Emerging antimicrobial resistance reporting: guide for emerging AMR event sharing: August 2018

Emerging antimicrobial resistance reporting Guide for emerging AMR event sharing August 2018 Emerging antimicrobial resistance reporting Guide for emerging AMR event sharing August 2018 Emerging antimicrobial resistance reporting: guide for emerging AMR event sharing ISBN 978-92-4-151458-3 © World Health Organization 2018 Some rights reserved. This work is available under the Creative Commons Attribution- NonCommercial-ShareAlike 3.0 IGO licence (CC BY-NC-SA 3.0 IGO; https://creativecommons.org/licenses/by-nc-sa/3.0/igo). Under the terms of this licence, you may copy, redistribute and adapt the work for non-commercial purposes, provided the work is appropriately cited, as indicated below. In any use of this work, there should be no suggestion that WHO endorses any specific organization, products or services. The use of the WHO logo is not permitted. If you adapt the work, then you must license your work under the same or equivalent Creative Commons licence. 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Printed in Switzerland 1 CONTENTS Introduction ........................................................................................................................................................ 3 GLASS-EAR reporting process: an overview ....................................................................................................... 4 Roles of GLASS-EAR-members ........................................................................................................................ 4 Selection of emerging AMR events to report to GLASS .................................................................................. 4 GLASS-EAR data and the data entry form ....................................................................................................... 4 Workflow ........................................................................................................................................................ 5 Using the GLASS-EAR IT module ......................................................................................................................... 6 Registration..................................................................................................................................................... 6 Accessing GLASS-EAR module ......................................................................................................................... 8 Adding, editing and submitting new events ................................................................................................... 8 Consulting and editing a pending event ......................................................................................................... 9 Consulting, editing and commenting a published event .............................................................................. 10 ANNEX 1. GLASS-EAR event form ..................................................................................................................... 12 2 ACKNOWLEDGEMENTS WHO would like to express its sincere appreciation and gratitude to all those who have supported and contributed to the development of this document. Executive group Martina Escher, Sergey Eremin, Carmem Pessoa da Silva Financial Support US Centers for Disease Control and Prevention Cooperative Agreement 3 INTRODUCTION The Emerging Antimicrobial Resistance Reporting (EAR) component within Global Antimicrobial Resistance Surveillance System (GLASS) was developed at the request of Member States to support detection, early warning and risk assessment capacities of national antimicrobial resistance (AMR) surveillance programmes. GLASS-EAR provides an IT module which is embedded in the GLASS IT platform and provides a space where experts can share information regarding emerging AMR events (as defined in the GLASS-EAR framework 1 ) to assess their importance, facilitate early information sharing, and stimulate epidemiological and microbiological discussion for coordinated actions. Launched in 2018, the GLASS-EAR IT module is open to those in charge of national AMR surveillance systems and constituencies that might discover new types of AMR in bacteria and fungi with potential relevance to public health. The GLASS-EAR community is constituted by all Member States, regardless their GLASS enrolment status, WHO Collaborating Centres, AMR surveillance networks and research institutions producing quality AMR data, and WHO IHR focal points. The GLASS-EAR component of GLASS implements a workflow process for notifying a diverse range of stakeholders on a timely basis, and in compliance with agreements such as the International Health Regulations (IHR) 2 . GLASS-EAR provides a tool for a standardized, transparent, timely and secure reporting and reactive information sharing through: • Defined criteria (see the GLASS-EAR framework 1 ) to select emerging AMR event in bacteria or fungi population to be reported to GLASS-EAR; • A standardized collection form for good information quality; • Defined roles for GLASS-EAR members and workflow for information sharing; • Implementation of the GLASS-EAR IT module, a web-based communication platform supporting the rapid and reactive exchange of technical information related to emerging AMR events according to the workflow and GLASS-EAR members’ roles; • Ensured confidentiality: emerging AMR events reported within the GLASS-EAR community are considered by definition confidential information to be shared only among EAR-GLASS team and GLASS-EAR-users from the concerned country. However, the level of confidentiality can be changed at any time as needed to facilitate data sharing; • Ensured data security: WHO has a formal and comprehensive policy for securely managing all databases and information sources hosted by the Organization. This policy includes information security, technical and physical data security, data access and retention procedures, and confidentiality agreements. As international civil servants, all WHO staff are required to adhere to the policy and its procedures (detailed under Staff Regulations), including full respect of Article 45 of the IHR 2 . This manual targets GLASS-EAR users at country level and aims at providing an overview of the GLASS-EAR process and an explanation on how to use the GLASS-EAR IT module. 