21st Century Challenges in Antimicrobial Therapy and Stewardship

Global Landscape of Microbial Resistance

Elsayed Aboulmagd*, Mervat A. Kassem, Alaa Abouelfetouh

Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt

Abstract

Antimicrobial agents are considered one of the most useful and successful forms of chemotherapeutics in the history of medicine. Unfortunately, resistance to such antimicrobial agents is widespread globally which represents a major challenge faced by the health authorities. Some species of microorganisms are intrinsically resistant to the effects of certain antimicrobial agents whereas the selective pressure of antimicrobials can cause others to acquire the resistance due to mutation of the target sites or horizontal gene transfer. The increased dissemination of microbes resistant to antibiotics may be caused by misuse/overuse of antibiotics, non-human use of antimicrobials or pharmaceutical manufacturing effluents. The emergence and spread of antimicrobial resistance influence many sectors in the healthcare system which will be negatively reflected on the whole community and can lead to many consequences which include high morbidity and mortality rates, loss of protection for patients and increased healthcare costs. The continuously increasing rate of antibiotic resistance to almost all traditional antimicrobial agents boosted the urgent need for the development of new non-traditional therapeutics. In addition, innovative strategies should be applied to reduce the emergence of new resistant pathogens. There are many alternative approaches and treatment options at different stages of investigation and development to combat multidrug-resistant pathogens including: development of new antibiotics, phage therapy, monoclonal antibodies, probiotics and anti-virulence factors. Because antibiotic resistance is a cross-border problem and microbes travel freely, international cooperation and coordination are required to solve such a problem. The use of antimicrobial agents should be optimized and misuse and overuse of such vital drugs should be avoided, and stewardship antibiotic programs should be implemented for the proper utilization of antibiotics. In addition, the non-human use of antimicrobial agents in agriculture and animal husbandry should be as limited as possible to reduce the unnecessary use that accelerates the development of antimicrobial resistance. In addition, global public awareness programs are urgently needed to educate everyone about the hazards and consequences of antimicrobial resistance and how such problems could be countered.

Keywords: Antimicrobial resistance, antibiotic misuse, selective pressure, gene transfer, intrinsic resistance, acquired resistance, economic cost, antimicrobial stewardship, alternative therapy, phage therapy, probiotics.

* Corresponding author Elsayed Aboulmagd: Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt; Tel: +2-03-5424642; Fax: +2-03-4873273;

E-mail: elsayed20@hotmail.com

The discovery of antibiotics in the first half of the 20th century made treating and preventing infections a real possibility, saving the lives of millions worldwide [1]. Following the discovery of penicillin, more antimicrobials joined the market and started being used in clinical practice. However, clinically relevant microorganisms soon started developing resistance to most antimicrobials, threatening once again the lives of those undergoing surgeries, organ transplantation or receiving chemotherapeutic agents [2]. In 1945, Alexander Fleming warned about the development of antimicrobial resistance (AMR) where he said It is not difficult to make microbes resistant to penicillin in the laboratory by exposing them to concentrations not sufficient to kill them, and the same thing has occasionally happened in the body. The time may come when penicillin can be bought by anyone in the shops. Because microorganisms know no boundaries, AMR is currently a global problem causing a staggering loss in lives and resources.

AMR develops when the microorganisms causing infections are no longer inhibited or killed by the agents that were effective in treating these infections. This leads to the emergence of superbugs capable of wide-spreading in the absence of competition from susceptible microorganisms already killed by exposure to the antimicrobials. These superbugs can also cause serious infections that are difficult to treat or are even untreatable [3]. Contrary to what was believed, that increased resistance can be energetically costly which limits the capacity of the resistant strain to survive in the absence of the antibiotic pressure [4], some of the super-resistant bugs are more virulent and show increased transmissibility [5]. The consequences are terrifying, with a reported annual death rate of 700000 lives in 2014. This figure is expected to increase to 10 million deaths, or one person dying every three seconds by 2050. The global economic waste is projected to amount to $100 trillion or a loss of $10,000 per person of 2016’s population by 2050 if the present spreading mechanisms remain unchecked, especially in low and middle-income countries [3].

Microbes can become resistant to antimicrobials naturally over the course of time due to genetic mutations as well as the horizontal transfer of resistance genes among different microbes [6]. As a matter of fact, the first penicillinase conferring penicillin resistance was discovered before penicillin became publicly available for use [7]. However, the extensive use of the antimicrobials in the last century and their subsequent disposal in the environment selected for antimicrobial- resistant microbes in a manner that far outweighed the effect of natural selection for survival purposes [6, 7]. A review of the available annotated bacterial genome sequences suggests the presence of over 20000 potential resistance genes [5]. Only a fraction of these genes is currently associated with resistance phenotypes [6].

