Against Antimicrobial Resistance Research Articles

A monitoring framework for reinforcing policies against antimicrobial resistance in Europe

Abstract In an attempt to overcome barriers to the effective implementation of policies against antimicrobial resistance (AMR) in the EU Member States, Norway and Iceland, One Health national action plans (NAPs) need to show improvements in both their formulation and their implementation. Research conducted by Tetra Tech, funded by the EU4Health Programme, has identified shortcomings to One Health national policies across all countries, such as limited political focus and awareness of the challenges brought by AMR; lack of operational plans for delivering on the NAPs; and lack of harmonised indicators and inadequate information systems for monitoring the implementation of plans. On this last issue, subsequent reseach by Tetra Tech has supported the design and development of monitoring indicators for reinforcing the expected improvements of NAPs and the implementation of policies aimed at EU Member States in the 2023 “Council Recommendation on stepping up EU actions to combat antimicrobial resistance in a One Health approach”. While drawing on existing data sources at EU and global level, the study has also worked with Member States representatives in identifying indicators for the monitoring framework and proposed new data collection activities at the national level. Key messages • EU countries face common barriers to the effective implementation of One health policies against AMR, and need to reinforce their national action plans. • Stepping up the fight against AMR in the EU requires a strong monitoring framework for following up on EU recommendations.

Interpenetrated Polymer Network Systems (PEG/PNIPAAm) Using Gamma Irradiation: Biological Evaluation for Potential Biomedical Applications

The potential antimicrobial and antibiofouling properties of previously synthesized PEG/NiPAAm interpenetrated polymer networks (IPNs) were investigated against three of the most common bacteria (E. coli, S. aureus, and S. epidermidis). The main goal was to evaluate the material’s biocompatibility and determine its potential use as an antifouling component in medical devices. This was intended to provide an alternative option that avoids drug usage as the primary treatment, thus contributing to the fight against antimicrobial resistance (AMR). Additionally, characterization and mechanical testing of the IPN were carried out to determine its resistance to manipulation processes in medical/surgical procedures. IPNs with different NiPAAm ratios exhibited excellent cytocompatibility with BALB/3T3 murine fibroblast cells, with cell viability values of between 90 and 98%. In addition, the results regarding the adsorption of albumin as a model protein showed a nearly constant adsorption percentage of almost zero. Furthermore, the bacterial inhibition tests yielded promising results, demonstrating effective pathogen growth inhibition after 48 h. These findings suggest the material’s suitability for use in biomedical applications.

Fast and Economic Microarray-Based Detection of Species-, Resistance-, and Virulence-Associated Genes in Clinical Strains of Vancomycin-Resistant Enterococci (VRE)

Today, there is a continuous worldwide battle against antimicrobial resistance (AMR) and that includes vancomycin-resistant enterococci (VRE). Methods that can adequately and quickly detect transmission chains in outbreaks are needed to trace and manage this problem fast and cost-effectively. In this study, DNA-microarray-based technology was developed for this purpose. It commenced with the bioinformatic design of specific oligonucleotide sequences to obtain amplification primers and hybridization probes. Microarrays were manufactured using these synthesized oligonucleotides. A highly parallel and stringent labeling and hybridization protocol was developed and employed using isolated genomic DNA from previously sequenced (referenced) clinical VRE strains for optimal sensitivity and specificity. Microarray results showed the detection of virulence, resistance, and species-specific genes in the VRE strains. Theoretical predictions of the microarray results were also derived from the sequences of the same VRE strain and were compared to array results while optimizing protocols until the microarray result and theoretical predictions were a match. The study concludes that DNA microarray technology can be used to quickly, accurately, and economically detect specifically and massively parallel target genes in enterococci.

