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AVIAN DISEASES 50:161–172, 2006
Invited Minireview—
Potential Impacts of Antibiotic Use in Poultry Production
Randall S. SingerAB and Charles L. HofacreC
A
Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota,
300A VSB, 1971 Commonwealth Avenue, St. Paul, MN 55108
B
Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN 55455
C
Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602-4875
Received 31 March 2006; Accepted 7 April 2006
SUMMARY. The ways in which antibiotics are used in poultry production have changed considerably during the past decade,
mainly because of concerns about potential negative human health consequences caused by these uses. Human health
improvements directly attributable to these antibiotic-use changes are difficult to demonstrate. Given that some antibiotics will
continue to be used in the poultry industry, methods are needed for estimating the causal relationship between these antibiotic uses
and actual animal and human health impacts. This is a challenging task because of the numerous factors that are able to select for
the emergence, dissemination, and persistence of antibiotic resistance. Managing the potential impacts of antibiotic use in poultry
requires more than a simple estimation of the risks that can be attributed to the use of antibiotics in poultry. Risk models and
empirical studies that evaluate interventions that are capable of minimizing the negative consequences associated with specific
antibiotic uses are desperately needed.
RESUMEN. Estudio Recapitulativo por Invitación—Impacto potencial del uso de antibióticos en la producción avı́cola.
La forma como los antibióticos son utilizados en la producción avı́cola ha cambiado considerablemente durante la década pasada,
principalmente debido a las preocupaciones sobre posibles consecuencias negativas en la salud humana causadas por la utilización de
los mismos. Los progresos en la salud humana atribuibles directamente a estos cambios en la utilización de antibióticos son difı́ciles
de demostrar. Sabiendo que algunos antibióticos continuarán siendo utilizados en la industria avı́cola, se requieren métodos para
estimar la relación causal entre los cambios en la utilización de antibióticos y el impacto real en la salud tanto humana como animal.
Esta es una tarea difı́cil debido al gran número de factores de selección que influyen en la aparición, diseminación y persistencia de
la resistencia a los antibióticos. El manejo de los impactos potenciales de la utilización de antibióticos en la avicultura requiere más
de un simple cálculo de los riesgos atribuibles al uso de los antibióticos en las aves domésticas. Existe una necesidad inmediata para
desarrollar modelos de riesgo y estudios empı́ricos que evalúen estrategias capaces de minimizar las consecuencias negativas
asociadas con la utilización de antibióticos especı́ficos.
Key words: antibiotic resistance, antibiotic use, causal inference, public health, risk assessment, unintended consequences
Abbreviations: APEC ¼ avian pathogenic Escherichia coli; FDA-CVM ¼ Food and Drug Administration, Center for Veterinary
Medicine; GRE ¼ glycopeptide-resistant enterococci; QAC ¼ quaternary ammonium compound; QD ¼ quinupristin–dalfopristin;
VRE ¼ vancomycin-resistant enterococci
Over the past decade, the ways in which antibiotics are used in
poultry production have changed. Antibiotic use in poultry is
changing globally, although perhaps more dramatically in the
European Union than in the United States (15). One reason for this
shift is the removal of specific antibiotic uses, as mandated by
regulatory agencies, such as the recent removal of fluoroquinolones
from poultry production in the United States and the removal of
growth-promotant use in many European countries (28,124).
Another reason is the voluntary reduction in growth-promotant
uses of antibiotics by some of the major poultry production
companies and restaurant chains (30). The major driving force
influencing these recent changes in antibiotic usage in poultry has
been the perceived public health risks associated with this practice
(88). Unfortunately, peer-reviewed documentation of these reductions, particularly in the United States, is difficult to find.
Agricultural antibiotic usage data have been requested by varying
groups but have not been easy to obtain (118,120), which has led
some groups to generate estimates based on crude calculations (55).
The notion that antibiotic uses in agriculture, and specifically in
poultry, may pose a risk to public health and animal health is not
new (121). Strains of Escherichia coli displaying resistance to
multiple antimicrobial agents have been recovered from the fecal
flora of broiler chickens since the earliest reports in the 1960s and
1970s (17,48,72,83,107,108,116). One of the first studies to
demonstrate resistance among E. coli isolates from poultry was
published in 1961 (111). The authors noticed that from 1957 to
1960, the practice of feeding broiler fowls on diets containing
tetracyclines increased greatly and progressively in Great Britain.
They further recorded the increasing incidence of tetracycline
resistance among pathogenic avian E. coli isolates during this same
time period from 3.5% in 1957, to 20.5% in 1958, 40.9% in 1959,
and 63.2% in 1960 (111). A later study reported by Smith in 1966
examined antimicrobial resistance among E. coli isolates obtained
from cases of human neonatal diarrhea, swine diarrhea, calf scours,
and avian colisepticemia (107). Among the avian E. coli isolates
tested, resistance was most often observed to sulfonamides (17.1%),
tetracyclines (17.1%), and to a lesser extent, streptomycin (2.9%).
Twenty-nine percent of avian isolates demonstrated resistance to one
or more drugs with the most common multidrug-resistant patterns
being streptomycin, sulfonamides, and tetracycline, or sulfonamides
and tetracycline (107).
The majority of publications from this time period echoed the
same conclusions: that the observed antimicrobial-resistance phenotypes reflected the wide use of antibiotics in the livestock industry,
and that these resistance phenotypes were primarily due to the
presence of resistance plasmids (initially referred to as R factors)
161
R. S. Singer and C. L. Hofacre
162
Table 1. Therapeutic antibiotics used in poultry productionA (19).
