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The New Country Doctor and the Clinical Diagnosis of the Farm


A new kind of professional

There are missing professions that would integrate epidemiology, farming and ecology.

These are professions that would deal not just with existing human pathogens on-farm and in the rural environment, but with emerging pathogens and their control or prevention. They would cover the interaction of human pathogens with current microbial ecology, including plant and animal pathogens, and the dynamic evolution of pathogens as they flow to, through, and from the farm and rural environment.

One example: In 2006-2007, I  proposed adding a new kind of medical/veterinary position to Cooperative Extension at Land Grant Colleges. I used the term Medical Extension Specialists. It was an example of one kind of new research professional engaged with human pathogens on-farm and in the farm environment. Although this received support from FDA (1) and from administrators at UC Davis, including the Western Institute for Food Safety and Security (WIFSS), as well as interest from the University of Wisconsin, the financial crisis in the fall of 2008 put an end to this kind of proposed innovation. At UC Davis, additional positions in Veterinary Medicine covered at least some of the same areas proposed for Medical Extension. The reasons for placing these research positions in Cooperative Extension will be discussed below.

A second example would be the “new country doctor” of the title of this article. The meaning is reversed from the usual order: the patient is the country, countryside, farm, watershed or local ecosystem. The resonance of the usual meaning for country doctor is the same: a person who is engaged, informal, knowledgeable, perceptive and skilled. Beyond research there is practice. Like other doctors, the new country doctor would preferentially be more engaged with maintaining the health of a “patient,” such as a farm, or rural community.

Both a traditional and a new country doctor would be concerned with human pathogens in the farm environment. The latter would be more concerned with the ecological dynamics of human pathogen movement between plants, animals and people, and, more specifically, with farming and other practices that prevent the introduction, establishment or development of new, worse human pathogens.

The biological and economic health of farms and ranches for crop and animal production may also increasingly be dependent on understanding and enhancing the microbial ecology of farming and ranching. A new country doctor would have the opportunity to integrate new genomic knowledge and other tools with the complexities of farming in a rural ecology. It could be one of the most interesting professional occupations in which to engage.

Emerging pathogens 

The problem with emerging pathogens is not just that they represent new diseases to combat, or older diseases with new evil twists. It’s that they keep emerging.

The older view was of a static situation: we win; the pathogens lose.

Here is MacFarlane Burnet, 1962 (2):One can think of the middle of the twentieth century as the end of one of the most important social revolutions in history, the virtual elimination of the infectious disease as a significant factor in social life.”

Burnet may have had in mind justifying his own new direction toward the immunology of cancers at a time when the only known infectious cause of cancer was in chickens (Rous sarcoma virus). One battle was won; on to the next one. It was a statement of confidence, if not of fact, and I think that confidence was general at the time: that the immunological, antibiotic and public health tools were available to control infectious diseases (3).

Most of America, including farming and ranching, still lives in Burnet’s conceptual world.

I should emphasize: not just farming and ranching. Otherwise, we would not have antibiotic soaps as common commercial goods, physicians would not prescribe antibiotics for viral diseases and, for clarity, we would call “antibiotics” antibacterials. It’s not just a problem of non-therapeutic antibiotic use in animal production, or apple growers wanting to use last-resort hospital antibiotics for control of bacterial plant pathogens such as fire blight (Erwinia spp., Enterobacteraceae (4a,b). This is still an active debate, in 2013).

The history of the epidemiological response to new pathogens and pathogen evolution can be found in the Centers for Disease Control and Prevention’s initial issue of the journal Emerging Infectious Diseases. Two reviews start the issue, by David Satcher (5) and by Stephen S. Morse (6). Morse’s article is particularly relevant here because of its section on “Ecological Change and Agricultural Development” in human pathogen emergence:

“Ecological changes, including those due to agricultural or economic development, are among the most frequently identified factors in emergence. They are especially frequent as factors in outbreaks of previously unrecognized diseases with high case-fatality rates, which often turn out to be zoonotic introductions….

“Agricultural development, one of the most common ways in which people alter and interpose themselves into the environment, is often a factor. Hantaan virus … causes over 100,000 cases a year in China …. Conversion of grassland to maize cultivation favored a rodent that was the natural host for this virus, and human cases increased in proportion with expansion of maize agriculture ….

“Perhaps most surprisingly, pandemic influenza appears to have an agricultural origin, integrated pig-duck farming in China ….

