This webpage comes from Myth*ing Links.

INDUSTRIAL
AGRICULTURE
aka Factory Farms or CAFO'S
[Concentrated Animal Feeding Operations]:

National / International Edition


E. coli Bacterium
Museum Victoria, Australia

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How & Why Are Pathogens
Getting Into Our Food Supply:
Cherchez la merde!
[Translation: "It's the shit, stupid!"]
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This is the google diary
of Stanley Cooper*
[*His name has been changed to keep the focus on the science and not the messenger]

6 March 2007:  Introduction from Dr. Kathleen Jenks of Myth*ing Links -- Stanley Cooper is educated in science and engineering. He has spent the last decade working on CAFO issues, earnestly investigating the problems of pathogens in the foods we eat.  He became especially concerned with multi-drug resistant pathogens in animal waste and the complete absence of state and federal regulations with respect to pathogen controls in such fecal matter.
When I recently discovered Cooper's work, I asked his permission to create this page so that more people could be made aware of it.  His witty, exasperated, frustrated annotations for his links are terrific. Much of the evidence he presents was buried in obscure online scientific papers and reports but the information in that material clearly shows what the Big Guys don't want any of us -- neither the small to medium farmers nor the nation's consumers -- to know about the dangerous bio-hazards being generated by current practices in industrial agriculture.  In reading his annotated links, you will be exploring the efforts of one person's keen interest in the microscopic interactions between waste, soils, air, and water that dictate where the pollution travels in our living environment.

As time permits, I will be adding more pages from Cooper's "google diary" containing his data on last year's contaminated spinach outbreak, as well as what he has discovered about noxious manure odors and other waste management hazards.

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           Subject:      up all night coughing so i googled peanut salmonella....
             Date:        Tue, 20 Feb 2007 05:29:27 EST
             From:        Stanley Cooper
...Testing Finds Salmonella in Peanut Butter Out of Georgia ConAgra Plant

1.  recall of ALL peter pan peanut butter purchased since may 2006 recalled........see the wall street journal

2.  http://abcnews.go.com/GMA/story?id=2886338  recent update on story

3.  peanut primer  http://edis.ifas.ufl.edu/AA258

4.  cotton crop using chicken litter.......followed by peanut or soy
http://southeastfarmpress.com/mag/farming_squeeze_fertilizer_dollar/

5.  chicken litter on peanut crops in georgia
http://agron.scijournals.org/cgi/content/full/93/6/1315

6.  cotton farmers use chicken litter to kill nematodes........then crop rotate with peanuts?
http://resources.caes.uga.edu/media/georgiaaudio/archive2001/040201.htm

7.  see table 1 -- double cropping peanut and canola with chicken litter
http://agron.scijournals.org/cgi/reprint/93/6/1315.pdf

8.  peanut yield increased with use of poultry litter
http://cat.inist.fr/?aModele=afficheN&cpsidt=14681027
Same study posted on the USDA website:
http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=137832

9.  poultry litter on peanut and canola (the hydrogenated part of peanut butter)
http://agron.scijournals.org/cgi/content/full/96/4/1125

10.  no increase in peanut yield with broiler litter application --- but there was an increase in canola production........hmmmm
http://www.ag.auburn.edu/aux/nsdl/sctcsa/Proceedings/1999/Gascho_b.pdf
 so maybe the source of salmonella is canola...........is it from chicken litter or other manure?

11.  canola yields increase with swine manure injection
http://www.agr.gov.sk.ca/agriarm/reports/MelfortHogManure.pdf

12.  canola 101
http://www.canola-council.org/nitrogenintro.aspx

13.  scroll down to discussion of pathogens and "chemical residues"
http://www.ars.usda.gov/research/programs/programs.htm?np_code=108&docid=395&pf=1&cg_id=27

14.  story on physical reactions to eating peanut butter
http://www.consumeraffairs.com/news04/2007/02/peanut_butter_recall02.html

15.  while i was googling peanut salmonella manure........california is looking to write some laws - oh boy
http://www.consumeraffairs.com/news04/2006/10/cspi_ca_farms.html

16.  don't ya love it when old research (1996) clearly speaks of pathogens in manure?  but current research wants to blame it on wild pigs or "dirty jars"........please.
http://jds.fass.org/cgi/reprint/80/10/2673.pdf

17.  fascinating on many levels.........never heard of feeding infants tea.......the aniseed was contaminated with salmonella......tied to animal manure on crop in Turkey.
http://www.cdc.gov/ncidod/EID/vol11no07/04-1022.htm

18.  just another interesting website on food pathogens.......
http://www.foodhaccp.com/memberonly/newsletter92.html

19.  this type of research just makes me pause and wonder how the heckfire we stay alive with folks just dying to put untreated feces and urine on vegetable crop land....
http://aem.asm.org/cgi/content/full/70/11/6420

20.  a republican blog about manure as hazardous waste.......check out the title "entreprenurial activist"
http://www.watchblog.com/republicans/archives/003792.html

21.  north carolina dissertation on salmonella........always good for references.
http://www.lib.ncsu.edu/theses/available/etd-07142005-161524/unrestricted/etd.pdf

well i finally quit coughing so am going back to bed........happy reading.  sc

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Salmonella bacterium
Subject:        pathogens in swine manure - Wing study
   Date:        Tue, 20 Feb 2007 10:11:10 EST
   From:        Stanley Cooper

http://www.ehponline.org/members/2000/108p685-699cole/108p685.pdf

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Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus:
This  virus, or bacteriophage, can attack and disable the salmonella bacterium.
Perdue University
[Note: there is intriguing data at this site (3rd article down) on the future
role of phages, instead of antibiotics, in combating bacteria like salmonella
(but see Cooper's 3 March 2007 thesis-entry below for downside of phages). KJ]
Subject:       more googling of salmonella, canola, and swine manure - a mixed bag of results
   Date:        Tue, 20 Feb 2007 12:34:50 EST
   From:        Stanley Cooper

hey sports fans -- after a few hours sleep i am wide awake and finding more good stuff === this is from googling: canola "swine manure" salmonella

 1.  some may have gotten this under separate email -- but it doesn't hurt to repeat a good report.  pathogens in swine manure -- Wing.
 http://www.ehponline.org/members/2000/108p685-699cole/108p685.pdf

2.  this is written from some of my most favorite folks -- the Bloomberg School.  yeah!
http://www.ehponline.org/members/2007/9760/9760.pdf

3.  this study is related to human source of pathogens.  good learning experience on the types of biological tests and procedures and groundwater monitoring.....
 http://www.ehponline.org/members/2007/9430/9430.pdf

4.  look for this study in theatres near you next summer...........Environmentally sound manure management for reduction of health-related microorganisms and odor........yeah!! by USDA no less.
http://www.ars.usda.gov/research/projects/projects.htm?accn_no=411418

5.  i think i am getting tired, but here is a slew of research abstracts from the community of microbiologists related to pathogens and animal production......
http://www.csm-scm.org/english/abstracts/public/list_date.asp?year=2003

6.  here is an interesting angle -- the non-nutrient side of manure application.  oh canada we stand on guard for you.....
http://www.ridgetownc.on.ca/research/documents/vaneerd_Non_Nutrient_Value_of_Manure.pdf

7.  here is a nice laundry list of ag industry whiners in DC.........i just shake my head
http://www.fass.org/fasstrack/archive.asp

8.  canadian manure management plan -- i just breezed through this plan and think it looks a hellava lot more intelligent than most of the CNMPs i have read here in the states....
http://www.toneag.com/sample.pdf

9.  see page 13 for my new favorite word:  vomitoxin
http://www.ianrpubs.unl.edu/epublic/live/ec273/build/ec273.pdf

10. another minnesota human health study -- animal impacts 1999
http://www.eqb.state.mn.us/geis/LS_Humanhealth.pdf

well, that is all for now..........sc

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Illinois Department of Public Health

Subject:       more articles on pathogen survival and other goodies
   Date:        Wed, 21 Feb 2007 11:05:16 EST
   From:        Stanley Cooper

i went back to pubmed site and started reading the articles related to salmonella survival in land application of manure (one of the items in yesterday's email list).

