scholarly journals Global genomic population structure of Clostridioides difficile

2019 ◽  
Author(s):  
Martinique Frentrup ◽  
Zhemin Zhou ◽  
Matthias Steglich ◽  
Jan P. Meier-Kolthoff ◽  
Markus Göker ◽  
...  
Keyword(s):  
Hierarchical Clustering ◽  
Global Scale ◽  
Comparative Genomic ◽  
Nucleotide Polymorphisms ◽  
Single Linkage ◽  
The Public ◽  
Bioinformatic Tools ◽  
Clostridioides Difficile ◽  
Recent Transmission ◽  
Public Health Officials

AbstractClostridioides difficile is the primary infectious cause of antibiotic-associated diarrhea. Local transmissions and international outbreaks of this pathogen have been previously elucidated by bacterial whole-genome sequencing, but comparative genomic analyses at the global scale were hampered by the lack of specific bioinformatic tools. Here we introduce EnteroBase, a publicly accessible database (http://enterobase.warwick.ac.uk) that automatically retrieves and assembles C. difficile short-reads from the public domain, and calls alleles for core-genome multilocus sequence typing (cgMLST). We demonstrate that the identification of highly related genomes is 89% consistent between cgMLST and single-nucleotide polymorphisms. EnteroBase currently contains 13,515 quality-controlled genomes which have been assigned to hierarchical sets of single-linkage clusters by cgMLST distances. Hierarchical clustering can be used to identify populations of C. difficile at all epidemiological levels, from recent transmission chains through to pandemic and endemic strains, and is largely compatible with prior ribotyping. Hierarchical clustering thus enables comparisons to earlier surveillance data and will facilitate communication among researchers, clinicians and public-health officials who are combatting disease caused by C. difficile.

scholarly journals A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics

2020 ◽  
Vol 6 (8) ◽  
Author(s):  
Martinique Frentrup ◽  
Zhemin Zhou ◽  
Matthias Steglich ◽  
Jan P. Meier-Kolthoff ◽  
Markus Göker ◽  
...  
Keyword(s):  
Hierarchical Clustering ◽  
Type Species ◽  
Global Scale ◽  
Comparative Genomic ◽  
Polymorphism Analysis ◽  
Genome Sequences ◽  
Single Linkage ◽  
Content Type ◽  
Link Type ◽  
Clostridioides Difficile

Clostridioides difficile is the primary infectious cause of antibiotic-associated diarrhea. Local transmissions and international outbreaks of this pathogen have been previously elucidated by bacterial whole-genome sequencing, but comparative genomic analyses at the global scale were hampered by the lack of specific bioinformatic tools. Here we introduce a publicly accessible database within EnteroBase (http://enterobase.warwick.ac.uk) that automatically retrieves and assembles C. difficile short-reads from the public domain, and calls alleles for core-genome multilocus sequence typing (cgMLST). We demonstrate that comparable levels of resolution and precision are attained by EnteroBase cgMLST and single-nucleotide polymorphism analysis. EnteroBase currently contains 18 254 quality-controlled C. difficile genomes, which have been assigned to hierarchical sets of single-linkage clusters by cgMLST distances. This hierarchical clustering is used to identify and name populations of C. difficile at all epidemiological levels, from recent transmission chains through to epidemic and endemic strains. Moreover, it puts newly collected isolates into phylogenetic and epidemiological context by identifying related strains among all previously published genome data. For example, HC2 clusters (i.e. chains of genomes with pairwise distances of up to two cgMLST alleles) were statistically associated with specific hospitals (P<10−4) or single wards (P=0.01) within hospitals, indicating they represented local transmission clusters. We also detected several HC2 clusters spanning more than one hospital that by retrospective epidemiological analysis were confirmed to be associated with inter-hospital patient transfers. In contrast, clustering at level HC150 correlated with k-mer-based classification and was largely compatible with PCR ribotyping, thus enabling comparisons to earlier surveillance data. EnteroBase enables contextual interpretation of a growing collection of assembled, quality-controlled C. difficile genome sequences and their associated metadata. Hierarchical clustering rapidly identifies database entries that are related at multiple levels of genetic distance, facilitating communication among researchers, clinicians and public-health officials who are combatting disease caused by C. difficile .

