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Shigella Draft Genome Sequences: Resources for Food Safety and Public Health

Authors:
Allison M Weis at University of Utah
Allison M Weis
Brent Gilpin at Institute of Environmental Science and Research
Brent Gilpin
Carol Huang at University of California, Davis
Carol Huang
Nguyet Kong at University of California, Davis
Nguyet Kong
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Abstract

Shigella is a major foodborne pathogen that infects humans and non-human primates and is the major cause of dysentery and reactive arthritis worldwide. This is the initial public release of 16 Shigella genome sequences from four species sequenced as part of the 100K Pathogen Genome Project.
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Shigella Draft Genome Sequences:
Resources for Food Safety and Public
Health
Allison M. Weis,
a
Brent Gilpin,
b
Bihua C. Huang,
a
Nguyet Kong,
a
Poyin Chen,
a
Bart C. Weimer
a
School of Veterinary Medicine, 100K Pathogen Genome Project, UC Davis, Davis, California, USA
a
; Institute of
Environmental Science & Research Ltd., Christchurch, New Zealand
b
ABSTRACT Shigella is a major foodborne pathogen that infects humans and non-
human primates and is the major cause of dysentery and reactive arthritis world-
wide. This is the initial public release of 16 Shigella genome sequences from four
species sequenced as part of the 100K Pathogen Genome Project.
Shigella spp. are Gram-negative enteric pathogens that infect humans and nonhu-
man primates. They are an important cause of dysentery, affecting more than 80
million people and causing more than 700,000 deaths each year worldwide (1, 2). The
burden of disease is carried by children, where 99% of infections occur in children in
developing nations, and most cases (70%) and deaths (60%) occur in children age 5 and
under (1, 2). Rare cases of shigellosis can lead to reactive arthritis (3). Shigella is spread
by direct contact with an infected person or by ingesting contaminated food or water
(1, 4). The infective dose can be as few as 10 organisms, making Shigella a foodborne
pathogen of global importance based on wide distribution, water quality concerns, and
an important risk for public health (4).
The genus Shigella is composed of four species: S. dysenteriae,S. flexneri,
S. boydii, and S. sonnei, all of which cause acute bloody diarrhea (2, 5). Shigella
genomics has emerged as an important tool in basic and clinical applications for
diagnosis and classification, and will inform treatment plans (5, 6), but the ability to
conduct source tracking using whole-genome sequencing remains challenging due
to the relatively few publically available genomes. In this release, the 100K Patho-
gen Genome Project sequenced and assembled the genomes of 16 novel Shigella
isolates of the four species: two S. boydii, three S. dysenteriae, nine S. flexneri, and
two S. sonnei isolates (Table 1).
The 100K Pathogen Genome Project (http://www.100kgenomes.org) is a large-scale
sequencing effort to inform food safety and public health in genome-based identifi-
cation and source tracking (7, 8). All Shigella isolates were shipped to Bart Weimer’s
laboratory (UC Davis, Davis, CA). DNA isolation, sequencing, and assembly were done
as previously described (7–9). Briefly, isolates were checked for purity (10) prior to
extracting genomic DNA (gDNA) from cultures grown on brain heart infusion agar
(catalog no. 241830; BD Difco, Franklin Lakes, NJ) for 1 to 2 days at 37°C. Cells were
lysed (11), gDNA was purified using the Qiagen QIAamp DNA minikit (catalog no.
51306), and quality was measured using the Agilent 2200 TapeStation system with the
Genomic DNA ScreenTape (12). After isolation, gDNA was fragmented using Covaris
E220 (13), end-repaired (5=), adenylated (3=), and ligated with double-stranded DNA
(dsDNA) adapters NEXTflex-96 DNA barcode (Bioo Scientific, Austin, TX), and gDNA
(1
␮
g) was used for library construction with the Kapa high-throughput (HTP) library
preparation kit (catalog no. KK8234; Kapa Biosystems, Boston, MA), using the Agilent
Bravo automated liquid handling platform workstation option B (Santa Clara, CA). The
Received 15 February 2017 Accepted 6
March 2017 Published 20 April 2017
Citation Weis AM, Gilpin B, Huang BC, Kong N,
Chen P, Weimer BC. 2017. Shigella draft
genome sequences: resources for food safety
and public health. Genome Announc 5:
e00176-17. https://doi.org/10.1128/
genomeA.00176-17.