Egg layer chickens
Antibiotic
Feed
Drinking
water
Bacitracin
Bambermycin
Chlortetracycline
Erythromycin
EnrofloxacinB
Lincomycin
Neomycin
Novobiocin
Oxytetracycline
Penicillin
Streptomycin
Sulfonamides
Tylosin
Virginiamycin
Yes
No
Yes
No
No
No
No
No
No
No
No
No
Yes
No
Yes
No
No
No
No
No
No
No
No
No
No
No
No
No
Broiler chickens
Growth
promotant
No
No
No
No
No
No
No
No
No
No
No
No
Yes
No
Turkeys
Feed
Drinking
water
Growth
promotant
Yes
Yes
Yes
Yes
No
Yes
No
Yes
Yes
Yes
No
Yes
Yes
No
Yes
Yes
Yes
Yes
Yes
Yes
Yes
No
Yes
No
Yes
Yes
No
No
Yes
Yes
Yes
No
No
Yes
No
No
Yes
Yes
No
No
Yes
Yes
Feed
Drinking
water
Growth
promotant
Yes
Yes
Yes
Yes
No
No
No
Yes
Yes
Yes
No
Yes
No
No
Yes
Yes
Yes
Yes
Yes
Yes
Yes
No
Yes
Yes
No
Yes
No
No
Yes
Yes
Yes
No
No
Yes
No
No
Yes
Yes
No
No
No
Yes
A
B
Gentamicin and ceftiofur are labeled for day-old chickens and turkeys by subcutaneous injection only.
Enrofloxacin is no longer approved for use in poultry production in the United States.
(48,79,83,107,116,122). These experiments increased both the
scientific and public scrutiny of the administration of therapeutic
and subtherapeutic doses of antimicrobials to animals and ultimately
led to the release of the Swann report in the United Kingdom in
1969, which recommended that antibiotics used to treat infections
in humans not be used as animal-feed additives (115). Despite
implementing these recommendations, the United Kingdom and
other countries have observed mixed results with regard to reducing
antimicrobial-resistance phenotypes among pathogenic E. coli
isolates. In fact, a survey conducted in 1980, 9 yr after the banning
of the use of tetracyclines as feed additives in the United Kingdom,
indicated that chickens and pigs were still a reservoir of tetracyclineresistant E. coli (109).
When the potential public health impacts of antibiotic use in
poultry are considered, antibiotic resistance is the major perceived
risk. Various approaches have been used to document and estimate
these potential risks and to relate resistance levels to actual human
health impacts. The goal of this review is to highlight the ways in
which antibiotics are used in poultry production, the ways in which
these uses can impact public health, and the data gaps that exist in
estimating this relationship. Hopefully, this brief review will identify
key areas to which researchers, poultry producers, and the pharmaceutical industry can supply useful data. Finally, the review has
the added goal of separating causality from association as we interpret the data collected from research projects, industry reports,
and surveillance systems.
ANTIBIOTIC USES IN POULTRY
Antibiotic use in commercial poultry can be divided into two use
categories: therapeutic antibiotics (Table 1) and growth-promotant
antibiotics (20). Antibiotics used in feed for growth promotion and
disease prevention purposes are administered at levels that are lower
than antibiotics given for the treatment of disease, and therefore,
these uses are termed subtherapeutic. These in-feed antibiotics are
capable of exerting a selection pressure on bacterial populations and
altering various microbial communities (74). Uses of antibiotics in
either category have the potential to select for bacterial strains that
are resistant to the antibiotic used while still having a positive impact
on the health of the animal population.
The antibiotics in the growth-promotant category are, in some
cases, the same antibiotics used in the therapeutic category; the
amount of the antibiotic administered to the birds is usually less for
growth promotion. The growth-promotant antibiotics are administered only in the birds’ feed (55). The decision to use growthpromotant antibiotics in commercial poultry is primarily based on
economic factors, i.e., whether the improvements in body weight,
feed efficiency, and/or growth rates are worth the cost of the
antibiotic (113). It should be noted that because there are limited
therapeutic antibiotics approved for poultry, these antibiotics are
rarely used by the commercial poultry producers as growth
promotants (50).
In the United States and many other countries, consumers of
poultry products are increasingly requesting that poultry suppliers
sell meat that has not been raised with growth-promotant antibiotics.
This has resulted in the need for nonantibiotic alternatives, such
as probiotics, intestinal acidifers, natural antibacterials, and enzymes
to reduce the growth of unfavorable intestinal bacteria, such as
Clostridium perfringens (32,51). These applications, in combination
with management changes, must also improve animal health and
promote size uniformity among animals in the herd or flock as the
growth-promotant uses have done (15). Without these effects, the
removal of the growth promotants could lead to the unintended
consequence of increased levels of pathogen contamination in meat,
as will be discussed later.
Therapeutic antibiotics are used in those cases in which a disease
has been introduced onto a farm. The poultry veterinarian must
decide whether the birds can be treated with an antibiotic, and if so,
which antibiotic and by what route of administration (in feed or in
drinking water). The choice of antibiotic is often limited by the
balance between the cost of the drug and the level of disease. In
addition, antibiotic decisions are influenced by the regulated
duration of withdrawal before slaughter to ensure that no drug
residue is found in the meat. The vast majority of therapeutic
treatments are given via the drinking water because sick birds may
stop eating but often continue to consume water. In layer chickens,
the antibiotics available to poultry veterinarians for the treatment of
bacterial infections are limited (Table 1).
Escherichia coli is the leading cause of economic loss due to disease
for the poultry industry throughout the world (9). Therefore, it is
the primary bacteria that therapeutic antibiotics are used to treat. In
Antibiotic use in poultry
most instances, these E. coli infections are secondary infections
following a primary viral or environmental insult (39). This can
mean that therapeutic antibiotics in commercial poultry are often
used to relieve the suffering of the sick birds and to minimize the
financial impact of the disease on bird performance until the primary
insult can be identified and eliminated. Another reason for the use
of therapeutic antibiotics is related to the potential increased public
health risk associated with slaughtering birds from farms with sick
birds. Poultry that are sick eat greater amounts of bedding material
(litter), which can result in higher rates of Salmonella spp. and
Campylobacter spp. in their intestinal tract (21). Also, one small
study found that birds from flocks having higher airsacculitis
condemnation rates had higher levels of E. coli and Campylobacter
spp. in the processed meat (91).