“Because humans are important agents of ecological and environmental change, many of these factors are anthropogenic. Of course, this is not always the case, and natural environmental changes, such as climate or weather anomalies, can have the same effect.”

Note that the original epidemiological focus on farms and the farm environment was not concerned with food safety. Joshua Lederberg led the team from the National Academy of Science’s Institute of Medicine whose report in 1992 was the foundation for developing institutional responses to emerging infections (7). I did not see any mention of foodborne diseases there either.

However, before it was decided to start a new CDC journal, there was briefly a new section in the CDC’s Morbidity and Mortality Weekly Report (MMWR). The April 16, 1993, issue started with an introduction describing a new series in MMWR on emerging infectious diseases.

The first report in the new section was on the West Coast O157:H7 hamburger outbreak (8), where Jack-in-the-Box is referred to anonymously as “chain A.” In practice, emerging foodborne diseases were an issue from the beginning.

It is easy to forget that finding the human pathogen O157:H7 as a non-pathogenic commensal in cattle was a shock. It was even more surprising to find O157:H7 in or on plants, starting with the apple cider and apple juice cases that were occurring around the same time as the Jack-in-the-Box outbreak (9).

The interaction between human pathogens and plants has continued to be even more surprising, up until today. A brief survey of the research projects and publications of only three labs can illustrate this: Fred Ausubel’s lab at Harvard/Massachusetts General Hospital (10); Maria Brandl’s lab at USDA Albany, CA (11); and Ariena H.C. van Bruggen’s lab at the University of Florida’s Emerging Pathogens Institute (12). There are many others.

A new country doctor, or a Medical Extension Specialist, would have to integrate veterinary, epidemiological, and ecological issues of pathogens, as well as the microbial interactions of healthy farm environments.

The transition from Burnet’s world to a view of dynamic pathogen evolution and emerging infectious diseases seems difficult enough.

For some years, there has been an attempt to create a paradigm shift  to integrate concepts of health and health disciplines “to obtain optimal health for people, animals and our environment.” The overall research program has often gone under the name of the One Health Initiative. The contributions of National Research Council and Institute of Medicine Reports on One Health are reviewed in the current issue of Emerging Infectious Diseases (December 2013) in an article by Carol Rubin, et al. (13). From a food safety perspective, “our environment” would include plants and crops, farms and the farm environment, and food production systems.

The research seems to be ahead of the paradigm shift, but as a concept that might integrate at least some perspectives on farming and food safety with integrated epidemiological approaches, it seems like a welcome approach. It might at least provide a common language.

I actually have higher hopes for integration of approaches in the farm environment and improving produce safety.  

The clinical diagnosis of the farm

“It takes three generations to grow a farmer.” (14)

Farming, in this country, is a highly skilled and complex integrated occupation. It’s also high-risk, both physically and economically. Mitigating economic risk is a constant challenge.

The complexity of farming is reflected in the need for 80 to 100 years worth of historical memory to intelligently guide decision-making. “A year like this one,” just in terms of weather, may most closely resemble a year in the late 1940s for farmers I work with in Eastern Washington. A particular combination of events – like a devastating fire at grain harvest – in my county, Yolo County, CA, may require going back to the 1920s. You may only live once, but over three or four generations, many rare combinations of circumstances have often occurred before.

Farmers have to integrate complex data into practical decision-making and action, all the time, year after year. In order to integrate decisions about human pathogens in the farm environment, they need well-founded and well-researched, reliable information.

They need people to work with who can help apply that information to the specific individual conditions of their farms and fields, crops and rotations, animals, and rangelands, soil types and climatic variations, ecologies and water sources.

Cooperative Extension has been one of the most effective research and technology transfer agencies in the history of the United States. It was one of the integral parts of the success of the Land Grant colleges. The training and culture within Cooperative Extension is both (neutral) research and solution-oriented: problem-solving. They are not an enforcement agency. They can do excellent research. They can work with farmers.

In California, we have been dependent on a small group of Extension Specialists for key field research on produce safety. Because the culture of an institution and profession is so important, we thought that Cooperative Extension was the best place to house Medical Extension Specialists as they developed their own approaches.

Extension has been repeatedly decimated over the past 20 years. In states such as California, there are fewer than half the professional staff positions (county- and university-based) remaining. It is surprising that the Land Grants have not been able to do more to protect this key part of their mission, nor to use it as a model for technology transfer in other areas besides agriculture (15).

