期刊
出版社
NATL ACAD SCIENCES
DOI: 10.1073/pnas.2024464118
关键词
antibiotic-resistance genes; ARG mobility; ARG host; PacBio sequencing; Nanopore sequencing
资金
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas at Northwest AF University
- Center for Health Impacts in Agriculture at Michigan State University
The environmental resistome is global, diverse, and influenced by human activities. By utilizing long-read sequencing, researchers were able to analyze antibiotic resistance genes (ARGs) in a ceftiofur-treated cow, revealing that multidrug-resistance genes comprise a significant portion of the resistome abundance, with some located on plasmids, and Enterobacteriaceae being dominant hosts of antibiotic-resistant plasmids.
While it is well recognized that the environmental resistome is global, diverse, and augmented by human activities, it has been difficult to assess risk because of the inability to culture many environmental organisms, and it is difficult to evaluate risk from current sequence-based environmental methods. The four most important criteria to determine risk are whether the antibioticresistance genes (ARGs) are a complete, potentially functional complement; if they are linked with other resistances; whether they are mobile; and the identity of their host. Long-read sequencing fills this important gap between culture and short sequencebased methods. To address these criteria, we collected feces from a ceftiofur-treated cow, enriched the samples in the presence of antibiotics to favor ARG functionality, and sequenced long reads using Nanopore and PacBio technologies. Multidrug-resistance genes comprised 58% of resistome abundance, but only 0.8% of them were plasmid associated; fluroquinolone-, aminoglycoside-, macrolide-lincosamide-streptogramin (MLS)-, and j3-lactam-resistance genes accounted for 2.7 to 12.3% of resistome abundance but with 19 to 78% located on plasmids. A variety of plasmid types were assembled, some of which share low similarity to plasmids in current databases. Enterobacteriaceae were dominant hosts of antibiotic-resistant plasmids; physical linkage of extended-spectrum j3-lactamase genes (CTX-M, TEM, CMY, and CARB) was largely found with aminoglycoside-, MLS-, tetracycline-, trimethoprim-, phenicol-, sulfonamide-, and mercury-resistance genes. A draft circular chromosome of Vagococcus lutrae was assembled; it carries MLS-, tetracycline- (including tetM and tetL on an integrative conjugative element), and trimethoprimresistance genes flanked by many transposase genes and insertion sequences, implying that they remain transferrable.
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