scholarly journals Phylogeographic Analysis Reveals Multiple International transmission Events Have Driven the Global Emergence of Escherichia coli O157:H7

2018 ◽  
Vol 69 (3) ◽  
pp. 428-437 ◽  
Author(s):  
Eelco Franz ◽  
Ovidiu Rotariu ◽  
Bruno S Lopes ◽  
Marion MacRae ◽  
James L Bono ◽  
...  
Keyword(s):  
United States ◽  
Disease Outbreaks ◽  
The United States ◽  
Human Case ◽  
Whole Genome Sequencing Data ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
E Coli ◽  
Phylogeographic Analysis ◽  
International Distribution

AbstractBackgroundShiga toxin–producing Escherchia coli (STEC) O157:H7 is a zoonotic pathogen that causes numerous food and waterborne disease outbreaks. It is globally distributed, but its origin and the temporal sequence of its geographical spread are unknown.MethodsWe analyzed whole-genome sequencing data of 757 isolates from 4 continents, and performed a pan-genome analysis to identify the core genome and, from this, extracted single-nucleotide polymorphisms. A timed phylogeographic analysis was performed on a subset of the isolates to investigate its worldwide spread.ResultsThe common ancestor of this set of isolates occurred around 1890 (1845–1925) and originated from the Netherlands. Phylogeographic analysis identified 34 major transmission events. The earliest were predominantly intercontinental, moving from Europe to Australia around 1937 (1909–1958), to the United States in 1941 (1921–1962), to Canada in 1960 (1943–1979), and from Australia to New Zealand in 1966 (1943–1982). This pre-dates the first reported human case of E. coli O157:H7, which was in 1975 from the United States.ConclusionsInter- and intra-continental transmission events have resulted in the current international distribution of E. coli O157:H7, and it is likely that these events were facilitated by animal movements (eg, Holstein Friesian cattle). These findings will inform policy on action that is crucial to reduce the further spread of E. coli O157:H7 and other (emerging) STEC strains globally.

scholarly journals Policy responses to foodborne disease outbreaks in the United States and Germany

2021 ◽  
Author(s):  
Kelsey D. Meagher
Keyword(s):  
United States ◽  
Disease Outbreaks ◽  
The United States ◽  
Policy Outcomes ◽  
Foodborne Disease ◽  
Structured Interviews ◽  
Health Crisis ◽  
E Coli ◽  
Archival Documents ◽  
Major Outbreak

AbstractThis paper explores differences in national responses to foodborne disease outbreaks, addressing both the sources of policy divergence and their implications for public health and coordinated emergency response. It presents findings from a comparative study of two multi-state E. coli outbreaks, one in the United States (2006) and one in Germany (2011), demonstrating important differences in how risk managers understood and responded to each nation’s first major outbreak associated with fresh produce. Drawing on a qualitative analysis of 36 semi-structured interviews with key stakeholders and hundreds of archival documents, this paper traces how social constructions of the E. coli risk interacted with organizational dynamics among state and industry actors to produce divergent policy outcomes: the U.S. outbreak was understood primarily as an agricultural problem that led to an industry-led agricultural solution, whereas the German outbreak was understood as a human disease problem that did not result in a substantial policy response once the acute health crisis passed. The paper concludes by discussing how these policy processes generate partial solutions to foodborne contamination that expose modern societies to systemic vulnerabilities.

The Western United States has Greater Antibiotic Resistance Among Salmonella Recovered from Intestinal Cecal Samples of Food Animals.

2020 ◽  
Author(s):  
Epiphanie Nyirabahizi ◽  
Gregory H. Tyson ◽  
Heather Tate ◽  
Michael S. Williams ◽  
Gurinder S. Saini ◽  
...  
Keyword(s):  
United States ◽  
The United States ◽  
Whole Genome Sequencing Data ◽  
Multiple Drug ◽  
Western Region ◽  
United States Department ◽  
Sequencing Data ◽  
Geographical Differences ◽  
Salmonella Newport ◽  
The Western Region

