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Article Edits: Antibiotic use in livestock
Original article: Antibiotic use in livestock

Topics to cover:

Molecular Biology

Effect in Humans

Risk Assessment

Mechanisms of Transfer

FDA and risk assessment
When it comes to quantifying the risks towards humans from antibiotic usage in live stock, there are several barriers to identifying direct causation. The topic itself covers everything from epidemiology, ecology, and molecular biology. Many models for risk assessment rely on the Impact Fraction, or the etiologic fraction, which is a specific link in an ecologic chain between animal antibiotic usage and epidemiological outbreaks. For example, tracking an epidemiological outbreak must incorporate the ecology of the source, the molecular biology of the organisms themselves, and then show correlation to an event.

The Food and Drug Administration categorizes potential antibiotic usage and negative effects in the human population in 3 tiers. These tiers categorize the likelihood that bacteria acquire resistance to antibiotics before ending up in food and subsequently result in adverse effects to human health as: low, medium or high probabilities .These categorizations determine the impact, or risk, of antibiotic resistance residing in human intestinal flora with calculation for an acceptable level of risk to human health.

In general, the work towards risk assessment models are very unfinished and often contradictory. These incongruences mostly result in hard to pinpoint generalities about usage and risk for adverse health effects. In the past 40 years of research on indirect effects of antibiotic usage, it is becoming harder to disprove the problem is directly linked to antibiotic usage. However, arguments still arise about the proportion of resistant infections that are caused by antibiotics used in livestock. Additionally, the research to better understand the molecular level of how bacteria spreads from livestock to human needs to be more concrete and unidirectional. In essence, resistance is difficult to predict and varies dependent on strain of bacteria and populations of people.

Regulation
The Food and Drug Administration allows four uses for antibiotics in livestock populations: Disease treatments, disease prevention, disease control, and growth promotion. Disease treatment differs from disease prevention in terms of when the antibiotics are used. Treatments are administered after bacterial infection has affected a group of animals. Prevention is prophylactic usage, or administered before there is an infection. This would be prevalent in a group of healthy animals not near or in the general vicinity of infected animals. Disease control is the targeting of animals in or near a group with a few infected animals. Growth promotion is beginning to be largely banned by countries or, in some cases, large meat suppliers choose to purchase livestock grown without antibiotics. The reasons why antibiotics increase growth efficiency are generally agreed to be due to modifications to the rumen flora microenvironment and the molecular biology of the intestinal bacteria.

The Food and Drug Administration estimates 80% of antibiotics, or 15.4 million kilograms of antimicrobial agents, in the United States are used on livestock. The rest is allocated for usage in the medical field.

Concentrated animal feeding operation (CAFO)
Concentrated animal feeding operations (CAFO) refer to large, often multi species, farming operations which lead to close animal housing quarters, rampant infections and disease, among many other malaises.

These animals are sedentary due to the lack of space in the cramped cages. They often catch disease due to the packed rooms and ease of transmission among the manure, blood and bodily fluids. The current justification for these conditions is the belief that due to the animals not roaming, they save energy and therefore better digest their food. This energy is reserved for growth of the animals. Antibiotics can also be administered to animals for the promotion of growth. This practice is being largely diminished however, as regulatory agencies limit it's practice. However, these animals are all fed from the same supply of food or water, so any antibiotics administered to a diseased minority would affect all the animals in a specific area. The conditions of these animals and the additive agents used to treat them contribute to a myriad of problems such as manure production, contaminations and effects on human populations.

Manure
The large amounts of manure produced in cattle livestock populations are a problem for many concentrated animal feeding operations. Dependent on size of the operation, there can be 2,800 to 1.6 million tons of manure produced per year. This range is approximately 3 to 20 times more manure than people in the United States produce annually. However, many operations lack ultimate sewage treatment plans for CAFO manure production, as opposed to humans in cities which have several water treatment practices.

