Abstract
Leuconostoc mesenteroides is a lactic acid bacterium (LAB) commonly associated with fermented foods. Here, we report the genome sequence of three selected dairy strains, showing atypical antibiotic resistances (AR). Genome analysis provided a better understanding of the genetic bases of AR in Leuconostoc and its potential transferability among foodborne bacteria.
GENOME ANNOUNCEMENT
Leuconostoc mesenteroides is a lactic acid bacterium (LAB) species commonly found in association with food substrates, both of plant and animal origin (1–3). In the dairy industry, strains of this species are naturally present as contaminants in many traditional cheese varieties or they are deliberately added as adjunct cultures (4–6). Indeed, their capacity to produce aromatic compounds, such as acetaldehyde, acetoin, and diacetyl, in addition to lactic and acetic acid, carbon dioxide, and dextrans, contribute to the development of desirable sensory traits of dairy products (7–10). An increasing number of L. mesenteroides genome sequences have been deposited in the GenBank database (11–13), including those of L. mesenteroides subsp. cremoris ATCC 19254T (ACKV00000000) and of two strains isolated from dairy starter cultures (6, 14).
Here, we report the genome sequence of three L. mesenteroides strains isolated from Italian soft cheese samples, namely, L. mesenteroides subsp. dextranicum LbE15, L. mesenteroides subsp. mesenteroides LbE16, and L. mesenteroides subsp. cremoris LbT16. These strains displayed atypical resistance to erythromycin and clindamycin (LbE15), kanamycin, streptomycin, tetracycline, and virginiamycin (LbE16), and tetracycline (LbT16).
Whole-genome sequencing was performed using the Illumina HiSeq2000 platform at the Beijing Institute of Genomics (BIG) (Beijing, China) with a paired-end library. Quality of reads was verified using the FastQC software and de novo assembly was performed with the SPAdes Assembler version 3.5.0 (15). The genome sequences of the three Leuconostoc strains were annotated by the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline. Genome information for each strain is reported in Table 1.
TABLE 1.
Whole-genome information of the three L. mesenteroides strains LbE15, LbE16, and LbT16
| Strain | Genome size (bp) | N50 (bp) | G+C content (%) | No. of genes | No. of coding sequences | No. of pseudo genes | Accession no. |
|---|---|---|---|---|---|---|---|
| LbE15 | 2,008,120 | 76,771 | 37 | 2,044 | 1,900 | 90 | LAYN00000000 |
| LbE16 | 2,036,196 | 160,323 | 37 | 2,100 | 1,949 | 97 | LAYU00000000 |
| LbT16 | 1,906,463 | 753,66 | 37 | 1,939 | 1,713 | 172 | LAYV00000000 |
Totals of 1,524,191, 1,682,147, and 1,416,327 paired-end reads (2- × 75-bp length on average) were assembled into 65, 86, and 66 contigs for strain LbE15, LbE16, and LbT16, respectively (genome coverage of about 200×). The lengths of the largest assembled contigs were 259,998 bp, 285,382 bp, and 382,195 bp for the genome of LbE15, LbE16, and LbT16, respectively. The three genomes contain 53 genes encoding RNAs, of which 3 are for rRNAs and 50 for tRNAs.
Preliminary analysis of the sequences revealed the presence of erm(B) in LbE15 and tet(S) in LbE16, coding for erythromycin (16) and tetracycline (17) resistance, respectively. However, these genotypes only partially explain the resistance phenotypes, and further studies will be necessary to gain a complete overview of the genetic background required for AR.
Increasing attention is paid to the presence of AR genes and their possible transferability to other species and eventually to pathogens (18). Therefore, the complete genomes of the three L. mesenteroides strains reported here represent a fundamental starting point to improve the current knowledge regarding the molecular basis of AR in LAB and to evaluate its transference capability via horizontal gene transfer among food-borne bacteria.
Nucleotide sequence accession numbers.
The whole-genome shotgun projects of the L. mesenteroides strains have been deposited in DDBJ/EMBL/GenBank under the accession numbers reported in Table 1. The versions described in this paper are the first versions, LAYN01000000 (L. mesenteroides subsp. dextranicum LbE15), LAYU01000000 (L. mesenteroides subsp. mesenteroides LbE16), and LAYV01000000 (L. mesenteroides subsp. cremoris LbT16).
ACKNOWLEDGMENT
The study was partially supported by a Spain-Italy bilateral collaboration program (Ref. IT2009-0080 and IT105MD12L).
Footnotes
Citation Campedelli I, Flórez AB, Salvetti E, Delgado S, Orrù L, Cattivelli L, Alegría Á, Felis GE, Torriani S, Mayo B. 2015. Draft genome sequence of three antibiotic-resistant Leuconostoc mesenteroides strains of dairy origin. Genome Announc 3(5):e01018-15. doi:10.1128/genomeA.01018-15.
