scholarly journals Advances in foodborne outbreak investigation and source tracking using whole genome sequencing

2019 ◽  
Vol 333 ◽  
pp. 012010
Author(s):  
W Ruppitsch ◽  
A Pietzka ◽  
A Cabal ◽  
A Chakeri ◽  
D Schmid ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Outbreak Investigation ◽  
Source Tracking ◽  
Whole Genome ◽  
Foodborne Outbreak

scholarly journals Whole Genome Sequencing Provides an Added Value to the Investigation of Staphylococcal Food Poisoning Outbreaks

2021 ◽  
Vol 12 ◽  
Author(s):  
Stéphanie Nouws ◽  
Bert Bogaerts ◽  
Bavo Verhaegen ◽  
Sarah Denayer ◽  
Lasse Laeremans ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Protein A ◽  
Food Poisoning ◽  
Gene Profiling ◽  
Added Value ◽  
Outbreak Investigation ◽  
Whole Genome ◽  
Foodborne Outbreak ◽  
Chain Reactions

Through staphylococcal enterotoxin (SE) production, Staphylococcus aureus is a common cause of food poisoning. Detection of staphylococcal food poisoning (SFP) is mostly performed using immunoassays, which, however, only detect five of 27 SEs described to date. Polymerase chain reactions are, therefore, frequently used in complement to identify a bigger arsenal of SE at the gene level (se) but are labor-intensive. Complete se profiling of isolates from different sources, i.e., food and human cases, is, however, important to provide an indication of their potential link within foodborne outbreak investigation. In addition to complete se gene profiling, relatedness between isolates is determined with more certainty using pulsed-field gel electrophoresis, Staphylococcus protein A gene typing and other methods, but these are shown to lack resolution. We evaluated how whole genome sequencing (WGS) can offer a solution to these shortcomings. By WGS analysis of a selection of S. aureus isolates, including some belonging to a confirmed foodborne outbreak, its added value as the ultimate multiplexing method was demonstrated. In contrast to PCR-based se gene detection for which primers are sometimes shown to be non-specific, WGS enabled complete se gene profiling with high performance, provided that a database containing reference sequences for all se genes was constructed and employed. The custom compiled database and applied parameters were made publicly available in an online user-friendly interface. As an all-in-one approach with high resolution, WGS additionally allowed inferring correct isolate relationships. The different DNA extraction kits that were tested affected neither se gene profiling nor relatedness determination, which is interesting for data sharing during SFP outbreak investigation. Although confirming the production of enterotoxins remains important for SFP investigation, we delivered a proof-of-concept that WGS is a valid alternative and/or complementary tool for outbreak investigation.

scholarly journals Characterization of emetic and diarrheal Bacillus cereus strains from a 2016 foodborne outbreak using whole-genome sequencing: addressing the microbiological, epidemiological, and bioinformatic challenges

2018 ◽  
Author(s):  
Laura M. Carroll ◽  
Martin Wiedmann ◽  
Manjari Mukherjee ◽  
David C. Nicholas ◽  
Lisa A. Mingle ◽  
...  
Keyword(s):  
New York ◽  
Bacillus Cereus ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Fast Food ◽  
Epidemiological Data ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Foodborne Outbreak

AbstractThe Bacillus cereus group comprises multiple species capable of causing emetic or diarrheal foodborne illness. Despite being responsible for tens of thousands of illnesses each year in the U.S. alone, whole-genome sequencing (WGS) has not been routinely employed to characterize B. cereus group isolates from foodborne outbreaks. Here, we describe the first WGS-based characterization of isolates linked to an outbreak caused by members of the B. cereus group. In conjunction with a 2016 outbreak traced to a supplier of refried beans served by a fast food restaurant chain in upstate New York, a total of 33 B. cereus group strains were obtained from human cases (n =7) and food samples (n = 26). Emetic (n = 30) and diarrheal (n = 3) isolates were most closely related to B. paranthracis (clade III) and B. cereus sensu stricto (clade IV), respectively. WGS indicated that the 30 emetic isolates (24 and 6 from food and humans, respectively) were closely-related and formed a well-supported clade relative to publicly-available emetic clade III genomes with an identical sequence type (ST 26). When compared to publicly-available emetic clade III ST 26 B. cereus group genomes, the 30 emetic clade III isolates from this outbreak differed from each other by a mean of 8.3 to 11.9 core single nucleotide polymorphisms (SNPs), while differing from publicly-available genomes by a mean of 301.7 to 528.0 core SNPs, depending on the SNP calling methodology used. Using a WST-1 cell proliferation assay, the strains isolated from this outbreak had only mild detrimental effects on HeLa cell metabolic activity compared to reference diarrheal strain B. cereus ATCC 14579. Based on both WGS and epidemiological data, we hypothesize that the outbreak was a single source outbreak caused by emetic clade III B. cereus belonging to the B. paranthracis species. In addition to showcasing how WGS can be used to characterize B. cereus group strains linked to a foodborne outbreak, we also discuss potential microbiological and epidemiological challenges presented by B. cereus group outbreaks, and we offer recommendations for analyzing WGS data from the isolates associated with them.

scholarly journals Agrobacterium spp. nosocomial outbreak assessment using rapid MALDI-TOF MS based typing, confirmed by whole genome sequencing