scholarly journals From Isolation to Containment: Perceived Fear of Infectivity and Protective Behavioral Changes during the COVID-19 Vaccination Campaign

2021 ◽  
Vol 18 (12) ◽  
pp. 6503
Author(s):  
Arielle Kaim ◽  
Maya Siman-Tov ◽  
Eli Jaffe ◽  
Bruria Adini
Keyword(s):  
Vaccination Campaign ◽  
Cross Sectional Study ◽  
Protective Behavior ◽  
Cross Sectional ◽  
Social Distancing ◽  
The Public ◽  
The Road ◽  
Israeli Population ◽  
Study Results ◽  
Public Health Officials

In the ongoing COVID-19 pandemic, maintenance of protective behavior is a continued challenge in the effort to contain the spread of the virus. A cross-sectional study via an internet questionnaire was utilized to elucidate changes in compliance to protective behavior among the Israeli population (n = 1120), after the beginning of the vaccination campaign. Comparison was made between individuals who were previously infected with the virus, those who received one dose of inoculation with the vaccine, and individuals that were neither infected or vaccinated. The study results indicate that those who were previously infected with the COVID-19 virus were less careful about mask wearing (18.8%) and social distancing (29.7%), as compared to the other examined groups (regarding mask wearing, 8.2% and 11.6% respectively, and with regard to social distancing 12.8% and 19.2%) and may require targeted risk communication campaigns to address this population. Furthermore, the study revealed that those that were non-Jewish (as compared to Jewish study counterparts) or that were older (19+) were more vigilant in their protective behavior (29.6% vs. 11.2% respectively for social distancing and 29.6% vs. 11.1% respectively for mask wearing). Despite a successful initial vaccination campaign in Israel, public health officials need to engage all members of the public to unremittingly observe compliance to directed health guidelines, to ensure that the results of previous governmental efforts in fighting the pandemic (such as lockdowns) will be effectively sustained, and the road to containment will be hastened.

scholarly journals Transmission of Multidrug/Rifampicin-Resistant Mycobacterium Tuberculosis in Chongqing, China: A Retrospective Observational Study Using Whole-Genome Sequencing

2021 ◽  
Author(s):  
Bing Zhao ◽  
Chunfa Liu ◽  
Jiale Fan ◽  
Aijing Ma ◽  
Wencong He ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Resistance Mutations ◽  
Treatment Information ◽  
Recent Transmission ◽  
Drugs Analysis ◽  
Lineage 2 ◽  
And Cluster Analysis

Abstract Background: Multidrug/rifampicin-resistant tuberculosis (MDR/RR-TB) is a global barrel for ‘Stop TB plan’. China has the second highest MDR/RR-TB burden in whole world wide. Understanding the transmission dynamic is facilitated for disease control. Methods: Whole genome sequencing (WGS) data from patients of Chongqing tuberculosis control institute were used for phylogenetic classifications, resistance predictions, and cluster analysis as indicator for recent transmission (RT). Factors associated with MDR/RR-TB were defined by a logistic regression model. Results: A total of 223 cases of MDR/RR-TB were recorded between Jan 1, 2018 and Dec 31, 2020, and 200 cases obtained relevant treatment information. The patients who are older than 55 year old were more likely to suffering from death. 178 MDR/RR strains were obtained WGS data, 152 were classified as lineage 2 strains. 80 (44.9%, 80 of 178) strains were in 20 genomic clusters that differed by 12 or fewer single nucleotide polymorphisms (SNPs), indicating RT. Patients who were infected with lineage 2 strains is a significant factor driving the epidemic towards MDR/RR-TB. Resistance mutations of first-line tuberculosis drugs analysis found that 79 (98.8%) of all 80 strains defined as RT have same mutations among each clusters totally. 55% (44 of 80) of the MDR/RR-TB strains accumulated additional drug resistance mutations along the transmission chain, especially fluoroquinolones (FQs) (63.6%, 28 of 44). Conclusions: The age is the most significant factor that causes death of MDR/RR-TB patients. RT of MDR/RR strains is not only drove the MDR/RR-TB epidemic, but also accumulated more serious resistance along the transmission chains.

