Antimicrobial Resistance: A Review

Kevin O’Malley UCD School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland



Antimicrobial resistance (AMR) poses an unprecedented and growing threat to modern medical practice. The implications of resistance are profound given that our ability to prevent, manage, and treat infection underscores most advances across the spectrum of healthcare disciplines in recent years. It has been suggested that ABR may surpass cancer as the leading cause of death worldwide within the first half of this century. Economist Jim O’Neill (Chairman of the UK Review on Antimicrobial Resistance) estimates that by 2050, unless radical action is taken, AMR may be responsible for up to 10 million deaths per year1. This paper seeks to provide a brief overview of antimicrobial resistance. Mechanisms of resistance are outlined alongside a number of factors identified as contributing to growing rates of AMR. Recent efforts to promote research and development of new antimicrobials are described, alternative and complementary therapies are examined, and recommendations are proposed.




Antimicrobial resistance (AMR)  

Mechanisms underlying resistance

Bacterial resistance to antimicrobials can occur via numerous mechanisms, either intrinsic or acquired. The most common example of an intrinsic resistance mechanism is the relatively impermeable outer membrane of Gram-negative bacteria, which reduces its susceptibility to many classes of antimicrobials. Chromosomally-encoded efflux pumps which transport and expel toxic antimicrobial molecules are another example [2].

Bacterial resistance can also be “acquired” via the transfer of plasmids or other mobile genetic elements. Resistance genes can be transferred in a number of ways, the most common of which are conjugation, transduction, and transformation3. Conjugation requires cell-to-cell contact and involves the transfer of plasmids to a recipient cell via pilli. Transduction involves the transfer of bacterial DNA from one cell to another of the same species via plasmids enclosed in bacteriophages. Transformation involves the uptake and integration of naked DNA from the environment by bacteria [3].

Finally, microorganisms may become resistant due to spontaneous chromosomal mutation.

Contributing factors

In the context of healthcare settings, many factors contribute to the development of antimicrobial resistance, including empiric treatment with broad-spectrum agents, inappropriate use of antimicrobials (e.g., in cases of viral illness), inappropriate duration of treatment, and patient non-adherence or failure to complete full course of treatment1. In countries with less regulation, the availability of antimicrobials without prescription exacerbates these issues, particularly in terms of overuse. In addition, the non-therapeutic use of antimicrobials in animals poses significant risks [4].

WHO Antimicrobial Resistance, Global Report on Surveillance (2014)

Following a rise in the incidence of infections caused by multidrug resistant organisms, global surveillance of resistant bacteria has come to the fore in the last decade. In their 2014 report on AMR surveillance, the World Health Organisation highlighted seven “bacteria of international concern”. These included Escherichia coli (resistant to third-generation cephalosporins and fluoroquinolones), Klebsiella pneumoniae (resistant to third-generation cephalosporins and carbapenems) and Staphylococcus aureus (resistant to methicillin) [5]. Of particular concern are findings that the proportion of these resistant strains exceeded 50% in certain WHO regions.

Reports from the Irish Health Protection Surveillance Centre (HPSC) show a promising decline in rates of methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infection in Ireland over the past decade following a concerted effort on the part of healthcare authorities. Of 1412 cases of S. aureusbloodstream infection reported in 2006, 592 (41.9%) were found to be resistant to methicillin. In 2015, just 199 (18.4%) of 1082 reported cases of S. aureus bloodstream infection were resistant to methicillin. In terms of proportion of MRSA versus MSSA (methicillin-susceptible S. aureus), this was a decrease of over 66% during this period [6].

In contrast, 16.7% of E. coli bloodstream isolates reported in Ireland in the first quarter of 2016 were classified as multi-drug resistant (MDR) [7]. The proportion found to be producers of Extended Spectrum Beta Lactamase (ESBL) has risen steadily from 5.8% in 2009 to 11.7% in 2016. ESBL- producing bacteria are resistant to the majority of the beta-lactam antimicrobial agents, including penicillins and cepharlosporins. Similarly, rates of MDR Klebsiella pneumoniae rose from 11.9% of bloodstream isolates in 2009 to 19.8% in 2015.

Antimicrobial use in agriculture

Antimicrobial resistance is emerging in domains beyond hospitals and healthcare facilities, particularly in agricultural settings.