The therapeutic antibiotics available to treat the respiratory
infections caused by E. coli are limited (40). The value of the
individual animal is so low that it is cost prohibitive to individually
dose each bird in a house, thus, eliminating the option of
aminoglycosides and cephalosporins. Because sick birds continue
to drink in a disease situation, therapeutic antibiotics labeled for use
in the drinking water are most often used. Bacitracin, lincomycin,
and neomycin are poorly absorbed from the intestine; therefore,
tetracyclines, fluoroquinolones, and sulfonamides are the only drugs
available to treat E. coli airsacculitis. It can be speculated that this
limited choice of antibiotics to treat E. coli infections has resulted in
many years of selection pressure on E. coli in the commercial poultry
environment, resulting in the high levels of sulfonamide and
tetracycline resistance in clinical E. coli isolates seen in many
diagnostic laboratories (127).
It is not the purpose of this review to comment on the amount of
antibiotic used in the poultry industry, on the feasibility of collecting
those data, or on the best ways to report them. Different organizations have arrived at different estimates of the amounts of
antibiotics used, and differences between estimates are due to
different equations for estimating usage as well as differences over
what constitutes an antibiotic (55,82). These estimates are generally
reported in gross amount of antibiotic used but do not provide
information about indications for use, route of administration, or
other qualitative information (104). A recent report by the Alliance
for the Prudent Use of Antibiotics, Facts about Antibiotics in Animals
and Their Impact on Resistance, addressed the ways in which these
data can be collected and used. A general conclusion of this report is
that we need new ways of describing antibiotic uses in animal
agriculture, such as the defined daily doses equivalent in human
medicine.
A topic that is in need of additional research is the utility of
antibiotic-use data in relation to the animal and public health
impacts of antibiotic usage in animal agriculture. With respect to
the poultry industry, data can be collected at the local, regional,
national, or international level. The pressures that select for
antibiotic resistance in bacteria may operate at many proximate
levels (within an animal, within a group of animals, or on the farm).
They may also operate on a broader scale, and therefore, it is
plausible that some aspects of the bacterial response to exposure
to antimicrobials may only be apparent when analyzed at the
ecological scale. Consequently, to make a general statement that
a national increase in the annualized amount of antibiotic used
in poultry represents an increased risk to human health is overly
simplistic and potentially fraught with biases (104). Better
analytical tools as well as more detailed descriptions of biological
mechanisms are needed to understand if and how these antibiotic
usage estimates will be useful in predicting changes in human
health risks.
163
ANTIBIOTIC USE, ANTIBIOTIC RESISTANCE,
AND HEALTH
With the changes being made in antibiotic use practices in
poultry, it would appear that many natural experiments have been
designed to determine the effects that antibiotic use has on antibiotic
resistance. The types of studies that have been conducted are of two
primary types. First, some investigators look for resistant bacteria in
flocks that have used antibiotics, and most of the time, comparisons
are made between poultry operations that use different levels of
antibiotics. Second, some investigators perform temporal studies in
which specific operations are followed before, during, and after they
implement changes in antibiotic use practices. Both of these study
designs have been used under experimental conditions as well as
in observational settings, where normal production operations are
compared.
In several classic studies of antibiotic use in chickens, antibiotic
administration resulted in an increased proportion of bacteria
resistant to the antibiotic in chickens administered tetracycline or
tylosin (49,68,69,71). In one of these studies, farm workers also
experienced increased levels of tetracycline-resistant bacteria following the administration of in-feed tetracycline to the chickens (68,69).
In another of these studies, a survey of resistance in normal broiler
flocks was included (71). Resistance was often detected in birds that
had received no antibiotics, a finding that, at the time, seemed to be
in conflict with the assumption that resistance was a consequence of
the selection pressure created by antibiotic use.
When specific antibiotics are used, especially as growth
promotants, resistance to that antibiotic is commonly detected in
bacterial populations from that operation. In a small study of
virginiamycin use in broilers in the United States, resistance to
streptogramins was common in the Enterococcus faecium isolates
(123). Unfortunately, that study had no comparison group, such as
farms that were not using virginiamycin. A prospective, controlled
trial was conducted in which virginiamycin was fed to chickens. No
effect was observed on resistance in E. faecium or on weight gain in
the birds (31). The study was very small, and the lack of an observed
effect could be attributed to the small sample size (one trial with two
groups of four chickens per group). In a larger study, multiple
feeding trials with virginiamycin were conducted (80). The groups
receiving virginiamycin in the feed had a higher prevalence of
streptogramin-resistant E. faecium than the control groups, but the
removal of virginiamycin from the feed resulted in a disappearance
of the streptogramin-resistant isolates. The authors concluded that
continuous feeding of virginiamycin was required to maintain the
resistance. In one study of broilers in their normal production
environment, there was no evidence that tetracycline usage for
therapeutic purposes altered the tetracycline-resistance levels in
E. coli, Enterococcus spp., or Campylobacter spp. (35). In that
investigation of two flock houses per farm on three farms, E. coli
and Enterococcus spp. isolates already had high tetracycline resistance
in flocks with and without historical tetracycline usage, and
Campylobacter spp. isolates remained largely susceptible, even after
tetracycline administration.
Perhaps one of the largest temporal investigations conducted
under natural conditions was performed in Denmark, where a
national surveillance system has assessed antibiotic-resistance levels
in bacteria of food-animal origin for many years. Within Denmark,
E. coli and Enterococcus spp. were monitored over time. Avoparcin
was banned as a growth promotant in Denmark and Norway in
1995 and in the rest of the European Union by the end of 1997.
