scholarly journals Comparison of de-duplication methods used by WHO Global Antimicrobial Resistance Surveillance System (GLASS) and Japan Nosocomial Infections Surveillance (JANIS) in the surveillance of antimicrobial resistance

2020 ◽  
Author(s):  
Toshiki Kajihara ◽  
Koji Yahara ◽  
John Stelling ◽  
Sergey Romualdovich Eremin ◽  
Barbara Tornimbene ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Nosocomial Infections ◽  
Surveillance System ◽  
Bacterial Species ◽  
World Health ◽  
Surveillance Period ◽  
E Coli ◽  
Specimen Type ◽  
Antimicrobial Resistance Surveillance ◽  
Number Of Patients

AbstractA major issue in the surveillance of antimicrobial resistance (AMR) is “de-duplication” or removal of repeated isolates, for which there exist multiple methods. The World Health Organization (WHO) Global Antimicrobial Resistance Surveillance System (GLASS) requires de-duplication by selecting only the first isolate of a given bacterial species per patient per surveillance period per specimen type per age group, gender, and infection origin stratification. However, no study on the comparative application of this method has been reported. The objective of this study was to evaluate differences in data tabulation between the WHO GLASS and the Japan Nosocomial Infections Surveillance (JANIS) system, which counts both patients and isolates after removing repeated isolates of the same bacterial species per multiresistance phenotype isolated from a patient within 30 days, regardless of specimen type. All bacterial data, consisting of approximately 8 million samples from 1795 Japanese hospitals in 2017 were exported from the JANIS database, and were tabulated using either the de-duplication algorithm of GLASS, or JANIS. We compared the tabulated results of the total number of patients whose blood and urine cultures were taken and of the percentage of resistant isolates of Escherichia coli for each priority antibiotic. The number of patients per specimen type tabulated by the JANIS method was always smaller than that of GLASS. There was a small (< 3%) difference in the percentage of resistance of E. coli for any antibiotic between the two methods in both out- and inpatient settings and blood and urine isolates. The two tabulation methods did not show considerable differences in terms of the tabulated percentages of resistance for E. coli. We further discuss how the use of GLASS tabulations to create a public software and website that could help to facilitate the understanding of and treatment against AMR.

scholarly journals Quality Assessment of an Antimicrobial Resistance Surveillance System in a Province of Nepal

2021 ◽  
Vol 6 (2) ◽  
pp. 60
Author(s):  
Jyoti Acharya ◽  
Maria Zolfo ◽  
Wendemagegn Enbiale ◽  
Khine Wut Yee Kyaw ◽  
Meika Bhattachan ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Surveillance System ◽  
Surveillance Data ◽  
World Health ◽  
Cross Sectional ◽  
Antimicrobial Resistance Surveillance ◽  
Data Collection Process ◽  
Data Compilation ◽  
Site Variation ◽  
Health Organization

Antimicrobial resistance (AMR) is a global problem, and Nepal is no exception. Countries are expected to report annually to the World Health Organization on their AMR surveillance progress through a Global Antimicrobial Resistance Surveillance System, in which Nepal enrolled in 2017. We assessed the quality of AMR surveillance data during 2019–2020 at nine surveillance sites in Province 3 of Nepal for completeness, consistency, and timeliness and examined barriers for non-reporting sites. Here, we present the results of this cross-sectional descriptive study of secondary AMR data from five reporting sites and barriers identified through a structured questionnaire completed by representatives at the five reporting and four non-reporting sites. Among the 1584 records from the reporting sites assessed for consistency and completeness, 77–92% were consistent and 88–100% were complete, with inter-site variation. Data from two sites were received by the 15th day of the following month, whereas receipt was delayed by a mean of 175 days at three other sites. All four non-reporting sites lacked dedicated data personnel, and two lacked computers. The AMR surveillance data collection process needs improvement in completeness, consistency, and timeliness. Non-reporting sites need support to meet the specific requirements for data compilation and sharing.

scholarly journals Establishment of the South Korean national antimicrobial resistance surveillance system, Kor-GLASS, in 2016

2018 ◽  
Vol 23 (42) ◽  
Author(s):  
Hyukmin Lee ◽  
Eun-Jeong Yoon ◽  
Dokyun Kim ◽  
Seok Hoon Jeong ◽  
Jong Hee Shin ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Surveillance System ◽  
Action Plan ◽  
World Health ◽  
Surveillance Systems ◽  
The South ◽  
South Korean ◽  
Antimicrobial Resistance Surveillance ◽  
The Status ◽  
Health Organization