Colistin use in pig-farming

The non-therapeutic use or overuse of antimicrobials in livestock poses another cause for concern. Perhaps the most serious example is the use of the antimicrobial colistin (a polymyxin) in pig-farming, which perfectly illustrates the risks associated with such casual practice. In humans, colistin is considered to be a last line agent for the treatment of multi-drug resistant gram negative bacteria, particularly carbapenemase-producing enterobacteriaceae. The toxic effects observed in humans are not seen in pigs, however, as colistin is not absorbed in the gastrointestinal tract of pigs. As such, colistin is seen as an ideal agent to treat gastrointestinal infection in swine and is widely used in pig-farming across the globe, including many European countries such as the United Kingdom, Germany, and Belgium [4, 9].  However, problems have arisen as a result of metaphylactic use of colistin, that is, the treatment of clinically healthy pigs alongside those with symptoms. Antimicrobials are not being used in cases of infection, but rather are given (often in excessive quantities) for purposes of growth promotion and weight gain. Alarmingly, scientists recently discovered a plasmid-mediated colistin-resistance gene (mcr-1) in pigs in China [10]. Another study in China, the world’s largest producer of pigs, has reported evidence of colistin resistance in patients without a history of colistin exposure but a history of contact with swine [11].

Environmental considerations

In the environment, transmissible plasmids may transfer between species and spread through various means including wind, surface water, and soil [12]. Levels of antimicrobials found in pig manure have been found to positively correlate with the quantity of the agent used in pig farms [4].

Waste water treatment

A number of studies have documented the presence of antimicrobials and AMR genes in urban waste water, including effluent discharges from hospitals and waste water treatment facilities [13]. Studies of treatment facilities in China found that the removal of pollutants such as antimicrobials (including parent compounds and transformation products) was incomplete, leaving residual levels in the environment [14]. Another study has described the presence of various sulphonamide resistance genes in seawater and sediment from the North Yellow Sea [12].

if these vegetables were consumed raw, there is a risk that the ESBL-genes may be transferred to opportunistic bacteria in the gut

A study conducted in the west of Ireland found that ESBL-producing E. coli can survive modern waste water treatment processes and recorded high levels of ampicillin resistance in E.coli discharged from the treatment facility [15]. This study noted the potential risk to food produce irrigated with contaminated water [15]. Other studies have also highlighted similar concerns of risk to public health. A 2014 Dutch study of supermarket vegetables (celery, carrots, lettuce, mushrooms) reported high levels of bacteria containing ESBL genes on the produce examined [16]. The authors acknowledge that the bacteria found is relatively harmless. However, if these vegetables were consumed raw, there is a risk that the ESBL-genes may be transferred to opportunistic bacteria in the gut [16].

Antimicrobial research and development

Since the 1980’s, few new antimicrobials have been developed. The small number that have entered clinical use include two new classes: oxazolidinones such as linezolid, and lipopeptides such as daptomycin [3]. These are the exception however, and not the rule.

Antimicrobial development does not represent an appealing investment for most companies. Estimates suggest the cost of bringing an antimicrobial agent to market stage is as high as £1 billion, or €1.2 billion. In addition, the risk of failure associated with research and development is considerable, and notably higher than other fields [3, 17].  Moreover, when prescribed, antimicrobials are used in limited doses for short durations, which ultimately translates into low returns. It is unsurprising that pharmaceutical organisations are instead focusing their energies on the significantly more profitable market of chronic disease management and the development of “lifestyle drugs” such as statins, anti-depressants, and anti-hypertensive medications [18].

Incentivising drugs companies

In response to the dearth of activity in this sphere, and in light of growing resistance, governments are now prioritising antimicrobial research and development. In 2012, the United States introduced the Generating Antibiotic Incentives Now (GAIN) Act, an initiative to incentivise pharmaceutical companies [19]. Under this legislation, companies that develop novel antimicrobial agents that are effective against specified pathogens will benefit from priority FDA review and expedited approval of qualifying agents, as well as an additional five years of patent exclusivity in the marketplace [3]. Similar efforts can be seen with the EU Innovative Medicines Initiative which represents the largest public-private partnership in Europe. Its “New drugs 4 bad bugs” programme aims to foster collaboration between academic researchers and pharmaceutical companies [20].

iChip technology

The vast majority of antimicrobials used in practice today originated from bacteria cultured from soil. Until recently, soil was cultured directly onto culture medium. This method embodied significant limitations such that a mere 1% of bacteria present in soil were actually cultivable. Novel technology has revolutionised this practice. Isolation chips (iChips) facilitate the culture of bacteria which previously could not be grown in laboratory conditions, allowing the growth of 40-60% of bacteria present in soil [21, 22].  Using dilutions of soil, iChip achieves this by placing a single bacterium in each of a vast number ofagar-filled microchambers. The device is then placed back in the original soil environment where a semi-permeable membrane allows the diffusion of nutrients to the bacteria within the chambers. In this natural environment the bacteria colonise and are then further cultivated on growth media [21]. This development has already led to the identification of new antimicrobials such as teixobactin (effective against S. aureus, M. tuberculosis, and C. difficile), and is thought to hold significant potential for similar discoveries in the future [20].

