Aeromonas bacteria are able to cause disease in a wide range of animals from humans to fish. In this article, we report the draft whole-genome sequences of 10 Aeromonas strains from clinical and environmental sources. These genome sequences will provide a repository of information for further investigations into the pathogenicity of this enigmatic pathogen.
ABSTRACT
Aeromonas bacteria are able to cause disease in a wide range of animals from humans to fish. In this article, we report the draft whole-genome sequences of 10 Aeromonas strains from clinical and environmental sources. These genome sequences will provide a repository of information for further investigations into the pathogenicity of this enigmatic pathogen.
ANNOUNCEMENT
Aeromonas species are aquatic bacteria found in brackish water and freshwater and are able to cause disease in both cold-blooded and warm-blooded animals (1). In humans, they can give rise to numerous clinical manifestations but are mostly associated with gastrointestinal disease and wound infections (2). A plethora of factors have been linked with aeromonad pathogenicity, including toxigenic factors, such as aerolysin and type III secretion systems (T3SS), and adhesins, such as type IV pili and both polar and lateral flagella (3–5). However, aeromonad pathogenicity is thought to be multifactorial and not reliant upon one virulence determinant. Aeromonas caviae strains Sch3 and Sch29 were isolated from children presenting with gastroenteritis at Sheffield Children's Hospital, and Aeromonas veronii biovar sobria BC88 was isolated from a child with dysentery in Western Australia (6); all the other aeromonads were environmental strains isolated from the River Don at various locations within South Yorkshire, United Kingdom. A. caviae Sch3 has been extensively studied due to its production of lateral flagella (4) and its ability to glycosylate its polar flagella (7, 8). A. veronii biovar sobria BC88 is a model for aeromonad adhesion, as it produces a type IV bundle-forming pilus (5). The analysis of the genomes presented here will allow a deeper understanding of the biology of aeromonads in relation to both their physiology and pathogenicity.
All environmental strains were isolated from river water by inoculation onto cystine lactose electrolyte-deficient (CLED) agar plus Andrade’s indicator (Oxoid) and Brilliance UTI clarity agar (Oxoid), as these were nonselective and provided a differential presumptive identification of organisms. Human clinical strains were isolated by the inoculation of feces onto Aeromonas isolation agar (Fluka) containing ampicillin. All strains were identified to the species level by multisequence alignment against the sequences of known aeromonad species. All strains were grown in tryptic soy broth (TSB), and genomic DNA was extracted using a QIAamp DNA minikit (Qiagen). For each of the 10 Aeromonas strains, genomic DNA libraries were prepared using the Nextera XT library kit (Illumina, San Diego, CA). The genomes were nucleotide sequenced using an Illumina HiSeq 2500 platform at MicrobesNG (University of Birmingham, UK). Sequencing used 2 × 250-bp paired-end reads that gave from 41 to 150× depth (Table 1). Trimmomatic v0.38 (9) was used to trim the reads with a sliding window quality cutoff of Q15, and read quality analyses were performed with FastQC software v0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The genomes were assembled and annotated using SPAdes v3.7 (10) and Prokka v1.12, respectively, using the standard default settings (11). Genome assembly metrics were calculated with QUAST, and the number of annotated coding sequences (CDS) for each aeromonad genome is shown in Table 1.
TABLE 1.
Genome accession numbers and characteristics of 10 Aeromonas strains taken from either a clinical or environmental source
| Strain | Species (source) | Mean coverage (×) | No. of reads | No. of contigs | Largest contig (bp) | Total length (bp) | GC content (%) | N50 (bp) | N75 (bp) | L50 (contigs) | L75 (contigs) | No. of CDS | ENA accession and assembly no. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sch29 | A. caviae (human clinical diarrhea) | 49.94 | 874,346 | 195 | 182,866 | 4,425,373 | 61.34 | 86,948 | 50,669 | 21 | 37 | 3,953 | ERS3090042, GCA_901202955 |
| Sch3N | A. caviae (human clinical diarrhea) | 84.83 | 1,155,915 | 192 | 240,555 | 4,737,922 | 61.39 | 90,385 | 43,401 | 18 | 37 | 4,313 | ERS3090043, GCA_901212305 |
| BC88 | A. veronii (human clinical dysentery) | 111.91 | 1,381,586 | 155 | 1,023,078 | 4,604,788 | 58.54 | 215,763 | 118,836 | 6 | 13 | 4,065 | ERS3090044, GCA_901212295 |
| KLG1 | A. hydrophila (environmental water) | 53.88 | 730,744 | 154 | 260,972 | 4,908,673 | 61.22 | 103,738 | 64,788 | 15 | 30 | 4,373 | ERS3090045, GCA_901212375 |
| KLG2 | A. allosaccharophila (environmental water) | 150.39 | 1,670,538 | 85 | 626,394 | 4,513,594 | 58.87 | 292,420 | 141,273 | 5 | 11 | 4,059 | ERS3090046, GCA_901212385 |
| KLG5 | A. veronii (environmental water) | 70.63 | 974,322 | 103 | 818,983 | 4,740,061 | 58.51 | 280,270 | 130,857 | 6 | 12 | 4,269 | ERS3090047, GCA_901212355 |
| KLG6 | A. media (environmental water) | 104.31 | 1,255,304 | 454 | 159,134 | 4,542,840 | 61.20 | 36,002 | 19,277 | 40 | 80 | 4,070 | ERS3090048, GCA_901212365 |
| KLG7 | A. veronii (environmental water) | 53.29 | 687,242 | 104 | 345,454 | 4,552,893 | 58.80 | 139,212 | 84,196 | 11 | 21 | 4,069 | ERS3090049, GCA_901212345 |
| KLG8 | A. veronii (environmental water) | 54.65 | 738,573 | 76 | 568,763 | 4,590,381 | 58.62 | 198,583 | 115,053 | 7 | 15 | 4,137 | ERS3090050, GCA_901212395 |
| KLG9 | A. veronii (environmental water) | 40.98 | 578,468 | 74 | 399,442 | 4,605,689 | 58.71 | 180,084 | 120,803 | 9 | 17 | 4,160 | ERS3090051, GCA_901212405 |
The sequences will provide a great resource for further investigations into the physiology and pathogenicity of the Aeromonas genus.
Data availability.
The reads used for assembly of the 10 annotated aeromonad genomes were deposited in the European Nucleotide Archive (ENA) at the European Molecular Biology Laboratory (EMBL) under the accession number PRJEB31025. The specific accession numbers for each sample are supplied in Table 1. The versions described in this paper are the first versions.
ACKNOWLEDGMENT
MicrobesNG provided genome sequencing, which was supported by the BBSRC (grant number BB/L024209/1).
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Associated Data
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Data Availability Statement
The reads used for assembly of the 10 annotated aeromonad genomes were deposited in the European Nucleotide Archive (ENA) at the European Molecular Biology Laboratory (EMBL) under the accession number PRJEB31025. The specific accession numbers for each sample are supplied in Table 1. The versions described in this paper are the first versions.