Avoparcin is a glycopeptide that can induce cross-resistance to
vancomycin (126), and therefore, there is concern that avoparcin use
164
R. S. Singer and C. L. Hofacre
in animal agriculture can impact human health by selecting for
vancomycin resistance and by aiding in the dissemination and
transfer of vancomycin-resistance genes (6). In some reports, the
removal of avoparcin from broilers in Denmark was followed by
a dramatic reduction in the percentage of E. faecium isolates resistant to vancomycin (vancomycin-resistant enterococci; VRE) (2),
whereas, in other studies, the prevalence of VRE on broiler farms
did not appear to change (46). A study in Denmark investigated the
genetic diversity of VRE in broiler houses after the avoparcin ban
(47). Based on high genetic similarity of isolates within a broiler
house over time and high heterogeneity among houses, the authors
concluded that the VRE may be persisting in the broiler house
environment over time in the absence of selection pressure. A similar
finding has been documented for E. coli in broiler houses (103).
Additional studies have been conducted on the dynamics of
antibiotic resistance following the removal of growth-promotant
antibiotics in other parts of Europe. A report from Germany
demonstrated a reduction in VRE prevalence in poultry meat and in
the gut flora of humans in the community following the ban of
avoparcin (61). The results following the ban of avoparcin in
Norway have been more confusing. In a study conducted up to 8 yr
after the ban of avoparcin, the prevalence of glycopeptide-resistant
enterococci (GRE) had not declined significantly in either the fecal
samples from broilers and turkeys or from poultry farmers (112).
This finding has been partially attributed to the presence of a
postsegregational killing system in the enterococci that maintains
the antimicrobial resistance through a physical genetic linkage in the
absence of selection pressure (112).
The effects of antibiotic use on resistance are also evaluated by
comparing farms that use antibiotics (conventional farms) to organic
farms. The assumption is that differences in antibiotic-resistance
levels between conventional and organic farms are due solely to the
differences in antibiotic use, an assumption that will be further
discussed later in this review. It is often assumed by the public that
animals raised in an organic setting produce healthier and more
wholesome meat products (63). One recent study compared VRE
from conventional and organic broiler operations in the United
Kingdom (37). Resistance was common in both types of operations,
although the prevalence appeared to be higher on the conventional
operations. Sampling was conducted in 2002 and 2003, years after
the 1997 ban of avoparcin use in animal agriculture, and still
resistance persisted.
Finally, the potential impacts of antibiotic use in poultry have
been assessed by analyzing bacterial populations on retail meat
samples. The assumption in this type of study is that the bacteria on
the meat reflect the organisms derived from the farm and that the
resistance in these isolates is related to antibiotic use practices on the
farm. These studies often include a comparison of conventional
to organically reared chickens and, therefore, make the same
assumption previously described. Some studies have shown that
organic chicken can have higher rates of disease and higher rates
of Campylobacter contamination at the time of slaughter than
conventionally reared chicken (45), although resistance levels can be
low in both types of operations. In one study conducted in Maryland
retail stores, organic chicken had a higher prevalence of Salmonella
and Campylobacter contamination than conventional chicken, but
the overall resistance level in those isolates was higher in
conventional product (26). Other studies have reported that the
prevalence of Campylobacter contamination was not higher in the
organic product but that the prevalence of fluoroquinolone-resistant
Campylobacter was much higher in the conventional chicken (87).
Importantly, these studies and most others that have investigated
food-borne pathogen contamination on meats have not enumerated
the microbial load on the product. These studies have focused on
prevalence of resistance and of contamination; prevalence of samples
on which specific bacteria can be found is not a measure of risk.
Microbial loads, which relate directly to the dose that is capable of
being ingested or disseminated, are more appropriate indicators of
risk. When actual microbial loads are considered, organic products
may have a food safety risk higher than that of the conventional
product (34).
With all of these different approaches to evaluating the relationship between antibiotic use and resistance, we are left asking
ourselves whether we can now quantify, and subsequently reduce,
the potential public health impacts of antibiotic use in poultry. How
is antibiotic use in poultry actually impacting animal and human
health? All antibiotic uses exert a selection pressure capable of
selection for resistance. Increased levels of bacterial resistance on the
farm will have obvious implications for the efficacy of therapeutic
treatment of animal diseases on the farm. How, then, does this relate
to human health?
The most commonly assessed pathway linking antibiotic use in
poultry to human health impacts is the farm-to-fork route.
Pathogens that are resistant to antibiotics can be passed through
the food chain. Following ingestion, these resistant pathogens might
cause disease that is difficult to treat because of the antibiotic
resistance. Therefore, human health outcomes that are used include
treatment failures, increases in morbidity or mortality, and qualityof-life measurements, such as quality-adjusted life years (5,84).
There are others ways in which antibiotic uses in poultry can impact
human health.
Instead of focusing on pathogens, some studies have begun to
investigate resistance in commensal bacteria. It is now well recognized
that commensals are capable of exchanging genes with other bacteria, including pathogens, in various environments (29,36,41,117).
If commensal bacteria possessing antibiotic-resistance genes are
ingested by humans through the same farm-to-fork pathway, the
potential exists for these commensals to share these resistance genes
with pathogens in the human gastrointestinal tract (92,93). The
probability of this transfer might increase if the individual has recently
taken antibiotics (73).
Finally, bacteria can be disseminated into the environment from
poultry farms. These bacteria can possess resistance genes and,
therefore, present the same risk to human health as organisms passed
through the farm-to-fork route. In that case, the organisms can be
disseminated in the waterways, or they can be spread onto fields with
poultry litter. Antibiotics and their metabolites are also capable of
being disseminated in that fashion.
