scholarly journals Large-scale assessment of antimicrobial resistance marker databases for genetic phenotype prediction: a systematic review

2020 ◽  
Vol 75 (11) ◽  
pp. 3099-3108
Author(s):  
Norhan Mahfouz ◽  
Inês Ferreira ◽  
Stephan Beisken ◽  
Arndt von Haeseler ◽  
Andreas E Posch
Keyword(s):  
Antimicrobial Resistance ◽  
Clinical Microbiology ◽  
Large Scale ◽  
Diagnostic Testing ◽  
Error Rates ◽  
Systematic Evaluation ◽  
Large Scale Assessment ◽  
Performance Requirements ◽  
Public Repositories ◽  
The Right

Abstract Background Antimicrobial resistance (AMR) is a rising health threat with 10 million annual casualties estimated by 2050. Appropriate treatment of infectious diseases with the right antibiotics reduces the spread of antibiotic resistance. Today, clinical practice relies on molecular and PCR techniques for pathogen identification and culture-based antibiotic susceptibility testing (AST). Recently, WGS has started to transform clinical microbiology, enabling prediction of resistance phenotypes from genotypes and allowing for more informed treatment decisions. WGS-based AST (WGS-AST) depends on the detection of AMR markers in sequenced isolates and therefore requires AMR reference databases. The completeness and quality of these databases are material to increase WGS-AST performance. Methods We present a systematic evaluation of the performance of publicly available AMR marker databases for resistance prediction on clinical isolates. We used the public databases CARD and ResFinder with a final dataset of 2587 isolates across five clinically relevant pathogens from PATRIC and NDARO, public repositories of antibiotic-resistant bacterial isolates. Results CARD and ResFinder WGS-AST performance had an overall balanced accuracy of 0.52 (±0.12) and 0.66 (±0.18), respectively. Major error rates were higher in CARD (42.68%) than ResFinder (25.06%). However, CARD showed almost no very major errors (1.17%) compared with ResFinder (4.42%). Conclusions We show that AMR databases need further expansion, improved marker annotations per antibiotic rather than per antibiotic class and validated multivariate marker panels to achieve clinical utility, e.g. in order to meet performance requirements such as provided by the FDA for clinical microbiology diagnostic testing.

scholarly journals Multimodal access control system combining RFID, fingerprint and facial recognition

2020 ◽  
Vol 20 (1) ◽  
pp. 405
Author(s):  
Mohamed El Beqqal ◽  
Mostafa Azizi ◽  
Jean Louis Lanet
Keyword(s):  
Large Scale ◽  
Facial Recognition ◽  
Recognition Rate ◽  
Error Rates ◽  
Identification System ◽  
Effective Measure ◽  
Acceptance Ratio ◽  
Performance Requirements ◽  
Biometric Systems ◽  
Access Control System

<span>Monomodal biometry does not constitute an effective measure to meet the desired performance requirements for large-scale applications, due to limita-tions such as noisy data, restricted degree of freedom and unacceptable error rates. Some of these problems can be solved through multimodal biometric systems that involve using a combination of two or more biometric modali-ties in a single identification system. Identification based on multiple biomet-rics represents an emerging trend. The reason for combining different modal-ities is to improve the recognition rate. In practice, multi-biometric aims to reduce the False Acceptance Ratio (FAR) and False Rejection Ratio (FRR) which are two standard metrics widely used in the accuracy of biometric sys-tems. In this paper, we will examine the different possible scenario in multi-modal biometric systems using RFID, fingerprint and facial recognition, that can be adopted to merge information and improve the overall accuracy of the system.</span>

scholarly journals Establishing Genotypic Cutoff Values To Measure Antimicrobial Resistance in Salmonella

