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Srinivasan V, Stedtfeld RD, Tourlousse DM, Baushke SW, Xin Y, Miller SM, Pham T, Rouillard JM, Gulari E, Tiedje JM, Hashsham SA. Diagnostic microarray for 14 water and foodborne pathogens using a flatbed scanner. J Microbiol Methods 2017; 139:15-21. [PMID: 28438642 DOI: 10.1016/j.mimet.2017.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/20/2017] [Accepted: 04/20/2017] [Indexed: 02/06/2023]
Abstract
Parallel detection approaches are of interest to many researchers interested in identifying multiple water and foodborne pathogens simultaneously. Availability and cost-effectiveness are two key factors determining the usefulness of such approaches for laboratories with limited resources. In this study, we developed and validated a high-density microarray for simultaneous screening of 14 bacterial pathogens using an approach that employs gold labeling with silver enhancement (GLS) protocol. In total, 8887 probes (50-mer) were designed using an in-house database of virulence and marker genes (VMGs), and synthesized in quadruplicate on glass slides using an in-situ synthesis technology. Target VMG amplicons were obtained using multiplex polymerase chain reaction (PCR), labeled with biotin, and hybridized to the microarray. The signals generated after gold deposition and silver enhancement, were quantified using a flatbed scanner having 2-μm resolution. Data analysis indicated that reliable presence/absence calls could be made, if: i) over four probes were used per gene, ii) the signal-to-noise ratio (SNR) cutoff was greater than or equal to two, and iii) the positive fraction (PF), i.e., number of probes with SNR≥2 for a given VMG was greater than 0.75. Hybridization of the array with blind samples resulted in 100% correct calls, and no false positive. Because amplicons were obtained by multiplex PCR, sensitivity of this method is similar to PCR. This assay is an inexpensive and reliable technique for high throughput screening of multiple pathogens.
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Affiliation(s)
- Vidya Srinivasan
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Dieter M Tourlousse
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Samuel W Baushke
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Yu Xin
- Department of Environmental Engineering, Nanjing University, China
| | - Sarah M Miller
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Trinh Pham
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Jean-Marie Rouillard
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Erdogan Gulari
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - James M Tiedje
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States.
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