Surveillance plays a pivotal role in overcoming antimicrobial resistance (AMR) in bacterial pathogens, and a variety of surveillance systems have been set up and employed in many countries. In 2015, the World Health Organization launched the Global Antimicrobial Resistance Surveillance System (GLASS) as a part of the global action plan to enhance national and global surveillance and research. The aims of GLASS are to foster development of national surveillance systems and to enable collection, analysis and sharing of standardised, comparable and validated data on AMR between different countries. The South Korean AMR surveillance system, Kor-GLASS, is compatible with the GLASS platform and was established in 2016 and based on the principles of representativeness, specialisation, harmonisation and localisation. In this report, we summarise principles and processes in order to share our experiences with other countries planning to establish a national AMR surveillance system. The pilot operation of Kor-GLASS allowed us to understand the national burden of specific infectious diseases and the status of bacterial AMR. Issues pertaining to high costs and labour-intensive operation were raised during the pilot, and improvements are being made.

scholarly journals Factors Obscuring the Role of E. coli from Domestic Animals in the Global Antimicrobial Resistance Crisis: An Evidence-Based Review

2020 ◽  
Vol 17 (9) ◽  
pp. 3061 ◽  
Author(s):  
Fernanda Loayza ◽  
Jay P. Graham ◽  
Gabriel Trueba
Keyword(s):  
Antimicrobial Resistance ◽  
Bacterial Species ◽  
Leading Edge ◽  
Domestic Animals ◽  
World Health ◽  
Clinical Settings ◽  
Key Factors ◽  
Animal Products ◽  
E Coli ◽  
Health Organization

Recent studies have found limited associations between antimicrobial resistance (AMR) in domestic animals (and animal products), and AMR in human clinical settings. These studies have primarily used Escherichia coli, a critically important bacterial species associated with significant human morbidity and mortality. E. coli is found in domestic animals and the environment, and it can be easily transmitted between these compartments. Additionally, the World Health Organization has highlighted E. coli as a “highly relevant and representative indicator of the magnitude and the leading edge of the global antimicrobial resistance (AMR) problem”. In this paper, we discuss the weaknesses of current research that aims to link E. coli from domestic animals to the current AMR crisis in humans. Fundamental gaps remain in our understanding the complexities of E. coli population genetics and the magnitude of phenomena such as horizontal gene transfer (HGT) or DNA rearrangements (transposition and recombination). The dynamic and intricate interplay between bacterial clones, plasmids, transposons, and genes likely blur the evidence of AMR transmission from E. coli in domestic animals to human microbiota and vice versa. We describe key factors that are frequently neglected when carrying out studies of AMR sources and transmission dynamics.

scholarly journals Trends in antimicrobial resistance in Europe: update of EARSS results

2007 ◽  
Vol 12 (11) ◽  
Author(s):  
M De Kraker ◽  
N Van de Sande-Bruinsma
Keyword(s):  
Antimicrobial Resistance ◽  
Antimicrobial Susceptibility ◽  
Surveillance System ◽  
Bacterial Species ◽  
Susceptibility Test ◽  
Test Results ◽  
Antimicrobial Susceptibility Test ◽  
The Past ◽  
Antimicrobial Resistance Surveillance

For the past seven years (1999 to 2006), the European Antimicrobial Resistance Surveillance System (EARSS) has collected antimicrobial susceptibility test results of invasive isolates in humans of seven bacterial species that serve as indicators for the development of antimicrobial resistance in Europe.

scholarly journals Evaluation of Emerging Antimicrobials Resistance in nosocomial infections caused by E. coli: The comparison results of observed cases and compartmental model

2021 ◽  
Author(s):  
mohammad kogani ◽  
babak eshrati ◽  
hamid reza baradaran ◽  
leila janani ◽  
mahshid nasehii
Keyword(s):  
Nosocomial Infections ◽  
Compartmental Model ◽  
Study Data ◽  
World Health ◽  
E Coli ◽  
Time Period ◽  
Comparison Results ◽  
Number Of Patients ◽  
Health Organization ◽  
The University

