Prevalence, Resistance Patterns and Risk Factors for Antimicrobial Resistance in Poultry Farms ...

111 Pages·2011·0.67 MB·English

Prevalence, Resistance Patterns and Risk Factors for Antimicrobial Resistance in Poultry Farms
and Retail Chicken Meat in Colombia and Molecular Characterization of Salmonella Paratyphi
B and Salmonella Heidelberg
by
Maria del Pilar Donado Godoy
DVM (Universidad Nacional de Colombia) 1988
M.Sc. (University of Guelph, Ontario Veterinary College) 1992
DISSERTATION
Submitted in partial satisfaction of the requirements for the degree of

DOCTOR OF PHILOSOPHY

in
Epidemiology
in the
OFFICE OF GRADUATE STUDIES
of the
UNIVERSITY OF CALIFORNIA
DAVIS
Approved:

_____________________________________
Ian Gardner, Chair

_____________________________________
Barbara Byrne

_____________________________________
Woutrina Miller
Committee in Charge
2010
Prevalence, Resistance Patterns and Risk Factors for Antimicrobial Resistance in Poultry Farms
and Retail Chicken Meat in Colombia and Molecular Characterization of Salmonella Paratyphi
B and Salmonella Heidelberg

Maria del Pilar Donado Godoy

2010
ii
Dedicated to

My parents, Guillermo and Bertha and,

Mi amor, Xavier

iii
ABSTRACT
The development of antimicrobial resistance among bacteria (AMR) is currently one of the world’s
most pressing public health problems. Misuse of antimicrobial agents both in humans and
animals has narrowed the potential use of antibiotics for the treatment of infections in humans. To
monitor the evolution of AMR and to develop control measures, some countries, such as the
USA, Canada and Denmark have set up national integrated monitoring systems. Surveillance
components in these programs help monitor changes in susceptibility/resistance of selected
zoonotic bacterial pathogens and commensal organisms recovered from animals, some retail
meats, and humans to antimicrobial agents. The growth of Colombia as an emerging economy
has resulted in the rapid development of its poultry industry and consequently new challenges in
food safety with the increased use of antibiotics. Since Colombia presents scenarios that can
potentially foster the emergence of antibiotic resistance and also does not have a monitoring
system, we conducted this pilot research to establish baseline data and to adapt processes for
the establishment of a Colombian Integrated Program for Antimicrobial Resistance Surveillance
(COIPARS).
We assessed the prevalence, risk factors and antimicrobial resistance profiles of a single food-
borne pathogen of importance for human health, Salmonella sp., and two commensal bacteria
Escherichia coli and Enterococcus, in commercial broiler farms of the two largest poultry
producing departments of Colombia and in retail meat chicken collected in Bogota, Capital District.
We further characterized isolates of the most prevalent Salmonella serovars, Salmonella
Paratyphi B dT+ and Heidelberg, using pulsed-field gel electrophoresis (PFGE) to evaluate their
genetic relatedness and to determine potential geographically predominant clones.
Our study found a high prevalence of Salmonella sp. in commercial broiler farms (41%) and
poultry houses (65%) and almost 26% in retail meat samples. Salmonella Paratyphi B dT+
represented 76% of Salmonella sp. isolated on farms and 51% of those isolated from retail meat
samples. Salmonella Heidelberg represented 23% and 16% of Salmonella isolates from farms
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and retail meat samples, respectively. This is the first time that Salmonella Paratyphi B dT+ has
been reported in the poultry chain in Colombia.
Salmonella isolated from farms and retail meat as well as Escherichia coli and enterococci
isolated from chicken meat showed extensive resistance to antimicrobial agents. Ninety-eight
percent of Salmonella sp. isolates were reported as multi-drug resistant. Ceftiofur, enrofloxacin,
nalidixic acid and tetracycline were the antimicrobials that showed the highest frequency of
resistance among Salmonella and E. coli isolates. For enterococci, we found that 62% of E.
faecium isolates were resistant to quinupristin/dalfopristin, which is used to treat nosocomial
human infections when vancomycin resistance is present.
The DNA fingerprinting of S. Paratyphi B dT+ and S. Heidelberg isolates revealed marked
heterogeneity. However, similar genotypes of both serovars were demonstrated to be present in
farms and in retail outlets as well as among isolates coming from different farms within each
region and from farms located in the two geographically distant departments. A possible
dissemination of similar genotypes of both serovars along the poultry chain was hypothesized.
Lack of rigorous biosecurity and some high risk management practices of the poultry industry in
Colombia were possible explanations.
In conclusion, we consider that the findings of our pilot project, the first of its kind conducted in
Colombia, indicate potential risks for human health related to food-borne pathogens present in
the poultry chain. Despite the fact that longitudinal studies are required to further characterize
these risks, we believe that these results confirm the utility of establishing the COIPARS. Our
findings also suggest that it is possible to follow the processes required for establishing a
surveillance system similar to the ones in the USA or Canada while adapting the protocols for
local conditions. Finally, a program like COIPARS can also provide scientific evidence for
implementation of the new Colombian biosecurity legislation (Resolution 001183 issued by the
Colombian Agricultural Institute on March 25, 2010) to decrease the prevalence of Salmonella in
poultry farms.
Approved: ________________________________________________________________
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ACKNOWLEDGEMENTS

