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Stedtfeld RD, Guo X, Stedtfeld TM, Sheng H, Williams MR, Hauschild K, Gunturu S, Tift L, Wang F, Howe A, Chai B, Yin D, Cole JR, Tiedje JM, Hashsham SA. Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements. FEMS Microbiol Ecol 2018; 94:5057470. [PMID: 30052926 PMCID: PMC7250373 DOI: 10.1093/femsec/fiy130] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/28/2018] [Indexed: 01/22/2023] Open
Abstract
The high-throughput antibiotic resistance gene (ARG) qPCR array, initially published in 2012, is increasingly used to quantify resistance and mobile determinants in environmental matrices. Continued utility of the array; however, necessitates improvements such as removing or redesigning questionable primer sets, updating targeted genes and coverage of available sequences. Towards this goal, a new primer design tool (EcoFunPrimer) was used to aid in identification of conserved regions of diverse genes. The total number of assays used for diverse genes was reduced from 91 old primer sets to 52 new primer sets, with only a 10% loss in sequence coverage. While the old and new array both contain 384 primer sets, a reduction in old primer sets permitted 147 additional ARGs and mobile genetic elements to be targeted. Results of validating the updated array with a mock community of strains resulted in over 98% of tested instances incurring true positive/negative calls. Common queries related to sensitivity, quantification and conventional data analysis (e.g. Ct cutoff value, and estimated genomic copies without standard curves) were also explored. A combined list of new and previously used primer sets is provided with a recommended set based on redesign of primer sets and results of validation.
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Affiliation(s)
- Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan 48824, USA
| | - Xueping Guo
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Tiffany M Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan 48824, USA
| | - Hongjie Sheng
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Maggie R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan 48824, USA
| | - Kristin Hauschild
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Santosh Gunturu
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Leo Tift
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Fang Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa 50010, USA
| | - Benli Chai
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Daqiang Yin
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - James R Cole
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
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