# Complete Genome Sequence of Salmonella enterica subsp. enterica Serotype Derby, Associated with the Pork Sector in France

Yann Sévellec, Sophie Granier, Nicolas Randomski, Arnaud Felten, Simon Le Hello, Carole Feurer, Michel-Yves Mistou, Sabrina Cadel-Six

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Yann Sévellec, Sophie Granier, Nicolas Randomski, Arnaud Felten, Simon Le Hello, et al.. Complete Genome Sequence of Salmonella enterica subsp. enterica Serotype Derby, Associated with the Pork Sector in France. Microbiology Resource Announcements, 2018, 7 (12), pp.e01027-18. 10.1128/MRA.01027-18. hal-02155343

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# Complete Genome Sequence of *Salmonella enterica* subsp. *enterica* Serotype Derby, Associated with the Pork Sector in France

Yann Sévellec,ª,>d Sophie A. Granier,ª,>d Nicolas Radomski,ª,>d Arnaud Felten,ª,>d Simon Le Hello,ᵇ Carole Feurer,ᶜ Michel-Yves Mistou,ª,>d Sabrina Cadel-Sixª,>d

**ABSTRACT** In the European Union, *Salmonella enterica* subsp. *enterica* serovar Derby is the most abundant serotype isolated from pork. Recent studies have shown that this serotype is polyphyletic. However, one main genomic lineage, characterized by sequence type 40 (ST40), the presence of the *Salmonella* pathogenicity island 23, and showing resistance to streptomycin, sulphonamides, and tetracycline (STR-SSS-TET), is pork associated. Here, we describe the complete genome sequence of a strain from this lineage isolated in France.

In the European Union, *Salmonella enterica* subsp. *enterica* serovar Derby (S. Derby) was the fifth serovar reported from human cases of salmonellosis in 2016 (0.7%; 325/44,462 confirmed cases) (1). European monitoring data linked this serovar predominantly to pigs and pork meat and, to a lesser extent, turkey and cattle (1). Recent studies based on whole-genome sequencing (WGS) have shown that distinct genomic lineages of S. Derby exist, associated with either pork or poultry (2, 3). The main genomic lineage associated with pork is characterized by multilocus sequence typing (MLST) profile 40 (sequence type 40 [ST40]), presence of genes mediating resistance to aminoglycosides, sulfonamides, and tetracyclines (3), and presence of *Salmonella* pathogenicity island 23 (SPI-23), which was previously associated with pork enterocyte invasion (2). We present here the complete genome sequence of S. *enterica* subsp. *enterica* serovar Derby strain 2014LSAL02547, which represents this genomic lineage.

Strain 2014LSAL02547 was isolated in 2014 from a pig carcass sampled at a slaughterhouse in Brittany, France, and identified as belonging to *Salmonella* serovar Derby, according to the White-Kauffmann-Le Minor scheme (4). Its genome was sequenced using Illumina HiSeq (i.e., paired-end read sequencing, 2 × 150 bp) and PacBio (i.e., long-read sequencing) technologies. Concerning the Illumina HiSeq sequencing, genomic DNA was isolated from overnight culture at 37°C on a tryptone soy yeast extract agar plate using the Wizard genomic DNA purification kit (Promega, France) according to the manufacturer's instructions for Gram-negative organisms. The DNA concentration was measured with a Qubit fluorometer, and a gel of 0.8% agarose was used to assess the quality of the extraction (and an eventual degradation of the DNA). Library preparation and sequencing were performed by the Institut du Cerveau et de la Moelle épinière (www.icm-institute.org) using NextEra XT technology and a NextSeq 500 sequencer, respectively (Illumina). Concerning the PacBio sequencing, DNA extraction and library preparation were performed by Genoscreen (Lille, France). DNA was extracted using a Gentra Puregene

**Received** 30 July 2018 **Accepted** 2 September 2018 **Published** 27 September 2018

**Citation** Sévellec Y, Granier SA, Radomski N, Felten A, Le Hello S, Feurer C, Mistou M-Y, Cadel-Six S. 2018. Complete genome sequence of *Salmonella enterica* subsp. *enterica* serotype Derby, associated with the pork sector in France. Microbiol Resour Announc 7:e01027-18. https://doi.org/10.1128/MRA.01027-18.