GLOBAL NATURE OF AMR PROBLEM

It would be naive to presume that the problem of AMR is restricted to those regions of the world where resistance levels are high or that the problem can be contained. That is for the simple reason that travelers to regions with high AMR prevalence can return home colonized with a superbug. Moreover, resistant strains can be carried on the body of an aircraft or transported goods, crossing the borders between high risk and lower risk regions [8].

AMR has recently been reported in 500,000 patients from 22 countries [9], with children up to 12 months of age and the elderly being more vulnerable to resistant infections, and men being more susceptible than women [10]. The rates and trends of resistance are different between countries. Among the Organization for Economic Co-operation and Development (OECD) countries, resistance grew from 14% in 2005 to 17% in 2015 for eight high-priority antibiotic-bacterium combinations, with Turkey, Greece and Korea showing seven times higher average resistance rates (35%) than Iceland, Netherlands and Norway (5%) (Fig. 1). Resistance to second and third-line antibiotics is expected to increase in 2030 by 70% relative to 2005 in OECD countries. In low and middle- income countries such as Brazil, Indonesia and Russia, resistance rates are between 40% and 60%, which is far greater than the average rate of 17% encountered among OECD countries. These high levels are projected to grow from four to seven times higher than OECD countries by 2050 [10].

Gram-negative bacteria pose the highest threat, following the development of resistance to carbapenems [1]. In developing countries, neonatal infections due to E. coli and Klebsiella spp. were found to be highly resistant to the WHO recommended regimens of gentamicin and ampicillin, with percentages as high as 71% resistance to gentamicin among Klebsiella spp. and 50% among E. coli [11]. Ampicillin resistance levels were higher, at 60-70% among E. coli and 100% among Klebsiella spp [12]. The spread of extended-spectrum β-lactamase producing Enterobacteriaceae strains made the use of cephalosporins to treat such infections impractical, shifting the medical attention towards carbapenem prescription as first-line drugs for cases of sepsis [13, 14]. However, carbapenem resistance among Enterobacteriaceae (CRE) due to the presence of β-lactamases [e.g. New Delhi metallo-β-lactamase (NDM) or extended spectrum β-lactamase (ESBL) and/or carbapenemases (e.g. Klebsiella pneumoniae carbapenemase (KPC)] has been increasingly reported worldwide [6, 15].

Fig. (1))

Average resistance proportions for eight priority antibiotic-bacterium combinations in 2015 [10].

In the USA, the prevalence of CRE, mostly Klebsiella spp., increased from 0% to 1.4% between 2001 and 2010 [16]. In Europe, the European Antimicrobial Resistance Surveillance Network reported rare carbapenem resistance among E. coli isolates, yet it was above 10% among Klebsiella pneumoniae and even higher among Acinetobacter baumannii and Pseudomonas aeruginosa [17]. The development of pan resistance among A. baumannii isolates decreased their susceptibility towards carbapenems making the management of such infections notably worrisome [14]. Carbapenem resistance among A. baumannii, P. aeruginosa and Enterobacteriaceae marks them as pathogens of critical priority on the WHO list of targets for the discovery of new antibiotics [18].

In the developed world, newer antibiotics and stricter infection control regimens are used to fight infections due to gram-positive bacteria. The prevalence of bacteremia due to methicillin-resistant Staphylococcus aureus (MRSA), figuring as a high priority pathogen on the WHO list [18], is decreasing between 2014 and 2017 in close to one-third of European countries, yet it remained higher than 25% in 30% of the countries mainly in central and southern Europe in 2017 [17]. The rates of decline were higher in the USA between 2005 and 2011, where a study in nine metropolitan areas reported a decrease in the adjusted national incidence rates of invasive MRSA infections by 54.2% among hospital-onset infections, 27.7% among healthcare-associated community-onset infections and by 5% among community-associated infections [19]. Nevertheless, community-associated MRSA infections seem to pose less of a threat in Europe than they do in the USA [20]; however, high nasal carriage and infection rates have been reported among humans who have contact with livestock, particularly pigs in many European countries, suggesting a role for pigs as a reservoir for MRSA transmission to humans [21-23].

On the other hand, in Africa and Asia, the prevalence rates were generally higher and the figures were derived from individual studies rather than national surveillance systems. A study conducted in eight Asian countries showed that the highest rates of hospital-associated S. aureus infections due to MRSA were reported in Sri Lanka at 86.5% and the lowest rate was 22.6% in India, with an average of 67.4%. The rates were lower in community-associated infections with an average of 25.5% and the highest rate of 38.8% again in Sri Lanka and the lowest rate of 2.5% in Thailand (Fig. 2) [24]. In most African countries, MRSA prevalence was below 50% but seemed to be increasing between 2000 and 2011 [25], except in South Africa that showed a decreasing trend from 36% in 2006 [26] to 24% between 2007 and 2011 [27]. The prevalence was lowest in Madagascar 6% between 2001 and 2005 [28], and highest in Ethiopia (55%) in 2006 [29] and Egypt (52%) then Algeria (45%) between 2003 and 2005 [30]. In Botswana, the prevalence varied between 23% and 44% between 2000 and 2007 [31, 32], and in Tunisia it increased from 16 to 41% between 2002 and 2007 [25] (Fig. 3).