As part of the National Antimicrobial Resistance Monitoring System (NARMS) activities, the United States Department of Agriculture (USDA) Food Safety Inspection Service (FSIS) collected cecal samples from food animal slaughter facilities throughout the country between 2014 and 2018. Of the 26,780 cecal samples from cattle, swine, chicken and turkey , 6,350 (23.71%) tested positive for Salmonella . NARMS tested Salmonella for susceptibility to aminoglycosides, folate pathway inhibitors, macrolides, phenicols, quinolones, beta lactams, and tetracyclines. Using the regional subdivisions defined in the USDA Office of Investigation, we used chi-square test to assess potential association between the region from which the samples were collected and both Salmonella prevalence and susceptibility. The results show a significant association between region and Salmonella prevalence, when accounting for source and establishment size, with the southeast region having the highest probability of finding Salmonella . However, the western region had the highest resistance probability across all antimicrobial classes except for macrolides, which showed no regional association. This association between region and resistance was strongest among isolates from cattle. Analysis of whole-genome sequencing data indicated that a significantly higher prevalence of Salmonella Newport in cattle in the western region (accounting for 9.52% of cattle isolates, compared to 3.44% in other regions) may account for the greater resistance to multiple drug classes. Approximately 90% of Salmonella Newport in the west exhibited the MDR-AmpC phenotype encoded by aph(3'')-Ib/aph(6)-Id , bla CMY-2 , floR , sul2 , and tetA. . Thus, differences in resistance across regions may be due to geographical differences in the prevalence of specific Salmonella serotypes and their accompanying resistance genes.

scholarly journals The landscape of genetic susceptibility correlations among diseases and traits

2017 ◽  
Vol 24 (5) ◽  
pp. 921-926 ◽  
Author(s):  
Jung Hun Ohn
Keyword(s):  
United States ◽  
Correlation Analysis ◽  
Genetic Susceptibility ◽  
Large Scale ◽  
The United States ◽  
Risk Scores ◽  
Whole Genome Sequencing Data ◽  
P Value ◽  
Sequencing Data ◽  
Pairwise Correlation

Abstract Objective: The aim of the study was to comprehensively explore the genetic susceptibility correlations among diseases and traits from large-scale individual genotype data. Materials and Methods: Based on a knowledge base of genetic variants significantly (P < 5 × 10−8) linked with human phenotypes, genetic risk scores (GRSs) of diseases or traits were calculated for 2504 individuals with whole-genome sequencing data from the 1000 Genomes Project. Associations between diseases/traits were statistically evaluated by pairwise correlation analysis of GRSs. Overlaps between the genetic susceptibility correlations and disease comorbidity associations from hospital claims data in more than 30 million patients in United States were assessed. Results: Correlation analysis of GRSs revealed 823 significant correlations among 78 diseases and 89 traits (false discovery rate adjusted P-value or Q-value < 0.01). It is noticeable that GRSs were correlated in 464 associations (56.4%) even if they were combinations of distinct sets of risk variants without chromosomal linkage, suggesting the presence of genetic interactions beyond chromosome position. When 312 significant genetic susceptibility correlations between diseases were compared to nationwide disease comorbidity correlations obtained from data from 32 million Medicare claims in the United States, 108 overlaps (34.6%) were found that had both genetic susceptibility and epidemiologic comorbid correlations. Conclusion: The study suggests that common genetic background exists between diseases and traits with epidemiologic associations. The GRS correlation approach provides a rich source of candidate associations among diseases and traits from the genetic perspective, warranting further epidemiologic studies.

scholarly journals Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes

2021 ◽  
Author(s):  
Eric S Tvedte ◽  
Mark Gasser ◽  
Benjamin C Sparklin ◽  
Jane Michalski ◽  
Carl E Hjelmen ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Hybrid Approach ◽  
Cost Effective ◽  
Fruit Fly ◽  
Drosophila Ananassae ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
E Coli ◽  
Hybrid Approaches ◽  
Long Read

Abstract The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.

scholarly journals 1675. Epidemiology of Urinary Tract Infections in the United States, 2009 - 2018

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S823-S823
Author(s):  
Kendra Foster ◽  
Linnea A Polgreen ◽  
Brett Faine ◽  
Philip M Polgreen
Keyword(s):  
United States ◽  
Urinary Tract ◽  
Klebsiella Pneumoniae ◽  
Urinary Tract Infections ◽  
Proteus Mirabilis ◽  
Antibiotic Use ◽  
The United States ◽  
Drug Resistant ◽  
E Coli ◽  
Tract Infections