**Editor** Iddo Friedberg, Iowa State University

**Copyright** © 2018 Sévellec et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

Address correspondence to Sabrina Cadel-Six, sabrina.cadelsix@anses.fr.

[This article was published on 27 September 2018 with Nicolas Radomski's surname misspelled as "Randomski" in the byline. The byline was updated in the current version, posted on 28 November 2018.]

<footnote>ªUniversité Paris-Est, Marne-la-Vallée, France</footnote>

<footnote>ᵇInstitut Pasteur, Centre National de Référence des *Salmonella*, Unité des Bactéries Pathogènes Entériques, Paris, France</footnote>

<footnote>ᶜFrench Institute for the Pig and Pork Industry (IFIP), Le Rheu, France</footnote>

<footnote>ᵈANSES, Laboratory for Food Safety, Maisons-Alfort, France</footnote>
<table><caption>TABLE 1 Structure of the SGI-1C and SPI-23 from S. Derby strain 2014LSAL02547<sup>a</sup></caption><thead><tr><th>Genomic island and position</th><th>CDS</th><th>Protein</th><th>Length (bp)</th></tr></thead><tbody><tr><td>SGI-1C</td><td></td><td></td><td></td></tr><tr><td>1</td><td>int</td><td>Integrase</td><td>1,158</td></tr><tr><td>2</td><td>s002</td><td>Helix-turn-helix domain protein</td><td>327</td></tr><tr><td>3</td><td>rep</td><td>Replication protein</td><td>954</td></tr><tr><td>4</td><td>S004</td><td>Hypothetical protein</td><td>228</td></tr><tr><td>5</td><td>S005</td><td>Hypothetical protein</td><td>2,760</td></tr><tr><td>6</td><td>S006</td><td>Hypothetical protein</td><td>534</td></tr><tr><td>7</td><td>S007</td><td>Hypothetical protein</td><td>612</td></tr><tr><td>8</td><td>S008</td><td>Hypothetical protein</td><td>210</td></tr><tr><td>9</td><td>S009</td><td>Hypothetical protein</td><td>291</td></tr><tr><td>10</td><td>S010</td><td>Hypothetical protein</td><td>255</td></tr><tr><td>11</td><td>traG</td><td>Pilus assembly protein TraG</td><td>3,405</td></tr><tr><td>12</td><td>S012</td><td>Conjugative relaxosome accessory transposon protein</td><td>1,425</td></tr><tr><td>13</td><td>S013</td><td>Hypothetical protein</td><td>858</td></tr><tr><td>14</td><td>S014</td><td>Hypothetical protein</td><td>411</td></tr><tr><td>15</td><td>S015</td><td>Hypothetical protein</td><td>270</td></tr><tr><td>16</td><td>S016</td><td>Hypothetical protein</td><td>213</td></tr><tr><td>17</td><td>S017</td><td>Hypothetical protein</td><td>243</td></tr><tr><td>18</td><td>intl1</td><td>Phage integrase</td><td>966</td></tr><tr><td>19</td><td>prokka_3715</td><td>Hypothetical protein</td><td>645</td></tr><tr><td>20</td><td>apII R</td><td>Type 2 restriction enzyme AplI</td><td>1,092</td></tr><tr><td>21</td><td>taqI M</td><td>Modification methylase TaqI</td><td>1,830</td></tr><tr><td>22</td><td>hin</td><td>DNA-invertase hin</td><td>588</td></tr><tr><td>23</td><td>intl1</td><td>Integrase Intl1</td><td>1,014</td></tr><tr><td>24</td><td>aadA2</td><td>Streptomycin 3"-adenylyltransferase</td><td>780</td></tr><tr><td>25</td><td>qacE delta1</td><td>Quaternary ammonium compound efflux small multidrug resistance transporter QacE delta 1</td><td>348</td></tr><tr><td>26</td><td>sulI</td><td>Sulfonamide-resistant dihydropteroate