Draft Genome Sequences of 23 Salmonella enterica Strains Isolated from Cattle in Ibadan, Nigeria, Representing 21 Salmonella Serovars.

To provide a better understanding of the diversity of Salmonella enterica, we report the assembled genome sequences of 23 Salmonella enterica strains isolated from fecal samples of cattle in Nigeria comprising 21 different Salmonella serovars.

GENOME ANNOUNCEMENT

The taxonomic classification of Salmonella enterica includes more than 2,600 serovars, which subsequently can be divided into typhoidal and nontyphoidal Salmonella (NTS) serovars (1). Typhoidal serovars (S. enterica subsp. enterica serovars Typhi, Sendai, Paratyphi A, Paratyphi B, and Paratyphi C) primarily infect humans, while NTS serovars have a broad spectrum of hosts, such as mammals (including humans), birds, and reptiles (2). Globalization has increased the availability of diverse strains of S. enterica across the world. Consequently, different serovars have crossed borders and emerging antimicrobial resistance (AMR) phenotypes have been described (3), thus presenting the need to study the genotypic diversity of S. enterica serovars. We announce here 23 draft genomes from S. enterica strains isolated from fecal samples of cattle in Nigeria, including genomes from serovars that are not currently available at GenBank, e.g., S. enterica subsp. enterica serovars Agoueve, Marseille, Sundsvall, Takoradi, Ekotedo, Tees, Plymouth, Hato, 47:z4,z23:-, Altendorf, Essen, and Glostrup.

Bacterial DNA was extracted from overnight cultures by using the DNeasy blood and tissue kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. Sequencing libraries were constructed with 0.2 ng/μl of prepared DNA using the Nextera XT DNA library prep kit (Illumina, San Diego, CA, USA).

Sequencing was performed on the MiSeq Illumina instrument with the 500-cycle MiSeq reagent V2 kit (2 × 250 bp) following the manufacturer’s guidelines. Raw data were subjected to genome assembly using SPAdes version 3.8 (4), and genome annotation was performed with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (5). Salmonella serotyping by whole-genome sequencing was predicted with the SeqSero version 1.0 software tool (6). The NCBI pathogen detection website (https://www.ncbi.nlm.nih.gov/pathogens) and annotation pipeline (5) were queried to extract information regarding AMR genes present in these genomes. In silico multilocus sequence typing (MLST) data were extracted from the Enterobase online tool (http://enterobase.warwick.ac.uk). Salmonella pathogenicity islands (SPIs) were identified using the SPIFinder version 1.0 online tool (https://cge.cbs.dtu.dk/services/SPIFinder).

The total lengths of these genomes range from 4.6 to 5.2 Mb, with an average GC content of 52%, and the numbers of contigs range from 25 to 102. The numbers of predicted genes, noncoding RNAs (ncRNAs), tRNAs, and clustered regularly interspaced short palindromic repeat (CRISPR) arrays range from 4,353 to 5,075, 10 to 18, 71 to 82, and 1 to 4, respectively, as previously described for Salmonella genomes (Table 1). In silico MLST analysis shows that each genome belongs to different sequencing types (STs), and 12 of them have not been previously reported. AMR genes were predicted in 6 out of 23 strains, including those encoding chloramphenicol, quinolone, tetracycline, and fosfomycin resistance. Up to seven SPIs were detected in these genomes, including SPI-1, SPI-2, and SPI-4, which encode a predicted type III and type I secretion system.

TABLE 1 

Sequencing metadata and MLST results for 23 Salmonella enterica strains, isolated from cattle in Nigeria

GenBank accession no.	No. of coding genes	No. of ncRNAs	No. of tRNAs	No. of CRISPR arrays	No. of contigs	Total length (bp)	GC content %	Predicted subspecies	Predicted serotype	MLST	Predicted AMR genesb
NPMJ00000000	4,485	13	77	2	48	4,616,478	52.16	enterica	Johannesburg	ST515	−
NPMI00000000	4,565	15	75	3	41	4,703,003	52.2	enterica	Stanleyville	ST2562	+
NPMH00000000	4,552	15	75	3	34	4,697,783	52.2	enterica	Stanleyville	ST2562	+
NPMG00000000	4,353	13	76		25	4,535,642	52.2	enterica	Eastbourne	ST414	−
NPMF00000000	4,538	12	74	2	54	4,743,981	52.24	enterica	Agoueve	ST3963a	−
NPME00000000	4,452	10	75	1	25	4,616,387	52.21	enterica	Give	ST3969a	−
NPMD00000000	4,761	18	79	2	43	4,915,736	52.2	enterica	Hadar	ST473	−
NPMC00000000	4,517	13	75		46	4,696,577	52.15	enterica	Marseille	ST3966a	−
NPMB00000000	4,390	11	78	2	31	4,562,440	52.2	enterica	Sundsvall	ST488	−
NPMA00000000	4,457	10	75	3	26	4,667,942	52.12	enterica	Takoradi	ST531	−
NPLZ00000000	4,443	14	75	2	42	4,637,247	52.18	enterica	Ekotedo	ST3968a	−
NPLY00000000	4,492	12	77	2	42	4,689,632	52.14	enterica	Tees	ST3955a	−
NPLX00000000	4,510	13	75	2	46	4,658,074	52.22	enterica	Bergen	ST1279	+
NPLW00000000	4,799	12	72	2	53	4,937,236	51.96	enterica	Plymouth	ST565	−
NPLV00000000	4,488	11	74	2	31	4,694,335	52.19	enterica	Hato	ST3997a	−
NPLU00000000	4,508	11	74	2	36	4,729,809	52.16	arizonae	47:z4,z23:-	ST3967a	−
NPLT00000000	5,075	11	82	4	102	5,266,492	51.79	enterica	Altendorf	ST3974a	+
NPLS00000000	4,730	14	71	1	33	4,876,578	52.09	enterica	Dublin	ST10	−
NPOH00000000	4,687	12	74	2	48	4,857,624	52.19	enterica	Essen	ST3964a	+
NPLR00000000	4,483	13	74	2	39	4,677,388	52.15	enterica	Ealing	ST2013	−
NPLQ00000000	4,570	18	77	2	33	4,739,515	52.09	enterica	Glostrup	ST3961a	−
NPLP00000000	4,442	11	73	2	30	4,637,671	52.18	enterica	Ekotedo	ST3972a	−
NPLO00000000	4,554	17	75	2	26	4,762,386	52.04	enterica	Corvallis	ST3962a	+

MLST analysis indicates these genomes belong to new STs.

−, absence of AMR genes; +, occurrence of AMR genes.

Analysis of these genomes will offer a better understanding of the genomic events responsible for AMR, disease transmission, and pathogenicity of Salmonella enterica.

Accession number(s).

The draft genome sequences reported here have been deposited in DDBJ/EMBL/GenBank under BioProject PRJNA186035. GenBank accession numbers are listed in Table 1.