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Antibiotic resistance

Antibiotic resistance is the ability of a microorganism to withstand the effects of antibiotics. It is a specific type of drug resistance. Antibiotic resistance evolves naturally via natural selection acting upon random mutation, but it can also be engineered by applying an evolutionary stress on a population. Once such a gene is generated, bacteria can then transfer the genetic information in a horizontal fashion (between individuals) by plasmid exchange. If a bacterium carries several resistance genes, it is called multiresistant or, informally, a superbug. The term antimicrobial resistance is sometimes use to explicitly encompass organisms other than bacteria.

Antibiotic resistance can also be introduced artificially into a microorganism through transformation protocols. This can aid in implanting artificial genes into the microorganism. If the resistance gene is linked with the gene to be implanted, the antibiotic can be used to kill off organisms that lack the new gene.

Causes and risk factors

Antibiotic resistance can be a result of horizontal gene transfer, and also of unlinked point mutations in the pathogen genome and a rate of about 1 in 10⁸ per chromosomal replication. The antibiotic action against the pathogen can be seen as an environmental pressure; those bacteria which have a mutation allowing them to survive will live on to reproduce. They will then pass this trait to their offspring, which will result in a fully resistant colony.

Several studies have demonstrated that patterns of antibiotic usage greatly affect the number of resistant organisms which develop . Overuse of broad-spectrum antibiotics, such as second- and third-generation cephalosporins, greatly hastens the development of methicillin resistance. Other factors contributing towards resistance include incorrect diagnosis, unnecessary prescriptions, improper use of antibiotics by patients, the impregnation of household items and children's toys with low levels of antibiotics, and the use of antibiotics as livestock food additives for growth promotion.

Researchers have recently demonstrated the bacterial protein LexA may play a key role in the acquisition of bacterial mutations.

Mechanisms

The four main mechanisms by which microorganisms exhibit resistance to antimicrobials are:

Drug inactivation or modification: e.g. enzymatic deactivation of Penicillin G in some penicillin-resistant bacteria through the production of β-lactamases.
Alteration of target site: e.g. alteration of PBP—the binding target site of penicillins—in MRSA and other penicillin-resistant bacteria.
Alteration of metabolic pathway: e.g. some sulfonamide-resistant bacteria do not require para-aminobenzoic acid (PABA), an important precursor for the synthesis of folic acid and nucleic acids in bacteria inhibited by sulfonamides. Instead, like mammalian cells, they turn to utilizing preformed folic acid.
Reduced drug accumulation: by decreasing drug permeability and/or increasing active efflux (pumping out) of the drugs across the cell surface.

Resistant pathogens

Staphylococcus aureus (colloquially known as "Staph aureus" or a Staph infection) is one of the major resistant pathogens. Found on the mucous membranes and the skin of around a third of the population, it is extremely adaptable to antibiotic pressure. It was the first bacterium in which penicillin resistance was found—in 1947, just four years after the drug started being mass-produced. Methicillin was then the antibiotic of choice, but has since been replaced by oxacillin due to significant kidney toxicity. MRSA (methicillin-resistant Staphylococcus aureus) was first detected in Britain in 1961 and is now "quite common" in hospitals. MRSA was responsible for 37% of fatal cases of blood poisoning in the UK in 1999, up from 4% in 1991. Half of all S. aureus infections in the US are resistant to penicillin, caca methicillin, tetracycline and erythromycin.

This left vancomycin as the only effective agent available at the time. However, strains with intermediate (4-8 ug/ml) levels of resistance, termed GISA (glycopeptide intermediate Staphylococcus aureus) or VISA (vancomycin intermediate Staphylococcus aureus), began appearing in the late 1990s. The first identified case was in Japan in 1996, and strains have since been found in hospitals in England, France and the US. The first documented strain with complete (>16ug/ml) resistance to vancomycin, termed VRSA (Vancomycin-resistant Staphylococcus aureus) appeared in the United States in 2002.

A new class of antibiotics, oxazolidinones, became available in the 1990s, and the first commercially available oxazolidinone, linezolid, is comparable to vancomycin in effectiveness against MRSA. Linezolid-resistance in Staphylococcus aureus was reported in 2003.

