Complete Genome Sequences of a Clinical Isolate and an
Environmental Isolate of Vibrio parahaemolyticus
Catharina H. M. Lüdeke,
Bart C. Weimer,
Jessica L. Jones
Gulf Coast Seafood Laboratory, Division of Seafood Science and Technology, Food and Drug Administration, Dauphin Island, Alabama, USA
; Hamburg School of Food
Science, University of Hamburg, Hamburg, Germany
; School of Veterinary Medicine
and 100K Pathogen Genome Project,
University of California, Davis, California, USA
Vibrio parahaemolyticus is the leading cause of seafood-borne infections in the United States. We report complete genome se-
quences for two V. parahaemolyticus strains isolated in 2007, CDC_K4557 and FDA_R31 of clinical and oyster origin, respec-
tively. These two sequences might assist in the investigation of differential virulence of this organism.
Received 13 February 2015 Accepted 18 February 2015 Published 26 March 2015
Citation Lüdeke CHM, Kong N, Weimer BC, Fischer M, Jones JL. 2015. Complete genome sequences of a clinical isolate and an environmental isolate of Vibrio
parahaemolyticus. Genome Announc 3(2):e00216-15. doi:10.1128/genomeA.00216-15.
Copyright © 2015 Lüdeke et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to Jessica L. Jones, firstname.lastname@example.org.
Vibrio parahaemolyticus is a halophilic Gram-negative bacte-
rium naturally occurring in estuarine environments (1).
Through consumption of raw or undercooked seafood, or contact
with contaminated seawater, V. parahaemolyticus can cause infec-
tions in humans; gastroenteritis is typical, but rarely, wound
and/or sepsis infections occur. V. parahaemolyticus is the leading
cause of seafood-borne gastroenteritis in the United States (2),
and there has been an increase in reported illnesses in the last two
V. parahaemolyticus can carry the thermostable direct hemoly-
sin (tdh) and tdh-related hemolysin (trh) genes, which are gener-
ally associated with pathogenicity and are used in outbreak inves-
tigations and assessing risk (4,5). Clinical isolates more frequently
carry the tdh and/or trh genes than environmental isolates (6).
However, in recent studies, clinical isolates lacking both of these
genes have been identiﬁed (7). Tissue culture studies have re-
vealed that the presence of tdh had no effect on cytotoxicity (8,9).
Hence, additional virulence factors likely exist for V. parahaemo-
We sequenced two V. parahaemolyticus isolates, CDC_K4557
and FDA_R31, to better understand the pathogenic potential of
these isolates and eventually improve risk assessment.
CDC_K4557 was isolated from the stool of a patient in Louisiana
in 2007 and submitted to the Centers for Disease Control and
Prevention (CDC). FDA_R31 was isolated by the Food and Drug
Administration (FDA) from an oyster sample harvested in Loui-
siana in 2007. As the clinical isolate is tdh
and the oyster
isolate is tdh
by PCR, these strains are ideal for identifying
new and/or additional virulence markers.
The genomes were sequenced within the University of Califor-
nia at Davis 100K Pathogen Genome Project using the PacBio RSII
sequencing platform (Paciﬁc Biomarkers, Menlo Park, CA, USA).
High-molecular-weight gDNA was extracted from overnight cul-
tures grown on Trypticase soy agar, lysed with an enzyme cocktail,
puriﬁed with the QIAamp DNA minikit (Qiagen, Valencia, CA,
USA), and analyzed on a 2200 TapeStation system with the
Genomic DNA ScreenTape (Agilent Technologies, Santa Clara,
CA, USA) assay for integrity of high molecular weight gDNA (10).
After evaluation of gDNA size and quantity, 10
g was used for
fragmentation using the Covaris g-TUBE device (Covaris,
Woburn, MA, USA) following the manufacturer’s instructions
(11). The fragmented gDNA was used for library construction
with the PacBio SMRTbell 10kb Library preparation kit, which
was normalized to 1 to 5
g input. Libraries were sequenced
utilizing PacBio RSII and C2 chemistry with 100⫻coverage per
the manufacturer’s instructions. For each isolate, the genomic
sequence single-pass reads were de novo assembled using the
Hierarchical Genome Assembly Process (HGAP) version 1.4
software (Paciﬁc Biosciences) and were then annotated using
the NCBI Prokaryotic Genomes Automatic Annotation Pipe-
(12). Through the annotation process, 4,771 and 4,937 genes for
the clinical and oyster isolates, respectively, as well as 4,579 and
4,731 coding regions were identiﬁed. The presence or absence of
the tdh and trh genes was conﬁrmed in both isolates.
Nucleotide sequence accession numbers. The closed genome
sequences of the two V. parahaemolyticus isolates are available
in GenBank under the accession numbers CP006004 and
CP006005 for chromosomes I and II of FDA_R31, respectively,
and CP006008 and CP006007 for CDC_K4557. The versions de-
scribed in this paper are the ﬁrst versions.
This project was supported by an appointment to the Research Fellowship
Program for the Center for Food Safety and Applied Nutrition adminis-
tered by the Oak Ridge Associated Universities through a contract with
the FDA. The 100K Pathogen Genome Project was supported by the FDA
and Agilent Technologies to produce these sequences.
We thank Whitney Ng and Kao Thao for their effort in the isolate
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