scholarly journals A Fresh Apple or a New Barrel: Business Ethics from an Individual to Corporate Level

2017 ◽  
Vol 8 (1) ◽  
pp. 8
Author(s):  
Sibel Oktar Thomas
Keyword(s):  
Business Ethics ◽  
Human Nature ◽  
Boards Of Directors ◽  
Ethical Issues ◽  
Holistic Approach ◽  
Codes Of Ethics ◽  
Global Scale ◽  
Economic Effects ◽  
The Public ◽  
Purpose Of Business

The moral nature of corporations has been discussed for a long time. But, since 2001, with enormous economic effects of the misconduct of some corporations this discussion gained another dimension, it moved into the public sphere, the subject became more sensitive. The anger and mistrust of the public toward business triggered legislators and corporations to take urgent action. For example, just after the collapse of Enron (2001) the American Congress passed the Sarbanes-Oxley Act (2002) that covers the responsibilities of boards of directors and requires compliance training at all levels. It also revived the old controversial arguments about the nature of business – whether the only purpose of business is to make profits, the relationship of business and ethics – whether business ethics is an oxymoron, and human nature – whether it is ‘bad apples’ or ‘bad barrels’. Yet, with new sets of regulations, in 2017, we are still witnessing the misconduct of corporations on a global scale. This article investigates the effectiveness of corporate efforts such as revisiting mission statements, polishing the codes of ethics and conducting training, by evaluating the nature of business, human nature and the understanding of ethics in the workplace. By looking through the lens of utilitarianism of ethical issues in business, I will argue that codes of ethics and ethics training are necessary but not sufficient. Within the scope of this paper I wish to pave the way to a holistic approach which is necessary and sufficient to create ethical businesses.

scholarly journals The Public Choice View at the “Deregulation” Movement: Analyzing the Experience of European Telecommunications

2019 ◽  
Vol 11 (1) ◽  
pp. 1-22
Author(s):  
Dimitrii Trubnikov
Keyword(s):  
Public Choice ◽  
Public Interest ◽  
Choice Theory ◽  
Current Trend ◽  
Telecommunications Industry ◽  
Global Scale ◽  
Open Market ◽  
The Real ◽  
The Public ◽  
Private Corporations

Purpose – The liberalization of European telecommunications has been expressed in highly concentrated markets with several major players at the pan-European level. Instead of fostering competitive marketplaces, the reform has created an oligopolistic landscape with powerful private corporations. This induces reasonable questions about the real objectives and the chosen ways of the reform. Methodology/approach/design – The deregulatory movement in the telecommunications sector is analyzed through contrasting perspectives of the public interest approach and public choice theory. Findings – The chance to change the landscape of the industry has been missed, and the current trend towards the global oligopolistic marketplace yields an unprecedented amount of economic power to narrow groups at the global scale. The liberalization movement introduced market mechanisms in the industry, but the real free and open market has never been formed, and it is possible to assert that it has never been among the real objectives and intentions of the policymakers. Originality/value – The recent surge of “liberalization” in the telecommunications industry speaks rather in favor of the hypothesis of vested private interests in the policy and that they have always been greatly covered by the sauce of public interest justifications. The case of telecommunications shows that ideas and understanding of economic phenomena played an important role in adoption of regulatory regimes, and it is apparent that people on the top of the social pyramid have opportunities to pick up and foster those ideas that better fit their private needs.

scholarly journals Unravelling A Regulation Machine

2018 ◽  
Vol 7 (1) ◽  
pp. 86-98
Author(s):  
Dionysia Mylonaki ◽  
Panagiotis Tigas
Keyword(s):  
Public Discourse ◽  
Fundamental Problem ◽  
Global Scale ◽  
Technical Aspect ◽  
Current Approach ◽  
Fake News ◽  
Public Attention ◽  
The Public ◽  
Machine Leraning

