SPIDAAR & ATLAS: Data sharing via AMR Surveillance partnerships

Dear All,

Building on the ATLAS database (link) that provides open access to data from 2004 to the present out of the multiple surveillance programs that Pfizer has run over that interval, Wellcome Trust and Pfizer have just announced that the underlying database will also be used to support SPIDAAR (Surveillance Partnership to Improve Data for Action on Antimicrobial Resistance), a new multi-year, public-private research collaboration with the governments of Ghana, Kenya, Malawi and Uganda to track resistance patterns and better understand the burden of antimicrobial resistance (AMR) on patients living in low- and middle-income countries.

To decode this, let’s start with some background on ATLAS. Pfizer has had a number of marketed antibacterial and antifungal agents over the past 20 years (tigecycline, ceftaroline, linezolid, fluconazole, and voriconazole … just to name a few). Triggered by conversations on the importance of sharing data on AMR (see, for example, this 2018 workshop at Wellcome trust, link), Pfizer created an open-access database in 2017 that provides access to data from all the surveillance programs that Pfizer has variously run since 2004 (link to an early press release on ATLAS; link to general current description of the project; link to ATLAS itself) . 

The scope of the data in the database is impressive: there are MICs on 680k bacterial isolates and 45 antibacterials from 76 countries as well as MICs on 15.5k fungi (mostly yeasts) and 10 antifungals from 40 countries. The database is very interactive and a great resource for graphics. Here, for example, is the distribution of carbapenem-resistant P. aeruginosa in 2004 vs. 2018:


You can also get the database to play back the timeline of the spread of resistance: after picking the bugs, drugs, and years, you just press play to watch the resistance creep across the globe! A little scary but also very instructive! I encourage you to have a look (and see below for more … you can download the entire 121MB database from the AMR Register).


So, what about SPIDAAR? As noted above, this is collaboration between Wellcome Trust, Pfizer, and the governments of Ghana, Kenya, Malawi, and Uganda to build capacity by initiating a surveillance program in these countries. Data from this work would obviously have value for each country’s National Action Plan on AMR. 

As noted above, SPIDAAR will use the ATLAS database as a vehicle for sharing its data. The SPIDAAR program also includes a separate real-world data study to examine the impact of antibiotic resistance on clinical as well as economic outcomes by recruiting a prospective cohort of patients with hospital-acquired infections.

As noted in an online article about the project by Wellcome Trust’s Gemma Buckland-Merrett (link), surveillance data is important at both the global (e.g., setting priorities) and local (e.g., guiding targeted action) level in efforts vs AMR. Indeed, The Access to Medicine Foundation recently called out the ATLAS project itself by noting (link) that through ATLAS, Pfizer was “… the first company to share raw data on the spread of resistance so that third parties can explore the potential for further research.”

This is really excellent to see! To my eye, this is a first of its kind public-private partnership supporting surveillance in countries with limited capacity and capability and is proof of how multiple sectors can come together to address AMR. 

More broadly, this is the type of initiative called for by the AMR Industry Alliance (AMR IA) in its reports on Industry commitments (link) to “Support collaboration and sharing of relevant non-proprietary data” and “Collect and share surveillance data.”


And, what does this mean for you? Well, ATLAS is one of the programs feeding in to the AMR Research Initiative (aka, the AMR Register), a Wellcome Trust-funded initiative (link). The AMR register website currently shows 13 surveillance programs where data are available either by request (12 of the 13) or by direct download (ATLAS: go here for descriptive webpage and here for the 121 MB (!!) Excel download).

The goal of all of this is to encourage creative re-use of these data. An example of this was noted in the 25 April 2019 announcement by Wellcome of the winners of their recent Data Re-Use Prize (link to general webpage on the prize). One of the two prizes went to a team who used the ATLAS dataset to derive a composite index of antibiotic resistance for common infection syndromes with the aim of creating a guide to empirical therapy (link). Although the authors concluded that there were not enough isolates to fully inform their model, the strategy is certainly sound and shows how extended data collection (e.g., SPIDAAR) could enable such goals.

Wow! Mighty oaks from little acorns grow … and I look forward to watching these programs progress as others add data.

All best wishes, –jr

John H. Rex, MD | Chief Medical Officer, F2G Ltd. | Operating Partner, Advent Life Sciences. Follow me on Twitter: @JohnRex_NewAbx. See past newsletters and subscribe for the future: https://amr.solutions/blog/. All opinions are my own.

Current funding opportunities:

  • Novo REPAIR Impact Fund is open for global applications through 31 Jul 2020. Go here for current details.
  • 2020 funding rounds for CARB-X have not been announced.
  • The Global AMR R&D Hub’s dynamic dashboard (link) summarizes funders and projects by geography, stage, and more.