The full extent of the global problem is not completely understood. In 2015, the WHO launched the Global Antimicrobial Resistance Surveillance System (GLASS) to standardize AMR surveillance worldwide. The system liaises with national and regional surveillance systems to gather data about enrolled countries, regarding their surveillance programs and AMR data on Acinetobacter spp., E. coli, K. pneumoniae, Neisseria gonorrhoeae, Salmonella spp., Shigella spp., S. aureus and Streptococcus pneumoniae, all of which figure on the WHO list of high-risk pathogens [18, 33]. These pathogens cause infections that are increasingly becoming antibiotic-resistant, necessitating the use of last resort agents which are sometimes less effective, more dangerous and not always available, especially in low resource settings, putting additional strain on healthcare budgets [33]. The system also incorporates data from other surveillance systems that can impact AMR in humans such as those monitoring antimicrobial consumption and resistance in the food chain in a One Health approach [34]. GLASS is expected to help estimate the real disease burden of bacterial infections, and to use evidence-based data to advise policymakers on the treatment and control measures and to evaluate the effectiveness of these measures to avoid the spread of resistance [33]. The system doesn’t monitor TB, HIV or malaria for which WHO already has well-established monitoring systems that have been generating data for years [9].

Fig. (2))

Prevalence of MRSA among S. aureus isolates from community-associated (CA) and hospital-associated (HA) infections in Asia [24].

A total of 25 (48%) high-income, 20 (38%) middle-income and 7 (14%) low-income countries are enrolled in the GLASS system as of 2018 [9]. The first GLASS report, released in January 2018, included national surveillance data from 40 countries, whereas 22 countries reported their levels of antibiotic resistance in 2016 [9, 33]. The quality of data and state of completeness of data reporting differ between countries, as many countries are still challenged regarding their infrastructure capacity and fund availability. However, the pathogens reported the most as being antibiotic-resistant are E. coli, K. pneumoniae, S. aureus, S. pneumoniae then Salmonella spp. Between zero and 82% of the isolates suspected of causing bloodstream infections were resistant to at least one of the antibiotics recommended to treat such infections. Resistance to ciprofloxacin ranged between 8% and 65% among E. coli causing urinary tract infection in reporting countries [9].

Fig. (3))

Prevalence of MRSA in Africa [25].

CAUSES OF AMR

Antibiotic Misuse as a Driver of Resistance

A number of factors have been associated with the increase in worldwide resistance. These include the increase in surgical operations, the world geriatric population, the substandard levels of sanitation and infection control in hospitals in developing countries and the low cost of older antibiotics which made antibiotics an open-access resource that is often abused [1, 6, 35]. Irrational prescription and the lack of regulations governing over-the-counter sales of antibiotics in many low and middle-income countries are further aggravating the problem, with patients having access to antibiotics even without a prescription, leading to misuse, including overuse and sometimes underuse [2, 6].

Inappropriate antibiotic use takes different forms, including antibiotics taken for the wrong indication, such as when antibiotics are prescribed, whether under patient pressure or otherwise, or in many cases self-administered to treat viral infections or self-limited diseases [36, 37]. It is estimated that up to 50% of the antibiotics are prescribed inappropriately, including the wrong antibiotic choice, incorrect dosing or wrong duration of treatment [38], which could be linked to limited diagnosing capabilities, especially in developing countries [39]. Moreover, self-medication, especially in developing countries, is very concerning as it may lead to unsuccessful therapy due to similar reasons [40]. Another form of antibiotic misuse is represented by the failure of the patients to comply with the antibiotic regimen, manifesting as dose missing or stopping the antibiotic prematurely when the patient starts to feel better or can’t tolerate the side effects [39, 41]. In most of these cases, the use of the wrong antimicrobial agent or the wrong dose exposes the bugs to concentrations of antimicrobials insufficient to kill them, which promotes resistance development [36].

Misuse can also take the form of or lead to the overuse of antimicrobials. A direct relationship and strong correlation exist between antibiotic consumption and the prevalence of antibiotic resistance [42]. In the case of P. aeruginosa, an important nosocomial pathogen that endangers the lives of cystic fibrosis patients, the lengthy antibiotic use has been linked to the development of antibiotic resistance [6, 43].

