Superbugs

While advances in technology have greatly affected nearly every aspect of modern farming, equivalent leaps in drugs and chemicals used with livestock and produce have led to higher yields, larger cattle producing more milk or meat, and greater resistance to disease, weather extremes, and nearly the entire range of problems that have decimated herds and frustrated farmers for millennia.

At the same time, the widespread and growing use of antibiotics, pesticides, and genetic engineering and bioengineering on or near what eventually will go on a consumer’s plate has raised concerns at state, federal, and international agencies, and with the general public.

The result has been a mixed bag of new regulations, potential international boycotts, both improvements in production and higher operating costs for farmers – and growing opportunities for the expansion of a new class of “niche” farms.

Antibiotic resistance tests; the bacteria in the culture on the left are sensitive to the antibiotics contained in the white paper discs. The bacteria on the right are resistant to most of the antibiotics. Photo by Dr. Graham Beards

Antibiotic resistance tests; the bacteria in the culture on the left are sensitive to the antibiotics contained in the white paper discs. The bacteria on the right are resistant to most of the antibiotics. Photo by Dr. Graham Beards

“In general, it’s clear that food and food-related issues are much more salient in the debate in Congress and across the country than even five years ago. Consumers are showing a lot more interest in how and where their food is being produced,” noted Pat Westhoff, Ph.D., an Iowa farm boy who served on the U.S. Senate Agriculture Committee staff (1992 to 1996) and now is director of the University of Missouri-Columbia Food and Agriculture Policy Research Institute.

“There definitely is a market for products seen as being safe and healthy for consumers and good for the environment. So those once very niche, small markets have become a larger share of the overall farm economy and have enabled a lot more very small farms to provide a living where conventional crops and farming would not.”

The bulk of research and data collection on many drug-related farm issues falls not to the U.S. Department of Agriculture (USDA), but to the Food and Drug Administration (FDA) and FDA programs such as the National Antimicrobial Resistance Monitoring System (NARMS).

NARMS was created in 1996 as a collaboration between the FDA, CDC (Centers for Disease Control and Prevention), and USDA. Data collected from humans, animals, and retail meat on antimicrobial resistance are tested for vulnerability to a battery of antimicrobial drugs and monitored for changes over time.

“The focus really is on foodborne pathogens, such as E. coli, and whether they are still susceptible to a variety of classes of antimicrobial drugs,” said Bill Flynn, D.V.M., Ph.D., a veterinarian who serves as the deputy director for science policy at the FDA’s Center for Veterinary Medicine. “It provides information to us and the public, more generally, relating not only to human populations but also what we’re seeing in food-producing animals and retail meat products.

“Antibiotics have been used in animals for many decades and play an important role. We have data we collect and report out on the quantity of antibiotics sold for that use, but sales and distribution data don’t necessarily represent actual use at the farm level. We don’t have current data on that, but efforts are under way to gather better data on use practices over time.”

The concern about antibiotic use on livestock mirrors those surrounding their use in humans. If too much is given too often, the targets of such treatments may develop immunities. The result would be “superbugs” – microbes against which current science has no other defense. A similar result can develop with the improper or overuse of pesticides or other chemicals.

According to data published by the FDA, more antibiotics are sold nationally for food-producing animals than for people, which contributes to the rise of antibiotic-resistant bacteria in food-producing animals. USDA photo by Lance Cheung

According to data published by the FDA, more antibiotics are sold nationally for food-producing animals than for people, which contributes to the rise of antibiotic-resistant bacteria in food-producing animals. USDA photo by Lance Cheung

In large part thanks to Hollywood, there has been a growing public aversion to plants or animals that have been genetically engineered for size, disease and pest resistance, or the ability to thrive in previously too-harsh environments, including those with minimal food and water.

“Strong financial pressures have driven the industrialization of U.S. livestock farms,” states a 2009 USDA Economic Research Service (ERS) report titled “The Transformation of U.S. Livestock Agriculture.” “Larger operations are able to realize lower costs and higher returns, while tighter coordination among firms at different processing stages can reduce financial risks.

“But growing to a more efficient scale also concentrates livestock in a limited area – and excess concentrations of manure-based nutrients can lead to increased air and water pollution. Large operations are also more prone to use antibiotics intensively in order to preempt the spread of animal disease and to accelerate animal growth. Extensive antibiotic use in livestock raises concerns about increased pathogen resistance and related risks to human health.”