There are many routes by which antibiotic use in poultry can
influence animal and public health (Fig. 1). As we use the prevalence
study to document changes in resistance levels or to compare
resistance levels among farms with differing levels of antibiotic usage,
how confident are we that we have assessed the causal impacts of
antibiotic use in poultry? Have we succeeded in measuring the public
health consequences caused by antibiotic use in poultry? How do we
quantify the causal effects of antibiotic use on antibiotic resistance
and public health risks?
CAUSAL INFERENCE
One of the primary goals of our research, surveillance,
monitoring, and modeling is to determine the animal and public
health impacts that are caused by antibiotic use. If the presence of
resistant bacteria is the surrogate for a potential public health impact,
then the question becomes how much of the observed bacterial
resistance is caused by antibiotic use in poultry? Various studies have
Antibiotic use in poultry
165
Fig. 1. Schematic representation of potential routes of transmission of antibiotic-susceptible or -resistant bacteria between animals, humans, and
the environment. (Adapted from Phillips et al. [86]).
conflicting results regarding the efficacy of growth-promotant
antibiotics in the current poultry production system. Given that
some antibiotic uses in poultry will remain, we must determine
which uses are absolutely necessary and which uses pose the greatest
risk to human and animal health. Unfortunately, a major factor in
determining that potential risk relates to identifying whether the
measured association between antibiotic use and antibiotic resistance
(or some other indicator of risk) is actually a causal association. One
goal of public health practitioners and veterinarians is to minimize
risks to human health that are caused, either directly or indirectly, by
the use of antibiotics in poultry. A healthy and safe food supply must
be maintained. Identifying causal relationships is needed for making
improvements to animal and human health, but unfortunately, that
task is not as simple as it might sound.
If we believe that antibiotic use in poultry causes antibiotic
resistance, and that such usage causes human health risks, then the
ideal study would be one in which all poultry farms are given the
same set of antibiotics, and the human health effects are then
characterized and quantified. At the exact same time, the exact same
farms are then NOT given those same antibiotics; the only difference
in the comparison trial, therefore, is the antibiotic usage, and
consequently, the human health effects that are observed can be
considered to be CAUSED by the antibiotic usage. That is an
impossible study because we can not both expose and unexpose the
same farms at the same time; therefore, the hypothetical alternative
is termed counterfactual (52,78,90). The relationship between those
two populations represents the real causal effect of antibiotic use on
resistance. Because we can not observe the counterfactual situation,
we use a substitute population, often called the control or comparison group. The relationship between the factual and substitute
groups is often incorrectly interpreted as a causal relationship. As the
differences between the counterfactual comparison group and the
substitute comparison group grow, the degree of epidemiologic
confounding and introduced bias also grows. Consequently, the
observed effect of antibiotic use on resistance is an uncertain distance
from the true causal effect.
There is a general perception that increased antibiotic use implies
an increased risk. However, not all antibiotic uses are equivalent in
terms of their selection pressure and potential animal and human
health risks. In addition, many of the studies that have assessed this
relationship would suffer when scrutinized under the counterfactual
model of causation. For example, in the case of antibiotic use in
poultry and its effects on public health, the counterfactual model
could sound like this: if poultry operations were simultaneously
exposed to high and low levels of antibiotics, would the public health
impacts be reduced when lower levels were used? As described
previously, the standard study designs are those that compare poultry
operations that use high levels to those that use low levels of
antibiotics or designs in which antibiotic usage is changed over time
in selected poultry operations. Public health impacts are then
estimated from these comparisons. Neither of these approaches is
a perfect substitute for the unobtainable counterfactual model, and
consequently, we must critically assess the interpretations of these
studies in light of their imperfections (78,81). Regardless, studies
will often make causal conclusions from imperfect comparisons,
often in the absence of any estimated epidemiological measure of
effect (14).
Finally, most studies compare the prevalence of resistant organisms in samples that have been affected by the antibiotic use (such as
farms treated with an antibiotic) to those that are supposedly free of
R. S. Singer and C. L. Hofacre
166
the selection pressure (farms that do not use the antibiotic). As was
described in a recent review of epidemiological interpretations of
antibiotic resistance data, prevalence data can lead to spurious
conclusions about the relationship between antibiotic use and
resistance (97). For example, an effective antibiotic might wipe out
all susceptible bacterial targets while the resistant population will
remain. There may be no effect on the resistant population, as
evidenced by no increase in the microbial load of the resistant
population. Based on prevalence data, a standard strength of
association criterion of causation (89) might lead to the erroneous
conclusion that antibiotic use in poultry was ineffective and caused
an increase in resistance levels. If the dose–response criterion of
causation is used (89), we might again reach the erroneous conclusion that higher levels of antibiotics result in increased resistance,
when in fact they are just more effective at eliminating the
susceptible bacteria.
COMPETING CAUSES
The aim of quantifying the causal association between antibiotic
use and resistance on poultry farms is far from simple. Without
precise and accurate estimates of that relationship, strategies aimed
at reducing animal and human health risks may be ineffective. A
major reason for the difficulty in assessing the relationship between
antibiotic use and potential public health risks is the diversity of
factors that can affect antibiotic-resistance levels other than antibiotic
usage. In other words, the substitute or control group rarely
resembles the causal counterfactual comparison group.
Antimicrobial-resistance genes can often be found in physically
linked assemblages within the bacterial cell (114). Consequently,
resistance to a specific antibiotic can be under positive selection in
the absence of a selection pressure from that antibiotic. Many
examples of these effects have been described. For example, as some
countries have reduced the amount of antibiotic used in animal
agriculture, specific resistances have persisted in the apparent absence
of primary selection pressure. In Norway, an isolate of Enterococcus
hirae was found in poultry that possessed the vanA and erm(B) genes,
conferring glycopeptide and macrolide resistance to this isolate (13).
