Effect of antimicrobial usage on enteric bacterial populations with focus on virulence and resistance profiles of Escherichia coli in growing pigs

Abstract

Microbial community in the gut of pigs provides a vast and complex microbial network of community diversity important for its health and development. Pathogenic Escherichia coli are responsible for acute profuse diarrhoea with resultant high morbidity and mortality. Antibiotics are used as growth promoters and for therapeutic purposes in pigs. Misuse, abuse and overuse of these antibiotics have led to development of resistant bacterial strains. This study reports the effect of antimicrobial usage on frequency in which growing pigs habour ETEC and VTEC virulence genes and compared phenotypic and genotypic antibiotic resistance pattern of E. coli and metagenomics analysis of fecal samples collected from; (i) pigs receiving normal farm treatment without antibiotics usage, over a 70 day period, and (ii) pigs allowed treatment with antibiotics and monitored over a 70 day period. Our hypothesis was that the use of antibiotics in commercial pig farms affect gut microbial population. A total of 241 E.coli strains were isolated and antibiotics resistance testing through disk diffusion and PCR was conducted. Sequencing was also done using the Miseq Illumina platform. Virulence genes were detected in [24.8% (Cl95%: 18.2-32.7)] of the antibiotic group isolates and [43.5% (Cl95%: 34.5-52.9)] of the non antibiotic group with a significant difference (P=0.002). Phenotypic resistance to oxytetracycline was most common and were significant (P = 0.03) in samples of days 10 (P = 0.02) and 21 (P = 0.01). Furthermore, [63.9% (Cl95%: 57.6, 69.7)] possesed one or more of the four tested tetracycline resistance genes. Significant statistical difference exists in bacterial structure and composition in the gut of growing pigs P<0.05. Firmicutes, Bacteriotedes and Proteobacteria were the three most abundant phyla and composition was statistically significant during the growing period. The study showed that antibiotics usage increases gut bacterial population in growing pigs. Disease causing virulence genes and antibiotics resistance genes may occur even without antibiotics usage in growing pigs and other factors may be involved.