Microbial shifts in the swine nasal microbiota in response to parenteral antimicrobial administration.

The continuous administration of antimicrobials in swine production has been widely criticized with the increase of antimicrobial-resistant bacteria and dysbiosis of the beneficial microbial communities. While an increasing number of studies investigate the effects of antimicrobial administration on swine gastrointestinal microbiota biodiversity, the impact of their use on the composition and diversity of nasal microbial communities has not been widely explored. The objective of this study was to characterize the short-term impact of different parenteral antibiotics administration on the composition and diversity of nasal microbial communities in growing pigs. Five antimicrobial treatment groups, each consisting of four, eight-week old piglets, were administered one of the antimicrobials; Ceftiofur Crystalline free acid (CCFA), Ceftiofur hydrochloride (CHC), Tulathromycin (TUL), Oxytetracycline (OTC), and Procaine Penicillin G (PPG) at label dose and route. Individual deep nasal swabs were collected immediately before antimicrobial administration (control = day 0), and again on days 1, 3, 7, and 14 after dosing. The nasal microbiota across all the samples were dominated by Firmicutes, proteobacteria and Bacteroidetes. While, the predominant bacterial genera were Moraxella, Clostridium and Streptococcus. Linear discriminant analysis, showed a pronounced, antimicrobial-dependent microbial shift in the composition of nasal microbiota and over time from day 0. By day 14, the nasal microbial compositions of the groups receiving CCFA and OTC had returned to a distribution that closely resembled that observed on day 0. In contrast, pigs that received CHC, TUL and PPG appeared to deviate away from the day 0 composition by day 14. Based on our results, it appears that the impact of parenteral antibiotics on the swine nasal microbiota is variable and has a considerable impact in modulating the nasal microbiota structure. Our results will aid in developing alternative strategies for antibiotics to improve swine health and consequently production.

Impact of parenteral antimicrobial administration on the structure and diversity of the fecal microbiota of growing pigs.

While antimicrobials are cost-effective tools for prevention and treatment of infectious disease, the impact of their use on potentially beneficent mucosal microbial communities of growing pigs has not been widely explored. The objective of this study was to characterize the impact of parenteral antibiotics administration on the composition and diversity of the resident fecal microbiota in growing pigs. Five antimicrobial treatment groups, each consisting of four, eight-week old piglets, were administered one of the antimicrobials; Ceftiofur Crystalline free acid (CCFA), Ceftiofur hydrochloride (CHC), Oxytetracycline (OTC), Procaine Penicillin G (PPG) and Tulathromycin (TUL) at label dose and route. Individual fecal swabs were collected immediately before antimicrobial administration (control = day 0), and again on days 1, 3, 7, and 14 after dosing. Genomic DNA was extracted, and the V1-V3 hypervariable region of 16S rRNA gene was amplified and sequenced using Illumina Miseq-based sequencing. Across all groups, the most abundant phyla were Firmicutes, Bacteroidetes, and Proteobacteria. Linear discriminant analysis and stacked area graphs, showed a pronounced, antimicrobial-dependent shift in the composition of fecal microbiota over time from day 0. By day 14, the fecal microbial compositions of the groups receiving CHC and TUL had returned to a distribution that closely resembled that observed on day 0, but differences were still evident. In contrast, animals that received PPG, OTC and CCFA, showed a tendency towards a balanced homeostatic microbiota structure on day 7, but appeared to deviate away from the day 0 composition by day 14. Based on our results, the observed changes in fecal microbiota showed antimicrobial-specific variation in both duration and extent. Understanding the impact of these important antimicrobial-induced changes will be a critical step in optimizing the use of antimicrobials in health management programs in the swine industry.