Publication Database

Using unique ORFan genes as strain-specific identifiers for Escherichia coli (2022)

Art

Zeitschriftenartikel / wissenschaftlicher Beitrag

Autoren

Ferrandis-Vila, Marta

Tiwari, Sumeet K.

Mamerow, Svenja

Semmler, Torsten

van der Putten, Boas

Trung, Nguyen V.

Oldenkamp, Rik

Bootsma, Martin

Matamoros, Sebastien

Ngo, Hoa T.

Alvarez, Julio

Ritchie, Jennifer M.

Fivian-Hughes, Amanda

Fruth, Angelika

Leng, Joy

La Ragione, Roberto M.

Ugarte-Ruiz, Maria

Bethe, Astrid (WE 7)

Schwarz, Stefan (WE 7)

Schultsz, Constance

Menge, Christian

Berens, Christian

Quelle

BMC microbiology

Bandzählung: 22

Heftzählung: 1

Seiten: Article number: 135

ISSN: 1471-2180

Sprache

Englisch

Verweise

URL (Volltext): https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02508-y

DOI: 10.1186/s12866-022-02508-y

Pubmed: 35585491

Kontakt

Institut für Mikrobiologie und Tierseuchen

Robert-von-Ostertag-Str. 7-13
14163 Berlin
+49 30 838 51843 / 66949
mikrobiologie@vetmed.fu-berlin.de

Abstract / Zusammenfassung

HECTOR consortium:
Marta Ferrandis-Vila, Sumeet K. Tiwari, Boas van der Putten, Nguyen V. Trung, Rik Oldenkamp, Martin Bootsma, Sebastien Matamoros, Hoa T. Ngo, Julio Alvarez, Jennifer M. Ritchie, Amanda Fivian-Hughes, Angelika Fruth, Joy Leng, Roberto M. La Ragione, Maria Ugarte-Ruiz, Astrid Bethe (WE07), Stefan Schwarz (WE07), Torsten Semmler, Constance Schultsz, Christian Menge & Christian Berens

Abstract:
Bacterial 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.

Most of the experimental strains (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.

The 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.