Long-term antibiotic exposure in soil is associated with changes in microbial community structure and prevalence of class 1 integrons

• Published in: FEMS microbiology ecology Vol. 92; no. 10; p. 1
• Main Authors: Cleary, David W., Bishop, Alistair H., Zhang, Lihong, Topp, Edward, Wellington, Elizabeth M. H., Gaze, William H.
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-10-2016
• Subjects: Abundance; Anti-Bacterial Agents - analysis; Anti-Bacterial Agents - toxicity; Antibiotic resistance; Antibiotics; Antimicrobial resistance; Bacteria; Bacterial diseases; Chlortetracycline; Communities; Community structure; Cyanobacteria; Distribution; Ecology; Environmental aspects; Gene sequencing; Growth promoters; Integrons; Livestock; Manure - microbiology; Microbial colonies; Microbiology; Microbiota; Microorganisms; Physiological aspects; Prevalence; Prophylaxis; Proteobacteria; Relative abundance; RNA, Ribosomal, 16S; rRNA 16S; Soil - chemistry; Soil analysis; Soil Microbiology; Soil Pollutants - analysis; Soil Pollutants - toxicity; Soil treatment; Soils; Sulfamethazine; Tylosin; Veterinary medicine; United Kingdom; class 1 integrons; soil; microbial diversity; antibiotic resistance; 16S rRNA gene
• ISSN: 1574-6941; 0168-6496; 1574-6941
• DOI: 10.1093/femsec/fiw159

Antimicrobial resistance is one of the most significant challenges facing the global medical community and can be attributed to the use and misuse of antibiotics. This includes use as growth promoters or for prophylaxis and treatment of bacterial infection in intensively farmed livestock from where antibiotics can enter the environment as residues in manure. We characterised the impact of the long-term application of a mixture of veterinary antibiotics alone (tylosin, sulfamethazine and chlortetracycline) on class 1 integron prevalence and soil microbiota composition. Class 1 integron prevalence increased significantly (P < 0.005) from 0.006% in control samples to 0.064% in the treated plots. Soil microbiota was analysed using 16S rRNA gene sequencing and revealed significant alterations in composition. Of the 19 significantly different (P < 0.05) OTUs identified, 16 were of the Class Proteobacteria and these decreased in abundance relative to the control plots. Only one OTU, of the Class Cyanobacteria, was shown to increase in abundance significantly; a curiosity given the established sensitivity of this class to antibiotics. We hypothesise that the overrepresentation of Proteobacteria as OTUs that decreased significantly in relative abundance, coupled with the observations of an increase in integron prevalence, may represent a strong selective pressure on these taxa.
We showed that the long-term addition of antibiotics into soils increased the level of antibiotic resistance genes and altered the number and types of bacteria present.