Antibiotic Resistant Bacteria

Animal Manure Management April 16, 2015 Print Friendly and PDF

Antibiotic resistant bacteria

               A major area of concern with the general public has focused on the potential for antibiotic resistant bacteria that reside in both animal manures and biosolids, due to the potential for subsequent transfer of the resistance to pathogens. Bacteria are prokaryotic organisms with the ability to metabolize and replicate very quickly.  They are also very adaptable genetically.  When confronted with an antibiotic, there need only be one bacterial cell with a genetic or mutational change that confers resistance to that antibiotic that subsequently allows for the proliferation of antibiotic resistant bacteria.  Thus the more that antibiotics are used, the greater the likelihood of antibiotic resistant strains developing.  The greatest concern with antibiotic resistance is the potential for human pathogenic strains to become resistant to overused antibiotics, which subsequently cannot contain the infectious agent.  As is typical in most niches, commensal bacteria tend to dominate the pathogenic bacteria at levels which are orders of magnitude greater than the pathogens.  This creates a haven for antibiotic resistance genes, which all have the potential to transfer to true or opportunistic pathogens.  The widespread, sometimes indiscriminant, use of antibiotics has raised the questions: i) “Can antibiotic resistant genes be transferred from nonpathogenic bacteria to human pathogenic strains in the environment?” ii) “Can antibiotic resistance in the environment, via residual land application, be transferred to the public?”

Brooks (2006) evaluated the incidence of antibiotic resistant bacteria (ARBs) in biosolids and a variety of other environmental samples and foodstuffs.  Table1.docx shows that Class B biosolids did not contain unusually high numbers of ARBs, and that in fact, the relative incidence was less than that found in pristine soil.  Interestingly, ARB concentrations were also lower than those found in common foodstuffs such as lettuce. Therefore food itself could be an important route of exposure to ARBs.  Rates of gene transfer in soil are thought to be a relatively infrequent event without selective pressure (Neilson et al., 1994), which reduces the risk of antibiotic resistant gene transfer to human pathogenic bacteria. Finally, note that soil itself is the original source of human antibiotics.

               Antibiotic use in the livestock and poultry industries has gradually increased over the past three decades in direct relation to the increasing number of CAFOs in operation.  Throughout this gradual cultural shift in livestock production, the need for antibiotics has increased as stocking densities and production cycles have increased.  The Union of Concerned Scientists predicted the number of antibiotics used in the industries at up to 50 million pounds annually (Chee-Sanford et al., 2009), with nearly half being used as a means to increase production.  The Animal Health Institute refutes this number stating that approximately 20.5 million pounds of antibiotic are used annually with approximately 1/10 of these used to increase production (Chee-Sanford et al., 2009).  These discrepancies highlight how little is known regarding this topic, and how contentious these issues truly are, particularly with news-cycles reporting increasing antibiotic resistance in our food supply or higher incidences of nosocomial infections.  Regardless, livestock industries account for a large amount of antibiotic use in the United States.  Antibiotics are used: 1) to treat infections and to prevent diseases; and 2) as a prophylactic, thus increasing production.  It is with the latter, that most concern or blame is placed. 

               In either case, as opposed to human antibiotic use, treating livestock with antibiotics is conducted in a manner that promotes the treatment of non-diseased animals.  Typically, CAFO animals are not individually treated for a disease.  If there is an outbreak of a disease-causing pathogen, farm managers typically react by not treating just the diseased individuals (perhaps only 100 of 20,000), but by treating the entire flock or herd.  This increases the likelihood for antibiotic resistance, as resistance genes can be promoted in healthy as well as diseased members of the host population.

               Brooks and McLaughlin (2009a) and Brooks et al. (2010) described the presence of antibiotic resistant bacteria in swine and poultry CAFOs.  The presence of antibiotic resistant bacteria in swine CAFOs appeared to be influenced by the type of management employed by the producer, specifically; the presence of younger piglets increased the amount of resistance in commensal E. coli.  In general, younger piglets led to resistance to an extra class of antibiotics (Brooks and McLaughlin, 2009a).  In some instances, regulatory and media pressures have forced industries to reduce antibiotic use, as has been noted in the poultry industry.  Brooks et al. (2010) noted the overall lack of antibiotic resistance in poultry CAFO manure, and an overall decrease among staphylococci, enterococci, and E. coli when compared to previous studies (Brooks et al., 2009a).    

                 Ultimately, the concern is for the potential movement of antibiotic resistant bacteria and genes from the “farm to the plate”.  Movement from the farm to the product and ultimately the consumer remains a poorly understood area (Marshall et al., 2011).  Three potential routes exist for the transfer to occur: 1) via consumption of undercooked food; 2) clonal spread from the occupationally exposed; 3) or from indirect manure contamination onto fresh food crops (e.g. environmental spread).  Sufficient evidence exists to support clonal spread from the occupationally exposed (Marshall et al., 2011), while the other two routes are poorly understood.  Contamination of fresh food crops either via runoff, land application of manure/biosolids, or feral animal has been hypothesized as a potential sources of contamination (Brooks et al., 2012a).  Antibiotic resistance phenotypes have been demonstrated to move via aerosols or runoff, though in very small amounts and over small distances from the CAFO (Brooks et al., 2009b, 2012b; Chinivasagam et al., 2009).  Brooks et al. (2009b) demonstrated that runoff from plots receiving litter was more concentrated with antibiotic resistant enterococci, which was characteristic of the litter and thus demonstrated that antibiotic resistant bacteria will transport as readily as any other bacteria.

Modified from Environmental Microbiology, 3rd Ed, Ed. I.L. Pepper, C.P. Gerba, and T.J. Gentry.  Chapter 26 "Land application of organic residuals: municipal biosolids and animal manures" by J.P. Brooks, C.P. Gerba, and I.L. Pepper.  

Question or concerns, contact John Brooks (

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This work is supported by the USDA National Institute of Food and Agriculture, New Technologies for Ag Extension project.