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. 2013 Oct 31;1(5):e00904-13. doi: 10.1128/genomeA.00904-13

Draft Genome Sequence of the Antibiotic-Producing Cystic Fibrosis Isolate Pantoea agglomerans Tx10

Derek D N Smith 1, Morgan W B Kirzinger 1, John Stavrinides 1,✉
PMCID: PMC3814576  PMID: 24179115

Abstract

Pantoea agglomerans is an enteric bacterium that is capable of causing both plant and human disease. Here, we report the genome sequence of a cystic fibrosis isolate, P. agglomerans Tx10, which produces an antibiotic that is effective against Staphylococcus aureus.

GENOME ANNOUNCEMENT

Pantoea agglomerans (formerly Enterobacter agglomerans and Erwinia herbicola) (1) is a member of the Enterobacteriaceae that has been noted to cause plant disease, as well as opportunistic infections in humans (2–4). P. agglomerans has also been shown to have unique metabolic capabilities, including antibiotic biosynthesis (4–10). Among these antibiotics are pantocins (11–14), herbicolins (15, 16), microcins (17–19), and phenazines (20), several of which target amino acid biosynthesis in the fire blight pathogen, Erwinia amylovora, and have been developed into biocontrol agents. Here, we report the complete genome sequence of the clinical isolate P. agglomerans Tx10, which was isolated from the sputum of a cystic fibrosis patient. This isolate produces multiple antibiotics that target E. amylovora and clinically relevant pathogens, including Staphylococcus aureus, Streptococcus epidermidis, and Escherichia coli.

Total DNA was sequenced using Illumina HiSeq 2000, 100-bp paired-end sequencing, resulting in 17,035,538 reads, with an average Phred quality score of 31. ABySS version 1.3.5 (21) was used for de novo paired-end assembly using the default parameters and an optimized k-mer value of 83. This resulted in 38 contigs with an N50 of 586,961 bp and an estimated genome size of 4,856,603 bp at 347× coverage. Contigs of ≥200 bp (25 total) were submitted to the NCBI Prokaryotic Genome Automatic Annotation Pipeline version 2.0, resulting in 4,627 predicted genes. Of these, there are 4,500 predicted coding genes, 32 pseudogenes, 24 rRNAs, and 71 tRNAs. Two contigs are predicted to represent plasmids of 173,724 bp and 681,148 bp.

The P. agglomerans Tx10 genome provides the means not only for identifying antibiotic biosynthetic clusters but also for evaluating the contribution of natural products to polymicrobial infections in cystic fibrosis.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at GenBank under the accession no. ASJI00000000. The version described in this paper is the first version, ASJI01000000.

ACKNOWLEDGMENTS

Genome sequencing was carried out by Genome Quebec.

This work was supported by grants from the Natural Sciences and Engineering Research Council of Canada, the Rx&D Health Research Foundation, and the Canada Foundation for Innovation. D.D.N.S. is supported by a Canadian Institutes of Health Research Master’s Award.

Footnotes

Citation Smith DDN, Kirzinger MWB, Stavrinides J. 2013. Draft genome sequence of the antibiotic-producing cystic fibrosis isolate Pantoea agglomerans Tx10. Genome Announc. 1(5):e00904-13. doi:10.1128/genomeA.00904-13.

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