1.  i like this first article for many reasons (and i have probably sent it to you before back during the spinach debacle).  it is an experiment where they innoculated the cattle with 157 and salmonella and then collected the manure for survival tests and also land applied the manure to determine survival rates in soils and finally planted lettuce to determine uptake into the plant.  the last part of the experiment is a bit weak, but the rest of the research goals have pretty intensive results.  i recommend reading the last two pages that are devoid of research gibberish.  depending on your background in statistics and graphing - you may also find all the graphs useful in discussions about diet versus pathogen survival.
 http://aem.asm.org/cgi/reprint/71/10/6165

2.  this article looks at composting dairy manure with straw and sawdust (ST and SD respectively) and the effects of temperature on nitrogen losses (see table 2 and figure 5.  There is a marked difference between composting at 25 degrees C and 55 degrees C - which should be considered when evaluating a nutrient management plan and total nitrogen land applied.  i haven't run across too many dairies that compost prior to land application other than the big one in Oregon.  The sample ID that matches a dairy lagoon without compost is DM-L-RT (stands for Dairy Manure-Lagoon-Room Temperature - see table 1 for descriptions of sample types).  see page 8 (discussion section) for a short paragraph about nitrogen concentration in dairy manure lagoons --- 17,000 ppm plus or minus 4000.  this is a lot higher than what i have thought would occur so my interest level is high --- compare to swine wastewater lagoons in oklahoma with N concentration around 1500-3000 ppm.  significantly higher -- so much more potent when land applying.

Micro tests included e coli, listeria, salmonella and M paratuberculosis (new one for me - will have to look that one up later).  remember your temperature conversions from celcius to farenheit...........multiply C by 9/5 and add 32........so 25C=77F and 55C=131F.  It appears the listeria did not survive either the composting or the lagoon storage.  salmonella seemed to die out by day 56...the paratuberculosis survived a long time at lower temperatures in a study sited on the last page (256 days).

the key to composting is the higher temperatures and the type of compost media (straw versus sawdust) affected the destruction of the pathogens.  uncomposted dairy manure allowed pathogens to stay viable longer.  a related article indicated that composting would make dairy waste safe for land application on food products.......
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=abstractplus&db=pubmed&cmd=Retrieve&dopt=abstractplus&list_uids=11563505
here is the link to the main article i discussed above
http://aem.asm.org/cgi/reprint/72/1/565

3.  this abstract indicates that salmonella did not transport through field tiles, but other fecal coliform did.  i hate when i can't access the full article, but good to know it is out there.  (i may have already sent this to you earlier)
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15387133&itool=iconabstr&query_hl=1&itool=pubmed_docsum

4.  and now for something completely different.......phosphorus leaching.
http://jeq.scijournals.org/cgi/reprint/33/3/1070

5.  this is a good article in that it explains in fairly simple terms why bacteria survive in some soils and not others.  mentions clays as a place for the organisms to hide out........no till verus tillage......swine waste.  they reproduced different rainfall events to test for bacteria movement.  good stuff here.  basically if you inject the manure, the bacteria survive at depth.  we knew that, but it is nice to have it said in a peer reviewed journal article.  also the last paragraph talks about the total coliform test as underestimating e coli.
 http://jeq.scijournals.org/cgi/reprint/32/5/1865

6.  this article concludes that tillage practice and soil type do not prevent e coli leaching and that soluble nitrogen may enhance the transport and fate of pathogens.  this study focused on dairy manure on no-till and tilled soil columns.  see table 3 to see that disturbed (till soil column) had an increase in pathogen population - meaning the bugs multiplied under a till scenario.  there seems to be some problems with the research that were corrected (volume of simulated rainfall) during the experiment.  the last sentence implies that even though a nutrient management plan that limits nitrogen may also address pathogen transport - they recommend pathogen treatment.  which i totally agree with.
http://aem.asm.org/cgi/reprint/66/3/877
 the author submitted new tables as a correction to the original publication.......
http://aem.asm.org/cgi/reprint/66/9/4172

7.  this study was a bit odd (the little cups buried in the dirt).........but the results are interesting when comparing fall manure application versus winter.  fall application without a fall crop resulted in higher nitrogen leaching the following spring possibly due to increased time for nitrogen mineralization.  the wording is a bit difficult to follow in the conclusions, but worth studying if you are interested in winter application issues.  the main thrust is that manure application during nongrowing seasons (fall/winter) resulted in the highest nitrogen leaching.
http://jeq.scijournals.org/cgi/reprint/33/4/1238

8.  this article is only available free by abstract (2006 pub date) but it has some good conclusions regarding the timing of manure application (dairy), soil type and nitrate leaching.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16510712&itool=iconabstr&query_hl=16&itool=pubmed_docsum

9.  this 3 year study used lysimeters to extract leachate from corn fields in central kentucky to study the effects of till/notill on nitrate leaching.  the amount of nitrogen land applied was estimated for dairy manure and reported in kilograms per hectare .........not my favorite set of units.  it would take a good belgium chocolate to make me do the conversion, but it can be done and i will do it upon receipt of said chocolate (smile).  the kicker is when soil nitrogen exceeds 25 kilograms per hectare - nitrate leaching can be expected (see page 5 right hand column for discussion).  look at figure 1 to see the spikes of nitrate leachate from manure application as compared to commercial fertilizer application (off the charts so to speak).  now the important stuff to remember -- the dairy cattle were not totally confined; they added less manure during the winter (oops), so the conclusions about less leachate from winter application as compared to spring is not entirely true and they as much say so on page 6.  there is good correlation between atrazine/arachlor leaching after first rainfall event on page 7 Figure 4 and is explained by transport through the macropores of the soil column when dry and then subjected to first rain.  so farmers, don't apply herbicides until after the first rain?  although the fertilizer caused nitrate leaching before manure, by the end of the study the manure treated land outleached the fertilizer treated land........page 8 conclusions.
http://jeq.scijournals.org/cgi/reprint/34/4/1354

10.  7 year corn/soybean crop rotatation study (minnesota) on nitrate leaching with tile drainage system. compared manure application with and without Nitrapyrin (nitrate inhibitor).  figure 2 illustrates the leaching as a direct result of higher rainfall.  and that subsequent rainfall increased the leaching without a dropoff (only a plateau) in between rain events (my interpretation).  see page 7/8 for conclusions.  most of the nitrate losses occurred when infiltration exceeded evapotransiration.   54% of nitrate in the tile drainage occurred during corn phase and 46% during soybean phase.  all greater than 10 ppm.
http://jeq.scijournals.org/cgi/reprint/34/2/590

11.  a model to predict nitrate leaching from manure application for 21 years shows 7 year timelapse between cause and effect.  see page 3 left hand column for reference to nitrate leaching greater than 10 ppm even when land applied according to "economic considerations".  this info is repeated on page 9.  the fact there is a model (several of them) is interesting all unto itself.  see page 11 right column for discussion of overapplication of nitrogen (what? couldn't be??)  see page 12 right hand column for long term projected effects from reduced nitrogen application.  See figure 3 for comparison of nitrate leaching with higher nitrogen application directly corresponding to higher nitrate leaching.  the key to the symbols is in the figure notation at bottom of figures.  the top figure on page 14 clearly shows the difference.  there is obviously a lot of information to assimilate in this article.  it is a predictive model for regional effects, not necessarily applicable to a particular site - or so the authors lament.
http://jeq.scijournals.org/cgi/reprint/32/1/247

that's all folks -- sc

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E. coli Bacteria
NASA
Subject        Re: Chatt Times: FDA food inspections down by half since 2003
                    [Note: AP article follows comments]
   Date:        Tue, 27 Feb 2007 10:12:00 EST
   From:        Stanley Cooper

i am sure we all appreciate articles like this written and put out on the AP.  but the backstory is still safely hidden from the public for some strange reason - the unfettered application of dairy, swine, and chicken wastewater to cropland that is planted with human consumptive food products.

