Implications of Foodborne pathogen survival during production and pre-harvest application of ...

280 Pages·2009·5 MB·English

by  David T. Ingram

ABSTRACT

Title of Dissertation: ASSESSMENT OF FOODBORNE
PATHOGEN SURVIVAL DURING
PRODUCTION AND PRE-HARVEST
APPLICATION OF COMPOST AND
COMPOST TEA

David T. Ingram, Ph.D. 2009

Directed By: Sam W. Joseph, Professor (Emeritus), CBMG
and Director, Maryland Institute for Applied
Environmental Health

Jianghong Meng, Professor, NFSC, and Interim
Director of the Joint Institute for Food Safety
and Nutrition

The use of compost in crop production systems as a soil amendment is
recognized by both conventional and organic plant production practitioners as
a means to increase yields and reduce the incidence of foliar diseases.
Compost tea (CT), an aqueous extract of the biological components of
compost, is also recognized as a means to broadcast the phytopathogen-
reducing components of compost directly to the surfaces of plants where
many foliar diseases become established. CT has been shown to control the
proliferation of a variety of foliar diseases in many turf, crop and horticulture
production systems when applied directly to the foliar surfaces of plants. This
dissertation research was designed to address several pre-harvest food safety
issues concerning compost and compost teas. Three objectives were pursued
to establish whether the use of compost and compost teas as pre-harvest
practices may introduce foodborne pathogens into the food supply and,
therefore, contribute to the incidence of foodborne illness. The first objective
involved a microbiological survey of commercially available compost in the
U.S. to determine the prevalence of fecal coliforms, Escherichia coli,
Salmonella and enterococci that might be reaching consumers through
contaminated fruit and vegetables. The second objective was to investigate
the ability of these foodborne pathogens to propagate during the production of
CT. The third objective involved a field study examining the potential of CT
to disseminate E. coli into organic and conventional strawberry production
systems. The effects of CT on the fruit yield, phytopathogen suppression, as
well as the potential for foodborne pathogen survival on the fruit surfaces
were examined. This project provided important information and
recommendations for the safe production and pre-harvest application of
compost and compost teas. It was contended that, with proper attention to the
manufacture and storage of compost and with simple modification of current
trends in CT production systems, the current threshold of pre-harvest
introduction of foodborne pathogens could be significantly reduced.
ASSESSMENT OF FOODBORNE PATHOGEN SURVIVAL DURING
PRODUCTION AND PRE-HARVEST APPLICATION OF COMPOST AND
COMPOST TEA

By

David Thomas Ingram

Dissertation submitted to the Faculty of the Graduate School of the
University of Maryland, College Park, in partial fulfillment
of the requirements for the degree of
Doctor of Philosophy
2009

Advisory Committee:

Professor Sam W. Joseph, Co-Chair
Professor Jianghong Meng, Co-Chair
Professor Thomas W. Castonguay
Dr. Mark A. Kantor
Dr. Patricia D. Millner
© Copyright by

David T. Ingram

2009
DEDICATION
This dissertation is dedicated first and foremost to my family who, through the
years have provided the strength, security and unconditional love every professional
graduate student needs to nurture his dreams, cultivate his ideas, wrestle with his
demons, and find his own path in life and career (with gentle prodding). I know that
no one will be more pleased than my father when he places a copy of this dissertation
on his bookshelf next to his own, also earned at the University of Maryland. Dad,
you will never know how much I have relied on your always sound advice, guidance
and much needed camaraderie to provide me with direction -- sometimes with a kick
in the gluteus maximus. Your pursuit of excellence is second to none, and our entire
family is all the stronger for your leadership.
Mom, you have no idea how often I have tapped into your unbounded energy
and amazing ability to remember the important things in life. Just thinking about you
always puts a smile on my face.
Kirsten, my sister, thank you for your patience and positive encouragement
that has kept me focused over the years. You have no idea how much I have enjoyed
watching you become a wonderful mother for my niece, Ella and nephew, Thomas.
If not for my fabulous wife, Shannon Leigh Kondrad, I could not have
accomplished this piece of work because of her selflessness and support. Words
cannot describe my gratitude for her love. You are truly the woman of my dreams.
Finally, the individual who probably most inspired me to complete this
dissertation is my daughter who will arrive this spring. I eagerly await your arrival so
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that I can share with you all that I have learned about life, love and the pursuit of
dreams.
This dissertation is dedicated to you all.

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ACKNOWLEDGEMENTS

“It may be poop to you, but it’s my bread and butter”

Sam W. Joseph, Ph.D.

