title: Evaluating the mobility potential of antibiotic resistance genes in environmental resistomes without metagenomics.
abstract: Antibiotic resistance genes are ubiquitous in the environment. However, only a fraction of them are mobile and able to spread to pathogenic bacteria. Until now, studying the mobility of antibiotic resistance genes in environmental resistomes has been challenging due to inadequate sensitivity and difficulties in contig assembly of metagenome based methods. We developed a new cost and labor efficient method based on Inverse PCR and long read sequencing for studying mobility potential of environmental resistance genes. We applied Inverse PCR on sediment samples and identified 79 different MGE clusters associated with the studied resistance genes, including novel mobile genetic elements, co-selected resistance genes and a new putative antibiotic resistance gene. The results show that the method can be used in antibiotic resistance early warning systems. In comparison to metagenomics, Inverse PCR was markedly more sensitive and provided more data on resistance gene mobility and co-selected resistances.
authors: University of Helsinki, Department of Food and Environmental Sciences, POB 56, 00014 University of Helsinki, Finland.
authors: Katariina
authors: K
authors: Pärnänen
authors: University of Helsinki, Department of Biosciences, POB 65, 00014 University of Helsinki, Finland.
authors: Antti
authors: A
authors: Karkman
authors: ETH Zürich, Department of Environmental Systems Science, Universitätstrasse 16, 8092 Zürich, Switzerland.|Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Überlandstrasse 611, 8600 Dübendorf, Switzerland.
authors: Manu
authors: M
authors: Tamminen
authors: University of Helsinki, Department of Food and Environmental Sciences, POB 56, 00014 University of Helsinki, Finland.
authors: Christina
authors: C
authors: Lyra
authors: University of Helsinki, Department of Food Hygiene and Environmental Health, POB 66, 00014 University of Helsinki, Finland.
authors: Jenni
authors: J
authors: Hultman
authors: University of Helsinki, Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, POB 56, 00014 University of Helsinki, Finland.
authors: Lars
authors: L
authors: Paulin
authors: University of Helsinki, Department of Food and Environmental Sciences, POB 56, 00014 University of Helsinki, Finland.
authors: Marko
authors: M
authors: Virta
mesh_terms: D001419:Bacteria / Q000187:drug effects / Q000235:genetics / Q000472:pathogenicity; D004269:DNA, Bacterial / Q000235:genetics; D004352:Drug Resistance, Microbial / Q000235:genetics*; D004783:Environmental Microbiology; D004784:Environmental Monitoring / Q000379:methods; D022761:Gene Transfer, Horizontal; D019015:Geologic Sediments / Q000382:microbiology; D006801:Humans; D020071:Interspersed Repetitive Sequences; D056186:Metagenomics; D005810:Multigene Family; D016133:Polymerase Chain Reaction / Q000379:methods
chemical_list: D004269:DNA, Bacterial