It seemed important not to further this decline. Additional funding for new positions could possibly come from non-traditional sources, including Health and Human Services, EPA, and DHS, while maintaining or improving funding for agricultural extension.

A new profession does not have to be university-based, but much of the training for a new profession will probably have to be. David Acheson, when at FDA, wrote about the positive impact this approach could have in medical education. In general, we thought that the starting place should be Land Grants that had both medical and veterinary schools and a strong foundation of epidemiology, microbiology and molecular biology.

There is more to disease and ecology than is reflected in my own focus, which has been mainly on emerging bacterial human pathogens, because of the food outbreak record, and on bacterial and fungal infections/symbioses of plants. Protozoan and viral diseases sourced from U.S. farms have seemed secondary. This is obviously a limited perspective. One of my friends in the 1970s studied the increase in schistosomiasis following the concrete lining of irrigation ditches in Sri Lanka, and there are many such counter-intuitive results. I tend to leave out parasitology, and– if you will pardon the older expression – fauna. In designing a broader program of training, these kind of gaps should be corrected.

What farmers need to increase food safety, more than regulations, are professionals who can carry out a clinical diagnosis of their farm. The goal is to maintain a dynamic equilibrium of healthy ecological interactions, to prevent human pathogen transmission, and to avoid new pathogen emergence.

Developing and maintaining a healthy dynamic equilibrium is going to be different in a complex and rich ecosystem, and more attainable, than in a sterile or semi-sterile environment (16).

In California, it is striking how many key researchers on human pathogens in the farm environment are in Veterinary Medicine and Veterinary Medicine Extension. This must reflect the continuing influence of the late Dr. Calvin W. Schwabe, who founded the first department of epidemiology in a veterinary school at UC Davis and worked to develop the integration of animal and human diseases, the one medicine concept, and the one health concept discussed above (17). UCD also has run an internationally oriented master’s degree program in Preventive Veterinary Medicine (18).

One can imagine a number of different types of professional training that would be good disciplinary backgrounds for this new profession.

My guess is that the first new country doctor will be a vet.

(1) Letter from Assistant Commissioner for Food Safety Dr. David Acheson to the author, received Aug. 23, 2007. Besides supporting the new positions proposed for UC Davis, he commented on curricula effects in medical education: “We believe that education in agriculture and human health, foodborne pathogens and zoonotic diseases are essential components of medical school programs….”  

(2) Quoted in James M. Hughes, Emerging Infectious Diseases: A CDC Perspective, 2001. Emerging Infectious Diseases, Volume 7, No. 3 Supplement, 494-496, June 2001. From: MacFarlane Burnet’s “Natural History of Infectious Diseases,” third edition, Cambridge University Press, 1962. 

(3) Burnet would probably have been appalled at the continuing devastation of then known and existing diseases 60 years later, including cholera, infant diarrhea and a plenitude of parasitical diseases. 

(4a) K.S. Bell, et al. 2004. Genome sequence of the enterobacterial phytopathogen Erwinia carotovora sussp. atroseptica and characterization of virulence factors. PNAS 101 (30): 11105-1110. Published online July 19, 2004. 

(4b) T.H.M. Smitz, et al. 2010. Complete genome sequence of the fire blight pathogen Erwynia amylovora CFBP 1430 and comparison to other Erwinia spp. Molecular Plant-Microbe Interactions. MPMI, 23 (4) pages 384-393, 2010. 

(5) David Satcher. 1995. Emerging infections: getting ahead of the curve. Emerging Infectious Diseases, Volume 1 (1), January-March 1995, pages 1-6. 

(6) Stephen S. Morse. 1995. Factors in the emergence of infectious diseases. Emerging Infectious Diseases, Volume 1 (1),  January-March 1995, pages 7-15. 

(7) Joshua Lederberg, et al. Emerging Infections, Microbial Threats to Health in the United States. Institute of Medicine. National Academy Press, Washington D.C., 1992.

(8) Multiple authors, starting with M. Davis and C. Osaki of the Seattle-King County Department of Public Health.  Update: Multistate outbreak of Escherichia coli O157:H7 infections from hamburgers – Western United States, 1992-1993. MMWR, 42 (14), 258-262. April 19, 1993.

(9) The hamburger outbreak overshadowed the May 1993 report in the Journal of the American Medical Association (JAMA) on hemolytic uremic syndrome (HUS) caused by drinking apple cider with O157:H7 in Massachusetts, and  similar cases in New York and Connecticut.  

