Abstract
Here, we report the draft genome sequence of the lactose-negative, rifampin-resistant, Escherichia coli strain 26R 793. This isolate has been widely used in conjugation experiments as a general recipient strain.
GENOME ANNOUNCEMENT
Since the isolation of the original Escherichia coli strain K-12 which was cultured from a feces sample taken from a diphtheria patient in 1922, a variety of mutant derivatives of E. coli K-12 have been generated for various laboratory assays (1). The lactose-negative, rifampin-resistant strain E. coli 26R 793 was one such derivative (2, 3). This strain has been used for over 20 years as a recipient for conjugation experiments with E. coli, Klebsiella, and Salmonella species (4–6).
In this study, we determined the draft genome sequence of E. coli 26R 793. Genomic DNA was purified from an overnight culture using the UltraClean Microbial DNA isolation kit (MO BIO Laboratories, Inc., USA) according to the manufacturer’s instructions. This template DNA was sequenced using the Illumina HiSeq 2500 platform (Illumina, San Diego, CA, USA) generating 100 bp paired-end reads from a library with an average insert size of 500 bp and a total amount of quality-filtered raw sequence of more than 600 Mbp. Reads were assembled de novo using SPAdes v3.6.2 (7) resulting in 102 contigs of over 200 bp. Annotation of these contigs was performed using RAST (8).
The E. coli 26R 793 genome was found to be 4.51 Mbp with a G+C content of 50.8%. It contained 4,335 predicted protein-coding sequences (CDS), five copies of rRNA operons, and 72 tRNA genes. An in silico multilocus sequence type (MLST) analysis was performed using the MLST targets. E. coli 26R 793 was assigned to sequence type (ST) 10 and the serotype was identified as H48.
When compared to the E. coli K-12 substrain MG1655 genome (GenBank accession number NC_000913.3), 42 genes of E. coli 26R 793 contained single nucleotide polymorphisms (SNPs) including seven synonymous and 19 non-synonymous mutations. Further, E. coli 26R 793 contained eight insertional mutations, six deletional mutations, and four indels located in the region of CDS. In addition to its rpoB gene variant (a single amino acid substitution at position 513, when compared with E. coli K-12 substrain MG1655) encoding resistance to rifampin, E. coli 26R 793 also possessed an enzymatic and inactivating tet(34) gene, and two virulence genes (gad and iss).
Accession number(s).
The complete genome sequence of E. coli 26R 793 has been deposited at EMBL/GenBank under the accession number FLKR02000000.
ACKNOWLEDGMENTS
We are grateful to Vivi Miriagou, Laboratory of Bacteriology, Hellenic Pasteur Institute, Athens, for kindly providing the strain.
This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.
Footnotes
Citation Wang J, Hurley D, McGrath K, Bai L, Hächler H, Stephan R, Fanning S. 2016. Draft genome sequence of Escherichia coli 26R 793, a plasmid-free recipient strain commonly used in conjugation assays. Genome Announc 4(5):e00707-16. doi:10.1128/genomeA.00707-16.
REFERENCES
- 1.Bachmann BJ. 1996. Derivations and genotypes of some mutant derivatives of Escherichia coli K-12, p 2460–2488. In Neidhardt FC, et al. (ed), Escheichia coli and Salmonella: cellular and molecular biology, 2nd ed. ASM Press, Washington, DC. [Google Scholar]
- 2.Tzouvelekis LS, Tzelepi E, Mentis AF, Tsakris A. 1993. Identification of a novel plasmid-mediated beta-lactamase with chromosomal cephalosporinase characteristics from Klebsiella pneumoniae. J Antimicrob Chemother 31:645–654. doi: 10.1093/jac/31.5.645. [DOI] [PubMed] [Google Scholar]
- 3.Clowes RC, Rowley D. 1954. Some observations on linkage effects in genetic recombination in Escherichia coli K-12. J Gen Microbiol 11:250–260. doi: 10.1099/00221287-11-2-250. [DOI] [PubMed] [Google Scholar]
- 4.Pournaras S, Ikonomidis A, Tzouvelekis LS, Tokatlidou D, Spanakis N, Maniatis AN, Legakis NJ, Tsakris A. 2005. VIM-12, a novel plasmid-mediated metallo-beta-lactamase from Klebsiella pneumoniae that resembles a VIM-1/VIM-2 hybrid. Antimicrob Agents Chemother 49:5153–5156. doi: 10.1128/AAC.49.12.5153-5156.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Wang J, Stephan R, Karczmarczyk M, Yan Q, Hächler H, Fanning S. 2013. Molecular characterisation of blaESBL-harbouring conjugative plasmids identified in multi-drug resistant Escherichia coli isolated from food-producing animals and healthy humans. Front Microbiol 4:188. doi: 10.3389/fmicb.2013.00188. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Balis E, Vatopoulos AC, Kanelopoulou M, Mainas E, Hatzoudis G, Kontogianni V, Malamou-Lada H, Kitsou-Kiriakopoulou S, Kalapothaki V. 1996. Indications of in vivo transfer of an epidemic R plasmid from Salmonella enteritidis to Escherichia coli of the normal human gut flora. J Clin Microbiol 34:977–979. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi: 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]