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Carlo Casanova ◽  
Elia Lo Priore ◽  
Adrian Egli ◽  
Helena M. B. Seth-Smith ◽  
Lorenz Räber ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Point Sources ◽  
University Hospital ◽  
Outbreak Investigation ◽  
Whole Genome ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Epidemiological Characteristics ◽  
Tof Ms

Abstract Background A number of episodes of nosocomial Agrobacterium spp. bacteremia (two cases per year) were observed at Bern University Hospital, Switzerland, from 2015 to 2017. This triggered an outbreak investigation. Methods Cases of Agrobacterium spp. bacteremias that occurred between August 2011 and February 2017 were investigated employing line lists, environmental sampling, rapid protein- (MALDI-TOF MS), and genome-based typing (pulsed field gel electrophoresis and whole genome sequencing) of the clinical isolates. Results We describe a total of eight bacteremia episodes due to A. radiobacter (n = 2), Agrobacterium genomovar G3 (n = 5) and A. pusense (n = 1). Two tight clusters were observed by WGS typing, representing the two A. radiobacter isolates (cluster I, isolated in 2015) and four of the Agrobacterium genomovar G3 isolates (cluster II, isolated in 2016 and 2017), suggesting two different point sources. The epidemiological investigations revealed two computer tomography (CT) rooms as common patient locations, which correlated with the two outbreak clusters. MALDI-TOF MS permitted faster evaluation of strain relatedness than DNA-based methods. High resolution WGS-based typing confirmed the MALDI-TOF MS clustering. Conclusions We report clinical and epidemiological characteristics of two outbreak clusters with Agrobacterium. spp. bacteremia likely acquired during CT contrast medium injection and highlight the use of MALDI-TOF MS as a rapid tool to assess relatedness of rare gram-negative pathogens in an outbreak investigation.

scholarly journals The utility of Escherichia coli as a contamination indicator for rural drinking water: Evidence from whole genome sequencing

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245910
Author(s):  
Saskia Nowicki ◽  
Zaydah R. deLaurent ◽  
Etienne P. de Villiers ◽  
George Githinji ◽  
Katrina J. Charles
Keyword(s):  
Escherichia Coli ◽  
Drinking Water ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Allelic Diversity ◽  
Source Tracking ◽  
Whole Genome ◽  
Faecal Contamination ◽  
Household Level ◽  
Phylogenetic Grouping

Across the water sector, Escherichia coli is the preferred microbial water quality indicator and current guidance upholds that it indicates recent faecal contamination. This has been challenged, however, by research demonstrating growth of E. coli in the environment. In this study, we used whole genome sequencing to investigate the links between E. coli and recent faecal contamination in drinking water. We sequenced 103 E. coli isolates sampled from 9 water supplies in rural Kitui County, Kenya, including points of collection (n = 14) and use (n = 30). Biomarkers for definitive source tracking remain elusive, so we analysed the phylogenetic grouping, multi-locus sequence types (MLSTs), allelic diversity, and virulence and antimicrobial resistance (AMR) genes of the isolates for insight into their likely source. Phylogroup B1, which is generally better adapted to water environments, is dominant in our samples (n = 69) and allelic diversity differences (z = 2.12, p = 0.03) suggest that naturalised populations may be particularly relevant at collection points with lower E. coli concentrations (<50 / 100mL). The strains that are more likely to have originated from human and/or recent faecal contamination (n = 50), were found at poorly protected collection points (4 sites) or at points of use (12 sites). We discuss the difficulty of interpreting health risk from E. coli grab samples, especially at household level, and our findings support the use of E. coli risk categories and encourage monitoring that accounts for sanitary conditions and temporal variability.

scholarly journals ON-rep-seq as a rapid and cost-effective alternative to whole-genome sequencing for species-level identification and strain-level discrimination of Listeria monocytogenes contamination in a salmon processing plant

2021 ◽  
Author(s):  
Gunn Merethe Thomassen ◽  
Lukasz Krych ◽  
Susanne Knøchel ◽  
Lisbeth Mehli
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Screening Method ◽  
Cost Effective ◽  
Strain Level ◽  
Source Tracking ◽  
Processing Plant ◽  
Whole Genome ◽  
Different Strains

Identification, source tracking, and surveillance of food pathogens is a crucial factor for the food-producing industry. Over the last decade, the techniques used for this have moved from conventional enrichment methods, through species-specific detection by PCR to sequencing-based methods, whole-genome sequencing (WGS) being the ultimate method. However, using WGS requires the right infrastructure, high computational power, and bioinformatics expertise. Therefore, there is a need for faster, more cost-effective, and more user-friendly methods. A newly developed method, ON-rep-seq, combines the classical rep-PCR method with nanopore sequencing, resulting in a highly discriminating set of sequences that can be used for species identification and also strain discrimination. This study is essentially a real industry case from a salmon processing plant. Twenty Listeria monocytogenes isolates were analyzed both by ON-rep-seq and WGS to identify and differentiate putative L. monocytogenes from a routine sampling of processing equipment and products, and finally, compare the strain-level discriminatory power of ON-rep-seq to different analyzing levels delivered from the WGS data. The analyses revealed that among the isolates tested there were three different strains. The isolates of the most frequently detected strain (n=15) were all detected in the problematic area in the processing plant. The strain level discrimination done by ON-rep-seq was in full accordance with the interpretation of WGS data. Our findings also demonstrate that ON-rep-seq may serve as a primary screening method alternative to WGS for identification and strain-level differentiation for surveillance of potential pathogens in a food-producing environment.

Sign in / Sign up

Export Citation Format

Share Document