Abstract Background Urinary tract infections (UTIs) are one of the most common bacterial infections. There is a lack of large epidemiologic studies evaluating the etiologies of UTIs in the United States. This study aimed to determine the prevalence of different UTI-causing organisms and their antimicrobial susceptibility profiles among patients being treated in a hospital setting. Methods We used the Premier Healthcare Database. Patients with a primary diagnosis code of cystitis, pyelonephritis, or urinary tract infection and had a urine culture from 2009- 2018 were included in the study. Both inpatients and patients who were only treated in the emergency department (ED) were included. We calculated descriptive statistics for uropathogens and their susceptibilities. Multi-drug-resistant pathogens are defined as pathogens resistant to 3 or more antibiotics. Resistance patterns are also described for specific drug classes, like resistance to fluoroquinolones. We also evaluated antibiotic use in this patient population and how antibiotic use varied during the hospitalization. Results There were 640,285 individuals who met the inclusion criteria. Females make up 82% of the study population and 45% were age 65 or older. The most common uropathogen was Escherichia Coli (64.9%) followed by Klebsiella pneumoniae (8.3%), and Proteus mirabilis (5.7%). 22.2% of patients were infected with a multi-drug-resistant pathogen. We found that E. Coli was multi-drug resistant 23.8% of the time; Klebsiella pneumoniae was multi-drug resistant 7.4%; and Proteus mirabilis was multi-drug resistant 2.8%. The most common antibiotics prescribed were ceftriaxone, levofloxacin, and ciprofloxacin. Among patients that were prescribed ceftriaxone, 31.7% of them switched to a different antibiotic during their hospitalization. Patients that were prescribed levofloxacin and ciprofloxacin switched to a different antibiotic 42.8% and 41.5% of the time, respectively. Conclusion E. Coli showed significant multidrug resistance in this population of UTI patients that were hospitalized or treated within the ED, and antibiotic switching is common. Disclosures All Authors: No reported disclosures

scholarly journals Epidemiologic and Microbiologic Characteristics of 28 Hospitalized Patients Cocolonized With Multiple Carbapenem-Resistant Enterobacteriaceae (CRE) in the United States

2020 ◽  
Vol 41 (S1) ◽  
pp. s62-s62
Author(s):  
Timileyin Adediran ◽  
Anthony Harris ◽  
J. Kristie Johnson ◽  
David Calfee ◽  
Loren Miller ◽  
...  
Keyword(s):  
United States ◽  
Secondary Analysis ◽  
Positive Culture ◽  
The United States ◽  
Healthcare Personnel ◽  
Surveillance Culture ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Multicenter Prospective Cohort Study ◽  
Epidemiological Significance

Background: As carbapenem-resistant Enterobacteriaceae (CRE) prevalence increases in the United States, the risk of cocolonization with multiple CRE may also be increasing, with unknown clinical and epidemiological significance. In this study, we aimed to describe the epidemiologic and microbiologic characteristics of inpatients cocolonized with multiple CRE. Methods: We conducted a secondary analysis of a large, multicenter prospective cohort study evaluating risk factors for CRE transmission to healthcare personnel gown and gloves. Patients were identified between January 2016 and June 2019 from 4 states. Patients enrolled in the study had a clinical or surveillance culture positive for CRE within 7 days of enrollment. We collected and cultured samples from the following sites from each CRE-colonized patient: stool, perianal area, and skin. A modified carbapenem inactivation method (mCIM) was used to detect the presence or absence of carbapenemase(s). EDTA-modified CIM (eCIM) was used to differentiate between serine and metal-dependent carbapenemases. Results: Of the 313 CRE-colonized patients enrolled in the study, 28 (8.9%) were cocolonized with at least 2 different CRE. Additionally, 3 patients were cocolonized with >2 different CRE (1.0%). Of the 28 patients, 19 (67.6%) were enrolled with positive clinical cultures. Table 1 summarizes the demographic and clinical characteristics of these patients. The most frequently used antibiotic prior to positive culture was vancomycin (n = 33, 18.3%). Among the 62 isolates from 59 samples from 28 patients cocolonized patients, the most common CRE species were Klebsiella pneumoniae (n = 18, 29.0%), Escherichia coli (n = 10, 16.1%), and Enterobacter cloacae (n = 9, 14.5%). Of the 62 isolates, 38 (61.3%) were mCIM positive and 8 (12.9%) were eCIM positive. Of the 38 mCIM-positive isolates, 33 (86.8%) were KPC positive, 4 (10.5%) were NDM positive, and 1 (2.6%) was negative for both KPC and NDM. Also, 2 E. coli, 1 K. pneumoniae, and 1 E. cloacae were NDM-producing CRE. Conclusion: Cocolonization with multiple CRE occurs frequently in the acute-care setting. Characterizing patients with CRE cocolonization may be important to informing infection control practices and interventions to limit the spread of these organisms, but further study is needed.Funding: NoneDisclosures: None