1 Emerging antimicrobial resistance reporting framework. Geneva: World Health Organization; 2018. 2 International Health Regulations (2005). Third edition. Geneva: World Health Organization; 2016 (http://www.who.int/ihr/publications/9789241580496/en/). 4 GLASS-EAR REPORTING PROCESS: AN OVERVIEW ROLES OF GLASS-EAR-MEMBERS Members from the EAR community can be classified in three groups according to their role: • EAR-GLASS: responsible WHO officers; • GLASS-EAR Users: GLASS-EAR members actively reporting information on emerging AMR events; • GLASS-EAR Readers: GLASS-EAR members that are not in the position to provide information on emerging AMR events but who needs to be informed GLASS-EAR members can be linked to one or more countries, according to their responsibilities. SELECTION OF EMERGING AMR EVENTS TO REPORT TO GLASS When an emerging AMR event is identified at a national or supranational level, it should be reported within two weeks from the event confirmation through the GLASS-EAR IT module. Additional information can always be added at a later stage, when it becomes available. GLASS-EAR users are expected to report to events 3 related to the following: • Pan-drug resistant (PDR) phenotypes and information on the responsible genes; • Pre-defined critical resistance phenotypes and information on the responsible genes; • Extensively drug-resistant (XDR) phenotypes which were not previously detected in a country and information on the responsible genes; • Novel (not previously reported globally) genetic determinants of resistance; The detailed explanations and definitions of emerging AMR events are available from the GLASS-EAR framework. GLASS-EAR DATA AND THE DATA ENTRY FORM The GLASS-EAR form (Annex 1) contains a set of both open and closed-ended questions, some of which are automatically filled in by the system. It allows for uploading of documents to be shared about the event and includes a space for comments and updates. The form is organized in four sections: 1) Reporting details: the details of the person reporting the event (i.e. reporter, institution, e-mail), the reporting country, the key dates (i.e. date of first reporting, last editing and last commenting), the reason of reporting and the level of confidentiality; 2) The event itself: the involved microorganism including the resistance details, source of the microorganism, its detection and laboratory confirmation; 3) Actions taken: data on whether the event was the issue of a national or an international reporting and/or of a risk assessment; 3 Currently the GLASS-EAR targets bacteria causing acute infections in humans and Candida auris 5 4) Comments: this is a “chatroom” where GLASS-EAR members can interact by posting additional information related to the event (e.g. similar findings in neighbouring countries), ask for clarifications or additional information, and request support from WHO and GLASS-EAR community. WORKFLOW The process of the emerging AMR event being reported follows a defined workflow that can be schematised in three main phases through which the event is: 1) created and submitted; 2) consolidated and published and 3) made available for consultation and information sharing Throughout the processes, the event goes from being a draft accessible only to the GLASS-EAR user generating it, to become a pending event open to EAR-GLASS team and GLASS-EAR members linked to the concerned country, and finally to acquiring the status of “published” event, available for consultation and information sharing to all GLASS-EAR members. Importantly, an event can always be edited when new information is available. To enhance the reactiveness of the GLASS-EAR community, throughout the process, the system automatically generates and sends e-mails to inform GLASS-EAR members that an emerging AMR event was submitted, or published, or commented or edited. E-mails have an explanatory title and provide a summary of the events and comments, and the link to the GLASS-platform. More details are provided in Figure 1 and in the text below Figure 1. GLASS-EAR workflow CREATING AND SUBMITTING AN EVENT GLASS-EAR users can create a new event, save it as a draft, edit or delete it as necessary. In this phase only the author can have access to the event. When the author considers that the event contains the necessary information (considering that the event can always been updated when new information is available), (s)he can submit the event: • An e-mail titled “New EAR event submitted” will be automatically sent to the EAR-GLASS team and to the GLASS-EAR members from the concerned country group • The event acquires the status of “Pending event” CONSOLIDATING AND PUBLISHING A PENDING EVENT 6 Shortly after the new event is submitted, GLASS team examines the event and together with the country users consolidates it. When appropriate, an EAR-GLASS team member publishes 4 it: • An e-mail titled “EAR event published” will be automatically sent to GLASS-EAR members according to the level of confidentiality • The event acquire the status of a “Published event” SHARING INFORMATION When the event is published, it becomes accessible to GLASS-EAR members according to the level of confidentiality. When the event becomes non-confidential, it is visible to all users of the GLASS-EAR module. Emerging AMR events can also be: • Edited: GLASS-EAR users of the concerned country group can edit the event at any time new information is available o An e-mail titled “EAR event edited” will be automatically sent to GLASS-EAR members according to the level of confidentiality • Commented: any GLASS-EAR users having access to the event can post a comment providing or asking for additional information o An