Abstract
Understanding the soil bacterial resistome is essential to understanding the evolution and development of antibiotic resistance, and its spread between species and biomes. We have identified and characterized multi-drug resistance (MDR) mechanisms in the culturable soil antibiotic resistome and linked the resistance profiles to bacterial species. We isolated 412 antibiotic resistant bacteria from agricultural, urban and pristine soils. All isolates were multi-drug resistant, of which greater than 80% were resistant to 16–23 antibiotics, comprising almost all classes of antibiotic. The mobile resistance genes investigated, (ESBL, bla NDM-1, and plasmid mediated quinolone resistance (PMQR) resistance genes) were not responsible for the respective resistance phenotypes nor were they present in the extracted soil DNA. Efflux was demonstrated to play an important role in MDR and many resistance phenotypes. Clinically relevant Burkholderia species are intrinsically resistant to ciprofloxacin but the soil Burkholderia species were not intrinsically resistant to ciprofloxacin. Using a phenotypic enzyme assay we identified the antibiotic specific inactivation of trimethoprim in 21 bacteria from different soils. The results of this study identified the importance of the efflux mechanism in the soil resistome and variations between the intrinsic resistance profiles of clinical and soil bacteria of the same family.
Highlights
Antibiotic resistance has developed over time from resistance to single classes of antibiotics to multi-drug resistance and extreme drug resistance
We aimed to identify the levels of culturable resistant bacteria, both antibiotic producers and non-antibiotic producers, and identify the roles of the different mechanisms of resistance such as efflux, novel enzymatic resistance mechanisms and selected plasmid mediated resistance genes in conferring multi-drug resistance within the soil bacterial community
While culture techniques will always bias the population of bacteria under study they have the advantage of being able to detect phenotypic resistances, including efflux mediated resistance and novel resistance mechanisms, and the resistance mechanism can be investigated in further detail
Summary
Antibiotic resistance has developed over time from resistance to single classes of antibiotics to multi-drug resistance and extreme drug resistance. With an every decreasing supply of novel antibiotics and increasing resistance research has started to focus on investigating the natural antibiotic resistome and understanding the ecology and evolution of antibiotic resistance in the non-clinical environment in order to identify reservoirs of both known and novel antibiotic resistance mechanisms. Despite the belief that the soil antibiotic resistome bacteria play an increasingly important role in the evolution, development and spread of antibiotic resistance in humans and animals, there is little known about the natural bacterial resistome in soil. There have been many calls for more information about the natural resistome and these have highlighted the importance of understanding the soil resistome in the preservation of antibiotics for the treatment of infections [1,2,3,4]. To date there have been few studies which have investigated the culturable soil resistome and these have been limited to the antibiotic producing bacteria Streptomyces, and an isolated cave microbiome [5,6]
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