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.

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