Abstract Background Early detection of Antimicrobials Resistance outbreaks is one of the most important goals of the World Health Organization. In this study, by comparing the observed cases of resistance with its expected cases, the outbreak of these resistances was investigated. It should be noted that this subject was not done in the country until the time of the study. Methods This study is a hospital-based study. Data related to all the university general of Iran (57 hospitals) were used. In these hospitals, all the patients who were infected by E.coli in time period of March 21 2017 to March 20 2018 were enrolled in the study. Then, using an index called the SIR; the observed cases of resistant E.coli were compared with the expected ones. This index is achieved from dividing the observed cases by its expected cases. If the obtained number is greater than one, it indicates the greater observed cases rather than the expected cases, which can represent Emerging. In order to compute SIR index, we divided the number of observed cases of Antimicrobials Resistance E.coli by the number of expected cases of each Antimicrobials Resistance E coli. To predict the expected cases of each Antimicrobials Resistance E coli, we developed one compartmental model. In this model, the number of patients is estimated using equations. Berkeley Madonna version 8.3.23 software was used to manipulate these equations. Results The SIR index for E.coli resistant to Ampicillin, Ceftazidime and Colistin were 1.2(1.1–1.3), 1.1(1.02–1.2) and 1.7(1.02–2.3) respectively. This index for E.coli resistant to Meropenem was .8 (.6-.9). In other cases, the calculated index was not statistically significant. Conclusions Ampicillin-resistant E.coli and Ceftazidime-resistant E.coli observed cases among nosocomial infections were greater than the expected cases. Hence it is necessary to reconsider using such type of antibiotics in treatment of nosocomial infections caused by E.coli. The results of this study could be important for health policy makers. In the future, outbreaks of this type of infection can be investigated with the help of the results of this study.

scholarly journals Evaluation of Emerging Antimicrobials Resistance in Nosocomial Infections Caused by E. Coli: The Comparison Results of Observed Cases and Compartmental Model

2021 ◽  
Author(s):  
Mahshid Nasehi ◽  
Babak Eshrati ◽  
Hamidreza Baradaran ◽  
Leila Janani ◽  
Sasan Ghorbani-Kalkhajeh ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
World Health Organization ◽  
Nosocomial Infections ◽  
World Health ◽  
Antibiotic Resistant ◽  
Microbial Resistance ◽  
E Coli ◽  
The World ◽  
Health Organization

Abstract Background: The World Health Organization repeatedly emphasizes the spread and association of nosocomial infections with microbial resistance. In a 2014 report, the World Health Organization cited microbial resistance as a global threat. In recent years, the world has seen the rapid growth of antibiotic-resistant E. coli in most areas, which poses a serious threat to public health. A high percentage of bacteria that cause nosocomial infections have been resistant to treatment. The most common bacterial agent among these nosocomial infections is E. coli. This bacterium is one of the main causes of nosocomial infections among hospitalized patients. One of the most important goals of the Global Antimicrobial Resistance and Use Surveillance System (GLASS) is timely identification and transmission of Emerging Antimicrobial Resistance (EAR) or outbreak of antibiotic resistance. One of the main ways to identify this "emerging" at the national or local level is to identify deviations from the expected resistance in drug compounds. As a result, if the observed cases of a drug-resistant pathogen are significantly higher than expected, it could indicate "emerging".Purpose: This study aimed to identify and transmit EAR or outbreak of antibiotic resistance among antibiotics used in the treatment of nosocomial infections caused by E. coli. This was done by comparing the observed cases of resistant E. coli with the predicted cases of resistant E. coli, which were predicted by the compartment model.Methods: This is a hospital-based study that used data from the nosocomial infection survelliance system to investigate observed cases of antibiotic resistance. In this study, the results of 12,954 antibiogram tests related to 57 hospitals located in 31 provinces of Iran were divided into two parts (results related to the first half of 2017 and results related to the second half of 2017). The model was developed in the second half of the year to predict expected cases. Before developeing model to predict the expected cases of resistant E. coli, the validity of the model was evaluated by implementing the model in the first half of the year. Finally, the predicted cases of resistant E. coli were compared with those observed in 2017. If the difference between the two was statistically significant, it indicated the outbreak of E.coli. This model evaluated 11 antibiotics recommended by the World Health Organization that are used to treat nosocomial infections caused by E. coli.Results: The results of this study showed that the outbreak of E. coli resistant to ampicillin and ceftazidime occurred in 2017 in hospitals of Iran. This means that resistance to ampicillin and ceftazidime antibiotics in nosocomial infections caused by E. coli is higher than expected and has become "emerging".Conclusion: This study showed how the outbreak of antibiotic resistance in the country's hospitals can be investigated. Using the method of this study, we can investigate the outbreak of antibiotic-resistant E. coli in the coming years and in different substrates. The results of this study showed that the administration and use of antibiotics should be reconsidered.

scholarly journals Automating the Generation of Antimicrobial Resistance Surveillance Reports: Proof-of-Concept Study Involving Seven Hospitals in Seven Countries

