title: Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients.
abstract: Antibiotic resistance genes are rapidly spread between pathogens and the normal flora, with plasmids playing an important role in their circulation. This study aimed to investigate antibiotic resistance plasmids in the gut microbiome of hospitalised patients. Stool samples were collected from seven inpatients at Siriraj Hospital (Bangkok, Thailand) and were compared with a sample from a healthy volunteer. Plasmids from the gut microbiomes extracted from the stool samples were subjected to high-throughput DNA sequencing (GS Junior). Newbler-assembled DNA reads were categorised into known and unknown sequences (using >80% alignment length as the cut-off), and ResFinder was used to classify the antibiotic resistance gene pools. Plasmid replicon modules were used for plasmid typing. Forty-six genes conferring resistance to several classes of antibiotics were identified in the stool samples. Several antibiotic resistance genes were shared by the patients; interestingly, most were reported previously in food animals and healthy humans. Four antibiotic resistance genes were found in the healthy subject. One gene (aph3-III) was identified in the patients and the healthy subject and was related to that in cattle. Uncommon genes of hospital origin such as blaTEM-124-like and fosA, which confer resistance to extended-spectrum β-lactams and fosfomycin, respectively, were identified. The resistance genes did not match the patients' drug treatments. In conclusion, several plasmid types were identified in the gut microbiome; however, it was difficult to link these to the antibiotic resistance genes identified. That the antibiotic resistance genes came from hospital and community environments is worrying.
authors.affiliation: Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Department of Biopharmacy, Faculty of Pharmacy, Silpakorn University, Bangkok, Thailand.
authors.forename: Tossawan
authors.initials: T
authors.lastname: Jitwasinkul
authors.affiliation: Bioinformatics and Data Management for Research Unit, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
authors.forename: Prapat
authors.initials: P
authors.lastname: Suriyaphol
authors.affiliation: National Center for Genetic Engineering and Biotechnology, Thailand.
authors.forename: Sithichoke
authors.initials: S
authors.lastname: Tangphatsornruang
authors.affiliation: Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Martin Asser
authors.initials: MA
authors.lastname: Hansen
authors.affiliation: Department of Biology, University of Copenhagen, Copenhagen, Denmark; Department of Environmental Science, Aarhus University, Aarhus, Denmark.
authors.forename: Lars Hestbjerg
authors.initials: LH
authors.lastname: Hansen
authors.affiliation: Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Søren Johannes
authors.initials: SJ
authors.lastname: Sørensen
authors.affiliation: Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
authors.forename: Chairat
authors.initials: C
authors.lastname: Permpikul
authors.affiliation: Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
authors.forename: Yong
authors.initials: Y
authors.lastname: Rongrungruang
authors.affiliation: Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand. Electronic address: chanwit.tri@mahidol.ac.th.
authors.forename: Chanwit
authors.initials: C
authors.lastname: Tribuddharat
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents; D002417:Cattle; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D000069196:Gastrointestinal Microbiome; D005798:Genes, Bacterial; D006801:Humans; D007297:Inpatients; D056186:Metagenomics; D008826:Microbial Sensitivity Tests; D010957:Plasmids / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013785:Thailand
chemical_list: D000900:Anti-Bacterial Agents
keywords: 454 high-throughput sequencing; Gut microbiome; Plasmid; Resistance gene