Whole-Genome Sequencing and Bioinformatic Analysis of Isolates from Foodborne Illness Outbreaks of Campylobacter jejuni and Salmonella enterica

Journal of Clinical Microbiology
Kelly F OakesonRobyn Atkinson-Dunn

Abstract

Whole-genome sequencing (WGS) via next-generation sequencing (NGS) technologies is a powerful tool for determining the relatedness of bacterial isolates in foodborne illness detection and outbreak investigations. WGS has been applied to national outbreaks (for example, Listeria monocytogenes); however, WGS has rarely been used in smaller local outbreaks. The current study demonstrates the superior resolution of genetic and evolutionary relatedness generated by WGS data analysis, compared to pulsed-field gel electrophoresis (PFGE). The current study retrospectively applies WGS and a reference-free bioinformatic analysis to a Utah-specific outbreak of Campylobacter jejuni associated with raw milk and to a national multistate outbreak of Salmonella enterica subsp. enterica serovar Typhimurium associated with rotisserie chicken, both of which were characterized previously by PFGE. Together, these analyses demonstrate how a reference-free WGS workflow is not reliant on determination of a reference sequence, like WGS workflows that are based on single-nucleotide polymorphisms, or the need for curated allele databases, like multilocus sequence typing workflows.

References

Oct 16, 1999·FEMS Microbiology Letters·B SteinbruecknerM Kist
Apr 28, 2001·Journal of Clinical Microbiology·E M RibotT J Barrett
Aug 3, 2001·International Journal of Food Microbiology·M L De BuyserV Lafarge
Nov 9, 2001·Journal of Dairy Science·B M Jayarao, D R Henning
Apr 10, 2008·Molecular Biology and Evolution·David Posada
Jun 21, 2008·Foodborne Pathogens and Disease·Justin DennyK Eckmann
Jan 7, 2010·BMC Bioinformatics·Ben C Stöver, Kai F Müller
Nov 11, 2010·Nucleic Acids Research·Rasko LeinonenUNKNOWN International Nucleotide Sequence Database Collaboration
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
May 18, 2012·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Elaine Scallan, Barbara E Mahon
May 16, 2012·Comparative Immunology, Microbiology and Infectious Diseases·Laurent-Xavier NouvelChristine Citti
Feb 21, 2013·Bioinformatics·Alexey GurevichGlenn Tesler
Oct 8, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Sergey NurkPavel A Pevzner
Mar 20, 2014·Bioinformatics·Torsten Seemann
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Jul 23, 2015·Bioinformatics·Andrew J PageJulian Parkhill
Jul 29, 2015·Frontiers in Genetics·Nathan D OlsonJustin M Zook
Mar 20, 2016·American Journal of Preventive Medicine·Robert L ScharffCraig W Hedberg
Apr 1, 2016·MMWR. Morbidity and Mortality Weekly Report·Kenneth R DavisAllyn K Nakashima
Aug 19, 2017·Emerging Infectious Diseases·Kelly F OakesonRobyn Atkinson-Dunn
Jul 1, 1983·Journal of Food Protection·Frank L Bryan

❮ Previous
Next ❯

Citations

Aug 15, 2019·Implementation Science : IS·Nina Van GoethemAnnie Robert
May 14, 2021·Clinical Microbiology Reviews·Carmen L CharltonEric P Bind
Jul 6, 2021·Pediatric Pulmonology·Harry S PorterfieldAnthony J Fischer

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRS1929599
SRS1929615
SRR5023223

Methods Mentioned

BETA
electrophoresis

Software Mentioned

SPAdes
Cladogram
QUAST
Phylogram
R Studio
JModelTest
Pegas
BioNumerics
Trimmomatic
Roary

Related Concepts

Related Feeds

Campylobacteriosis (ASM)

Campylobacteriosis is caused by the bacteria Campylobacter jejuni and is a common cause of gastroenteritis in humans. Discover the latest research on Campylobacteriosis here.