[USCC] antibiotic resistant microbes in livestock manure-compost

[Allison L H Jack]

Hi everyone,

I wanted to make a few comments on this older thread from before the July 
4th holiday.

Dr. Chaney mentioned that the human pathogens present in livestock manures 
are not thermophiles, and would be killed during composting (full posting 
at the end of this message). This is true, but the main concept behind 
antibiotic resistance is that bacteria can transfer this resistance between 
completely unrelated species via plasmids. The following is a possible 
scenario. An E. coli bacterium living in a cow gut acquires resistance to 
the sub-therapeutic antibiotics administered to the cow. This bacterium is 
shed from the gut and ends up in the manure. The antibiotic resistance gene 
is carried on a mobile plasmid (small circular extra-chromosomal DNA) that 
is transferred to 3 totally different bacterial species. If one of these 
species is a thermophile, it is possible that it could survive the 
composting process and transfer the plasmid to mesophilic bacteria in the 
finished compost and in the soil. Many human pathogens, especially 
opportunistic ones, are soil dwellers, hence the widespread concern over 
this issue of multi drug resistant bacteria. The American Society for 
Microbiology has a whole section of their website devoted to the issue of 
antibiotic resistance due to medical and agricultural use of antibiotics. 
[http://www.asm.org/Policy/index.asp?bid=531].

The transfer of antibiotic resistance genes from bacteria in manure to 
bacteria in soil is well documented (see a selection of literature below 
[1-2]), but little is known about how manure management affects this 
process. There is growing evidence that intensively managing manure (i.e. 
composting) can reduce the spread of antibiotic resistance genes in soil 
bacterial populations [3]. I would argue that more studies of this kind 
need to be done. I believe documenting that composting could partially 
ameliorate this emerging environmental problem would be a benefit to the 
industry. But of course, without the involvement and support of the entire 
composting community, this field of research will continue to focus on raw 
manure and not take a critical look at the potential benefits of the 
composting process.

Scientific knowledge is a moving target, and I would argue that successful 
industries need to be flexible and respond rapidly to new information. For 
example, when McDonald's executives learned about the emerging issue of 
antibiotic resistant microbes, they very rapidly banned the use of 
sub-therapeutic antibiotics for all of their meat suppliers worldwide 
[<http://www.mcdonalds.com/corp/values/purchasing/antibiotics/global_policy.html>www.mcdonalds.com/corp/values/purchasing/antibiotics/global_policy.html]. 
The 503 rules were researched and written decades before horizontal gene 
transfer was documented in soil bacterial communities. Environmental 
microbiology is one of the fastest growing fields of science right now due 
to the new molecular tools at our disposal. Which news story would you like 
to see first; "Compost can contain antibiotic resistant microbes, be 
afraid!" or "Composting can help reduce the presence of antibiotic 
resistant microbes"? I hope the industry chooses to be proactive and 
collaborate with scientists working on this issue so that we can all better 
understand the effect of composting on the persistence of antibiotic 
residues and antibiotic resistance genes in manures.

Dr. Chaney's point on endocrine disrupting compounds in personal care 
products is a good one. Many people, myself included, chose not to use 
products that contain these compounds. There's an extensive searchable 
database run by the Environmental Working Group where you can research the 
ingredients in these products (most have which have been banned in Europe) 
[http://www.cosmeticsdatabase.com/index.php?nothanks=1]. Adverse human 
health effects are one issue, but this is an environmental issue as well. 
Fish can't choose which deodorant they're exposed to! Endocrine disrupting 
compounds from sewage effluent have a feminization effect on fish at very 
low concentrations. Feminization means that male fish can't develop 
properly and a population can shift to almost entirely females, or sterile 
intermediates which can cause the whole population to crash. There's an 
excellent PNAS paper on this subject that's available online [4].  I 
believe this will be one of the largest environmental stories of our 
generation behind climate change, and it will definitely affect the 
biosolids composting industry. Again, this was not a documented issue when 
the 503 rules were developed. I would argue that the industry needs to 
decide on adopting a proactive or reactive response to these emerging 
issues in manure management.

