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ABSTRACT

Here, we describe the Salmonella enterica serovar Heidelberg phage Matapan. A myophage with a 157,408-kb genome, Matapan is most closely related to Vi01-like phages.

ANNOUNCEMENT

Salmonella enterica serovar Heidelberg is a member of Enterobacteriaceae and a zoonotic pathogen (1). Strains in this serovar cause human salmonellosis, are multidrug resistant, and are detectable in poultry and other meat processing plants across the United States (1, 2). Salmonellosis is spread through infected animal products, feces, contaminated water, and human-to-human contact. Using bacteriophage therapy to reduce S. Heidelberg transmission among animals during transport and during processing is desired to lower the number of human infections (3). Here, we present the genome sequence of Matapan, a myophage that infects S. Heidelberg.
Matapan was collected from filtered (0.2-μm pore size) municipal wastewater in College Station, TX, via enrichment on S. Heidelberg. Host bacteria were cultured on tryptic soy broth or agar (Difco) at 37°C with aeration, and phage isolation and propagation were done using the soft agar overlay method (4). Phage morphology was determined by negatively staining samples with 2% (wt/vol) uranyl acetate and imaging by transmission electron microscopy at the Texas A&M Microscopy and Imaging Center (5). The genomic DNA for Matapan was purified using the Promega Wizard DNA clean-up system, according to the modification in the shotgun library preparation protocol given by Summer (6). Libraries were prepared with an Illumina TruSeq Nano low-throughput kit, according to the manufacturer's recommendations. Sequencing was performed on an Illumina MiSeq instrument with v2 500-cycle chemistry in a paired-end, 250-bp run, yielding 1,167,981 total reads. Sequence reads were quality controlled with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed with the FASTX-Toolkit 0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/). The genome was assembled to 26.9-fold coverage with SPAdes v3.5.0, with default parameters, and closed by PCR (forward primer, 5′-GCCACAGAGAACCCATGAA-3′; reverse primer, 5′-ATAAACCTGAATGTCCAGACCA-3′) and Sanger sequencing (7). The analysis and annotation tools are hosted on the Center for Phage Technology Galaxy and Web Apollo instances (https://cpt.tamu.edu/galaxy-pub/) (8, 9). Genes were predicted using Glimmer v3.0 and MetaGeneAnnotator v1.0 and ARAGORN v2.36 for tRNAs (1012). The presence of Rho-independent terminators was predicted with TransTermHP v2.09 (13). Predicted protein functions were assigned using InterProScan v5.22-61 and BLAST v2.2.31 versus NCBI nonredundant (nr), UniProtKB Swiss-Prot, and TrEMBL databases, with a 0.001 maximum expectation cutoff (1416). Whole-genome sequence identities were calculated with progressiveMauve v2.4.0 (17).
Matapan is a Vi01-like myophage with a 157,408-kb genome with a G+C content of 44.9%, a 93.0% coding density, 214 protein-coding genes, and 3 tRNAs. As determined by progressiveMauve, Matapan shares nucleotide similarities of 91.3%, 89.5%, 88.2%, and 87.9% with Salmonella phage Vi01 (GenBank accession number FQ312032), Escherichia phage ECML-4 (GenBank accession number JX128257), Salmonella phage STML-13-1 (GenBank accession number JX181828), and Salmonella phage Marshall (GenBank accession number KF669653), respectively, and 196 similar proteins with phage Vi01. Similar to other Vi01-like phages, Matapan is predicted to use headful or pac-type packaging using PhageTerm (18). About one-third of the predicted proteins were assigned putative functions. Similarities to phage T4 in the structural region led to reopening the genome according to convention, in front of the rIIA-like gene.

Data availability.

The genome sequence and associated data for phage Matapan were deposited under GenBank accession number MN066127, BioProject accession number PRJNA222858, SRA accession number SRR8869240, and BioSample accession number SAMN11360418.

ACKNOWLEDGMENTS

This work was supported by funding from the National Science Foundation (awards EF-0949351 and DBI-1565146) and from the National Cattlemen’s Beef Association and Texas Beef Cattle to J.J.G. Additional support came from the Center for Phage Technology (CPT), an Initial University Multidisciplinary Research Initiative supported by Texas A&M University and Texas AgriLife, and from the Department of Biochemistry and Biophysics at Texas A&M University.
We are grateful for the advice and support of the CPT staff.
This announcement was prepared in partial fulfillment of the requirements for BICH464 Bacteriophage Genomics, an undergraduate course at Texas A&M University.

REFERENCES

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Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 8Number 3819 September 2019
eLocator: e01017-19
Editor: John J. Dennehy, Queens College
PubMed: 31537677

History

Received: 23 August 2019
Accepted: 29 August 2019
Published online: 19 September 2019

Contributors

Authors

Jasmine Juliette
Center for Phage Technology, Texas A&M University, College Station, Texas, USA
Yicheng Xie
Center for Phage Technology, Texas A&M University, College Station, Texas, USA
Heather Newkirk
Center for Phage Technology, Texas A&M University, College Station, Texas, USA
Mei Liu
Center for Phage Technology, Texas A&M University, College Station, Texas, USA
Center for Phage Technology, Texas A&M University, College Station, Texas, USA
Center for Phage Technology, Texas A&M University, College Station, Texas, USA

Editor

John J. Dennehy
Editor
Queens College

Notes

Address correspondence to Jolene Ramsey, [email protected].

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