e-mail titled “EAR event commented” will be automatically sent to GLASS-EAR members according to the level of confidentiality USING THE GLASS-EAR IT MODULE The GLASS-EAR module is part of the GLASS IT platform, a WHO web-based platform for sharing global data on antimicrobial resistance (AMR). Launched in 2016, the platform is hosted on the WHO server and serves as common environment for sharing data generated in the framework of several WHO AMR surveillance activities. GLASS IT platform is a secure web-based platform with user-specific roles and access rights. REGISTRATION National Focal Points from countries enrolled in GLASS are already registered in the GLASS-IT platform and can access the system using their username and password; Other GLASS-EAR members shall request access to the GLASS-EAR module by sending an email to the GLASS secretariat at glass-ear@who.int: • The email should have a title “EAR member new request” and provide a minimum set of information (i.e. name, institution, country and reason for applying); • GLASS secretariat will process the request and send two separate emails providing the user name and password as well as the link to the GLASS IT platform. The new user profile will be linked to one of the three GLASS-EAR member’s roles (EAR GLASS, EAR user or EAR reader) and to one or more countries. 4 While certain GLASS-EAR events, according to their assessment, will be reported to public via the WHO website and other means described in the GLASS-EAR framework document, “publication” here refers to publication on the GLASS-EAR IT platform when the information becomes available to all GLASS-EAR members. 7 When you open the link in your browser, you will see the login page. Enter your user name and password and click on the “Log in” button. Please note that you can retrieve your password by clicking on the “Forgot your password?” link. To recover your password, you will need to enter your email address and the CAPTCHA letters shown on your screen. Once you have logged in, you will reach the WHO GLASS IT platform main page. According to your profile setting, you will be able to see one or more of the buttons displayed below, in addition to the EAR button. Please provide and keep up-to-date your personal information: click on the “My account” button to access “My account” page and fill in all the fields. Some of this data will appear automatically in the data entry form when submitting an event. 8 ACCESSING GLASS-EAR MODULE From the WHO GLASS IT platform starting page click on the “EAR” button to access the home page of the Emerging AMR Reporting (GLASS-EAR). Here, buttons are organised following the GLASS-EAR workflow and will be visible according to the GLASS-EAR- user role (e.g. GLASS-EAR readers will see only “Pending events” and “Published events”): • Add an event: here a GLASS-EAR user can open a new data entry form • Draft events: here are listed only events that have been created by the GLASS-EAR user and that are in the process to be submitted • Pending events: here GLASS-EAR users and GLASS-EAR readers can access events that have been submitted by an EAR user, linked to their country and in the process of being consolidated and published • Published events: here GLASS-EAR users and GLASS-EAR readers can access the published event related to the country/ies his/her profile is linked to and the non-confidential events from other countries ADDING, EDITING AND SUBMITTING NEW EVENTS By clicking on the “Add an event” button, an empty form will open. The user can provide the information requested and submit the event by clicking on “Save and submit” button. Alternatively, the user can save the event by clicking on the “Save and exit” button. The event will be saved as a draft event and the GLASS-EAR user will be redirected to the home page of the Emerging AMR Reporting. Please don’t forget submitting the event when the draft is finalized! 9 To access all your draft events, click on the “Draft events” button. A list of the draft events will appear as shown on the screenshot below. Click on the “View” button to open the event. At this stage the author can edit and save the draft event as many times as needed. When necessary, the event can be deleted by clicking on the “Delete” button. It is advisable to keep here only the event you are still working on and to discharge the others. When the author of the event considers that the event contains all the necessary information, (s)he can submit the event. • The event is now a pending event and can be accessed in the “pending event” section. • An e-mail will be automatically sent to the GLASS-EAR GLASS team and to the GLASS-EAR users from the concerned country. CONSULTING AND EDITING A PENDING EVENT Users can access a pending event from their country by clicking on the “Pending events” button. 10 The events will be listed by day of submission, starting from the most recent. If needed, events can be filtered by “Event ID” and “Reporting Year”. The user can access the form by clicking on the “View” button. From here (s)he will be able to edit it and export as a .pdf file. When appropriate, EAR GLASS members in agreement with the submitting country will publish the event: • The event will acquire status of a “Published event”; • An e-mail will be sent to inform all the EAR users having the rights to access the event CONSULTING, EDITING AND COMMENTING A PUBLISHED EVENT Users can access the published event by clicking on the “Published events” button. The events will be listed by day of submission, starting from the most recent. If needed, events can be filtered by “Event ID”, “Reason for reporting”, “Country”, “Reporting period”, “Type of microorganism” “Source” and “Confidentiality”. The user can open the form by clicking on the “View” button. From here GLASS-EAR-members can: • Export the event as a .pdf file; • Edit: only GLASS-EAR users linked to the concerned country can edit the form. o An e-mail will be sent to inform all the GLASS-EAR users having the rights to access the event 11 • Comment: all GLASS-EAR users can post a comment. By clicking on the “Add a comment” button a comment window will open and the user can add the text and save it: o An e-mail will be sent to inform all the GLASS-EAR users having the rights to access the event. 