scholarly journals Whole genome sequencing provides possible explanations for the difference in phage susceptibility among two Salmonella Typhimurium phage types (DT8 and DT30) associated with a single foodborne outbreak

2015 ◽  
Vol 8 (1) ◽  
Author(s):  
Manal Mohammed ◽  
Martin Cormican
2018 ◽  
Vol 15 (5) ◽  
pp. 285-292 ◽  
Author(s):  
Laura Ford ◽  
Qinning Wang ◽  
Russell Stafford ◽  
Kelly-Anne Ressler ◽  
Sophie Norton ◽  
...  

2017 ◽  
Author(s):  
Adriana Munoz ◽  
Boris Yamrom ◽  
Yoon-ha Lee ◽  
Peter Andrews ◽  
Steven Marks ◽  
...  

AbstractCopy number profiling and whole-exome sequencing has allowed us to make remarkable progress in our understanding of the genetics of autism over the past ten years, but there are major aspects of the genetics that are unresolved. Through whole-genome sequencing, additional types of genetic variants can be observed. These variants are abundant and to know which are functional is challenging. We have analyzed whole-genome sequencing data from 510 of the Simons Simplex Collections quad families and focused our attention on intronic variants. Within the introns of 546 high-quality autism target genes, we identified 63 de novo indels in the affected and only 37 in the unaffected siblings. The difference of 26 events is significantly larger than expected (p-val = 0.01) and using reasonable extrapolation shows that de novo intronic indels can contribute to at least 10% of simplex autism. The significance increases if we restrict to the half of the autism targets that are intolerant to damaging variants in the normal human population, which half we expect to be even more enriched for autism genes. For these 273 targets we observe 43 and 20 events in affected and unaffected siblings, respectively (p-value of 0.005). There was no significant signal in the number of de novo intronic indels in any of the control sets of genes analyzed. We see no signal from de novo substitutions in the introns of target genes.


2018 ◽  
Author(s):  
Laura M. Carroll ◽  
Martin Wiedmann ◽  
Manjari Mukherjee ◽  
David C. Nicholas ◽  
Lisa A. Mingle ◽  
...  

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.


2016 ◽  
Vol 54 (8) ◽  
pp. 1975-1983 ◽  
Author(s):  
Marc W. Allard ◽  
Errol Strain ◽  
David Melka ◽  
Kelly Bunning ◽  
Steven M. Musser ◽  
...  

The FDA has created a United States-based open-source whole-genome sequencing network of state, federal, international, and commercial partners. The GenomeTrakr network represents a first-of-its-kind distributed genomic food shield for characterizing and tracing foodborne outbreak pathogens back to their sources. The GenomeTrakr network is leading investigations of outbreaks of foodborne illnesses and compliance actions with more accurate and rapid recalls of contaminated foods as well as more effective monitoring of preventive controls for food manufacturing environments. An expanded network would serve to provide an international rapid surveillance system for pathogen traceback, which is critical to support an effective public health response to bacterial outbreaks.


2021 ◽  
pp. 147-159
Author(s):  
Jasna Kovac ◽  
Edward G. Dudley ◽  
Erin M. Nawrocki ◽  
Runan Yan ◽  
Taejung Chung

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S388-S389
Author(s):  
Mary Beth Dorr ◽  
Zhen Zeng ◽  
Mark Wilcox ◽  
Junhua Li ◽  
Ian Poxton ◽  
...  

Abstract Background Bezlotoxumab (BEZ) and actoxumab (ACT) are monoclonal antibodies against C. difficile toxins B and A, respectively. Patients receiving a single infusion of BEZ alone or with ACT in the MODIFY I/II trials showed an absolute 10% (relative ~40%) reduction in rCDI over 12-weeks compared with placebo (PBO). The addition of ACT did not improve efficacy. This post hoc analysis investigated whether BEZ prevented relapse with the same strain and/or reinfection with a new strain. Methods C. difficile strains isolated from patient stool samples were typed by PCR ribotyping, PCR free library construction and Illumina whole genome sequencing (WGS). rCDI was defined as diarrhea with toxigenic C. difficile in stool. Reinfection and relapse were differentiated by comparing ribotype (RT) and pair-wise single-nucleotide WGS variations (PWSNV). Relapse was assigned if the baseline RT and the RT isolated during rCDI were the same and PWSNVs were ≤2. Reinfection was defined as rCDI cases with a different RT compared with baseline or the same RT with >10 PWSNVs. Patients receiving BEZ or ACT+BEZ were pooled and patients receiving PBO or ACT were pooled. The effect of BEZ on the cumulative incidence of relapse and reinfection was estimated by Fine & Gray’s competing risks survival model. Results Among 514 patients with rCDI in MODIFY I/II, 259 (50.4%) had a baseline and a post-baseline C. difficile isolate. There were 198 (76.4%) relapse and 50 (19.3%) reinfection cases (Table). Among rCDI cases, proportions of reinfection and relapse were similar between treatments. Proportion of relapses was higher for RT 027. Significant differences in crude cumulative incidence for relapse (P < 0.001) were observed for BEZ and ACT+BEZ groups compared with PBO and ACT groups. Similar changes were observed for reinfection but results were not significant. Cumulative incidence curves showed that relapses occurred earlier and at a higher rate than reinfections, but the reduction in rCDI was similar (Figure). Conclusion The BEZ-induced reduction in rCDI observed in MODIFY I/II reflects the prevention of relapses due to the same strain. A reduction in reinfections was also observed, but likely due to a smaller number of reinfection cases, the difference was not significant. Disclosures M. B. Dorr, Merck & Co., Inc.: Employee and Shareholder, may own stock/hold stock options in the Company; Z. Zeng, Merck & Co., Inc.: Employee, May own stock/hold stock options in the Company ; M. Wilcox, Merck & Co., Inc.: Consultant, Consulting fee; Cubist: Consultant, Grant Investigator and Speaker’s Bureau, Consulting fee, Grant recipient and Speaker honorarium; Alere, Actelion Pharma, Astellas, Optimer, sanofi pasteur, Summit Pharma, bioMerieux, Da Volterra, Qiagen, Cerexa, Abbott, AstraZeneca, Pfizer, Durata Therapeutics, Seres Therapeutics, Valneva, Nabriva Therapeutics, Roche, The Medicines Company, Basilea P: Consultant, Consulting fee; Alere, Actelion Pharmaceuticals, Pharmaceuticals, Astellas, Optimer Pharmaceuticals, sanofi pasteur, Summit Pharmaceuticals, bioMerieux, Da Volterra, Qiagen, Cerexa, and Abbott: Grant Investigator, Grant recipient; J. Li, BGI-Shenzhen: Employee, Salary; H. Zhao, BGI-Shenzhen: Employee, Salary; X. Li, BGI-Shenzhen: Employee, Salary; D. Guris, Merck & Co., Inc.: Employee, may own stock/hold stock options in the Company; P. Shaw, Merck & Co., Inc.: Employee, May own stock/hold stock options in Company


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