Alternative therapeutic options

In spite of the above efforts, it is likely to be a number of years before any new antimicrobials enter the market. Other avenues which are being explored with renewed interest are therapeutic options which complement or enhance current agents. Phage therapy and nanoparticle optimisation are two such examples.

Phage therapy

it is highly specific to particular pathogens with no harmful effects on commensal flora, and exhibits significant bactericidal effects against MDR strains of bacteria [

The use of bacteriophages to target and kill bacteria is not a new concept. Bacteriophages (also referred to as “phages”) are viral entities which target only bacterial cells, penetrating the cell wall and inserting genetic material into the cytoplasm. In the case of lytic phages (also referred to as virulent phages), this material replicates exponentially once inside the bacterial cell, synthesising more phage particles before lysing the bacterium. This process facilitates very high concentrations at the infective site [23]. Chief among the advantages conferred by phage therapy is that it is highly specific to particular pathogens with no harmful effects on commensal flora, and exhibits significant bactericidal effects against MDR strains of bacteria [24]. In addition, phage therapy exhibits strong action on bacterial biofilm, particularly those of P. aeruginosa, which can be found in hospital water networks [25]. Used in combination with antimicrobials, phage therapy is extremely effective and may prove a key player in antimicrobial treatment in the future. Few trials involving humans have been conducted to date, however early indications suggest the therapy is safe. The scope to treat numerous infections with the same agent is limited by the specificity of phage therapy for individual strains of bacteria, which prevents empiric or presumptive use. Concerns have been raised, however, that phage therapy may induce antibody production in patients, thus rendering its potential obsolete [26].


Another option described in recent literature involves the use of metallic nanoparticles to enhance the bactericidal effects of antimicrobials [24]. Penetration of the bacterial membrane is facilitated by the small scale of the particles. One study outlined the biosynthesis of amoxicillin and gold nanoparticles. The conjugate agents were found to not only exhibit broad-spectrum activity against both Gram-positive and Gram-negative species, but successfully cleared MRSA infection in experimental animals [27].


In terms of what lessons can be drawn from the literature, a number of recommendations are outlined:

  • Antimicrobial stewardship should be integrated into medical education and training, to shift away from the current tendency of empiric treatment [28].
  • A concerted effort must be made to reduce demand for antimicrobials via increased public awareness, improved sanitation and hygiene, promotion of vaccination, and employment of rapid diagnostic facilities in the acute setting [1].
  • Curbing agricultural antimicrobial use via the introduction of additional antimicrobial fees (based on usage) to prevent overconsumption, revenue from which could be directed toward the cost of researching and developing newer drugs [29].
  • Restrictions should be placed on hospital effluent discharges and requirements made that waste water must be treated appropriately before being discharged into urban waste water systems [25].


There is no question that antimicrobial resistance poses a unique threat and formidable challenge for the medical profession. In light of the substantial negative effects exerted by resistance in terms of mortality, morbidity and consumption of healthcare resources, it is in society’s best interest to prioritise this issue.





1.     O'Neill J. Tackling drug-resistant infections globally: Final report and recommendations. London, United Kingdom:; 2016.

2.     Cox G, Wright GD. Intrinsic antibiotic resistance: mechanisms, origins, challenges and solutions. International journal of medical microbiology. 2013; 303.

3.     Sabtu N, Enoch DA, Brown NM. Antibiotic resistance: what, why, where, when and how? British Medical Bulletin. 2015 October.

4.     Rhouma M, Beaudry F&LA. Resistance to colistin: what is the fate for this antibiotic in pig production? International journal of antimicrobial agents. 2016; 48.

5.     WHO WHO. Antimicrobial resistance: Global report on surveillance. Surveillance report. Geneva, Switzerland: WHO World Health Organisation; 2014. Report No.: 9789241564748.

6.     HPSC HPSC. Data on S. aureus/ MRSA bloodstream infections from acute hospitals, 2004 - Q1 2016. Dublin, Ireland: Health Protection Surveillance Centre HPSC; 2016. Available at:

7.     HPSC HPSC. EARSS Surveillance report 2016: Net data on antimicrobial resistance in Ireland , Quarter 1 2016. Dublin: HPSC, European Antimicrobial Resistance Surveillance System; 2016 Available at: SurveillanceSystemEARSS/EARSSSurveillanceReports/2016Reports/.