The manure produced from concentrated populations of animals can be diseased and have negatives on the environment itself. Some of this manure can be treated and used as fertilizers, but larger operations often revert to storing it until it can be disposed of properly. Livestock manure can be tainted by blood, pathogens such as E.coli, antibiotics, growth hormones, chemical additives, etc. Dependent on the operation, manure is managed by ground application plans. This involves the liquefying and spraying of waste for fertilizer. Manure is also trucked off site, stored in containers, or held in holding ponds. Typically, there can be problems associated with storing manure. Manure can have detrimental effects on the surrounding area due to leaking containers or holding ponds. This event, known as manure leaching, can lead to manure run off effecting the ground or soil water by percolation or direct contamination.

Groundwater contamination
When manure run off or percolation enters a water system, the infecting agents thrive in that environment. Previous studies have shown private well-water in Idaho found high levels of veterinary antibiotics as well as additive chemicals. The surrounding areas of concentrated animal feeding operations are at particular risk for groundwater or soil water sources of contamination. When manure enters a water source, either underground or above ground, whatever pathogens inhabiting the manure enters the water as well. All the agents inside the manure can contaminate a water source. This is because pathogens survive longer in groundwater than surface water due to lower temperatures and protection from the sun and other harsher elements. Additionally, this water will not be treated until far later in the process, allowing bacterial colonies to grow.

Groundwater is one of the larger sources of water that humans are supplied from. As of 2010, 53% of people in the United States relied on groundwater as their primary source of drinking water. Groundwater also gradually leads to surface waters, such as rivers and streams. Thus, leading to surface water contaminations. Water as a contaminant is a major source of outbreak in human populations. In several reviews of epidemiological outbreaks, the areas around concentrated animal feeding operations are typically at a higher risk of exposure to antibiotic resistant bacteria strains and subsequent outbreak event.

Antibiotic usage
The living conditions of animal feeding operations leads to a shotgun approach at targeting a sick population of livestock. Due to denser amounts of animals in smaller spaces, illness spreading and affecting a few animals can signal a precursor that more animals in an area will be infected by pathogens. In the United States, 80% of all antibiotics are given as feed additives .The antibiotics given to treat all the animals in dense area are not specific to each animal's illness and use a general approach to dosing. This leads to the antibiotics not being fully metabolized by the animals. This has been tested by levels of antibiotics still present in the manure of these animals.

Vectors
A vector, in this context, is an organism that transmits disease to another organism. Insects such as flies and mosquitoes have high amounts of breeding grounds and nests of eggs around manure waste, allowing rapid reproduction and fresh vectors for potential disease. Typically with dense populations of livestock, transmission of disease from one animal to another can be on account of insects, such as flies, mosquitoes or ticks, spreading blood from one animal to another. This can be particularly dangerous for sick animals spreading diseases to healthier animals, promoting general malaise in a concentrated area. Additionally, the animals can be infected from other animals' manure making contact with their food. In fact, fecal-oral transmission are one of the largest sources for pathogen transmission. Within concentrated animal farming operations, there is no mandatory testing of novel viruses, only reporting known illnesses to the World Organization for Animal Health. Thus, certain mutations or recombinant bacteria strains, which are more efficient in translation to human to human events, can be unnoticed.

Additionally, insect beds around manure pools or containers are a particular threat for contamination. These insects feed and reproduce in the runoff of treated manure, so they can acquire resistant strains of bacteria from blood and the manure of livestock treated with antibiotics. Since most manure holding ponds are on or near the sites of the operations, the insects are not far from livestock populations. These insects are also particularly dangerous because they can spread bacteria or other pathogens to humans by infecting human food. This is prevalent when treated manure is used as fertilizers of liquefied for spraying. Additionally, as a result of the unsanitary handling of meat in kitchens.

Horizontal Gene Transfer
A vector, in this context, regards the genetic definition, describing that in horizontal gene transfer, a resistant bacteria can transfer mutation traits in the form of vectors. These mobile genes, or plasmids, carry the necessary genetic information to spread resistant traits to bacteria of different species.

