Abstract

Antimicrobial resistance (AMR) is the resistance of a microorganism to an antimicrobial drug to which it was previously sensitive. Resistant organisms that include bacteria, viruses and some parasites are able to withstand attack by antibiotics, antivirals, and antimalarial, so that standard treatments become ineffective and futile. Therefore, AMR is a consequence of the misuse and overuse of antibiotics and develops when a microorganism mutates or acquires a resistance gene. Moreover, genes can be transferred between bacteria in a horizontal fashion by conjugation, transduction, or transformation. Thus a gene for antibiotic resistance which had evolved via natural selection may be shared and gradually as the bacterium acquires multiple resistance genes it becomes superbug. The antibiotics misuse and overuse has significantly contributed to the resistance which therefore requires timely testing and management and an efficient containment and surveillance system and rational prescription of antimicrobial therapy in the clinical practice. Possibly Mother Nature holds an answer to this problem of AMR.

History
In 1928 , Scottish scientist Alexander Fleming discovered a substance called Penicillin while working with Staphylococcus in the laboratory. Thereafter an era of using natural and synthetic drugs began,to treat bacterial infections.1

The Problem: Genetic Evolution?

After more than 50 years of widespread use, evolution of disease-causing microbes also has resulted in many antimicrobials losing their effectiveness. As microbes evolve, they adapt to their environments and if something stop them from growing and spreadingsuch as an antimicrobialthey evolve new mechanisms to resist the antimicrobials by changing their genetic structure so that changing the genetic structure ensures that the offspring of the resistant microbes also are resistant.2 Moreover, genes can be transferred between bacteria in a horizontal fashion by conjugation, transduction, or transformation. Thus a gene for antibiotic resistance which had evolved via natural selection may be shared. Evolutionary stress such as exposure to antibiotics then selects for the antibiotic resistant trait. Many antibiotic resistance genes reside on plasmids, facilitating their transfer. If a bacterium carries several resistance genes, it is called multiresistant or,

informally, a superbug or super bacterium. . The greater the duration of exposure, the greater the risk of the development of superbugs.AMR makes it harder to eliminate infections from the body. As a result of a microbes ability to survive in spite of antimicrobials, some infectious diseases are now more difficult to treat than they were just a few decades ago.3 AMR therefore poses a significant global problem.2-4

Causes
Antibiotic misuse, overuse and underuse
The widespread misuse of antibiotics both inside and outside of hospitals is playing a significant role in the emergence of resistant bacteria.Inappropriate sale and prescription of antibiotics has been attributed to a number of causes like over the counter sale,physicians heavily burdened with the patients and dont have time to listen to them therefore reckless prescribing to get rid of the patients early or else are overtly cautious due to medico legal reasons.1,5 Sub optimum antibiotic concentrations in critically ill people increase the frequency of antibiotic resistance organisms. While taking antibiotics doses less than those recommended may increase rates of resistance.Also, Poor hand hygiene by hospital staff has been associated with the spread of resistant organisms and an increase in hand washing compliance results in decreased rates of these organisms.5

Inadequate Diagnostics
More often, healthcare providers use incomplete or imperfect information to diagnose an infection and thus prescribe an antimicrobial irrationally or prescribe a broad-spectrum antimicrobial when a specific antibiotic might be better. These situations contribute to selective pressure and accelerate antimicrobial resistance.5

Hospital Use
Suboptimal antibiotic concentration in critically ill patients increase the frequency of resistant organisms by selective pressure.1,5 The extensive use of antimicrobials and close contact among sick patients creates a fertile environment for the spread of antimicrobial-resistant germs.6

Agricultural Use
Scientists also believe that the practice of adding antibiotics to agricultural feed promotes drug resistance. More than half of the antibiotics produced in the United States are used for agricultural purposes.6,7 However; there is still much debate about whether drug-resistant microbes in animals pose a significant public health burden.