Copyright © 2017 Weis et al. This is an open-
access article distributed under the terms of
the Creative Commons Attribution 4.0
International license.
Address correspondence to Bart C. Weimer,
bcweimer@ucdavis.edu.
PROKARYOTES
crossm
Volume 5 Issue 16 e00176-17 genomea.asm.org 1
libraries were size selected using dual SPRI selection (0.2⫻to 0.6⫻) to produce libraries
with fragments between 300 and 450 bp. Final library amplification was done with
eight cycles using the Kapa HiFi HotStart ReadyMix, followed by a 1⫻SPRI bead
cleanup. Prior to sequencing, the library size was confirmed using the Agilent 2100
Bioanalyzer system with high-sensitivity DNA kit (14, 15), quantified with a quantitative
PCR (qPCR)-based Kapa library quantification kit (catalog no. KK4824), pooled with
multiplexing up to 96 isolates, and sequenced on the Illumina HiSeq 2000 with PE100
plus index read at BGI@UC Davis (Sacramento, CA). The paired-end reads were assem-
bled using CLC Genomics Workbench version 6.5.1 (Qiagen).
Accession number(s). Sequences can be found in the NCBI SRA 100K Project
BioProject PRJNA186441 and in GenBank (Table 1).
ACKNOWLEDGMENTS
We thank the Weimer lab and all their efforts in isolate logistics and technical
assistance and all of the collaborators for the 100K Pathogen Genome Project.
This project was funded by the 100K Pathogen Genome Project with initial funding
from Agilent Technologies to produce these sequences.
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control using the Agilent 2200 TapeStation system. Application note.
Agilent Technologies, Santa Clara, CA. http://www.agilent.com/cs/
library/applications/5991-5442EN.pdf.
TABLE 1 Shigella species draft genome sequence information
GenBank accession no. Strain ID Species Depth (ⴛ) No. of contigs No. of bases
MSJS00000000 BCW_4868 S. boydii 115 243 4,863,576
MSJT00000000 BCW_4869 S. boydii 108 297 4,246,029
MSJU00000000 BCW_4870 S. dysenteriae 114 285 4,018,103
MSJV00000000 BCW_4871 S. dysenteriae 117 299 4,078,019
MSJW00000000 BCW_4872 S. dysenteriae 72 292 4,490,659
MSJX00000000 BCW_4874 S. flexneri 109 269 4,252,909
MSJY00000000 BCW_4875 S. flexneri 90 249 4,196,256
MSJZ00000000 BCW_4876 S. flexneri 101 293 4,396,898
MSKA00000000 BCW_4877 S. flexneri 100 296 4,330,224
MSKC00000000 BCW_4879 S. flexneri 124 287 4,167,963
MSKB00000000 BCW_4880 S. flexneri 106 267 4,224,783
MSKD00000000 BCW_4881 S. flexneri 170 253 4,334,622
MSKG00000000 BCW_4882 S. flexneri 96 297 4,099,589
MSKF00000000 BCW_4883 S. flexneri 118 289 4,305,926
MSKE00000000 BCW_4885 S. sonnei 101 299 4,392,417
MSKH00000000 BCW_4886 S. sonnei 100 286 4,530,575
Weis et al.
Volume 5 Issue 16 e00176-17 genomea.asm.org 2
13. Jeannotte R, Lee E, Arabyan N, Kong N, Thao K, Huang BH, Kelly L,
Weimer BC. 2014. Optimization of Covaris settings for shearing bacterial
genomic DNA by focused ultrasonication and analysis using Agilent
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14. Kong N, Ng W, Foutouhi A, Huang BH, Kelly L, Weimer BC. 2014. Quality
control of high-throughput library construction pipeline for KAPA HTP
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library/applications/5991-4296EN.pdf.
Genome Announcement
Volume 5 Issue 16 e00176-17 genomea.asm.org 3
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