Computational censorship in the form of fake news and toxic comments regulation is a subject that comes up quite often in the public discourse, as a result of the volatile political circumstances on a global scale and due to the unquestionable impact of journalism on these circumstances. Public attention has been directed to the role of mainstream and other media in the formation of public opinion, either in the form of articles or in the form of usergenerated comments. The purpose is to analyse and allow a deeper understanding of a project that is under development, namely, computational-censorship and to show that algorithmic regulation is not a solution, but rather another layer to a more fundamental problem. This article examines the implicationsof developing Machine Leraning/Artificial Iintelligence (ML/AI) which aims to regulate the internet and we attempt to allow a glimpse into the technical aspect of the problem as a way to back arguments that could be re-jected by the ML/AI research community as “non-pragmatic”. Finally, it aims to highlight the absurdity of the current approach to research in this area, which is the exact opposite of the rationalism that the field claims to be embracing.

The Challenge of Climate Change

2017 ◽  
Author(s):  
Mario J. Molina ◽  
Adolfo Plasencia
Keyword(s):  
Climate Change ◽  
Nobel Prize Winner ◽  
Global Scale ◽  
Ozone Layer ◽  
Decision Makers ◽  
The Public ◽  
Continuous Release ◽  
It Education ◽  
Industrial Compounds ◽  
And Training

In this conversation, Nobel Prize winner Mario J. Molina reflects on the ethical side of science. He explains how several decades ago, together with the scientist F. Sherwood Rowland, he predicted that human activity was endangering the ozone layer. They discovered the mechanisms which could bring about the destruction of the layer due to the continuous release of industrial compounds, such as the so-called chlorofluorocarbons (CFCs), into the atmosphere. Professor Molina relates how the issue with the ozone layer was the first example of a problem on a truly global scale for science and, as such, had to be tackled, because without the ozone layer, life on our planet would not have evolved as we know it. Education and training are proving a great help with how the present challenge of stopping or mitigating the daunting problem of global warming should be approached. In the dialogue, different courses of action for persuading both decision-makers and the public are proposed. It is however proving rather difficult to achieve and something which, according to Professor Molina, is also related to education.

scholarly journals Municipal public health officials and the Public Health Act

2016 ◽  
Vol 1 ◽  
Author(s):  
Heidi Lyshol
Keyword(s):  
Public Health ◽  
Health Workers ◽  
Relevant Literature ◽  
Vocational Teachers ◽  
The Public ◽  
New Public Health ◽  
New Public ◽  
Public Health Officials ◽  
Public Health Workers ◽  
Public Health Act

Introduction: The Norwegian Public Health Act of 2012 was intended to give the municipalities a bigger stake in the health of the population by emphasizing public health at a municipal level. The aim of this study was to investigate the effects of the Act on public health officials in the execution of their vocational roles.Research questions: How do public health officials in Norwegian municipalities balance the requirements of the new Public Health Act and what their local leaders, both politicians and bureaucrats, want? How do they use the Act in the performance of their vocational roles? Does this have any relevance for vocational teachers? Method :After a literature search, semi-formal interviews were conducted with 13 municipal public health officials who were also given practical tasks and short questionnaires. The interview transcripts were analysed using Thematic Analysis. This qualitative research technique is defined and described. Discussion and Results: The study shows that the public health workers see the Act as a useful tool and actively use it to leverage the public health field into greater importance. They feel that the Act is empowering, gives them greater pride in their work, and that it helps both them and their superiors to achieve greater understanding of public health workers’ roles in their municipalities. Using the informants’ own words, changes in the municipal public health workers’ roles and vocational self-definitions are discussed in the context of the new Act and selections from the relevant literature. Conclusion: The Public Health Act has changed the roles of municipal public health workers and helped them to further public health by giving them more responsibility and expanded their duty to safeguard health in all policies. The Act is seen as empowering, giving public health professionals pride in their work and greater role understanding, and should be heavily featured in the curriculum of future public health workers.

