Here we report the whole-genome sequences of 15 clinical Streptococcus suis strains isolated from pigs in Switzerland. Although they originated from the same host and geographic origin, the strains showed a large amount of diversity.
ABSTRACT
Here we report the whole-genome sequences of 15 clinical Streptococcus suis strains isolated from pigs in Switzerland. Although they originated from the same host and geographic origin, the strains showed a large amount of diversity.
ANNOUNCEMENT
Streptococcus suis is a Gram-positive, facultative, anaerobic bacterium that is mainly found in the nasal mucosa and the tonsils of healthy pigs. Under predisposing circumstances, like inadequate sanitation or reduced immunity, S. suis can cause various diseases such as meningitis, septicemia, arthritis, pneumonia, and endocarditis (1). Besides being an important pig pathogen causing major economic losses, S. suis is considered a relevant zoonotic agent, especially in China and Southeast Asia (1–3). Currently, there are 29 described S. suis serotypes. Worldwide, serotype 2 is the most common reported serotype to cause infections in pigs, followed by serotypes 9 and 3 (1). In humans, the most frequently identified serotypes are serotype 2, followed by serotype 14 (1).
We have sequenced 15 clinical S. suis strains (Table 1). The strains were originally isolated between 2006 and 2018 by streaking pig samples onto Columbia agar with sheep blood (Thermo Fisher Diagnostics AG, Pratteln, Switzerland). The plates were incubated at 37°C for 48 hours under aerobic conditions. Strains were identified by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) (Biotyper Compass Explorer software v.4.1.60, Bruker Daltonics, Bremen, Germany) and serotyped by multiplex PCR according to Kerdsin et al. (4).
TABLE 1.
Overview of strains
| Strain | Serotype | Yr | Source | GenBank accession no. | SRA accession no. | No. of contigs | Genome size (bp) | N50 | GC content (%) |
|---|---|---|---|---|---|---|---|---|---|
| PP203 | 9 | 2015 | Blood from heart | RSDR00000000 | SRR8290481 | 27 | 2,127,065 | 6 | 41.4 |
| PP269 | 1 or 14 | 2015 | Blood from heart | RSDQ00000000 | SRR8290480 | 63 | 1,968,146 | 12 | 41.3 |
| PP386 | 6 | 2016 | Blood from heart | RSDP00000000 | SRR8290479 | 53 | 1,878,848 | 12 | 41.5 |
| PP422 | 9 | 2016 | Lung | RSDO00000000 | SRR8290478 | 48 | 2,075,657 | 8 | 43.7 |
| PP423 | 2 or 1/2 | 2016 | Blood from heart | RSDN00000000 | SRR8290477 | 51 | 2,068,343 | 8 | 41.2 |
| PP425 | 6 | 2016 | Brain | RSDM00000000 | SRR8290476 | 54 | 1,881,239 | 11 | 41.5 |
| PP463 | 2 or 1/2 | 2016 | Blood from heart | RSDL00000000 | SRR8290475 | 52 | 2,135,450 | 9 | 41.1 |
| PP464 | NDa | 2016 | Lung | RSDK00000000 | SRR8290474 | 94 | 2,340,449 | 15 | 41.5 |
| PP536 | 9 | 2016 | Heart | RSDJ00000000 | SRR8290473 | 24 | 2,122,156 | 4 | 41.4 |
| PP730 | 1 or 14 | 2018 | Joint | RSDI00000000 | SRR8290472 | 58 | 1,912,461 | 11 | 41.4 |
| PP735 | 1 or 14 | 2018 | Joint | RSDH00000000 | SRR8290484 | 59 | 1,912,627 | 11 | 41.4 |
| SS1014 | ND | 2010 | Kidney | RSDG00000000 | SRR8290483 | 208 | 2,504,491 | 37 | 41.2 |
| SS29 | 6 | 2006 | No information | RSDF00000000 | SRR8290486 | 49 | 1,894,451 | 11 | 41.5 |
| SS470 | 2 or 1/2 | 2007 | Heart | RSDE00000000 | SRR8290485 | 49 | 2,079,888 | 8 | 41.1 |
| SS8 | 6 | 2006 | No information | RSDD00000000 | SRR8290482 | 48 | 1,893,520 | 11 | 41.5 |
ND, not determined.
Genomic DNA was extracted using a DNA blood and tissue kit (Qiagen, Hombrechtikon, Switzerland) and prepared for sequencing with a Nextera DNA Flex sample preparation kit (Illumina, San Diego, CA, USA) on an Illumina MiniSeq sequencer with 150-bp paired-end reads.
The sequencing resulted in an output of paired-end read sets containing 596,559 to 1,666,705 reads of 150 bp. The quality of the reads was checked using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads passed all quality steps with the exception of the control step “per-base sequence content.” Failure to pass this step, however, is typical for transposon-based libraries (FastQC manual [see https://www.bioinformatics.babraham.ac.uk/projects/fastqc/]) and was ignored. Reads were assembled de novo using Spades 3.12 (5) with activation of the “–careful” option. Raw assemblies were filtered for size larger than 1,000 bp and coverage of more than 25-fold.
The final assemblies resulted in 13 genomes with a size between 1,878,848 and 2,135,450 bp and coverages between 50- and 120-fold (Table 1). The genomes consisted of 24 to 64 contigs per strain, and the largest contigs were 129 to 333 kbp. Strains SS1014 and PP464 had large genomes of 2,340,449 and 2,504,491 bp, with coverages of 50- and 39-fold, respectively. The SS1014 and PP464 genomes consisted of 204 and 94 contigs, the largest of which were 76 kb and 174 kb, respectively.
