Evaluating the use of whole-genome sequencing for outbreak investigations in the lack of closely related reference genome

2018 ◽  
Vol 59 ◽  
pp. 1-6 ◽  
Author(s):  
Mohamed M.H. Abdelbary ◽  
Laurence Senn ◽  
Estelle Moulin ◽  
Guy Prod'hom ◽  
Antony Croxatto ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Reference Genome ◽  
Whole Genome ◽  
Outbreak Investigations

Utility of Whole Genome Sequencing To Describe the Persistence and Evolution of Listeria monocytogenes Strains within Crabmeat Processing Environments Linked to Two Outbreaks of Listeriosis

2018 ◽  
Vol 82 (1) ◽  
pp. 30-38 ◽  
Author(s):  
RICHARD ELSON ◽  
ADEDOYIN AWOFISAYO-OKUYELU ◽  
TREVOR GREENER ◽  
CRAIG SWIFT ◽  
ANAÏS PAINSET ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Surveillance Data ◽  
Control Measures ◽  
Whole Genome ◽  
Typing Method ◽  
Outbreak Investigations ◽  
Molecular Typing Method ◽  
Clinical Cases

ABSTRACT This article describes the identification and investigation of two extended outbreaks of listeriosis in which crabmeat was identified as the vehicle of infection. Comparing contemporary and retrospective typing data of Listeria monocytogenes isolates from clinical cases and from food and food processing environments allowed the detection of cases going back several years. This information, combined with the analysis of routinely collected enhanced surveillance data, helped to direct the investigation and identify the vehicle of infection. Retrospective whole genome sequencing (WGS) analysis of isolates provided robust microbiological evidence of links between cases, foods, and the environments in which they were produced and demonstrated that for some cases and foods, identified by fluorescent amplified fragment length polymorphism, the molecular typing method in routine use at the time, were not part of the outbreak. WGS analysis also showed that the strains causing illness had persisted in two food production environments for many years and in one producer had evolved into two strains over a period of around 8 years. This article demonstrates the value of reviewing L. monocytogenes typing data from clinical cases together with that from foods as a means of identifying potential vehicles and sources of infection in outbreaks of listeriosis. It illustrates the importance of reviewing retrospective L. monocytogenes typing alongside enhanced surveillance data to characterize extended outbreaks and inform control measures. Also, this article highlights the advantages of WGS analysis for strain discrimination and clarification of evolutionary relationships that refine outbreak investigations and improve our understanding of L. monocytogenes in the food chain.

scholarly journals Outbreaks of Salmonella illness associated with frozen raw breaded chicken products in Canada, 2015–2019

2019 ◽  
Vol 147 ◽  
Author(s):  
V. K. Morton ◽  
A. Kearney ◽  
S. Coleman ◽  
M. Viswanathan ◽  
K. Chau ◽  
...  
Keyword(s):  
Risk Factor ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Retail Sale ◽  
Outbreak Investigations

Abstract Frozen raw breaded chicken products (FRBCP) have been identified as a risk factor for Salmonella infection in Canada. In 2017, Canada implemented whole genome sequencing (WGS) for clinical and non-clinical Salmonella isolates, which increased understanding of the relatedness of Salmonella isolates, resulting in an increased number of Salmonella outbreak investigations. A total of 18 outbreaks and 584 laboratory-confirmed cases have been associated with FRBCP or chicken since 2017. The introduction of WGS provided the evidence needed to support a new requirement to control the risk of Salmonella in FRBCP produced for retail sale.

scholarly journals Utility of Combining Whole Genome Sequencing with Traditional Investigational Methods To Solve Foodborne Outbreaks of Salmonella Infections Associated with Chicken: A New Tool for Tackling This Challenging Food Vehicle