Vermicomposting reduces the antimicrobial resistance in livestock waste

Vermicomposting, a process in which housefly larvae are used to decompose organic waste, has attracted attention as a method for managing antimicrobial-resistant bacteria (ARB) in livestock manure. Vermicomposting effectively reduces antimicrobial resistance genes (ARGs) and residual antimicrobials. However, the evaluation of live bacteria, including ARB, remains scarce. Additionally, conventional DNA extraction methods include DNA from dead bacteria, impeding the accurate evaluation of ARG-associated risk in compost and the microbiome. This study assesses the effectiveness of vermicomposting pig manure against antimicrobial resistance (AMR) by evaluating the ARB, ARGs (focusing on DNA from live bacteria), and microbiome associated with vermicomposting processes. Vermicomposting significantly reduces the abundance of bacteria, including ARB, and decreases the ARG (tetA, tetB, blaTEM, and blaCTX−M) copy number in live bacteria. Bacterial community analysis revealed an increase in the abundance of Gammaproteobacteria. Moreover, the vermicomposted samples effectively cultivated myriad plants. Overall, vermicomposting effectively reduces the ARB and ARGs in pig manure, with potential benefits for plant growth and sustainable waste management. Hence, it can be widely applied to treat livestock manure and other organic wastes to combat AMR.

Enhanced Suppression of Stenotrophomonas maltophilia by a Three-Phage Cocktail: Genomic Insights and Kinetic Profiling.

In our era of rising antibiotic resistance, Stenotrophomonas maltophilia (STM) is an understudied, gram-negative, aerobic bacterium widespread in the environment and increasingly causing opportunistic infections. Treating STM infections remains difficult, leading to an increase in disease severity and higher hospitalization rates in people with Cystic Fibrosis (pwCF), cancer, and other immunocompromised health conditions. The lack of effective antibiotics has led to renewed interest in phage therapy; however, there is a need for well-characterized phages. In response to an oncology patient with a respiratory infection, we collected 18 phages from Southern California wastewater influent that exhibit different plaque morphology against STM host strain B28B, cultivated from a blood sample. Here, we characterize the genomes and life cycle kinetics of our STM phage collection. We hypothesize that genetically distinct phages give rise to unique lytic life cycles that can enhance bacterial killing when combined into a phage cocktail compared to the individual phages alone. We identified three genetically distinct clusters of phages, and a representative from each group was screened for potential therapeutic use and investigated for infection kinetics. The results demonstrated that the three-phage cocktail significantly suppressed bacterial growth compared to individual phages when observed for 48 hours. We also assessed the lytic impacts of our three-phage cocktail against a collection of 46 STM strains to determine if a multi-phage cocktail can expand the host range of individual phages. Our phages remained strain-specific and infect >50% of tested strains. The multi-phage cocktail maintains bacterial growth suppression and prevents the emergence of phage-resistant strains throughout our 40-hour assay. These findings suggest specialized phage cocktails may be an effective avenue of treatment for recalcitrant STM infections resistant to current antibiotics.

Mandatory vs. Voluntary? How to Conceive and Implement the ‘Right’ Measures to Fight AMR

SummaryThe fight against antimicrobial resistance (AMR) usually relies on a large set of measures, such as banning or restricting the use of certain molecules, promoting preventive approaches to animal health, monitoring antibiotic use and prescription, training farmers and veterinarians, developing quality schemes and labels, etc. These measures can be mandatory (i.e. regulations) or voluntary (i.e. private standards, professional guidelines, etc.), depending on the policy style adopted in each country: imposing the same framework of action for everyone or trying to stimulate stakeholders’ initiatives. It is however difficult to say that one option is better than another, given that reduction of antimicrobial use in livestock has been achieved in different European countries using different options. Based on a cross‐reflection from three ROADMAP case studies, this Point de Vue argues that an efficient and legitimate AMR policy has to adopt a combination of voluntary and mandatory measures which is carefully thought through and which is adapted to local contexts and dynamics.