10.2196/19762 ◽  
2020 ◽  
Vol 22 (10) ◽  
pp. e19762 ◽  
Author(s):  
Cherry Lim ◽  
Thyl Miliya ◽  
Vilada Chansamouth ◽  
Myint Thazin Aung ◽  
Abhilasha Karkey ◽  
...  
Keyword(s):  
Open Access ◽  
Antimicrobial Resistance ◽  
Surveillance System ◽  
World Health ◽  
Data Repository ◽  
Hospital Data ◽  
User Input ◽  
Antimicrobial Resistance Surveillance ◽  
Data Files ◽  
Health Organization

Background Reporting cumulative antimicrobial susceptibility testing data on a regular basis is crucial to inform antimicrobial resistance (AMR) action plans at local, national, and global levels. However, analyzing data and generating a report are time consuming and often require trained personnel. Objective This study aimed to develop and test an application that can support a local hospital to analyze routinely collected electronic data independently and generate AMR surveillance reports rapidly. Methods An offline application to generate standardized AMR surveillance reports from routinely available microbiology and hospital data files was written in the R programming language (R Project for Statistical Computing). The application can be run by double clicking on the application file without any further user input. The data analysis procedure and report content were developed based on the recommendations of the World Health Organization Global Antimicrobial Resistance Surveillance System (WHO GLASS). The application was tested on Microsoft Windows 10 and 7 using open access example data sets. We then independently tested the application in seven hospitals in Cambodia, Lao People’s Democratic Republic, Myanmar, Nepal, Thailand, the United Kingdom, and Vietnam. Results We developed the AutoMated tool for Antimicrobial resistance Surveillance System (AMASS), which can support clinical microbiology laboratories to analyze their microbiology and hospital data files (in CSV or Excel format) onsite and promptly generate AMR surveillance reports (in PDF and CSV formats). The data files could be those exported from WHONET or other laboratory information systems. The automatically generated reports contain only summary data without patient identifiers. The AMASS application is downloadable from https://www.amass.website/. The participating hospitals tested the application and deposited their AMR surveillance reports in an open access data repository. Conclusions The AMASS is a useful tool to support the generation and sharing of AMR surveillance reports.

scholarly journals Evaluation of Emerging Antimicrobials Resistance in Nosocomial Infections Caused by E. Coli: the Comparison Results of Observed Cases and Compartmental Model

2021 ◽  
Author(s):  
Mahshid Nasehi ◽  
Babak Eshrati ◽  
Hamid Reza Baradaran ◽  
Leila Janani ◽  
Sasan Ghorbani Kalkhajeh ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
World Health Organization ◽  
Nosocomial Infections ◽  
World Health ◽  
Antibiotic Resistant ◽  
Microbial Resistance ◽  
E Coli ◽  
The World ◽  
Health Organization

Abstract Background: The World Health Organization repeatedly emphasizes the spread and association of nosocomial infections with microbial resistance. In a 2014 report, the World Health Organization cited microbial resistance as a global threat. In recent years, the world has seen the rapid growth of antibiotic-resistant E. coli in most areas, which poses a serious threat to public health. A high percentage of bacteria that cause nosocomial infections have been resistant to treatment. The most common bacterial agent among these nosocomial infections is E. coli. This bacterium is one of the main causes of nosocomial infections among hospitalized patients. One of the most important goals of the Global Antimicrobial Resistance and Use Surveillance System (GLASS) is timely identification and transmission of Emerging Antimicrobial Resistance (EAR) or outbreak of antibiotic resistance. One of the main ways to identify this "emerging" at the national or local level is to identify deviations from the expected resistance in drug compounds. As a result, if the observed cases of a drug-resistant pathogen are significantly higher than expected, it could indicate "emerging".Purpose: This study aimed to identify and transmit EAR or outbreak of antibiotic resistance among antibiotics used in the treatment of nosocomial infections caused by E. coli. This was done by comparing the observed cases of resistant E. coli with the predicted cases of resistant E. coli, which were predicted by the compartment model.Methods: This is a hospital-based study that used data from the nosocomial infection survelliance system to investigate observed cases of antibiotic resistance. In this study, the results of 12,954 antibiogram tests related to 57 hospitals located in 31 provinces of Iran were divided into two parts (results related to the first half of 2017 and results related to the second half of 2017). The model was developed in the second half of the year to predict expected cases. Before developeing model to predict the expected cases of resistant E. coli, the validity of the model was evaluated by implementing the model in the first half of the year. Finally, the predicted cases of resistant E. coli were compared with those observed in 2017. If the difference between the two was statistically significant, it indicated the outbreak of E.coli. This model evaluated 11 antibiotics recommended by the World Health Organization that are used to treat nosocomial infections caused by E. coli.Results: The results of this study showed that the outbreak of E. coli resistant to ampicillin and ceftazidime occurred in 2017 in hospitals of Iran. This means that resistance to ampicillin and ceftazidime antibiotics in nosocomial infections caused by E. coli is higher than expected and has become "emerging".Conclusion: This study showed how the outbreak of antibiotic resistance in the country's hospitals can be investigated. Using the method of this study, we can investigate the outbreak of antibiotic-resistant E. coli in the coming years and in different substrates. The results of this study showed that the administration and use of antibiotics should be reconsidered.

