Abstract
Staphylococcus aureus is presently regarded as an emerging zoonotic agent due to the spread of specific methicillin-resistant S. aureus (MRSA) clones in pig farms. Studying the microbiota can be useful for the identification of bacteria that antagonize such opportunistic veterinary and zoonotic pathogen in animal carriers. The aim of this study was to determine whether the nasal microbiome of pig S. aureus carriers differs from that of non-carriers. The V3-V5 region of the 16S rRNA gene was sequenced from nasal swabs of 44 S. aureus carriers and 56 non-carriers using the 454 GS FLX titanium system. Carriers and non-carriers were selected on the basis of quantitative longitudinal data on S. aureus carriage in 600 pigs sampled at 20 Danish herds included in two previous studies in Denmark. Raw sequences were analysed with the BION meta package and the resulting abundance matrix was analysed using the DESeq2 package in R to identify operational taxonomic units (OTUs) with differential abundance between S. aureus carriers and non-carriers. Twenty OTUs were significantly associated to non-carriers, including species with known probiotic potential and antimicrobial effect such as lactic acid-producing isolates described among Leuconostoc spp. and some members of the Lachnospiraceae family, which is known for butyrate production. Further 5 OTUs were significantly associated to carriage, including known pathogenic bacteria such as Pasteurella multocida and Klebsiella spp. Our results show that the nasal microbiome of pigs that are not colonized with S. aureus harbours several species/taxa that are significantly less abundant in pig carriers, suggesting that the nasal microbiota may play a role in the individual predisposition to S. aureus nasal carriage in pigs. Further research is warranted to isolate these bacteria and assess their possible antagonistic effect on S. aureus for the pursuit of new strategies to control MRSA in pig farming.
Highlights
The composition of the microbiota is known to directly influence the host’s health and disease
Sequencing, quality filtering and mapping resulted in 701,304 mapped V3-V5-region sequences, ranging between 1,686–46,096 copies per sample, which corresponded to 296 operational taxonomic units (OTUs)
We found 20 bacterial candidates that were associated with non-carriage of S. aureus in the nasal cavity of pigs highly exposed to this bacterium at the pen and the farm level
Summary
The composition of the microbiota is known to directly influence the host’s health and disease. The study of the microbiota in healthy and diseased livestock can lead to identification of bacteria that antagonize specific animal or zoonotic pathogens. These bacteria may be useful in the prevention and eventually treatment of diseases. Some probiotics have been shown to be promising in the reduction of zoonotic bacteria in livestock such as Campylobacter jejuni in broiler chickens [8]. This resource remains largely unexplored for control of zoonotic bacteria
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