scholarly journals Population Genomics of American Mink Using Whole Genome Sequencing Data

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 258
Author(s):  
Karim Karimi ◽  
Duy Ngoc Do ◽  
Mehdi Sargolzaei ◽  
Younes Miar
Keyword(s):  
Population Genomics ◽  
Association Studies ◽  
American Mink ◽  
Population History ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Effective Population ◽  
Cross Validation Error

Characterizing the genetic structure and population history can facilitate the development of genomic breeding strategies for the American mink. In this study, we used the whole genome sequences of 100 mink from the Canadian Centre for Fur Animal Research (CCFAR) at the Dalhousie Faculty of Agriculture (Truro, NS, Canada) and Millbank Fur Farm (Rockwood, ON, Canada) to investigate their population structure, genetic diversity and linkage disequilibrium (LD) patterns. Analysis of molecular variance (AMOVA) indicated that the variation among color-types was significant (p < 0.001) and accounted for 18% of the total variation. The admixture analysis revealed that assuming three ancestral populations (K = 3) provided the lowest cross-validation error (0.49). The effective population size (Ne) at five generations ago was estimated to be 99 and 50 for CCFAR and Millbank Fur Farm, respectively. The LD patterns revealed that the average r2 reduced to <0.2 at genomic distances of >20 kb and >100 kb in CCFAR and Millbank Fur Farm suggesting that the density of 120,000 and 24,000 single nucleotide polymorphisms (SNP) would provide the adequate accuracy of genomic evaluation in these populations, respectively. These results indicated that accounting for admixture is critical for designing the SNP panels for genotype-phenotype association studies of American mink.

Food-Borne Disease Outbreaks in the United States, 1973

1975 ◽  
Vol 132 (2) ◽  
pp. 224-228 ◽  
Author(s):  
J. M. Hughes ◽  
M. H. Merson ◽  
R. A. Pollard
Keyword(s):  
United States ◽  
Disease Outbreaks ◽  
The United States ◽  
Food Borne

Military Technology Races

1999 ◽  
Vol 53 (3) ◽  
pp. 537-565 ◽  
Author(s):  
Vally Koubi
Keyword(s):  
United States ◽  
World War Ii ◽  
Soviet Union ◽  
The United States ◽  
Military Technology ◽  
The Soviet Union ◽  
International Distribution ◽  
Strategic Defense ◽  
Distribution Of Power ◽  
The Military

Because of the nature of modern weapons, significant innovations in arms technology have the potential to induce dramatic changes in the international distribution of power. Consider, for example, the “strategic defense initiative” (SDI), a program initiated by the United States in the early 1980s. Had the program been successfully completed, it might have led to a substantial devaluation of Soviet nuclear capabilities and put the United States in a very dominant position. It should not then come as a surprise that interstate rivalry, especially among super powers, often takes the form of a race for technological superiority. Mary Acland-Hood claims that although the United States and the Soviet Union together accounted for roughly half of the world's military expenditures in the early 1980s, their share of world military research and development (R&D) expenditures was about 80 percent. As further proof of the perceived importance of R&D, note that whereas the overall U.S. defense budget increased by 38 percent (from $225.1 billion to $311.6 billion in real terms) from 1981 to 1987, military R&D spending increased by 100 percent (from $20.97 billion to $41.96 billion). Moreover, before World War II military R&D absorbed on average less than 1 percent of the military expenditure of major powers, but since then it has grown to 11–13 percent. The emphasis on military technology is bound to become more pronounced in the future as R&D becomes the main arena for interstate competition.

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