12 ANNEX 1. GLASS-EAR EVENT FORM5 Information in green is automatically filled in by the system Mandatory field are marked with * EMERGING AMR EVENT Title of the event (includes microorganism(s); resistance pattern/resistance mechanism; country involved; year) REPORTING DETAILS Reporting Institution: __________________________________________________________________________________ Country: ____________________________________________________________________________________________ Reporting person (name surname): ___________________________________ ___________________________________ Date of reporting to GLASS: First reporting: dd/mm/yy Date of last edit: dd/mm/yy Date of last comment: dd/mm/yy Reason for reporting: □ Isolation of pan-drug (PDR) resistant phenotypes □ Occurrence of a pre-defined critical resistance □ Extensive drug-resistant (XDR) phenotypes not previously detected in the country □ Novel (not previously reported globally) genetic determinants for resistance □ Unusual increase in critical resistance or in extensive resistant phenotypes □ Other, please specify ________________________________________________________________________ Level of confidentiality*: □ Not-confidential (the event will be shared within the EAR network) □ Confidential (only a person from the country and GLASS have access to the event) THE EVENT Involved microorganism(s): □ Bacteria □ Fungi Name(s) of the involved microorganism(s): _________________________________________________________________ Phenotypic R details (including original MICs or zone diameters) ________________________________________________ Genotypic R details (molecular mechanism(s)) ______________________________________________________________ Source(s) of the microorganism(s): From which source(s) has the microorganism(s) been isolated (more than one option is possible)? □ Human _____________________ (Date/period of sampling) 5 Paper-based version 13 □ Animal _____________________ (Date/period of sampling) □ Food _____________________ (Date/period of sampling) □ Environment _____________________ (Date/period of sampling) □ Other (please specify) ____________________________________________________________________________ _____________________ (Date/period of sampling) Event detection: Date of first identification of the event: dd/mm/yyyy Event Confirmation: has this event/finding been confirmed by a (national/regional) reference laboratory? Yes/No/Not applicable Name of reference laboratory: ___________________________________________________________________________ Confirmatory test(s) used: ______________________________________________________________________________ Date of confirmation: dd/mm/yyyy Summary of the event: Please provide a short description of the event, including:  Geographical location where the specimen was collected (country, region and location)  Setting where the specimen was collected (e.g. community, hospital, farm);  Reason for sampling: e.g. routine clinical activities, screening/monitoring program, research;  Source and type of specimen: human (blood, urine etc.), animal (animal species-blood, urine), food (food items) and environment (water, sewage));  Any other information you consider useful to characterize the event _________________________________________________________________________________________________ _________________________________________________________________________________________________ _________________________________________________________________________________________________ _________________________________________________________________________________________________ _________________________________________________________________________________________________ _________________________________________________________________________________________________ _________________________________________________________________________________________________ _________________________________________________________________________________________________ ACTIONS TAKEN National reporting Has this event been reported to the respective national body/authorities? Yes/no Reporting date: dd/mm/yyyy International reporting other than GLASS Has this event been the issue of international reporting other than GLASS-EAR? Yes/No International body name and reporting framework (e.g. WHO-IHR, WHO-INFOSAN, OIE-WAHID...): __________________________________________________________________________________________ Reporting date: dd/mm/yyyy Risk assessment: Has a risk assessment been conducted? Yes/no 14 Please provide a summary of the results (and a web link, if publicly available) ____________________________________________________________________________________________________ ____________________________________________________________________________________________________ ____________________________________________________________________________________________________ If available, please upload the document Other actions: please list any other action conducted at local or national level: ____________________________________________________________________________________________________ ____________________________________________________________________________________________________ ____________________________________________________________________________________________________ COMMENT Commenting person: Date of comment: dd/mm/yyyy Reporter: ____________________________________ Country: _______________________________________ Comment____________________________________________________________________________________________ ____________________________________________________________________________________________________ ____________________________________________________________________________________________________ 15 16