Abstract
BackgroundThe 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.ResultsNasal 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.ConclusionsFarm 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.
Highlights
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)
Initial screening of 100 pigs from two farms resulted only in identification of farms where all or no pigs were carrying MRSA. Both MRSA positive (n = 5) and negative (n = 8) pigs were subsequently identified on a farm that used a liquid feeding system that consisted of corn, wheat shorts, soybean and whole whey
CatchAll analysis of richness predicted a mean of 1749 Operational taxon unit (OTU)
Summary
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 microbial composition of a body site (the microbiota) and the sum of its genetic materials (the microbiome) are of increasing interest since it is clear that they can play critical roles in health and disease. Most microbiota studies have focused on the intestinal tract or feces, but various other body sites harbour important microbial populations, including the nasal passages. There has been limited investigation of the nasal microbiota in pigs, with culture-based studies focusing on selected pathogens [1]. It is likely that the tonsillar and nasal microbiotas are similar, but this has not been investigated
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