In that case, the potential existed for macrolide use in poultry to aid
in the persistence of VRE; tylosin was also banned from use in
poultry, thus, limiting that scenario. In Denmark, VRE has persisted
after the ban of avoparcin in poultry (46). Tylosin use was continued
for a short time after the avoparcin ban, and in swine, glycopeptideresistant E. faecium (GRE) prevalence did not decline rapidly. The
same genetic linkage between vanA and erm(B) was detected (1), and
following the decrease in tylosin usage in pigs, the GRE prevalence
declined (2).
Commonly used disinfectants can also help explain certain
patterns of antimicrobial resistance. For example, quaternary
ammonium compounds (QAC) are commonly used in hatcheries,
as well as in processing plants and in retail establishments, and
resistance can develop to these disinfectants (94,100). There are
many examples of QAC-resistance genes having a genetic linkage
with antimicrobial-resistance genes (98,99). The location of the
QAC-resistance gene is often on a plasmid, enabling an increased
potential for horizontal gene transfer among bacteria. In addition,
a QAC-resistance gene cassette has been found within the class I
integron in various bacteria, including Salmonella spp. (42). In this
example, QAC usage may select for resistance to many other
antibiotics.
Many bacteria possess mechanisms of resistance to specific metals
to prevent potential toxicity from metal exposure. Copper is
commonly used in food-animal production, for example, in poultry
feed in the form of copper sulfate (65). Copper has been shown to
select for copper-resistant bacterial isolates (12), and this process is
also capable of selecting for increased antibiotic resistance (12). A
recent study of E. faecium from broiler and turkey farms
demonstrated the presence of copper resistance conferred by the
tcrB gene. Of concern was the finding that the tcrB gene was linked
to the vatE gene on the same plasmid, thus enabling a copperselection pressure to maintain virginiamycin resistance, even in the
absence of virginiamycin use (101). Continued use of copper sulfate
in swine production in Denmark did not appear to maintain the
combined resistance to copper, glycopeptides, and macrolides in E.
faecium, suggesting that the resistance genes might not be directly
linked to metal resistances in all cases (44). Another metal resistance
that has been commonly linked to antibiotic-resistance genes is
mercury, which is commonly found in the environment. Mercuryresistance genes can be found in association with mobile genetic
elements (8), and these mercury-resistance genes are often linked to
other antibiotic-resistance genes (125). For example, the transposon
Tn21 possesses the mercury-resistance mer operon and a class 1
integron that includes antibiotic-resistance genes (11,42,70). Overall, the selection of antibiotic resistance in poultry production, which
includes the poultry environment, may have more to do with the
presence of additional genes that confer resistance to chemicals and
metals or that provide an ecological fitness advantage to the cell than
to the presence of a primary antibiotic-resistance gene (3).
Environmental-selection pressures also exist in the form of
antibiotics and antibiotic metabolites. Given that certain microorganisms, especially those that live predominantly in the soil, are
capable of producing antibiotics, increased levels of resistance would
be expected in areas where these antibiotic-producing organisms are
in abundance (27). However, antibiotics can also be found in the
waterways (62) after release from hospitals, sewage treatment plants,
factories, and agricultural runoff (64). When poultry litter is used as
fertilizer, the potential exists for spreading resistant organisms and
active antibiotic compounds into the environment. This route of
potential risk to public health has been understudied.
Perhaps the most difficult aspect of the design of antibioticresistance studies is the inclusion of the routes and probabilities of
transmission of antibiotic resistant organisms. When considering
the effects of antibiotic use, the indirect effects (which include
transmission) might represent the most important contributors to
antibiotic-resistance emergence and dissemination at the ecological
level (73). Bacteria are capable of being disseminated among sites,
and therefore, resistant organisms can be transmitted through
a variety of routes. Resistance can be found in areas irrespective of
any selection pressures. For example, effluents from hospitals and
sewage treatment plants represent just one source of resistant
organisms. When considering the dissemination of organisms,
agricultural runoff will, of course, be an important contributor.
Airborne dissemination of resistant bacteria from farms has been
observed (16,38). People returning to the community after hospital
stays can carry resistant organisms (73). Foreign travel is always
a major risk factor for the acquisition of resistant food-borne
infections (33,56,85). Finally, organisms can be moved from site to
site, and potentially at large geographic distances, via mechanical
transmission or via biological vectors. Antibiotic use in poultry can
have public health impacts through the selection of resistant
organisms and subsequent dissemination by one of these understudied routes. It must be emphasized that resistant organisms are
also capable of being introduced into the poultry farm via these same
processes (60), further complicating our ability to distinguish and
quantify the causal impact of antibiotic usage in poultry on
antibiotic resistance or on public health.
Antibiotic use in poultry
RISK ASSESSMENT AND MANAGEMENT
Quantifying the causal relationship between antibiotic use in
poultry and public health impacts is challenging and difficult to do
in empirical studies. Related to the ways in which antibiotic use can
impact public health, we know that antibiotic use in poultry
can increase the pool of resistant bacteria and resistance genes. This
can potentially lead to increased carriage of resistant bacteria and
resistance genes in the human community. These antibiotic uses can
also lead to the release of resistant organisms and selection pressures
into the environment. There should be no need to find the ‘‘smoking
gun’’ example of an actual instance in which antibiotic use in poultry
causes an antibiotic resistant organism to cause harm in humans; the
risks associated with any antibiotic use are well known, and thus, the
potential risk to human health exists from antibiotic use in poultry.
The question is, how do we begin to estimate the strength of this
causal relationship and then manage the potential risks? For this
purpose, a variety of mathematical models and quantitative risk
assessments have been developed to predict the effects of antibiotic
usage on resistance and human health. These models have been used
to estimate the likely impacts of continued antibiotic use but rarely
to evaluate management changes and efficacious interventions for
reducing public health risks.