before the spinach debacle i never knew that anyone would be stupid enough to put dairy waste on land used to grow spinach - a plant that humans eat raw in every salad bar across america.  of course, that disaster is still being spun as a wild pig running across grazing cattle poop, rather than the application of dairy waste which is so obvious from the pathogen.

then most folks missed the lettuce/tacobell/oops.its.the.tomatos whirlwind tour on CDC website - the one where it was decided the tomatos were probably all thrown out so no need to alarm anyone and washing wouldn't help cause the e coli was "under the skin".

now the public is wondering if all that gas and diarrhea and flu-like symptons are because they have a cold or ate too much or ate something uncooked like peanut butter with a little feces pathogens in it.  the peanut butter plant claims it has high enough temperatures to kill the pathogen when the literature clearly shows salmonella withstands temps up to 194 F (as compared to 165 in the factory).  but whoa now -- must be "dirty jars".........are they freaking serious?

how about thinking real hard about which mass produced animals near the peanut cropland is know for excreting ecoli.......like poultry and pigs.  (dairy does also, but georgia is a big chicken state).   the georgia extension office bulletins are full of advice to not apply chicken litter on peanut crop land because the high zinc levels after a time will reduce crop yields (when zinc reaches 100-200 lbs/acre).......now why would anyone have to warn you to not do something that you aren't doing?  hmmm.  but chicken litter is great for cotton crops cause it kills a pesky nematode........then double crop with peanuts and shazam.  salmonella in your peanut butter.

what we need more of is research on the uptake of bacteria and viral pathogens by plants and the partitioning of those bacteria in the leaf, stem, flower, and seed of the plant.  research has confirmed that e coli is uptaken by the spinach plant into the root system.........but it has not been confirmed that the bacteria travel into the leaf and stem.........my question is what is there to stop it?  if the bacteria are in the circulatory system of the plant (ie., inside the root).......then they should be able to travel wherever the fluids travel granted the size and chemical nature is not prohibitive.

and if a peanut butter plant temperature of 165 F can't kill the salmonella --- the compost temperatures of 130 to 150 won't either. and half-assed attempts at composting (ie., piling up litter in a barn and mixing it with dead chickens) certainly won't get the job done.

and word has it that the delmarva chicken folks are being delivered peanut shells rather than sawdust for their chicken houses..........

the food production industry on the ground appears to be an industry that doesn't have the wherewithal to (1) admit they have a serious pathogen problem, (2) understand the biology of the problem, and (3) have the personal initiative to drastically improve their attitude and do something smart about it.

but then, that is just 10 years of observation talking.  stanley cooper

[Article follows directly below]:


E. coli Bacterium
In a message dated 2/27/2007 4:44:26 AM Central Standard Time,
neillherring{at}earthlink.net writes:
Government inspections of food decrease nearly 50% since 2003
By Andrew Bridges and Seth Borenstein, The Associated Press
WASHINGTON: The federal agency that's been front and center in warning the public about tainted spinach and contaminated peanut butter is conducting just half the food safety inspections it did three years ago.

The cuts by the Food and Drug Administration come despite a barrage of high-profile food recalls.

"We have a food safety crisis on the horizon," said Michael Doyle, director of the Center for Food Safety at the University of Georgia.

Between 2003 and 2006, FDA food safety inspections dropped 47 percent, according to a database analysis of federal records by The Associated Press.

That's not all that's dropping at the FDA in terms of food safety. The analysis also shows:

There are 12 percent fewer FDA employees in field offices who concentrate on food issues.

Safety tests for U.S.-produced food have dropped nearly 75 percent, from 9,748 in 2003 to 2,455 last year, according to the agency's own statistics.

After the Sept. 11, 2001, attacks, the FDA, at the urging of Congress, increased the number of food inspectors and inspections amid fears that the nation's food system was vulnerable to terrorists. Inspectors and inspections spiked in 2003, but now both have fallen enough to erase the gains.

"The only difference is now it's worse, because there are more inspections to do, more facilities, and more food coming into America, which requires more inspections," said Tommy Thompson, who as secretary of the Department of Health and Human Services pushed to increase the numbers. He's now part of a coalition lobbying to turn around several years of stagnant spending.

The Bush administration's budget request for 2008 includes an additional $10.6 million for food safety at the FDA; the lobbying group said 10 times that increase is needed. Even though the FDA increased its overall spending on food between 2003 and 2006, those increases failed to keep pace with rising personnel costs.

"It's not just outsiders like us who have been watching it for a while. People who worked in the Bush administration are coming out and saying the agency is not working at its current resource levels. It just can't manage the job," said Caroline Smith DeWaal, director of food safety at the Center for Science in the Public Interest, an advocacy group.

Members of Congress also have renewed the focus on the safety of the nation's food supply amid highly publicized recalls sparked by food poisoning, including last year when E. coli was found to taint fresh spinach sold coast to coast. That outbreak killed three people and sickened nearly 200.

The latest big recall involves peanut butter believed tainted with salmonella, a bacterium found in feces that can cause severe diarrhea. The outbreak has sickened at least 329 people in 41 states since August, federal health officials say.

Food safety experts say it would be impossible to know whether increased numbers of inspectors and inspections      would have prevented the outbreak, linked to Peter Pan and Great Value brands made by ConAgra Foods Inc., or other recent food poisoning scares.

The FDA had last inspected ConAgra's peanut butter plant in Sylvester, Ga., in February 2005 and had found no      problems, agency spokesman Michael Herndon said.

Firms that produce high-risk foods more susceptible to contamination, such as fresh fruit and vegetables, are supposed to be inspected every year, unless they have a good safety record. Then inspections are done every two or three years, Herndon said.

For other foods, the FDA rotates inspections, depending on resources.

The shrunken ranks of inspectors have left the nation once again vulnerable, especially to problems in imported food, Thompson and others said. Doyle, whose center studies ways to improve food safety, called the nation's growing appetite for imported foods the "coming threat."

The United States last year imported about $10 billion more in food, feed and beverages than it exported, according to census figures. Even as imports grow in volume and diversity, the number of FDA inspections is shrinking: Agency inspectors physically examined just 1.3 percent of food imports last year, about three-quarters as much as in 2003.

The FDA, meanwhile, says it is concentrating its efforts on areas where the potential threat to the public's health is greatest.