The world human consumption of antibiotics increased by 36% between 2000 and 2010, three- quarters of this increase occurred in Brazil, Russia, India, China and South Africa (BRICS) [44]. India’s retail sales volume represented 23% of BRICS’ volume, probably owing to the under-regulation of the over-the-counter sale of antibiotics in India [45]. Moreover, China was responsible for 57% of the increase in antibiotic sales in the hospitals among BRICS countries, which could be explained by the dependence of some hospitals on pharmaceutical sales to increase their revenue [45, 46]. Another factor expanding antibiotic consumption in some developing countries is poor to no antibiotic sales/use regulations, allowing antibiotic purchase without medical prescription and sometimes even through unregulated supply chains [47]. This phenomenon is compounded by the economic growth and prosperity in the above-mentioned countries [45] and in high-income countries, patients sometimes put pressure on physicians to prescribe an antibiotic conforming to what patients consider the norm [48]. Moreover, the use of poor quality and/or counterfeit antimicrobials, especially in low and middle-income countries, has dire consequences for communities and healthcare settings. The presence of low concentrations of the active pharmaceutical ingredients in the falsified medicines will expose the pathogens to sub-lethal antimicrobial concentrations that may lead to the evolution of an MDR mutant [49]. The consumption of two last-resort antibiotics: carbapenems and polymyxin was notably high at 45% and 13%, respectively, together with broad-spectrum cephalosporins, broad-spectrum penicillins and fluoroquinolones [45]. However high the rates of antibiotic consumption are, access to antibiotics isn’t equitable, with many patients in rural and resource-poor areas lacking proper access to the antibiotics they need, which results in more deaths than those caused by antibiotic resistant infections [1, 3, 50].

The rising consumption of antibiotics in humans and animals together with the high levels of antibiotic waste polluting the environment drive resistance development [51-53]. This occurs through the killing of the susceptible clones, selecting for resistant mutants that thrive and dominate the population, a good example of the Darwinian notion of selection and survival [6, 51]. The use of broad-spectrum antibiotics may exacerbate the problem by selecting for multidrug-resistant strains [51]. This is hardly surprising regarding that half of the antimicrobials used in human healthcare and even higher levels among livestock in countries that are members of OECD are inappropriate [54]. This occurs mostly when patients receive antibiotics to treat viral infections or for self-limited conditions [36, 37]. Moreover, the prolonged use of antibiotics, in particular broad-spectrum ones, can lead to the death of susceptible normal intestinal microbiota allowing the super-growth of hard to treat Clostridium difficile [55]. The incidence of such infections was 453000 cases in 2011 in the USA alone, with a mortality rate of about 6.4% [56].

Use of Sub-therapeutic Concentrations of Antibiotics in Animals as Growth Promoters

Animal husbandry is another area where antibiotics are massively used as growth promoters in sub-therapeutic concentrations as well as for disease prevention, especially when the animals are kept in poor conditions. Livestock consumes about 70% of the antibiotics that are medically important for humans in the USA and about 50% in other countries around the world [57]. In the USA, about three-quarters of these antibiotics are also used to treat human pathogens and about half of the remaining agents are structurally similar to human antibiotics [58, 59]. The consumption of antibiotics in animals by 2030 is expected to increase by 67% globally and to nearly double in BRICS countries [60]. In India, it is expected to increase by 312% to meet the growing demands for meat and animal products for human consumption as a result of rising incomes in China and Southeast Asia [60]. The use of antibiotics in sub-therapeutic concentrations in agriculture has been linked to the increase in the prevalence of antibiotic resistance genes [61]. The benefit of using antibiotics as growth promoters is questionable in modern farming and tends to vary with the age, species and lineage of the animal as well as the sanitary and management conditions [62]. Consequently, the European Union has already forbidden the use of antibiotics as growth promoters, and in the USA, the FDA is taking action to limit the use of sub-therapeutic doses of medically important antibiotics in livestock [57].

Antibiotics as Environmental Waste

Another contributor to the problem is the way the factories manufacturing the Active Pharmaceutical Ingredients (API) of antibiotics dispose of their waste [57]. There are few to no standards governing the disposal of API effluent around the world [63]. China and India are examples where a significant amount of APIs are being manufactured. This may be due to lower production cost which is generally a reflection of more relaxed standards [57, 64]. It is estimated that more than 50% of the antibiotics produced in China are released in the rivers [65]. The situation is disconcerting, especially that ciprofloxacin concentration in an Indian river where 90 manufacturers of APIs disposed of their effluent was 1000 fold higher than the concentration toxic to bacteria and was greater than the expected serum concentration in patients taking ciprofloxacin [66, 67]. Even when the effluent was treated, in some cases the level of antibiotic was still considerably high following treatment [68]. Such environments laden with antibiotics or their APIs can act as reservoirs for resistance genes [52, 53]. Moreover, insufficient treatment of water released from other sources, such as livestock, agriculture and healthcare settings, etc. compounds the problem, posing a considerable environmental risk and impacting different ecosystems [69]. Regarding the current lack of binding regulations of waste disposal in many countries, efforts are being made to determine the levels of antibiotics in waste that would drive resistance development [70].

Selective Pressure, Gene Transfer and Mutation

In addition to selective pressure induced and encouraged by frequent or irrational administration of antibiotics, both horizontal transfer of the genes encoding antibiotic resistance by transferring plasmids and vertical transfer by mutation of the target sites of the different antimicrobial agents play an essential role in the evolution and spread of microbial resistance [71]. Moreover, the administration of an antibiotic may not only select for resistance to such a drug but also to other antimicrobials of the same class which are structurally related.