Plectasin’s Odyssey

The seminar "Plectasin's Odyssey: From Hopeful Beginnings to Untimely End," held on the 16th of November 2023 at University of Copenhagen, Denmark, gives us an overview of the challenges in developing new antibiotics inside the antimicrobial pipeline. The seminar focused on the story of Plectasin, the first antimicrobial peptide found in a fungus, discovered by Novozymes back in 2002. A group of twelve people was invited, including key figures of the original discovery team of Plectasin, as well as academic historians and researchers. The story of Plectasin highlighted how complex and challenging it is to bring a new drug into pharmaceutical development. The participants reflected on the initial excitement of discovering Plectasin and its potential as a good antimicrobial candidate. Subsequently, discussions focused on market obstacles, including the crucial roles of regulatory and economic stakeholders. The issue of a visible gap between the health system’s needs and the pharmaceutical industry’s focus, the importance of innovative funding and development models, and the potential for repurposing shelved antimicrobial candidates were addressed. However, it was agreed that publication of the discovery in prestigious journals such as Nature and Science added to the perceived competence by the public of Novozymes as a company. In summary, a common thread in the discussion was the urgent need for a shift towards more collaborative, community-focused, and sustainably financed strategies in antibiotic development. Such a change is essential if we are to stand a chance in the global fight against antimicrobial resistance (AMR).

Escherichia coli isolates from vegetable farms in Addis Ababa, Ethiopia: Antimicrobial susceptibility profile and associated resistance genetic markers.

The use of animal manure to fertilize soil is an emerging concern contributing to the transfer of antimicrobial-resistant pathogens to vegetables. Hence, assessing antimicrobial susceptibility profile of Escherichia coli in vegetable farms is essential to design appropriate interventions against antimicrobial resistance (AMR) in the food chain. This study assessed antimicrobial resistance profile and associated genetic markers among E. coli isolated from vegetable farms fertilized with animal manure in Addis Ababa, Ethiopia. A total of 1044 samples were collected using convenience sampling: soil (n = 271), manure (n = 375), and vegetables (n = 398) from 81 vegetable farms in Addis Ababa, Ethiopia. Antimicrobial susceptibility test was conducted for 100 E. coli isolates and antimicrobial resistance genes (ARGs) were tested by polymerase chain reaction (PCR). Of the 1044 collected samples, 25.3% were positive for E. coli, with significantly higher prevalence in the manure sample and samples collected from Akaki Kality sub-city (p < .05). The highest resistance rate was recorded for tetracycline (72%), followed by streptomycin (63%), and sulfamethoxazole +trimethoprim (56%). Multidrug resistance was detected in 61% of the E. coli isolates. The aac(3)-IV (76.9%), bla TEM (65.4%), aadA (60.3%), tet(A) (58.3%), and sulI (51.7%) were the commonly detected resistance genes. The current study showed a high burden of antimicrobial resistance among E. coli isolated from manure-amended vegetable farms, with potential of playing a significant role in the dissemination of antimicrobial resistance in the food chain. Efforts should be made to reduce the burden of resistant organisms and ARGs through prudent use of antimicrobials in livestock and application of appropriate composting techniques before using manure as fertilizer.

Participatory antimicrobial stewardship: fostering patient and public engagement to counter antimicrobial resistance.

International governments defined antimicrobial stewardship (AS) as an essential ally against antimicrobial resistance (AMR). Patient and public engagement (PPE) in AS was pointed out as an imperative requirement to be embraced. We discuss PPE state of the art in AS and methodological reflections on how to achieve its effective implementation.

Detection of veterinary antibiotic residues in fresh fecal samples collected from selected pig farms in the City of Baybay, Leyte, Philippines

Investigations on the presence of antibiotic residues in livestock manure are becoming an integral part on the quest against antimicrobial resistance (AMR). Moreover, as a potential hazard to human health and the environment, the threat of antibiotic residues cannot be taken lightly. As one of the biggest pig producers in Eastern Visayas, the Province of Leyte, Philippines is presented with the challenge to sustain the pork requirements of the region despite its limited overall production. This study aims to determine the prevalence of antibiotic residues present in the swine manure among selected commercial piggery farms in Baybay City, Leyte. Using147 fecal samples collected from different classes of pigs and following standard microbial inhibition plate technique, this study consistently found inhibitory action against the growth of Bacillus subtilis across three pH levels from fecal samples collected from grower-finishers, and breeders unlike samples collected from both the lactating and farrowing sows. These results may provide insights and baseline information useful for similar studies on antibiotic residues in meat and meat products that may have implications on human health.