Veterinary use
Drugs used in food producing animals like cows, pigs, chickens etc. to improve the quality of meat, milk,eggs etc can affect their safety 7,8 and can be the source of superbugs. For example, farm animals, particularly pigs, are believed to be able to infect people with MRSA. The resistant bacteria in animals due to antibiotic exposure can be transmitted to humans via three pathways, those being through the consumption of meat, from close or direct contact with animals, or through the environment. If infection in animals are left untreated, there is a greater risk of potentially unsafe food entering the human food chain 9 Development of resistant bacteria in food animals can result from chromosomal mutations but is more commonly associated with the horizontal transfer of resistance determinants borne on mobile genetic elements. Food may represent a dynamic environment for the continuing transfer of antibiotic resistance determinants between bacteria. Current food preservation systems that use a combination of environmental stresses to reduce growth of bacteria, may serve to escalate development and dissemination of antibiotic resistance among food related pathogens. The increasing reliance on biocides for pathogen control in food production and processing, heightens the risk of selection of biocide-resistant strains.9,10 A 2006 study published in the Journal of Infectious Diseases found that bacteria from conventional chicken and from people who ate the chicken became resistant to Synercid, a strong antibiotic used to treat antibiotic-resistant bacteria. It also found that it was rare to find resistant bacteria among antibiotic-free chicken, while the majority of bacterial isolates from conventional poultry were resistant.11

Antiviral drug Resistance

In the setting of intensive immunosuppression for the management of rejection in solid organ transplant (SOT) recipients, or graft-versus-host disease (GVHD) in hematopoietic stem cell transplant recipients, antiviral therapy is commonly used and drug resistant viruses are increasingly encountered. Prolonged antiviral drug exposure and ongoing viral replication due to immunosuppression are key factors in the development of antiviral drug resistance, which may manifest as persistent or increasing viremia or disease despite therapy. 12 More than 200 mutations are associated with antiretroviral resistance to drugs belonging to six licensed antiretroviral classes 13

Mechanisms of AMR
The 4 main mechanisms by which microbes acquire resistance are mainly:

1. Drug inactivation or modification: for example, enzymatic deactivation of Penicillin G in some penicillin-resistant bacteria through the production of -lactamases.2-4 2. Alteration of target site: for example, alteration of PBPthe binding target site of 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. Fluor quinolone resistance is mainly (but not exclusively) due to mutations in the target enzymes, DNA topoisomerases.14 3. Alteration of metabolic pathway: for example, some sulfonamide.15 4. Reduced drug accumulation: by decreasing drug permeability and/or increasing active efflux (pumping out) of the drugs across the cell surface.3,4 Drug efflux pumps play a key role in drug resistance and also serve other functions in bacteria. There has been a growing list of multidrug and drug-specific efflux pumps characterized from bacteria of human, animal, plant and environmental origins. These pumps are mostly encoded on the chromosome although they can also be plasmid-encoded. 2-4 5. Many of the resistance genes apparently have their evolutionary origins in the antibioticproducing microbes, which must defend themselves from the antibiotics produced. Many also come from the environmental organisms, especially soil microorganisms, which have been exposed to various antibiotics throughout their evolutionary history. An alarming trend is the recent selection of mutants of widespread resistance genes that resulted in the broadening of the substrate range of the inactivated drugs, as in the extended-spectrum -lactamases from the common TEM -lactamase.16

Ambiguity of Fluoroquinolones14
There are three known unique mechanisms of fluoroquinolone resistance. Some types of efflux pumps can act to decrease intracellular quinolone concentration. In gram-negative bacteria, plasmid- mediated resistance genes produce proteins that can bind to DNA gyrase, protecting it from the action of quinolones. Finally, mutations at key sites in DNA gyrase or Topoisomerase IV can decrease their binding affinity to quinolones, decreasing the drug's effectiveness. Research has shown that the bacterial protein LexA may play a key role in the acquisition of bacterial mutations giving resistance to quinolones and rifampicin.