“Tarda en llegar y al final, al final, siempre hay recompensa…en la zona de promesas”. Gustavo
Cerati
“It takes time to arrive and in the end, in the end, there is always a reward… in the zone of
promises”. Gustavo Cerati
Before entering the ”zone of promises”, I want to thank a thousand of times over, to each and
every one of the people who were alongside in one way or another. Today it is hard for me to
write… please forgive me because the words are not flowing as they could. I have been
submerged in this journey for so long now that some of the words have slowly gotten lost…
“Life also gives you people with beautiful hearts” …
and for all those nice individuals, I am filled with gratitude; even though you may not hear the
melody, there is music accompanying me in my thanks to each one of you.
I would like to thank Ian Gardner for his marvelous patience and support even though “all the
roads seemed to get farther and farther away from Rome.” Thank you for being there and
believing that it was possible to begin in Kenya and end up in Colombia. Thank you for
supporting me in each of the many episodes of “magical realism” that can only be enjoyed or
suffered in countries like mine. I would also like to thank Barbara Byrne and Woutrina Miller for
their involving in this bodywork that came from such a different, distant, and unknown place. To
all three of you, I offer my most profound appreciation and gratitude for providing me the
guidance and support that culminated in this dissertation.
My enormous gratitude to Enrique Pérez, one of those “winged” human beings who saved me
twice from deep abysses and took me by the hand until I was free from all harm. My special
thanks to Enrique Perez from PAHO-WHO and Richard Reid-Smith from CIPARS for
brainstorming and helped me to setting up the Colombian Integrated Program for Antimicrobial
Resistance Surveillance (COIPARS) and for making it possible by giving me scientific, logistical
and financial support to make this initiative working. A special acknowledgment to you, Enrique,
Richard and to Ole Heuer from DANMAP, for coming to Colombia and believing that was the
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appropriate country to launch the pilot integrated program for the antimicrobial resistance
surveillance in Latin America. Also, special thanks to Ezra Barzilay and Jane Wichard from CDC
for participating in this initiative and for the scientific support that you have provided to me.
Thanks also to the Instituto Colombiano Agropecuario (ICA) for funding most of the research
activities related to this PhD Project. Thank you for providing me with the reagents, tools,
equipment, two laboratories, and related infrastructure that facilitated my research so successfully
in Colombia. Special thanks to each of my friends and colleagues at ICA for believing in the
importance of this project and for helping me build the support network with the official and
private Colombian entities that participated in making this project possible: Deyanira Barrero,
McAllister Tafur, Fabiola Rodriguez, Miryam Gallego,Mariluz Villamil, Paula Castaneda, Alex
Barbosa, Alvaro Pedraza, Anita Puentes, Aida Rojas, Ivonne Hernandez, Claudia Calderon,
Myriam Wilches, Dilmer, Jhon Leon, David Urdaneta, all the personnel of the LNDV, and finally to
Yesid Gonzales, Yenny and Jaime and the personnel of the Centro de Diagnostico de
Bucaramanga, Santander.
To the Instituto Nacional para la Vigilancia de Medicamentos y Alimentos (INVIMA) and
especially thak you to Mercedes Vanegas for the serotypification of Salmonella sp. that originated
in retail stores. I would also like to thank Adriana Coral and her staff (Claudia Carrillo and Fabián
Torres) from the Grupo Éxito as well as to Consuelo Vanegas, the director of the LEMA,
Universidad de Los Andes and her students Ricardo Castellanos, and Andrés Valderrama for
participating in the COIPARS network and providing technical and laboratory support for the
retail store meat analyses.
Thanks to the Instituto Colombiano de Salud (INS) and specially to Jaime Moreno, Sandra
Escobar and Caterin Rodriguez, for participating in the COIPARS network and giving me the
basic training and ongoing support necessary for characterizating Salmonella sp. using PFGE.
Special thanks to Martha Vives, Angelita Holguin, and Vivi Clavijo from Los Andes University, for
launching the molecular characterization of Salmonella using PFGE in the Salmonella laboratory
of the ICA. And finally, thank you Michael Hume, from the USDA, for the support and guidance in
the analysis of the salmonella isolates and for assisting with the scientific advice you graciously
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provided in development of the dendograms. Michael, I promise you a wonderful night of salsa in
Bogota.
Special thanks to Adriana León and Alex Garcia for introducing me to the Colombian poultry
industry who opened doors for me to be able to work on this project, and who open the doors of
the poultry industry to work in this area. I also thank the companies of Cundinamarca and
Santander.
Remerciements chaleureux à Alba Marina Cotes, director of CBB, at Corpoica in Colombia, for
rescuing me and believing in the goals of this research and the impact that my findings may have
for Colombia. It was refreshing that you were always sure that I was going to finish. Merci Alba
Marina! My special gratitude to Patricia Diaz, the best secretary assistant ever, for facilitating the
things…I always trusted you. I hope we can work together again in the future. Thank to my other
working colleagues at Corpoica.
To Colciencias and Fulbright for funding me with a scholarship the first three years of the PhD,
and specially to Jimmy Quintero for being patient and understanding with challenges that I faced