2016 ◽  
Vol 61 (3) ◽  
Author(s):  
Gregory H. Tyson ◽  
Shaohua Zhao ◽  
Cong Li ◽  
Sherry Ayers ◽  
Jonathan L. Sabo ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Large Scale ◽  
Acquired Resistance ◽  
Resistance Mechanisms ◽  
Wild Type ◽  
Content Type ◽  
Phenotypic Resistance ◽  
Large Scale Assessment ◽  
Resistance Determinants ◽  
Cutoff Values

ABSTRACT Whole-genome sequencing (WGS) has transformed our understanding of antimicrobial resistance, helping us to better identify and track the genetic mechanisms underlying phenotypic resistance. Previous studies have demonstrated high correlations between phenotypic resistance and the presence of known resistance determinants. However, there has never been a large-scale assessment of how well resistance genotypes correspond to specific MICs. We performed antimicrobial susceptibility testing and WGS of 1,738 nontyphoidal Salmonella strains to correlate over 20,000 MICs with resistance determinants. Using these data, we established what we term genotypic cutoff values (GCVs) for 13 antimicrobials against Salmonella. For the drugs we tested, we define a GCV as the highest MIC of isolates in a population devoid of known acquired resistance mechanisms. This definition of GCV is distinct from epidemiological cutoff values (ECVs or ECOFFs), which currently differentiate wild-type from non-wild-type strains based on MIC distributions alone without regard to genetic information. Due to the large number of isolates involved, we observed distinct MIC distributions for isolates with different resistance gene alleles, including for ciprofloxacin and tetracycline, suggesting the potential to predict MICs based on WGS data alone.

scholarly journals How to choose the right real-time RT-PCR primer sets for the SARS-CoV-2 genome detection? 

2020 ◽  
Author(s):  
Ahalieyah Anantharajah ◽  
Raphael Helaers ◽  
Jean-Philippe Defour ◽  
Nathalie Olive ◽  
Florence Kabera ◽  
...  
Keyword(s):  
World Health Organization ◽  
Large Scale ◽  
Diagnostic Testing ◽  
Detection Sensitivity ◽  
World Health ◽  
Coding Region ◽  
Viral Loads ◽  
The World ◽  
Health Organization ◽  
The Right

Abstract The SARS-CoV-2 pandemic has created an unprecedented need for rapid large-scale diagnostic testing. Currently, several quantitative reverse-transcription polymerase chain reaction (RT-qPCR) assays recommended by the World Health Organization are being used by clinical and public health laboratories and typically target regions of the RNA-dependent RNA polymerase (RdRp), envelope (E) and nucleocapsid (N) coding region. However, it is currently unclear if results from different tests are comparable. The present study demonstrates substantial differences in SARS-CoV-2 RNA detection sensitivity among the primer/probe sets recommended by the World Health Organization especially for low-level viral loads. The alignment of thousands of European SARS-CoV-2 sequences against the primers/probe highlights single mismatches which might also contribute to false negatives. An understanding of the limitations depending on the targeted genes and primer/probe sets may influence the selection of molecular detection assays by clinical laboratories.

Using Web-based Testing for Large-Scale Assessment

2013 ◽  
Author(s):  
Laura S. Hamilton ◽  
Stephen P. Klein ◽  
William Lorie
Keyword(s):  
Large Scale ◽  
Web Based ◽  
Large Scale Assessment ◽  
Scale Assessment

Optical Scanning for Large-Scale Studies

1975 ◽  
Vol 14 (01) ◽  
pp. 32-34
Author(s):  
Elisabeth Schach
Keyword(s):  
Large Scale ◽  
Error Rates ◽  
Data Reporting ◽  
Reading Error ◽  
Optical Scanning ◽  
Rejection Rates

Data reporting the experience with an optical mark page reader is presented (IBM 1231Ν1). Information from 52,000 persons was gathered in seven countries, decentrally coded and centrally processed. Reader performance rates (i.e. sheets read per hour, sheet rejection rates, reading error rates) and costs (coding, verification, reading, etc.) are given.

Why Has There Been No People’s Power Rebellion in North Korea?