CA-MRSA (Community-acquired MRSA) has now emerged as an epidemic that is responsible for rapidly progressive, fatal diseases including necrotizing pneumonia, severe sepsis and necrotizing fasciitis. Methicillin-resistant Staphylococcus aureus (MRSA) is the most frequently identified antimicrobial drug-resistant pathogen in US hospitals. The epidemiology of infections caused by MRSA is rapidly changing. In the past 10 years, infections caused by this organism have emerged in the community. The 2 MRSA clones in the United States most closely associated with community outbreaks, USA400 (MW2 strain, ST1 lineage) and USA300, often contain Panton-Valentine leukocidin (PVL) genes and, more frequently, have been associated with skin and soft tissue infections. Outbreaks of community-associated (CA)-MRSA infections have been reported in correctional facilities, among athletic teams, among military recruits, in newborn nurseries, and among active homosexual men. CA-MRSA infections now appear to be endemic in many urban regions and cause most CA-S. aureus infections.

Enterococcus faecium is another superbug found in hospitals. Penicillin-Resistant Enterococcus was seen in 1983, vancomycin-resistant enterococcus (VRE) in 1987, and Linezolid-Resistant Enterococcus (LRE) in the late 1990s.

Streptococcus pyogenes (Group A Streptococcus: GAS) infections can usually be treated with many different antibiotics. Early treatment may reduce the risk of death from invasive group A streptococcal disease. However, even the best medical care does not prevent death in every case. For those with very severe illness, supportive care in an intensive care unit may be needed. For persons with necrotizing fasciitis, surgery often is needed to remove damaged tissue. Strains of S. pyogenes resistant to macrolide antibiotics have emerged, however all strains remain uniformly sensitive to penicillin.

Resistance of Streptococcus pneumoniae to penicillin and other beta-lactams is increasing worldwide. The major mechanism of resistance involves the introduction of mutations in genes encoding penicillin-binding proteins. Selective pressure is thought to play an important role, and use of beta-lactam antibiotics has been implicated as a risk factor for infection and colonization. Streptococcus pneumoniae is responsible for pneumonia, bacteremia, otitis media, meningitis, sinusitis, peritonitis and arthritis.

Proteus can cause urinary tract infections and hospital-acquired infections. Proteus is unique, however, because it is highly motile and does not form regular colonies. Instead, Proteus forms what are known as "swarming colonies" when plated on non-inhibitory media. The most important member of this genus is considered to be Proteus mirabilis, a cause of wound and urinary tract infections. Fortunately, most strains of Proteus mirabilis are sensitive to ampicillin and cephalosporins. Unlike its relative, Proteus vulgaris is not sensitive to these antibiotics. However, this organism is isolated less often in the laboratory and usually only targets immunosuppressed individuals. Proteus vulgaris occurs naturally in the intestines of humans and a wide variety of animals; also manure, soil and polluted waters. More than 80% of human urinary tract infections (UTI) are due to the bacterium Escherichia coli but urinary infections due to Proteus mirabilis are also well documented. Proteus mirabilis once attached to urinary tract, infects the kidney more commonly than E. coli. Proteus mirabilis belongs to family Enterobacteriaceae and is a gram-negative motile swarmer bacterium. Proteus mirabilis are often found as free-living organisms in soil and water but they are also parasitic in the upper urinary tract of human beings.

Penicillin-resistant pneumonia caused by Streptococcus pneumoniae (commonly known as pneumococcus), was first detected in 1967, as was penicillin-resistant gonorrhea. Resistance to penicillin substitutes is also known as beyond S. aureus. By 1993 Escherichia coli was resistant to five fluoroquinolone variants. Mycobacterium tuberculosis is commonly resistant to isoniazid and rifampin and sometimes universally resistant to the common treatments. Other pathogens showing some resistance include Salmonella, Campylobacter, and Streptococci.

In November 2004, the Centers for Disease Control and Prevention (CDC) reported an increasing number of Acinetobacter baumannii bloodstream infections in patients at military medical facilities in which service members injured in the Iraq/Kuwait region during Operation Iraqi Freedom and in Afghanistan during Operation Enduring Freedom were treated. Most of these showed multidrug resistance (MRAB), with a few isolates resistant to all drugs tested.