One of the first mathematical models relating antibiotic use in
animals and humans to human health risks predicted that animal
use of antibiotics would decrease the efficacy duration of antibiotics
in human medicine but that human uses of antibiotics would
not only decrease the efficacy but also would increase the overall
prevalence of resistance (105). In a subsequent model, virginiamycin
use in poultry was assessed as a risk for the emergence of
streptogramin resistance (106). Although this model did not
explicitly consider the risks of infection with a streptograminresistant isolate and subsequent treatment failure, the model
evaluated the combined medical and agricultural use of streptogramins and predicted that virginiamycin use in poultry would reduce
the efficacy of quinupristin–dalfopristin (QD). In other models that
have included actual health outcomes, the risks of increased
morbidity and mortality due to QD-resistant E. faecium infection in humans associated with virginiamycin use in poultry were
predicted to be very low (24) and were highly sensitive to QD
prescription rates in humans (23). The model assumed that transfer of resistant E. faecium actually occurs and that it is caused
by virginiamycin use in chickens. The model suggested that the
benefit of removing virginiamycin use from poultry rapidly
decreased as human QD use increased and high-level QD resistance spreads. The impact of virginiamycin use appears to depend
on the rate of transmission of the QD resistance in humans
(more precisely modeled as R0, the basic reproductive rate of
transmission) (57). The lower the potential spread of resistance
among humans, the more important the virginiamycin use in
poultry becomes.
Risk analysis methodologies have also been used to determine the
likelihood of specific outcomes, including negative public health
impacts, resulting from the use of antibiotics in animal agriculture
(18,119). A recent publication has reviewed many of the microbial
risk assessments that have been conducted in the area of
antimicrobial resistance (110). In one high-profile example, a risk
assessment was conducted by the U.S. Food and Drug Administration, Center for Veterinary Medicine (FDA-CVM) to estimate the
public health burden associated with fluoroquinolone-resistant
Campylobacter infections in people that were caused by the use
of fluoroquinolones in chickens (10). The model was a major
contributor to the recent decision to remove fluoroquinolones from
167
use in poultry production. In a farm-to-fork type of risk assessment
model, the impacts of macrolide use in animal agriculture were
assessed (53). In this model, resistance that was generated in
animal production as a result of macrolide use was followed
through the food chain to determine how many people would be
infected with these resistant strains, would subsequently seek
medical care, and would be treated with a macrolide. Risk was
defined as the probability of this chain of events, combined with
the consequence of macrolide-treatment failure due to resistant
Campylobacter spp. or E. faecium. In general the estimated risks were
very small, with the largest risk being an annual probability of less
than 1 in 10 million for macrolide-resistant Campylobacter derived
from poultry.
Many mathematical and risk assessment models have now been
developed, and each seems to take a different approach to
quantifying and predicting the human health risks associated with
antibiotic use in animal agriculture. Some of these have been used
for regulating the uses of animal antibiotics, even though some have
argued that the models do not actually predict causal relationships
(22). Many of these models have been subjected to a rigorous
sensitivity analysis, in which all model parameters are assessed for
their relative importance in influencing the outcome of the model.
The sensitivity analysis can reveal not only those parameters that
appear to be biologically important in affecting the outcome but also
those parameters about which we need to know more information.
For example, a parameter to which the model is highly sensitive
might indicate the need to generate more precise estimates for the
value of this parameter. In a recent review, the argument was made
that some of these mathematical and risk assessment models are
missing key parameters, and others have very broad and potentially
biased assumptions, and thus, the estimated risks may be over- or
underestimated (7).
One of the primary reasons for conducting a rigorous modeling
exercise is to enable management to make informed decisions.
Ultimately, though, there are two ways in which antibiotic use in
poultry can be managed. One approach is to employ the precautionary principle. In this argument, the consequences of an action
are often unknown, such as the actual public health risks associated
with animal antibiotic use. There is a perceived potential for serious
negative consequences of this action, and therefore, it is better to
avoid the action rather than to suffer the potential consequences.
Under this principle, which on the surface makes good public health
sense, certain antibiotic uses have been withdrawn from animal
agriculture. One reason why this approach is often needed, especially
in the case of antibiotic use and resistance, is the difficulty in
designing, implementing, and analyzing the decisive studies that will
prove a negative health effect. By the time such a study is complete,
the negative effects associated with continued antibiotic use might
be irreversible. Consequently, the precautionary principle approach
to managing antibiotic use in poultry has only one real option:
withdraw the antibiotic use that might result in a negative human
health consequence.
Another way to evaluate the potential consequences of antibiotic
use in poultry is to develop scientifically based predictions, and
through these models, to evaluate interventions that reduce the
human and animal health risks associated with the continued
antibiotic use in poultry. Unfortunately, most risk assessments
conducted to date in antibiotic resistance that have been used for
regulatory purposes have not been based on interventions. Instead,
the assessments have attempted to qualify the risks associated with
the antibiotic use or else to quantify the risks for the sole purpose
of making the dichotomous decision of whether or not to withdraw
the antibiotic from use.
