e. coli and emerging pathogens - nebraska extension · 2019. 11. 5. · e. coli and emerging...
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E. coli and Emerging Pathogens2019 USDA-NRCS & Nebraska Extension Ag Production Training
Presented by Tiffany Messer, Amy Schmidt, and Lisa Durso
[email protected]@unl.edu [email protected]
Overview of various types of confined livestock operations and recommended practices to reduce runoff of E. coli
Recommended practices to reduce E. coli runoff from grazing land
E. coli Hot Spots and Hot Times in a Reservoir System Impacted by Cattle Grazing and Migratory Waterfowl
Antibiotic Resistance Pathogens and Genes
E. coli & Emerging Pathogens
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Overview of various types of confined livestock operationsand recommended practices to reduce runoff of E. coli
Other sources of E. coli include land-applied human biosolids & aquaculture.
Graphic Source: Durso and Schmidt. Antimicrobial resistance related to agricultural wastewater and biosolids. In Antimicrobial Resistance in the Wastewater Treatment Process. P. Keen Raphaël Fugure, Eds. 2017
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Why E. coli?
"Know Your Enemy. Impure water.”(Reeve 088266-11), National Museum
of Health and Medicine
Drawn by Pfc. Andrew M. Hube and Cpl. Charles W. Brannan
Two main strategies to reduce E. coli contributions to surface water
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Vegetative Treatment Systemsfor feedlot runoff collection and utilization
Runoff from feedlot surface collected
Effluent pumped to vegetated area sized to utilize nutrients
Runoff from vegetated area returned to storage
Pump Station
Basin
Treatment Cells (1-8) Cattle Pens
The Vegetative Treatment System effectively reduces the concentration of manure-associated bacteria in the soil over time.
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Pump Station
Basin
Treatment Cells (1-8) Cattle Pens
The Vegetative Treatment System effectively reduces the concentration of manure-associated bacteria in the soil over time.
If properly managed, 100% of fecal indicator bacteria and pathogens can be prevented from entering surface waters.
Runoff from feedlot surface is collected in one of four sediment basins and gravity flows to a pump station.
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Only one treatment area is used at a time.
Runoff is applied to the vegetated areavia a gated pipe or other system.
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Overflow is collected at the downslope endof the vegetated area.
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Flow onto the vegetative area and return flow of runoff is measured using a pump station.
Buffer strips slow nutrient and pathogen transport.
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Manure application methods impact nutrientand pathogen transport.
Take Home Messagefor Controlling E. coli
Microbes tend to stay suspended in the liquid portion of the runoff and do not
settle out as quick as nutrients.
Infiltration is keyfor microbes like E. coli.
For more info: [email protected]
402-472-9622
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Recommended practices to reduce E. coli runoff from grazing land
The same basic principles apply:
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E. coli Sources
Bacterium found inintestines of warmblooded animals
(including humans)
Methods of E. coli contribution to environment:1 – Runoff from manured or grazed land2 – Direct fecal deposition in surface water3 – Wildlife and waterfowl
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E. coli in Grazing Systems
Sources: Oliver et al., 2005. Transfer of Escherichia coli to Water from Drained and Undrained Grassland After Grazing. JEQ 34:918-925.Martinez et al., 2013. Using the Q10 model to simulate E. coli survival in cowpats on grazing lands. Enivron Internat 54:1-10.Wagner et al. 2012. Assessment of cattle grazing effects on E. coli runoff. ASABE 55:2111-2122.
E. coli may first increase in fresh cowpats, but declines over about 3 months.
No difference between drained/undrained fields
High-flow storm events release more E. coli than low-flow events.
Larger animals and higher stocking density equate to more risk.
Wildlife contributions vary.
Soil, topography and proximity to water are factors.
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Reducing E. coli in Grazing Land Runoff
Sources: Wagner et al. 2012. Assessment of cattle grazing effects on E. coli runoff. ASABE 55:2111-2122.
Maintain adequate ground cover.
Balance stocking rate with available forage.
Avoid grazing in vulnerable areas of pasture during wet weather periods.
Provide adequate pasture recovery time following grazing.
Utilize rotational grazing to achieve these goals.
E. coli hot spots and hot times in a reservoir systemImpacted by cattle grazing and migratory waterfowl
Research by Dr. Tiffany [email protected]
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Study on E. coli in Surface Water
U.S. Meat Animal Research Center (USMARC)35,000 acres
NAD during WWII, USDA in 1964US Army Corp of Engineers monitors two groundwater plumes.