Pseudomonas

Pseudomonas aeruginosa is a highly relevant opportunistic pathogen. One of the most worrisome characteristics of P. aeruginosa consists in its low antibiotic susceptibility. This low susceptibility is attributable to a concerted action of multidrug efflux pumps with chromosomally-encoded antibiotic resistance genes and the low permeability of the bacterial cellular envelopes. Besides intrinsic resistance, P. aeruginosa easily develop acquired resistance either by mutation in chromosomally-encoded genes, or by the horizontal gene transfer of antibiotic resistance determinants. Development of multidrug resistance by P. aeruginosa isolates requires several different genetic events that include acquisition of different mutations and/or horizontal transfer of antibiotic resistance genes. Hypermutation favours the selection of mutation-driven antibiotic resistance in P. aeruginosa strains producing chronic infections, whereas the clustering of several different antibiotic resistance genes in integrons favours the concerted acquisition of antibiotic resistance determinants. Some recent studies have shown that phenotypic resistance associated to biofilm formation or to the emergence of small-colony-variants may be important in the response of P. aeruginosa populations to antibiotics treatment.

Role of animals

Methicillin Resistant Staphylococcus Aureus (MRSA) is acknowledged to be a human commensal and pathogen. MRSA has been found in cats, dogs and horses, where it can cause the same problems as it does in humans. Owners can transfer the organism to their pets and vice-versa, and MRSA in animals is generally believed to be derived from humans. The United States Food and Drug Administration has responsibility for determining the safety of food as well as drugs. Drugs are frequently used for animals the same way they are used in people – to treat illness and improve the health of the animals. Drugs are used in animals that are used as human food, such as cows, pigs, chickens, fish, etc., and these drugs can affect the safety of the meat, milk, and eggs produced from those animals. Therefore, FDA has the responsibility to review drugs intended for use in food animals, and to be sure that the use of the drugs does not result in harmful residues in food or create resistant pathogens that can harm human health. For example, farm animals, particularly pigs, are believed to be able to infect people with MRSA. In 1951, the FDA approved the use of antibiotics in animal feed without a veterinary medical prescription; Concerns about resistance have been revisited several times since then, and most antimicrobials have not been shown to be a hazard. Europe quickly followed suit. As the spread of drug-resistant bacteria became a concern, countries began questioning the practice. In 1969, Britain issued the Swann Report, which recommended that human therapeutic antibiotics be banned from being used as growth promoters in agriculture. The report was largely ignored. It's pointed out by industry, that most of the routine feed drugs are either not used in human medicine, or are older compounds that have long been superseded by later-generation drugs.

Nearly 30 years later, char the World Health Organization concluded that antibiotics as growth promoters in animal feeds should be prohibited (in the absence of risk assessments). And in 1998, European Union health ministers voted to ban four antibiotics widely used to promote animal growth (despite their scientific panel's recommendations). Regulation banning the use of antibiotics in European feed, with the exception of two antibiotics in poultry feeds, became effective in 2006. With good animal husbandry and hygiene, there shouldn't be adverse effects, health-wise or production-wise, from not using antibiotics in animal feed. In Scandinavia, there's evidence that the ban has led to a lower prevalence of antimicrobial resistance in (non-hazardous) animal bacterial populations. Meanwhile, in the poultry industry, the ban hasn't had a deleterious effect. Economic performance in poultry production wasn't adversely affected either. Whether banning feed drugs has had any actual benefit to public health has been the topic of several reviews. Foodborne incidence and resistance patterns in humans, have not declined in countries featuring animal bans, in fact some have increased. Meanwhile, there were higher mortality in swine populations following bans. the "success" of Scandinavain and EU bans is therefore highly questionable as a useful policy, according to several published reviews. In the United States, antibiotic use in animal feeds remains controversial, due to a well-financed anti-agricultural campaign. The FDA first called for restrictions in 1997, which generated many studies and reports on the issue. In 1980, the Institute of Medicine reviewed the subject and recommended that more studies be conducted. In 1999, the General Accounting Office (GAO) also concluded that the evidence was inconclusive. A follow-up 2004 GAO study found that evidence existed of antibiotic-resistant bacteria being transferred from animals to humans. But since federal agencies don't collect data on antibiotic use in animals, conclusions on the potential impact on human health couldn't be made. Therefore, antibiotics are still used in U.S. animal feed--along with evidence of other worrisome ingredients.

