In a 1945 interview with The New York Times, Alexander Fleming, who won a Nobel Prize
that year for his discovery of pencillin, warned that misuse of the drug could result
in selection for resistant bacteria. True to this prediction, resistance began to
emerge within 10 years of the widescale introduction of penicillin. Indeed, although
antibiotics have transformed the medical response to bacterial illness and rendered
easily treatable many formerly deadly infections, the mishandling and misprescription
of these drugs have transformed the bacterial population such that many antibiotics
have partially or entirely lost their efficacy. The problem is severe enough that
many experts believe the value of existing antibiotic therapies over the next 100
years is now uncertain. However, some also believe that with a proper response to
the current trend in antibiotic resistance, these drugs might once again serve their
original function.
The Cure Is the Catalyst
Antibiotics fight bacteria through a variety of mechanisms. Penicillins, cephalosporins,
carbapenems, and vancomycin kill bacteria by damaging or inhibiting the synthesis
of bacterial cell walls. Other antibiotics act through effects on bacterial DNA or
RNA (quinolones and rifampin), proteins (aminoglycocides, chloramphenicol, tetracyclines,
and macrolide antibiotics), or metabolism (trimethoprim and sulfonamides).
Bacteria are said to have “intrinsic resistance” to an antibiotic when their normal
characteristics render them immune to the antibiotic’s mechanism of effect. Intrinsic
resistance is not affected by misuse of antibiotics. In fact, it is valuable in determining
which antibiotic will be most effective against a certain microbe. For example, the
outer membrane of gram-negative bacteria makes them relatively impermeable to hydrophobic
compounds such as macrolide antibiotics, thus conferring intrinsic resistance to these
drugs. Some bacteria can also use temporary strategies in which different genes are
expressed or suppressed in order to enable survival in the presence of antibiotics,
with expression patterns returning to normal once the threat posed by those particular
drugs has passed.
In contrast, bacteria may acquire resistance to an antibiotic by taking on a new characteristic
through gene mutation or the transfer of genetic material between bacteria. Acquired
characteristics that can make bacteria resistant to an antibiotic include changes
to the bacterial membrane that prevent antibiotics from entering the cell. Bacteria
may also use enzymes to break down antibiotics, or they may employ “efflux pumps”
to remove the antibiotic entirely or reduce its concentration below effective levels.
If a bacterium is able to perform more than one of these functions, it may be resistant
to more than one type of antibiotic, resulting in multidrug resistance, according
to P.M. Bennett, writing in the March 2008 issue of the British Journal of Pharmacology.
At the same time, the possession of even a single form of efflux pump can lead to
the export of—and protection against—more than one form of antibiotic, thus also conferring
multi-drug resistance, adds David McDowell, a professor of food studies at the University
of Ulster.
Mutations are relatively rare, occurring in only 1 event per 107–1010 bacteria, according
to a review by Michael R. Mulvey and Andrew E. Simor in the 17 February 2009 issue
of the Canadian Medical Association Journal. As an example, Mulvey and Simor pointed
to isoniazid resistance among Mycobacterium tuberculosis. “This form of resistance
is not transferable to other organisms,” they wrote. “The probability of multiple
resistance mutations occurring in a single organism is equal to the product of their
individual probabilities. This is the rationale behind the use of combination therapy
for the management of tuberculosis.”
Of greater concern are “promiscuous” gene transfer systems that allow the sharing
of genetic material between bacteria. One genetic transfer strategy is the exchange
of conjugative plasmids. These circles of DNA, which are separate from the bacterial
chromosome, can replicate independently and move between bacteria carrying antibiotic
resistance genes, thereby multiplying antibiotic resistance among successive generations
within a bacterial colony. Bacteria may also acquire resistance genes through the
spread of transposons or integrons, groups of linked genetic elements.
In the July 2008 issue of the Journal of Bacteriology, Michael Gillings and colleagues
wrote that class 1 integrons (the most extensively studied type of integron) now appear
in 40–70% of gram-negative pathogens in clinical and agricultural samples. “The rapid
spread of class 1 integrons through gram-negative and, more recently, into gram-positive
species has been facilitated by their location on mobile DNA elements, such as plasmids
and transposons, coupled with the selective advantage conferred by their associated
antibiotic resistance genes,” they wrote. The authors noted about 10% of sequenced
bacterial genomes carry integrons.