E. coli in surface water
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E. coli in surface water
Avian Detection
• Time-lapse camera installation
• 3 cameras at MARC: 2 at Reservoir; 1 at GCS1
• Bird counts were estimated on weekly basis
• Densities were calculated using ArcMap
Conclusions
1. Cattle density w/in 50 m of stream up to 30 days prior to rainfall events impacted E. coli concentrations in stream corridor
2. Avian presence significantly impacted E. coli concentrations during fall.
3. E. coli concentrations increased moving downstream.
4. Downstream reservoir exceeded EPA freshwater quality criteria ~85% of the study period following rainfall events.
Study on E. coli in Surface Water
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Antibiotic Resistant Pathogens and Resistance Genes
$$Bacteria
$Genes
$$$Drugs
Cost of Studying Antibiotic Resistance
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Clinical vs. Environmental Resistance
In clinical settings, the term “resistance” is
inexorably linked DIRECTLY to
“pathogen” and “treatment failure”.
In environmental settings, most bacteria are not
pathogens and pathogenicity of zoonotic
and opportunistic bacteria is assumed, but not known.
Relationships are generally INDIRECT.
Given that we want to reduce antibiotic resistance in agricultural settings, what is the target that we want to set for reduction?
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Given that we want to reduce antibiotic resistance in agricultural settings, what is the target that we want to set for reduction?
What is a normal, or “natural”, level of antibiotic resistance?
Zero?
Source: http://scopeblog.stanford.edu/files/2011/09/woolly_mammoth.jpg
Antibiotic resistance is ancient.
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30,000-year-old Beringian permafrost sedimentsand the identification of a highly diverse
collection of genes encodingresistance to b-lactam, tetracycline
and glycopeptide antibiotics.
Source: Nature 2011, 477:457
Antibiotic resistance is found in pristine
habitats.
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Sample of the culturable microbiome from a region ofLechuguilla Cave, New Mexico, that has been
isolated for over 4 million yearsrevealed that, like surface microbes, these bacteria
were highly resistant to antibiotics…with some strainsresistant to 14 different commercially-available antibiotics.
Source: PLoS ONE 2012, 7(4): e34953
Antibiotic resistant bacteria are found on meat raised in organic, antibiotic-free systems.
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No statistically significant differences were observedfor the prevalence of S. aureus in general, or MSSA or MRSA, specifically,
when comparing pork productsfrom conventionally raised swine and swine raised without antibiotics,
a finding that contrasts with a prior study from the Netherlands examining both conventional and “biologic” meat products.
Source: PLoS ONE 2012, 7(1): e30092
Antibiotic resistance is common in environmental samples.
Source: becauseitsawesome.com
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Source: Curr Opin Micobiol 2007, 10:485
Antibiotic resistance has largely been studied in the context of failure of drugs in clinical settings. Growing evidence shows that
bacteria that live in the environment (e.g. soil)are multi-drug-resistant.
Antibiotic resistant bacteria are found in organic farming systems.
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Even in the absence of farm use of antibiotics, antibiotic resistance persistedin the organically raised swine. The reasons for the persistence of antibiotic
resistance are likely to be multiple.These findings suggest approaches in addition to prudent antibiotic usewill be important in effectively reducing resistant bacterial populations
in swine.
Source: AEM 2011, 77:7167
Measuring antibiotic resistance in ungrazed prairie soils, Nebraska
Year 15 prairies
10 locations within each
9-mile Prairie sampled over time
Year 2
20 prairies
5 locations within each
All samples collected in 3-d window
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Contact InformationQuestions and comments welcome!
Tiffany Messer
Assistant ProfessorWater Quality Scientist
Biological Systems EngineeringSchool of Natural ResourcesPhone: (402) 472-2232Email: [email protected]
Identify, Trace, and Treat Contaminants in Agroecosystems and
Downstream Communities.
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Amy Millmier Schmidt, P.E.
Associate ProfessorManure Management Specialist
Biological Systems EngineeringAnimal SciencePhone: (402) 472-0877Email: [email protected]
Identify and promote livestock manure management practices to mitigate
potential social and environmental risks from manure nutrients and contaminants.
Lisa Durso
Research MicrobiologistUSDA Ag Research Service
National Program 212, Soil & AirAdjunct at UNL, AgronomyPhone: (402) 472-9622Email: [email protected]
“Microbes in Manure”Using manure to improve soil and plant
health while minimizing adverse environmental impacts (pathogens, fecal
indicators, antibiotic resistance)
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