Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients. (September 2016)

• Record Type: Journal Article
• Authors: Jitwasinkul, Tossawan; Suriyaphol, Prapat; Tangphatsornruang, Sithichoke; Hansen, Martin Asser; Hansen, Lars Hestbjerg; Sørensen, Søren Johannes; Permpikul, Chairat; Rongrungruang, Yong; Tribuddharat, Chanwit
• Is Part Of: Journal of global antimicrobial resistance. Volume 6(2016:Sep.)
• Page Start: 57
• Page End: 66
• Publication Date: 2016-09
• Subjects: Resistance gene -- Gut microbiome -- Plasmid -- 454 high-throughput sequencing; Drug resistance -- Periodicals; Drug resistance -- Periodicals; Drug resistance; Periodicals; 616.9041
• DOI: 10.1016/j.jgar.2016.03.001
• Languages: English
• ISSNs: 2213-7165

Abstract

Highlights: Plasmid-derived drug resistance gene pool of hospital inpatients' gut microbiome was investigated. Multiple antibiotic resistance gene classes shared by patients' gut microbiome. Most genes were previously reported in food animals and healthy humans. Uncommon genes of hospital origin were identified among patients' gut microbiome. Antibiotic usage in hospital and community requires better regulation. 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 bla TEM-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.