ABSTRACT

Pseudomonas aeruginosa is a Gram-negative nosocomial pathogen that is a leading cause of morbidity and mortality in cystic fibrosis patients and immunocompromised individuals worldwide. The isolate examined in this study, PA14-UM, is a well-characterized isolate utilized in studies from the University of Maryland.

ANNOUNCEMENT

Pseudomonas aeruginosa is an opportunistic pathogen that is associated with significant global morbidity and mortality among hospitalized burn and cystic fibrosis patients, as well as immunocompromised individuals (1). P. aeruginosa PA14, originally isolated by the Ausubel laboratory (2), was acquired by the laboratory of Steven Lory and passed on to the laboratory of Vincent Lee, where it has been named PA14-UM to indicate the version of PA14 that resides at the University of Maryland (310). PA14 is a commonly used strain for studies of P. aeruginosa and represents a lineage that is distinct from another commonly used reference isolate, PAO1. Since PA14 is investigated for studies in signal transduction, motility, biofilm formation, and virulence, a comprehensive sequence of strain derivatives will allow comparison of data generated from different labs, such as those completed with PAO1 (11).
The isolate has been stored in the Lee laboratory at −80°C as a 20% glycerol stock. This genome will serve as the reference for this isolate utilized in studies from the University of Maryland, as it has been noted recently that isolates from different stocks of supposedly the same isolate often have genomic and phenotypic differences (11). This isolate was grown for DNA isolation in LB medium overnight at 37°C with agitation, and the purified genomic DNA was collected from 1 ml of culture using a commercially available kit (ArchivePure DNA cell/tissue kit; 5 Prime, Hilden, Germany). Sequencing was performed by the Microbial Genome Sequencing Center (https://www.migscenter.com/). Library prep was conducted using a modified version of the Nextera DNA kit with no size selection, and the library was sequenced on the NextSeq 550 platform (12). A total of 5,943,300 raw read pairs of 150 bp were generated. Raw sequencing reads were filtered to remove contaminating phiX reads using BBDuk of the BBTools software suite (https://sourceforge.net/projects/bbmap/). The raw reads were also filtered to remove contaminating Illumina adapter sequences and quality trimmed using Trimmomatic v0.36 (13). All software was used with default values unless otherwise noted. The resulting filtered reads were assembled using SPAdes v3.14.1 (14). The assemblies were then filtered to contain only contigs longer than 500 bp with a k-mer coverage of ≥5×. The genome sequence consists of 461 contigs with an N50 value of 26,344 bp and a sequencing coverage of 137.8×. The resulting genome size is 6,467,793 bp with a G+C content of 66.33%. The genome was annotated with PGAP v4.12 (15). Comparison of the PA14-UM isolate to the parental strain, UCBPP_PA14 (GenBank accession number CP000438.1) (16), using nucmer v4.0 (17) identified a total of 283 single nucleotide variants.
This genome sequence serves as the reference for this isolate to be utilized in future studies from the University of Maryland.

Data availability.

All data have been released, and the accession numbers are as follows. The genome assembly is at GenBank under accession number JACFYT000000000, and the raw reads have been submitted to the SRA under accession number SRR12339385.

ACKNOWLEDGMENT

This project was funded in part by federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under grant numbers U19AI110820 to D.A.R. and R01AI110740 and R01AI142400 to V.T.L.

REFERENCES

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2.
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Roelofs KG, Wang J, Sintim HO, Lee VT. 2011. Differential radial capillary action of ligand assay for high-throughput detection of protein-metabolite interactions. Proc Natl Acad Sci U S A 108:15528–15533.
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Cole SJ, Records AR, Orr MW, Linden SB, Lee VT. 2014. Catheter-associated urinary tract infection by Pseudomonas aeruginosa is mediated by exopolysaccharide-independent biofilms. Infect Immun 82:2048–2058.
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Lieberman OJ, Orr MW, Wang Y, Lee VT. 2014. High-throughput screening using the differential radial capillary action of ligand assay identifies ebselen as an inhibitor of diguanylate cyclases. ACS Chem Biol 9:183–192.
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Orr MW, Donaldson GP, Severin GB, Wang J, Sintim HO, Waters CM, Lee VT. 2015. Oligoribonuclease is the primary degradative enzyme for pGpG in Pseudomonas aeruginosa that is required for cyclic-di-GMP turnover. Proc Natl Acad Sci U S A 112:E5048–E5057.
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Zhou E, Seminara AB, Kim S-K, Hall CL, Wang Y, Lee VT. 2017. Thiol-benzo-triazolo-quinazolinone inhibits Alg44 binding to c-di-GMP and reduces alginate production by Pseudomonas aeruginosa. ACS Chem Biol 12:3076–3085.
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Orr MW, Weiss CA, Severin GB, Turdiev H, Kim S-K, Turdiev A, Liu K, Tu BP, Waters CM, Winkler WC, Lee VT. 2018. A subset of exoribonucleases serve as degradative enzymes for pGpG in c-di-GMP signaling. J Bacteriol 200:e00300-18.
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Cole SJ, Hall CL, Schniederberend M, Farrow JM, III, Goodson JR, Pesci EC, Kazmierczak BI, Lee VT. 2018. Host suppression of quorum sensing during catheter-associated urinary tract infections. Nat Commun 9:4436.
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Kim S-K, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT. 2019. A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation. Elife 8:46313.
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Chandler CE, Horspool AM, Hill PJ, Wozniak DJ, Schertzer JW, Rasko DA, Ernst RK. 2019. Genomic and phenotypic diversity among ten laboratory isolates of Pseudomonas aeruginosa PAO1. J Bacteriol 201:e00595-18.
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Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 9Number 4612 November 2020
eLocator: 10.1128/mra.00978-20
Editor: Catherine Putonti, Loyola University Chicago

History

Received: 30 August 2020
Accepted: 13 October 2020
Published online: 12 November 2020

Contributors

Authors

Vincent T. Lee
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, Maryland, USA
Reza Ghodssi
Department of Electrical and Computer Engineering, Institute for Systems Research, Fischell Department of Bioengineering, Fischell Institute for Biomedical Devices, University of Maryland, College Park, College Park, Maryland, USA
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, Maryland, USA
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, Maryland, USA
Rena D. Malik
Department of Surgery, Division of Urology, University of Maryland School of Medicine, Baltimore, Maryland, USA
Olga G. Goloubeva
Department of Epidemiology & Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
Tracy H. Hazen
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA

Editor

Catherine Putonti
Editor
Loyola University Chicago

Notes

Address correspondence to Vincent T. Lee, [email protected].

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