Resistant Pathogens and their Global Burden

1. Multidrug resistance Tuberculosis: About 440 000 new cases of multidrug-resistant tuberculosis (MDR-TB) emerge annually, causing at least 150 000 deaths. Extensively drugresistant tuberculosis (XDR-TB) has been reported in 64 countries to date.17 2. Staphylococcus aureus: 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 human skin of around a third of the population, it is extremely adaptable to antibiotic pressure. It was one of the earlier bacteria in which penicillin resistance was foundin 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.18-22 MRSA (methicillin-resistant Staphylococcus aureus) , first detected in Britain in 1961, is one of the most important nosocomial pathogens globally18-25 and a major cause of morbidity and mortality in high risk wards such as intensive care units.23-25 In India, the few studies there have been suggest that the prevalence of MRSA in hospitals is rising, and nationally MRSA is now thought to account for about 30% of S. aureus infections in hospital.26 Half of all S. aureus infections in the US are resistant to penicillin, methicillin, tetracycline and erythromycin, chloramphenicol, and lincosamides.21 Such strains are also resistant to disinfectants, and MRSA can act as a major source of hospital-acquired infections. .This left vancomycin as the only effective agent available at the time. However, strains with intermediate (4-8 g/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 (>16 g/ml) resistance to vancomycin, termed VRSA (Vancomycin-resistant Staphylococcus aureus) appeared in the United States in 2002.27 The emergence of pan-resistant gram-negative strains, notably those belonging to Pseudomonas aeruginosa and Acinetobacter baumanii, occurred more recently, after most major pharmaceutical companies stopped the development of new antibacterial agents.28 Hence, there are almost no agents that could be used against these strains, in which an outer membrane barrier of low permeability and an array of efficient multidrug efflux pumps are combined with multitudes of specific resistance mechanisms.18-24 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.29 Linezolid-resistance in Staphylococcus aureus was reported in 2003.29 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.18-25 The epidemiology of infections caused by MRSA is rapidly changing.24 In the past 10 years, infections caused by this organism have emerged in the community..

3. Streptococcus and Enterococcus:. Resistance of Streptococcus pneumonia 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.30 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.30 Streptococcus pneumonia is responsible for pneumonia, bacteremia, otitis media, meningitis, sinusitis, peritonitis and arthritis. Penicillin-resistant pneumonia caused by Streptococcus pneumonia (commonly known as pneumococcus), was first detected in 1967, as was penicillin-resistant gonorrhea.30,31 Multidrug-resistant Enterococcus faecalis and Enterococcus faecium are associated with nosocomial infections. [42] Among these strains, penicillin-resistant Enterococcus was seen in 1983, vancomycin-resistant Enterococcus (VRE) in 1987, and linezolid-resistant Enterococcus in the late 1990s. 32 4. Pseudomonas aeruginosa: Pseudomonas aeruginosa is a highly prevalent 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 (for example, MexABand Mex-XY) and the low permeability of the bacterial cellular envelopes.28 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.28 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. 5. Salmonella and E. coli: Escherichia coli and Salmonella come directly from contaminated food. Of the meat that is contaminated with E. coli 34, eighty percent of the bacteria are resistant to one or more drugs made; it causes bladder infections that are resistant to antibiotics (HSUS Fact Sheet). Salmonella was first found in humans in the 1970s and in some cases is resistant to as many as nine different antibiotics (HSUS Fact Sheet)33. When both bacteria are spread, serious health conditions arise. Many people are hospitalized each year after becoming infected, and some die as a result.

6. Drug Resistance Malaria: Resistance to earlier generation antimalarial medicines such as chloroquine and sulfadoxine- pyrimethamine is widespread in most malaria-endemic countries. P. falciparum becomes resistant to antimalarial drugs by acquiring resistance mutations, genetic changes that prevent these drugs from killing the parasite. A mutation in the gene encoding a protein called the chloroquine resistance transporter causes resistance to chloroquine, a specific group of mutations in the dihydrofolate reductase gene causes resistance to

pyrimethamine, and several mutations in dhps, the gene that encodes dihydropteroate synthase, are associated with resistance to sulfadoxine. Scientists have discovered that the mutations causing chloroquine and pyrimethamine resistance originated in Asia and spread into Africa (probably multiple times) in the late 1970s and mid-1980s, respectively. These Asian-derived mutations are now common throughout Africa and, consequently, it is not possible to determine how they spread across the continent.34,35

Diagnosis
Diagnostic tests are designed to determine which microbe is causing infection and to which antimicrobials the microbe might be resistant. This information would be used by a healthcare provider to choose an appropriate antimicrobial. However, current diagnostic tests often take a few days to give results. Oftentimes, healthcare providers need to make treatment decisions before the results are known. While waiting for test results, healthcare providers may prescribe a broad-spectrum antimicrobial when a more specific treatment might be better. The common practice of treating unknown infections with broad-spectrum antimicrobials is another factor in the emergence of antimicrobial resistance

Treatment of AMR
If you think you have an infection of any typebacterial, viral, or fungaltalk with your healthcare provider. Some infections will go away without medical intervention. Others will not and can become extremely serious. Ear infections are a good example: Some middle ear infections are caused by a virus and will get better without treatment. However, other middle ear infections caused by bacteria can cause perforated eardrums, or worse, if left untreated. The decision to use antimicrobials should be left to your healthcare provider. In some cases, antimicrobials will not shorten the course of the disease, but they might reduce your chance of transmitting it to others, as is the case with pertussis (whooping cough). Antibiotics cannot fight against infections caused by viruses. Antibiotics are appropriate to use when 1. There is a known bacterial infection 2. The cause of the infection is unknown. In that case, the consequences of not treating a condition could be devastating (e.g., in early meningitis). Of note, the color of your sputum (saliva) does not indicate whether you need antibiotics. For example, most cases of bronchitis are caused by viruses. Therefore, a change in sputum color does not indicate a bacterial infection.

