Abstract
Here, we report the availability of draft genomes of several Salmonella serotypes, isolated from poultry sources from Nigeria. These genomes will help to further understand the biological diversity of S. enterica and will serve as references in microbial trace-back studies to improve food safety.
GENOME ANNOUNCEMENT
Nontyphoidal salmonellosis is one of the common causes of bacterial diarrhea worldwide (1). Globally, 94 million cases of gastroenteritis and 115,000 deaths each year are estimated to be caused by nontyphoidal salmonellosis (2). While North America and Europe have constituted active salmonella surveillance programs, very limited epidemiological data are available in developing countries, particularly in sub-Saharan Africa. Therefore, we have conducted an epidemiological investigation of Salmonella enterica prevalence in poultry samples from South-West and North-Central Nigeria in 2014. Here, we report the draft genome sequences of the 37 S. enterica strains, isolated as part of this study (Table 1).
TABLE 1 .
Characteristics of 37 Salmonella enterica strains, isolated from poultry sources in Nigeria
| Strain name | Accession no. | Serotype | Genome size (bp) | G+C content (%) | No. of proteins |
|---|---|---|---|---|---|
| NGUA01 | BCNZ00000000 | Kentucky | 4,881,836 | 52.2 | 4,524 |
| NGUA02 | BCOA00000000 | Kentucky | 4,876,582 | 52.2 | 4,534 |
| NGUA03 | BCOB00000000 | Herston | 4,887,324 | 52.1 | 4,567 |
| NGUA04 | BCOC00000000 | Herston | 4,853,780 | 52.2 | 4,508 |
| NGUA05 | BCOD00000000 | 13:d:e,n,z15 | 4,707,314 | 52.2 | 4,350 |
| NGUA06 | BCOE00000000 | Zega | 4,680,950 | 52.2 | 4,294 |
| NGUA07 | BCOF00000000 | Kentucky | 4,950,201 | 52.1 | 4,571 |
| NGUA08 | BCOG00000000 | Zega | 4,723,274 | 52.2 | 4,325 |
| NGUA09 | BCOH00000000 | Herston | 4,828,175 | 52.2 | 4,495 |
| NGUA10 | BCOI00000000 | Herston | 5,059,871 | 52 | 4,692 |
| NGUA12 | BCOK00000000 | Zega | 4,689,083 | 52.2 | 4,290 |
| NGUA13 | BCOL00000000 | Colindale | 4,872,659 | 52.1 | 4,541 |
| NGUA14 | BCOM00000000 | Nima | 4,536,192 | 52.3 | 4,198 |
| NGUA16 | BCOO00000000 | Kentucky | 4,970,350 | 52.1 | 4,635 |
| NGUA17 | BCOP00000000 | Zega | 4,687,717 | 52.2 | 4,300 |
| NGUA18 | BCOQ00000000 | Kentucky | 5,259,276 | 52 | 4,879 |
| NGUA19 | BCOR00000000 | Zega | 4,721,675 | 52.2 | 4,350 |
| NGUA20 | BCOS00000000 | Kentucky | 4,871,939 | 52.2 | 4,512 |
| NGUA21 | BCOT00000000 | Kentucky | 4,947,233 | 52.1 | 4,617 |
| NGUA22 | BCOU00000000 | Herston | 4,801,625 | 52.1 | 4,485 |
| NGUA23 | BCOV00000000 | Kentucky | 4,975,494 | 52.2 | 4,642 |
| NGUA24 | BCOW00000000 | Herston | 4,847,498 | 52.1 | 4,536 |
| NGUA25 | BCOX00000000 | Zega | 4,702,417 | 52.2 | 4,310 |
| NGUA26 | BCOY00000000 | Lingwala | 4,783,830 | 52.1 | 4,374 |
| NGUA27 | BCOZ00000000 | Zega | 4,875,130 | 52.2 | 4,488 |
| NGUA28 | BCPA00000000 | Kentucky | 4,885,381 | 52.2 | 4,538 |
| NGUA29 | BCPB00000000 | Zega | 4,699,130 | 52.2 | 4,321 |
| NGUA30 | BCPC00000000 | Kentucky | 4,867,532 | 52.2 | 4,528 |
| NGUA31 | BCPD00000000 | Zega | 4,731,115 | 52.2 | 4,355 |
| NGUA32 | BCPE00000000 | Kentucky | 4,827,432 | 52.2 | 4,472 |
| NGUA33 | BCPF00000000 | 13:d:e,n,z15 | 4,708,185 | 52.2 | 4,356 |
| NGUA34 | BCPG00000000 | Zega | 4,682,708 | 52.2 | 4,288 |
| NGUA35 | BCPH00000000 | Herston | 4,879,810 | 52.1 | 4,557 |
| NGUA36 | BCPI00000000 | Nima | 4,523,766 | 52.3 | 4,183 |
| NGUA37 | BCPJ00000000 | Kentucky | 4,873,902 | 52.2 | 4,524 |
