Abstract
We report on nine draft genomes of Pseudomonas aeruginosa isolates, assembled using a hybrid paired-end and Nextera mate-pair library approach. Eight are of clinical origin, and one is the ATCC 27853 strain. We also report their multilocus sequence types.
GENOME ANNOUNCEMENT
Pseudomonas aeruginosa is an important pathogen, associated with infections in burn wounds, ventilated patients, patients with cystic fibrosis, and so on. It is intrinsically resistant to a number of antimicrobial agents and may acquire resistance to any of the available antimicrobics. Further, P. aeruginosa may be nosocomially transmitted. The complete genome sequences of eight clinical isolates from a single facility were obtained for epidemiological studies of relatedness (i.e., clonality). ATCC 27853 was also studied.
Isolates were cultivated on 5% sheep blood agar and genomic DNA obtained using the Maxwell 16 Tissue DNA purification kit (Promega, Madison, WI, USA) and the Genomic DNA Clean and Concentrator kit (Zymo Research, Irvine, CA, USA).
Paired-end and two Nextera mate-pair DNA libraries from each cultured isolate were prepared with target fragment lengths of 500 bp for the paired-end reads, and 4 to 6 kbp, and 8 to 10 kbp for the mate-pair reads, respectively. A total of 60,176,290 read pairs were produced on the Illumina MiSeq platform run for 600 cycles across all nine genomes. Reads were processed for adapter removal and quality filtering using Trimmomatic version 0.32 (1) with parameters “ILLUMINACLIP:adapters.fasta:2:30:10 LEADING:3 TRAILING:3 MAXINFO:220:0.1 MINLEN:70.” Reads were then error corrected using SPAdes version 3.1.0 (2) in error-correction-only mode. Read coverage was decreased to 80× by randomly choosing read pairs. Reads were then assembled in two passes. First pass assembly was performed using Velvet version 1/2/10 (3) with k-mers from 31 to 99, selecting contigs from the assembly with the longest contig. The final pass assembly was performed using SPAdes in assembly-only mode, using as input the same unassembled reads as the first pass assembly, plus the contigs from Velvet passed as “untrusted contigs” to SPAdes. For each isolate, we identified the genes used for multilocus sequence typing of P. aeruginosa, and submitted them for typing using the PubMLST (4) database (http://pubmlst.org/paeruginosa). The resulting genomes, their multilocus sequence types (MLSTs), and assembly statistics are listed in Table 1.
TABLE 1 .
List of accession numbers, sequence types, and assembly statistics for the genomes submitted under this announcement
| Isolate | Accession no. | MLST | No. of contigs (>300 bp) | G+C content (%) | Assembled length (bp) | N50 length (bp) |
|---|---|---|---|---|---|---|
| ATCC 27853 | LFMN00000000 | ST-155 | 21 | 66.08 | 6,847,745 | 2,097,247 |
| BTP031 | LFMO00000000 | ST-235 | 15 | 65.98 | 6,878,781 | 1,039,251 |
| BTP032 | LFMP00000000 | ST-235 | 32 | 66.11 | 7,547,174 | 2,492,409 |
| BTP033 | LFMQ00000000 | ST-235 | 22 | 65.95 | 6,899,762 | 1,220,050 |
| BTP034 | LFMR00000000 | ST-654 | 16 | 65.99 | 6,924,697 | 1,036,494 |
| BTP035 | LFMS00000000 | ST-235 | 19 | 65.97 | 6,873,380 | 2,067,829 |
| BTP036 | LFMT00000000 | ST-235 | 1 | 65.98 | 6,879,005 | 6,879,005 |
| BTP037 | LFMU00000000 | ST-235 | 44 | 65.99 | 6,857,129 | 5,465,220 |
| BTP038 | LFMV00000000 | ST-823 | 41 | 66.00 | 7,085,577 | 1,371,882 |
Nucleotide sequence accession numbers.
The complete genome sequences have been deposited at DDBJ/EMBL/GenBank under the accession numbers provided in Table 1.
ACKNOWLEDGMENTS
This research was supported by the Center for Individualized Medicine at Mayo Clinic, the Mayo Illinois Alliance for Technology Based Healthcare, and the Division of Clinical Microbiology, Department of Laboratory Medicine, Mayo Clinic.
This publication made use of the PubMLST website (http://pubmlst.org) developed by Keith Jolley (4) and sited at the University of Oxford. The development of that website was funded by the Wellcome Trust.
Footnotes
Citation Jeraldo P, Cunningham SA, Quest D, Sikkink RA, O’Brien D, Eckloff BW, Patel R, Chia N. 2015. Draft genome sequences of nine Pseudomonas aeruginosa strains, including eight clinical isolates. Genome Announc 3(5):e01154-15. doi:10.1128/genomeA.01154-15.
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