The Antibiotic Paradox: Effects on the Microbiome

Is antimicrobial resistance (AMR) the greatest threat to human health? In this episode, we discuss how the misuse and overuse of antimicrobials in humans and agriculture have accelerated bacteria, viruses, and other pathogens’ ability to mutate and develop resistance against the treatments designed to curb and control them. 

We talked with molecular biologist Stephen Baker, virologist Ian Goodfellow and infectious disease epidemiologist Caroline Trotter about the magnitude of the problem and how it is not a problem of the future, but of the now. Along the way, we discuss whether post COVID19, are we in a better position now to deal with the next pandemic? Can we predict when it might happen? And if it does happen, will we deal with it any differently?

This episode was produced by Nick Saffell, James Dolan, Naomi Clements-Brod and Annie Thwaite. 

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Timestamps: 

[00:00] - Introductions

[01:10] - A bit about the guests’ research

[02:03] - What are antimicrobials and what is antimicrobial resistance (AMR)?

[03:00] - How do antimicrobials kill bacteria? How do the chemicals interact and stop a process? How were they discovered? 

[04:20] - Antibiotic means anti-life. How long have they been around? 

[05:10] - How does the process of antimicrobial resistance (AMR) work?

[06:40] - What are the consequences of antimicrobial resistance? The example of drug-resistant typhoid

[08:50] - How do you use vaccines to prevent diseases like drug-resistant typhoid? Vaccines, sanitation, and how vaccination is implemented and reformulated. 

[10:15] - Is antimicrobial resistance (AMR) the greatest threat to human health? Do we underestimate the impact that antibiotics have had?

[11:15] - Do we understand the scale of the resistance out there? What about mortality and morbidity because of antimicrobial resistance?

[13:00] - Antimicrobial resistance-specific diseases. What about meningitis? The power of early action?

[13:45] - The magnitude of the problem. The terrifying realisation that antimicrobials are irrelevant in some countries because of the sheer amount of biomass of drug resistance out there. 

[15:00] - The overuse of antimicrobrials, human microbiome and the community of bacteria that live in your body. 

[15:50] - Does the human microbiome recover from an antibiotic. How antibiotics work -  basically an atomic bomb going off. 

[17:00] - Do we have a full picture of how important a microbiome is. Links to obesity and the long-term effects of early exposure to antibiotics. 

[17:45] - What is the impact of microbiome variation on vaccines? 

[19:10] - Have we misused antibiotics? Is this on us? Or is inevitable? 

[19:45] - Resistance is inevitable. Resistance is reported within two years of a drug being licensed and used. We created is this arms race. This will be known as the antimicrobial era.   

[21:05] - Do we need a better diagnosis before we administer antimicrobials? 

[21:45] - The volume use of antimicrobials - healthcare vs agriculture. 

[22:35] - The overuse of antimicrobials. gentamicin being spread on tomatoes is ludicrous. 

[23:30] - Time for a recap! 

[31:50] - What can we do about combating resistance? What role do vaccines play? 

[33:15] - The Shigella infection. There isn’t a vaccine available for it yet. And the difference a vaccine for diarrhoeal diseases could have on AMR

[34:30] - Key messages on the use of antibiotics. Full dose or not to full dose. Should we complete a course of antibiotics. What is the best clinical result small dose over a period or one massive amount in one go? 

[37:00] - Do we have vaccines against bacterial infections? How do viruses work? The differences between bacteria and viruses. 

[38:00] - How important is MRNA for the future of vaccines? 

[39:00] - When can a vaccine be used to prevent disease and what are the big vaccine-preventable diseases that are causing ill health? HIV, Malaria. Global access

[41:30] - the speed of protein changes in viruses and how that impacts vaccines 

[43:00] - Do we have a good understanding of how all of the vaccines actually work? 

[43:50] - Is it possible to have a vaccine for Ebola? How would that work? How does Ebola spread? Ian’s experience working on Ebola in Sierra Leone

[45:50] - Ebola kickstarted epidemic preparedness across the world. 

[47:25] - The importance of rapid diagnosis and sequencing

[50:20] - COGUK and sequencing COVID to understand mutations.  

[51:10] - Post COVID19. Are we in a better position now to deal with this next time? Can we predict when it might happen? And if it does happen, will we deal with it any differently?

[54:30] - The importance of surveillance in between these events. Funding drops off and why should be investing in surveillance. How does this help with predictions? 

[57:35] - Time for another recap! 

[1:05:00] - How do we create an international network of skills and knowledge going forward to deal with future events? 

[1:07:25] - The role of Cambridge International Infection Initiative (Ci3) and Cambridge Africa

[1:10:45] - The link between climate change and global infectious diseases

[1:12:00] - The geographical distribution of insects and birds due to climate change and rising temperatures, and how that will impact infectious diseases

[1:13:20] - Flooding and diarrhoeal diseases. The threat of cholera and drug resistance 

[1:14:40] - The threat of dengue is cities and rising temperatures.

[1:15:35] - The hitlist. Reeling off the number of diseases that they’ve all had 

[1:16:00] - Let's break this episode down and close this thing out

Guests

Dr Caroline Trotter is a Principal Research Associate and Director of Cambridge-Africa, sharing her time between the Departments of Veterinary Medicine and Pathology. She is an infectious disease epidemiologist with particular interest in vaccine evaluation. Her research into the epidemiology and control of bacterial meningitis has been used to inform vaccine policy in Europe and Africa and she regularly acts as a consultant to the World Health Organisation.

Professor Ian Goodfellow  @igoodfel is a Wellcome Senior Fellow and deputy head of the Department of Pathology at the University of Cambridge. His research focuses on the mechanisms of RNA virus replication and pathogenesis as well as the identification of control measures for the prevention or treatment of infections.

Professor Stephen Baker @Baker_Lab_Cam was located at the Wellcome Africa- Asia programme in Vietnam for 11 years, where he established an internationally recognised programme of research on enteric (gastrointestinal) infections. The work in Stephen’s group focusses on understanding how specific bacteria that cause infectious disease in humans in low-middle income countries evolve and spread with a specific focus on typhoid fever, bacillary dysentery (Shigella), as well as other diarrheal diseases such as cholera and rotavirus.