Growing U.S. consumer concern about using antibiotics in animal feed has led to a niche market of "antibiotic-free" animal products, but this small market is unlikely to change entrenched industry-wide practices. Within FDA, the animal drug review duties have been assigned to one of the Agency’s operating units, the Center for Veterinary Medicine. Their guidance is used to evaluate all types and uses of antimicrobials, including what some refer to as subtherapeutic use. Although that term has not been defined by regulation, it describes the use of a product to boost an animal’s ability to grow and produce more food, instead of treating or preventing an infectious disease. It could also be used to evaluate antimicrobials if they are used for growth promotion, and for antimicrobials that are products of genetic engineering. Animals that we use to produce food for human consumption, including cows (for beef and milk production), pigs, chickens, turkeys, fish, and sheep. Antimicrobials are used to cause animals to increase production of food. Antimicrobials are used in feeds for some species, and the animals fed the antimicrobial feeds often grow faster while consuming less feed than animals not given antimicrobials in feed. In addition to determining whether the use of a drug would result in residues left in the meat, milk, or eggs, FDA must ensure that the use of antimicrobials in food-producing animals does not lead to the development of resistant bacteria that can become a public health concern. This document is one way that drug sponsors can submit information that address the issue of the microbial safety of antimicrobial new animal drugs. A sponsor is free to use other scientifically valid approaches to demonstrate the safety of their proposed product. CVM first said in December 1999 that it would consider the question of the fostering of antimicrobial resistance when reviewing antimicrobials for use in animals. That announcement was followed a year later with what was called FDA’s “Framework Document,” which first described the FDA’s plan to use risk assessments of the development of antimicrobial resistance in determining the safety of antimicrobials for food-producing animals. The guidance document was first published as a draft in September 2002, to allow the scientific community to comment on the concept and on the science FDA used to develop the guidance document. The FDA allows the use of antimicrobials because they are a valuable tool that veterinarians can use to treat sick animals, and so livestock producers can use antimicrobials to produce meat, milk, and eggs more efficiently.

In 2001, the Union of Concerned Scientists estimated that greater than 70% of the antibiotics used in the US are given to food animals (e.g. chickens, pigs and cattle) in the absence of disease. This 2001 report, however, has been shown to over-estimate animal usage rates. Antibiotic use in food animal production has been associated with the emergence of antibiotic-resistant strains of bacteria including Salmonella, Campylobacter, Escherichia coli and Enterococcus, among others. There is substantial evidence from the US and European Union that these resistant bacteria cause antibiotic-resistant infections in humans. The American Society for Microbiology (ASM), the American Public Health Association (APHA) and the American Medical Association (AMA) have called for substantial restrictions on antibiotic use in food animal production including an end to all "non-therapeutic" uses. The food animal and pharmaceutical industries have fought hard to prevent new regulations that would limit the use of antibiotics in food animal production, pointing out that while concerns exist, risk assessments and actual data have demonstrated little to no risk in this area. For example, in 2000 the US Food and Drug Administration (FDA) announced their intention to rescind approval for fluoroquinolone use in poultry production because of substantial evidence linking it to the emergence of fluoroquinolone resistant Campylobacter infections in humans. The final decision to ban fluoroquinolones from use in poultry production was not made until 5 years later because of challenges from the food animal and pharmaceutical industries. Today, there are two federal bills (S. 549 and H.R. 962) aimed at phasing out "non-therapeutic" antibiotics in US food animal production. These bills are nominally endorsed by many public health and medical organizations including the American Nurses Association (ANA), the American Academy of Pediatrics (AAP), and the American Public Health Association (APHA). Other professional groups, notably animal science, food science, veterinary, and industry groups do not support this legislation, however, pointing out that current uses are not shown to be hazardous and have legitimate disease prevention roles.

Alternatives

Prevention

Rational use of antibiotics may reduce the chances of development of opportunistic infection by antibiotic-resistant bacteria due to dysbacteriosis. In one study the use of fluoroquinolones are clearly associated with Clostridium difficile infection, which is a leading cause of nosocomial diarrhea in the United States, and a major cause of death, worldwide.

Vaccines do not suffer the problem of resistance because a vaccine enhances the body's natural defenses, while an antibiotic operates separately from the body's normal defenses. Nevertheless, new strains may evolve that escape immunity induced by vaccines.

While theoretically promising, anti-staphylococcal vaccines have shown limited efficacy, because of immunological variation between Staphylococcus species, and the limited duration of effectiveness of the antibodies produced. Development and testing of more effective vaccines is under way.