Changes related to larger farms, often with more pen-fed beef and dairy cattle, hogs, and chickens, has benefitted from economies of scale in applying new technologies, drugs, and chemicals, ultimately resulting in lower consumer prices. However, the researchers added, “structural change in livestock agriculture has had less felicitous effects, as well,” especially as animal wastes become more geographically concentrated in the United States.

“High concentrations of animal manure can lead to increased air and water pollution, with adverse health and environmental consequences. … A heavy reliance on antibiotics for growth promotion and for disease prevention may spawn antibiotic-resistant strains of bacteria, with human health risks,” they wrote. “Changes in farm structure are intertwined with these concerns because larger operations concentrate manure more and rely more heavily on growth-promoting antibiotics than smaller operations.”

Growth-promoting antibiotics also are a feature of industrialized hog and poultry operations, where sub-therapeutic doses of antibiotics routinely go into their feed and water. However, many producers still reject the routine use of antibiotics, relying instead on alternative strategies, such as extensive testing and sanitary protocols, to prevent disease and promote growth. In some cases, such alternatives involve little or no additional cost, but in others, labor and resources may be both expensive and time consuming.

“Individual producers may have little incentive to take costly actions to mitigate the harmful effects of livestock industrialization. Livestock production is highly competitive and operations with high costs may jeopardize their own survival in policing themselves. However, steps can be taken, at modest cost, that preserve the benefits of industrialized livestock production while limiting its harmful effects,” the report concluded.

chicken superbug salmonella

While it is not unusual for raw poultry from any producer to have Salmonella bacteria, it is uncommon to have multidrug-resistant Salmonella bacteria. USDA photo by Alice Welch

ERS researchers previously reported a number of high-profile cases of Salmonella and bovine spongiform encephalopathy (BSE) – aka, “mad-cow disease” – which brought heightened international attention to the use of antibiotics in food animals. That was further complicated by the limited scientific understanding – by the public, news media, and government officials – of the implications for human health. The U.K. cattle industry, in particular, was nearly destroyed by repeated BSE crises, each of which led to reduced beef consumption in the European Union (EU) and stricter import controls, both within the EU and by other nations, including the United States.

The negative impact of BSE was not limited to food, however. Because bovine byproducts are used in a wide range of industries, including cosmetics, medical, pharmaceutical, animal feed, and others, trade restrictions are felt across many sectors. That demonstrated not only the breadth of markets for agricultural products, but the widespread negative impact such increasingly common practices as antibiotic use can have on local, regional, and even global economies.

Members of the World Trade Organization are not bound by a common set of export controls on farm products, but can create their own – often quite different – regulations. The science and technology revolution in agriculture also comes into play there, where increasingly sensitive monitors have greatly improved the ability to detect pathogens. That has led some countries to adopt a zero tolerance standard. However, as some pathogens appear to be common in the global environment, precision detection tools may combine with efforts to achieve zero risk to result in some nations banning all imports.

Since the development of antibiotics decades ago, the U.S. Congress and lawmakers worldwide have debated the prohibition or severe restriction of their use in food animals.

“Resistance is a very complicated issue, with multiple ways in which bacteria can become resistant to various drugs. That can occur naturally, but using these products can drive resistance to emerge in bacteria,” Flynn said. “Bacteria can be shared between animals and humans, including disease-causing bacteria. Food products derived from animals could be exposed to those and so humans downstream could become sick as a result. That is further compounded if that bacteria also is resistant to a drug doctors typically use to fight it, which would affect the outcome of a patient’s treatment.

“Looking at it from an animal health perspective, these drugs have played an important role in treating and preventing disease, so having bacteria become resistant could be detrimental to managing disease in animal agriculture. We are looking at what options we have to gather additional information to get a better understanding of use practices at the farm level and hope to seek further public input this year.”