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"Beware of Manure Pit Hazards"
National Ag Safety Database
[Excellent charts & sobering specifics about what happens to workers
who accidentally fall into "lagoons" full of CAFO manure --
this is the same stuff  being sprayed on our farmlands.  KJ]

Subject:       Re: Chatt Times: FDA food inspections down by half since 2003 - part II
   Date:        Tue, 27 Feb 2007 10:43:28 EST
   From:        Stanley Cooper

for example, the following research shows salmonella uptake by carrots and radishes.......comparing uptake rates between poultry compost, dairy compost, and pH amended cattle compost.......result -- uptake.  end of conversation.  of course, the article has lots more interesting things to read such as the length of time the pathogen survived in the test fields........and other research along the same lines.  basically 200+ days.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=383101

and for those who get curious enough to want to know the application rate of compost, the article uses metric tons per hectare.  the conversions are:

1 metric ton = 2,204.62 pounds
1 hectare = 2.47 acres
1 kilogram = 2.2 lbs
my new concern after reading this article is the concentration of nitrate in the three composts....which are given in units of kilograms per hectare..........which is converted to lbs/acre  (2.2/2.47 = 0.89) ....or basically 10% less.
the amount of nitrate in the dairy compost is huge.  6053 lbs/acre but the phosphorus seems low.  296 lbs/acre

the research did not give total nitrogen in the compost, which is the most useful comparative value for us.  but cripes almighty if the nitrates is 6000 then the total is some value more than that.  i would hope none more - meaning all the urea ammonia was converted to nitrate.  anyone have an idea about that???

my concern is whether the application rate was extraordinarily higher than what industry uses.  will get back to you on that..........sc

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http://www.all-creatures.org/anex/cattle.html
Subject:       googling on a sunny tuesday
   Date:        Tue, 27 Feb 2007 13:20:01 EST
   From:        Stanley Cooper

i found the following articles while googling pathogens in compost and pathogens in silage....

1.  salmonella in roma tomatos in 2004?  never heard about it.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=383101\
http://www.cdc.gov/mmwr/preview/mmwrhtml/mm5413a1.htm

2.  10 years ago, separation of urine from feces was known to fastly affect pathogen survival in the urine... but gosh 6 years in the solids portion???? maybe it is better to mix it up?
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=abstractplus&db=pubmed&cmd=Retrieve&dopt=abstractplus&list_uids=8767690

3.  survivability of salmonella species in swine feces -2001 study from Ames Iowa - again looking at survival rates in dry manure.  this is important when considering the exhaust from the barns includes dry fecal matter.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=abstractplus&db=pubmed&cmd=Retrieve&dopt=abstractplus&list_uids=11456201

4.  money spent in new york state to combat negative effects of agriculture.  i don't know about you, but this kind of stuff depresses me.  nearly a half million to study silage leachate?  seriously?  of course the NY farm bureau is all over this free money....
http://www.agmkt.state.ny.us/ad/release.asp?ReleaseID=1495

5.  the ole grass is better for the cattle type journal article and seasonal preferences for shedding of e coli and other pathogens.
http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1065162&blobtype=pdf

6.  i always wonder when they claim "no pathogens in the edible lettuce parts"......does that mean there was some in the nonedible parts?
http://cat.inist.fr/?aModele=afficheN&cpsidt=17165538

7.  great pictures of composting dead animals......
http://www.ncagr.com/oep/powerpoints/Wilson.pdf

8.  interesting white paper (full test available from Midwest Plan Services) on treatment methods for pathogens in manure waste.
http://www.cals.ncsu.edu/waste_mgt/natlcenter/whitepapersummaries/pathogens.pdf

9.  and now for something completely different.......on farm detection methods for pathogens by the FDA.   considering it takes an acronym dictionary to read the darn thing......wonder who actually does this?
http://www.fda.gov/cvm/SumWebPage.htm

guess that will do for now.........my brain is fried again.  sc

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From: How Stuff Works

Subject:       googling multi-drug resistance part I
   Date:        Fri, 2 Mar 2007 15:32:10 EST
   From:       Stanley Cooper

i sent this out this morning as one email and apparently it got stuck somewhere and never got posted to the listserve -- so am breaking it up into two parts:

PART ONE
good morning.........i feel BETTER.  i think i am totally not sick today.  AWESOME.

so to start out my day right, i am googling multi-drug resistant bacteria in poop.  i bet you all do that at least once in awhile right? hey the sun is shining, the coffee is made, and i only have two lawyers to talk to today.  so today is a good day to learn about germs and why they are in my food.

1.  here is an example of the agriculture perspective of multi-drug resistance..........gosh we just don't know why it is happening, but it is on the rise........nothing to be concerned about.  we will just tinker around a bit and get back to you.
http://www.uoguelph.ca/research/publications/Assets/PDF/PigPens/Winter2005.pdf

2.  here is the WHO's perspective.  a bit more serious.  probably more accurate.  and i find the fact that this problem started being a big problem in about 1990..........just about the time CAFOs were pumping up around the country.  they get straight to the point and discuss the GENETIC changes to salmonella that cause multi-drug resistance even if the drug is no longer applied.  this particularly caught my eye:

"A Danish study found that although persons with susceptible Salmonella infections had a higher mortality than the general population, persons with resistant Salmonella infections had an even higher mortality. The death rate for persons with multidrug-resistant infections was estimated to be 10 times higher in the two years following specimen collection than for the general population."
be sure to scroll down to the bottom for all the other urls on the subject
http://www.who.int/mediacentre/factsheets/fs139/en/

3.  one of the urls in the WHO fact sheet in item 2 is worth reading for sure --- a 1997 summary of drug resistant bacteria.  very easy to read.  alarming in its content especially when we find ourselves ten years later with absolutely no improvement in the regulation of pathogens in manure.
http://whqlibdoc.who.int/hq/1997/WHO_EMC_ZOO_97.4.pdf

4.  another url from the WHO article dated 1998 talks about quinolone use in animals and the emergence of fluoroquinolone resistance in salmonella...........right after the ag industry started using it.  the resistance is due to chromosonal mutations related to the "efflux pump of the bacteria"........that's a new one for me.  sounds like a bug poop chamber.
http://whqlibdoc.who.int/hq/1998/WHO_EMC_ZDI_98.10.pdf

5.  in 2000, the WHO gets a bit more serious - calling on proactive legislation to regulate antibiotic use and to phase out growth promoters (i believe their words were "rapidly" and terminated - pretty strong words).  this one is peppered with a lot of "only" "prudent" "evaluate" and "responsibility"..........you know if someone lectured me on a topic and used all those words over and over -- i would get the distinct impression they were absolutely serious and if i ignored them i would be in big fat trouble......
http://whqlibdoc.who.int/hq/2000/WHO_CDS_CSR_APH_2000.4.pdf

6.  in 2001, the WHO has some more to say --- emphasis is on controls and monitoring and public reporting of the monitoring results of antimicrobial uses.  Denmark started in 1995 to monitor animal use of microbials and the antibiotics are only available by prescription......the guys from the US had to admit they don't know how much antibiotics are used cause no prescriptions are required - end users buy directly from the drug companies. oh and FDA does not require the drug companies to state whether a new drug is intended for use in the US or abroad...?  what's that about?
http://whqlibdoc.who.int/hq/2002/WHO_CDS_CSR_EPH_2002.11.pdf

7.  Denmark quit using antimicrobials as growth promoters in 1998 in the ag industry.  dang that is exactly when we saw a huge increase in pork production in the US that never existed - large scale confined feeding operations in the size of 10,000 head finishing operations...27,000 head sow facilities.....90,000 head nursery facilities........and tons of 4000 head finishers and 2000 head sow facilities......rather than 100 to 500 head.  upon further reading, the impact of stopping the use of growth promoters in pigs only affected weaners not the finishers.........so why are we still doing it here in the US?  wonder who is running the farms out here -- the drug companies or the farmers?  the pork production in denmark continued to increase after the termination of growth promoters..........bet the drug companies didn't like THAT.  they probably hoped there would be a big rise in death rates or big change in weight gains or something?  sounds like the only big expense was the rewiring of the feed systems.  it also sounds like the industry just used other drugs not listed in the ban.........this is a long report - gives names, dosages, etc by animal type and drug class. http://whqlibdoc.who.int/hq/2002/WHO_CDS_CSR_EPH_2002.11.pdf

