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Draft Genome Sequence of Multidrug-Resistant Abortive Campylobacter jejuni from Northern California

April 2017
Genome Announcements 5(15)

DOI:10.1128/genomeA.00171-17

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CC BY 4.0

Authors:

Allison M Weis

University of Utah

Kris Clothier

University of California, Davis

Carol Huang

University of California, Davis

Nguyet Kong

University of California, Davis

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Campylobacter jejuni is an enteric bacterium that can cause abortion in livestock. This is the release of a multidrug-resistant Campylobacter jejuni genome from an isolate that caused an abortion in a cow in northern California. This isolate is part of the 100K Pathogen Genome Project.

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Draft Genome Sequence of Multidrug-

Resistant Abortive Campylobacter jejuni

from Northern California

Allison M. Weis,

Kristin A. Clothier,

Bihua C. Huang,

Nguyet Kong,

Bart C. Weimer

School of Veterinary Medicine, 100K Pathogen Genome Project, UC Davis, Davis, California, USA

; California

Animal Health and Food Safety, Davis, California, USA

ABSTRACT Campylobacter jejuni is an enteric bacterium that can cause abortion in

livestock. This is the release of a multidrug-resistant Campylobacter jejuni genome

from an isolate that caused an abortion in a cow in northern California. This isolate

is part of the 100K Pathogen Genome Project.

Campylobacter jejuni is an enteric pathogen that affects humans worldwide with

infection accompanied by symptoms such as fever and bloody diarrhea, and can

lead to autoimmune diseases (1–6). C. jejuni is zoonotic, and in livestock it can lead to

gastroenteritis and occasionally abortion (7–12). In recent years, several regions in the

United States have noted the emergence of an abortive hypervirulent C. jejuni isolate

(13–15).

Multidrug resistant bacteria are a major worldwide problem, leading to untreatable

infection and mortality among humans and other animals (16, 17) that can be trans-

mitted to the human microbiome (18). Here, we describe a multidrug-resistant abortive

C. jejuni strain from northern California that was isolated from a bovine fetus from a

third trimester abortion in 2009 and was uniquely multidrug resistant. This C. jejuni

genome contains tetO, which confers resistance to tetracycline and its derivatives. It

also contains aphA, a kanamycin resistance gene that is an aminoglycoside phospho-

transferase. Lastly, it also contains a Thr-86-Ile mutation in the GyrA protein that results

in ﬂuoroquinolone resistance. The tetO and aphA genes are located on a putative

plasmid, whereas gyrA is in the chromosome. The genome assembly comprised 54

contigs, 1,708,778 bp, and 1,717 coding sequences, and the sequence depth was 59⫻.

This C. jejuni isolate was among a set of animal source isolates that was given to the

100K Pathogen Genome Project (http://www.100kgenomes.org) in the laboratory of

Bart Weimer (UC Davis). The isolate was checked for purity (19) and genomic DNA

(gDNA) was extracted from culture grown on 5% blood agar plates (UC Davis, VetMed

Biological Services) for 1 to 2 days, lysed with an enzyme cocktail (20), puriﬁed with a

Qiagen QIAamp DNA minikit (51306), and analyzed on the Agilent 2200 TapeStation

system with the Genomic DNA ScreenTape assay for integrity of gDNA, as described

previously (21–23). Approximately one microgram of gDNA was used for library con-

struction with the KAPA Hyper library preparation kit (Kapa Biosystems, Boston, MA,

USA; KK8514), on a PerkinElmer Sciclone NGS Workstation (Waltham, MA, USA). In this

process, fragmented double-stranded gDNA molecules were end-repaired (5=), adeny-

lated (3=), and ligated with double stranded DNA adapters (Weimer 384 TS-LT DNA

Barcodes, Integrated DNA Technologies, Inc., Coralville, IA, USA), followed by dual-SPRI

size selection for targeting a library size of 250 to 500 bp. Final library quality

assessment to verify size distribution was performed on a Perkin Elmer Caliper Lab Chip

GX using the PerkinElmer Caliper HT 1K kit (CLS701879), and library quantiﬁcation was

completed using a SYBR Green– based qPCR kit and a KAPA library quantiﬁcation kit

Received 13 February 2017 Accepted 21

February 2017 Published 13 April 2017

Citation Weis AM, Clothier KA, Huang BC, Kong

N, Weimer BC. 2017. Draft genome sequence

of multidrug-resistant abortive Campylobacter

jejuni from northern California. Genome

Announc 5:e00171-17. https://doi.org/10.1128/

genomeA.00171-17.

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 15 e00171-17 genomea.asm.org 1

(KK4824). Pooled libraries were sequenced on the Illumina HiSeq X TEN platform with

a PE150-plus index read at Novogene (Sacramento, CA, USA). Paired-end sequence

reads were assembled using ABySS version 1.9.0 (k-mer ⫽64) and annotated with

Prokka (24, 25).

Accession number(s). This sequence can be found at NCBI SRA BioProject

PRJNA186441 under genome SRA accession number SRR5210995, and at NCBI GenBank

under the accession number MUJW00000000.

ACKNOWLEDGMENTS

We thank all contributors of the 100K Pathogen Genome Project and members of

the Weimer Lab for technical assistance. We thank the individuals associated with the

isolation of the unique and important C. jejuni strain presented here. This project was

funded by the 100K Pathogen Genome Project to produce this sequence.

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