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

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.

ANNOUNCEMENT

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 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).

TABLE 1

Structure of the SGI-1C and SPI-23 from S. Derby strain 2014LSAL02547

Genomic island and position	CDS	Protein	Length (bp)
SGI-1C
1	int	Integrase	1,158
2	s002	Helix-turn-helix domain protein	327
3	rep	Replication protein	954
4	S004	Hypothetical protein	228
5	S005	Hypothetical protein	2,760
6	S006	Hypothetical protein	534
7	S007	Hypothetical protein	612
8	S008	Hypothetical protein	210
9	S009	Hypothetical protein	291
10	S010	Hypothetical protein	255
11	traG	Pilus assembly protein TraG	3,405
12	S012	Conjugative relaxosome accessory transposon protein	1,425
13	S013	Hypothetical protein	858
14	S014	Hypothetical protein	411
15	S015	Hypothetical protein	270
16	S016	Hypothetical protein	213
17	S017	Hypothetical protein	243
18	intI1	Phage integrase	966
19	prokka_3715	Hypothetical protein	645
20	aplIR	Type 2 restriction enzyme AplI	1,092
21	taqIM	Modification methylase TaqI	1,830
22	hin	DNA-invertase hin	588
23	intI1	Integrase Int1	1,014
24	aadA2	Streptomycin 3″-adenylyltransferase	780
25	qacEdelta1	Quaternary ammonium compound efflux small multidrug resistance transporter QacE delta 1	348
26	sul1	Sulfonamide-resistant dihydropteroate synthase	840
27	ypeA	Putative acetyltransferase	501
28	intB	Transposase/IS protein	786
29	istA	Integrase core domain IS26	1,515
30	tniB	Bacterial TniB protein	861
31	tnsB	Transposon Tn7 transposition protein TnsB	1,680
32	cph2	Phytochrome-like protein cph2	708
33	merE	Mercury resistance protein MerE	237
34	mta	Zinc-responsive transcriptional regulator	363
35	merA	Mercuric reductase	1,695
36	merC	Mercuric resistance protein MerC	423
37	merP	Mercuric transport protein periplasmic component precursor	276
38	merT	MerT mercuric transport protein	351
39	merR	Mercuric resistance operon regulatory protein	435
40	prokka_3736	Hypothetical protein (putative relaxase)	243
41	tetR	Tetracycline repressor protein class A from transposon 1721	678
42	tetA	Tetracycline resistance protein, class C	1,200
43	yedA	Putative inner membrane transporter YedA	783
44	tnsB	Transposon Tn7 transposition protein TnsB	708
45	prokka_3741	Hypothetical protein	1,035
SPI-23
1	intA3	Integrase A	1,275
2	prokka_01810	Hypothetical protein	252
3	prokka_01811	Abortive infection phage resistance protein	1,113
4	prokka_01812	Bacterial shuffle protein	1,488
5	prokka_01813	Major subunit of bundle-forming pilus precursor	558
6	bfpA	Conjugal transfer protein TraD	306
7	traD	Hypothetical protein	1,515
8	prokka_01816	Hypothetical protein	735
9	prokka_01817	Hypothetical protein	576
10	prokka_01818	Hypothetical protein	531
11	prokka_01819	Hypothetical protein	342
12	prokka_01820	Hypothetical protein	471
13	prokka_01821	Hypothetical protein	552
14	prokka_01822	Hypothetical protein	180
15	prokka_01823	Hypothetical protein	240
16	prokka_01824	Hypothetical protein	1,251
17	prokka_01825	Hypothetical protein	282
18	prokka_01826	Hypothetical protein	438
19	prokka_01827	Hypothetical protein	558
20	prokka_01828	Hypothetical protein	183
21	prokka_01829	Hypothetical protein	477
22	prokka_01830	Hypothetical protein	2,730
23	prokka_01831	Hypothetical protein	504
24	prokka_01832	Hypothetical protein	93
25	prokka_01833	Hypothetical protein	870
26	prokka_01834	Hypothetical protein	588
27	prokka_01835	Hypothetical protein	984
28	prokka_01836	RNA pyrophosphohydrolase	444
29	prokka_01837	Hypothetical protein	519
30	prokka_01838	Hypothetical protein	261
31	prokka_01839	Hypothetical protein	735
32	prokka_01840	Hypothetical protein	738
33	prokka_01841	hypothetical protein	480
34	hns_2	DNA binding protein H_NS	405
35	prokka_01843	Hypothetical protein	549
36	prokka_01844	Hypothetical protein	1,272
37	prokka_01845	Hypothetical protein	297
38	prokka_01846	Hypothetical protein	291
39	prokka_01847	Hypothetical protein	219
40	prokka_01848	Hypothetical protein	876
41	prokka_01849	Hypothetical protein	525

GenBank 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).

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).