I would first like to acknowledge Sam W. Joseph, Ph.D., my long-time
mentor, counselor, professor, and friend who recognized the potential microbiologist
in me back in the days when E. coli O157:H7 and other foodborne pathogens were
mostly implicated in red meat and poultry. I cherished our time together and
mentally processed every bit of advice that you gave me over the many research
projects, “coffee house” discussions, golf outings, manuscript drafting, the
completion of my M.S. Thesis, and the ups and downs associated with completing,
finally, this dissertation. I would not be where I am today in my career without your
guidance on coping with the many pitfalls and entrapments associated with putting
pen-to-paper. My father repeatedly said, “David, you owe Sam Joseph much more
than you realize right now.” He was right. Your efforts to help me to earn the Ph.D.
enable me to continue tinkering in the laboratory and exploring a science that I have
learned to love. Thank you for your patience and all you have done for me.
Dr. Jianghong Meng, your interest in me as one of your first lab-technicians in
the NFSC Department and later your support as I embarked on this Ph.D. journey will
never be forgotten. Thank you. I hope that this dissertation will mark the beginning
of more opportunities to collaborate with you.
Before I met Patricia Millner, Ph.D., I thought compost was simply a pile of
poop, and that there was only one type of strawberry. Bless you for introducing me to
the incredibly diverse and wonderful world of agriculture. Giving me the
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opportunity, freedom and financial support to pursue my experiments, (even some
you surely knew would fail), strengthened my instincts and methods and enabled me
to find my scientific legs. Engaging me in your diverse and fruitful research
programs in the USDA-ARS family has helped me to understand the interactions of
medical, food and environmental microbiology. Thank you for all your support,
guidance and friendship that enabled a seed, planted in a cooperative research
agreement with the University, to grow through the medium of a Student-Career
Experience Program into a full-bloom government career. In my book, you are a
renaissance leader.
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TABLE OF CONTENTS

LIST OF TABLES ...................................................................................................... IX

LIST OF FIGURES .................................................................................................... XI 

CHAPTER 1 : LITERATURE REVIEW ..................................................................... 1 
Overview ................................................................................................................... 1 
Compost : evolution from historical reference to state-of-the-art ............................ 5 
Modern compost production methods .................................................................. 8 
Physico-chemical factors affecting the composting process .................................. 13 
Carbon:Nitron ratio ............................................................................................. 13 
Moisture .............................................................................................................. 14 
pH ........................................................................................................................ 15 
Temperature ........................................................................................................ 15 
Uses and benefits .................................................................................................... 16 
Soil conditioner ................................................................................................... 17 
Plant disease suppression .................................................................................... 19 
Compost as an energy source .............................................................................. 21 
Human pathogens in compost ................................................................................. 23 
United States composting standards ................................................................... 23 
Pathogen reduction in compost ........................................................................... 26 
Pathogen indicators ............................................................................................. 28 
Gaps in Part 503 Regulations .............................................................................. 28 
Compost Tea ........................................................................................................... 31 
Definitions and development .............................................................................. 31 
Uses and benefits ................................................................................................ 34 
Evolution of U.S. compost tea production methods ........................................... 44 
Food safety concerns........................................................................................... 46 
Human pathogens in compost tea ....................................................................... 49 
Compost Tea Task Force recommendations ....................................................... 54 
Scope of dissertation ............................................................................................... 56 

CHAPTER 2 : FECAL BACTERIAL PATHOGENS AND INDICATORS IN
COMMERCIALLY AVAILABLE COMPOST ........................................................ 58 
Abstract ................................................................................................................... 58 
Introduction ............................................................................................................. 61 
Materials and Methods ............................................................................................ 64 
Compost sampling and processing ...................................................................... 64 
Dry weight determination ................................................................................... 68 
Microbiological analyses .................................................................................... 69 
MIDI protocol ..................................................................................................... 79 
Real-time PCR detection of virulence genes in E. coli isolates .......................... 83 
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Statistical analysis ............................................................................................... 84 
Results ..................................................................................................................... 86 
Composting facilities .......................................................................................... 86 
Physical and chemical parameters of compost samples ..................................... 87 
Coliform and Salmonella concentrations in compost samples ........................... 94 
Heterotrophic, gram negative and enterococci populations in compost samples.
............................................................................................................................. 98 
Monthly analysis for fecal coliform, E. coli and Salmonella content ............... 101 
Analysis of compost samples based on biosolids content ................................ 106 
Characterization of E. coli and Salmonella isolates .......................................... 107 
Summary for fecal coliform, E. coli and Salmonella content ........................... 114 
Discussion ............................................................................................................. 115 

CHAPTER 3 : POTENTIAL MULTIPLIER FACTORS EFFECTING COMPOST
TEA AS A SOURCE OF ESCHERICHIA COLI AND SALMONELLA .................. 128 
Abstract ................................................................................................................. 128 
Introduction ........................................................................................................... 129 
Materials and Methods .......................................................................................... 133 
Bacteria and culture conditions. ........................................................................ 133 
Compost source and nutrient supplements. ...................................................... 134 
Compost tea method (ACT, NCT) comparison ................................................ 135 
Component bioassays........................................................................................ 138 
Analysis of four compost tea brewing systems. ................................................ 138 
Competition study ............................................................................................. 139 
Microbiological characterization of compost teas. ........................................... 140 
Physical and chemical characterization of compost ......................................... 141 
Statistical analyses ............................................................................................ 141 
Results ................................................................................................................... 142 
ACT/NCT compost tea comparison study ........................................................ 142 
Component bioassays........................................................................................ 144 
Brewer comparison ........................................................................................... 144 
Competition study ............................................................................................. 145 
Discussion ............................................................................................................. 159 

CHAPTER 4 : EFFECT OF COMPOST AND COMPOST TEA ON THE
MICROBIOLOGICAL SAFETY AND HARVEST QUALITY OF STRAWBERRY
FRUITS ..................................................................................................................... 166 
Abstract ................................................................................................................. 166 
Introduction ........................................................................................................... 168 
Materials and Methods .......................................................................................... 173 
Strawberry plot design and statistical analysis ................................................. 173 
Strawberry field preparation ............................................................................. 174 
Preparation and application of compost tea (foliage treatments) ...................... 176 
Microbiological and chemical analysis of compost tea .................................... 178 
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