According to APHIS, antibiotic selection should be based upon the following key factors:  characteristics of suspected or confirmed bacterial organism(s); prevalence of antibiotic resistance mechanisms in the suspected or confirmed bacterial organism(s); ability to reach site of infection at an effective concentration; animal species and their potential for human consumption; and dose, frequency, duration of therapy, and route of administration of available antibiotic formulations. Photo source: Dani Ausen; Iowa State University

According to APHIS, antibiotic selection should be based upon the following key factors: characteristics of suspected or confirmed bacterial organism(s); prevalence of antibiotic resistance mechanisms in the suspected or confirmed bacterial organism(s); ability to reach site of infection at an effective concentration; animal species and their potential for human consumption; and dose, frequency, duration of therapy, and route of administration of available antibiotic formulations. Photo source: Dani Ausen; Iowa State University

The pharmaceutical industry also is looking at new uses of their products as part of the drug approval process and Flynn expects good cooperation with the most recent FDA proposal regarding antibiotics.

“In December 2013, we published a three-year plan that asked the pharmaceutical companies marketing these products to work with the FDA in changing them from over-the-counter [OTC] status to requiring a veterinarian’s oversight. Once that is done, it becomes mandatory for users downstream to get prescriptions in order to acquire and use those drugs. Even though it is voluntary for the pharms, we expect a high rate of cooperation,” he said.

“We need to be judicious about how and when we use these important tools for treating disease in animals. Our proposal to take all medically important antibiotics currently being marketed OTC for food-producing animals and create a new labeling status requiring an authorized prescription would be a significant change in how these products have been available for decades – and in how animal producers work and consult with veterinarians.”

USDA’s Agricultural Research Service (ARS) also works with the Animal and Plant Health Inspection Service (APHIS) and NARMS on periodic surveys of various industry segments on related issues and supports studies into alternative approaches to animal husbandry.

At the ARS Jornada Experimental Range near Las Cruces, N.M., for example, research animal scientist Dean M. Anderson is studying range animal ecology – so-called “free range” livestock raised without the use of special feeds or drugs.

“Many people might think an animal scientist is focused on feedlot nutrition, but I look at animals that gain their nutrition foraging on native rangeland – and, where I’m at, [it’s] mostly arid land. There obviously are some exceptions, but every bovine starts its life tied to a foraging environment rather than a confinement situation,” he explained.

As has been true for more than a century, domestic cattle and sheep raised in 17 western states gain most of their nutrition from the sparse vegetation they find while walking across hundreds or even thousands of acres of barbed wire fence-enclosed rangeland.

“Our area at Jornada has been trying to improve the efficiency of the plant-animal interface, to use innate animal behaviors to improve efficiency of production, both in terms of how we harvest the forage and the labor requirements to manage free-ranging livestock,” he said. “My focus has been to use the best genetics adapted to this area.”

Anderson said he was not referring to genetic engineering, but in finding those animals best suited by natural selection or breeding to forage on wild grasses and native shrubs, normally growing without any chemicals or irrigation. The key is to achieve uniform use of all range land; in his case, by combining 21st century technology with natural behavior to move animals over the landscape to prevent both over- and underuse and, in so doing, produce healthy food animals free from drugs and chemicals.

“Before humans became involved, animals moved freely, according to the ‘green-up’ – when the temperature rises and plants start growing in the spring, compared to dormant forage, which is basically brown. Think of it like fresh bread versus bread that has been sitting on the shelf for a week or so. When animals were domesticated, herding became the art form used to place them in the right location for the right amount of time,” he explained.

“But when barbed wire fencing came along, we basically did away with the herding approach and stocked the enclosed area based on the relationship between what each cow needs and what the land can provide. But that’s what led to over- and underuse. Since 1926, there have been at least 68 different things tried to improve animal distribution – change the location of water or supplements, place shade or fertilizer in certain areas, burn other areas, and so on. Some have been beneficial, some not; some worked synergistically, some not.”

How and when antibiotics are used in food animals has become an international concern, leading researchers to look both forward to new ways to treat disease and increase production and back to the best practices of animal herders through the centuries.

“The steps we’re taking are not out of line with what other countries have done to address this issue. We also make an effort to collaborate as much as we can with other countries and learn what we can from their experiences and actions taken,” Flynn concluded. “Given the multi-factorial nature of this issue, which is very complicated – there is no one single problem that can be pointed to – and challenging to articulate, it is hard to ensure everyone is well informed. But it is important that we do a better job of informing the public.

“Obviously, based on the sheer scale of the U.S. agriculture industry, a lot of variables may play into driving the need for the use of antibiotics. This is a cost for producers, so there is some incentive for them to find ways that are more efficient, but that also will vary considerably among the different types of operations we have out there. And vets will play an increasingly important role in making sure these drugs are used properly.”

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