In some instances, resistance mechanisms are induced by the presence of an antibiotic,
says José L. Martínez, a microbiologist at the Spanish National Center of Biotechnology,
but in most cases resistance arises when susceptible bacteria are killed by the antibiotic
and only those resistant few prevail and reproduce. In other words, antibiotics don’t
cause resistance. Instead, they select for resistant bacteria and increase the proportional
prevalence.
Ironically, the impulse to scour equipment and surfaces may sometimes end up worsening
this situation, as M. Ann S. McMahon and colleagues pointed out in the January 2007
issue of Applied and Environmental Microbiology: “Detergents and solvents have been
shown, among other compounds, to induce the [multiple antibiotic resistance] operon,”
they wrote, describing food-preservation processes. “This operon regulates the expression
of a large number of genes, including those coding for at least one broad-specificity
efflux pump (the arcAB efflux pump), which are more strongly expressed under conditions
of environmental stress. This suggests a direct linkage between environmental stresses,
such as those occurring in foods and the domestic environment, efflux pump expression,
and the development of antibiotic resistance.” The authors suggest that the increased
use of sublethal bacteriostatic food preservation methods (as opposed to bactericidal
methods) may be contributing to antibiotic resistance among food-related pathogens.
Case in Point
The problem of antibiotic resistance has become widely known in large part because
of the emergence of methicillin-resistant Staphylococcus aureus (MRSA), an increasingly
common bacterial agent with frightening consequences. Initially, most MRSA infections
were contracted by hospital in-patients suffering from other underlying conditions.
Such infections were dubbed hospital-acquired MRSA (sometimes called healthcare-associated
MRSA, and abbreviated in both cases as HA-MRSA). In 1974, 2% of all S. aureus infections
in the United States were HA-MRSA, according to the Centers for Disease Control and
Prevention. By 1995 this figure rose to 22% and by 2004 had reached 64%. More recently,
MRSA infections have been reported among otherwise apparently healthy members of the
general population who have not undergone hospitalization or any invasive medical
procedure within the past year. These infections are known as community-acquired MRSA
(CA-MRSA).
In the September 2008 issue of the Journal of Clinical Microbiology Fred C. Tenover
and colleagues from the CDC reported on an extended study undertaken to characterize
MRSA isolates collected as part of the National Health Examination and Nutrition Survey
between 2001 and 2004. A total of 19,412 nasal samples had been collected from noninstitutionalized
individuals. Between 2001–2002 and 2003–2004, the incidence of S. aureus in nasal
samples decreased. However, during the same period, the prevalence of MRSA increased,
reaching 1.5%.
Moreover, colonization with MRSA can persist even after several years. In a study
reported in the 1 April 2009 issue of Clinical Infectious Diseases, Ari Robicsek and
colleagues examined 1,564 patients after positive MRSA identification and then retested
them over a 4-year period. After one year, 48.8% of the patients were still colonized
with MRSA. After four years, 21.2% were still colonized. The lesson to be learned,
according to the authors, is that “even in the fourth year after a positive clinical
culture result, the risk of MRSA colonization does not subside to that of the general
patient population.”
Risk factors for acquiring HA-MRSA include recent hospitalization, outpatient visits
to the hospital, and nursing home admission. CA-MRSA infections are also associated
with antibiotic exposure, chronic illness, injection drug use, athletics (particularly
contact sports such as wrestling or those that involve handling a communal object
such as a volleyball), or close contact with someone who has one of these characteristics
or exposures. Any sharing of equipment, clothing, or athletic facilities, or skin-to-skin
contact, also increases the likelihood of acquiring MRSA. However, HA-MRSA and CA-MRSA
have started to blend, with traditional risk factors predicting infection less accurately.