while developing this research.
Special thanks to Phil Kass, my winged professor, for being a wonderful human being and a
professor that unconditionally supported me. You shared your amazing epidemiology knowledge,
your family and your life. For me you are a paradigm of how a professor should be for graduate
students.
My gratitude to Maria Victoria Ovalle, my colleague and friend, part of the staff of the new
Salmonella Laboratory of the ICA, and participating fully for standardizing the antimicrobial
susceptibility automated system and the Salmonella serotyping procedures in the laboratory.
Working with you was fabulous and I look forward to continue working in the near future. Also,
thanks to Aura Lucia Leal from GREBO, for being part of the COIPARS initiative since the
beginning.
My overwhelming gratitude to Maribel León, DVM, for having working as my assistant through all
the activities of this project, for pushing me to continue, for her unwavering energy in the face of
numerous challenges, for travelling with me though farewell places to sample and for accepting
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all financial limitations of this project. It is now my turn to help you with your dream of pursuing a
PhD.
On Friday, I went to my last day of school, hand in hand with Tina, who also brought me to school
at UCDavis my first day of class, when I had so many expectations, fears, so much excitement to
begin my studies again after a twenty year hiatus. Tina and Jose, thank you for being my home
in Davis, my parents’ home, the home of my brothers and sisters, the home where there has
always been a place for me, where I have laughed and cried, the home where I began everything
anew, and where I am beginning everything again. To Monica, thank you for taking me to the
home of the “Moras” family and the home of my love from which I never want to leave…
To my close friends and roommates in Davis with whom I shared my language, table, sunrises
and sunsets, laughter and tears, complicity, scoldings, little fights, thank you; you always knew
what to do or say to help me along this road, you will always be in my heart. Thank you Montse
Canedo, for accompanying me in everything, both the good and the bad, for talking and talking,
for analyzing, for being my companion and partner; Ricardo Ertze, the “man of the house”, for
your sweetness, your support, and for being there from the very first day; Rossio Motta for
making me laugh when you thought I was crying and for sharing profoundly my sorrows and joys;
and Miryam Gallego for your friendship and solidarity that is still going strong.
Enormous thank you’s to my gang, my friends, my companions in the Epi-group, Poh-Sin Yap,
Naila Baig-Ansari, Sophia Papageorgiou , Banafsheh Sadeghi and Anup Srivastav (Anupi-rat) for
sharing with me wonderful working times and laughs. Special thanks to Poh-Sin for your immense
generosity and your never-ending friendship, you have shown so much about the meaning of
friendship. I am so glad that your life is now painted by many beautiful colors, Bogota is waiting
for you. My warm thanks to Naila, my Pakistani connection, and my sister in this journey. I thank
life for putting you in my way and allowing us to work together side by side until the very end. Our
Pakistani-Colombian connection cannot be broken. Sophie, my deepest gratitude for listening to
me, for working closely with me day and night and for giving me your lovely friendship--we have
to be sure that we also share, in the future, a space to rest our minds and bodies. Bani,, special
gratitude for being close to me in the first and the last times of my PhD, for your generosity and
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for sharing with me the warmest and most courageous part of your heart. Even though I will be far
away, you know you can count on me. To Locksley, a marvelous human being, warm thanks for
listening to me and give me his wise advice the first years of the PhD. Anupi-rat, thank you for
everything and more, for making me feel like a child enjoying the classes I took with you. You
know where to find me if you ever need me. In the final part of this road, Syrukh appeared and
she was my mouse companion in the office of Tupper Hall, that she called “the dungeon”. Thank
you for the company and being here in the long nights of working.
I want to express my giant gratitude to the rest all my friends for standing with me in this long
voyage where I appeared and disappeared without reason and for waiting patiently for better
times to come. To write the acknowledgments to every one of you would take days and I want to
get back home to celebrate with all of you--now it is time to party!!! Los quiero mucho: Sonia,
Anny, Fredy, Alberto, Pilar, Nohora, Fernando, Richard, Fanny, Loly, Pepa, Coco, Sara y Rober.
Thank you to my parents, Bertha y Guillermo, for your understanding and for your whole life
strong support “pase lo que pase”. I love you deeply and now the times I will spend with you will
be more and more. Thank you to my sister Rocio for being in my side always with her wonderful
smile: I am so proud of you, of your way to face the life and I am sorry for not being in Rome
when the times where so difficult. Thank you to the rest of my family for the all the understanding.
I will be back soon.
And finally, my heart to you Xavi, my quotidian support, my companion in life, thank you for
sharing one wing with me, for being the best “razon de vivir mi vida”. This song by Victor Heredia
is for you completamente Mon Amour de ma vie:

Para decidir si sigo poniendo
Esta sangre en tierra
Este corazón que bate su parche
Sol y tinieblas.
Para continuar caminando al sol
Por estos desiertos
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