ANTIOBIOTIC RESISTANCE TRANMISSION AND MOLECULAR ECOLOGY OF SALMONELLA ...

103 Pages·2006·0.47 MB·English

ANTIOBIOTIC RESISTANCE TRANMISSION AND MOLECULAR ECOLOGY
OF SALMONELLA ENTERICA SUBTYPES FROM NEW YORK STATE

A Thesis
Presented to the Faculty of the Graduate School
of Cornell University
In Partial Fulfillment of the Requirements for the Degree of
Master of Science

by
Samuel David Alcaine
January 2007
© 2007 Samuel David Alcaine
ABSTRACT

Salmonella enterica is a gram-negative, rod shaped bacillus, which inhabits the
intestines of mammals, reptiles and birds. In the United States, Salmonella is one of
the leading causes of food-borne illness, and is typically acquired through the
consumption of contaminated food or water. Modern public health practises have lead
to a decrease in the number of Salmonella infections, however, there has been rise in
the number of infections caused by antimicrobial-resistant Salmonella.
The rise of antimicrobial-resistant Salmonella subtypes, including the
appearance of subtypes resistant to ceftriaxone, represents a particular concern.
Ceftriaxone is used to treat invasive cases of Salmonella in children, and is closely
related to ceftiofur, an antibiotic commonly used to treat diseases of cattle. In order to
develop a better understanding of the evolution and transmission of ceftiofur
resistance in Salmonella, we characterized ceftiofur resistant and sensitive Salmonella
isolates from seven New York dairy farms. A total of 39 isolates from these seven
farms were analyzed for evolutionary relatedness (by DNA sequencing of the
Salmonella genes fimA, manB, and mdh), antibiotic-resistance profiles, and the
presence of bla , a beta-lactamase gene associated with resistance to
CMY-2
cephalosporins. Our data indicate that (i) resistance to ceftriaxone and ceftiofur were
highly correlated with the presence of bla ; (ii) ceftiofur resistant Salmonella were
CMY-2
geographically widespread as shown by their isolation from farms located throughout
New York state; (iii) ceftiofur resistant Salmonella isolated from farms represent
multiple distinct subtypes and evolutionary lineages as determined by serotyping,
DNA sequence typing, and antimicrobial-resistance profiles; and (iv) ceftiofur
resistant Salmonella evolved by multiple independent acquisitions of an identical
bla allele and by clonal spread of ceftiofur resistant subtypes.
CMY-2
A collection of 179 human and 166 bovine clinical Salmonella isolates
obtained from across New York State over the course of one year were characterized
using serotyping and multilocus sequence typing (MLST) scheme based on the
sequencing of three genes (fimA, manB, and mdh). The 345 isolates were
differentiated into 52 serotypes and 75 sequence types (STs). Serotypes and STs were
not randomly distributed among human and bovine isolates and selected serotypes and
STs were exclusively associated with human and bovine isolates. A number of
common STs were geographically widely distributed, including isolates representing
the emerging Salmonella serotype 4,5,12:i:-, which was found among human and
bovine isolates in a number of counties in New York state. Phylogenetic analyses
supported that serotype 4,5,12:i:- is closely related to Salmonella Typhimurium and
that Salmonella Newport represents two distinct evolutionary lineages that differ in
their frequency in human and bovine isolates. A number of isolates carried two copies
of manB (48 isolates) or showed small deletion events in fimA (9 isolates). Our data
indicate that (i) serotyping and MLST typing both provide for sensitive subtype
discrimination of Salmonella; (ii) bovine and human Salmonella subtypes represent
distinct and overlapping populations; (iii) a number of Salmonella clonal groups,
including emerging subtype 4,5,12:i:-, are geographically widespread among human
and/or bovine populations; (iv) Salmonella Newport represents two distinct
phylogenetic lineages that appear to be host specific; and (v) duplication and deletion
events in manB and fimA may provide a mechanism for rapid diversification of
Salmonella surface molecules.
BIOGRAPHICAL SKETCH
Samuel Alcaine was born on a cold Thanksgiving Day in 1979. He is
considered a hero by some, a legend by others, and completely unknown to the
majority of the world. Exactly why he was selected by Dr. Martin Wiedmann to join
the Food Science Lab at Cornell University, he will never know. What he does know
is that his time in Ithaca and the Wiedmann Lab was one of the most important
experiences in his life, and the people he met there have shaped him for the better, or
so he hopes. His greatest triumphs were achieved either while chilling with the
members of I-ETA-PI at the hip and exclusive bar known as Korova, or while
streaking plates and singing La Ley late at night in the Wiedmann lab. While those
moments arguably changed the world we live in, they are not recorded in the
following pages. What follows is Samuel Alcaine’s attempt, with much help and
prodding from Dr. Martin Wiedmann, to do something useful for society.