8.  2006 in Indianapolis - abstract for conference - 100% of the isolates shown to be multi-drug resistant in large sample size on north carolina hog nursery and finisher lagoon.....
http://a-c-s.confex.com/crops/2006am/techprogram/P27209.HTM

9.  from that same conference, here is an abstract that shows the manure itself prevents the attachment of e coli onto soil --- due to pH and conductivity (salts)..........so more likely to be in stormwater runoff.  Makes sense to me.......the only way the bacteria are going to attach to soil is by postive/negative attractive forces.  The soils that contain clays, which are negatively charged surfaces, will attract positively charged things such as ions of calcium, magnesium, etc and any appendages on the bacteria that have a positive charge.  if there are lots of positively charged items in the water -- they compete for the negatively charged surface and the one that wins is the one that has low solubility and high affinity for adsorption.....the other kids have to stay in the water until another negatively charged surface becomes available.  the pH of the solution dictates which positively charged particles are in solution (dissolved) rather than involved in precipitation (like calcium ion versus calcium carbonate molecule).........low pH - lots of stuff dissolved -- lots of competition for adsorption sites........high pH -- lots of stuff in molecular form rather than ionic form -- much less competition.
http://a-c-s.confex.com/crops/2006am/techprogram/P24605.HTM

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"Dirty Dozen Most Contaminated Foods"
Prevention Magazine
(Also see their article:  Is your Produce Poisoned? KJ)

Subject:       googling multi-drug resistance PART II
   Date:        Fri, 2 Mar 2007 15:32:53 EST
   From:        Stanley Cooper

i am particularly proud of the last entry............very good fun indeed.  s.c.

10.  ahhhhh my favorite topic - internalization of bacteria in plants --- in other words the bacteria are on the inside of the plant you are eating.........not on the outside.  i hate it when they start out the abstract with "we don't know much"............uh, yeah they do - over in the botany and microbiology departments of non-land grant universities.
http://a-c-s.confex.com/crops/2006am/techprogram/P24990.HTM

11.  now this is just plain funny ---- biopiles --- euphemism for piles of dead animals.  they say they don't know much about pathogens in dead animals.  are they kidding?  if your head is buried in the sand is it really dark outside?
http://a-c-s.confex.com/crops/2006am/techprogram/P27658.HTM

12.  man - where was i in november? i should have been at this conference in indianapolis........i recommend traversing all the urls back and forth in this website to get all the research abstracts.  i am going on to the next item on my google search, but will return to this baby later.........current research.
http://a-c-s.confex.com/crops/2006am/techprogram/P20427.HTM
and this one is from canada...........a bunch of smart fellows looking at pathogen survival in large scale hog production.  why don't we have these guys down here in the states?
http://a-c-s.confex.com/crops/2006am/techprogram/P20395.HTM
oh and just in case you forgot about cotton/peanut crop rotation.........
http://a-c-s.confex.com/crops/2006am/techprogram/P22774.HTM

13.  houseflys in fast food restaurants carry MDR (multi-drug resistant) bacteria..........creepy (oh and by the by -- just by sending this url to someone i got a popup window that asked me if i was a health professional and to emphasize that this information is NOT for predicting adverse impacts....just so's you know....i am not a medical professional.......just well read engineer.
http://a-c-s.confex.com/crops/2006am/techprogram/P22774.HTM

14.  another new term - horizontal gene transfer...........the dos-e-doe of MDR in your colon...seems the bugs hang out together, its kinda dark, no one is regulating their behavior and before you know it they start sharing their bad habits, like multi-drug resistance............you are who your friends are so to speak.
http://aem.asm.org/cgi/content/abstract/67/2/561

15.  now this fly study that says flys play an important role in MDR transfer from cattle manure to wherever the fly lands.........did not give me a popup when i sent the url to someone.........gosh those medical magazines are parnoid.
http://esa.confex.com/esa/2006/techprogram/paper_25510.htm

16.  february 2007 publication restating many of the facts found on the WHO website and emphasizing the termination of nontherapuetic use of antibiotics in the United States no less.  strong words.  great article.
http://www.ehponline.org/members/2006/8837/8837.pdf

17.   hey check out the cool picture taken by Johns Hopkins (yeah Kellogg)....you got to scroll to the bottom of this webpage and read the comment about the National Pork Producers.........classic.
http://whyfiles.org/221odd_air_hazards/index.php?g=2.txt

18.  i love the comment in this report.............."resistance is real"...........next favorite comment........"this thinking may be flawed" (referring to the unfettered use of antibiotics) poultry and antibiotics.  2002 report.  be sure to read to at least page 4 to capture the counter to the argument that reducing growth promoters causes increase use of antibiotics -- the answer -- well, at least those uses are for situations that need them and do not cause the types of resistance we see otherwise.  i changed my mind... you have to read until page 5 to capture the table that shows comparison of rates of resistance in pigs and chickens before and after drug use termination in denmark...........very dramatic differences (drop not rise).  okay maybe to page 7 where it talks about feedint wheat, barley and rye to poultry causes digestion problems that lead to disease.........bad digestion in birds leads to disease.  this is such a wonderful report.  easy to read, full of great information.  oooh page 14 attacks the use of "natural".  and the topper --- "we need to learn the lessons presented by other countries".........god forbid.
http://ag.ansc.purdue.edu/poultry/multistate/Multi-state.pdf

19.  face book of bacteria.......
http://www.ucsusa.org/food_and_environment/antibiotics_and_food/foodborne-illnesses.html

20.  okay...........a nematode is a worm.  worm lives in dirt.  farmer puts manure on dirt.  worm eats dirt.  when scientist splits open worm and looks in the gut --- e coli 157 is right there staring back.  this and other delightful bits of knowledge can be found in the following url.  there is one study putting soil and a worm innoculated with salmonella newport and then they put a leaf or a strawberry or a carrot on top of the soil and closed the lid.........within a day, the salmonella was on the plant material........but without the worm...no salmonella on the plant material.  so the worms are pooping on the plants and excreting the pathogen?  oh lordy. and wouldn't you know it -- the nematodes are ATTRACTED to cattle manure.  so it is inevitable.  some great new phrases.........."harbor in their gut" ..........is one of them.    oooh and then they cook the worms to see if the e coli 157 is still prevalent........hot worms actually had more e coli population....and if you make it hot and humid woowee.......population soars.  they used that green flourescent protein indicator...sweet.  if i read the words "important food safety issue" one more time i am going to scream - its human safety man, the food seems to be doing just fine.
http://www.ugacfs.org/research/pdfs/SALMONELLA2004.pdf

21.  i don't know the date of the food and drug administration proposal but the bibliography doesn't have anything more current than 1999.  after reading the other stuff, i am not sure i trust what the FDA "believes" is very useful, good for me or otherwise worth the paper it is printed on.
http://www.fda.gov/cvm/antimi18.html
or a bit easier to read in pdf:  http://www.fda.gov/cvm/Documents/antim18.pdf

