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Title:The role of antibiotics metaphylaxis on developmental dynamics of fecal microbiota and persistence of antimicrobial resistome in piglets
Author(s):Zeineldin, Mohamed Moselhy
Advisor(s):Lowe, James F
Contributor(s):Aldridge, Brian M.; Lima, Fabio
Department / Program:Vet Clinical Medicine
Discipline:VMS-Veterinary Clinical Medcne
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:M.S.
Genre:Thesis
Subject(s):Antimicrobial
Piglets
Microbiome
Resistome
Abstract:The swine gastrointestinal microbiota is comprised of a diverse and complex microbial population that coexists in a coordinated, complex mucosal ecosystem that contributes to host gastrointestinal and immunological development. While antimicrobial are cost-effective tools for prevention and treatment of infectious diseases, the impact of their use on potentially beneficent mucosal microbial communities has not been widely explored. Optimization of antimicrobial use in swine management systems requires full understanding of antimicrobial-induced changes on developmental dynamics of gut microbiota and prevalence of antimicrobial resistance genes (ARGs). While the antibiotic resistance profiles of pathogens have been characterized, the antimicrobial resistance bacteria and ARGs from the whole gut microbiota have received far less attention. The objective of this study was to characterize the impact of parenteral antibiotics administration on composition and diversity of the resident fecal microbiota in pigs. In commercial swine farm, five antimicrobial treatment groups, each consisting of four, eight-week old piglets, were administered one of the antimicrobial; Tulathromycin (TUL), Ceftiofur Crystalline free acid (CCFA), Ceftiofur hydrochloride (CHC), Oxytetracycline (OTC), and Procaine Penicillin G (PPG) 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. Additionally, a randomized complete block design was used to study the impacts of early-life antimicrobial intervention on fecal microbiota structure, and their accompanying antimicrobial resistome in neonatal piglets. Forty-eight litters were blocked to one of six treatments; Control (CONT), TUL, CCFA, CHC, OTC and PPG. Two piglets per litter were individually identified and weights and deep fecal swabs were collected at days 0 (prior to treatment), 5, 10, 15 and 20. All fecal swabs were processed for DNA extraction. Sequencing analysis of the V3-V4 hypervariable region of 16S rRNA gene and the selected ARGs were performed using Illumina Miseq platform. Moreover, whole genome, metagenomics sequencing approach was performed on subset of samples from the CONT and TUL groups, to assess the fecal microbiota structure and their accompanying antimicrobial resistome. In growing piglets, the most abundant phyla were Firmicutes, Bacteroidetes, and Proteobacteria. Linear discriminant analysis, 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 normalized microbiota structure on day 7, but appeared to deviate away from the day 0 composition by day 14. In neonatal piglets, our results show that, while early-life antibiotics prophylaxis had no effect on individual weight gain, or mortality, it was associated with noticeable changes in the prevalence of selected ARGs, and minor shift in the composition of the fecal microbiota during this developmental stage. Relative to CONT, only TUL treated piglet exhibited significant decline in chao1 richness index at day 20. Compared to the CONT, the PPG treated piglets exhibited a significant increase in the prevalence of ermB and tetW at day 20 of life. Tulathromycin intervention was also resulted in significant increase in the abundance of tet W at days 10 and 20, and erm B at day 20. Using whole genome metagenomics sequencing on subset of samples from the CONT and TUL groups, a total of 127 antimicrobial resistome related to 19 different classes of antibiotics were identified across all samples. The majority of identified antimicrobial resistome were observed in both experimental groups and at all-time points. The magnitude and extent of differences in microbial composition, and antimicrobial resistome, between the TUL and CONT groups were statistically insignificant. However, both the fecal microbiota composition and antimicrobial resistome were changed significantly between the sampling days. Based on our results, the observed changes in fecal microbiota in growing piglets showed antimicrobial-specific variation in both duration and extent. While in the perinatal piglets, the shifts in fecal microbiota structure caused by perinatal antimicrobial intervention are modest and limited to particular groups of microbial taxa. However, early life PPG and TUL intervention could promote selection of ARGs in herds. While additional investigations are required to explore the consistency of these findings across larger populations, these results could open the door to new perspectives on the utility of early life antimicrobial administration to healthy neonates in swine management systems.
Issue Date:2019-02-25
Type:Text
URI:http://hdl.handle.net/2142/104748
Rights Information:Copyright 2019 Mohamed Moselhy Zeineldin
Date Available in IDEALS:2019-08-23
Date Deposited:2019-05


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