Phage therapy

Phage therapy, an approach that has been extensively researched and utilized as a therapeutic agent for over 60 years, especially in the Soviet Union, is an alternative that might help with the problem of resistance. Phage Therapy was widely used in the United States until the discovery of antibiotics, in the early 1940s. Bacteriophages or "phages" are viruses that invade bacterial cells and, in the case of lytic phages, disrupt bacterial metabolism and cause the bacterium to lyse. Phage Therapy is the therapeutic use of lytic bacteriophages to treat pathogenic bacterial infections.

Bacteriophage therapy is an important alternative to antibiotics in the current era of multidrug resistant pathogens. A review of studies that dealt with the therapeutic use of phages from 1966–1996 and few latest ongoing phage therapy projects via internet showed: phages were used topically, orally or systemically in Polish and Soviet studies. The success rate found in these studies was 80–95% with few gastrointestinal or allergic side effects. British studies also demonstrated significant efficacy of phages against Escherichia coli, Acinetobacter spp., Pseudomonas spp and Staphylococcus aureus. US studies dealt with improving the bioavailability of phage. Phage therapy may prove as an important alternative to antibiotics for treating multidrug resistant pathogens.

Development of new drugs

Until recently, research and development (R&D) efforts have provided new drugs in time to treat bacteria that became resistant to older antibiotics. That is no longer the case. The potential crisis at hand is the result of a marked decrease in industry R&D, government inaction, and the increasing prevalence of resistant bacteria. Infectious disease physicians are alarmed by the prospect that effective antibiotics may not be available to treat seriously ill patients in the near future.

The pipeline of new antibiotics is drying up. Major pharmaceutical companies are losing interest in the antibiotics market because these drugs may not be as profitable as drugs that treat chronic (long-term) conditions and lifestyle issues.

The resistance problem demands that a renewed effort be made to seek antibacterial agents effective against pathogenic bacteria resistant to current antibiotics. One of the possible strategies towards this objective is the rational localization of bioactive phytochemicals. Plants have an almost limitless ability to synthesize aromatic substances, most of which are phenols or their oxygen-substituted derivatives such as tannins. Most are secondary metabolites, of which at least 12,000 have been isolated, a number estimated to be less than 10% of the total. In many cases, these substances serve as plant defense mechanisms against predation by microorganisms, insects, and herbivores. Many of the herbs and spices used by humans to season food yield useful medicinal compounds including those having antibacterial activity.

Traditional healers have long used plants to prevent or cure infectious conditions. Many of these plants have been investigated scientifically for antimicrobial activity and a large number of plant products have been shown to inhibit growth of pathogenic bacteria. A number of these agents appear to have structures and modes of action that are distinct from those of the antibiotics in current use, suggesting that cross-resistance with agents already in use may be minimal. For example the combination of 5'-methoxyhydnocarpine and berberine in herbs like Hydrastis canadensis and Berberis vulgaris can block the MDR-pumps that cause multidrug resistance. This has been shown for Staphylococcus aureus.

Archaeocins is the name given to a new class of potentially useful antibiotics that are derived from the Archaea group of organisms. Eight archaeocins have been partially or fully characterized, but hundreds of archaeocins are believed to exist, especially within the haloarchaea. The prevalence of archaeocins is unknown simply because no one has looked for them. The discovery of new archaeocins hinges on recovery and cultivation of archaeal organisms from the environment. For example, samples from a novel hypersaline field site, Wilson Hot Springs, recovered 350 halophilic organisms; preliminary analysis of 75 isolates showed that 48 were archaeal and 27 were bacterial.

Applications

Antibiotic resistance is an important tool for genetic engineering. By constructing a plasmid which contains an antibiotic resistance gene as well as the gene being engineered or expressed, a researcher can ensure that when bacteria replicate, only the copies which carry along the plasmid survive. This ensures that the gene being manipulated passes along when the bacteria replicates.

The most commonly used antibiotics in genetic engineering are generally "older" antibiotics which have largely fallen out of use in clinical practice. These include:

Industrially the use of antibiotic resistance is disfavored since maintaining bacterial cultures would require feeding them large quantities of antibiotics. Instead, the use of auxotrophic bacterial strains (and function-replacement plasmids) is preferred.