Barriers to the effective implementation of One health policies against AMR in the EU

Abstract Funded by the EU4Health 2021 Programme, Tetra Tech conducted a study for the European Commission on the “Barriers to the effective implementation of policies against antimicrobial resistance (AMR)” in the EU Member States, Norway and Iceland. The study provides input to support the EU's overall goal to combat AMR by improving the development and implementation of One Health national action plans (NAPs) which, in turn, shall contain effective measures in infection prevention and control and prudent use of antimicrobials. The research was conducted under the following study areas: development and implementation of One Health NAPs, infection prevention and control (IPC) measures in hospitals and long-term care facilities (LTCFs); antimicrobial stewardship measures (AMS) in hospitals, LTCFs, primary care and pharmacies. The research revealed some common problems across all countries, such as insufficient funding to deliver on the measures foreseen in the NAPs, the shortages of qualified staff at all levels of care, the lack of measures targeting LTCFs specifically, the limited involvement of pharmacies in AMS, and the disruptions caused by the COVID-19 pandemic in the health sector. The barriers affect each country differently but they are nevertheless common to all, independently of their size and socio-economic situation. Limitations to deliver on the NAPs objectives were also due to lack of other resources besides funding and staff: old infrastructure, insufficient material and equipment, as well as testing capacity, inadequate information systems. Other barriers identified include: limited political focus and awareness of the challenges brought by AMR; lack of operational plans for delivering on the NAPs; lack of harmonised indicators for monitoring the implementation of plans; limited coverage of AMR, AMS and IPC in education and training; and limited public awareness of AMR. Key messages • Countries face common barriers to the effective implementation of One health policies against AMR, such as lack of dedicated funds, shortages of qualified staff, and disruptions caused by the pandemic. • Actions are needed for improving the implementation of One Health national action plans in the EU, including effective measures in infection prevention and control and prudent use of antimicrobials.

Supertool for Superbugs—Smart “Nano-ointment of Graphene Usnic Acid Nanoparticles” Against Antimicrobial Resistance (AMRs)

Supertool for Superbugs—Smart “Nano-ointment of Graphene Usnic Acid Nanoparticles” Against Antimicrobial Resistance (AMRs)

The best laid plans?: international governance perspectives in AMR national action plans in Europe.

There is a broad consensus in the European public health community that international collaboration and coordination are key in the fight against antimicrobial resistance (AMR). Yet, while experts typically testify the importance of cross-national learning and a coordinated effort to reduce the spread of multi-resistant bacteria, there are mixed views about how that is best realized in practice, particularly on the dichotomy between horizontal and vertical activities. National action plans (NAP) from all EU member states were systematically overviewed by two independent researchers. We followed a fixed procedure for locating a broad and comparable content on the international dimensions, and letting these vary on scales. We find that countries adhere to four different strategies for international coordination, varying between 'high' and 'low' on values of vertical and horizontal activities. Most countries spend none or very little space to discuss international activities, while some countries use their NAPs to outline their aspiration for taking leading roles in the international struggle. Moreover, in line with previous research, we find that many countries directly mimic the Global Action Plan, but also that a large share of countries describe independent arrangements in their international strategies. European countries recognize AMR and its inherent international governance challenge differently in their NAPs, which may have implications for coordinated action to address the issue.

Vaccine development for bacterial pathogens: Advances, challenges and prospects.

The advent and use of antimicrobials have played a key role in treating potentially life-threatening infectious diseases, improving health, and saving the lives of millions of people worldwide. However, the emergence of multidrug resistant (MDR) pathogens has been a significant health challenge that has compromised the ability to prevent and treat a wide range of infectious diseases that were once treatable. Vaccines offer potential as a promising alternative to fight against antimicrobial resistance (AMR) infectious diseases. Vaccine technologies include reverse vaccinology, structural biology methods, nucleic acid (DNA and mRNA) vaccines, generalised modules for membrane antigens, bioconjugates/glycoconjugates, nanomaterials and several other emerging technological advances that are offering a potential breakthrough in the development of efficient vaccines against pathogens. This review covers the opportunities and advancements in vaccine discovery and development targeting bacterial pathogens. We reflect on the impact of the already-developed vaccines targeting bacterial pathogens and the potential of those currently under different stages of preclinical and clinical trials. More importantly, we critically and comprehensively analyse the challenges while highlighting the key indices for future vaccine prospects. Finally, the issues and concerns of AMR for low-income countries (sub-Saharan Africa) and the challenges with vaccine integration, discovery and development in this region are critically evaluated.