Upcoming meetings of interest to the AMR community:

  • 30 Jun 2020 (online, 17:00-18:30 CEST): GARDP REVIVE webinar. Title: “Clinical development of antimicrobials – Phase 1 development challenges.” Speaker: Markus Zeitlinger. Go here to register.
  • 9 Jul 2020 (online, 09:00-10:30 CEST): GARDP REVIVE webinar. Title: “The challenges and opportunities for antimicrobial R&D in low- and middle-income countries – India case study.” Speaker: Anand Anandkumar and Kamini Walla. Go here to register.
  • 17 Jul-2 Aug 2020 (Marine Biology Laboratory, Woods Hole, MA): Residential course entitled “Molecular Mycology: Current Approaches to Fungal Pathogenesis.” This 2-week intensive training program has run annually for many years and gets outstanding reviews. Go here for details.
  • 27 Jul-31 Jul 2020 (online): Small World Initiative Instructor Training Workshop – training for undergraduate professors and high school teachers in wet lab techniques, parallel curricula, & pedagogical instruction to engage students in the hunt to find new antibiotics in soil (also covering distancing learning options). Go here to register.
  • 4 Aug 2020 (Silver Spring): FDA workshop entitled “Development Considerations of Antifungal Drugs to Address Unmet Medical Need.” Go here to register.
  • 5 Aug 2020 (Silver Spring): FDA workshop entitled “Developing Antifungal Drugs for the Treatment of Coccidioidomycosis (Valley Fever) Infection.” Go here to register.
  • September 2020. University of Sheffield (UK). Applications are being taken for a new 1-year (full-time) or 2-year (part-time) Masters of Science course in Antimicrobial Resistance. The program runs annually from September and covers microbiology, clinical practice and policy. The course webpage is here.
  • 9-10 Sep 2020 (Washington, DC): US PACCARB public meeting. Go here for details.
  • 26-29 Oct 2020 (online meeting), Annual ESPID meeting (European Society for Pediatric ID, #38)
  • 10-13 Apr 2021 (Vienna): Annual ECCMID meeting (#31)
  • 20-24 June 2021 (Toronto): International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD-12). Go here for details.
  • 3-7 Jun 2021 (Anaheim), ASM Microbe 2021. Go here for details.
  • 8-11 Oct 2021 (Aberdeen, Scotland): 10th Trends in Medical Mycology. Go here for details.
  • 16-24 Oct 2021 (Annecy, France): Interdisciplinary Course on Antibiotics and Resistance (ICARe). This is a soup-to-nuts residential course on antibiotics, antibiotic resistance, and antibiotic R&D. The course is very intense, very detailed, and gets rave reviews. Registration is here and is limited to 40 students.
  • 18-21 May 2021 (Albuquerque, New Mexico): Biannual meeting of the MSGERC (Mycoses Study Group Education and Research Consortium). Save-the-date announcement is here, details to follow.

Dear All,
 
The IDWeek 2024 program committee is again seeking programs on novel antimicrobial agents and novel diagnostics for presentation in pipeline sessions! Here’s what is sought:

  • “Industry partners are invited to submit antimicrobials that are in preclinical stages of development (Phase II and III preferred) or recently approved after January 2024.
  • “The pipeline sessions will include antibacterials, antifungals, and antivirals (excluding COVID-19 and HIV).
  • “The committee also invites companies developing novel diagnostic technologies with a minimum of some preliminary proof of concept data to submit.” 

This is a great opportunity to tell the story of your development project! The deadline to submit is Wednesday, June 26 via the application portal. Any questions should be directed to program@idsociety.org. Please share this email with anyone you think might be interested in applying!
 
In addition, I’ll also note that those with a more general story to tell should look at the BugHub Stage (and the Global BugHub stage). Both BugHub variants seek “presentations that touch on your experience of working in infectious diseases and presentations that ultimately lead to a greater understanding of our diverse field” via a TED Talk-esque speech about your work. The deadline for applications is 26 June, the same as for the pipeline sessions.

I look forward to seeing you there! All best wishes, –jr

John H. Rex, MD | Chief Medical Officer, F2G Ltd. | Operating Partner, Advent Life Sciences. Follow me on Twitter: @JohnRex_NewAbx. See past newsletters and subscribe for the future: https://amr.solutions/blog/. All opinions are my own.

