Abstract
Here, we present the draft genome sequences of 19 Salmonella enterica serovar Typhimurium monophasic variant [4,5:i:−] strains involved in a long-term salmonellosis outbreak that occurred in central Italy in 2013 to 2014.
GENOME ANNOUNCEMENT
Salmonella is a Gram-negative foodborne pathogen distributed worldwide. Even if few lineages have been detected, its antibiotic resistance pattern is very heterogeneous, spanning from multidrug-resistant to largely susceptible strains (1). According to Garcia et al. (2), two major profiles circulate in Europe, the Spanish clone and the ASSuT clone. The ASSuT clone, which is common in Italy, harbors a genomic region that confers resistance to ampicillin, streptomycin, sulfonamides, and tetracycline (3). In central Italy, in the period of September 2013 to August 2014, a non-ASSuT long-term salmonellosis outbreak was reported; the clinical isolates were epidemiologically associated with strains isolated from wastewater, while no source attribution was possible (F. Cito, F. Baldinelli, P. Calistri, E. Di Giannatale, G. Scavia, M. Orsini, S. Iannetti, L. Sacchini, I. Mangone, L. Candeloro, A. M. Conte, C. Ippoliti, C. Cammà, M. Marcacci, M. Ancora, A. M. Dionisi, S. Ocwzarek, and I. Luzzi, unpublished data). The distinctive trait of both clinical and environmental strains was the resistance to nalidixic acid; this antibiotic resistance profile is not common, and it was observed in Europe in 2011 only (4).
Nineteen strains, chosen among clinical and environmental isolates on the basis of their spatial-temporal distribution and familiar kinship, were subjected to whole-genome sequencing together with three unrelated strains as outgroups. Genomic DNA was extracted by Qiagen EasyPrep, libraries were prepared using the Hi-Q sequencing kit, and sequencing was performed on a PGM Ion Torrent platform. Raw reads were submitted to the SRA repository (5), while biosamples were registered under the project ID PRJNA266093. Reads were trimmed and assembled using a dedicated de novo workflow under the Orione framework (6) plus some ad hoc-developed python scripts; contig annotation was performed by the NCBI team using the PGAP pipeline (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html).
The results from the genome annotation (numbers of coding sequences [CDSs], rRNAs, and tRNAs) are summarized in Table 1, together with N50 values and GenBank accession numbers.
TABLE 1 .
Genome annotation statistics and accession numbers
| BioSample accession no. | No. of contigs | N50 (bp) | No. of CDSs | No. of rRNAs | No. of tRNAs | GenBank accession no. |
|---|---|---|---|---|---|---|
| SAMN03162139 | 9 | 794,381 | 3,863 | 25 | 84 | LDPA00000000 |
| SAMN03162140 | 8 | 921,005 | 3,551 | 27 | 82 | LDYH00000000 |
| SAMN03162153 | 14 | 838,841 | 3,474 | 27 | 80 | LECB00000000 |
| SAMN03162151 | 10 | 478,653 | 3,799 | 25 | 81 | LECA00000000 |
| SAMN03162157 | 14 | 695,105 | 3,707 | 25 | 83 | LECD00000000 |
| SAMN03162156 | 12 | 705,141 | 3,825 | 25 | 82 | LECC00000000 |
| SAMN03162148 | 13 | 627,564 | 3,780 | 27 | 83 | LFCI00000000 |
| SAMN03162144 | 28 | 476,560 | 3,635 | 26 | 86 | LFCH00000000 |
| SAMN03162141 | 10 | 566,971 | 3,536 | 26 | 82 | LFCG00000000 |
| SAMN03162145 | 14 | 694,859 | 3,409 | 24 | 80 | LFDZ00000000 |
| SAMN03162146 | 28 | 435,395 | 3,758 | 26 | 84 | LFDY00000000 |
| SAMN03162147 | 11 | 628,011 | 3,719 | 25 | 79 | LFDX00000000 |
| SAMN03162150 | 11 | 723,217 | 3,906 | 25 | 84 | LFDW00000000 |
| SAMN03162161 | 14 | 579,418 | 4,114 | 26 | 85 | LFGN00000000 |
| SAMN03162155 | 12 | 628,734 | 3,828 | 23 | 82 | LFGR00000000 |
| SAMN03162159 | 20 | 628,218 | 3,891 | 29 | 82 | LFGP00000000 |
| SAMN03162162 | 14 | 579,418 | 3,822 | 25 | 83 | LFGM00000000 |
| SAMN03162160 | 11 | 872,758 | 3,678 | 26 | 80 | LFGO00000000 |
| SAMN03162158 | 15 | 695,105 | 3,820 | 24 | 83 | LFGQ00000000 |
The availability of the assembled sequences allowed us to better understand antibiotic resistance mechanisms and to clarify genomic relationships among the isolates.
Nucleotide sequence accession numbers.
The sequences described here have been deposited at GenBank under the accession numbers indicated in Table 1.
ACKNOWLEDGMENT
This work was supported by the National Ministry of Public Health (MSRCTE0212).
Footnotes
Citation Orsini M, Mangone I, DiPasquale A, Perticara S, Sacchini L, Cito F, Iannetti S, Marcacci M, Ancora M, Calistri P, Di Giannatale E, Cammà C. 2015. Draft genome sequences of 19 Salmonella enterica serovar Typhimurium [4,5:i:−] strains resistant to nalidixic acid from a long-term outbreak in Italy. Genome Announc 3(4):e00911-15. doi:10.1128/genomeA.00911-15.
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