High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak.
BACKGROUND
A large, multi-province outbreak of listeriosis associated with ready-to-eat meat products contaminated with Listeria monocytogenes serotype 1/2a occurred in Canada in 2008. Subtyping of outbreak-associated isolates using pulsed-field gel electrophoresis (PFGE) revealed two similar but distinct AscI PFGE patterns. High-throughput pyrosequencing of two L. monocytogenes isolates was used to rapidly provide the genome sequence of the primary outbreak strain and to investigate the extent of genetic diversity associated with a change of a single restriction enzyme fragment during PFGE.


RESULTS
The chromosomes were collinear, but differences included 28 single nucleotide polymorphisms (SNPs) and three indels, including a 33 kbp prophage that accounted for the observed difference in AscI PFGE patterns. The distribution of these traits was assessed within further clinical, environmental and food isolates associated with the outbreak, and this comparison indicated that three distinct, but highly related strains may have been involved in this nationwide outbreak. Notably, these two isolates were found to harbor a 50 kbp putative mobile genomic island encoding translocation and efflux functions that has not been observed in other Listeria genomes.


CONCLUSIONS
High-throughput genome sequencing provided a more detailed real-time assessment of genetic traits characteristic of the outbreak strains than could be achieved with routine subtyping methods. This study confirms that the latest generation of DNA sequencing technologies can be applied during high priority public health events, and laboratories need to prepare for this inevitability and assess how to properly analyze and interpret whole genome sequences in the context of molecular epidemiology.
Gilmour
Matthew W
MW
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada. Matthew_Gilmour@phac-aspc.gc.ca
Graham
Morag
M
Van Domselaar
Gary
G
Tyler
Shaun
S
Kent
Heather
H
Trout-Yakel
Keri M
KM
Larios
Oscar
O
Allen
Vanessa
V
Lee
Barbara
B
Nadon
Celine
C
D002170:Canada / Q000453:epidemiology; D019295:Computational Biology; D004269:DNA, Bacterial / Q000235:genetics; D004196:Disease Outbreaks; D005506:Food Contamination; D005516:Food Microbiology; D005517:Foodborne Diseases / Q000382:microbiology; D016680:Genome, Bacterial; D044404:Genomic Islands; D057166:High-Throughput Screening Assays; D054643:INDEL Mutation; D008089:Listeria monocytogenes / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D008088:Listeriosis / Q000453:epidemiology; D008461:Meat Products / Q000382:microbiology; D010802:Phylogeny; D010957:Plasmids; D020641:Polymorphism, Single Nucleotide; D039002:Prophages; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012703:Serotyping; D014774:Virulence
D004269:DNA, Bacterial