Antibiotic resistance and meat: why we should be careful in assigning blame

C Tilli

Antibiotic resistance and meat: why we should be careful in assigning blame

C Tilli

5 min readJun 17, 2020

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JP Addison🔸

I just want to say that this is a great first post. It's a hallmark of EA to be able to say "I think your conclusion is correct, but this argument in favor isn't valid."

C Tilli

Thanks a lot!!

poppinfresh

Great post, thanks for this. I'll stop chucking in "antibiotic resistance" as a reason to reduce factory farming. I'll focus on stronger reasons. I think a longer post on this topic would be useful.

On horizontal gene transfer, you write "This last mechanism could potentially be the most important one, but we do not know how common such transfer is or what share of the resistance burden for humans it causes." Without more information this is not particularly reassuring for me. Do we truly know nothing about how common or potentially important this is? I'd love to see you give a sense of your intuitions here, even if they're based on theorizing, speculating, or very weak evidence.

C Tilli

Edit: I originally made mistakes in the calculation below, have edited to correct this. See comment below by willbradshaw for details of the calculation.

Thanks! I completely agree there are other strong reasons to reduce (or eliminate) factory farming.

About your other comment – I also don’t think the situation is reassuring at all. I think it’s very plausible that the antibiotic use in agriculture could be an important driver of antibiotic resistance.

I think that we need more research on both the jumping of species barriers and on horizontal gene transfer. This paper could be interesting if you want to read more on how common horizontal gene transfer is, but I haven’t been able to find anything that gives a good assessment on how important this is for resistance (I will be very grateful for suggestions if you or someone else know good research on this!).

I know an analogous problem is that human patients often develop resistant bacteria in the normal gut microbiota when they take antibiotics, and this could also be transferred to pathogens through horizontal gene transfer – again, we don’t know how much it happens. Another thing is that some bacteria can both be living in the environment or on animals or in the normal bacterial flora, and then act as pathogens when they end op in the “wrong” place – for example bacteria that is harmless in the gut flora could cause urinary tract infection. If these develop resistance, they don’t need to do any gene transfer but simply change location to cause problems.

Personally, if I try to speculate, I would reason that it’s very unlikely that antibiotic use on animals drives resistance in human infections as much per kg used as antibiotic use on humans. So if we assume that 75% of the kg of antibiotics is used on animals, I would say that it’s unlikely to drive as much as 75% of the resistance burden on humans. It could be that it is 10% as efficient in driving resistance on humans because of the “transfer barriers”, that would mean that 7.5% (CORRECTION: should be 23%, see comments below) of the resistance burden on humans would go away if we eliminated antibiotic use in agriculture. That would still be very significant and worth pursuing. Of course, I don’t know at all if the number should be 10% or 50% or 1%, and I could also not answer if that makes it a more significant driver than for example the misuse of antibiotics for viral infections.

Apart from speculative, this reasoning is also very simplified, since there are many different classes of antibiotics that target different bacteria. It is unclear which would be the best way to measure “resistance burden”. If we would mean it as QALYs lost, it will make a big difference which bacteria is resistant and to which antibiotic(s). In some cases resistance would just mean switching over the patient to another drug and the patient recovers a couple of days later. In some cases, such as with tuberculosis, resistance could mean the alternative treatment is prolonged by years, has serious side-effects and is also much more expensive. In some cases, the patient would die. Resistance to so-called last-line antibiotics is much more severe than others. This report lists the WHO priority pathogens, I think it’s quite good in how it gives an understanding of how much worse the treatment for resistant tuberculosis is compared to “regular” tuberculosis, for example (p 21).

Even if I think we need more research to understand this better (and thereby how to design interventions and allocate resources), I don’t think that should be taken as a reason to wait with reforming agriculture to eliminate (non-therapeutic) antibiotic use. We know the mechanisms are there, and we also know that it’s possible to remove the antibiotics from production, and I don’t think we can afford to wait and see. This urgency to achieve change is also why I think it unwise to tie this cause too closely to elimination of factory farming, for example – even if that would be good, I think it would take too long time, and I think it’s possible to eliminate the antibiotic use much faster if we keep that as a (relatively) separate issue. In context where one can be nuanced I don't think it's wrong to bring up antibiotic use and resistance as a negative effect of factory farming, but I think as you say that there are stronger arguments to front to end factory farming.

Will Bradshaw

This feels a bit petty, since I don't really disagree with any of your conclusions, but there are some mistakes in the mathematics here.

Let's assume a fraction $p$ of all antibiotics used are used in animals, and a fraction $1 - p$ are used in humans. (In your example, $p = 0.75$ .)

Let's also assume that antibiotics use in animals is $k \times$ as effective at causing a resistance burden in humans per unit antibiotics used. (In your main example, $k = 0.1$ .)

Then the total resistance burden in humans is given by $B = (use in animals) \times (burden from animal use) + (use in humans) \times (burden from human use)$ , which in algebraic terms is $B = p \times k + (1 - p) \times 1 = 1 + p (k - 1)$ .