22.  okay this is a slide show -- when you get to the slide that shows the steer there are letters superimposed on the various parts of the hide where feces samples were taken.  just for fun, this is what i think the letters stand for:
O (near the mouth) means okay i will sample there
N (on the neck) means not so bad really, sure i will sample there
B (back of animal) means that's better actually cause i can just lean over the railing and scoop that poop
V (down below near the belly) means very funny guys, now i have like bend over and rub his belly
F (by the you know) means forget it you guys are sick
P (somewhere near the butt) means for pete's sake don't let go of the tail - he just wacked me in the head and why or why didn't i got to business school
H (hind leg) means hahahahaha so he can kick me - right
RA --- means really awful
FG --- means fuh-get it
the next slide shows the prevalence of bacteria (e coli and salmonella) at each of these locations. don't you think it is weird that the lowest numbers for salmonella and the highest numbers for e coli 157 were at the fug-get it site?   a few slides later you see boy meets cow and come to an agreement....keep going and you see the slide that shows e coli 157 survival based on temperature at 37 degrees C (98.6 degrees F) FINALLY a drop off in survival after a DAY.....otherwise.......bugs keep on keeping on.  okay - now go a few more slides to find the fecal "pat" and the method of sampling one........hilarious.  north, east, south and west portions of the fecal pattie.........are they serious?  the next slide actually shows the more samples you take the more variation in the number of bacteria detected.  i think i need a drink and i don't mean cherry coke.  one of their conclusions is "no optimum sampling site determined" jeez guess there is still some argument among the grad students on which is worse P or RA......i mean surely there can't be any argument about FG?  There are a couple of slides about DFM or direct fed microbial.  not sure what that is exactly but it sure seems to be a good way to get rid of e coli 157........there is a slide comparing salmonella swabs on clean and dirty trailers at the feedlot and at the slaughterhouse.  what i do not understand but am beginning to have my suspicions is why the clean truck at the slaughterhouse has almost twice as much e coli as the dirty truck at the feedlot.........could this be a difference in washing techniques or airborne transmission?  there is almost no difference in salmonella swabs on the cattle held in clean trailers or dirty trailers...and the larger value is on the midsection not the poop end......so does that mean the guy pooping on ya is worse than the poop you got inside ya?  or is this cummulative guys pooping on ya?  there is a slide on using trichloromelamine to kill e coli 157........and it reminds me of other 99% effective things...its that 1% that gets ya pregnant......so it doesn't kill ALL the bacteria -- just a large percentage of it.  of course, salmonella does not find the disinfectant to be much of a disinfectant, more like dessert.

conclusion - effective.  jeez i only got through the first half of this presentation.  hope you find my comments alluring enough to go at least get that far.  this is our industry that we are watching.  and this shows they need to be watched.
http://www.orgs.ttu.edu/icfie/Additional%20Information/combofoodsafety.ppt

later - sc

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Salmonella
University of Wisconsin, Eau Claire

Subject:       just one thesis on antiobiotic resistance
   Date:        Sat, 3 Mar 2007 13:24:40 EST
   From:       Stanley Cooper

by the by -- when i refer to a page number i am referring to the pdf page number, not the thesis page no.

1.  this master's thesis contains a history of antibiotic discovery and emergence of multi-drug resistance.  on page 35, he discusses the "efflux pump" and how that prevents the antibiotic from working - ie., entering the bacterium and killing it by lysing or basically blowing it up.  Great source of info of the types of antibiotics, when they were discovered, when resistance first started and why.  page 39 -- 25 million pounds of antibiotics used in animal feed in 1998........it is frustrating that most of the ag studies were done in denmark, germany and the like (not in the US) but you have to remember - those countries actually keep track of antibiotic use in animals (by prescription) and we don't so the researchers actually have a database to work with.  see page 57 for reference to article about antibiotic resistant bacteria in groundwater samples near pig farm.  also references groundwater study in virginia and washington state and alabama, florida, orgeon and maryland.  (gosh - i may have to check out this fellow's bibliography very closely - specifically items 52, 82, 175, and 211).  see page 61 for paragraph on paradigm shift from thinking bacteria die out quickly when exposed to atmosphere to understanding they can survive very long periods of time (up to and even exceeding a year) to finding bacteria that don't care and may even thrive.  see page 62 for a pretty simple description of how a bacteria can have a one-step mutation to fight off the antibiotic mainly by changing the ability of the antibiotic to bind to the bacteria (he calls it binding affinity).  if the antibiotic drug cannot bind to the cell wall of the bacteria -- then there is no interaction.  the drug molecule must be attached to cause a change in the bacteria that causes the death of the bacteria - either by screwing around with its cell wall causing the cell wall to be perforated or by getting deeper inside and messing around with the genetics of the bacteria.  he is describing horizontal gene transfer (3 mechanisms) - one of which occurs by the bacteria being eaten by a bacteriophage and the bacteriophage "warehouse" causes a mixing of genetic material.  correct me if i am wrong - but kinda like putting a bunch of folks in prison and finding out later they taught each other a thing or two....and another mechanism where after you kill the bad bacteria, its dna is just floating around (called naked dna) and some other bacteria eats it --- and through the apparent magic of genetic engineering, the smarts from the naked dna get transferred into the dna bank of the consumer.  i have to put it in simple terms for myself in order to remember this.  if anyone out there has a better analogy -- please speak up.  and then the last method of horizontal gene transfer appears to be when two bacteria are close together that they just automatically share or steal each others genetic info.  not sure if this is a pickpocket on the bus or a community bake sale approach where there is actually an economic gain associated with the exchage (i'll tell you about a cool way to break carbon chains if you give me something in return........ah sure, ah here take this bit of info that i think is useless to me but might rock your world).  on page 65 he talks about resistance transfer between two or more resistant bacteria even though only one drug is administered to get rid of one bacteria.  consider this -- you have two or more drug resistant bacteria but resistant for different antibiotics......you get treated with antibiotic A which kills bacteria A usually, but bacteria B just happens to have the resistance to antibiotic A and gives it to bacteria A which then says -- bring it on doctor cause i got a new tool in my toolbox.  it is amazing that they could interact so well, but maybe it can be explained in a simple way..........bacteria B which is resistant to antibiotic A expels resistance information automatically when exposed to antibiotic A in case some of bacteria B's relatives haven't yet acquired resistance to A and it just so happens serenditiously that bacteria A gets the info.....in ASCII format or some such nonsense whereby the info can be reformatted quickly for bacteria A to immediately or at least quickly acquire resistance to antibiotic A.  all this info sharing is done with plasmids - i liken them to dictionaries, textbooks, or encyclopedias -- they contain genetic material on specific topics - and they are excreted by the bacteria into the great wide open..........and like the fellow says on page 66, just cause there is a plasmid doesn't mean the plasmid has your answer........we have all experienced that late the night before a term paper is due (smile).  transposons kinda remind me of the cut and paste function in word processing -- very specific info that can travel between the plasmid and the chromosone....an abbreviated version of the plasmid - and be inserted in the correct gene sequence on the chromosone.  integrons seem to be analogous to being able to cut and paste several distinct paragraphs and carry them over to the chromosone and then they are inserted in the correct places.......but probably not all in the same place.  we certainly don't have that ability in word (hahahaha) - just think you could pick four or five statements in one paper and transfer them to the correct places in the second paper in one click cause each statement would carry its own info on where it is supposed to go and how.........guess that is represented in the computer software as a database entry that is controlled by a program that takes each data according to its place in the database and inserts it into another program that only receives that type of data.  see this is not so complicated really -- ha.  page 68 talks about horizontal gene transfer in soils after application of manure.....just to keep this on topic.  so antibiotic resistant bacteria land applied with the manure can teach the pre-existing soil bacteria how to be antibiotic resistant as well........iowa study showed 10 fold increase in such a phenomena.  you might want to read page 74 very carefully on how resistance is passed around at the CAFO.

the remaining portion of the thesis focuses on poultry in chesapeake bay.   Univ of Maryland 2005
https://drum.umd.edu/dspace/bitstream/1903/2641/1/umi-umd-2552.pdf

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Feeding Pigs
North Carolina Division of Water Quality

Subject:       more googling on multi-drug resistance
   Date:        Sat, 3 Mar 2007 22:46:30 EST
   From:       Stanley Cooper

i am on page 11 of my original google of "multi-drug resistance" manure

just when you think there can't be anymore new stuff, alas, two theses in a row that have fantastic summaries of the issue..........so here we go again.  remember, my page numbers refer to pdf pages, not the thesis page numbers........