8.     Pitout JD, Laupland KB. Extended-spectrum beta-lactamase-producing Enterobacteriaceae: an emerging public health concern. The Lancet: Infectious diseases. 2008; 8(3).

9.     Kempf I, Fleury MA, Drider D, Bruneau M, Sanders P, Chauvin C, et al. What do we know about resistance to colistin in enterobacteriaceae in avian and pig production in Europe? International journal of antimicrobial agents. 2013; 42.

10.   Liu YY, Wang Y, Walsh TR, Yi LX, Zhang R, Spencer J, et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. The Lancet: Infectious Diseases. 2016; 16(2).

11.   Olaitan AO, Morand S, Rolain JM. Emergence of colistin-resistant bacteria in humans without colistin usage: a new worry and cause for vigilance. International journal of antimicrobial agents. 2016; 47.

12.   Na G, Zhang W, Zhou S, Gao S, Lu Z, Wu Xea. Sulfonamide antibiotics in the Northern Yellow Sea are related to resistant bacteria: Implications for antibiotic resistance genes. Marine pollution bulletin. 2014; 84.

13.   Rodriguez-Mozaz S, Chamorro S, Marti E, Huerta B, Gros M, Sanchez-Melsio A, et al. Occurence of antibiotics and antibiotic resistance genes in hospital and urban wastewaters and their impact on the receiving river. Water research. 2015; 69.

14.   Dong H, Yuan X, Wang W, Qiang Z. Occurence and removal of antibiotics in ecological and conventional wastewater treatment processes: A field study. Journal of Environmental Management. 2016; 178.

15.   Galvin S, Boyle F, Hickey P, Vellinga A, Morris D, Cormican M. Enumeration and characterisation of antimicrobial-resitant Escherichia coli bacteria in effluent from municipal hospital, and secondary treatment facility sources. Applied and Environmental Microbiology. 2010 July; 76.

16.   Blaak H, van Hoek A, Veenman C, van Leeuwen A, Lynch G, van Overbeek Wea. Extended spectrum beta-lactamase- and constitutively AmpC-producing enterobacteriaceae on fresh produce and in the agricultural environment. International journal of food microbiology. 2014; 168.

17.   Morgan S, Grootendorst P, Lexchin J, Cunningham C, Greyson D. The cost of drug development: a systematic review. Health Policy. 2011; 100(1).

18.   Arias CA&MBE. A new antibiotic and the evolution of resistance. The New England Journal of Medicine. 2015; 372(12).

19.   Chaudhary AS. A review of global initiatives to fight antibiotic resistance and recent antibiotics’ discovery. Acta Pharmaceutica Sinica B. 2016; IN PRESS(IN PRESS).

20.   Kirby T. New antibiotic development hailed as game changing. The Lancet: Infectious Disease. 2015 March; 15.

21.   Nichols D, Cahoon N, Trakhtenberg EM, al. e. Use of iChip for high throughput in situ cultivation of "uncultivable" microbial species. Applied Environmental Microbiology. 2010; 76.

22.   Ling LL, Schneider T, Peoples AJ, al. e. A new antibiotic kills pathogens without detectable resistance. Nature. 2015; 517.

23.   Rios AC, Moutinho CG, Pinto FC, Del Fiol FS, Jozala A, Chaud MV. Alternatives to overcoming bacterial resistances: State-of-the-art. Microbiological Research. 2016; 191.

24.   Chatterjee M, Anju CP, Biswas L, Kumar VA, Mohan C, Biswas R. Antibiotic resistance in Pseudomonas aeruginosa and alternative therapeutic options. International journal of medical microbiology. 2016; 306.

25.   Hocquet D, Muller A, Bertrand X. What happens in hospitals does not stay in hospitals: antibiotic-resistant bacteria in hospital wastewater systems. Journal of hospital infection. 2016; 93.

26.   Lusiak-Szelachaowska M, Zaczek M, Weber-Dabrowska B, Miedzybrodzki R, Klak M, Fortuna W. Phage neutralisation by sera of patients receiving phage therapy. Viral Immunology. 2014; 27.

27.   Kalita S, Kandimalla R, Sharma KK, Kataki A, Deka M, Kotoky J. Amoxicillin-functionalised gold nanoparticles reverts MRSA resistance. Materials Science and Engineering C. 2016; 61.

28.   Fortman JL&MA. The future of antibiotics: Emerging technologies and stewardship. Trends in microbiology. 2016 July; 24(7).

29.   Hollis A, Ahmed Z. The path of least resistance: Paying for antibiotics in non-human uses. Health Policy. 2014; 118.