The fraction of the total burden caused by animal use is then $A = \frac{p k}{B}$ . If $p = 0.75$ and $k = 0.1$ , this is $A = \frac{0.075}{0.325} \approx 23 %$ . So, quite a bit more than 7.5%.

If $k = 0.01$ (use in animals is 1% as efficient at causing a resistance burden in humans), then $A = \frac{0.0075}{0.2575} \approx 3 %$ . If $k = 0.5$ , $A = 60 %$ .

So the fraction of the human burden caused by animal use could be quite high even if the per-unit efficiency is quite low.

C Tilli

That was sloppy of me, thanks a lot for the correction! Edited in the comment.

Will Bradshaw

Cool, thanks.

One comment: while all your caveats about simplified reasoning and so on are well-made and still apply, I would generally be surprised if you could substitute a number like this in your analysis with another number three times the size, without affecting anything else, such that you could make the substitution and leave the wording unchanged.

That is to say, if a contribution of 7.5% was "very significant and worth pursuing", I'd expect a contribution of 23% to be extremely significant, and worth making a high (or near-top) priority.

Of course, that's the result for 10%, and 10% is just a made-up number. But I think the general point stands.

C Tilli

Good point. I'm unsure what the best practise in editing previous comments is - I don't want to change it so much that the subsequent comments don't make sense to another reader. Clarified now by leaving in the original number that fits with the reasoning around it while keeping the correction in brackets.

Jc_Mourrat

I think it would also be worth keeping in mind how hard it is to make progress on each front. Given that there seems to be widespread non-therapeutic use of antibiotics for farmed animals, and that (I believe) most people have accepted that antibiotics should be used sparingly, I would be surprised if there were no "low-hanging fruits" there. This is not meant as a complete solution, but rather is an attempt to identify our "next best move". I would believe that cheap in-farm diagnostic tools should now be within reach as well, or already existing.

Separately from this, I admit being confused about the nature of the question regarding the importance of dealing with over-use of antibiotics in farmed animals. My understanding is that we know that inter-species and horizontal gene transfers can occur, so is the question about knowing how much time it takes? I just don't have a clear model of how I'm supposed to think about it. Should I think that we are in a sort of "race against bacteria" to innovate faster than they evolve? Why would a delay in transfer to humans be a crucial consideration? Is it that antibiotic innovation is mostly focused on humans? Is there such a thing as a human-taylored antibiotic vs. farmed animal antibiotic? I suppose not? I cannot wrap my head around the idea that this delay in transmission to humans is important. So I guess I'm not thinking about it right?

[Added later:] Maybe the point is that if some very resistant strain emerges in a farmed animal species, we have time to develop a counter-measure before it jumps to humans?

wen

Thank you for this post! I gave a strong upvote because this claim has been growing in strength in animal advocacy communities, and I have often thought that we need to examine it and make sure it actually makes sense, or it damages our credibility.

I realise now that I've actually been sceptical about the claim 'More than half of the antibiotics today are used for meat production'. This seems to be correct; this article says 73% of antimicrobials^[1] sold are used in animals (which I think cites an article by Van Boeckel et al 2017, in Science, but I can't access these articles). I also formerly believed this was predominantly a US issue, given the scale of poorly regulated factory farming there, but it's actually China that is the biggest consumer of veterinary microbials, in both absolute and relative terms.

This paper suggests 'user fees', i.e. taxes, on veterinary antimicrobials. This seems like it could have very bad consequences on food prices, supply, and thus nutrition in low and middle-income countries, which the paper says have more elastic demand. Do you have views on this?

Additionally, one potential negative consequence of this narrative is that improved farm biosecurity might be a strong solution to prevent antibiotic resistance from crossing over to humans. And this would probably entail making farms more technologically sophisticated, more intensive, and bigger, which tends to be much worse for animals.

Not sure if the distinction between antimicrobials and antibiotics makes a big difference. ↩︎

Will Bradshaw

If taxation on vetinary antimicrobials increases the price of meat (both because of the need to pay for antimicrobials and the reduced growth rate if less is used), that seems strongly positive to me. Higher prices means less demand for meat means fewer animals in factory farms.

It's not obvious to me that improved biosafety on factory farms would entail making them bigger; they're already pretty enormous, and it's not clear to me how the costs of biosafety would scale with size (this is a weak opinion, I wouldn't be surprised to change it). But in any case, are smaller (but still very big) factory farms any worse for animals than even bigger factory farms? If I imagine doubling the size of a modern (enormous) chicken factory farm, that doesn't obviously seem like it makes the lives of the chickens any more torturous than they already are.

wen

Ah, I was thinking primarily about low and middle-income countries for both of these.

I am a big fan of 'internalising the externalities' of meat production by making prices higher in developed countries, but I think this becomes a more ethically and strategically complex tactic when we're looking at places where people are already spending large proportions of their incomes on food, are in calorie deficits, etc.

You're probably right that improving biosecurity on factory farms might not make a big difference to antibiotic resistance and animal welfare. I'm thinking of improving biosecurity on smaller farms / closing smaller farms and encouraging larger farms because of their better biosecurity, which is already happening in China (haven't read this particular article but seems like an appropriate source).