Spotted in the Wild
In the 2001 report Hogging It! Estimates of Antimicrobial Abuse in Livestock, the
Union of Concerned Scientists estimated that 70% of all antibiotics used in the United
States—more than 24 million pounds per year—is routinely put in the food and water
of healthy livestock. Antibiotics are used in feed animals to not only control disease
but also improve metabolism and reduce dietary requirements by stimulating the growth
of microbes that produce vitamins and amino acids. In a review in the May 2007 issue
of EHP, Amy R. Sapkota and colleagues wrote that the practice of using antibiotics
at non-therapeutic levels “has been shown to select for antibiotic resistance in both
commensal and pathogenic bacteria in a) the animals themselves; b) subsequent animal-based
food products; and c) water, air, and soil samples collected around large-scale animal
feeding operations.”
Veterinary antibiotics often are excreted unchanged. In the April 2001 issue of Applied
and Environmental Microbiology, for instance, J. C. Chee-Sanford and colleagues reported
that up to 75% of tetracycline administered to swine was excreted unaltered. The excreted
drugs can persist in the environment, creating an opportunity for resistance selection
within exposed bacterial populations.
Animal waste handling practices vary considerably between farms, but generally include
“land application,” the spreading of waste on the soil surface as a fertilizer, which
can result in contamination of soil and surface or ground water. Many conventional
farming operations also use waste lagoons, which provide an alternative route by which
birds and insects can pick up antibiotic-resistant bacteria.
A study by Jay P. Graham and colleagues in the 1 April 2009 issue of Science of the
Total Environment reported that flies collected from the areas surrounding a poultry
production facility demonstrated resistance consistent with the types of antibiotics
being used there. Graham and colleagues suggested that “the carriage of antibiotic
resistant enteric bacteria by flies in the poultry production environment increases
the potential for human exposure to drug resistant bacteria.”
And there is evidence that antibiotic-resistant bacteria are traveling far. In the
January 2008 issue of Emerging Infectious Diseases, Maria Sjöland and colleagues documented
an unexpectedly high presence in Arctic wildlife of drug-resistant Escherichia coli,
which the authors speculate may have been transported by migratory birds. In another
recent study, published in the March 2009 issue of FEMS Microbiology Ecology, Julie
M. Rose and colleagues took 472 bacterial isolates from vertebrates in coastal waters
off the northeastern United States, including marine mammals, sharks, and birds, and
found that 58% demonstrated resistance to at least one antibiotic, whereas 43% were
multidrug-resistant.
In 1996, the National Antibiotic Resistance Monitoring System (NARMS) was formed as
a joint effort of the Food and Drug Administration (FDA), the Centers for Disease
Control and Prevention, and the U.S. Department of Agriculture to collect data on
bacteria present in humans and animals. In 2001, NARMS expanded to include sampling
of retail meats collected through random purchases from randomly selected groceries.
NARMS first began sampling at locations in 6 states in 2002, then increased to 8 states
in 2003, 10 in 2004, and 11 in 2008. The most recent NARMS report, 2006 NARMS Retail
Meat Annual Report, presents some staggering numbers. In tests of chicken breast samples
collected between 2002 and 2006, an average of 51.1% tested positive for Campylobacter,
11.9% for Salmonella, 97.7% for E. coli, and 82.6% for Enterococcus. In many cases,
these bacterial isolates also tested positive for resistance to one or more drugs.
One of the first studies to closely examine the occurrence of MRSA on U.S. farms looked
at two swine production systems. As reported by Tara C. Smith and colleagues in the
23 January 2009 edition of PLoS ONE, one farm had extremely high levels of the ST398
strain of MRSA in both its animal population (49% overall, with 100% occurrence in
animals aged 9–12 weeks) and its workers (64%). Yet, none of the animals or workers
in the second farming system had MRSA, which may have to do with the source of the
animals. Smith explains, “Because the farms got their animals from different sources,
we’re guessing MRSA is moving via importation, bringing in pigs already colonized.”
Pharmaceutical factories, themselves, can be another source of antibiotics entering
the environment. As Meghan Hessenauer, an environmental scientist at the U.S. Environmental
Protection Agency, points out, guidelines for pharmaceutical manufacturing wastes
are geared toward the discharge of chemicals used in the process of manufacturing
rather than active pharmaceutical ingredients. This, she says, means “there is no
regulation and no limits on antibiotics themselves.”
