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On-site genetic analysis for species identification using lab-on-a-chip.

ABSTRACT: This paper presents a microfluidic device capable of performing genetic analysis on dung samples to identify White Rhinoceros (Ceratotherium simum). The development of a microfluidic device, which can be used in the field, offers a portable and cost-effective solution for DNA analysis and species identification to aid conservation efforts. Optimization of the DNA extraction processes produced equivalent yields compared to conventional kit-based methods within just 5 minutes. The use of a color-changing loop-mediated isothermal amplification reaction for simultaneous detection of the cytochrome B sequence of C. simum enabled positive results to be obtained within as little as 30 minutes. Field testing was performed at Knowsley Safari to demonstrate real-world applicability of the microfluidic device for testing of biological samples.

SUBMITTER: Wimbles R

PROVIDER: S-EPMC7882957 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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On-site genetic analysis for species identification using lab-on-a-chip.

Wimbles Ryan R Melling Louise M LM Cain Bradley B Davies Naomi N Doherty Jason J Johnson Bridget B Shaw Kirsty J KJ

Ecology and evolution 20210129 4

This paper presents a microfluidic device capable of performing genetic analysis on dung samples to identify White Rhinoceros (<i>Ceratotherium simum</i>). The development of a microfluidic device, which can be used in the field, offers a portable and cost-effective solution for DNA analysis and species identification to aid conservation efforts. Optimization of the DNA extraction processes produced equivalent yields compared to conventional kit-based methods within just 5 minutes. The use of a ...[more]

PMID: 33613987

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Project description:Campylobacter spp. have been recognized as major foodborne pathogens worldwide. An increasing frequency of antibiotic-resistant pathogens, including Campylobacter spp., have been identified to transmit from food products to humans and cause severe threats to public health. To better mitigate the antibiotic resistance crisis, rapid detection methods are required to provide timely antimicrobial resistance surveillance data for agri-food systems. Herein, we developed a polymer-based microfluidic device for the identification and antimicrobial susceptibility testing (AST) of Campylobacter spp. An array of bacterial incubation chambers were created in the microfluidic device, where chromogenic medium and antibiotics were loaded. The growth of Campylobacter spp. was visualized by color change due to chromogenic reactions. This platform achieved 100% specificity for Campylobacter identification. Sensitive detection of multiple Campylobacter species (C. jejuni, C. coli, and C. lari) was obtained in artificially contaminated milk and poultry meat, with detection limits down to 1?×?102 CFU/ml and 1?×?104 CFU/25 g, respectively. On-chip AST determined Campylobacter antibiotic susceptibilities by the lowest concentration of antibiotics that can inhibit bacterial growth (i.e., no color change observed). High coincidences (91% to 100%) of on-chip AST and the conventional agar dilution method were achieved against several clinically important antibiotics. For a presumptive colony, on-chip identification and AST were completed in parallel within 24 h, whereas standard methods, including biochemical assays and traditional culture-based AST, take several days for multiple sequential steps. In conclusion, this lab-on-a-chip device can achieve rapid and reliable detection of antibiotic-resistant Campylobacter spp.IMPORTANCE Increasing concerns of antibiotic-resistant Campylobacter spp. with regard to public health emphasize the importance of efficient and fast detection. This study described the timely identification and antimicrobial susceptibility testing of Campylobacter spp. by using a microfluidic device. Our developed method not only reduced the total analysis time, but it also simplified food sample preparation and chip operation for end users. Due to the miniaturized size of the lab-on-a-chip platform, the detection was achieved by using up to 1,000 times less of the reagents than with standard reference methods, making it a competitive approach for rapid screening and surveillance study in food industries. In addition, multiple clinically important Campylobacter species (C. jejuni, C. coli, and C. lari) could be tested by our device. This device has potential for wide application in food safety management and clinical diagnostics, especially in resource-limited regions.

Dataset Information

On-site genetic analysis for species identification using lab-on-a-chip.

Publications

On-site genetic analysis for species identification using lab-on-a-chip.

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