Diagnosing Antimicrobial Resistance in Which the Drugs Are Likely to Improve the Health Status of an Individual

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ANTIMICROBIAL RESISTANCE of antimicrobial resistance, as it limits the VIEWPOINT exposure of patients and environments to antibacterials under only those circumstances Diagnosing antimicrobial resistance in which the drugs are likely to improve the health status of an individual. The more inappropriately antibacterials are used, the Carey-Ann D. Burnham, Jennifer Leeds, Patrice Nordmann, Justin O’Grady more we risk the erosion of the utility of a and Jean Patel drug due to resistance. With the immense Abstract | Antimicrobial resistance constitutes a global burden and is one of amount of time and resources that it takes to discover new safe and effective antibiotics, the major threats to public health. Although the emergence of resistant diagnostics help the medical community to microorganisms is a natural phenomenon, the overuse or inappropriate use of preserve the utility of these precious drugs. antimicrobials has had a great effect on resistance evolution. Rapid diagnostic tests that identify drug-resistant bacteria, determine antimicrobial susceptibility Patrice Nordmann. Diagnostic techniques and distinguish viral from bacterial infections can guide effective treatment may contribute to the identification of rapidly emerging resistance traits. First, strategies. Moreover, rapid diagnostic tests could facilitate epidemiological such a rapid identification can contribute surveillance, as emerging resistant infectious agents and transmission can be to better antibiotic stewardship. Rapid monitored. In this Viewpoint article, several experts in the field discuss the adaptation of the antibiotic therapy to drawbacks of current diagnostic methods that are used to identify antimicrobial the resistance phenotype of the infecting resistance, novel diagnostic strategies and how such rapid tests can inform drug organism may save the lives of patients, as development and the surveillance of resistance evolution. it has been shown that the optimization of the antibiotic therapy during the first 6–12 h of infection is crucial for the treatment The evolution of drug resistance can have a positive effect at the individual of life-threatening infections. This is mechanisms in pathogenic patient level, diagnostics have a broader particularly true for infections caused by microorganisms poses a global health crisis, role in managing antimicrobial resistance. Gram-negative bacteria, such as those species and millions of people are at risk if the Rapid susceptibility testing is essential to that are currently the main focus of antibiotic problem is not addressed in the laboratory support clinical trials for new anti-infective resistance research. For example, species and translated to the clinic. What role do agents, and aggregate contemporary in the Enterobacteriaceae family that may diagnostics have in managing the challenge data on local and regional antimicrobial produce extended-spectrum β-lactamases of antimicrobial resistance? resistance trends can facilitate antimicrobial that confer resistance to extended-spectrum stewardship, epidemiological surveillance and cephalosporins, carbapenemases that confer Carey-Ann D. Burnham. Antibiotic epidemiological efforts. resistance to carbapenems (imipenem, resistance has emerged as a global health meropenem or ertapenem), or that are crisis and if we cannot reverse the trend we Jennifer Leeds. From my perspective as resistant to polymyxins. Second, the rapid are on a course towards a post-antibiotic era. a leader of an antibacterial drug discovery identification of resistance traits may There are several ways that diagnostic testing group in the pharmaceutical industry, contribute to the identification of patients can assist in managing this challenge. diagnostics enable the appropriate use of new who are infected with resistant pathogens At a very high level, rapid near-patient drugs when they are introduced into clinical but do not show symptoms, particularly in diagnostic assays to distinguish viral practice and throughout their commercial hospital settings. In turn, the immediate from bacterial infections may prevent lifespan. It is important for medical staff and isolation of an infected individual in treatment with unnecessary antibiotics. treating physicians to understand which healthcare facilities could prevent the If a bacterial infection is present, defining drugs will benefit an individual patient, and it development of outbreaks that are associated the aetiology and antibiotic susceptibility is important for the antimicrobial stewardship with multidrug-resistant bacteria and profile is essential to optimize and narrow committees to understand how to address save costs. antimicrobial therapy as quickly as possible. overall patient needs at their institutions Whereas traditional methods used in clinical with respect to antimicrobial resistance. Justin O’Grady. Rapid and comprehensive microbiology laboratories would typically Without a diagnostic device that indicates diagnostics are key for managing require 48 h (or longer) for definitive results, whether a patient is likely to benefit from a antimicrobial resistance; they enable the rapid diagnostic methods are becoming specific drug, the drug could be misused or improved management of patients who are available for routine clinical use; some of not used at all, even if it was available and infected, improved antimicrobial stewardship these methods can provide results within able to save the lives of patients. Appropriate and the development of new antimicrobials. hours. Although rapid tests for infection use is a cornerstone in the management The first clinical question is whether the