scholarly journals Surveillance of antimicrobial resistance of invasive pathogens: the Estonian experience

2006 ◽  
Vol 11 (2) ◽  
pp. 9-10 ◽  
Author(s):  
K Loivukene ◽  
K Kermes ◽  
E Sepp ◽  
V Adamson ◽  
P Mitt ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Antimicrobial Resistance ◽  
Surveillance System ◽  
Gram Negative ◽  
E Coli ◽  
Invasive Pathogens ◽  
Susceptibility Data ◽  
Antimicrobial Resistance Surveillance ◽  
Klebsiella Spp

The aim of the present study was to evaluate the needs for surveillance of invasive Gram-negative pathogens in Estonia. The antimicrobial susceptibility data of invasive isolates of Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella spp, Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae and enterococci were collected in accordance with EARSS (European Antimicrobial Resistance Surveillance System) protocols. Despite the higher rate of Gram positive pathogens, their resistance to antimicrobials was low in contrast to the elevated resistance established for Gram negative pathogens. The higher resistance to antimicrobials was particularly associated with A. baumannii and P. aeruginosa. Also, the proportion of extended spectrum betalactamase (ESBL)-producing strains was 23% among Klebsiella spp. and 3.6% among E. coli. The inclusion of invasive Gram negative pathogens in antimicrobial resistance surveillance provides useful information concerning local pathogen susceptibility, as well as for the empirical treatment of suspected infections.

scholarly journals Automating the generation of antimicrobial resistance surveillance reports: a proof-of-concept study in seven hospitals in seven countries

2020 ◽  
Author(s):  
Cherry Lim ◽  
Thyl Miliya ◽  
Vilada Chansamouth ◽  
Myint Thazin Aung ◽  
Abhilasha Karkey ◽  
...  
Keyword(s):  
Open Access ◽  
Antimicrobial Resistance ◽  
Surveillance System ◽  
Local Level ◽  
Research Unit ◽  
World Health ◽  
Hospital Data ◽  
Antimicrobial Resistance Surveillance ◽  
Data Files ◽  
Automated Tool

ABSTRACTBackgroundReporting cumulative antimicrobial susceptibility testing data on a regular basis is crucial to inform antimicrobial resistance (AMR) action plans at local, national and global levels. However, analysing data and generating a report are time-consuming and often require trained personnel. We illustrate the development and utility of an offline, open-access and automated tool that can support the generation of AMR surveillance reports promptly at the local level.MethodsAn offline application to generate standardized AMR surveillance reports from routinely available microbiology and hospital data files was written in the R programming language. The application can be run by a double-click on the application file without any further user input. The data analysis procedure and report content were developed based on the recommendations of the World Health Organization Global Antimicrobial Resistance Surveillance System (WHO GLASS). The application was tested in Microsoft Windows 10 and 7 using open-access example data sets. We then independently tested the application in seven hospitals in Cambodia, Lao People’s Democratic Republic (PDR), Myanmar, Nepal, Thailand, the United Kingdom, and Vietnam.FindingsWe developed the AutoMated tool for Antimicrobial resistance Surveillance System (AMASS), which can support clinical microbiology laboratories to analyse their microbiology and hospital data files (in CSV or Excel format) onsite and promptly generate AMR surveillance reports (in PDF and Excel formats). The data files could be those exported from WHONET and/or other laboratory information systems. The automatically generated reports contain only summary data without patient identifiers. The AMASS application is downloadable from www.amass.website. The participating hospitals tested the application and deposited their AMR surveillance reports in an open-access data repository.InterpretationThe AMASS application can be a useful tool to support the generation and sharing of AMR surveillance reports.FundingMahidol Oxford Tropical Medicine Research Unit (MORU) is funded by the Wellcome Trust (Grant no. 106698/Z/14/Z). Oxford University Clinical Research Unit (OUCRU) is funded by the Wellcome Trust (Grant no. 106680/B/14/Z). The investigators are funded by the Wellcome Trust (CL is funded by a Training Research Fellowship [Grant no. 206736] and DL is funded by an Intermediate Training Fellowship [Grant no. 101103]). BSC is funded by the UK Medical Research Council and Department for International Development (Grant no. MR/K006924/1). The funder has no role in the design and conduct of the study, data collection, or analysis and interpretation of the data.

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