TYPES AND MECHANISMS OF AMR

Some microorganisms are intrinsically resistant to the action of certain antimicrobials, whereas others become tolerant to previously inhibitory concentrations of antimicrobials, the former is referred to as intrinsic resistance and the latter as acquired resistance [72].

Intrinsic Resistance

Intrinsic resistance occurs as a result of inherent, and mostly chromosomally mediated, particular traits in the microorganism that make them unresponsive to the action of the antimicrobial. These characteristics include: (1) reduced affinity or lack of target site as exemplified in the insensitivity of Mycoplasma devoid of cell wall to the action of the β-lactams, (2) production of inactivating enzymes such as the β-lactamases produced by some gram-negative bacteria to hydrolyze β-lactams or the enzymes that alter the structure of the antibiotic to prevent its binding to the target such as aminoglycoside acetyltransferases, (3) decreased permeability seen in vancomycin resistance among members of the Enterobacteriaceae as a result of the outer membrane acting as a permeability barrier, and finally (4) efflux systems among gram-positive and gram-negative bacteria which together with decreased permeability result in reduced drug uptake [72-76]. Overexpression of some efflux pumps can render previously susceptible bacteria resistant to clinically useful antibiotics [77, 78]. Some efflux pumps have narrow substrate specificity (for example, the tetracycline pumps), but many transport a wide range of structurally dissimilar substrates and are known as multidrug resistance (MDR) efflux pumps [79]. Some of these mechanisms can also be disseminated to susceptible microorganisms through horizontal gene transfer rendering them MDR as well. Table 1 shows some selected intrinsic resistance mechanisms. Another form of phenotypic resistance is provided by the persister cells. These are cells that represent 10-6 to 10-4 of the population and that survive antimicrobial chemotherapy [80]. They are especially important in a biofilm setting, where, following antimicrobial chemotherapy, surviving planktonic persisters are killed by the immune system, whereas biofilm persister cells encased in the extracellular matrix of the biofilm escape. Once the antimicrobial is discontinued, these cells re-establish the biofilm that sheds more planktonic cells causing a relapse of the infection [81]. The cyclical use of one, and preferably two different antimicrobials, has been suggested to treat such infections. The first application of the antimicrobial is meant to kill the majority of the population, leaving the persisters to grow and potentially lose the persister phenotype allowing for eradication when the second antimicrobial is applied [82].

Table 1 Selected examples of intrinsic resistance mechanisms [74].

Acquired Resistance

For most known classes of antimicrobials, their use in clinical practice predisposed for the development of resistance. The length of time it takes for resistance to develop is a factor of the complexity of the acquired resistance mechanism [72, 83]. For penicillin, it took a couple of years for resistance to develop as a result of the product of one gene, whereas for vancomycin it took the enterococci 29 years to acquire the five genes required for high-level vancomycin resistance [72, 84, 85].

Acquired resistance can be either the result of mutations in chromosomal genes or the acquisition of foreign DNA coding for antibiotic resistance genes, often obtained from intrinsically resistant organisms present in the environment through horizontal gene transfer (HGT) [86, 87]. Such changes in the bacterial genome may alter the nature of proteins expressed by the organism and consequently the structural and functional features of the bacteria leading to resistance against a particular antibiotic [88]. Table 2 shows some selected acquired resistance mechanisms.

Bacterial cells can mutate their genes, at a mutation rate of 1 in 10⁷. Some strains are hypermutable (mutators) with a mutation rate that is up to 1000 fold higher than in normal cells, mainly due to defects in DNA repair and proofreading mechanisms [89, 90]. A notable example is P. aeruginosa isolated from cystic fibrosis patients where mutators can represent 20% of the population [91]. When such mutations confer resistance to a particular antibiotic and in the presence of selective pressure due to the exposure to such antibiotics, all susceptible cells are killed allowing the resistant ones to thrive and dominate the population. Resistance development following exposure to sub-therapeutic concentrations of an antibiotic is an illustrative example of the role of selective pressure in resistance development [72]. Selective pressure was also demonstrated in the transition from methicillin susceptibility to resistance among S. aureus isolated from hospitalized patients postoperatively, due to mutation in the PBPs [92, 93]. Quinolone resistance in E. coli can be caused by point mutations in the gyrA gene or the parC gene leading to changes in at least seven and three amino acids, respectively. On the other hand, a single point mutation in the rpoB gene is associated with complete resistance to rifampin [94]. Mutations within the coding sequences of the porin channels in the outer membrane of gram-negative bacteria possibly reduce the permeation rates of bulky drug molecules without affecting those of smaller nutrient molecules. Clinically important bacterial pathogens like Serratia marcescens, Salmonella enterica, K. pneumonia and P. aeruginosa, have utilized this reduced drug uptake system to resist important antimicrobial agents, such as the β-lactams, fluoroquinolones, aminoglycosides, as well as chloramphenicol [95]. In prokaryotic genomes, mutations also frequently occur due to base changes caused by exogenous agents, DNA polymerase errors, deletions, insertions and duplications. Moreover, a mutation increases the prevalence of genetic recombination, providing diversity to antibiotic resistance mechanisms [96, 97].

