Distribution of Medically Relevant Antibiotic Resistance Genes and Mobile Genetic Elements in Soils of Temperate Forests and Grasslands Varying in Land Use

Abstract

Antibiotic-resistant pathogens claim the lives of thousands of people each year and are currently considered as one of the most serious threats to public health. Apart from clinical environments, soil ecosystems also represent a major source of antibiotic resistance determinants, which can potentially disseminate across distinct microbial habitats and be acquired by human pathogens via horizontal gene transfer. Therefore, it is of global importance to retrieve comprehensive information on environmental factors, contributing to an accumulation of antibiotic resistance genes and mobile genetic elements in these ecosystems. Here, medically relevant antibiotic resistance genes, class 1 integrons and IncP-1 plasmids were quantified via real time quantitative PCR in soils derived from temperate grasslands and forests, varying in land use over a large spatial scale. The generated dataset allowed an analysis, decoupled from regional influences, and enabled the identification of land use practices and soil characteristics elevating the abundance of antibiotic resistance genes and mobile genetic elements. In grassland soils, the abundance of the macrolide resistance gene mefA as well as the sulfonamide resistance gene sul2 was positively correlated with organic fertilization and the abundance of aac(6′)-lb, conferring resistance to different aminoglycosides, increased with mowing frequency. With respect to forest soils, the beta-lactam resistance gene blaIMP-12 was significantly correlated with fungal diversity which might be due to the fact that different fungal species can produce beta-lactams. Furthermore, except blaIMP-5 and blaIMP-12, the analyzed antibiotic resistance genes as well as IncP-1 plasmids and class-1 integrons were detected less frequently in forest soils than in soils derived from grassland that are commonly in closer proximity to human activities.

Living in a Puddle of Mud: Isolation and Characterization of Two Novel Caulobacteraceae Strains Brevundimonas pondensis sp. nov. and Brevundimonas goettingensis sp. nov.

“…Antibiograms and the in silico investigations of both strains revealed a resistance potential with respect to medically relevant antibiotics. These results might be an indication of how far antibiotic contamination of our environment has progressed [79], especially as both isolates were isolated from protected habitats. However, this could also indicate that presence of antibiotic resistance genes are a natural phenomenon, as the presented isolates originate from a complex environment where they likely face natural producers of antibiotics, e.g., Streptomyces [80].…”

Fate of Horizontal-Gene-Transfer Markers and Beta-Lactamase Genes during Thermophilic Composting of Human Excreta

“…Abundances did not differ among different land use strategies. However, a positive correlation with fungal diversity was detected [ 47 ]. This might explain rising bla IMP abundances in the compost, since fungi contribute to composting rise in abundance during the composting process [ 4 ].…”

“…Plasmids of the IncP-1 group have a broad host range and are self-transmissible [ 45 , 46 ]. They have been found in diverse environments such as soil [ 47 , 48 , 49 ], the rhizosphere [ 49 , 50 ], manure [ 51 ], wastewater [ 52 ], rivers [ 53 ] and estuarine water [ 54 ]. IncP-1 plasmids are associated with antibiotic and metal resistance, as well as catabolic functional genes.…”

A database on the abundance of environmental antibiotic resistance genes

“…Willms, et al . 40 utilized real-time quantitative PCR to quantify medically relevant ARGs and MGEs in the soil in Germany, and Delgado-Baquerizo, et al . 41 generated a global atlas of soil ARG abundance detected by HT-qPCR.…”