Other Environmental Inputs
There are best management practices in place to prevent such industrial releases,
says Hessenauer. Nevertheless, drugs are still making their way out of at least some
manufacturing plants. In one survey of a wastewater treatment plant that received
effluent from a penicillin G production facility, published online 18 February 2009
ahead of print in Environmental Microbiology, Dong Li and colleagues demonstrated
that, compared with upstream samples, effluent and downstream samples showed significantly
high levels of resistance for almost all the antibiotics they tested for.
At the household level, recent studies have found a correlation between the disposal
of antibiotics and the emergence of resistance. In research performed by Dean A. Seehusen
and John Edwards and described in the November–December 2006 issue of the Journal
of the American Board of Family Medicine, more than half the patients surveyed had
flushed unused or expired pharmaceuticals down the toilet. Only 22.9% reported returning
unused medication to a pharmacy, and still fewer had received information from a health
care provider about proper medication disposal. In the December 2005 issue of EHP,
Jonathan Bound and Nikolaos Voulvoulis reported similar numbers from a U.K. study
in which only 21.8% of survey respondents returned unused medications to their pharmacies.
As with farm animals, antibiotics may be excreted by humans in their original active
form. Up to 80% of amoxicillin, for example, may be excreted unaltered in urine. In
the October 2000 issue of Antimicrobial Agents and Chemotherapy, for instance, Niels
Høiby and colleagues reported that excretion of ceftriaxone and ceftazidime in sweat
“may have contributed significantly to the present worldwide selection for and spread
of MRSA.” When excreted antibiotics do make their way to sewage treatment plants,
they aren’t necessarily removed from the water, nor are antibiotic-resistance bacteria.
In the December 2005 issue of The Journal of General and Applied Microbiology Xavier
Vilanova and Anicet R. Blanch reported finding vancomycin- and erythromycin-resistant
bacteria in liquid and dried sludge from a treatment plant.
Researchers are still evaluating how disinfectants and antibacterial products such
as handsoap may impact antibiotic resistance. In the April 2003 issue of Clinical
Microbiology Reviews, Peter Gilbert and Andrew J. McBain wrote, “While the regular
application and use of antimicrobial handwashing products have been noted to bring
about a change in skin flora, this has not been associated with fluctuations in resistance.”
The following year, the Board of the International Scientific Forum on Home Hygiene
issued a consensus statement declaring “there is no evidence that biocide use has
been a significant factor to date in the development of antibiotic resistance in clinical
practice—antibiotic misuse is the most significant causative factor.”
The board noted, however, that “it is important to ensure that biocides are used responsibly
as part of a good hygiene routine in the domestic setting in order to avoid the possibility
of any impact on antimicrobial resistance in the future.” Indeed, the same holds true
for community-scale hygiene. In the June 2004 issue of Ecotoxicology and Environmental
Safety, Richa Shrivastava reported that suboptimal chlorination of water taken from
India’s River Gomti appeared to select for multidrug-resistant Pseudomonas aeruginosa,
an opportunistic pathogen.
On the Trail of the Resistance Footprint
David Patrick and James Hutchinson suggested in the 17 February 2009 issue of the
Canadian Medical Association Journal that a “resistance footprint” can help identify
and measure antibiotic hazards. That is, everyone connected with antibiotics through
production, prescription, consumption, and disposal should consider their own potential
contributions to the problem (their “footprint”) as well as their role in preventing
the spread of antibiotic resistance. Says Patrick, “The price for use of a specific
course of antibiotics isn’t necessarily suffered by the person who takes them. In
addition to potential therapeutic benefits from using antibiotics, there is a contribution
to the selective pressure to resistance that affects other people.”
Effective stewardship programs that promote the “resistance footprint” concept must
acknowledge and address financial incentives for antibiotic use among farmers, on
whom the burden of maintaining their herds rests and for whom financial constraints
are often a great concern. Patrick says, “When I speak with food producers about pressure
to get rid of antibiotics, they say a complication in North America is that we have
a common food market between the United States and Canada, so if one side moves and
perceives an economic disadvantage, they worry about putting themselves out of business.