Effects in humans
The effects of antibiotic usage in livestock transferring to humans has been well documented for over 40 years. It was first documented in 1976, where a study followed a novel antibiotic being used in livestock. The bacteria in animals and workers were regularly followed to record translational effects. The findings revealed that within 2 weeks, the bacteria found in the guts of animals fed antibiotics were resistant to the new antibiotic. Additionally, the resistant bacteria had spread to farm's laborers within 6 months. The bacteria in the stool of the laborers were tested and contained more than 80% resistance to the initial antibiotic given to the livestock. Since the primary study, there have been many well documented events showing that antibiotic usage in livestock results in direct influence of antibiotic resistance in humans.

Major bacterial infections in humans can be traced back to livestock. The family of bacteria, Enterobacteriaceae, include many opportunistic pathogens. These bacteria are commonly found in livestock and commercial meats. These include Escherichia coli, Klebsiella and Staphylococcus aureus. Representing urinary and digestive tract infections, skin infections and bloodstream infections- they account for a significant portion of antibiotic resistant bacterial infections.

These resistant strains of bacteria are easily transmitted between one farm animal to another, between humans, and between animals and humans. Besides being a threat to health in essence, they also carry genetic information that can lead to other bacteria spreading and gaining resistant traits in humans, or acting as a vector for desirable plasmids. Thus, not only is there a direct threats of infection from them, but also the implication that other bacteria in a person can acquire the mutant traits of antibiotics resistance.

Spread to humans
Antibiotic resistant bacteria can spread to humans through a variety of routes including: soil and groundwater, direct contamination of farm workers, insect vectors, and infecting meat during the butchering process. From the livestock to worker perspective, this puts entire communities of people at risk of acquiring antibiotic resistant bacteria. Articles such as clothes or materials can indirectly and unintentionally aid the transmission of these resistant strains of bacteria to larger human populations.

Sampling of retail meats such as turkey, chicken, pork and beef consistently show high levels of Enterobacteriaceae. Rates of resistant bacteria in these meats are high as well. Sources on contaminated meat put humans at direct risk by handling the meat or ingesting it before it is completely cooked. In these instances, we are ingesting the living bacteria as well. Ingesting contaminated meat sources, as mentioned above, account for 20% of antibiotic resistant infections in humans.

Potential Article Editing
Antibiotic prophylaxis

I would like to focus specifically on use in cattle and the effects in human populations. I have some background knowledge here so that would be helpful, and I found good starting materials here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3234384/

Additional sources in my notes from a course I took a few years ago

Dan Brock

bioethicist with views on cloning. This would be more in line with bioethics, but his wiki page itself is bland and doesnt have information on the work he has done and arguments he has. More information can be added relating it to what ethical views he has, etc.

Broad overviews of his arguments can be found on many .edu sources http://hettingern.people.cofc.edu/Nature_Technology_Society_Fall05/Brock_Cloning_Human_Beings.htm

John Lacy

Bioethicist with views on physician assisted suicide. As above, can be written with his arguments presented and some arguments directly against his. His wiki page is really a biography but doesn't go in on this rather sensitive subject. His arguments can be found in published papers and .edu sources.

http://frontiersmag.wustl.edu/2016/04/02/the-reality-of-physician-assisted-suicide/

Article Evaluation :
Antibiotic resistance in gonorrhea

Notes:

The majority of citations in a paragraph or section are from the same source, and there are recurring sources throughout the paper. The sources for the most part are of reputable, world wide data base sites so that'd good.

The position is quite neutral. it really just presents facts on multiple aspects of antibiotic resistance.

The only non neutral positions are when the article posts on why some treatments don't work. But that's more of the history and mechanisms behind why something works, which is rather scientific and historical at times. No real bias in the paper.

Large amount of history to the article. Showing gramatical misunderstanding and making sure courses are better cited.

Edits are relatively recent, so information seems to be up to date.

The real distractions to the paper are that some of the information is dense, and not well translated from data bases. So it can be inaccessible to some readers, and not well read back to other readers.

The article is a part of three wikiprojects, all related to microbiology or medicine and health. Pages seem well composed.