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Using unique ORFan genes as strain-specific identifiers for Escherichia coli
Marta Ferrandis-Vila1, Sumeet K Tiwari2, Svenja Mamerow1
1Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Straße 96a, 07743, Jena, Germany.
BMC Microbiology
|May 18, 2022
Summary
This study developed a novel method for identifying individual bacterial strains using unique ORFan genes and strain-specific primers. This approach efficiently detects and tracks specific strains in vitro and in vivo.
Area of Science:
- Microbiology
- Genetics
Background:
- Bacterial strain identification is crucial but challenging.
- Current methods are often arduous and time-consuming.
- The need for selective and specific strain identification is high.
Purpose of the Study:
- To develop a method for differentiating individual bacterial strains within the same species.
- To utilize unique or rare ORFan genes for strain-specific identification.
- To create strain-specific primers for accurate detection.
Main Methods:
- Targeted unique ORFan genes from 17 Escherichia coli strains.
- Developed strain-specific primers based on these genes.
- Employed multiplex PCR and quantitative PCR (qPCR) for detection.
Main Results:
- Successfully developed strain-specific primers for 14 out of 17 strains.
- Identified strains using a combination of PCR and selection for the remaining three.
- Demonstrated successful in vitro and in vivo identification in spiked fecal material and experimental infections.
Conclusions:
- The developed method is efficient and reliable for identifying single strains in mixtures.
- It provides a fast and inexpensive alternative to existing methods.
- The technique is effective for both in vitro and in vivo strain tracking.
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