REFERENCES
- 1.Bjorkroth J, Holzapfel W. 2006. Genera Leuconostoc, Oenococcus and Weissella, p 267–319. In Dworkin M, Falkow S, Rosemberg E, Schleifer KH, Stackebrandt E (ed), The prokaryotes, A handbook on the biology of bacteria, vol 4, 3rd ed. Springer Verlag, New York, NY. [Google Scholar]
- 2.Nionelli L, Curri N, Curiel JA, Di Cagno R, Pontonio E, Cavoski I, Gobbetti M, Rizzello CG. 2014. Exploitation of Albanian wheat cultivars: characterization of the flours and lactic acid bacteria microbiota, and selection of starters for sourdough fermentation. Food Microbiol 44:96–107. doi: 10.1016/j.fm.2014.05.011. [DOI] [PubMed] [Google Scholar]
- 3.Silva LF, Casella T, Gomes ES, Nogueira MC, De Dea Lindner J, Penna AL. 2015. Diversity of lactic acid bacteria isolated from Brazilian water buffalo mozzarella cheese. J Food Sci 80:M411–M417. doi: 10.1111/1750-3841.12771. [DOI] [PubMed] [Google Scholar]
- 4.Alegría Á, Delgado S, Flórez AB, Mayo B. 2013. Identification, typing, and functional characterization of Leuconostoc spp. strains from traditional, starter-free cheeses. Dairy Sci Technol 93:657–673. doi: 10.1007/s13594-013-0128-3. [DOI] [Google Scholar]
- 5.Ali Y, Kot W, Atamer Z, Hinrichs J, Vogensen FK, Heller KJ, Neve H. 2013. Classification of lytic bacteriophages attacking dairy Leuconostoc starter strains. Appl Environ Microbiol 79:3628–3636. doi: 10.1128/AEM.00076-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Pedersen TB, Kot WP, Hansen LH, Sørensen SJ, Broadbent JR, Vogensen FK, Ardö Y. 2014. Genome sequence of Leuconostoc mesenteroides subsp. cremoris strain t26, isolated from mesophilic undefined cheese starter. Genome Announc 2:e00485-14. doi: 10.1128/genomeA.00485-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.McSweeney PLH, Sousa MJ. 2000. Biochemical pathways for the production of flavour compounds in cheeses during ripening: a review. Lait 80:293–324. doi: 10.1051/lait:2000127. [DOI] [Google Scholar]
- 8.Hemme D, Foucaud-Scheunemann C. 2004. Leuconostoc, characteristics, use in dairy technology and prospects in functional foods. Int Dairy J 14:467–494. doi: 10.1016/j.idairyj.2003.10.005. [DOI] [Google Scholar]
- 9.Nieto-Arribas P, Seseña S, Poveda JM, Palop L, Cabezas L. 2010. Genotypic and technological characterization of Leuconostoc isolates to be used as adjunct starters in Manchego cheese manufacture. Food Microbiol 27:85–93. doi: 10.1016/j.fm.2009.08.006. [DOI] [PubMed] [Google Scholar]
- 10.Kothari D, Goyal A. 2015. Gentio-oligosaccharides from Leuconostoc mesenteroides NRRL B-1426 dextransucrase as prebiotics and as a supplement for functional foods with anti-cancer properties. Food Funct 6:604–611. doi: 10.1039/c4fo00802b. [DOI] [PubMed] [Google Scholar]
- 11.Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A, Pavlova N, Karamychev V, Polouchine N, Shakhova V, Grigoriev I, Lou Y, Rohksar D, Lucas S, Huang K, Goodstein DM, Hawkins T, Plengvidhya V, Welker D, Hughes J, Goh Y, Benson A, Baldwin K, Lee JH, Díaz-Muñiz I, Dosti B, Smeianov V, Wechter W, Barabote R, Lorca G, Altermann E, Barrangou R, Ganesan B, Xie Y, Rawsthorne H, Tamir D, Parker C, Breidt F, Broadbent J, Hutkins R, O’Sullivan D, Steele J, Unlu G, Saier M, Klaenhammer T, Richardson P, Kozyavkin S, Weimer B, Mills D. 2006. Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci USA 103:15611–15616. doi: 10.1073/pnas.0607117103. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Jung JY, Lee SH, Lee SH, Jeon CO. 2012. Complete genome sequence of Leuconostoc mesenteroides subsp. mesenteroides strain j18, isolated from kimchi. J Bacteriol 194:730–731. doi: 10.1128/JB.06498-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Riveros-Mckay F, Campos I, Giles-Gómez M, Bolívar F, Escalante A. 2014. Draft genome sequence of Leuconostoc mesenteroides P45 isolated from pulque, a traditional Mexican alcoholic fermented beverage. Genome Announc 2(6):e01130-14. doi: 10.1128/genomeA.01130-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Erkus O, de Jager VC, Spus M, van Alen-Boerrigter IJ, van Rijswijck IM, Hazelwood L, Janssen PW, van Hijum SA, Kleerebezem M, Smid EJ. 2013. Multifactorial diversity sustains microbial community stability. ISME J 7:2126–2136. doi: 10.1038/ismej.2013.108. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.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]
- 16.Roberts MC. 2008. Update on macrolide-lincosamide-streptogramin, ketolide, and oxazolidinone resistance genes. FEMS Microbiol Lett 282:147–159. doi: 10.1111/j.1574-6968.2008.01145.x. [DOI] [PubMed] [Google Scholar]
- 17.Thaker M, Spanogiannopoulos P, Wright GD. 2010. The tetracycline resistome. Cell Mol Life Sci 67:419–431. doi: 10.1007/s00018-009-0172-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 18.Morandi S, Cremonesi P, Silvetti T, Brasca M. 2013. Technological characterisation, antibiotic susceptibility and antimicrobial activity of wild-type Leuconostoc strains isolated from north Italian traditional cheeses. J Dairy Res 80:457–466. doi: 10.1017/S0022029913000447. [DOI] [PubMed] [Google Scholar]