2018 ◽  
pp. 1-34
Author(s):  
Andrew Jackson
Keyword(s):  
Rural Areas ◽  
North Korea ◽  
Large Scale ◽  
Political Elite ◽  
Information Control ◽  
Al Jazeera ◽  
The North ◽  
New Information ◽  
Effective System ◽  
The Right

One scenario put forward by researchers, political commentators and journalists for the collapse of North Korea has been a People’s Power (or popular) rebellion. This paper analyses why no popular rebellion has occurred in the DPRK under Kim Jong Un. It challenges the assumption that popular rebellion would happen because of widespread anger caused by a greater awareness of superior economic conditions outside the DPRK. Using Jack Goldstone’s theoretical expla-nations for the outbreak of popular rebellion, and comparisons with the 1989 Romanian and 2010–11 Tunisian transitions, this paper argues that marketi-zation has led to a loosening of state ideological control and to an influx of infor-mation about conditions in the outside world. However, unlike the Tunisian transitions—in which a new information context shaped by social media, the Al-Jazeera network and an experience of protest helped create a sense of pan-Arab solidarity amongst Tunisians resisting their government—there has been no similar ideology unifying North Koreans against their regime. There is evidence of discontent in market unrest in the DPRK, although protests between 2011 and the present have mostly been in defense of the right of people to support themselves through private trade. North Koreans believe this right has been guaranteed, or at least tacitly condoned, by the Kim Jong Un government. There has not been any large-scale explosion of popular anger because the state has not attempted to crush market activities outright under Kim Jong Un. There are other reasons why no popular rebellion has occurred in the North. Unlike Tunisia, the DPRK lacks a dissident political elite capable of leading an opposition movement, and unlike Romania, the DPRK authorities have shown some flexibility in their anti-dissent strategies, taking a more tolerant approach to protests against economic issues. Reduced levels of violence during periods of unrest and an effective system of information control may have helped restrict the expansion of unrest beyond rural areas.

White Backlash

2015 ◽  
Author(s):  
Marisa Abrajano ◽  
Zoltan L. Hajnal
Keyword(s):  
Ethnic Diversity ◽  
Republican Party ◽  
Large Scale ◽  
White Americans ◽  
Political Beliefs ◽  
White Backlash ◽  
Political Spectrum ◽  
Racial Divide ◽  
The Right ◽  
Political Backlash

This book provides an authoritative assessment of how immigration is reshaping American politics. Using an array of data and analysis, it shows that fears about immigration fundamentally influence white Americans' core political identities, policy preferences, and electoral choices, and that these concerns are at the heart of a large-scale defection of whites from the Democratic to the Republican Party. The book demonstrates that this political backlash has disquieting implications for the future of race relations in America. White Americans' concerns about Latinos and immigration have led to support for policies that are less generous and more punitive and that conflict with the preferences of much of the immigrant population. America's growing racial and ethnic diversity is leading to a greater racial divide in politics. As whites move to the right of the political spectrum, racial and ethnic minorities generally support the left. Racial divisions in partisanship and voting, as the book indicates, now outweigh divisions by class, age, gender, and other demographic measures. The book raises critical questions and concerns about how political beliefs and future elections will change the fate of America's immigrants and minorities, and their relationship with the rest of the nation.

Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects

2020 ◽  
Author(s):  
Christina Schindler ◽  
Hannah Baumann ◽  
Andreas Blum ◽  
Dietrich Böse ◽  
Hans-Peter Buchstaller ◽  
...  
Keyword(s):  
Free Energy ◽  
Drug Discovery ◽  
Large Scale ◽  
Active Drug ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculation ◽  
Large Scale Assessment ◽  
New Public ◽  
Binding Free Energy Calculations

Here we present an evaluation of the binding affinity prediction accuracy of the free energy calculation method FEP+ on internal active drug discovery projects and on a large new public benchmark set.<br>

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