Highly resistant bacterial infections in hospitalized COVID-19 patients: A report from India

Dear All,

I was made aware today of this important paper and wanted to share it promptly:

Vijay S, Bansal N, Rao BK, Veeraraghavan B, Rodrigues C, Wattal C, Goyal JP, Tadepalli K, Mathur P, Venkateswaran R, Venkatasubramanian R, Khadanga S, Bhattacharya S, Mukherjee S, Baveja S, Sistla S, Panda S, Walia K. Secondary Infections in Hospitalized COVID-19 Patients: Indian Experience. Infect Drug Resist. 2021;14:1893-1903; https://doi.org/10.2147/IDR.S299774.

Let me excerpt the key sentences from the abstract:

  • “A retrospective study of secondary infections in patients admitted in intensive care units (ICUs) and wards of ten hospitals of the Indian Council of Medical Research (ICMR) AMR surveillance network, between June and August 2020, was undertaken.
  • “Out of 17,534 admitted patients, 3.6% of patients developed secondary bacterial or fungal infections.
  • “The mortality among patients who developed secondary infections was 56.7% against an overall mortality of 10.6% in total admitted COVID-19 patients.
  • “Gram-negative bacteria were isolated from 78% of patients.
  • Klebsiella pneumoniae (29%) was the predominant pathogen, followed by Acinetobacter baumannii (21%).
  • “High levels of carbapenem resistance were seen in A. baumannii (92.6%) followed by K. pneumoniae (72.8%).”

In the discussion, the authors further note that “Among secondary infections in patients with COVID-19, extremely drug-resistant (XDR) K. pneumoniae and XDR A. baumannii constituted almost 50% of the isolates.” They caveat this by noting that “There is a possibility that many cultures may have been sent only when the initial empirical antibiotics did not help the patients, which may have led to isolation of pathogens with drug resistance”, but the resistance rates are very worrisome nonetheless!

As this project was organized by the Indian Council of Medical Research in its hospitals (note also that the first two authors as well as the last two are all ICMR-affiliated), this paper has the weight of a very substantial report from the Indian government. Further, these are data from last summer (e.g.,  India’s v1.0 COVID-19 experience), so one can only speculate on what is happening now during the new wave they are experiencing … the reports of rising rates of mucormycosis could well be just the tip of the iceberg.

Scary! The paper makes very appropriate calls for implementing best infection control practices and I’m sure that those would help. Nonetheless, this paper also proves that AMR is progressing inexorably … and we are all threatened by these pathogens. The time for new fire extinguishers is NOW! Get busy and discover something!

All best wishes, –jr

Post-newsletter addendum: Jason Gale and Bhuma Shrivastava have written a 25 May 2021 discussion for Bloomberg of the paper that provides a great quote from Kamini Walia, the paper’s senior author about the challenge of prescribing and over-prescribing: “The culture of over-medicating through antibiotics predates the pandemic. Antimicrobials are a shield, and as long as the patient is feeling better, doctors don’t want to de-escalate the antibiotic regimen. And the price for that comes three to six months down the line.” Well said! 

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 (most current list is here):

  • MTEC has announced an RFP seeking proposals focused on diagnostics, prevention of endemic diarrhea, and selected antivirals. Go here for the full RFP and search for “FA2.13” to find the infection-focused topics. White papers are due 17 June 2021.
  • GNA NOW (part of the IMI AMR Accelerator) has an open call to identify a novel mechanism antibacterial to add to its portfolio. The selected project would receive resources equivalent up to several million € (to be defined according to project needs); see also this 11 May 2021 newsletter for details. Expressions of interest are due by 18 June 2021.
  • CARB-X recently announced that their existing resources will be reserved to fund their existing portfolio (more than 80 total awards, and counting, as they include contracting from prior rounds). New rounds from CARB-X will occur only after new funding is obtained in 2021.
  • It’s not a funder, but AiCuris’ AiCubator offers incubator support to very early stage projects. Read more about it here.
  • The Global AMR R&D Hub’s dynamic dashboard (link) summarizes the global clinical development pipeline, incentives for AMR R&D, and investors/investments in AMR R&D.
  • In addition to the lists provided by the Global AMR R&D Hub, you might also be interested in my most current lists of R&D incentives (link) and priority pathogens (link).


Upcoming meetings of interest to the AMR community (most current list is here):

  • 24-29 May 2021 (virtual and in Geneva): ESPID 2021, the 39th Annual Meeting of the European Society for Paediatric Infectious Diseases. Save-the-date announcement is here, details to follow. 
  • [NEW] 26 May 2021 (virtual, 15.00-16.00 CEST): Webinar on the GNA NOW open call. See this 11 May 2021 newsletter for details on GNA NOW. Go here to register for the webinar.
  • 27 May 2021 (virtual, 9.30a-11.00 CEST): GARDP-sponsored webinar entitled “New clinical trial designs for evaluation of antimicrobial agents.” Go here to register.
  • 7-9 Jun 2021 (virtual, various times): 5th International Conference on Responsible Use of Antibiotics in Animals. This conference runs only every few years … the 4th instance was in 2016. Go here to register.
  • 20-24 Jun 2021 (Toronto): International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD-12). Go here for details.
  • 20-24 Jun 2021 (virtual, various times): World Microbe Forum sponsored by the American Society for Microbiology (ASM) and the Federation of European Microbiological Societies (FEMS). Go here for more details and to register.
  • 27 Jun-2 Jul 2021 (Ventura, CA): Gordon Research Conference entitled “Antimicrobial Peptides”. Go here for details, go here for the linked 26-27 Jun Gordon Research Seminar that precedes it.
  • 9-12 Jul 2021 (virtual): Annual ECCMID meeting (#31)
  • 26 Jul-30 Jul 2021 (online): Small World Initiative Instructor Training Workshop – training for undergraduate professors in the wet lab techniques, parallel curricula, & pedagogical instruction to engage students in the hunt to find new antibiotic-producing soil microbes. Go here to register.
  • 14-29 Aug 2021 (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.
  • 24-26 Aug 2021 (virtual, timings not stated but presumably EU-centered): The 5th edition of the annual AMR conference sponsored by the BEAM Alliance, CARB-X, the Novo REPAIR Impact Fund, the IMI Accelerator, and the European Biotechnology Network. The in-person version of this meeting is consistently excellent; the video-based version will have to do for 2021. Go here for details. 
  • 8-11 Oct 2021 (Aberdeen, Scotland): 10th Trends in Medical Mycology. Go here for details.
  • 11-15 Oct 2021 (physical, somewhere in the UK): UK-focused Innovation Mission sponsored by Innovate UK in collaboration with AMR Insights and Oxford innovation. This free event seeks to connect AMR-focused start-ups, SMEs and Multinationals, Academia, Research Institutes, Regional Development Companies and other interested stakeholders in the UK, Europe and other parts of the world. Go here for more 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. Bonus feature: For obvious reasons, the course didn’t happen in 2020! But as a celebration of the course’s 5th year, a webinar version was held on 29 Oct 2020: go here to stream it. 
  • 25-28 Oct 2021 (Stellenbosch, South Africa): The University of Cape Town’s H3D Research Centre will celebrate its 10th anniversary with a symposium covering the Centre’s research on Malaria, TB, Neglected Tropical Diseases, and AMR. Go here to register.
  • 5-8 Nov 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.
  • 6-11 Mar 2022 (Il Ciocco, Tuscany): Gordon Research Conference entitled “New Antibacterial Discovery and Development”. Go here for details, go here for the linked 5-6 Mar Gordon Research Seminar that precedes it.

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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