ABSTRACT
We report whole-genome sequences for 10 Listeria monocytogenes sequence type 6 isolates associated with a large listeriosis outbreak in South Africa, which occurred over the period of 2017 to 2018. The possibility of listeriosis spreading beyond South Africa’s borders as a result of exported contaminated food products prompted us to make the genome sequences publicly available.
GENOME ANNOUNCEMENT
Listeria monocytogenes is a Gram-positive bacterium that causes listeriosis. Acquisition of the pathogen occurs mainly by consumption of contaminated food. Infections with L. monocytogenes can result in mild febrile gastroenteritis in healthy individuals; however, invasive diseases such as bacteremia, meningitis, pneumonia, endocarditis, and sepsis can occur in high-risk groups (1).
In South Africa, a large, multiprovince outbreak of listeriosis caused by L. monocytogenes began in 2017. As of 27 April 2018, a total of 1,019 laboratory-confirmed clinical listeriosis cases were reported to the National Institute for Communicable Diseases, South Africa (http://www.nicd.ac.za/index.php/nicd-listeriosis-situation-report-27-april-2018). Multilocus sequence typing (MLST) of 521 clinical isolates using a whole-genome sequencing approach determined that 443 of 521 (85%) isolates belonged to L. monocytogenes sequence type 6 (ST6). Isolates of the same sequence type were found in a widely consumed ready-to-eat processed meat product called “polony” and in the processing environment (production facility) of the manufacturer of this implicated meat product. Here, we provide 10 whole-genome sequences of the ST6 outbreak strain representing isolates from three different source types (human, environmental, and food).
Standard microbiological techniques were performed to confirm identification of L. monocytogenes. Genomic DNA from each isolate was extracted using the QIAamp DNA minikit (Qiagen, Germany), and paired-end libraries were prepared using the Nextera XT DNA library kit, followed by 2 × 300-bp sequencing on a MiSeq platform (Illumina, Inc., USA). The paired-end reads were quality trimmed using Sickle version 1.33 and de novo assembled using SPAdes version 3.11 (2).
For the 10 isolates, genome assemblies contained an average of 161 contig sequences longer than 200 bp and covered an average total of 3,037,729 bp. The contigs for each isolate were then submitted to GenBank, where gene annotations were implemented using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (3). The average total number of 3,207 genes predicted by PGAP includes 3,085 protein-coding genes, 36 pseudogenes, and 86 RNA genes on average. Key genomic features for the 10 isolates are summarized in Table 1.
TABLE 1.
Isolate information and key genomic features of 10 L. monocytogenes whole-genome sequences from the 2017 to 2018 outbreak in South Africa
| Isolate reference no. | Source | GenBank accession no. |
No. of contigs |
Size (bp) | No. of coding genes |
No. of RNAs |
No. of pseudogenes |
Total no. of genes |
|---|---|---|---|---|---|---|---|---|
| HM00110618 | Production facility | QEXB00000000 | 333 | 3,098,720 | 3,255 | 78 | 44 | 3,377 |
| YA00078529 | Human blood culture | QEXC00000000 | 101 | 3,081,235 | 3,112 | 83 | 43 | 3,238 |
| YA00071388 | Human blood culture | QEXD00000000 | 222 | 2,972,956 | 3,034 | 60 | 31 | 3,125 |
| YA00082404 | Food | QEXE00000000 | 116 | 3,078,799 | 3,111 | 77 | 33 | 3,221 |
| YA00079283 | Human throat swab | QEXF00000000 | 83 | 3,085,415 | 3,107 | 80 | 41 | 3,228 |
| YA00072733 | Human blood culture | QEXG00000000 | 255 | 2,974,005 | 3,052 | 57 | 28 | 3,137 |
| YA00066964 | Human blood culture | QEXH00000000 | 124 | 3,028,045 | 3,044 | 114 | 36 | 3,194 |
| YA00075880 | Human blood culture | QEXI00000000 | 166 | 3,016,857 | 3,044 | 121 | 35 | 3,200 |
| IG01149260 | Human blood culture | QEXJ00000000 | 98 | 3,023,744 | 3,048 | 95 | 36 | 3,179 |
| HM00108598 | Food | QEXK00000000 | 114 | 3,017,512 | 3,039 | 99 | 35 | 3,173 |
Accession number(s).
The draft genome sequences reported here have been deposited at NCBI/GenBank under the accession numbers QEXB00000000 to QEXK00000000 (BioProject number PRJNA451422, BioSample numbers SAMN08970424 to SAMN08970415, respectively).
ACKNOWLEDGMENTS
We thank the Listeria outbreak response team at the National Institute for Communicable Diseases, National Health Laboratory Service, South Africa, and the National Department of Health, South Africa, including all provincial, metropolitan, and district environmental health departments.
Footnotes
Citation Allam M, Tau N, Smouse SL, Mtshali PS, Mnyameni F, Khumalo ZTH, Ismail A, Govender N, Thomas J, Smith AM. 2018. Whole-genome sequences of Listeria monocytogenes sequence type 6 isolates associated with a large foodborne outbreak in South Africa, 2017 to 2018. Genome Announc 6:e00538-18. https://doi.org/10.1128/genomeA.00538-18.
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