2017 ◽  
Vol 80 (4) ◽  
pp. 654-660 ◽  
Author(s):  
Samuel J. Crowe ◽  
Alice Green ◽  
Kimberly Hernandez ◽  
Vi Peralta ◽  
Lyndsay Bottichio ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Food Samples ◽  
Clinical Isolates ◽  
Whole Genome ◽  
Salmonella Infections ◽  
Outbreak Investigations ◽  
Consumption Rates ◽  
Foodborne Outbreaks

ABSTRACT High consumption rates and a multitude of brands make multistate foodborne outbreaks of Salmonella infections associated with chicken challenging to investigate, but whole genome sequencing is a powerful tool that can be used to assist investigators. Whole genome sequencing of pathogens isolated from clinical, environmental, and food samples is increasingly being used in multistate foodborne outbreak investigations to determine with unprecedented resolution how closely related these isolates are to one another genetically. In 2014, federal and state health officials investigated an outbreak of 146 Salmonella Heidelberg infections in 24 states. A follow-up analysis was conducted after the conclusion of the investigation in which 27 clinical and 24 food isolates from the outbreak underwent whole genome sequencing. These isolates formed seven clades, the largest of which contained clinical isolates from a subcluster of case patients who attended a catered party. One isolate from a chicken processed by a large producer was closely related genetically (zero to three single-nucleotide polymorphism differences) to the clinical isolates from these subcluster case patients. Chicken from this large producer was also present in the kitchen of the caterer on the day before the event, thus providing additional evidence that the chicken from this producer was the outbreak source. This investigation highlights how whole genome sequencing can be used with epidemiologic and traceback evidence to identify chicken sources of foodborne outbreaks.

scholarly journals 864. Whole Genome Sequencing is Unable to Track Candida auris Transmission

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S470-S471
Author(s):  
Scott C Roberts ◽  
Egon A Ozer ◽  
Teresa Zembower ◽  
Chao Qi
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Illumina Miseq ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Candida Auris ◽  
Healthcare Settings ◽  
Long Read ◽  
Outbreak Investigations ◽  
Phylogenetic Grouping

Abstract Background Candida auris (C. auris), an emerging yeast species, is often drug-resistant and has caused outbreaks in healthcare settings. Surging C. auris cases at our institution prompted whole genome sequencing (WGS) of patient and environmental specimens and comparison to local and international isolates. Methods WGS was performed on clinical and environmental isolates obtained from Northwestern Memorial Hospital (NMH) from June 2018 to December 2019. Genome sequences were compared against isolates from other institutions in the Chicagoland area obtained from a reference lab (ACL) and from the CDC. Two isolates underwent long-read sequencing on the Oxford Nanopore GridION platform to obtain closed genomes. WGS was performed on the remaining isolates with the Illumina MiSeq platform. Results Twenty isolates from NMH, five from ACL, and two from the CDC underwent WGS to yield 12.6 Mb genomes. Any two NMH isolates differed from each other by a maximum of 36 single nucleotide variants (SNV) (Figure 1). Two patients thought to be part of a transmission cluster (isolates CA06 and CA07), differed by 7 SNVs. No phylogenetic grouping between hospital systems across Chicagoland was observed. Isolates from room surfaces from a C. auris patient differed by 1-6 SNVs from each other and from 7-8 SNVs from the patient isolate. Samples taken from different body sites of another patient differed by 4-9 SNVs. Average SNV counts were lower among nosocomially acquired cases when compared to C. auris isolates present on admission (Figure 2). All NMH isolates were fluconazole sensitive, but a fluconazole resistant ACL isolate differed from a sensitive NMH isolate by only 4 SNVs. Figure 1: Phylogenetic tree of all NMH and ACL isolates with fluconazole sensitivities Figure 2: Observed pairwise SNP differences between nosocomial and POA strains Conclusion WGS of C. auris did not reveal identical isolates in any instance, even from the same patient or the patients and their environment. Generally, lower numbers of SNVs were observed for intra- versus inter-institutional isolates. More work is needed to determine the use, if any, of WGS in outbreak investigations. Disclosures All Authors: No reported disclosures

scholarly journals Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015

2018 ◽  
Vol 23 (33) ◽  
Author(s):  
Ivo Van Walle ◽  
Jonas Torgny Björkman ◽  
Martin Cormican ◽  
Timothy Dallman ◽  
Joël Mossong ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
National Level ◽  
European Economic Area ◽  
Whole Genome ◽  
The European Union ◽  
Allelic Differences ◽  
Outbreak Investigations ◽  
Country Clusters ◽  
Sequence Quality

