Bacterial species singled out from a diverse crowd

Nguyen, Jen; Tropini, Carolina

doi:10.1038/d41586-020-03315-z

Cited by 1 publication

(1 citation statement)

References 13 publications

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“…The ORFan gene approach allows the combination with other visualization techniques to expand strain-speci c detection to other types of biological sample. Recently, a FISH ( uorescence in situ hybridization)-based strain identi cation technique was described (32). It has proved to be very useful at the species identi cation level, based on 16S rDNA sequence speci city.…”

Section: Discussionmentioning

confidence: 99%

Using Unique ORFan Genes as Strain-specific Identifiers for Escherichia Coli

Ferrandis-Vila¹,

Tiwari²,

Mamerow³

et al. 2021

Preprint

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BackgroundBacterial identification at the strain level is a much-needed, but arduous and challenging task. This study aimed to develop a method for identifying and differentiating individual strains among multiple strains of the same bacterial species. The set used for testing the method consisted of 17 Escherichia coli strains picked from a collection of strains isolated in Germany, Spain, the United Kingdom and Vietnam from humans, cattle, swine, wild boars, and chickens. We targeted unique or rare ORFan genes to address the problem of selective and specific strain identification. These ORFan genes, exclusive to each strain, served as templates for developing strain-specific primers.ResultsMost of the strains to be deployed experimentally (14 out of 17) possessed unique ORFan genes that were used to develop strain-specific primers. The remaining three strains were identified by combining a PCR for a rare gene with a selection step for isolating the experimental strains. Multiplex PCR allowed the successful identification of the strains both in vitro in spiked faecal material in addition to in vivo after experimental infections of pigs and recovery of bacteria from faecal material. In addition, primers for qPCR were also developed and quantitative readout from faecal samples after experimental infection was also possible.ConclusionsThe method described in this manuscript using strain-specific unique genes to identify single strains in a mixture of strains proved itself efficient and reliable in detecting and following individual strains both in vitro and in vivo, representing a fast and inexpensive alternative to more costly methods.

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Section: Discussionmentioning

confidence: 99%