John’s Top Recurring Meetings

Virtual meetings are easy to attend, but regular attendance at annual in-person events is the key to building your network and gaining deeper insight. My personal favorites for such in-person meetings are below. Of particular value for developers are the AMR Conference and the ASM-ESCMID conference. Hope to see you there!

  • 27-30 April 2024 (Barcelona, Spain): 34th ECCMID, the annual meeting of the European Society for Clinical Microbiology and Infectious Diseases. Go here for details. 
  • 17-20 Sep 2024 (Porto, Portugal): ASM/ESCMID Joint Conference on Drug Development to Meet the Challenge of Antimicrobial Resistance. Go here for the meeting’s general website. You can’t register (yet) for the 2024 event, but save the date!
  • 16-20 Oct 2024 (Los Angeles, USA): IDWeek 2024, the annual meeting of the Infectious Diseases Society of America. Save the date! More details to come!
  • 25-26 February 2025 (Basel, Switzerland): The 9th AMR Conference 2025. Go here to register

Upcoming meetings of interest to the AMR community:

  • [NEW]  9 Apr 2024 (virtual, 830a-10a ET): GARDP’s next REVIVE webinar entitled “Progressing a discovery project – Criteria and challenges.” Register here.
  • [NEW] 9 Apr 2024 (virtual, 10a-1130a ET): CDC webinar “Impacts of Antimicrobial Resistance on Cancer Care.” Click here for details and to register.
  • 10-11 Apr 2024 (virtual): Sepsis Alliance AMR Conference, a 2-day conference focused on “Practical technologies to manage sepsis and counteract the expanding challenge of antimicrobial resistance.” Go here for details and to register.
  • 26 Apr 2024 (Barcelona, Spain): ESCMID workshop entitled “Using Data Science and Machine Learning for Infection Science: A Hands-on Introduction.” Click here to register or here for more details. 
  • 27-30 April 2024 (Barcelona, Spain): 34th ECCMID, the annual meeting of the European Society for Clinical Microbiology and Infectious Diseases. See Recurring Meetings list, above.
  • 26-31 May 2024 (Montreal, Canada): EDAR7, the McGill AMR Centre’s 7th edition of their Environmental Dimension of Antimicrobial Resistance conference. Go here for details; final abstract deadline is 21 Dec 2023.
  • 28-29 May 2024 (in person, Uppsala, Sweden): Uppsala Antibiotic Days, a broad-ranging 2-day program hosted by the Uppsala Antibiotic Center. Go here for details and to register.
  • [NEW] 30-31 May 2024 (face-to-face in Rockville, Maryland as well as online, 8.30-5.30p ET on 30 May, 9-2.40p on 31 May): NIAID-sponsored workshop entitled “Towards realizing the promise of adjunctive immune therapy for invasive fungal infections”. The agenda covers host immunity to invasive fungal infections, immune modulators in the context of fungal infections; and strategies for testing immune modulators as adjunctive therapy. Go here for more details and to register.
  • 9-13 June 2024 (in person, Ascona, Switzerland): “New Approaches to Combat Antibiotic-Resistant Bacteria, 2nd Edition” is a Sunday-Thursday residential workshop focused on the deep biology of AMR. Sponsored by NCCR AntiResist (a Swiss National Science Foundation consortium), the scientific program has the feel of a Gordon Conference. Space is limited, so you are encouraged to apply promptly — go here for details.
  • 13-17 June 2024 (Atlanta, Georgia): ASM Microbe, the annual meeting of the American Society for Microbiology. You can’t register yet, but you can go here for general details.
  • 17-20 Sep 2024 (Porto, Portugal): ASM/ESCMID Joint Conference on Drug Development to Meet the Challenge of Antimicrobial Resistance. See Recurring Meetings list, above.
  • 16-20 Oct 2024 (Los Angeles, USA): IDWeek 2024, the annual meeting of the Infectious Diseases Society of America. See Recurring Meetings list, above. 
  • 19-27 Oct 2024 (Annecy, France, residential in-person program): ICARe (Interdisciplinary Course on Antibiotics and Resistance). Now in its 8th year, Patrice Courvalin directs the program with the support of an all-star scientific committee and faculty. The resulting soup-to-nuts training covers all aspects of antimicrobials, is very intense, and routinely gets rave reviews! Seating is limited, so mark your calendars now if you are interested. Applications open in March 2024 — go here for more details.
  • 4-5 Dec 2024 (in person, Washington, DC): “Fungal Dx 2024: Fungal Diagnostics in Clinical Practice” is a 2-day in-person workshop organized by ISHAM‘s Fungal Diagnostics Working Group. The program and registration links are available at https://fungaldx.com/; the agenda is comprehensive and features an all-star global list of speakers.

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