synthase</td><td>840</td></tr><tr><td>27</td><td>ypeA</td><td>Putative acetyltransferase</td><td>501</td></tr><tr><td>28</td><td>intB</td><td>Transposase/IS protein</td><td>786</td></tr><tr><td>29</td><td>istA</td><td>Integrase core domain IS26</td><td>1,515</td></tr><tr><td>30</td><td>tniB</td><td>Bacterial TniB protein</td><td>861</td></tr><tr><td>31</td><td>tnsB</td><td>Transposon Tn7 transposition protein TnsB</td><td>1,680</td></tr><tr><td>32</td><td>cph2</td><td>Phytochrome-like protein cph2</td><td>708</td></tr><tr><td>33</td><td>merE</td><td>Mercury resistance protein MerE</td><td>237</td></tr><tr><td>34</td><td>mta</td><td>Zinc-responsive transcriptional regulator</td><td>363</td></tr><tr><td>35</td><td>merA</td><td>Mercuric reductase</td><td>1,695</td></tr><tr><td>36</td><td>merC</td><td>Mercuric resistance protein MerC</td><td>423</td></tr><tr><td>37</td><td>merP</td><td>Mercuric transport protein periplasmic component precursor</td><td>276</td></tr><tr><td>38</td><td>merT</td><td>MerT mercuric transport protein</td><td>351</td></tr><tr><td>39</td><td>merR</td><td>Mercuric resistance operon regulatory protein</td><td>435</td></tr><tr><td>40</td><td>prokka_3736</td><td>Hypothetical protein (putative relaxase)</td><td>243</td></tr><tr><td>41</td><td>tetR</td><td>Tetracycline repressor protein class A from transposon 1721</td><td>678</td></tr><tr><td>42</td><td>tetA</td><td>Tetracycline resistance protein, class C</td><td>1,200</td></tr><tr><td>43</td><td>yedA</td><td>Putative inner membrane transporter YedA</td><td>783</td></tr><tr><td>44</td><td>tnsB</td><td>Transposon Tn7 transposition protein TnsB</td><td>708</td></tr><tr><td>45</td><td>prokka_3741</td><td>Hypothetical protein</td><td>1,035</td></tr><tr><td>SPI-23</td><td></td><td></td><td></td></tr><tr><td>1</td><td>intA3</td><td>Integrase A</td><td>1,275</td></tr><tr><td>2</td><td>prokka_01810</td><td>Hypothetical protein</td><td>252</td></tr><tr><td>3</td><td>prokka_01811</td><td>Abortive infection phage resistance protein</td><td>1,113</td></tr><tr><td>4</td><td>prokka_01812</td><td>Bacterial shuffle protein</td><td>1,488</td></tr><tr><td>5</td><td>prokka_01813</td><td>Major subunit of bundle-forming pilus precursor</td><td>558</td></tr><tr><td>6</td><td>bfpA</td><td>Conjugal transfer protein TraD</td><td>306</td></tr><tr><td>7</td><td>traD</td><td>Hypothetical protein</td><td>1,515</td></tr><tr><td>8</td><td>prokka_01816</td><td>Hypothetical protein</td><td>735</td></tr><tr><td>9</td><td>prokka_01817</td><td>Hypothetical protein</td><td>576</td></tr><tr><td>10</td><td>prokka_01818</td><td>Hypothetical protein</td><td>531</td></tr><tr><td>11</td><td>prokka_01819</td><td>Hypothetical protein</td><td>342</td></tr><tr><td>12</td><td>prokka_01820</td><td>Hypothetical protein</td><td>471</td></tr><tr><td>13</td><td>prokka_01821</td><td>Hypothetical protein</td><td>552</td></tr><tr><td>14</td><td>prokka_01822</td><td>Hypothetical protein</td><td>180</td></tr><tr><td>15</td><td>prokka_01823</td><td>Hypothetical protein</td><td>240</td></tr><tr><td>16</td><td>prokka_01824</td><td>Hypothetical protein</td><td>1,251</td></tr></tbody></table>