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patient needs antimicrobial therapy, and, empirical therapy and facilitating the early to be available before the administration second, if a microbial infection is present, initiation of targeted narrow-spectrum of empirical treatment, particularly when what antimicrobial is appropriate for treatment with proven antibiotic activity dealing with life-threatening infections. successful treatment. Any delay in appropriate against the causative agent of infection. The Providing a comprehensive microbiological antimicrobial therapy can lead to increased ultimate goal for rapid diagnostics should diagnosis before the second dose of empirical mortality in the case of certain infections; for be the identification of the pathogen and treatment may be sufficient to improve example, ventilator-associated pneumonia antimicrobial susceptibility directly from patient outcomes and stewardship until and sepsis1. The rapid identification of clinical samples at point of care within more rapid diagnostic technologies are pathogens and antimicrobial resistance or approximately 30 min. However, currently, available. Moreover, rapid and comprehensive susceptibility will change the way clinicians the fastest diagnostic testing methods diagnostics will enable the development manage infection, reducing the duration of still take hours, and results are unlikely and use of narrow-spectrum antimicrobials by providing pathogen and resistance information in hours rather than days, The contributors* and enabling early targeted therapy. Carey-Ann D. Burnham is an associate professor of pathology and immunology, molecular microbiology, and pediatrics at Washington University School of Medicine, St. Louis, Missouri, Jean Patel. Antimicrobial use is a USA. She is also the Medical Director of Clinical Microbiology for Barnes Jewish Hospital, St. Louis, primary driver of resistance. The CDC Missouri, USA. Her research programme focuses on the development of diagnostic assays for estimates that the use of 50% of antibiotics infectious diseases and the transmission and epidemiology of antimicrobial resistance in bacteria. (antimicrobials used to treat bacterial Jennifer Leeds is an Executive Director and head of Antibacterial Discovery in the Infectious infections) administered in hospitals Diseases Area at the Novartis Institutes for Biomedical Research, Emeryville, California, USA, is inappropriate or unnecessary. New where she is responsible for the strategy and execution of the new antibacterial portfolio, from diagnostics could fundamentally change target discovery through to clinical validation. She is an expert in bacterial genetics and when and how antibiotics are used. physiology, antibacterial mechanisms of action and resistance, drug discovery, clinical A diagnostic test that could accurately microbiology and clinical development. She co‑invented and co‑led the international discovery differentiate a bacterial infection from a project team for the novel antibacterial LFF571, which demonstrated safety and efficacy in viral infection or non-infectious condition humans for the treatment of infection with Clostridium difficile. Recently, her group disclosed the would eliminate most of the unnecessary preclinical discovery programme for LYS228, a novel antibacterial in phase 1 that is being use of antibiotics. A test that could rapidly developed to treat infections caused by carbapenem-resistant members of the Enterobacteriaceae. She represents Novartis in drafting and reviewing recommendations for vehicles to incentivize determine whether a bacterial infection antimicrobial research and development, and is a member of the International Federation of was likely to respond to a specific antibiotic Pharmaceutical Manufacturers Associations (IFPMA) Antimicrobial Resistance (AMR) Research (that is, if it is susceptible) would mean that Working Group. She has chaired several recent meetings and symposia on antimicrobial research doctors could pick an appropriate drug and development and antimicrobial resistance, and is a member of the Finance Committee of the faster, thereby improving patient outcomes, American Society for Microbiology. She received her Bachelor’s degree in microbiology from decreasing the risk of adverse drug events Cornell University, Ithaca, New York, USA, and her Ph.D. in medical microbiology and immunology and reducing the potential for pathogen from the University of Wisconsin-Madison, USA. Prior to joining the pharmaceutical industry in spread. Another crucial role for diagnostics 2001, she was a postdoctoral fellow in microbiology and molecular genetics at Harvard Medical is identifying patients who are colonized, but School, Boston, Massachusetts, USA, where she trained in the laboratory of Jon Beckwith. may not be infected, with resistant bacteria. Patrice Nordmann is Chair of Microbiology in the Department of Medicine, and Head of the These test results can identify hidden Emerging Antibiotic Resistance Unit and of the Foreign Research Unit INSERM (Paris, France) at the reservoirs for transmission, especially in University of Fribourg, Switzerland. He is co‑author of more than 680 peer-reviewed publications. healthcare settings. His research focuses on the emerging antibiotic resistance traits in Gram-negative bacteria, from fundamental genetics to biochemistry and clinical applications. His latest research topics include What are the drawbacks of the methods carbapenemases and acquired resistance to polymyxins in Gram-negative bacteria. currently used to identify antimicrobial Justin O’Grady carried out his Ph.D. (2003–2006) and first postdoctoral position (2006–2008) at resistance? the National University of Ireland, Galway, followed by a 2 year period in industry at Beckman Coulter (2008–2010), Galway, Ireland, all of which were in the area of infection diagnostics. He C.-A.D.B. Most of the commercially subsequently took up a postdoctoral position at University College London, UK, where he focused available rapid methods for identifying on tuberculosis diagnostics. In 2013, he was appointed Assistant Professor in Medical Microbiology antimicrobial resistance are genotypic at Norwich Medical School, University of East Anglia, UK, and was promoted to Associate Professor methods — that is, methods that rely on in 2016. His research focuses on the rapid diagnosis of infectious disease and antimicrobial resistance using molecular methods, with a recent focus on nanopore metagenomic sequencing. the detection of resistance genes or gene Justin O’Grady’s homepage. https://www.uea.ac.uk/medicine/people/profile/justin-ogrady products. There are several limitations to these approaches. The first is that genotypic Jean Patel is a clinical microbiologist who has specific expertise in the laboratory detection of methods can be effective at predicting antimicrobial resistance. She has experience leading the CDC Antimicrobial Resistance Laboratory antimicrobial resistance, but they do not and prior to working for the CDC she worked as the Assistant Director of the Clinical Microbiology Laboratory at the Hospital of the University of Pennsylvania, Philadelphia, USA. She has served as inform antimicrobial susceptibility. In chair and vice chair of the Clinical and Laboratory Standards Institute Subcommittee for addition, with these approaches ‘you only get Antimicrobial Susceptibility Testing and works with the WHO to develop technical guidance for what you look for’ (typically a small panel detecting resistance and strengthening the global surveillance of antimicrobial resistance. of resistance determinants is evaluated). Furthermore, not all resistance phenotypes *Listed in alphabetical order. are conferred by a straightforward genotype,

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and genotypic methods would not detect antibacterial discovery and development resistance has changed this situation, emerging resistance patterns for which the arena, in clinical practice. In addition, it highlighting the need for rapid diagnostics. genotype has not been defined. is not straightforward to add new drugs Increasing antimicrobial resistance is also Phenotypic methods have the advantage to existing testing device platforms, so the forcing changes in recommended first-line of predicting both resistance and susceptibly availability of all approved test formats for a treatments, replacing drugs to which in a relatively unbiased way. However, particular drug typically does not coincide pathogens have developed resistance with microbial growth-based methods have with the introduction of a new drug onto drugs that pathogens are susceptible to but the major disadvantages of requiring a the market. This potentially limits the use are often less effective or cause unwanted relatively large number of viable organisms of the new drug, even when otherwise adverse effects. An example includes the for analysis and of the methods being slow. appropriate. Finally, the current FDA recent change from using trimethoprim to In addition, these growth-based methods guidelines for antimicrobial susceptibility using nitrofurantoin for the treatment of are best suited for central laboratory testing testing devices licensed for use in the United uncomplicated urinary tract infections in and not near-patient testing. Furthermore, States do not allow the use of these devices the United Kingdom; nitrofurantoin must although phenotypic methods used to provide susceptibility data for organisms be avoided in patients with reduced kidney in clinical laboratories today produce that are not part of the approved indication function owing to poor activity (reduced reproducible results2,3, these in vitro assays for a new drug4, so the use of a drug to treat renal elimination of nitrofurantoin, leading cannot approximate the complex ecology of pathogens that are otherwise sensitive to an to a decreased concentration in the urinary infection and do not account for other factors antibiotic is hampered by the lack of available tract) and toxic adverse effects (increased that can influence the outcome of infection, susceptibility testing for those pathogens that concentration of the drug in the blood). such as host response, biofilm formation, might be treatable with a particular drug on Another example is the switch from using interactions with other microorganisms and the basis of preclinical and non-clinical data. ciprofloxacin to cephalosporins for the bioavailability in tissue. treatment of gonorrhoea, as cephalosporins A logistical challenge is that when new P.N. The techniques that are currently used are less effective for the treatment of anti-infective agents are cleared for use, there for the identification of antibiotic resistance pharyngeal infection. Trimethoprim or may be a great lag (sometimes years) before (broth dilution and disk diffusion techniques) ciprofloxacin could still be used in the methods to measure in vitro susceptibility are sometimes time-consuming, expensive approximately 60% of infections caused are developed and/or before these laboratory and not broad enough. Many diagnostic by susceptible pathogens5,6, if these could reagents have regulatory clearance for techniques used for antibiotic susceptibility be identified in a timely fashion using routine diagnostic use. A lack of methods testing still require culturing of the infective rapid diagnostics. PCR tests, particularly for routine susceptibility testing may limit agent, which can take at least 6–18 h. Such more recent sample-to‑answer multiplex the clinical use of these new agents. culture-dependent methods can thus delay PCR technologies (for example, Biofire Last, there are some important gaps the choice of an appropriate antimicrobial Filmarray and Curetis Unyvero panels), are in diagnostic methods; for example, we therapy; that is, the choice of the antibiotic becoming more commonly used in clinical have very limited tools for the diagnosis to which the bacteria is susceptible. Many microbiology. However, the resistance of fungal and mycobacterial infections, molecular techniques are already available markers on these panels are not sufficiently and even fewer for the rapid detection of for the detection of several resistance traits. comprehensive to provide clinically antimicrobial resistance in these pathogens. However, their main drawbacks are that they actionable results in most cases and their Another example is drug-resistant Neisseria are still expensive, they only detect known future use is questionable, as they are used in gonorrhoeae infections, which are an genes, they cannot be used directly for many parallel to culture-based methods but cannot urgent public health threat. Although rapid clinical samples that contain too few bacterial replace them. molecular assays exist that provide sensitive isolates (for example, for blood samples), and specific detection of this pathogen and the presence of a resistance gene does J.P. Current testing methods for selecting in clinical specimens, the detection of not necessarily correlate with the resistance an effective antibiotic can be too slow or antimicrobial resistance genes is not a phenotype. In fact, gene expression level and provide limited information. Specifically, component of these assays. A potential combined mechanisms of resistance may traditional phenotypic susceptibility downside to these rapid molecular make those resistance traits difficult to predict testing results are usually available 36–72 h methods is an absence of culture isolates for through the use of molecular techniques after the sample is collected from the susceptibly testing, which could be important alone. Indeed, several and different combined patient. This is too slow to help with both for the care of an individual patient biochemical mechanisms may provide the initial treatment decisions and, because but also for gathering population-level same resistance phenotype. of the delay, results are often not used to surveillance data. de‑escalate or update the treatment plan J.O’G. In light of rapidly increasing when such action is warranted. Molecular J.L. For many infection types, the turnaround antimicrobial resistance, current tests, such as PCR or hybridization tests for time for diagnosis and the implementation culture-based methods are no longer fit resistance mechanisms, are much faster, with of diagnostic information is rather slow, for purpose for the diagnosis of infection, turnaround times of 1–4 h. These tests can so changes from empirical to targeted particularly acute infection, owing to the slow be very useful for treatment decisions for treatment, or inappropriate to appropriate turnaround time of results. Until relatively infections caused by Gram-positive bacteria, therapy, may not occur on an effective recently, empirical broad-spectrum treatment such as Staphylococcus aureus, because the timescale. This could limit the benefit worked for the vast majority of infections, and number of resistance mechanisms in this of niche or narrow-spectrum agents, culture results were only used clinically when species is limited. By contrast, resistant which are a growing emphasis within the treatment failed. Increasing antimicrobial Gram-negative bacteria, such as species in

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the Enterobacteriaceae, Acinetobacter spp. breadth of the panel of microorganisms and P.N. The novel strategies for detecting and Pseudomonas spp., have many different antimicrobial agents that can be detected, emerging resistance traits may be based on resistance determinants (resistance genes and the flexibility of the system to expand molecular biology techniques, immunology, and mutations), and often the phenotypic testing to additional microorganisms and biochemistry and rapid culture techniques. resistance results from a combination antimicrobial agents as required. Novel molecular techniques will involve of determinants that encode resistance novel machines based mostly on a PCR mechanisms acting together at different J.L. There are some new rapid image-based technique. However, the costs associated with sites in the bacterial cell. As resistance is technologies that could provide the purchasing and maintaining such devices so complex, tests that detect only a subset turnaround of information more quickly are currently still too high for them to be of resistance mechanisms provide limited in a clinical setting. Current culture-based available to many institutions and hospitals. information for picking a therapeutic agent. methods that require isolated colonies Following the development and approval, to grow before susceptibility data can such novel technologies can be used as a What novel diagnostic strategies and be acquired can take up to 48 h or more, point‑of‑care technology in hospital settings, approaches can be implemented to depending on the time lag from patient such as intensive care units, as well as for identify antimicrobial drug resistance? What sampling to the start of the clinical general healthcare providers in medical parameters need to be considered when microbiology laboratory processes, the practices. The spread of techniques such as developing phenotypic and genotypic tests testing time and the time to turn data around the whole-genome sequencing may provide for the rapid and accurate detection (or and have it reviewed by a physician. New some help for the rapid identification confirmation) of antimicrobial resistance and methods that can use direct-from-sample of specific resistance traits. However, when selecting useful therapeutic agents? testing and that can report drug susceptibility whole-genome sequencing takes at least without the need for standard culture several hours to obtain results. Currently, C.-A.D.B. There are several novel strategies techniques may shorten that time window by this technique is widely used to compare that can be implemented. It is well established at least one day, perhaps more. For example, susceptible strains that could be a potential that outpatient visits for respiratory infections on the basis of the information disclosed on source of outbreaks. are the setting in which the most unnecessary their website, the Accelerate PhenoTest BC kit Immunological techniques that are based antimicrobials are prescribed. Near-patient can identify species from blood culture in less on antibody–antigen reactions are also testing to rule out bacterial infection or than 90 min and antibiotic susceptibility in being developed, as they provide simple, confirm viral aetiology may be a simple less than 7 h7. There are also some hand-held cost effective and convenient solutions approach to reducing the unnecessary use nucleic acid-based rapid diagnostic devices for the identification of several antibiotic of antimicrobials. being developed that may be useful in field resistance traits. Moreover, rapid culture In the setting of serious bacterial infection, settings, especially when the practicality of methods, such as those for identifying rapid phenotypic methods are needed. The culture-based diagnostics is not feasible but resistance to polymyxins in members of the ideal method would provide definitive results the likelihood of certain pathogens is high8. Enterobacteriaceae (rapid polymyxin NP directly from the clinical specimen within What parameters need to be considered test), as well as biochemical approaches, such 5–8 h of specimen collection; with these when developing phenotypic and genotypic as those used to identify broad-spectrum performance characteristics, the second tests for the rapid and accurate detection (or enzymes (such as extended-spectrum dose of antibiotics administered could be confirmation) of antimicrobial resistance and β-lactamases or carbapenemases, using the directed therapy. when selecting useful therapeutic agents? To rapid ESBL NP test and rapid Carba NP Although phenotypic methods to me, as a drug discoverer, the most important test, respectively), already enable the rapid detect both resistance and susceptibility aspect of new diagnostic tools is that they identification of resistance markers, although to antibiotics are desired, conventional provide clarity about when it is appropriate the underlying molecular mechanisms growth-based systems are slow, and to use a particular agent. However, knowing of resistance remain unknown. These attempts to increase the doubling time of that an organism contains genes that could techniques provide results within 2 h. microorganisms have resulted in very limited confer resistance to a particular drug still Overall, the parameters of any novel success. Thus, there is a need to focus on the does not necessarily inform what that diagnostic technique to be studied are development of new methods to detect this organism is susceptible to. Thus, a treating sensibility, specificity, and positive and growth with improved sensitivity, an example physician really benefits when they are negative predictive values. In addition, of which could be measuring metabolic end given a list of agents that will work against a a particular concern is that rapid tests should products as a surrogate for microbial growth. particular pathogen, not just what will not take into account that there is not necessarily In addition, methods that measure the host work. To achieve this, a device will need to a correlation between the resistance response to therapy are desired. For many robustly report susceptibility data, not just phenotype and genotype. infections, the optimal duration of antibiotic the presence of a resistance determinant, treatment is not known, but measuring the to a panel of available drugs. In addition, J.O’G. Recently, agnostic metagenomic host response could be an effective tool the presence of genetic material does not sequencing has been tested for the to establish an appropriate end point to always correlate with the expression levels rapid and comprehensive diagnosis of antimicrobial therapy. of those genes, nor does it necessarily take pathogens and antimicrobial resistance, Thus, factors that should be considered into account other intrinsic or acquired with a first trial currently ongoing for when developing new assays include sample mechanisms that contribute to the loss of hospital-acquired pneumonia. Rapid requirements (that is, can testing be carried susceptibility; therefore, a phenotypic test nanopore metagenomic sequencing can out directly on a clinical specimen or on a method will often need to be paired with a identify a pathogen (bacteria, viruses, fungi pure culture of organism), analysis time, the genotypic method to capture that complexity. and parasites) and its associated resistance

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profile within hours (for example, 4 h for including metagenomics, will initially be Aside from antibiotics, novel therapeutic the diagnosis of urinary tract infections9) most important for pathogens such as approaches are necessary. Academics and in a single test. This is a very powerful Mycobacterium tuberculosis, N. gonorrhoeae industry must work together to improve technique that is likely to have a big effect on and Salmonella spp. our understanding of the microbial clinical microbiology in the coming years. Sequencing will be a powerful tool for disruption that occurs when antimicrobial However, the detection of antimicrobial the rapid identification of antimicrobial therapy is administered and what can resistance (rather than susceptibility) is not resistance, but phenotypic antimicrobial be done to combat this. Furthermore, ideal, as it informs clinicians on what not susceptibility testing is likely to remain the an improved understanding of how our to prescribe rather than providing clear ‘gold standard’ testing strategy for selecting a resident microbiota contributes to health treatment options. Also, genotypic resistance therapeutic agent. This is because genotypic and disease, and what microorganisms are may not always correlate with phenotypic testing can only tell us about resistance most important to resistant colonization or resistance (for example, resistance related to mechanisms and determinants that have infection with pathogens, is an important area gene expression levels), and many resistance already been discovered, which means of investigation. mechanisms are multifactorial and not that new resistance could be missed and yet fully understood. Rapid susceptibility spread undetected. Although phenotypic J.L. It is an exciting time in antibacterial testing directly from clinical samples is susceptibility methods have slow turnaround drug discovery and diagnostic innovation. challenging, but should be the ultimate goal times, technological advances are shortening I attended the American Society for for diagnostic technologies attempting to these delays. Recent phenotypic innovations Microbiology (ASM) Microbe meeting replace culture-based methods. include single-cell light microscopy, mass 2017 and there was a session called “Bad MALDI-TOF and rapid microscopy- spectrometry and measuring genomic Bugs, New Drugs — but No Tests!”. The based susceptibility testing methods are transcription after antibiotic exposure. These room was packed as a panel consisting available (for example, Accelerate PhenoTest methodological strategies are all faster than of a drug developer, a hospital-based BC), but these systems currently rely on waiting for bacteria to grow overnight in the clinical microbiologist, a diagnostic device cultured clinical samples and/or isolates, presence of antibiotics. These methods can manufacturer, and an infection control which are typically only available 24 h post- become even faster if coupled with advances specialist and Jean Patel (an epidemiology incubation. Although combining quantitative in technologies that capture and test low expert from the CDC), helped the PCR (qPCR)-based detection (or, in the numbers of infectious agent from clinical microbiology community to understand future, rapid metagenomics) of pathogen specimens. This would eliminate or shorten the latest developments in the diagnostic nucleic acid and shortened culture of isolates the incubation time required to have enough device arena. In my opinion, every academic in media containing antibiotics has been bacteria for testing using current methods. and industry scientist who is innovating shown to be an effective method for testing The FDA recently approved a phenotypic diagnostic approaches should attend events antimicrobial susceptibility, the requirement susceptibility method that can produce such as this one so that they can become for isolated bacteria increases the turnaround results within about 6.5 h of a positive blood aware of the needs and limitations of all time for results. It remains to be seen whether culture10. This is a great advancement and aspects of the field. This also gives them a such technologies can be optimized to work hopefully even faster phenotypic methods few points of contact with whom to interact directly on clinical samples, particularly will be available in the future. and begin to learn more about the practical those that contain high bacterial loads, nature of diagnostics and where innovation such as samples from patients with urinary What opportunities are there for can truly have an effect. Working across tract infections. academics, clinicians and scientists in drug development and device development industry to work together to innovate and as a coordinated and collaborative effort J.P. Genotypic testing is fast and implement diagnostics that improve patient is crucial, both from a regulatory and reproducible, and whole-genome care and public health? from a practical standpoint. Open lines of sequencing is becoming more affordable. communication among clinical laboratory Sequencing data can more accurately detect C.-A.D.B. Translational research — an staff, healthcare providers, drug developers antibiotic resistance because databases that ongoing process of iteration — is essential and device innovators is crucial to appreciate correlate molecular findings to phenotypic to drive the innovation that is needed to the goals and the needs of each partner, so resistance, such as ResFinder, are more improve patient outcomes and public health. that innovators can deliver products that meet robust. Sequencing has the additional For the success of this translation, academics and exceed the expectations of the individual benefits of providing molecular typing and clinicians will need to work with stakeholders, and the decision makers who data to help with outbreak detection industry partners to develop and evaluate back them, by providing necessary resources. and helping infection control experts to new products and move them forward Spending time ‘walking in each other’s shoes’ better understand transmission dynamics. towards market, and diagnostic methods can teach you a lot about what excites each Advances in metagenomic techniques need to be developed in conjunction with party and what barriers may lie in the way hold promise that we will soon be able to new antimicrobial agents. Equally important of a great idea being adopted into clinical obtain crucial antimicrobial resistance data is the need for ongoing surveillance to practice. Finally, we need to really support from slow-growing pathogens, fastidious identify emerging mechanisms of resistance training and careers in clinical microbiology. pathogens or pathogens that are now as early as possible and the characterization Without trained staff who can implement commonly detected by culture-independent of resistance mechanisms; this knowledge the use of new devices and provide accurate diagnostics, which, although rapid, is essential for the ongoing development of information back to physicians and other provide less data-rich results. For these diagnostic methods and antimicrobial agents healthcare personnel, the true societal value and other reasons, sequencing approaches, for emerging resistance mechanisms. of new devices is at risk.

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P.N. Academics who are working in prospects (very few new classes of antibiotic Preventative medicine, in addition to association with hospitals have a privileged have been discovered since the 1980s) and education on health and the appropriate situation to detect emerging resistance diminishing returns on investment (the use of anti-infective agents, is fundamental phenomena, as they have access to samples development pipeline is extremely expensive in the battle against the post-antibiotic and patients who are infected. On the basis and antibiotics are relatively cheap drugs). era. Coordinated, global surveillance and of their observations, they may be in a Hence, there is a dearth of new antimicrobials antibiotic-sparing efforts are needed. position to develop specific novel diagnostic in the pipeline. Governments must look Laboratories are challenged to rapidly tests that correspond to a clinical need, beyond big pharma to, for example, small respond with diagnostic testing methods such as the detection of new drug-resistant and medium-sized enterprises (SMEs) and for emerging resistance mechanisms and pathogens. However, the development of universities, who can team up to advance pathogens. We should view diagnostics, resistance tests mostly relies on industry, as the discovery and development of novel therapy and antibiotic resistance as a single the microbiological diagnostic industry has antibiotics and companion diagnostic tests. continuous process. Results of laboratory extensive know-how and the money to invest Clearly, the appropriate mechanisms and testing must be integrated into diagnostic rapidly in the field. As extensively done in the government funding need to be in place for pathways; collaboration and integration of past, clinicians and clinical microbiologists this approach to be successful. laboratory medicine professionals in patient will have a key role in the evaluation and care continuum is essential. Academics implementation of any novel diagnostic tests J.P. The CDC has several networks for and industry must work together to build that are being developed by industry, and evaluating and implementing novel robust, curated repositories of pathogen they will have the main role in choosing diagnostics that will improve antibiotic use sequence data and corresponding phenotypic and retaining the most suitable technique and the containment of antibiotic-resistant and clinical data. These data are necessary to identify a resistance trait as a source of infections. Specifically, the CDC has a to realize the potential of sequence-based infection or at the carrier state, based on the network of academic centres, the Prevention diagnostics, computational pipelines, and the clinical value of each test and their cost. Epicenters, which develops and evaluates development of both new diagnostics and innovative ways, including novel diagnostics, new anti-infective agents. J.O’G. Innovation, translation and to improve antibiotic stewardship and implementation skills are all required prevent healthcare-associated infections. J.L. We need to continue to monitor trends for new diagnostic tests to reach the In addition, the CDC has established the in the epidemiology of resistant pathogens bedside; hence, diagnostics innovators in Antibiotic Resistance Laboratory Network through global surveillance, as well as different areas naturally collaborate closely. (ARLN), which leverages public health point prevalence studies. The availability Recently, governments have provided more laboratory capacity to fill the gaps in testing of diagnostics is crucial to help generate funding for research and development that is usually carried out in healthcare meaningful data sets. The data around the into antimicrobial resistance and this has settings. The ARLN consists of seven regional epidemiology and spread of resistance are opened many additional opportunities for laboratories for advanced antimicrobial what help drug discoverers and developers academic, industrial and clinical innovators resistance testing capacity, one national to understand current, and predict future, to work together. The quality and scope tuberculosis whole-genome sequencing medical need. It takes a long time to discover of diagnostic clinical trials have improved laboratory, and additional testing in 57 state and bring a new antibacterial drug to market; with investment, with recent studies and large city laboratories. In the ARLN, the thus, if we only react once a threat is urgent, considering more than test specificity and CDC will use innovative tools evaluated by we are constantly ‘fighting the last war’. The sensitivity, and turnaround time, addressing other programmes to improve our ability to availability of robust diagnostics can keep us antimicrobial stewardship, cost–benefit generate antimicrobial resistance data for ahead of the threat posed by antimicrobial analysis and scientist and clinician behaviour containment and prevention. The CDC is also resistance and help us to place resources in relation to new diagnostics (for example, working to make sure that new diagnostics where they will have the biggest effect with the INHALE hospital-acquired pneumonia can detect all types of antibiotic resistance by respect to managing resistance. With such diagnostic trial). These multidisciplinary making ARLN samples of resistant bacteria accurate and implementable diagnostics, and approaches are crucial if better diagnostics gathered nationwide available in the CDC the necessary information technology (IT) are to be developed and implemented in and FDA Antibiotic Resistant Isolate Bank. systems to support these efforts, we as drug clinical microbiology. An example of a discoverers would have access to up‑to‑date potential area for future multidisciplinary Looking beyond the development of information, on a global scale, of where the collaboration is combining the detection diagnostics, what else is needed in the biggest threats and unmet medical needs lie. of human biomarkers of infection, such as battle against antimicrobial resistance? For blood transcriptional biomarkers11, with example, how will diagnostics inform drug P.N. Beyond the development of diagnostic the detection of the pathogen and the development and the surveillance of resistance techniques, the development of novel drugs antimicrobial resistance profile in a single evolution in the laboratory? What other tools is of the utmost importance to control the test. For example, using host and pathogen are needed in this pursuit? development of antimicrobial resistance. metatranscriptomics for the diagnosis of This development will most likely be driven sepsis could determine whether an infection C.-A.D.B. Even better than rapidly by industry, through the development of is present and, if an infection is present, could diagnosing and treating an infection would novel chemical agents with antibacterial guide appropriate antimicrobial therapy. be preventing it from occurring in the activity. The extensive reports of emerging ‘Big pharma’ are pulling out of first place. Vaccines are one component resistance traits will pave the way for antimicrobial discovery and development, of this, as are infection prevention efforts choosing the antibiotic to be developed. as they are faced with poor discovery in both hospital and community settings. Moreover, antimicrobial resistance in

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Gram-negative bacteria will continue to agencies will be able to monitor pathogens Justin O’Grady is at Norwich Medical School, increase, as they emerge in the community in real time, making it feasible to track Faculty of Medicine and Health Sciences, University of East Anglia, Norwich NR4 7TJ, UK. setting (in which their spread is difficult outbreaks as they occur, monitor resistance [email protected] or impossible to control) and resistance evolution and spread, identify transmission Jean Patel is at the Antibiotic Resistance Coordination traits are being transmitted in the hospital events, and improve infection control and Strategy Unit, National Center for Emerging settings. It is of vital importance to develop and prevention. The depth and richness Zoonotic and Infectious Diseases, Centers for Disease simple computer-based strategies for the of the data will far outweigh current Control and Prevention, 1600 Clifton Road, Atlanta, identification of patients who are diagnostics data. However, there are many Georgia 30329–4027, USA. [email protected] possibly infected with an antimicrobial- barriers to replacing culture-based methods. resistant pathogen at the hospital level Both the personnel and infrastructure need doi:10.1038/nrmicro.2017.103 to detect possible carriers of antibiotic to be in place to handle big data, manage Published online 12 October 2017 1. Kuti, E. L., Patel, A. A. & Coleman, C. I. Impact of resistance. For example, in many hospitals rapid results so that they reach clinicians in inappropriate antibiotic therapy on mortality in worldwide, it is still impossible to know a timely fashion and analyse and interpret patients with ventilator-associated pneumonia and blood stream infection: A meta-analysis. J. Crit. Care whether the patient has been transferred the sequence data. Governments, regulatory 23, 91–100 (2008). from a hospital in which the patient could authorities, clinicians and scientists all 2. Doern, G. V. & Brecher, S. M. The clinical predictive value (or lack thereof) of the results of in vitro have been infected with a multidrug-resistant need to be willing to accept, and to drive, antimicrobial susceptibility tests. J. Clin. Microbiol. 49, bacterium. In addition, the extensive this change. S11–S14 (2011). 3. Clinical and Laboratory Standards Institute. use of precise and rapid diagnostics will Development of in vitro Susceptibility Testing Criteria facilitate epidemiological surveillance of J.P. A key aspect of our efforts to combat and Quality Control Parameters. 4th edn (CLSI, 2008). 4. Kircher, S. M. et al. The Susceptibility Testing resistance worldwide in ‘real time’. Many antibiotic resistance is a robust IT Manufacturers Association presents an opinion for the important resistance traits are still only infrastructure; this affects all aspects of delay of current susceptibility tests. Clin. Infect. Dis. 63, 1531–1532 (2016). being identified after the resistance trait antimicrobial resistance. In healthcare 5. Kahlmeter, G., Åhman, J. & Matuschek, E. has spread worldwide, as exemplified facilities, we need to ensure that diagnostic Antimicrobial resistance of Escherichia coli causing uncomplicated urinary tract infections: A European by the global spread of the extended- tests are rapidly and clearly reported to update for 2014 and comparison with 2000 and spectrum β-lactamase CTX‑M-15, and the healthcare providers at the bedside. Too 2008. Infect. Dis. Ther. 4, 417–423 (2015). 6. Public Health England. Surveillance of antimicrobial carbapenemases OXA‑48 and more recently often, laboratory information systems and resistance in Neisseria gonorrhoeae: key findings from New Delhi metallo-β-lactamase. electronic medical records have limited the Gonococcal Resistance to Antimicrobials Surveillance Programme (GRASP). GOV.UK https://www.gov.uk/ capability to communicate complex test government/uploads/system/uploads/attachment_data/ J.O’G. file/567602/GRASP_Report_2016.pdf (2016). Rapid diagnostics will enable the results. Public health also needs advances 7. Accelerate Diagnostics. Accelerate Pheno system. targeted recruitment of patient samples that in IT. The CDC is addressing this need by Accelerate Diagnostics http://acceleratediagnostics.com/ products/accelerate-pheno-system/#features (2017). contain specific pathogens with specific building surveillance program to capture 8. Nather, D. Inside the Pentagon’s biotech strike force. resistance profiles in clinical trials of both antibiotic use and resistance data from STAT News https://www.statnews.com/2015/11/24/ darpa-biotech-infectious-disease/ (2015). antimicrobials and inhibitor combinations. electronic medical records. Healthcare 9. Schmidt, K. et al. Identification of bacterial pathogens This is currently very important; for example, facilities, as well as local, state and regional and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. in the development of β‑lactamase inhibitor public health authorities, can use these data J. Antimicrob. Chemother. 72, 104–114 (2017). combinations. Currently, it is commonplace to implement containment and prevention 10. US Food and Drug Administration. FDA allows marketing of test to identify organisms that cause bloodstream for more than 75% of the recruited patients measures. The CDC is also working to create infections and provide antibiotic sensitivity results. in a trial to be infected with a pathogen that interactive tools so that the data are easily FDA https://www.fda.gov/NewsEvents/Newsroom/ PressAnnouncements/ucm543150.htm (2017). is sensitive to the antibiotic alone, which accessible by the public, including academic 11. McHugh, L. et al. A molecular host response assay to means that less than 25% of the samples can and industry partners who need such data discriminate between sepsis and infection-negative systemic inflammation in critically ill patients: discovery be used to test the inhibitor. Moreover, if for strategic decision making. and validation in independent cohorts. PLoS Med. 12, we can replace culture-based methods with e1001916 (2015). Carey-Ann D. Burnham is at the Department of rapid diagnostics, clinicians can prescribe Pathology & Immunology, Washington University Competing interests statement targeted narrow-spectrum agents. This will The authors declare competing interests: see Web version for School of Medicine, 660 South Euclid Avenue, details. reinvigorate the antimicrobial development Campus Box 8118, St. Louis, Missouri 63110, USA. [email protected] Publisher’s note pipeline by creating a more diverse market. Springer Nature remains neutral with regard to jurisdictional Novel narrow-spectrum agents are easier to Jennifer Leeds is at Novartis Institutes for claims in published maps and institutional affiliations. discover than broad-spectrum agents (as their Biomedical Research, Inc., Infectious Diseases Area, activity is for a specific pathogen or pathogen 5300 Chiron Way, Emeryville, California 94608, USA. FURTHER INFORMATION [email protected] ResFinder: https://cge.cbs.dtu.dk/services/ResFinder/ group rather than across a broad range of INHALE hospital-acquired pneumonia diagnostic trial: pathogens) and are hence potentially cheaper http://www.ucl.ac.uk/inhale-project/overview Patrice Nordmann is at the Medical and Molecular Prevention Epicenters: to develop, but they can only be developed Microbiology Department of Medicine, INSERM https://www.cdc.gov/hai/epicenters/index.html and used if better diagnostics are in place. European Laboratory (French National Institute for Antibiotic Resistance Laboratory Network (ARLN): Health and Medical Research, Paris), https://www.cdc.gov/drugresistance/solutions-initiative/ The implementation of rapid and ar-lab-networks.html Natural Reference Center for Emerging Antibiotic comprehensive diagnostics, such as CDC and FDA Antibiotic Resistant Isolate Bank: https:// Resistance, University of Fribourg, Chemin du www.cdc.gov/drugresistance/resistance-bank/index.html metagenomic sequencing, will change Musée 18, 1700 Fribourg, Switzerland. ALL LINKS ARE ACTIVE IN THE ONLINE PDF public health globally. Public health [email protected]