-Allison Jack
Cornell University



[1]

Title: Short-term effects of amoxicillin on bacterial communities in 
manured soil
Author(s): Binh CTT, Heuer H, Gomes NCM, et al.
Source: FEMS MICROBIOLOGY ECOLOGY   Volume: 62   Issue: 3   Pages: 
290-302   Published: DEC 2007

Abstract: Antibiotic-resistant bacteria, nutrients and antibiotics that 
enter the soil by means of manure may enhance the proportion of bacteria 
displaying antibiotic resistance among soil bacteria and may affect 
bacterial community structure and function. To investigate the effect of 
manure and amoxicillin added to manure on soil bacterial communities, 
microcosm experiments were performed with two soil types and the following 
treatments: (1) nontreated, (2) manure-treated, (3) treated with manure 
supplemented with 10 mg amoxicillin kg(-1) soil and (4) treated with manure 
supplemented with 100 mg amoxicillin kg(-1) soil, with four replicates per 
treatment. Manure significantly increased the total CFU count and the 
amoxicillin-resistant CFU count of both soil types. However, only the soil 
with a history of manure treatment showed a significant increase in the 
relative number of amoxicillin-resistant bacteria as a result of 
amoxicillin amendment. The majority of plasmids exogenously isolated from 
soil originated from soil treated with amoxicillin-supplemented manure. All 
16 characterized plasmids carried the bla-TEM gene, and 10 of them belonged 
to the IncN group. The bla-TEM gene was detected in DNA directly extracted 
from soil by dot-blot hybridization of PCR amplicons and showed an 
increased abundance in soil samples treated with manure. Molecular 
fingerprint analysis of 16S rRNA gene fragments amplified from soil DNA 
revealed significant effects of manure and amoxicillin on the bacterial 
community of both soils.


[2]

Title: The effects of subtherapeutic antibiotic use in farm animals on the 
proliferation and persistence of antibiotic resistance among soil bacteria
Author(s): Ghosh S, LaPara TM
Source: ISME JOURNAL   Volume: 1   Issue: 3   Pages: 191-203   Published: 
JUL 2007

Abstract: The use of antibiotics at subtherapeutic concentrations for 
agricultural applications is believed to be an important factor in the 
proliferation of antibiotic- resistant bacteria. The goal of this study was 
to determine if the application of manure onto agricultural land would 
result in the proliferation of antibiotic resistance among soil bacteria. 
Chlortetracycline- resistant bacteria were enumerated and characterized 
from soils exposed to the manure of animals fed subtherapeutic 
concentrations of antibiotics and compared to the chlortetracycline- 
resistant bacteria from soils at farms with restricted antibiotic use ( 
dairy farms) and from non- agricultural soils. No significant differences 
were observed at nine different study sites with respect to the numbers and 
types of cultivated chlortetracycline- resistant bacteria. Genes encoding 
for tetracycline resistance were rarely detected in the resistant bacteria 
from these sites. In contrast, soils collected from a tenth farm, which 
allowed manure to indiscriminately accumulate outside the animal pen, had 
significantly higher chlortetracycline- resistance levels. These resistant 
bacteria frequently harbored one of 14 different genes encoding for 
tetracycline resistance, many of which ( especially tet( A) and tet( L)) 
were detected in numerous different bacterial species. Subsequent bacterial 
enumerations at this site, following the cessation of farming activity, 
suggested that this farm remained a hotspot for antibiotic resistance. In 
conclusion, we speculate that excessive application of animal manure leads 
to the spread of resistance to soil bacteria ( potentially by lateral gene 
transfer), which then serve as persistent reservoir of antibiotic resistance.

[3]

Title: Response of antibiotics and resistance genes to high-intensity and 
low-intensity manure management
Author(s): Storteboom HN, Kim SC, Doesken KC, et al.
Source: JOURNAL OF ENVIRONMENTAL QUALITY   Volume: 36   Issue: 6   Pages: 
1695-1703   Published: NOV-DEC 2007

Abstract: This purpose of thid study was to determine the response of 
antibiotics and antibiotic resistance genes (ARG) to manure management. A 
pilor field study was conducted using horse manure containing no 
antibiotics, into which chlorretracycline (CTC), tylosin (TYL), and 
monensin (MON) were spiked and compared to unspiked controls. Subsequently, 
a large-scale field study was conducted comparing manure from a dairy with 
minimal use of antibiotics and a feedlot with regular subtherapeutic use of 
antibiotics. The manures were subjected tp high-intensity management (HIM) 
(amending watering, and turning) and low-intensity management (LIM) (no 
amending, watering, or turning) and were monitereed for antibiotic 
concentrations and levels of tetracycline ARG [tet(W) and tet(O)] using 
quantitative real-time polymerase chain reaction. All three antibiotics in 
the pilot study disipated more rapidly in HIM manure, with half-lives 
ranging from 4 to 15 d, compared to LIM manure, with half-lives ranging 
from 8 to 30 d. Levels of tet(W) were significantly higher after 141 d of 
treatment, but levels of tet(O) were significantly lower in all treatments. 
In the large-scale study, the feedlot manure had higher initial 
concentrations than the dairy manure of tetracycline (TC), oxytetracycline 
(OTC), and CTC as well as tet(W) and tet(O). Tetracycline and OTC 
dissipated more rapidly in HIM manure, with half-lives ranging from 7 to 31 
d. After 6 mo of treatment, tet(W) and tet(O) decreased significantly in 
feedlot manure, whereas dairy manure required only 4 mo of treatment for 
similar results.