[R.E. Besser et al. An outbreak of diarrhea and hemolytic uremic syndrome from Escherichia coli O157:H7 in fresh pressed apple cider. JAMA 269 (17) 2217 - 2220. May 05, 1993.] 

With hindsight, similar cases are probably traceable to the 1980s, including in Sacramento, CA, where the linkage between apple juice and HUS was made but not with pathogenic O157:H7. Similarly the Listeria monocytogenes 1981 Canadian outbreak was actually the first demonstration of foodborne listeriosis.

[E.T. Ryser and E.H. Marth (editors). Listeria, Listeriosis and Food Safety, Third Edition. CRC Press, 2007 (page 94)]. 

Cabbage grown with raw and composted sheep manure, from a herd which had had listeriosis deaths, was made into coleslaw.

Outbreaks traced to sprouts and lettuce in the 1990s and early 2000s continued to implicate fresh produce, as did the Odwalla (unpasteurized) juice O157:H7 outbreak. Finally, with the 2006 spinach outbreak, FDA had had enough, and human pathogens on leafy greens and other raw produce were unquestionably a national and regulatory issue.

[FDA Statement on Foodborne E. coli O157:H7 Outbreak in Spinach. Oct. 06, 2006. See “Next Steps” section.  http://www.fda.gov/NewsEvents/Newsroom/PressAnnouncements/2006/ucm108761.htm ].

(10)  http://ausubellab.mgh.harvard.edu 

(11)  http://www.ars.usda.gov/pandp/people/people.htm?personid=10920 

(12)  http://www.epi.ufl.edu/?q=node/167 

(13) Carol Rubin, et al., 2013. Review of Institute of Medicine and National Research Council Recommendations for One Health Initiative. Emerging Infectious Diseases, Volume 19, Number 12, pages 1913-1917. December 2013. 

(14) This common saying seems to evade Internet search terms. “It takes three generations to make a farmer” is quoted in “The Promised Land” by Leavitt Ashley Knight, “Everybody’s Magazine” Volume 28, page 788, 1913. But this was a play on the more common “It takes three generations to make a gentleman.” I’ve heard it in the rural West for more than 35 years, and it was quoted (with “make”) by Oklahoma Labor Commissioner Mark Costello in 2012.

(15) As an observation, the decline of Extension in CA seems to be in an inverse function to the number of university positions at the vice chancellor level and above.

(16) One of the most protected and controlled medical environments is the hospital intensive care unit (ICU). Yet the control of methicillin-resistant Staphylococcus aureus (MRSA) and other multi-drug resistant organisms in ICUs is not only difficult but also the subject of considerable controversy on even the research results of control methods. See:

K.T. Kavanagh, et al., 2013. A perspective on how the United States fell behind Northern Europe in the battle against methicillin-resistant Stapylococcus aureus. Antimicrobial Agents and Chemotherapy, volume 57, number 12, pages 5789-5791. December 2013. Published ahead of print, Oct. 7, 2013.

The analogy in food safety is sprout production, also under the most protected and sealed environment imaginable, in this case for crop production, where pathogen introduction and spread is facilitated by the absence of any ecological controls of pathogens in a semi-sterile environment.

Similarly, control of human pathogens in the crop phyllosphere (the above-ground aerial surface layers of plants) seems to be more difficult because of the reduced richness of plant surface ecology relative to soil and roots (rhizosphere ecology). Control systems still may be possible, but any biocontrol or beneficial microbial treatment is going to be much less well-buffered.

(17) R.S. Nolan, 2013. Legends: the accidental epidemiologist. Dr. Calvin W. Schwabe fathered a generation of veterinary epidemiologists. JAMA News, July 01, 2013. Posted June 19, 2013. https://www.avma.org/News/JAVMANews/Pages/130701m.aspx 

(18) http://www.vetmed.ucdavis.edu/mpvm/

© Food Safety News
  • Marge Mullen

    Excellent and informative! Thank you Daniel Cohen!!

  • Oginikwe

    Thank you for this well-researched, informative article.

    You are correct about the Extensions: we don’t even bother with ours because it is stuck in the factory-farm paradigm and that it what got us here in the first place. Because we can’t depend upon our extension, we tend to “think outside the box” and share our results.
    A lot like this “revolutionary” gentleman: Citrus Greening Forces Florida Growers To Trust A Controversial Savior (Huff Po) 8/30/2013: