Series

Antimicrobials: access and sustainable effectiveness 2

Understanding the mechanisms and drivers of antimicrobial
resistance
Alison H Holmes, Luke S P Moore, Arnfinn Sundsfjord, Martin Steinbakk, Sadie Regmi, Abhilasha Karkey, Philippe J Guerin, Laura J V Piddock

To combat the threat to human health and biosecurity from antimicrobial resistance, an understanding of its Published Online
mechanisms and drivers is needed. Emergence of antimicrobial resistance in microorganisms is a natural November 18, 2015
http://dx.doi.org/10.1016/
phenomenon, yet antimicrobial resistance selection has been driven by antimicrobial exposure in health care, S0140-6736(15)00473-0
agriculture, and the environment. Onward transmission is affected by standards of infection control, sanitation,
This is the second in a Series of
access to clean water, access to assured quality antimicrobials and diagnostics, travel, and migration. Strategies to five papers about access to and
reduce antimicrobial resistance by removing antimicrobial selective pressure alone rely upon resistance imparting a sustainable effectiveness of
fitness cost, an effect not always apparent. Minimising resistance should therefore be considered comprehensively, by antimicrobials

resistance mechanism, microorganism, antimicrobial drug, host, and context; parallel to new drug discovery, broad National Institute of Health
Research Health Protection
ranging, multidisciplinary research is needed across these five levels, interlinked across the health-care, agriculture,
Research Unit in Healthcare
and environment sectors. Intelligent, integrated approaches, mindful of potential unintended results, are needed to Associated Infection and
ensure sustained, worldwide access to effective antimicrobials. Antimicrobial Resistance, and
Department of Infectious
Diseases, Imperial College
Introduction synthetic modifications of them, with only a few drugs
London, London, UK
The increasing challenge to health care attributable to (eg, sulphonamides and fluoroquinolones) being wholly (Prof A H Holmes MD,
antimicrobial resistance, and the subsequent absence of synthetic. The protective mechanisms that have evolved L S P Moore MPH); Norwegian
access to effective antimicrobials, is of worldwide include preventing entry of or exporting the drug, National Advisory Unit on
Detection of Antimicrobial
concern. There is a real threat that the public health producing enzymes that destroy or modify the Resistance, Department of
gains from improved access to antimicrobials, including antimicrobial, or making changes to the antimicrobial Clinical Microbiology and
the improvements in childhood survival, could be target. Therefore, antimicrobial resistance could Infection Control, University
undermined.1 Understanding the scientific basis of be considered to simply represent the darwinian Hospital of North Norway, and
Department of Medical
antimicrobial resistance is essential to combating this competition from natural microorganism-derived anti- Biology, University of Tromsø,
public health threat. This understanding should cover microbial molecules. Functional meta-genomic studies Tromsø, Norway
the resistance mechanisms, enabling novel approaches of soil microorganisms have shown a widespread (A Sundsfjord MD); Department
to diagnostics and therapeutics, through to the drivers of
antimicrobial resistance in society and the environment,
essential for the development of appropriate inter- Key messages
ventional policies.2–4 The many factors contributing to • The emergence of antimicrobial resistance is a natural evolutionary response to
the present worldwide status of antimicrobial resistance antimicrobial exposure. At a societal level, complex and interlinking drivers are
are reviewed in this Series paper, with a particular focus increasing the prevalence of antimicrobial-resistant microorganisms, predominantly
on emergence of resistance, transmission, bacterial arising from use in human beings and agriculture and the pollution of the
fitness, and potential for reversibility. The evidence for, environment.
and the role of, important drivers of antimicrobial • Acquisition of antimicrobial resistance mechanisms does not necessarily compromise
resistance are considered and assessed in the context of microbial fitness. Worldwide clonal spread and long-term persistence of resistant
the community (including the environment and bacteria are also seen in the absence of direct antibiotic selection pressure.
agriculture) and in health-care systems. Please see • Reversibility of antimicrobial resistance after withdrawal of antimicrobial selective
appendix for a list of supplementary references. From pressure is consequently not clear cut; minimisation of emergence of resistance to
this evidence, stakeholders can engage with issues new and future agents is therefore essential.
specific to their area of practice, yet also be mindful of • Gaining insight into the mechanisms of antimicrobial resistance, long-term
cross-sectoral interconnectivity and the need for a One persistence, and successful clonal spread, is fundamental to the development of novel
Health approach to antimicrobial resistance. targets for both diagnostic tests and therapeutic agents with integration of these into
sustainable antimicrobial resistance strategies.
Emergence of resistance • Gaps in understanding and areas for innovation are clear, yet progress towards these
1) Why does resistance emerge within a micro-organism? goals is still urgently needed, with a careful awareness of any potential effect on access
Through a darwinian selection process microorganisms to effective antimicrobial treatment.
have developed robust mechanisms to evade destruction • There is no single solution and several, synergistic, overlapping, and complementing
from many toxic substances. Most antimicrobial drugs approaches will be needed, with a strong overarching shared goal to ensure and
are naturally produced by microorganisms, including sustain access to effective antimicrobial therapies.
environmental fungi and saprophytic bacteria, or are

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of Bacteriology and diversity of genetic determinants conferring antibiotic noted that at 1-day old, 14·3% harboured
Immunology, Division of resistance, of which only a fraction have been described Enterobacteriaceae that contained an enzyme that
Infectious Disease Control,
Norwegian Institute of Public
in human pathogens.5 One example where a naturally inactivates β-lactam drugs, an extended-spectrum
Health, Oslo, Norway occurring resistance mechanism has had an effect on β-lactamase (ESβL), yet this increased to 41·5% of babies
(M Steinbakk MD); Institute for human health is the resistance developed against by day 60.14 The environment, drinking water, and food
Science, Ethics and Innovation β-lactam antimicrobial drugs, in which the enzymes are probably the most important means for establishing
(iSEI), University of
Manchester, Manchester, UK
(β-lactamases) that inactivate these antimicrobial the normal (healthy) gut microflora. Antimicrobial-
(S Regmi MBChB); Oxford molecules have existed for millions of years.6 resistant bacteria have been found in every environment
Clinical Research Unit, Patan The production of antimicrobial molecules by examined so far including Antarctica, the sea, soil,
Academy of Health Sciences, saprophytic organisms were originally thought to inhibit drinking water,15 and various food products.16 This
Kathmandu, Nepal
(A Karkey DPhil); Worldwide
the growth of neighbouring organisms, providing a polymicrobial, variably antimicrobial-resistant, com-
Antimalarial Resistance competitive advantage in the local environment; however, mensal microbiome (microorganisms that are not
Network (WWARN), and some studies suggest a more complex interaction. First, causing infection at that body site eg, the gastrointestinal
Centre for Tropical Medicine the concentration of antimicrobial molecules in the soil tract or skin) is established at an early age.
and Global Health, Nuffield
Department of Medicine,
seems to be too low to inhibit growth of other bacteria.7 In a pristine (ie, free from external antimicrobial
University of Oxford, Oxford, Second, evidence suggests that even sublethal concen- selection pressure) ecosystem, antimicrobial-resistant
UK (P J Guerin MD); and trations of antimicrobials have substantial effects on and non-resistant species coexist in a stable balance.17
Antimicrobials Research Group,
bacterial physiology, increasing the rate of microbial The human microbiota is no exception, and commensal
Institute for Microbiology and
Infection, University of adaptive evolution and possibly acting as signalling microorganism populations in human beings include
Birmingham, Birmingham, UK molecules influencing microbial and host gene species that are naturally resistant to some
(L J V Piddock PhD) expression.8 Of particular note are some saprophytic antimicrobials. Selective pressure is exerted by any
Correspondence to: bacteria that produce carbapenems (an important class of condition (eg, antimicrobial exposure) that allows
Prof Alison H Holmes, NIHR broad-spectrum antimicrobials in clinical use) in which microorganisms with inherent resistance or newly
Health Protection Research Unit
in Healthcare Associated
the genes implicated in the synthesis of carbapenems acquired mutations or resistance genes to survive and
Infection and Antimicrobial might also have a role in the quorum-sensing apparatus proliferate.6 Antimicrobial use exerts such selective
Resistance, Imperial College (the mechanism through which a colony of pressure on commensal human microflora, and
London, London W12 0HS, UK microorganisms coordinates growth and gene expression) pathogens, increasing the risk of recovery of resistant
[email protected]
or formation of biofilms.6 This process leads to further organisms from patients.12
See Online for appendix questions about the unintended effects of antimicrobial Use of antimicrobials in clinical medicine has exposed
drugs, with our understanding of their potential effect on the human microbiota to unprecedented high
microorganisms, beyond their inhibitory action, concentrations of these drugs. In-vivo development of
remaining incomplete.9 de-novo resistance within a human individual has been
Emergence of resistance to synthetic antimicrobials also recorded during treatment courses with a range of
occurs. This resistance has unfortunately been widely antimicrobials including, worryingly, carbapenems.18 In
exemplified in the case of fluoroquinolones, for which some patients, such as those with cystic fibrosis, there
in Escherichia coli isolated from patients in Europe, are increased rates of mutation in the infecting bacteria
fluoroquinolone resistance is now at 10–40%.10 Many (ie, they are hypermutable). Some antimicrobials
resistance mechanisms have emerged including alteration exacerbate this hypermutability, promoting selection of
of target (a DNA-gyrase), increased efflux (export of a drug resistance.19
out of the microorganism), fluoroquinolone inactivation
(by an aminoglycoside N-acetyltransferase), and protection 3) Why does resistance emerge at the population
of the target by DNA-binding proteins (known as Qnr).11 level in humans and animals?
Even though many microorganisms in the environ- Antimicrobials are among the most commonly prescribed
ment, and organisms including plants and animals, drugs used in human medicine, yet up to 50% of all
naturally produce antimicrobial substances, little antimicrobials prescribed to people are considered
evidence exists to suggest that this contributes unnecessary.20 This use, misuse, or overuse of
significantly to the selection of antimicrobial-resistant antimicrobial drugs is considered to be a major driving
microorganisms in their native environment.7 Therefore, force towards antimicrobial resistance.21,22
the many and varied human, animal, and agricultural In human beings, the concentration of antibiotic
uses of antimicrobials should be considered key prescribing might be highest in inpatient settings, with
worldwide drivers of antimicrobial resistance.2,12,13 30–40% of patients on antibiotics in European hospitals.23
However, the overall quantity of antimicrobial prescribing
2) Why does antimicrobial resistance emerge at the is highest in the community.24 Even though guidelines
individual human level? recommend prudent use, needless prescriptions are seen
Neonates are rapidly colonised by Enterobacteriaceae even in countries with low rates of prescription.25 However
after birth, irrespective of whether they are breast fed or an overall reduction in prescriptions for antimicrobials
not. A study in India of a cohort of breast fed babies has been reported in some settings over the past decade,

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with a modest reduction in antimicrobial resistance

Transduction
recorded.26 The role of educating prescribers is crucial in Bacteriophages (viruses that
overcoming antimicrobial misuse or overuse and is seen infect bacteria) mediate
transfer of DNA between
to be effective in primary care27 and secondary care.28 bacteria via transduction,
Additionally, raising awareness of the fundamentals of whereby DNA from a
antimicrobial use in the general public is equally donor bacterium is packaged
into a virus particle and
essential.29 transferred into a recipient
However, although the link between human bacterium during infection.
antimicrobial use and resistance seems clear cut, this
association is complex.30 Confounding factors mean a
uniform approach to understanding resistance cannot be
Conjugation
taken. These factors include pathogen–drug interactions, The mechanism of gene transfer
pathogen-host interactions, mutation rates of the responsible for the most concerning
pathogen, emergence of successful antimicrobial- aspects of antimicrobial resistance.
A sex pilus (small tube) forms
resistant clones, the transmission rates of pathogens between two bacterial cells through
between human beings, animals, and the environment, which a plasmid is transferred from
one to the other.
cross-resistance, and selection of co-resistance to Transformation
unrelated drugs. Importantly, at the human population Some bacteria are able to take up free DNA
from the environment and incorporate it
level, public health factors such as rates of vaccine into their chromosome.
uptake,31 different systems of health care, the role of
migration and tourism, sanitation, and population Figure 1: Transmission of genetic material between microorganisms
Genetic material is transferred between microorganisms through three main routes: (i) transformation—
densities, also influence the prevalence of resistance.30 examples include recombination of foreign DNA from Streptococcus mitis to Streptococcus pneumoniae,
More antimicrobials are used in food production than conferring penicillin resistance via the formation of mosaic genes, and Neisseria gonorrhoeae where a mosaic
in human beings,22 with marked national differences in penA gene is associated with ceftriaxone resistance;38 (ii) transduction—where antimicrobial resistance genetic
the number of antimicrobial drugs used in food- material has been identified in phage DNA isolated from waste water treatment,36 and both extended-spectrum
β-lactamase genes and mecA genes (the latter responsible for meticillin resistance in Staphylococcus aureus)
producing animals, varying a 100-fold from 4 mg to have been identified in bacteriophage extracted from faecal samples at farms and abattoirs;37 and (iii)
400 mg of antimicrobial per kg of meat produced in conjugation—with plasmids being responsible for example for the global dissemination of genes encoding
European countries.32 Various studies have shown that carbapenemases such as New Delhi metallo-β-lactamase,15 as well as ESβLs.39 Furthermore integrative
antimicrobial resistance has, at least in part, emerged as chromosomal elements (ICEs) can transfer these resistance genes between plasmids and the bacterial host
chromosome in a range of Gram-negative species and streptococci.40
a result of the selective pressure exerted by antimicrobial
use outside of human medicine, namely in veterinary
medicine,33 food-animal and fish production,34,35 and 2) How does human-human transmission drive
agriculture.22 resistance?
In summary, the role of antimicrobial use in driving Modelling of transmission dynamics has improved
the emergence of resistance is likely to be specific to each understanding of how human–human transmission
drug and to each microorganism, as is the effect of contributes to the spread of pathogens and antimicrobial
changes in this use. This means that policies need to be resistance.21,22 In the community, faecal–oral
mindful of this complexity in addressing selection transmission, often through failures in sanitation, plays
pressure and that an integrated approach is adopted an important part, particularly for resistant
across both the community (including agriculture and Enterobacteriaceae.42 Transmission can also occur
the environment) and health-care structures. through sexual encounters; for Neisseria gonorrhoeae,
core groups have contributed to widespread
Transmission of resistance dissemination of resistant clones.43 Perhaps where the
1) How does transmission of resistance occur between dynamics of transmission are best understood is in the
micro-organisms? context of health-care-associated infections. Using
In addition to selection of antimicrobial resistance meticillin-resistant Staphylococcus aureus (MRSA) as an
through mutations in genes encoded on a microbe’s example, modelling suggests duration of patient stay
chromosome, new genetic material can also be exchanged and contamination of health-care workers’ hands both
between organisms. This process can provide the host contribute to continuing transmission.44 Use of
cell and its progeny with new genetic material encoding whole-genome sequencing has enabled more detailed
antimicrobial resistance and can occur through several epidemiological analysis, providing rapid, fine resolution
mechanisms, of which perhaps the most important is sequencing to help with mapping outbreaks and
plasmid transmission (figure 1).15,36–40 Antimicrobials delineating transmission points.45 What is missing,
influence this, not only by exerting a selective pressure perhaps, is a better understanding of how movement
towards emergence of antimicrobial resistance, but also and flow of patients, and the built environment, affect
by inducing transfer of resistance determinants between resistance transmission within,46 and between,47
microorganisms.41 health-care institutions. Moreover, the inability to rapidly

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Linezolid-resistant enterococci
Cephalosporin-resistant N gonorrhoea
Carbapenemase-producing Gram-negative organisms
New Delhi metallo-β-lactamase

Figure 2: Worldwide travel routes and emergence of antimicrobial resistance

Although extended-spectrum β-lactamase-producing Enterobacteriaceae and MRSA are now nearly ubiquitous, certain novel types of resistance, among both Gram-
negative and Gram-positive organisms, are of particular concern. The mechanisms of human-to-human transmission for these organisms are likely to be complex,
but include association with travel. Data shown includes NDM-positive bacteria from patients with an epidemiological link to the Indian subcontinent,52 linezolid-
resistant enterococci,53 and reported cefixime/ceftriaxone treatment failures for Neisseria gonorrhoea.54 Flight path data developed by Dr Jonathan Read and Professor
Tom Solomon, based on the number of commercial flight bookings made (number of travellers might be higher).

identify resistant microorganisms with appropriate and drug resistance has been suggested, and provision of even
efficient diagnostic tests is likely to further contribute to slightly higher rates of protection for drug-resistant over
continuing transmission in health-care settings. drug-sensitive strains might be an effective method in
During the last 10 years the human microbiota has controlling antimicrobial resistance.57 Finally, controlling
acquired antimicrobial resistant Enterobacteriaceae on an antimicrobial resistance through use of targeted,
unprecedented scale. In some parts of the world the carrier vaccine-induced replacement strains has been proposed.58
rate of ESβL-positive Enterobacteriaceae in the gut is more
than 50%,48 and travel has been clearly associated with 3) What is the role of animals and the environment in
increased risk of gut colonisation with these organisms. In driving transmission of resistance?
a prospective study from the Netherlands, 8·6% of The potential for transmission of antimicrobial-resistant
travellers were colonised with ESβL-producing microbes from animals to human beings, and the
Enterobacteriaceae before travel, but 30·5% acquired gut association between use of antimicrobial growth promoters
colonisation during travel, with independent risk factors in farm animals and transmission of resistant bacteria,
being travel to south and east Asia.49 More recently, and were recognised in the 1960s.59 Antimicrobial resistance
perhaps more worryingly, is the spread of carbapenem that arises in animal husbandry is now well established and
resistance mechanisms across the world, and between affects zoonotic pathogens such as Salmonella serovars60 and
organisms, with New Delhi metallo-β-lactamase (NDM),15 Campylobacter spp;61 the mechanisms of resistance are
Klebsiella pneumoniae carbapenemase,50 and OXA-4851 indistinguishable in bacteria isolated from animals or
enzymes being among those of greatest concern human beings. Bacteria, and mobile genetic elements
(figure 2).52–54 Travel-related human–human spread has also conferring resistance, linger on animal skin and in faeces
been evident for Gram-positive organisms, notably in the and by various means can be transferred between bacteria,
spread of antimicrobial-resistant Streptococcus pneumoniae and bacteria can make their way to human beings.62 Despite
from Spain to Iceland.55 the subsequent accumulation of this and other evidence,
Population-based strategies to interrupt human–human and the publication of the seminal report by Swann on this
transmission, including through interventions such as issue more than 40 years ago,30,63 a European ban on the use
mass drug administration and vaccination, might alter the of antimicrobials for growth promotion in livestock did not
transmission dynamics of pathogens and resistance occur until 2006, and outside the European Union such
determinants. Evidence for this approach is strongest for use still occurs widely, including in the USA. The effect on
vaccines, in which their use can result in reduction or patterns of resistance from changing use of antimicrobials
elimination of the target organism, reducing the need for in animal health care continues to be well described.21,22
antimicrobial treatment and selection of antimicrobial This interweaving of animal and human microbial
resistance.56 Targeting vaccines against strains with ecosystems extends to both commensals and opportunistic

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pathogens, including species such as E coli, enterococci, Human antimicrobial misuse or overuse Suboptimal dosing, including
and Staphylococcus aureus. Evidence supporting Animal antimicrobial misuse or overuse from substandard and falsified
Environmental contamination drugs
transmission from livestock to human beings of ESβL and Health-care transmission Travel
AmpC-β-lactamase genes on plasmids and of E coli clones, Suboptimal rapid diagnostics Mass drug administration for
most likely through the food chain, have been reported.64 Suboptimal vaccination human health

Phylogenetic evidence from whole-genome analyses of

51 Enterococcus faecium strains goes further and supports

Relative contribution of factor as a driver

High
the hypothesis that the epidemic hospital-adapted lineage

for antimicrobial resistance

emerged from a population that included mostly animal
strains.65 Human infections with MRSA have been
classified by their putative sources, such as health-care
Moderate
associated or community associated. However, human
MRSA cases associated with exposure to pigs (livestock-
associated MRSA [LA-MRSA]) have been described,66 as
have MRSA skin and soft-tissue infections associated with Low
proximity to crop field pig manure and livestock
operations.67
The contribution of the environment to antimicrobial Low Moderate High
Evidence that factor is contributing to antimicrobial resistance
resistance is also concerning. Use of metals in agriculture
(for example when copper is applied directly as a Figure 3: Role of modifiable drivers for antimicrobial resistance: a conceptual
bactericide or fungicide),68 and even natural occurrence of framework
An infographic to show the considered potential contribution of each factor as
metals in certain geographical areas,69 can select for a driver for antimicrobial resistance. Associated relative contribution,
resistance; of more concern is that many metals co-select supporting evidence, and potential population affected (diameter of bubble)
for antimicrobial resistance.7,70 Even the commonly used was created from a two round Delphi method of contributing authors. Factors
nitrogen fertilisers could affect the soil content of were identified from review of the national and international antimicrobial
resistance literature. The Grades of Recommendation, Assessment,
antibiotic resistance genes, causing shifts in the relative Development, and Evaluation (GRADE) approach was used to identify the
abundance of microorganisms.5 The importance of quality of the evidence (the study with the highest GRADE estimate was cited)
sewage and waste processing in environment–human supporting each driver as being contributory to the rise in antimicrobial
transmission is also clear. This stems from antimicrobials resistance (appendix).
and antimicrobial metabolites entering not only from
human waste processing, but also from pharmaceutical an infection) than their antimicrobial susceptible
industry pollution. As a result, many potentially counterparts. This situation would mean that reducing
pathogenic antimicrobial resistance microbes have the burden of resistance might simply be achieved
been isolated from pre-treatment and (importantly) through removing the selective pressure of antimicrobials,
post-treatment sewage systems.42,71 The subsequent leading to antimicrobial-resistant microbes losing out in
detection of antimicrobials and antimicrobial-resistant darwinian competition with the susceptible strains.
microbes in surface water and ground water35,42 reinforces Unfortunately, this is frequently not the case and can be
the environmental need for preventive action to be taken. seen in two important classes of antimicrobials, the
In summary, the worldwide acquisition, persistence, fluoroquinolones and the β-lactams.72
and transmission of antimicrobial-resistant microbes by In the case of fluoroquinolones (man-made anti-
people, animals, and the environment is hugely affected microbials), clonal expansion has given rise to a
by no access to clean water, open rather than closed worldwide high prevalence of resistance in several
sewage systems, variation in health-care infection-control bacteria. This increase is exemplified by whole-genome
practices, inadequate provision of antimicrobials and sequencing of an epidemic MRSA strain (EMRSA-15;
diagnostics, farming systems with suboptimum ST22)73 and Clostridium difficile O27.74 Furthermore,
regulation of antimicrobials, and high population widespread dissemination of fluoroquinolone-resistant
densities (figure 3, appendix). Although some of these clones of E coli ST131 exists,75 whereas fluoroquinolone-
issues exist in high resource settings, they are likely to resistant Salmonella enterica serovar Typhi72 and
represent particularly important drivers of antimicrobial N gonorrhoeae76 are not uncommon.
resistance in low-income and middle-income countries. This development and worldwide spread of
fluoroquinolone-resistant bacteria suggests resistance to
The complex issues of fitness and reversibility of this class of drugs is unlikely to be a burden to the
antimicrobial resistance bacterium. Mutations that alter the target of
1) Does antimicrobial resistance affect the fitness of antimicrobials (such as gyrA, in the case of fluoro-
micro-organisms? quinolones) can change bacterial physiology, potentially
There is a perception that antimicrobial-resistant making them less fit. Yet compensatory mutations that
microbes might be less fit (ie, less able to grow or cause restore fitness to wild-type levels might explain, in part,

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Panel 1: Reversibility of antimicrobial resistance after withdrawal of antimicrobial selective pressure in human and animal
populations: a complex picture
Human health Animal health
Evidence of correlation between reduction of antimicrobial Complexity is also evident in animal health when correlating
use and decrease in antimicrobial resistance is complex, yet it reduced antimicrobial use to a decrease in antimicrobial
has been seen in some Gram-positive organisms. In a French resistance. In Denmark and Norway, after an avoparcin
prospective trial,82 a reduction in antimicrobial use (a glycopeptide antimicrobial) agricultural ban, a marked
corresponded to significantly decreased pharyngeal reduction in the proportion of glycopeptide-resistant
colonisation of penicillin-non-susceptible S pneumoniae. In enterococci (GRE) was seen in broilers from poultry farms
Finland, reductions in macrolide use led to a decrease in previously exposed to avoparcin.86 However, although post-ban
erythromycin resistance in Streptococcus pyogenes,83 although studies suggested that the amount of faecal GRE in broilers
this was possibly due to clonal replacement rather than might have decreased significantly, the prevalence of animals
reduced selection pressure. Correlation has also been seen in colonised with GRE was still high several years after the ban.11587
Gram-negative organisms. In bloodstream infections in the A similar situation was seen in pigs. In the UK, after the 1971
UK, non-susceptibility to cephalosporins and quinolones in ban of tetracycline as an animal growth promoter, the
Enterobacteriaceae has shown a modest decrease over the past proportion of tetracycline-resistant E coli isolated from the
decade, probably reflecting prescribing shifts.26 However, the exposed pig population decreased, but the prevalence of
relative contribution of reductions in antimicrobial use and colonised pigs remained at 100% several years later.88
concomitant infection control interventions is difficult Yet, importantly, reduction of animal antimicrobial use might
to quantify. not alter production volumes. The avoparcin ban for
By contrast, evidence also exists where reduced antimicrobial antimicrobial growth promotion noted above had no deleterious
use has not equated to a decrease in antimicrobial resistance. In effect on production volume.89 Similarly in Danish pigs, a 60%
a prospective trial in Sweden, an 85% reduction in reduction in pig antimicrobial consumption had no negative
trimethoprim consumption resulted in only a marginal slowing effect on productivity.90 However the European ban on
of the rise in trimethoprim resistance in uropathogenic antimicrobials as growth promoters has seen a modest increase
Escherichia coli.84 In the UK, a 98% decrease in cotrimoxazole in infections and an attributable increase in therapeutic use of
consumption did not result in reduction of antimicrobial antimicrobials in classes of direct importance to human health.91
resistance, instead it was inexplicably followed by a 6% increase Although reduction in animal antimicrobial use might not
in sulphonamide resistance in clinical isolates of E coli.85 clearly decrease antimicrobial resistance, it will delay further
This absence of clear correlation between reduced use of development and spread, without adversely affecting
antimicrobials and decreased antimicrobial resistance urgently production volumes. Policies to restrict novel classes to either
needs a greater understanding to enable the design of animal or human health might further help prevent the
effective interventions. crossover of resistance.

why clinical isolates resistant to this class of drugs have CTX-M-14) has no detectable fitness effect when
proliferated and spread. As a specific example, mutations introduced into new host strains and has spread worldwide
detected in a fluoroquinolone-resistant strain of E coli in diverse E coli strains from animals, human beings, and
were experimentally reconstructed. Strains with single the environment.79 As such, absence of antimicrobials
mutations were less fit than the parental strain; however, might not lead to a reduction in the prevalence of this type
two or more mutations in combination increased the of third generation cephalosporin-resistance.80
fitness of the bacterium to similar or greater levels than
that of the antimicrobial-susceptible strain.77 Therefore, 2) Is emergence of resistance reversible?
once selected, fluoroquinolone-resistant mutants are One strategy to reduce the development and spread of
able to persist and thrive even in the absence of antimicrobial resistance is to lower the selective pressure
fluoroquinolone antimicrobials.77 by limiting or suspending the use of antimicrobials. This
The carriage of mobile genetic elements such as strategy is based on the assumption that resistant
plasmids, which often contain several antimicrobial microorganisms will be outnumbered by susceptible
resistance genes, has also been proposed to reduce strains if the selective advantage of possessing the
bacterial fitness. However, carriage of natural plasmids resistance determinant is diminished,81 but as noted, this
with no antimicrobial resistance genes is common, and is not always true (panel 1). Mathematical models have
might confer a benefit to hosts, thereby promoting increasingly been used to identify, predict, and help design
expansion of plasmid-carrying strains.78 For example, an intervention programmes for antimicrobial resistance.92
IncK plasmid (named pCT), which carries one These models support antimicrobial exposure as central
antimicrobial resistance gene (encoding the ESβL to resistance emergence and spread, but importantly do

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Panel 2: Potential approaches to prolong the useful therapeutic life of antimicrobials available at present
Maintain heterogeneity of antimicrobial agents Repurposing of withdrawn and underused antimicrobial
Excessively homogeneous antimicrobial use might contribute drugs
to selective pressure. Maintaining prescribing diversity can be Repurposing previously discovered (often FDA-approved)
achieved through several methods. One such method is drug pharmacotherapies might provide a potentially less economically
cycling (replacing an antimicrobial belonging to one class risky pursuit than de-novo drug discovery. This approach has
with one or more belonging to different classes, sequentially, already been evident with the return of colistin and fosfomycin
at the level of the unit or hospital). However, cycling might use for multidrug-resistant Gram-negative infections,
only be useful if implemented before resistance to the repurposing of older drugs for bacteria such as
replacement drug has emerged or if resistance to the first Acinetobacter baumannii, and more widespread consideration of
drug imposes a fitness cost.77 Another approach is drug fusidic acid in clinical practice in some countries since the 1960s.
mixing (diversification of antimicrobial prescription at the Incentives advocating new drug discovery, including mechanisms
individual level allowing for patient variation), which to accelerate clinical trials, and making these drugs attractive to
maintains personalisation of infection treatment. However, industry for production might also need to be adapted to such
implementing personalised medicine effectively would repurposed drugs.
require accurate and rapid diagnosis of pathogens,
Combination therapy
antimicrobial resistance, and host factors.
Combination therapy is use of several antimicrobials to which the
Assure and ensure adequate serum drug concentrations targeted organisms do not show cross-resistance. This relies on
Subtherapeutic concentrations contribute to poor treatment microbial populations containing singly resistant mutants, but
responses and exert non-lethal selective pressures. none that are resistant simultaneously to several drugs. However,
Unfortunately, suboptimal drug exposures have many causes: the increasing prevalence of multidrug-resistant strains needs
use of poor quality drug (falsified, substandard, or degraded), careful assessment to ensure efficacy of drug combinations. This
systematic under-dosing (small infants, overweight adults, strategy has been successful in preventing or delaying resistance
infrequent dosing), inadequate drug absorption (malnutrition in tuberculosis, HIV, and malaria. However, combination therapy
and drug interactions), unusual large apparent volume of successes for the organisms causing these diseases are not directly
distribution (pregnancy), or particularly rapid clearance.2 translatable to bacterial infections and have not been widely
Taken individually, populations exposed to sub-therapeutic recommended so far, often because of the increased cost, but also
concentrations might seem small, but they represent a high from fear of incremental, unwanted disturbance of the
proportion of the patients receiving antimicrobials in microbiome. Furthermore, the differentials in half-life of drugs
low-income and middle-income countries. Optimisation of used in combination should be carefully considered, or
dosage and guarantee of drug quality could reduce unintentional monotherapy might ensue. In conclusion, the
sub-therapeutic drug exposure and reduce this modifiable risk–benefit of combination therapy is unclear and further work is
driver of resistance. urgently needed to clarify these issues.

find correlations between reduction in antimicrobial use include the nature of the resistance mechanisms (and
and reduction in antimicrobial resistance, at both the level of fitness cost), the propensity for horizontal gene
individual patient93 and human population levels.94 transfer and transmissible elements, and cross-selection
Complete eradication of antimicrobial resistance in and co-selection mechanisms.77 Cross-selection and
populations of microbes after reduced selective pressure co-selection are highly pertinent because many bacteria
from antimicrobials is not straightforward. Resistance are multidrug resistant owing to the presence of several
determinants are easy for microbes to acquire and might antimicrobial resistance genes; therefore, only by reducing
persist at low, but detectable, levels for many years in use of all drugs to which resistance is encoded will the
the absence of particular antimicrobials,95 and in turn, prevalence of a multidrug-resistant microbe decrease, and
antimicrobial resistant microbes can persist for only then if this is beneficial to the bacterium.
many years on human and animal skin and as faecal flora
without any further exposure or selection pressure.96 The Approaches to optimising antimicrobial use
absence of a clear correlation between reduced use of 1) How should antimicrobials be used to preserve
antimicrobials and decreased antimicrobial resistance can effectiveness and delay resistance in humans?
be explained by the interplay of several factors. One factor The published work on antimicrobial resistance across
is context, such as whether the system is open (ie, many different diseases converges on a remarkably
continuous inflow and outflow, in which the incoming consistent set of recommendations for prevention and
population has a differing frequency of antimicrobial containment.10,20–22,97,98 These principles focus on improve-
resistance) or closed (ie, a community in which migration ment of diagnosis and prescription practices, reduction
is restricted). At the level of the microbe, other factors of antimicrobial use in animal husbandry, fish farming,

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agriculture, and environmental exposure in general, cohesively addressed. The construction of a worldwide
development of new antimicrobials, guarantee of database of previous and present antimicrobial resistance
access to essential medicines of assured quality, and projects has been advocated,102 but irrespective of this,
improvement of surveillance. Despite these generic several areas have particular priority.
principles being acknowledged, implementation has First, understanding of how to minimise the selection
been slow.99 However, some disease-specific approaches of antimicrobial resistance is fundamental, including
have been tried, and the evidence suggests that several understanding of how to optimise antimicrobial use.
approaches could be beneficial if tested and validated on This approach requires detailed analysis to define
a wide range of infectious diseases (panel 2). optimum durations and dosage of therapy in specific
In a world where patients often need urgent effective patient groups (including infants, pregnant women,
treatment, some antimicrobial optimisation strategies undernourished, obese, and co-infected patients).103,104
present practical challenges. Analysis of antimicrobial The absence of basic knowledge about ideal prescribing
stewardship programmes, and their implementation in regimens represents a significant gap. Furthermore, as
varied health-care settings, is an area of vigorous noted (panel 2), some previously advocated strategies
academic pursuit, and although many lessons have to combat antimicrobial resistance need further
clearly been learnt,28 gaps in our knowledge still exist.100 assessment, including investigation of antimicrobial
The human and economic costs of overcoming these prescribing combinations. Many of these matters can
challenges, and filling these gaps, are likely to be small only be investigated through translational research,
compared with unchecked resistance, which might mean including novel educational methods,105 and through
drugs have to be withdrawn and replaced with newly implementation of international networking and
developed alternatives, or worse, the inability to treat at collaborations. A reorganisation of antimicrobial
all.101 Furthermore, beyond optimisation of antimicrobial resistance funding to support such translational work
use, development and implementation of robust is needed.102
infection prevention and control initiatives at national Second, in support of optimisation of antimicrobial
and local levels should be established to curtail onwards use, improved targeting through rapid infection
transmission of antimicrobial-resistant microbes.22 diagnostics should be enabled. Although this method has
been widely advocated,20,21,97 it has been slow to be
2) How should antimicrobials be used to preserve implemented, due partly to technical and financial
effectiveness and delay resistance in animals? barriers,22 but also issues around innovation adoption.106
The evidence for reversibility of antimicrobial resistance An example is next generation sequencing, which is likely
in the context of animal health has been noted as complex to radically change microbiological diagnostics, but costs,
(panel 1); however, three principles are clear. First, data pipelines, and clinical confidence in interpreting
antimicrobials used as animal growth promoters and for results have yet to be resolved.107 An alternative
inappropriate routine infection prevention in herds technological development already widely in use, namely
should be banned. Second, access to non-medicated matrix-assisted laser desorption/ionisation time-of-flight,
animal feed for farmers should be improved. Third, use allows rapid microorganism identification, and potentially
of specific classes of antimicrobials should be restricted also antimicrobial susceptibility testing.108 These avenues
to either human beings or animals.4 are suitable for secondary care, but for primary care
Approaches to optimisation of antimicrobial use in optimising antimicrobial use through near-patient
both human and animal health should be integrated and inflammatory marker assays has growing evidence.109 For
coordinated, with shared learning, understanding, and low-income and middle-income countries, diagnostic
participation in environmental interventions. Such a options several-fold cheaper, with less need of logistic
One Health approach, integrating human medicine, infrastructure, are needed and a focus on chromogenic
veterinary medicine, public health, and environmental tests might provide avenues for exploration.110
science in specialties including surveillance, development Third, although new drug discovery is essential (and
of new diagnostics and therapeutics, and interlinking through use of novel laboratory methods, drug discovery
research and education should enable creation and has taken a leap forward)111 research on the quality of
implementation of more comprehensive and effective currently used antimicrobials is also urgently needed.
policies. Coordinated action and application of these The issue of substandard antimicrobials is a potentially
might prolong the therapeutic life of present significant driver of resistance and little is known on the
antimicrobials, and should be a high priority for all. international extent of the problem.2 Engaging policy
makers, prescribers, antimicrobial providers, and the
What gaps in our knowledge need addressing? public in ensuring access and assuring quality of
The need to address the research gaps in antimicrobial antimicrobials should be an essential component of
resistance has never been more keenly felt. However, addressing antimicrobial resistance.
identification of priorities, increase of research funding, Fourth, understanding of how to effectively reduce the
and targeting research activity should be coordinated and prevalence of resistant organisms and their transmission

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underpins much of the research needed. In the context the existing evidence base is sufficient to allow targeted
of human–human transmission, delineating not just policies to be developed in several areas.2–4 Such strategies
effective, but cost-effective interventions to optimise to reduce antimicrobial resistance should consider the
antimicrobial use, reduce transmission, and prevent role and effect of many factors, including the resistance
environmental contamination with antimicrobial resis- mechanisms, species of microorganism, the particular
tance and antimicrobials is essential. To address this antimicrobial, as well as the setting and context. So far,
balance through minimisation of antimicrobial use all evidence suggests that no single solution exists and
in agriculture and aquaculture while meeting the several overlapping and synergistic approaches will be
ever-increasing worldwide food demands, is also a needed. Furthermore these approaches should be
fundamental challenge. Adopting a One Health lens to coordinated at national and international levels, while
identify gaps in understanding at these interfaces, and engaging local stakeholders to ensure widespread
then construct integrated research strategies to bridge implementation. The approaches should be mindful of
them, is likely to be a productive way forward. Inherent any potential unintended consequences (including
in this area of research is improvement towards a greater possible impact on access to necessary antimicrobials2
level of detail from surveillance (ie, fine resolution and patient outcomes) and should share a strong
geographical and temporal information) to identify overarching goal to ensure access to effective
associations between antimicrobial use and misuse, and antimicrobial therapies for this generation and for
to clearly identify successful interventions. However, the future.
present surveillance data are rarely standardised or Contributors
reported in a timely way and are often aggregated, All authors contributed to the literature search, interpretation of
making interpretation problematic; without access to published information, writing, and contribution to figure content for
their respective areas of expertise. AHH and LSPM edited, structured,
individual patient outcomes data are of little use. Making and coordinated the complete manuscript and the figures and panels.
primary data available internationally, and standardising All authors reviewed and approved the final version of the manuscript.
which markers of resistance and species are tracked Declaration of interests
across international boundaries, might be one avenue to AHH and LSPM have previously consulted for bioMérieux. All other
harmonise these efforts22,97 and is potentially possible to authors declare no competing interest.
a fine resolution112 with automated methods.113 Such Acknowledgments
information can provide early warning of emerging AHH and LSPM receive support from the National Institute of Health
resistance and allow prompt implementation of efforts to Research Imperial Biomedical Research Centre, the UK Clinical
Research Collaboration who fund the Centre for Infection Prevention
preserve and maximise the useful therapeutic life of and Management (UKCRC G0800777), and the National Institute for
present antimicrobials. This coordinated approach has Health Research Health Protection Research Unit (NIHR HPRU) in
been successfully implemented for malaria and could be Healthcare Associated Infection and Antimicrobial Resistance at For more on malaria
productively applied to other pathogens. Imperial College London in partnership with Public Health England surveillance see www.wwarn.org
(PHE). AS receives support from The Research Council of Norway,
Finally, at the level of the microorganism, continued Northern Norway Regional Health Authority Medical Research
investigation is needed to generate new insights into Programme, and the Norwegian Ministry of Health and Care Services.
the basic mechanisms of resistance, gene transfer, and MS acknowledges support from the Norwegian Institute of Public
Health. LJVP acknowledges support from the UK BBSRC and MRC, and
adaptive bacterial evolution. This includes investigating
has a Roche Extending Innovation Network award. We thank Dr
the role of persistence and host–pathogen interactions Jonathan Read and Prof Tom Solomon in depicting the flight path
and their contribution to antimicrobial resistance114 and concentration data. The views expressed in this Series paper are those of
antimicrobial resistance reversal. Pursuing areas such the authors and not necessarily those of the NHS, the NIHR, the UK
Department of Health, Public Health England, or the Norwegian
as these might uncover new targets for improved
Ministry of Health and Care Services.
therapeutics and diagnostics. Areas of particular
References
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