| NGUA38 | BCPK00000000 | Livingstone | 4,860,227 | 51.9 | 4,462 |
| NGUA39 | BCPL00000000 | Kentucky | 4,878,399 | 52.2 | 4,505 |
S. enterica strains were isolated by enrichment culture in tetrathionate broth followed by growth on XLT4 agar. The identities of the strains were further confirmed by Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF). Genomic DNA from each strain was isolated from 1.0 ml of grown cultures using the E.Z.N.A. bacterial DNA kit (Omega Bio-tek, Norcross, GA). Following the manufacturer’s protocol, sequencing libraries were prepared using 1.0 ng of genomic DNA using the Nextera XT kit (Illumina, San Diego, CA). Genomes were sequenced on an Illumina MiSeq platform using V2 paired-end chemistry (2 × 250-bp). De novo genome assembly was performed using SPAdes version 3.5.0 (3). Genome annotation was performed using Prokka version 1.11 (4). Genome size and G+C content were estimated with all contigs of each strain. Among the 37 strains, median values for genome size and G+C content were 4.87 (Mb) and 52.2 (%), respectively (Table 1), and were similar to those of the S. enterica complete genomes. The serotypes of the isolates were determined using SeqSero (5).
As shown in Table 1, we obtained a diverse collection of S. enterica isolates from poultry sources in Nigeria. S. enterica serotype Enteritidis, the most common serotype associated with poultry worldwide, was not found in our study. The most common serotype among our isolates was S. Kentucky, followed by S. Zega and S. Herston. Other serotypes found were S. Nima, S. Livingston, and S. Colindale. The genomes of several Salmonella serotypes that we report here are the first reports, or are relatively rare. For example, only one genome of an S. Livingston isolate, from a lake in Canada, has been reported (6). To our knowledge, the genomes described in Table 1 belonging to S. Zega, S. Herston, S. Nima, and S. Colindale are the first genomes being reported for these serotypes. S. Nima has been reported to have caused an international outbreak through contaminated chocolate (7). S. Zega was previously isolated from Zaire (8). S. Colindale is one of the common Salmonella serotypes isolated from fresh lettuce in Burkina Faso (9). S. Herston has been isolated from diarrheal cases in children from Niger. The genomes we report here will help to understand more fully the biological diversity of S. enterica and will serve as references in microbial trace-back studies to improve food safety.
Nucleotide sequence accession numbers.
The sequences have been deposited in DDBJ/EMBL/GenBank under the accession numbers listed in Table 1.
ACKNOWLEDGMENTS
This work was supported in part by the USDA National Institute of Food and Agriculture, Hatch projects SD00H532-14 and SD00R540-15 awarded to J.S. and by research funding from Yamagata Prefecture and Tsuruoka City awarded to H.S. and M.T. We also acknowledge the use of the High Performance Computing (HPC) cluster managed by the University Networking and Research (UNRC) group at South Dakota State University. The funding agencies had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Footnotes
Citation Useh NM, Ngbede EO, Akange N, Thomas M, Foley A, Keena MC, Nelson E, Christopher-Hennings J, Tomita M, Suzuki H, Scaria J. 2016. Draft genome sequences of 37 Salmonella enterica strains isolated from poultry sources in Nigeria. Genome Announc 4(3):e00315-16. doi:10.1128/genomeA.00315-16.
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