1.  2005 Agriculture Economics thesis from michigan state -- economic impacts on US hog industry from ban of subtherapeutic use of antibiotics in feed.  by Michael Hogberg............

page 10 -- europe bans all subtherapeutic use in 2006 (ooh that was last year - is this another global warming behavior -- wait until every last country in the free world does something and THEN we get off our butts? or should i say - then the pocketbooks of corporate america find a way to profit from action? its freaking embarrassing.).  page 11 - figure showing the relationship between ag-sourced bacteria and your vegetable drawer in your refrigerator.......also shows where pet food fits in in all of this.......cause if you ain't eating it they sure are.....nothing goes to waste.

page 16 reflects this kid's naivete of our industry when he talks about the possible heterogeneity of the hog industry --- good managers and poor managers -- not sure about you guys, but i have only run into the poor managers ??  seems pretty homogeneous to me.............unless, he is referring to the older model of a real family farm with dad and the kids working at wee hours of the morning doing chores?  see, i don't think dad and the kids are responsible for multi-drug resistant pathogens.......and i bet you don't either.

page 18 refers to United Feeds (for those in indiana area that may interest you)......over 100 producers participated in the study.......

page 20 talks about market weight of 230 pounds back in the 1950's..........it is now about 270 pounds.  see page 39 for confirmation of this

pgs 23 - interesting that sweden and denmark used a tax to help phase out subtherapeutic use of antibiotics.

the next 10 pages or so describe the cooperative markets in sweden and denmark as compared to private ownership in america.....as a shortcut to establishing the ban on antibiotics.  their goal was to improve public perception of their product. management practices were dictated by the government -- larger space allocation per animal and type of housing per species (page 29).  see, we know this but the big ag PR machine makes us worry we are PETA if we try to talk about animal welfare.........example, sows in open stalls rather than crate system.  another government mandate related to farm size, animal
density and use of slatted floors (whaaat, i hope he explains that in more detail.........).  ooh ooh ooh -- and then they mandated that weaning time be extended four weeks from lactation.........cripes almighty.  and here in good ole america the ag schools are busy trying to figure out the second the piglet can be snatched from mama's teat and turned out to the nursery only to discover that health problems abound at the finishing stage......hence our need for subtherapeutic antibiotics

page 31-32 talks about the post-weaning diarrhea problems that occurred when antibiotics were removed from the diet.........stress related.  called "failure to survive"  sounds tragic.

page 36 - FDA tries to ban antibiotics and congress responds by threatening FDA budget.  he also mentions that FDA approves drugs but does not license their use.  someone help me here -- so who does?

page 41 -- in 1990, the US used 8 million kilograms of antibiotics in ag industry.......that equals 17.6 million pounds when using a conversion of 1000 grams per kilogram and 454 grams per pound or 2.2 kilograms per pound.  ask yourself why an 800% increase in antibiotics from 1970 to 1990?  cause the cost of antibiotics dropped 1000%..........the ole volume of sales allows for lower prices, especially if poorly regulated.

page 42, using antibiotics allowed the producers to house the animals closer together -- hence concentrated animal feeding operations as compared to "confined".........big difference in those two words.  see graph on page 43 for change of farm size over time.   i don't suppose the big rise in farm size had anything to do with the legislative politics in 1988-1989?

page 43 - 83% of nursery and 64% of finishers fed antibiotics (2000 study) - most often used - tetracyclerine table 3-1 lists all the common antibiotics used in the ag industry feed system.

page 47 - graph of change in number of producers (drop) to rise in hog production from 1990 to present.

the rest of the thesis is the economic evaluation using university of kentucky data and the United Feeds data.  it's a bit over my head - but i am sure some of you bean counters will find it very useful.
http://www.aec.msu.edu/theses/fulltext/hogberg_ms.pdf

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Subject:       my epiphany - manure pathogen transport mechanisms in plants
   Date:        Sun, 4 Mar 2007 11:51:24 EST
   From:       Stanley Cooper

first of all -- my sauce came out great last night.  i changed my google criteria to:
       manure pathogen transport mechanisms in plants
and voila -- loads of stuff i have never read before and the first good one is:

1.  2002 Rutgers (Soloman, et al) lettuce study -- the proverbial smoking gun -- e coli viable inside the lettuce leaf.  thank you good night.  the pictures tell the story really.........used flourescence to identify the ecoli at 45 micrometers into the lettuce leaf.  i can't say enough about it really. (when i send you links to the pdf file on the asm website you usually see the "manual download" message to the left and an info bar to the right --- i just use my cursor to highlight the border and get the two-sided arrow and then drag the border to the right - then you can increase the size of the article using the zoom function).  considering this is the first time i have seen this article and i google just about every day on pathogens........well, i think it is tragic.  when i was first interested in pathogens and spinach - i read dozens of related articles using lettuce as the media - but none of them indicated plant uptake into the leaves -- some begrudingly agreed that the pathogens were in the roots........and then when i read articles from USDA they claim the uptake is "controversial".  what is controversial about SEEING the pathogen INSIDE the plant leaf?
 http://aem.asm.org/cgi/reprint/68/1/397

2.  here is the USDA/EPA spin.  the organization that sponsored this webcast Q&A session is run by Rick Koelsch of Univ of Nebraska..........not a friend of human health and environment - i have run into him at rulemaking hearings - friend of corp ag.  see the answer to the uptake of e coli by the spinach.  see the answers regarding temperature effects on bacteria.  not correct.  not true.  spin.  the comment that EPA response to a lawsuit regarding CAFO rules was that there is no need for pathogen regulation in manure??????
http://lpe.unl.edu/pdfs/qanov06.pdf

3.  i have sent this before, but just to have it handy right after the comments made on item 2........the epa risk management report of may 2004.  pablum.  disappointing.
http://www.epa.gov/nrmrl/pubs/600r04042/600r04042.pdf

4.  i include this brief abstract because it introduces a new term for me:  The bacterial family Enterobacteriaceae contains some of the most devastating human and animal pathogens, including Escherichia coli, Salmonella enterica and species of Yersinia and Shigella.
http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.phyto.44.070505.143444

5.  i tried to cut and paste but gave up ..........scroll down to about 75% of the way through and see the section on pathogens.......related to biosolids disposal from domestic wastewater systems.  even this reference does not reflect the current understanding of pathogen survival in the soils but does at least forbid the application on human consumptive food products.  why would we allow untreated animal waste on human consumptive food products?
http://lgu.umd.edu/lgu_v2/homepages/home.cfm?trackID=31

6.  while we are on the topic of comparing biosolids to untreated manure catch a load of this one (yellow is animal waste, blue is treated municipal waste e coli counts):

Evans and Owens (1972) and Dean and Foran (1992) reported the application of liquid manures to tile drained fields resulted in elevated levels of nutrients and bacteria compared to normal tile discharges from unmanured sites. Fleming and Bradshaw (1992) reported maximum levels of 88.2 mg/l of NH4-N, and 1020 mg/l total suspended solids; and McLellan et al. (1993) reported peak concentrations of 53,000 organisms/100 nil of E. Coli in tile discharges shortly after application of liquid manures which originally contained 149 mg/l NH4-N and 7,000,000 organisms/100 tnl of E. Coli. For comparison, the accepted maximum effluent standard for most municipal wastewater treatment plants is 400 organisms/100 rnl of E. Coli and 37 mg/l of total suspended solids
http://www.p2pays.org/ref/21/20528.htm

7.  industry spin..........about half way down you will find "smorgasboard...."  buried deep in the paragraph it mentions that "pathogens may also cause problems"
http://beef-mag.com/mag/beef_capturing_manures_value/index.html

