间存在显著差异，但使用Yue&Clayton指数（P = 0.26）时无显著差异。MRSA阳性猪和阴性猪之间无显著差异（P = 0.133和0.175）。属于厚壁菌门的操作分类单元是MRSA阴性猪的主要指标，包括乳酸杆菌属以及另一个乳酸杆菌科和葡萄球菌属。
农场管理可影响猪的鼻腔微生物群，但未发现微生物群对MRSA携带的影响。需要进一步开展研究，以明确管理对微生物群的影响以及微生物群对病原体携带的影响。