Will Bradshaw

Yeah, I agree that biosafety concerns leading to consolidation, and thus reducing animal welfare, is more of a concern in countries that are on the threshold of industrialising farming. Though I'd guess it would usually be a fairly minor effect compared to the general rising demand for meat as wealth increases, (a) that might not always be the case (China had a catastrophic pig pandemic recently, so I bet safety incentives there are very strong right now), and (b) given how ethically disastrous factory farms are, a small effect could be enough for the thing that caused it to be net bad. (I also haven't read the article)

As far as people in poorer countries getting cheaper meat, I agree it becomes more complex, but I'm still pretty confident that fewer factory farms is robustly net-good. I don't think meat is sufficiently important to a healthy diet that giving people more of it in exchange for torturing vast numbers of animals is a good trade-off anywhere, even instrumentally, and I'd also guess that if meat gets more expensive there are other dietary luxuries people can transition to on the margin that are only slightly less pleasant.

That's just concerning the direct ethical effects, though. I can't speak to strategic considerations.

C Tilli

Thanks a lot for your comments! I don’t have a strong view on what is the best way to reduce the use of antibiotics in agriculture, but it seems important to adapt to the specific context. I live in Sweden where it’s forbidden to use antibiotics for prophylactic or growth-purposes in agriculture, and that works well here, but in some countries a ban might be hard to enforce, or lead to corruption and unmonitored use, or else have very negative consequences for financially vulnerable farmers. I remember reading somewhere about some kind of insurance/compensation program for poor farmers that reduce or quit use of antibiotics, but I couldn’t find it right now – will look and see if I can and add a link.

When it comes to the adaptations in farming that could reduce risk (apart from reducing meat production), I would think it’s likely they would be related to improved animal welfare since you need to keep the animals in better conditions to prevent infections if you don’t want to prevent or treat them with antibiotics. To lessen the risk of transmission would be a matter of improved hygiene, which I don’t see as having obvious negative consequences.

In general I would think (without having thought a lot about possible scenarios) that higher meat prices should be a good thing, as long as there are other good alternatives for nutritious and affordable food that people choose instead. But I don’t know what the actual effects of such price changes are.

talk2sarahw

Antibiotic resistance (AR) in animals is a formidable threat as a One Health issue. One Health means that a disease crosses all boundaries to infect animals, humans, and the environment. Noticeably, there is a high death toll from AR from food and animals: 20-30% of over 2.8 million cases are caused by such bacteria, according to the Center for Disease Control and Prevention (CDC) (2019; 2020). In essence, this equates to over 560,000-840,000 cases. Overall, this discussion will address the key considerations of USDA's mechanisms to prevent AR, AR in animals being overlooked, and effective primary prevention methods.

Currently, the USDA has mechanisms like the "withdrawal period" and random meat inspection to prevent antibiotic resistance. Specifically, the "withdrawal period" is the amount of time that needs to be passed for an animal to metabolize the antibiotic fully and excrete the antibiotic residue so that the farmer can legally slaughter the animal (USDA, n.d.; The Meat We Eat, 2017). Although this seems safe, the USDA's Food Safety Inspection Service (FSIS) randomly samples meat upon slaughter to discard meat with dangerous levels of antibiotic residue, rather than systematically sampling all products (USDA, n.d.; The Meat We Eat, 2017). As a result, there is still a noticeable risk for AR meat.

My main concern is the existence of AR in animals that flies below the public radar. AR causes common infections to be nearly untreatable: this may occur among millions of animals to cause excruciating pain. Specifically, inadequate animal rights, profit-driven industry, and inadequate inspection frequencies may cause ineffective oversight of proper antibiotic administration. This is concerning because the most common antibiotic uses are for growth and prophylaxis--as a means to prevent production diseases. After speaking to an Animal Charity Evaluators representative, I learned that a significant pervasive issue is the inadequate frequency of auditing on animal farms. As a result, farmers are given adequate opportunities to neglect animals via legal loopholes. Overall, antibiotic resistance causing suffering animals is an important point that should be considered.

Lastly, people should focus on primary, rather than tertiary prevention. Primary prevention occurs before the disease occurs, while tertiary prevention occurs after the disease occurs to prevent disability. Primary prevention includes creating sanitary farm conditions and using vaccination over antibiotic use. For example, Norway eliminated antibiotic use in fish over the past decades by transitioning to vaccination, a safe and effective method to prevent antibiotic resistance (AR) and infection, according to the World Health Organization (WHO) (WHO, 2015). To counter concerns of vaccination causing fish stress, immersion vaccination is known to cause much less pain while being relatively effective compared to injection vaccination (Komar et al., 2006). Overall, antibiotic stewardship to animals should be the last resort via opting for primary prevention.

Comments

C Tilli

Edit: I originally made mistakes in the calculation below, have edited to correct this. See comment below by willbradshaw for details of the calculation.

Thanks! I completely agree there are other strong reasons to reduce (or eliminate) factory farming.

Not sure if the distinction between antimicrobials and antibiotics makes a big difference. ↩︎