R. S. Singer and C. L. Hofacre
168
FUTURE DIRECTIONS
Estimating the potential impacts of antibiotic use in poultry
production is complex. To make more accurate assessments of these
impacts and to manage these antibiotic uses in a rational and
efficacious manner, research must continue in specific directions. An
area in which more work is needed is in relation to the physical
linkage of genes in the bacterial chromosome and in mobile
genetic elements, such as plasmids (29,36,41,117). For example,
a plasmid from an avian pathogenic E. coli (APEC) was recently
sequenced in its entirety (54). This plasmid, labeled pAPEC-O2-R,
contains many different types of genes, such as heavy metal–
resistance genes, a QAC-resistance gene, and up to eight different
antibiotic-resistance genes. All of these genes can be under
selection pressure in the poultry environment, resulting in the coselection and potential persistence of many different antibiotic
resistances in the absence of antibiotic pressure. In some of the early
studies of antibiotic use and resistance in chickens, these R
plasmids were found to be moveable to humans and were considered
a risk in the form of a potential reservoir of antibiotic-resistance
genes (69). As described earlier, there are few therapeutic options
available for treating infections such as airsacculitis, and these
limited choices may have helped contribute to the presence and
persistence of tetracycline- and sulfonamide-resistance genes residing on this APEC plasmid. Until we have a better understanding of the diversity of factors that can select for the
persistence of antibiotic-resistance genes, it will be difficult to
find management strategies that can actually reduce the levels of
antibiotic resistance currently circulating in the poultry production
system.
In addition to elucidating the diversity and interdependence of
genes located within the bacterial cell, we also need to evaluate how
the entire bacterial community is affected by antibiotic uses. Bacteria
are known to transfer resistance genes, even among distantly related
bacteria (36,41,117). The selection pressures exerted by antibiotic
uses affect the entire population of bacteria, not just those that are the
intended targets. The emerging field of metagenomics, which assesses
the genomic composition of the bacterial community in complex
samples, is being used more frequently to fill this data gap (43). Some
studies have begun to characterize this bacterial community, for
instance, in the intestinal tract of the maturing broiler chicken (75),
in the broiler litter (76), and in the cecal bacterial community,
following exposure to oxytetracycline (35).
There is still the common belief that resistance will decrease when
an antibiotic is removed. The assumption is based primarily on the
ecological theory that the bacterium incurs a fitness cost for maintaining the resistance gene but that this cost is less than the benefit
when an antibiotic is present. In the absence of the selection
pressure, the theory would state that the susceptible strain will either
out-compete the resistant strain or the resistant strain will lose the
resistance gene. Unfortunately, recent studies indicate that the
maintenance of resistance may not impose a significant fitness cost or
that this cost can be overcome (4,58,59,66,67,77,95,96). To better
manage our current antibiotic uses, we need to better comprehend
the ways in which bacteria can harbor resistance and how resistant
strains are likely to persist and spread, even in the absence of the
antibiotic-selection pressure.
The models that we build to assess the potential risks of antibiotic
use in poultry must begin to take a more holistic view of health.
Specifically, these models need to include the potential risks and the
potential benefits associated with antibiotic use. Phrased another
way, are there potential unintended consequences of removing
antibiotics from use in poultry? Recent models have predicted that
there might be some significant negative human health consequences
associated with the removal of certain antibiotics from poultry
production (25,102). In these models, it is assumed that the
antibiotics are helping maintain a healthier population of birds as
well as promoting size uniformity of the birds in the flock. These
factors can potentially lead to reduced microbial loads on the
carcass, which is a direct measure of the potential risk of
foodborne illness associated with consumption of that product.
Consequently, antibiotic use has potential benefits and risks, and
all of these potential consequences should be a part of our future
assessments of the ways in which antibiotics are used in poultry
production.
Finally, and probably most important, the assessments that are
used to determine the potential impacts of antibiotic use in animal
agriculture must be improved: these assessments must include
evaluations of potential interventions for reducing the risks to
human and animal health. This is especially true given that the
United States and some other countries have explored a sciencebased approach to assessing and managing risk. For example, in the
United States FDA-CVM risk assessment of fluoroquinolone use in
chickens, the aim was never to evaluate potential interventions for
reducing the risks to human health associated with fluoroquinoloneresistant Campylobacter infections that were caused by fluoroquinolone use in poultry; the model only estimated the potential human
health impact. By using a different modeling format, however,
potential interventions could have been evaluated, and many
different solutions could have been assessed. For example, the
processing of flocks that have received fluoroquinolones in a
separated fashion from flocks that have not been treated could
have been evaluated as a risk-reduction strategy. In this case, treated
flocks could be processed as the final group of birds before a full
processing plant cleaning and disinfection. This would reduce the
chance of cross-contamination of chicken meat from nontreated
houses with the bacteria from treated houses. In another potential
intervention, houses or farms that have received fluoroquinolones
could be cleaned in a more intensive manner than the normal
cleaning, and all litter from these flocks could be sterilized. Perhaps,
flocks from these farms during successive grow-outs would have
to be processed in a similar manner as the treated flocks. Finally,
an intervention in which flocks that have been treated with
antibiotics would have to wait for a longer period of time before
processing could have been assessed. This type of approach would
resemble the mandatory withdrawal times associated with antibiotic
residues. Feeding studies of other antibiotics have shown that
resistance increases after exposure to the antibiotic but that the
feeding of the antibiotic might be required to maintain the
resistance (80). Consequently, management strategies could also
include guidelines of when antibiotic uses should be ceased in flocks
before they go to processing to reduce the load of resistant organisms
in the birds.
These types of interventions might sound labor-intensive and
costly. They are, and that is the point. Under certain circumstances,
it might be cost-effective and ethical for a producer to use a powerful
antibiotic to control a severe disease in the flock, but this use would
then have major repercussions on how the flock and the farm are
subsequently managed. Producers might not opt for this intensive
measure, but at least, they would have a choice that is accepted as
scientifically sound for reducing both the human and animal risks
associated with the antibiotic use in their flocks. As we begin to gain
a better understanding of the ecology of resistance and its relation
to animal and human health, we will need these scientifically based
strategies for minimizing the impacts of antibiotic use on animal,
human, and environmental health.
Antibiotic use in poultry
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ACKNOWLEDGMENTS
R. Singer was partially supported by USDA National Research
Initiative Competitive Grant 00-35212-9398. C. Hofacre was partially
supported by USDA National Research Initiative Competitive Grant
01-35212-10877.