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ACKNOWLEDGMENTS
First off, none of this would have happened if not for Dr. Martin Wiedmann. I
owe him a big thank you for putting up with me and taking the time to teach me how
to think like a scientist. Like any lab there were always up and downs, but in the end,
if given the chance, I would happily do it again.
I also owe a thank you to Dr. Lorin Warnick for being my advisor and
providing the Salmonella collection that was the basis of my studies. He gave me an
important second point of view to turn to for help on my work and my knowledge. I
will never forget about bacteriocins again.
I would also like to thank Dr. Kathryn Boor for her support while I was
working in the Food Safety Lab. Thank you to Dr. Patrick McDonough for storing,
sending, and testing the hundreds of isolates I would later streak up and type late at
night.
Thanks to all my lab mates and friends: Marker, Paddy, and Eric for being my
partners in crime. Alphina, Jesse, Yesim and Reed for all their help. A huge thanks-
from-keeping-me-from-going-crazy to Esther, you are the glue, we are the pieces.
Thanks to all the undergrads and visitors that helped with the sometimes thankless
grunt work: Wan-lin (I hope you’re still driving), Jessica O, and Marlin.
Finally a shout out to my family, friends, I-ETA-PI, and everyone at Korova,
without your support, ears, beers, and laughter, I would be as gray as the Ithaca skies.

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TABLE OF CONTENTS

Page
CHAPTER 1 ANTIMICROBIAL RESISTANCE IN SALMONELLA: A 1
REVIEW

CHAPTER 2 CEFTIOFUR RESISTANT SALMONELLA ISOLATED 37
FROM DAIRY FARMS REPRESENT MULTIPLE
WIDELY DISTRIBUTED SUBTYPES THAT EVOLVED
BY INDEPENDENT HORIZONTAL GENE TRANSFER

CHAPTER 3 MULTILOCUS SEQUENCE TYPING SUUPORTS THAT 60
BOVINE AND HUMAN ASSOCIATED SALMONELLA
REPRESENT DISTINCT AND OVERLAPPING
POPULATIONS INCLUDING CLONAL GROUPS WITH
DUPLICATION AND DELETION EVENTS IN GENES
ENCODING CELL SURFACE PROTEINS

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LIST OF FIGURES
Page
FIGURE 2.1 Distribution of MLST types across New York dairy farms 48

FIGURE 2.2 Phylogenetic tree of Salmonella isolates based on the 51
concatenated manB, mdh, and fimA sequences

FIGURE 3.1 Phylogenetic trees based on Salmonella mdh and fimA gene 79
sequences

FIGURE 3.2 DNA and amino acid sequences of fimA deletion types 85

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LIST OF TABLES
Page
TABLE 1.1 Drug-resistant Salmonella Outbreaks 5

TABLE 1.2 Summary of Antibiotic Resistance in 7
Salmonella

TABLE 2.1 PCR primers and conditions 43

TABLE 2.2 Allelic profiles and MLST types of 49
Salmonella isolates

TABLE 2.3 Serotype, MLST, and antibiotic 53
resistance profiles of Salmonella isolates

TABLE 3.1 Farms with multiple sample-submission 71
dates resulting in Salmonella isolation
from clinically infected animals

TABLE 3.2 Distribution of Salmonella serotypes 75
among sequence types (STs) and
human andbovine isolates

TABLE 3.3 Salmonella Sequence Type (ST) 76
Distribution among different counties in
New York State

TABLE 3.4 Serotypes that include at least one isolate 82
that carries two manB copies

TABLE 3.5 Serotypes that include at least one isolate 84
that carries a deletion in the 3’ end of
fimA

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CHAPTER 1
ANTIMOCROBIAL RESISTANCE IN SALMONELLA: A REVIEW*

*S. D. Alcaine, L. Warnick, and M. Wiedmann

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