scholarly journals Utility of Routine Genomic Sequencing for Infection Control Surveillance

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S35-S35
Author(s):  
Richard T Ellison ◽  
Andrew Hoss ◽  
Jomol Mathew ◽  
Jeff Halperin ◽  
Brian Gross ◽  
...  
Keyword(s):  
Infection Control ◽  
Medical Center ◽  
Academic Medical Center ◽  
Microbial Pathogens ◽  
Genomic Sequencing ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Philips Healthcare ◽  
Recent Transmission ◽  
Research Grant

Abstract Background Recent work indicates that comprehensive genomic sequencing can be a highly effective tool in defining the transmission of microbial pathogens. We have studied the utility of the routine use of genomic sequencing for infection control surveillance in an academic medical center. Methods The genomes of inpatient and emergency department isolates of Staphylococcus aureus, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Enterococcus faecium were sequenced. Within each species, single-nucleotide polymorphisms (SNP) were identified in the core genome for all isolates using alignment-based methods. The number of SNP differences between isolate pairs was determined and used, in combination with the patient’s electronic medical records to identify potential transmission events. Results Between September 2016 and March 2017, 388 S. aureus, 66 P. aeruginosa, 48 K. pneumoniae, and 29 E. faecium isolates were sequenced from 373 patients. There was variation in the distribution of SNP differences between intrapatient isolates for the four pathogens; with the least variability for E. faecium and greatest for P. aeruginosa. The majority of the bacterial isolates from separate patients appeared to be genetically unique exhibiting marked SNP differences from other isolates. There were 19 sets of isolates where the SNP variation between interpatient isolates was either comparable to that of intrapatient variation (12) and suggestive of recent transmission events, or with SNP variation somewhat greater than the intrapatient SNP variation (7) suggesting relative relatedness. Only one of the highly related sets had been previously identified by standard infection control surveillance. Likely transmissions appeared to have occurred both in the inpatient and outpatient settings, and the transmission routes were not always apparent. Conclusion The routine use of genomic sequencing analysis identified previously unrecognized likely transmission events within the institution’s patient population that are of relevance to infection control surveillance. This capacity should significantly enhance our understanding of the epidemiology of hospital acquired infections, and assist in developing and implementing new prevention strategies. Disclosures R. T. Ellison III, Philips Healthcare: Consultant and Grant Investigator, Consulting fee and Research grant; A. Hoss, Philips: Employee, Salary; J. Mathew, Philips Healthcare: Investigator, Research grant; J. Halperin, Philips Healthcare: Employee and Shareholder, Salary; B. Gross, Philips: Employee and Shareholder, Salary; D. V. Ward, Philips Healthcare: Consultant, Investigator and Research Contractor, Consulting fee, Research support and Salary

Public health challenges during the COVID-19 outbreak in Nepal: a commentary

2020 ◽  
Vol 34 (4) ◽  
pp. 373-376 ◽  
Author(s):  
Sharmistha Sharma ◽  
Jeevan Bhatta
Keyword(s):  
Public Health ◽  
Design Methodology ◽  
Health Workers ◽  
Health Interventions ◽  
Content Type ◽  
The Public ◽  
Public Health Challenges ◽  
Current Scenario ◽  
Public Health Officials ◽  
The Government

PurposeThe purpose of this paper is to depict the current scenario of coronavirus diseases 2019 (COVID-19) in Nepal, how the government is tackling this pandemic as well as look at the public health challenges that Nepal is facing and might face in the future.Design/methodology/approachThis paper is a viewpoint of COVID-19 activities conducted in Nepal.FindingsNepal is vulnerable to COVID-19, as it shares borders with China and India. Cases have started to be seen in different parts of Nepal. Government of Nepal has started various measures to control the spread of the virus such as deploying health workers, information sharing via different mediums. However, there are still many challenges that the government and public health officials need to be concerned about as well.Originality/valueThis paper provides information about the situation of COVID-19 in Nepal, how the government is handling, and public health challenges that may arise. This paper can be beneficial for further public health interventions.

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