Abstract
Salmonella enterica is principally a foodborne pathogen that shows considerable serovar diversity. In this report, we present two draft genome sequences of Salmonella enterica subsp. enterica serovar Lubbock, a novel serovar.
GENOME ANNOUNCEMENT
Salmonella enterica is a foodborne pathogen, showing considerable antigenic diversity with more than 2,500 serovars characterized to date (1, 2). This bacterium inhabits and colonizes a large variety of hosts and environments. Recent studies (3, 4) have highlighted the presence of Salmonella in bovine peripheral lymph nodes, which may be incorporated with meat to produce ground beef and therefore become a source of food contamination. We isolated atypical strains initially identified as serovar Montevideo. However, molecular interrogation of targeted genetic clades (5) revealed an atypical profile for Salmonella enterica serovar Montevideo. Further serological characterization of these isolates provided the antigenic formula of S. I. 6,7:g,m,s:e,n,z15, representing a novel serovar that has been designated Lubbock. The strains sequenced in this announcement are 10TTU468 and 11TTU1590; both were isolated from subiliac lymph nodes from cattle at a commercial abattoir. Initial subtyping using multilocus sequence typing (6) or CRISPR locus content characterization showed subtypes previously associated with Salmonella enterica serovar Mbandaka.
Paired-end 151-bp reads were generated using an Illumina MiSeq platform. Reads were de novo assembled using the a5-pipeline version 20141120 (7), resulting in 38 and 36 contigs for 10TTU468 and 11TTU1590, respectively. The total assembly size was 4.95 Mbp for both strains, with N50 values of 263 kbp and 264 kbp and a median read depth of the assemblies of 85× and 74× for 10TTU468 and 11TTU1590, respectively. The draft genomes were annotated using the NCBI Prokaryotic Genome Automated Annotation Pipeline (8). Prophages were identified using PHAST (9). High-quality single nucleotide polymorphisms (hqSNPs) were called using software and parameters described previously by Den Bakker et al. (10), using the concatenated genome sequence of 10TTU468 as a reference, with rRNA and prophage regions excluded.
A total of 4,712 (10TTU468) and 4,709 (11TTU1590) protein-coding sequences were annotated in each genome. No plasmid-associated sequences were found, and both genome sequences contain seven intact prophages and five incomplete prophage regions. A kSNP-based (11) phylogenetic comparison using a representative variety of S. enterica serovars (12) and additional serovar Mbandaka isolates showed that both strains are closely related to S. enterica serovar Mbandaka 2009k-0807 (GenBank accession no. AMRS00000000.1) and 2012K-0273 (GenBank accession no. ARYT00000000.1). Further hqSNP-based comparison of the two isolates with 128 S. Mbandaka isolates publicly available from the NCBI Sequence Read Archive (SRA) (February 2015) showed that 10TTU468 and 11TTU1590 differ by 187 shared hqSNPs from the most closely related S. enterica serovar Mbandaka strain (NY_IDR1200021873-04, SRA accession no. SRX426108). Fifty-two hqSNPs mapped to a 4.5-kbp region containing the fliC gene. The high SNP density suggests homologous recombination within this region, and a BLASTn (13) search of the fliC sequences of Lubbock strains shows that this gene has a 100% identity to fliC in S. enterica serovar Montevideo strain 507440-20.
Nucleotide sequence accession numbers.
These whole-genome shotgun projects have been deposited in DDBJ/EMBL/GenBank under the accession numbers JXYU00000000 (10TTU468) and JXYV00000000 (11TTU1590). The versions described in this paper are JXYU01000000 and JXYV01000000.
ACKNOWLEDGMENTS
This work was funded in part by the U.S. Department of Agriculture, National Institutes of Food and Agriculture’s National Integrated Food Safety Initiative award no. 2011-51110-31081 and by the Beef Checkoff Program.
We acknowledge the laboratory of Food Safety of the French Agency for Food, Environmental and Occupational Health and Safety (Maisons-Alfort, France) and the national reference laboratory for Salmonella at the Pasteur Institute (Paris, France) that performed the serological characterization of these strains, leading to the confirmation of the identification of the novel serovar Lubbock.
We report no financial conflicts of interest that arise because of material reported herein.
Footnotes
Citation Bugarel M, den Bakker HC, Nightingale KK, Brichta-Harhay DM, Edrington TS, Loneragan GH. 2015. Two draft genome sequences of a new serovar of Salmonella enterica, serovar Lubbock. Genome Announc 3(2):e00215-15. doi:10.1128/genomeA.00215-15.
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