8. the EPA has such a split personality.......for example, this draft report 2004 is very useful and even though it is missing some critical research knowledge related to pathogen survival and occurrence, it is pretty straightforward and comprehensive.  good reading.
http://www.manure.umn.edu/regulatory/4Pharmaceuticals%20and%20Pathogens.pdf

9.  this study compares the breakthrough curves of chloride ion, e coli, and manure wastewater (pg 4 graphical presentation of results).  To understand a breakthrough curve........the y axis represents the concentration of the outlet divided by the original concentration of the item studied (C/Co)...........so high values means most of the item passed right through the media.........low values means there was retention inside the cores for various reasons.... delayed breakthrough indicates whatever did cause the retention was overcome and the concentration at the outlet starts to increase.  the soil used is described as silty with a clay fraction of 29% - which is a size delineation NOT an indicator of clay minerals.... (ie., a negative and highly reactive colloidal surface)...page 5 has one sentence that infers the bacteria prefer a postiively charged site for adsorption.......which explains some things and not others......if the bacteria are negatively charged and they added potassium chloride (chloride ion being a strongly negative charge) then i wonder about the actual competition between bacteria and chloride when chloride has a high solubility constant.... likes to remain in solution.  they make an argument that the individual bacteria get trapped in small pore spaces and dead ends in the matrix.  worth the effort to read.
http://vzj.scijournals.org/cgi/reprint/4/3/828

10.  some conference proceedings at the university of florida... odd bit of information.  the risk model for salmonella is ridiculous........considering the survivability in the soil and the ability of the microbes to multiply - although he uses a decay curve over 5 weeks.  doesn't match any decay curves i have read recently with salmonella lasting 200+ days in soil.....it almost seems like the main author understands that.   from the text:

Sludge treatment destroys 99% of the Salmonella allowing 1% remaining in the treated sludge. On application to the soil, 99% decay occurs in  5 weeks leaving 1% of that applied. Undoubtedly further decay will occur.  Dilution may be modeled as the probability of a tonne of potato crops colliding with a sludge particle. The dilution factor is 900. Therefore a potato has a 899/900 = 0.99888 probability of colliding with a soil particle. The probability of collision with a sludge particle is 1/900 = 0.00111.  Since each tonne of potatoes contains 0.02 tonnes of soil/sludge at point of harvest, 0.02 / 5 = 0.004 = 4% of the 5 tonnes dry solids of sludge applied to the hectare will be transmitted to the potato on collision with a sludge particle. 4.98 tonnes of the 5 tonnes of sludge applied = 0.996 = 99.6% will remain on the soil.  So starting with a tonne of raw sludge containing 5.4 x 108 salmonellas, one ends up with a tonne of potatoes potentially containing 44 salmonellas following treatment and dilution.
http://conference.ifas.ufl.edu/landapp/pathogens.htm
11.  and then you read this kind of crap coming out of north carolina state and no wonder the industry doesn't do anything.  i quote: "livestock and poultry shed a number of viruses and bacteria in manure.  While some of these can infect humans, it is relatively unlikely that they will unless the manure has direct access to a drinking water supply"
http://www.cals.ncsu.edu/waste_mgt/natlcenter/modules/Module%201.doc

12.  this article is about funding ag research (not pathogen transport) but has some great numbers broken down by regions of the US........useful in working with legislature on why your particular state is not doing more or if they are - why is the money spent on mundane repetitive notions rather than more creative and useful topics.
http://www.csrees.usda.gov/nea/ag_systems/pdfs/research_sanantonio.pdf

13.  you may remember my rant with the peanut crop planted after the cotton and the chicken litter used to kill a particular nematode that affected cotton yield and the potential for salmonella in the chicken litter to enter the peanut and thus end up in your kitchen cupboard in the peanut butter jar.  well this study looks at hog manure and its effect at killing a nematode --- the volatile organic acids is what does it........hahahaha.  the stuff that makes hog manure stink so bad is being used to kill nematodes with complete disregard for the pathogens that come with it.  swell.  this is kinda like when the kids do the laundry and shrink everything  - you are caught in a quandry - do you put a smile on your face and feel joy that they are doing the chores or do you freak out at the hundreds of dollars of clothes that were ruined cause someone apparently forgot to tell another someone what hot water does to fabric dyes?
http://www.publish.csiro.au/paper/AP01009.htm

14.  okay -- they referenced Solomon, et al so this review is at least up to date on the Rutgers lettuce research.  good article, summarizes a lot of the journal articles i have sent in the past.  In the same paragraph on page 6 (pdf page, not journal page) they mention research by Jablasome in 2005 that showed internalization of pathogens in seeds.......but that internalization did not extend into the growing plant.  I think the fact that it internalized in the seed goes back to my concern about rapeseed and Canola oil from that seed....and any other seed that humans eat -- almonds for example - which i have seen references to as a concern by the almond growers right after the spinach debacle.  also in that paragraph - Cooley, et al found e coli in the roots and the vasculature (ie., the fluid transport system of the plant).

the next paragraph discusses Zhuang, et al 1995 study on internalization of salmonella in tomatos - increases with increasing ambient temperature.  the next paragraph after that sums up the problem -- if the bugs are inside the plant, no amount of washing the outside will help you so emphasis must be on pre-harvest contamination control. amen.  cleaning the outside of the plant material only affects the surfaces that came in contact with manure laden soils.  and that is good.  don't get me wrong - the problems are on the outside and the inside of the plant.  but when the focus goes back to cleaning the plant material - i am sorely disappointed because the next logical step is to treat the manure to kill the pathogens or god forbid go straight to the animal and feed it differently.  here we find corporate agriculture succeeding in putting the burden on the crop farmer (the guy that was convinced the manure is beneficial and wonderful) to keep the food chain safe.  ACK.

see page 5 right hand column - paragraph starting with "wells and butterfield" - discusses the change in pH of the plant itself by fungi (raising pH to 7) assists the salmonella in surviving on the plant at the damaged area.  the bottom of that paragraph talks about a decrease in pH to 3.7 caused by a different microbe that resulted in no growth of salmonella at the plant wound.  basically we are talking about tag team microbes - with salmonella winning when the pH is adjusted towards neutral.  the term "epiphyte" means living on the plant surface.......helps a lot when reading the info on page 5.  i recommend reading the first paragraph on page 5 as well.........fairly clear discription of how the plant tries to identify a pathogen and prevent its entry so the pathogen mutates and gets in anyway.  there was rumor that if you carried a clipboard and wore a particular color shirt to the basketball arena that you could slip in without paying........never tried it myself cause i was always studying, but did hear the success stories....(smile).  we are not that much different than pathogens - if at first you don't succeed, try try again.

what is this about a 1974 study of bacteria in cucumbers?  that "enterobacteracea" is the family of all our favorites - see my item 4.  yikes.  that was 32 years ago.  seriously, this article and the one with the flourescent photos of e coli inside the lettuce should be sufficient to attract the attention of even the most dullest legislator.  i saved this article in a folder labeled "very important pathogen reports"  just so's ya know how much i think about it.
http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1750-3841.2006.00157.x

15.  this is a 1998 study of dairy manure transport from field application to the tile drainage system.  looked at soluble phosphorus and fecal coliform transport.  clear and concise.  good reading for those folks in the midwest with thousands of miles of field tiles.
http://asae.frymulti.com/request.asp?JID=3&AID=19428&v=14&i=6&CID=aeaj1998&T=2

well that should do it for now............hope you guys find this stuff even remotely as interesting as i do.  if not, please share with some of your odder friends okay? sc

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INDEX for Factory Farms / Industrial Agriculture Pages

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[19 April 2007]:
Another Stanley Cooper page --
Behind the Odors From Factory Farms: What the Nose Doesn't Know:


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4-6 March 2007
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