Using Machine Learning to Predict Antimicrobial Resistance-A Literature Review.

Machine learning (ML) algorithms are increasingly applied in medical research and in healthcare, gradually improving clinical practice. Among various applications of these novel methods, their usage in the combat against antimicrobial resistance (AMR) is one of the most crucial areas of interest, as increasing resistance to antibiotics and management of difficult-to-treat multidrug-resistant infections are significant challenges for most countries worldwide, with life-threatening consequences. As antibiotic efficacy and treatment options decrease, the need for implementation of multimodal antibiotic stewardship programs is of utmost importance in order to restrict antibiotic misuse and prevent further aggravation of the AMR problem. Both supervised and unsupervised machine learning tools have been successfully used to predict early antibiotic resistance, and thus support clinicians in selecting appropriate therapy. In this paper, we reviewed the existing literature on machine learning and artificial intelligence (AI) in general in conjunction with antimicrobial resistance prediction. This is a narrative review, where we discuss the applications of ML methods in the field of AMR and their value as a complementary tool in the antibiotic stewardship practice, mainly from the clinician's point of view.

Investigating Knowledge of Antibiotics, Antimicrobial Resistance and Antimicrobial Stewardship Concepts Among Final Year Undergraduate Pharmacy Students in Northern Nigeria.

Well trained, knowledgeable and competent pharmacists are indispensable in the fight against antimicrobial resistance (AMR), which is a current global public health problem. The aim of this work was to assess knowledge of antibiotics, antimicrobial resistance and antimicrobial stewardship of fifth year pharmacy students at three universities in Northern Nigeria. A descriptive cross-sectional study that used a paper-based questionnaire to collect data from July to September 2021 was conducted. The questionnaire was self-administered and divided into four sections. The first section collected information about the demographic data of respondents, while section B explored their knowledge of antibiotics and AMR. Section C contained six questions assessing knowledge of various aspects of antimicrobial stewardship (AMS), while the final part assessed respondents' preparedness to work with antibiotics and perceptions of their current knowledge of these concepts. Descriptive statistics were used to report the results obtained. A total of 164 questionnaires were retrieved. Majority of respondents were male (58.3%) and aged between 21 and 25 years (53.4%). Most of them had some knowledge of antibiotics and AMR, however several misconceptions with respect to these concepts were identified. Only 80 (48.8%) of respondents indicated that they knew what AMS was, although most of these students were correctly knowledgeable about the goals and scope of AMS and composition of the AMS team. Generally, less than half of respondents agreed that their current knowledge of antibiotics, AMR or AMS was adequate for their future careers, and over 90% of them agreed that they would like more education about these topics. Many of the study's' respondents were somewhat knowledgeable about these concepts, although several knowledge gaps were also observed. Improving undergraduate pharmacy education with respect to these concepts is recommended.

Global Action Against Antimicrobial Resistance (AMR): L-forms, How to Recognize Them Under the Optical Microscope

The Lancet published a systematic review of the global burden of bacterial antimicrobial resistance in 2019, which found a worrying increase. In 2017, World Health Organization (WHO) published a list of priority antibiotic-resistant pathogens, which included the 12 most dangerous bacterial families for human health. We would like to draw attention to the L-forms that are poorly understood at the clinical level in hospital laboratories and have great potential to improve diagnosis and avoid underdiagnosis.