Table 2 Selected examples of acquired resistance mechanisms [72].

Acquisition of foreign DNA material through HGT is one of the most important drivers of bacterial evolution and it is frequently responsible for the development of AMR. Methicillin resistance among S. aureus can occur when the pathogen acquires mecA encoding PBP2’ or PBP2a that has a lower affinity towards the β-lactams [92, 93, 98]. Bacteria acquire external genetic material through three main strategies: transformation, transduction and conjugation.

Transformation is the uptake of short fragments of naked DNA by naturally transformable bacteria. This DNA is normally present in the external environment due to the death and lysis of another bacterium. Transformation is perhaps the simplest type of HGT. Bacteria capable of taking up DNA from the environment are termed competent. Some microorganisms, such as many streptococci and A. baumannii, are competent at a specific stage in their growth [99, 100].

Transduction involves the transfer of DNA from one bacterium into another via bacteriophages. In this case, the phage particles are packaged with bacterial DNA instead of phage. Although it is uncommon, there have been examples of antibiotic resistance genes, and even entire mobile genetic elements, being mobilized by transduction [101].

Conjugation is considered the main mechanism of HGT, it involves the transfer of DNA via sexual pilus and requires cell-to-cell contact. DNA fragments that contain resistance genes from resistant donors can then make previously susceptible bacteria express resistance as coded by the newly acquired resistance genes. This mechanism of transfer permits genetic exchange between many different bacterial genera [102]. The emergence of resistance in the hospital environment often involves conjugation and is likely to occur at high rates in the gastrointestinal tract of humans under antibiotic treatment. As a rule, conjugation uses mobile genetic elements as vehicles to share valuable genetic information, although direct transfer from chromosome to chromosome has also been well characterized [103]. The most important mobile genetic elements are plasmids that mediate the lion’s share of resistance, transposons and integrons [104, 105].

Multidrug Resistance Caused by Altered Physiological States

The antibiotic susceptibility of bacterial cells is also affected by their physiological states. Even high concentrations of antibiotics do not kill all of the bacterial population, leaving behind a persister population that is genetically identical to the susceptible cells. The presence of persisters is one of the mechanisms explaining the increased resistance of biofilms to antibiotics [106]. The presence of persisters is now thought to be an example of the strategy whereby bacteria naturally generate mixtures of phenotypically different populations so that one of them can be advantageous to a changing environmental demand [107].

CONSEQUENCES OF AMR

Treatment Failure and Loss of Activity

A direct consequence of AMR development is that antimicrobial agents lose their activity towards microbes. A case in point is gonorrhea that was treatable by penicillin till the 1980s when Neisseria gonorrhea developed resistance to both penicillin and tetracycline, then to quinolones in the mid-2000s, necessitating the use of third-generation cephalosporins to which the bacterium is currently developing resistance [108, 109].

High Morbidity and Mortality and Ensuing Economic Cost

AMR can seriously compromise the health and life of many patients [1], mainly because of the initial use of antimicrobials to which the infectious agent is resistant and the resulting delay in starting the right therapy [110, 111]. This burden is often borne by low and middle-income countries where patients can’t afford to use more expensive second and third-line drugs when treatment fails as a result of the infectious agent becoming resistant to the action of first-line antimicrobials [45]. AMR can also lead to the inability to carry out surgical procedures in the elderly and other vulnerable populations because of the high risk of untreatable infections, once more raising morbidity and mortality rates [1]. It is expected that AMR will become one of the leading causes of death by the year 2050 [3, 112].

A measure of increasing morbidity is the lengthier hospital stay and need for intensive care for patients suffering from infections due to resistant bugs [113, 114]. This amounts to 1.29 fold increase in the length of hospital stay in case of MRSA bacteremia [115], 2.6 fold in case of extended spectrum beta-lactamase producing strains of K. pneumoniae and 1.7 fold in case of carbapenem-resistant P. aeruginosa [116], and an added cost of $10,000 to $40,000 to treat such infections [117, 118], attributable to patient isolation with extra measures for infection control, prolonged treatment and laboratory testing and more expensive antibiotics [119]. In addition, AMR increased the risk of death by 1.2 in the case of pneumonia and bloodstream infections [120]. In neonates, the increased risk of death is even higher and can reach as high as twice the risk in infections with susceptible strains [121]. In Europe alone, it is estimated that complications associated with antibiotic resistance cost €9 billion annually [122]. In the USA, AMR costs about $20 billion and $35 billion for excess direct healthcare costs and loss of productivity due to infection, respectively [123]. On a global scale, the lost productivity associated with AMR infections is projected to be 2% to 3.5% and to amount to a cumulative $100 trillion by 2050 [3, 112].

