Plant resistome profiling in evolutionary old bog vegetation provides new clues to understand emergence of multi-resistance

• Published in: The ISME Journal Vol. 15; no. 3; pp. 921 - 937
• Main Authors: Obermeier, Melanie Maria, Wicaksono, Wisnu Adi, Taffner, Julian, Bergna, Alessandro, Poehlein, Anja, Cernava, Tomislav, Lindstaedt, Stefanie, Lovric, Mario, Müller Bogotá, Christina Andrea, Berg, Gabriele
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01-03-2021; Nature Publishing Group
• Subjects: 45/22; 45/23; 45/47; 631/158/855; 631/326/171; 631/326/41/2142; 82/80; 82/83; Anti-Bacterial Agents - pharmacology; Antibiotic resistance; Antibiotics; Antimicrobial resistance; Biomedical and Life Sciences; Bogs; Culture collections; Drug Resistance, Microbial; Ecological effects; Ecology; Efflux; Europe; Evolutionary Biology; Genes; Genes, Bacterial; Life Sciences; Metagenome; Metagenomics; Microbial activity; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Microbiomes; Microorganisms; Plant communities; Sphagnum; Vegetation; Wetlands; β Lactamase; Europe
• ISSN: 1751-7362; 1751-7370; 1751-7370
• DOI: 10.1038/s41396-020-00822-9

The expanding antibiotic resistance crisis calls for a more in depth understanding of the importance of antimicrobial resistance genes (ARGs) in pristine environments. We, therefore, studied the microbiome associated with
Sphagnum
moss forming the main vegetation in undomesticated, evolutionary old bog ecosystems. In our complementary analysis of culture collections, metagenomic data and a fosmid library from different geographic sites in Europe, we identified a low abundant but highly diverse pool of resistance determinants, which targets an unexpectedly broad range of 29 antibiotics including natural and synthetic compounds. This derives both, from the extraordinarily high abundance of efflux pumps (up to 96%), and the unexpectedly versatile set of ARGs underlying all major resistance mechanisms. Multi-resistance was frequently observed among bacterial isolates, e.g. in
Serratia
,
Rouxiella, Pandoraea, Paraburkholderia
and
Pseudomonas
. In a search for novel ARGs, we identified the new class A β-lactamase Mm3. The native
Sphagnum
resistome comprising a highly diversified and partially novel set of ARGs contributes to the bog ecosystem´s plasticity. Our results reinforce the ecological link between natural and clinically relevant resistomes and thereby shed light onto this link from the aspect of pristine plants. Moreover, they underline that diverse resistomes are an intrinsic characteristic of plant-associated microbial communities, they naturally harbour many resistances including genes with potential clinical relevance.