[4]

Title: Collapse of a fish population after exposure to a synthetic estrogen
Author(s): Kidd KA, Blanchfield PJ, Mills KH, et al.
Source: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED 
STATES OF AMERICA   Volume: 104   Issue: 21   Pages: 8897-8901   Published: 
MAY 22 2007

Absract: Municipal wastewaters are a complex mixture containing estrogens 
and estrogen mimics that are known to affect the reproductive health of 
wild fishes. Male fishes downstream of some wastewater outfalls produce 
vitellogenin (VTG) (a protein normally synthesized by females during oocyte 
maturation) and early-stage eggs in their testes, and this feminization has 
been attributed to the presence of estrogenic substances such as natural 
estrogens [estrone or 17 -estradiol (E2)], the synthetic estrogen used in 
birth-control pills [17 -ethynylestradiol (EE2)], or weaker estrogen mimics 
such as nonylphenol in the water. Despite widespread evidence that male 
fishes are being feminized, it is not known whether these low-level, 
chronic exposures adversely impact the sustainability of wild populations. 
We conducted a 7-year, whole-lake experiment at the Experimental Lakes Area 
(ELA) in northwestern Ontario, Canada, and showed that chronic exposure of 
fathead minnow (Pimephales promelas) to low concentrations (5–6 ng·L 1) of 
the potent 17 -ethynylestradiol led to feminization of males through the 
production of vitellogenin mRNA and protein, impacts on gonadal development 
as evidenced by intersex in males and altered oogenesis in females, and, 
ultimately, a near extinction of this species from the lake. Our 
observations demonstrate that the concentrations of estrogens and their 
mimics observed in freshwaters can impact the sustainability of wild fish 
populations.

PNAS is open access, read the full article here: 
http://www.pnas.org/content/104/21/8897


Allison Jack
Cornell University


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Dear USCC:

I believe some perspective is needed following some of the comments that
have come from the original question about destruction of antibiotics
during composting.

It is clear that many antibiotics are readily biodegraded during either
anaerobic digestion or composting of manure and biosolids. But not all
are so rapidly biodegraded. Just as with herbicides and pesticides; some
are easily biodegraded and others not. The unexpected residue of the
herbicide clopyralid discovered several years ago required changes in
registration so that it would not be used for home weed control and then
contaminate home composts or yard-debris composts that are increasingly
important to North American cities.

Mr. McGowan reminded us of some of this, but then over-stated the
reality of pathogen destruction by composting. Yes, there may be some
antibiotic resistant microbes in livestock and human wastes, but these
are human pathogens that are readily killed by the temperatures required
for effective composting. Of course, not all composting is conducted to
comply with the 503 requirements, but increasingly that has become the
management goal for the composting industry which needs to show they
have killed animal and plant pathogens by the combination of temperature
and time.

I wanted to remind us all again that toxic chemicals are present in all
the plants we eat. Bruce Ames (of Ames test fame) has evaluated toxicity
and mutagenicity of chemicals in foods and found that 99.98% of all
pesticicds that are present in foods are the natural pesticides made in
plants to prevent microbial infection or reduce insect feeding on the
plant in nature. Residues of synthetic pesticides are miniscule in
comparison. I note this information because some who communicate here
seem to think that only industrial chemicals are dangerous. These
natural chemicals include some which are complex enough that
biodegradation is slower than for more metabolic compounds in plants.

And others have made a big deal about possible residues of antibiotics
from personal care products in biosolids and biosolids composts. They
seem to forget that the highest exposure of humans to these chemicals is
to the materials in the products as they use them in their homes. And
the selection of antibiotic resistant microbes is much greater in the
home where such materials are used than due to the low concentrations
present in biosolids or manure. Similarly for other chemicals in
personal care products.

Just hoping to help us find a balanced perspective on these issues that
fairly considers the value of composting and of compost products.

Regards,

Rufus Chaney
Beltsville, MD

**************************************************************************************
Allison L H Jack
Graduate Student
Department of Plant Pathology and Plant-Microbe Biology
http://pppmb.cals.cornell.edu
Cornell University
335 Plant Science
Ithaca, NY 14850
607.273.5762
************************************************************************************* 


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