(Continued on next page)
<figure><img src="image_3.png" /></figure>

<table><caption>TABLE 1 (Continued)</caption><thead><tr><th>Genomic island and position</th><th>CDS</th><th>Protein</th><th>Length (bp)</th></tr></thead><tbody><tr><td>17</td><td>prokka_01825</td><td>Hypothetical protein</td><td>282</td></tr><tr><td>18</td><td>prokka_01826</td><td>Hypothetical protein</td><td>438</td></tr><tr><td>19</td><td>prokka_01827</td><td>Hypothetical protein</td><td>558</td></tr><tr><td>20</td><td>prokka_01828</td><td>Hypothetical protein</td><td>183</td></tr><tr><td>21</td><td>prokka_01829</td><td>Hypothetical protein</td><td>477</td></tr><tr><td>22</td><td>prokka_01830</td><td>Hypothetical protein</td><td>2,730</td></tr><tr><td>23</td><td>prokka_01831</td><td>Hypothetical protein</td><td>504</td></tr><tr><td>24</td><td>prokka_01832</td><td>Hypothetical protein</td><td>93</td></tr><tr><td>25</td><td>prokka_01833</td><td>Hypothetical protein</td><td>870</td></tr><tr><td>26</td><td>prokka_01834</td><td>Hypothetical protein</td><td>588</td></tr><tr><td>27</td><td>prokka_01835</td><td>Hypothetical protein</td><td>984</td></tr><tr><td>28</td><td>prokka_01836</td><td>RNA pyrophosphohydrolase</td><td>444</td></tr><tr><td>29</td><td>prokka_01837</td><td>Hypothetical protein</td><td>519</td></tr><tr><td>30</td><td>prokka_01838</td><td>Hypothetical protein</td><td>261</td></tr><tr><td>31</td><td>prokka_01839</td><td>Hypothetical protein</td><td>735</td></tr><tr><td>32</td><td>prokka_01840</td><td>Hypothetical protein</td><td>738</td></tr><tr><td>33</td><td>prokka_01841</td><td>Hypothetical protein</td><td>480</td></tr><tr><td>34</td><td>hns_2</td><td>DNA binding protein H_NS</td><td>405</td></tr><tr><td>35</td><td>prokka_01843</td><td>Hypothetical protein</td><td>549</td></tr><tr><td>36</td><td>prokka_01844</td><td>Hypothetical protein</td><td>1,272</td></tr><tr><td>37</td><td>prokka_01845</td><td>Hypothetical protein</td><td>297</td></tr><tr><td>38</td><td>prokka_01846</td><td>Hypothetical protein</td><td>291</td></tr><tr><td>39</td><td>prokka_01847</td><td>Hypothetical protein</td><td>219</td></tr><tr><td>40</td><td>prokka_01848</td><td>Hypothetical protein</td><td>876</td></tr><tr><td>41</td><td>prokka_01849</td><td>Hypothetical protein</td><td>525</td></tr></tbody></table>