Background and aim The trend in reported case counts of invasive Listeria monocytogenes (Lm), a potentially severe food-borne disease, has been increasing since 2008. In 2015, 2,224 cases were reported in the European Union/European Economic Area (EU/EEA). We aimed to validate the microbiological and epidemiological aspects of an envisaged EU/EEA-wide surveillance system enhanced by routine whole genome sequencing (WGS). Methods: WGS and core genome multilocus sequence typing (cgMLST) were performed on isolates from 2,726 cases from 27 EU/EEA countries from 2010–15. Results: Quality controls for contamination, mixed Lm cultures and sequence quality classified nearly all isolates with a minimum average coverage of the genome of 55x as acceptable for analysis. Assessment of the cgMLST variation between six different pipelines revealed slightly less variation associated with assembly-based analysis compared to reads-based analysis. Epidemiological concordance, based on 152 isolates from 19 confirmed outbreaks and a cluster cutoff of seven allelic differences, was good (sensitivity > 95% for two cgMLST schemes of 1,748 and 1,701 loci each; PPV 58‒68%). The proportion of sporadic cases was slightly below 50%. Of remaining isolates, around one third were in clusters involving more than one country, often spanning several years. Detection of multi-country clusters was on average several months earlier when pooling the data at EU/EEA level, compared with first detection at national level. Conclusions: These findings provide a good basis for comprehensive EU/EEA-wide, WGS-enhanced surveillance of listeriosis. Time limits should not be used for hypothesis generation during outbreak investigations, but should be for analytical studies.

scholarly journals Whole-Genome Sequencing Revealed a Late-Maturing Isogenic Rice Koshihikari Integrated with Hd16 Gene Derived from an Ise Shrine Mutant

2022 ◽  
Vol 2022 ◽  
pp. 1-12
Author(s):  
Motonori Tomita ◽  
Ryotaro Tokuyama ◽  
Shosuke Matsumoto ◽  
Kazuo Ishii
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Reference Genome ◽  
Recurrent Parent ◽  
Whole Genome ◽  
Linkage Relationship ◽  
Late Maturity ◽  
Key Genes ◽  
Late Maturation ◽  
Relationship Of

We identified the key genes controlling the late maturation of the Japonica cultivar Isehikari, which was found at Ise Jingu Shrine and matures 6 days later than Koshihikari. We conducted a genetics-based approach through this study. First, the latest mature plants, which flowered later than Isehikari, were segregated in the F2 and F3 generations of Koshihikari×Isehikari. Next, the linkage relationship of a single late-maturing gene with the SSR markers on the long arm of chromosome 3 was inferred by using late-maturing homozygous F2 segregants. Moreover, genetic analyses of late maturity were conducted through the process of six times of continuous backcross with Koshihikari as a recurrent parent by using the late-maturing homozygous F3 line as a nonrecurrent parent, thus developing a late-maturing isogenic Koshihikari (BC6F2). As a result, we elucidated a single late-maturing gene with incomplete dominance that caused the 14-day maturation delay of Koshihikari. The whole-genome sequencing was conducted on both of Koshihikari and the late-maturing isogenic Koshihikari. Then, the SNP call was conducted as the reference genome of Koshihikari. Finally, a single SNP was identified in the key gene Hd16 of the late-maturing isogenic Koshihikari.

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