We need joint Canadian and U.S. support of agricultural regulations.” If farmers could
be shown the longer-term economic benefits of stewardship and “footprint” management,
he adds, they might be more inclined to adopt strategies that would limit use of antibiotics
and reduce resistance.
So far, the majority of efforts to prevent and reduce antibiotic resistance have occurred
in the field of health care, with infectious disease practitioners and researchers
leading a call to reduce unnecessary use of antibiotics and adopt other stewardship
strategies. Hospitals have implemented stewardship programs that bring interested
parties together to identify problem drugs, retrieve historical patient data, and
review standing formulary policies in order to develop strategies to manage antimicrobial
use and monitor resistance patterns.
In 2007, the Infectious Diseases Society of America and the Society for Health-care
Epidemiology of America issued its “Guidelines for Developing an Institutional Program
to Enhance Antimicrobial Stewardship.” Some of these guidelines are well validated,
such as optimizing antimicrobial dosing based on the individual patient, infectious
agent, and site of infection. Others—such as substituting one antibiotic for another—have
not yet been validated.
Research to identify new antibiotics for which resistance has not yet developed also
is ongoing. However, the high cost of new drug development, combined with the more
stringent approval criteria adopted in recent years by the FDA, is prohibitive for
many larger pharmaceutical companies. The FDA’s desire to prevent further resistance
from emerging also means that a “new compound that makes it through regulatory approval
will be put on a restricted list to be used only when other antibiotics have failed,
thereby limiting its market,” wrote Julian Davies in volume 8, number 7 (2007) of
EMBO Reports.
New drug development, says Stuart Levy, a professor of molecular biology and microbiology
at Tufts University, may therefore end up in the hands of academia or smaller pharmaceutical
companies. “The smaller companies are able to focus on a single organism or a single
product, devoting their energies and people to that singular focus,” he explains.
“In large companies, particularly when you get to the level of animal studies, you
have to wait in a queue in order to do your analysis.”
Meanwhile, reining in antibiotic use is easier said than done. With cephalosporin
resistance occurring at alarming rates, the FDA on 3 July 2008 proposed a withdrawal
of extra-label uses of this class of antibiotics in food-producing animals, meaning
farmers could no longer legally use these drugs for anything other than FDA-approved
uses listed on the label. However, on 25 November 2008, the agency withdrew the proposal
“in order for FDA to fully consider the comments” received from groups such as the
American Association of Swine Veterinarians (AASV), which argued the ban was based
on unsubstantiated data. A news item in the January/February 2009 issue of the AASV’s
Journal of Swine Health and Production notes that “It seems . . . that given the fact
that antimicrobials affect all susceptible bacteria in the animal being treated, whether
or not that bacteria is on the approved label, the more rational approach would be
to use an approved product for the [animal] species being treated rather than a product
labeled for a different [animal] species.”
The presence of antibiotic resistance genes in surface water, groundwater, at sewage
treatment plants, landfills, and a variety of agricultural and aquacultural locations
means pollution of the environment has not only been chemical. And although limiting
antibiotic use and creating programs that control dissemination of antibiotics can
prevent the problem of resistance from worsening and may even reduce the problem,
it’s unclear whether resistant strains will necessarily be replaced by susceptible
ones, says Martínez. Moreover, says Gillings, “The natural disappearance of antibiotic-resistant
strains is very slow—much slower than the rate of their appearance.”
Still, some studies suggest that reducing use of antibiotics at the level of an individual
medical practice is associated with reduced local antibiotic resistance. For instance,
in the 1 October 2007 issue of The British Journal of General Practice, Chris C. Butler
and colleagues showed that antibiotic resistance could be effectively reduced within
an observable period. Specifically, they observed an overall reduction of resistance
to ampicillin (1% per year) and trimethoprim (0.6% per year) in practices that reduced
their prescriptions of those drugs. Although modest, these findings may suggest the
possibility of a sustained decline in resistance, wrote Butler and colleagues, thus
“preserving the international reservoir of antibiotic susceptibility.”