HOW TO MITIGATE THE AMR PROBLEM?

Due to the dryness of new antimicrobials’ pipelines, containment and prevention of antibiotic resistance should be a major priority. Since human health is directly connected to the environment and animal health, and due to the strong relationship between the development of antibiotic resistance and using of antibiotics in agriculture, any containment program should adopt a One Health approach [38, 124].

Surveillance and Antimicrobial Stewardship

The size, severity and widespread nature of AMR make it imperative to find solutions to curb its spread. Seeing as antibiotic misuse/overuse is at the root of the problem, antibiotic use needs to be regulated, especially in those countries where people can purchase an antibiotic even without a prescription. As a first step, there is an immediate need for robust surveillance and tracking systems to monitor the extent of antibiotic use on local and global levels. WHO launched the GLASS system in 2015 to achieve this goal and published its first report in 2018 with updates to follow regularly (Fig. 4) [33]. This requires the commitment of policymakers to put in place and enforce antimicrobial stewardship to prevent the unnecessary and often excessive use of antibiotics in humans [125]. Another measure to extend the life span of antimicrobials is to restrict or control the use of certain agents, especially last resort ones and/or to rotate the use of antimicrobials [126]. In this respect, the use of information and communication technology in the form of e-health can help prescribers make the proper antibiotic choice and decide on the right dose and duration [127]. In line with antimicrobial stewardship measures, there is a need to restrict the use of antibiotics in agriculture and animal husbandry as growth promoters or to prevent infections rather than to treat actual ones and to shift to agents not medically important for humans [3].

These measures need the national commitment of local health authorities to devise national action plans, and because microbes know no borders international cooperation is also needed to bring about the successful implementation of such plans. WHO is already coordinating such efforts on regional and global levels [3, 128]. All action plans require a multi-sectoral One Health approach involving humans, animals, and environmental health [124]. The aim of the plan is to ensure ongoing successful treatment via the preservation of the usefulness of the existing antimicrobial agents and the effective prevention of infections caused by multi-resistant pathogens. As of May 2017, one-third of the WHO member states had already developed their action plans to tackle AMR with another third working on theirs [129]. To achieve these goals, it is important to improve awareness of AMR and to reduce the incidence of infection [128]. Raising awareness can occur via campaigns to educate the general public on the risks of antibiotic misuse and ensuing resistance. These campaigns can also reduce patients’ pressure on prescribers to prescribe antibiotics even when they are not called for as in the treatment of viral infections like the common cold [37].

Fig. (4))

Distribution of countries enrolled in the GLASS system (2018) [33].

Reducing the incidence of infection by improving hygiene and sanitation, the application of stricter infection control measures in healthcare settings and efficient vaccination programs will undoubtedly decrease the need for antimicrobial agents [3]. To help reduce antibiotic overuse, an improvement in diagnostics is called for to expedite antibiotic sensitivity testing and to properly and rapidly identify resistant bacteria. This has the potential to help physicians stop prescribing antibiotics just in case one is needed when the diagnostics are not available or are too expensive to afford in some resource-limited settings [3].

Chemical Modifications and Discovery of New Antibiotics

The discovery of penicillin in 1928 started a golden age of antibiotic discovery that lasted till the 1960s, with enough new agents still being discovered till the 1980s to overcome the ever occurring problem of antibiotic resistance [130, 131]. However, since the 1980s and with the exception of some new drug discoveries between 2011 and 2016 [37, 132], the interest of the pharmaceutical companies to discover new entities has waned [130], and very few agents have been approved for the treatment of infectious diseases [133]. A potential hypothesis is that pharmaceutical companies acquire large financial incentives from the increased demand on their agents when they become last resort options due to pathogens acquiring resistance to most other agents. By this time the last resort antibiotic might be already out of patent protection or close to being so which limits the incentive to invest in newer agents. In addition, because antibiotics are used for relatively short periods due to the rapid development of MDR pathogens, investment in the development of new antimicrobial agents is no longer profitable. There is an urgent need to amend this situation. Governments are encouraged to invest in research and development of new antimicrobials, to reward such innovative discoveries while limiting the unnecessary use of antibiotics to preserve the newly discovered ones. This requires cumulative global efforts with the United Nations and the G20 (Group of Twenty) taking active roles to ensure the success of such initiatives. A market entry reward of about one billion USD is suggested to celebrate the successful introduction in the market of new drugs, this is to ensure that these antimicrobials can be made available to anyone who needs them regardless of whether they come from a high or limited resource country. It is also to ensure that the new drugs won’t be over-marketed or overpriced to cover the expenses that went into drug discovery and still make them profitable. This is especially true considering that the total profit from sales of patented antibiotics is 4.7 billion USD annually which is equivalent to one top-selling anticancer drug, reducing the attractiveness to pharmaceutical companies to invest in antimicrobials. However, to make the market entry reward initiative successful, governments must review and adjust their purchasing and distribution systems [3].