The solution to the problem

1. Surveillance of antimicrobial resistance Surveillance of antimicrobial resistance tracks changes in microbial populations, permits the early detection of resistant strains of public health importance, and supports the prompt notification and investigation of outbreaks. Surveillance findings are needed to inform clinical therapy decisions, to guide policy recommendations, and to assess the impact of resistance containment interventions. Types of surveillance Appropriate strategies for surveillance of antimicrobial resistance should reflect identified scientific or public health objectives, resources and available technical capacity for testing, and sustainability. A combination of complementary approaches is often desirable.

Alert organism tracking: the identification, confirmation, and communication of specific organisms of great public health importance, such as vancomycin-resistant Staphylococcus aureus or extensively drug-resistant Mycobacterium tuberculosis (XDRTB). Enhanced routine surveillance: the active review, interpretation, confirmation, and investigation of results generated in the course of routine clinical care. Targeted surveys: one-time or periodic study protocols to address specific scientific or public policy needs not adequately addressed by routine diagnostic test results

2. 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 (antibiotic) 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. There is clinical evidence that topical skin preparations such as those containing tea tree oil and thyme oil may be effective in preventing transmittal of CA-MRSA. 3. Vaccination 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; for example an update Influenza vaccine is needed each year. While theoretically promising, antistaphylococcal 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.

4. Reduction of antibiotic use: The Australian Commonwealth Scientific and Industrial Research Organization (CSIRO), realizing the need for the reduction of antibiotic use, have been working on two alternatives. One alternative is to prevent diseases by adding cytokines instead of antibiotics to animal feed. These proteins are made in the animal body "naturally" after a disease and have the potential to achieve the animal growth rates traditionally sought by the use of antibiotics without the contribution of antibiotic resistance associated with the widespread non-therapeutic uses of antibiotics currently utilized in the food animal production industries. Additionally, CSIRO is working on vaccines for diseases.

5. Phage therapy:
Phage therapy is therapeutic use of lytic bacteriophages to treat pathogenic bacterial infections. This 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 Bacteriophage therapy is an important alternative to antibiotics in the current era of multidrug resistant pathogens. A review of studies showed: phages were used topically, orally or systemically in Polish and Soviet studies. The success rate found in these studies was 8095% 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.

6. Research: Possible Hope For Future

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, and the increasing prevalence of resistant bacteria. Physicians are alarmed by the prospect that effective antibiotics may not be available to treat seriously ill patients in the near future. As bacterial antibiotic resistance continues to exhaust our supply of effective antibiotics, a global public health disaster appears likely. Poor financial investment in antibiotic research has exacerbated the situation. A call to arms raised by several prestigious scientific organizations a few years ago rallied the scientific community, and now the scope of antibacterial research has broadened considerably 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.

Does Nature have an answer to AMR?

One of the possible strategies towards AMR 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 [citation needed]. 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. In research published on October 17, 2008 in Cell, a team of scientists pinpointed the place on bacteria where the antibiotic myxopyronin launches its attack, and why that attack is successful. The myxopyronin binds to and inhibits the crucial bacterial enzyme, RNA polymerase. The myxopyronin changes the structure of the switch-2 segment of the enzyme, inhibiting its function of reading and transmitting DNA code. This prevents RNA polymerase from delivering genetic information to the ribosomes, causing the bacteria to die. One of the major causes of antibiotic resistance is the decrease of effective drug concentrations at their target place, due to the increased action of ABC transporters. Since ABC transporter blockers can be used in combination with current drugs to increase their effective intracellular concentration, the possible impact of ABC transporter inhibitors is of great clinical interest. ABC transporter blockers that may be useful to increase the efficacy of current drugs have entered clinical trials and are available to be used in therapeutic regimes.

Application of AMR in Research work

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: ampicillin kanamycin tetracycline Chloramphenicol 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.

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