kit (Qiagen), the DNA concentration was assessed using a Qubit fluorometer, and the DNA extract's quality was checked by agarose gel electrophoresis. Library preparation was made by DNA fragmentation and ligation of single-molecule real-time (SMRT) adaptors. Prior to sequencing, BluePippin size selection (Sage Science) was set at 15 kb in order to achieve identical sequence overlaps. PacBio sequencing was performed on one SMRT cell. Quality of the Illumina and PacBio reads was examined using FastQC v0.11.5 (5). Prinseq v0.20.4 (6) was used to select Illumina long reads of good quality (no undefined bases; Phred, >30; length, >60 kb). SMRT Analysis v2.3.0 software was used to assemble PacBio reads. In SMRT Analysis, the Hierarchical Genome Assembly Process (HGAP) v3.0 (7) was invoked to correct the subreads (length, >1,000 bases; read score, 0.8), and Celera v8.3 (8) was used for assembly (subread length, >500 bases; deep coverage, >25×). SAMtools v1.5 (9) was used to map the Illumina short paired-end reads against the PacBio assembly to correct potential assembly mistakes and to determine the depth of the final assembly. The final deep coverage obtained was 146×. A unique 4.86-Mb contig was obtained, with a GC content of 51.12%. The genome was annotated using Prokka (10). It included 4,549 coding sequences (CDS) and 88 tRNAs.

Genes mediating antimicrobial resistance phenotype STR-SSS-TET (showing resistance to streptomycin, sulfonamides, and tetracycline) are part of the *Salmonella* genomic island 1 (SGI-1) (3), described in Table 1. This SGI-1 element integrated a cluster of mercury resistance genes (*merA*, *merC*, *merP*, *merT*, and *merR*) located in a Tn7 transposon. SPI-23 from the 2014LSAL02547 genome was 36,603 bp long and was located between the *DAD50_12070* and *mftA* genes (Table 1).

**Data availability.** This whole-genome assembly sequence was deposited in the NCBI database under the accession number CP029486. The SRA accession numbers are SRX3643218 (Illumina reads) and SRX4523973 (PacBio reads).

## ACKNOWLEDGMENTS

This study was funded by the French Ministry of Agriculture, Food and Forestry, by the *Salmonella* Network from the French Agency for Food, Environmental and Occu-

<footnote>ªGenBank accession number CP029486. SGI-1C, *Salmonella* genomic island 1 type C (bases 427735 to 472096); SPI-23, *Salmonella* pathogenicity island 23 (bases 2369809 to 2406412).</footnote>
<figure><img src="image_4.png" /></figure>

pational Health and Safety (ANSES) Laboratory for Food Safety and by INAPORC. Y.S. is
the recipient of a doctoral fellowship (DGER-ANSES) cofunded by AgroParisTech and
the ANSES.

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<figure><img src="image_5.png" /></figure>

# Correction for Sévellec et al., “Complete Genome Sequence of *Salmonella enterica* subsp. *enterica* Serotype Derby, Associated with the Pork Sector in France”

Yann Sévellec,ª,>d Sophie A. Granier,ª,>d Nicolas Radomski,ª,>d Arnaud Felten,ª,>d Simon Le Hello,ᵇ Carole Feurer,ᶜ Michel-Yves Mistou,ª,>d Sabrina Cadel-Sixª,>d

Volume 7, no. 12, e01027-18, 2018, https://doi.org/10.1128/MRA.01027-18. Page 1:
The author byline should appear as given in this correction.

**Citation** Sévellec Y, Granier SA, Radomski N, Felten A, Le Hello S, Feurer C, Mistou M-Y, Cadel-Six S. 2019. Correction for Sévellec et al., "Complete genome sequence of *Salmonella enterica* subsp. *enterica* serotype Derby, associated with the pork sector in France." *Microbiol Resour Announc* 8:e01597-18. https://doi.org/10.1128/MRA.01597-18.

**Copyright** © 2019 Sévellec et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

Address correspondence to Sabrina Cadel-Six, sabrina.cadelsix@anses.fr.

**Published** 3 January 2019

<figure><img src="image_6.png" /></figure>

<footnote>ªUniversité Paris-Est, Marne-la-Vallée, France</footnote>

<footnote>ᵇInstitut Pasteur, Centre National de Référence des Salmonella, Unité des Bactéries Pathogènes Entériques, Paris, France</footnote>

<footnote>ᶜFrench Institute for the Pig and Pork Industry (IFIP), Le Rheu, France</footnote>

<footnote>ᵈANSES, Laboratory for Food Safety, Maisons-Alfort, France</footnote>