The average nucleotide identity (ANI) of the strains was calculated according to Richter et al. (6) using PyANI (https://github.com/widdowquinn/pyani). The ANI of strain PP422 was only 88 to 89% compared to the other strains in this study, thus showing a high genomic diversity which was already observed previously in this species (7). The other strains had an ANI of at least 94.6%, which is below the ANI cutoff for species differentiation of 95 to 96% (6), confirming again the diversity of the species S. suis.
Our results highlight the massive diversity within the pathogenic species S. suis, even between strains from the same host and region. Since the breeding of pigs is quite consolidated in Switzerland, this opens up possibilities for strain tracing in case of human disease outbreaks.
Data availability.
All these sequences have been published in GenBank under SRA accession no. SRR8290481 (PP203), SRR8290480 (PP269), SRR8290479 (PP386), SRR8290478 (PP422), SRR8290477 (PP423), SRR8290476 (PP425), SRR8290475 (PP463), SRR8290474 (PP464), SRR8290473 (PP536), SRR8290472 (PP730), SRR8290484 (PP735), SRR8290483 (SS1014), SRR8290486 (SS29), SRR8290485 (SS470), and SRR8290482 (SS8). All these sequences have also been published in GenBank under the genome accession no. RSDR00000000 (PP203), RSDQ00000000 (PP269), RSDP00000000 (PP386), RSDO00000000 (PP422), RSDN00000000 (PP423), RSDM00000000 (PP425), RSDL00000000 (PP463), RSDK00000000 (PP464), RSDJ00000000 (PP536), RSDI00000000 (PP730), RSDH00000000 (PP735), RSDG00000000 (SS1014), RSDF00000000 (SS29), RSDE00000000 (SS470), and RSDD00000000 (SS8).
ACKNOWLEDGMENT
This work was supported by funding from the University of Zurich.
REFERENCES
- 1.Dutkiewicz J, Sroka J, Zając V, Wasiński B, Cisak E, Sawczyn A, Kloc A, Wójcik-Fatla A. 2017. Streptococcus suis: a re-emerging pathogen associated with occupational exposure to pigs or pork products. Part I—epidemiology. Ann Agric Environ Med 24:683–695. doi: 10.26444/aaem/79813. [DOI] [PubMed] [Google Scholar]
- 2.Dutkiewicz J, Zając V, Sroka J, Wasiński B, Cisak E, Sawczyn A, Kloc A, Wójcik-Fatla A. 2018. Streptococcus suis: a re-emerging pathogen associated with occupational exposure to pigs or pork products. Part II—pathogenesis. Ann Agric Environ Med 25:186–203. doi: 10.26444/aaem/85651. [DOI] [PubMed] [Google Scholar]
- 3.Xia X, Wang X, Wei X, Jiang J, Hu J. 2018. Methods for the detection and characterization of Streptococcus suis: from conventional bacterial culture methods to immunosensors. Antonie Van Leeuwenhoek 111:2233–2247. doi: 10.1007/s10482-018-1116-7. [DOI] [PubMed] [Google Scholar]
- 4.Kerdsin A, Akeda Y, Hatrongjit R, Detchawna U, Sekizaki T, Hamada S, Gottschalk M, Oishi K. 2014. Streptococcus suis serotyping by a new multiplex PCR. J Med Microbiol 63:824–830. doi: 10.1099/jmm.0.069757-0. [DOI] [PubMed] [Google Scholar]
- 5.Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov AS, Lesin V, Nikolenko S, Pham S, Prjibelski A, Pyshkin A, Sirotkin A, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi: 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Richter M, Rosselló-Móra R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106:19126–19131. doi: 10.1073/pnas.0906412106. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Baig A, Weinert LA, Peters SE, Howell KJ, Chaudhuri RR, Wang J, Holden MT, Parkhill J, Langford PR, Rycroft AN, Wren BW, Tucker AW, Maskell DJ. 2015. Whole genome investigation of a divergent clade of the pathogen Streptococcus suis. Front Microbiol 6:1191. doi: 10.3389/fmicb.2015.01191. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
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Data Availability Statement
All these sequences have been published in GenBank under SRA accession no. SRR8290481 (PP203), SRR8290480 (PP269), SRR8290479 (PP386), SRR8290478 (PP422), SRR8290477 (PP423), SRR8290476 (PP425), SRR8290475 (PP463), SRR8290474 (PP464), SRR8290473 (PP536), SRR8290472 (PP730), SRR8290484 (PP735), SRR8290483 (SS1014), SRR8290486 (SS29), SRR8290485 (SS470), and SRR8290482 (SS8). All these sequences have also been published in GenBank under the genome accession no. RSDR00000000 (PP203), RSDQ00000000 (PP269), RSDP00000000 (PP386), RSDO00000000 (PP422), RSDN00000000 (PP423), RSDM00000000 (PP425), RSDL00000000 (PP463), RSDK00000000 (PP464), RSDJ00000000 (PP536), RSDI00000000 (PP730), RSDH00000000 (PP735), RSDG00000000 (SS1014), RSDF00000000 (SS29), RSDE00000000 (SS470), and RSDD00000000 (SS8).