The majority of the new agents target gram-positive bacteria, leaving the resistant gram-negative pathogens that figure as a critical priority on the WHO list of priority pathogens with few effective treatment options. The complex nature of the cell wall of gram-negative bacteria makes it especially difficult to find new agents that can permeate the cell wall and stay inside [131]. Most of the new agents in the clinical pipelines are modifications of older agents with a narrow therapeutic spectrum against one or a few specific pathogens and aim to overcome resistance problems [131]. As of May 2017, only 51 antibiotics, including combinations, and 11 biologicals, mainly monoclonal antibodies and endolysins to be used as adjuncts to antibiotic therapy, are in the different phases of the clinical pipeline, with 16 targeting critical priority pathogens, including carbapenem-resistant A. baumannii, carbapenem-resistant P. aeruginosa and carbapenem-resistant Enterobacteriaceae. Of the 16, three are considered innovative and only one is developed for oral formulation. Oral preparations are especially needed in low resource countries for the treatment of infections in outpatients. Also of the 16 agents, five agents are in phase 3, one in phase 2 and ten in phase 1. With the potential of 14% of the agents in phase 1 to be approved for use in clinical practice, only one to two agents out of these ten are expected to reach the market. The narrow spectrum of action of these agents makes it hard to use them for the empirical treatment of severe infections during that window of time before the antimicrobial susceptibility results become available and where the choice of the right antibiotic could prove life-saving [131]. Because of the challenges that face the discovery of new antimicrobial agents and the huge investment and long period needed to sponsor such discoveries, it is paramount to maintain the efficacy of the already present antimicrobial agents through the development of new combination therapies [134-136]. A cocktail of antibiotics is nowadays recommended for the treatment of TB to decrease resistance development. However, for a variety of reasons, strains of Mycobacterium tuberculosis resistant to four or more agents have occurred to the extent that there are now strains that are totally drug resistant [137-139].

Alternative Approaches to Treat Resistant Infections

Nowadays, there are many alternative approaches and treatment options at different stages of investigation and development to combat different bacterial infections caused by MDR pathogens [140, 141].

Virulence factors are a group of molecules and structures that enable microorganisms to initiate and establish microbial infections and diseases. Drugs with anti-virulence potential are considered attractive candidate drugs to control MDR pathogens. These anti-virulence drugs can interfere with vital processes essential for microbial pathogenesis such as adherence, invasion, colonization, biofilm formation, intracellular replication, damage of host tissues and evasion of host immune system [142].

Quorum sensing inhibition is another potential approach for combating bacterial pathogens by disrupting the communication between bacterial cells [39, 143]. Inhibition of quorum sensing doesn’t kill the bacterial cells, resulting in no selective pressure and hence the rate of emergence of microbial resistance will be low [143].

Vaccines are used primarily as a prophylactic tool to prevent infectious diseases, reduce the severity of the disease and raise the threshold load of pathogenic microorganisms required for induction of infection. The development of new vaccines to different pathogens could play an important role in limiting the spread of microbial resistance by reducing and preventing the need for antimicrobial agents [144, 145].

Bacteriophages and phage lytic proteins are emerging as potentially attractive non-conventional therapeutic agents to eradicate resistant bacteria and combat the development of newly arising multidrug-resistant pathogens [146, 147]. They are safe, highly specific thus minimizing the chance of secondary infections, able to effectively eradicate bacterial biofilm and environmentally friendly [147]. In addition, phage-antibiotic combinations showed promising and significant synergistic activity against different resistant pathogens [40, 147-149].

Probiotics are living good microorganisms that have many benefits for human health. They minimize, either alone or in combination with antibiotics, the risk of different bacterial infections and the need for antibiotics. Therefore, probiotics reduce the emergence and spread of antibiotic resistance [150]. Moreover, there are currently many other alternative approaches at different research levels such as monoclonal antibodies [142], antimicrobial peptides [143], immune stimulants [144], antibiofilms [145] and new antibiotic combinations [146]. The possible side effects and limitations of such alternative therapies are depicted in Table 3.

Table 3 Side effects and/or limitations of alternative therapies against multidrug-resistant pathogens.

CONCLUSION

Antimicrobial resistance is a global problem that jeopardizes the achievements of modern medicine and is a harbinger to the return to a time when simple infections were fatal. Injudicious antibiotic use in human healthcare as well as animal husbandry, together with the slowdown in the discovery of new antimicrobials are at the root of the problem. Regulating antimicrobial use and encouraging the discovery of novel agents and alternative therapies seem the way forward to win the human fight against pathogenic microbes.

CONSENT FOR PUBLICATION

Not applicable.

CONFLICT OF INTEREST

The authors confirm that the contents of this chapter have no conflict of interest.

ACKNOWLEDGEMENTS

Declared none.

REFERENCES