Vaccination coverage in Italian children and antimicrobial resistance: an ecological analysis

BackgroundAlthough a general consensus that vaccines could be a complementary strategy against antimicrobial resistance (AMR), there is still the need for studies investigating the relationship between childhood vaccination coverage and AMR proportions in the overall population.MethodsWe performed an ecological analysis of available Italian data (vaccination coverages, AMR proportions, number of isolates tested, and antibiotic use) to evaluate the relationships between vaccination coverages in children and AMR proportions in the last 2 decades.ResultsAfter adjusting for covariates, we showed that AMR proportions decreased with increasing vaccination coverages, especially for some combinations of vaccines, pathogens, and antimicrobials. Vaccination coverages for pertussis, diphtheria, and tetanus were inversely related to proportions of E. coli resistant to fluoroquinolones and third generation cephalosporins, K. pneumoniae resistant to carbapenems and third generation cephalosporins, and P. aeruginosa resistant to piperacillin and tazobactam. Polio vaccination coverage was inversely related to proportions of E. coli and K. pneumoniae resistant to third generation cephalosporins.ConclusionsThese results, however, should be interpreted cautiously due to the ecological nature of our analysis. For this reason, further studies designed ad hoc should be encouraged to measure the impact of increasing childhood vaccination coverage on AMR.

Use of antibiotics in livestock in Nigeria: Curbing antimicrobial resistance and developing a national regulatory guideline towards monitoring antibiotic use in animal and animal foods

Despite all efforts and resources channelled towards the fight against Antimicrobial Resistance (AMR), it manages to remain one of the top public health challenges of the 21st century. It is almost as if the problem itself has developed resistance. Numerous researches have been conducted to unravel its persistence and seek ways to reduce or eradicate AMR. This has increased awareness and emphasized the urgency to which effective measures have to be taken to alleviate AMR. Among the factors discovered to contribute to this menace is the use of antibiotics in livestock/animal rearing. It has come to light that most antibiotics used in animal rearing are done with little or no expert consultation and some of these antimicrobials are available over the counter in many countries. Lack of awareness, unavailability of agricultural extension services, inadequate instructions supplied by manufacturers, and the need for profit by animal rearers culminates in the irrational use of antibiotics. To solve this problem, the decision for antimicrobial use in livestock production should primarily lie with veterinarians or agricultural workers who can effectively diagnose diseases in such animals and recommend the appropriate treatment, dose, and treatment duration. Proper control of drug use by regulatory authorities and agricultural workers, observation of the prescribed withdrawal period for drugs, educating local farmers, as well as monitoring the antibiotic residues, will go a long way in curbing the menace of antibiotic resistance. This is what this review addresses.

Whole Genome Sequence Analysis of Multidrug Resistant Escherichia coli and Klebsiella pneumoniae Strains in Kuwait.

The spread of carbapenem-resistant Escherichia coli and Klebsiella pneumoniae is a global concern. The management of infections caused by multidrug resistance (MDR) isolates poses substantial clinical challenges in both hospitals and communities. This study aimed to investigate the genetic characteristics and variations of MDR E. coli and K. pneumoniae isolates. Bacterial identification and antibiotic susceptibility testing against 19 antibiotics were performed by standard methods. Whole genome sequencing (WGS) was carried out on eight carbapenem-resistant isolates using an Illumina MiSeq platform. The assembled draft genomes were annotated, then sequences were blasted against antimicrobial resistance (AMR) genes database. WGS detected several resistance genes mediating the production of β-lactamases, including carbapenems and extended-spectrum β-lactamase genes as (blaOXA-1/-48, blaKPC-2/-29, blaCMY-4/-6, blaSHV-11/-12, blaTEM-1, blaCTX-M-15, blaOKP-B, blaACT and blaEC). Furthermore quinolone resistance including oqxA/oqxB, aac(6′)-Ib-cr5, gyrA_D87N, gyrA_S83F, gyrA_S83L, parC_S80I, parE_S458A, parE_I355T, parC_S80I, and qnrB1. In addition to aminoglycoside modifying enzymes genes (aph(6)-Id, aph(3″)-Ib, aac(3)-IIa, aac(6′)-Ib, aadA1, aadA2 and aadA5), trimethoprim-sulfamethoxazole (dfrA12/A14/A17 and sul1/sul2), tetracycline (tetA and tetB), fosfomycin (fosA and uhpT_E350Q) resistance genes, while other genes were detected conferring chloramphenicol (floR, catA2, and efflux pump cmIA5), macrolides resistance (mph(A) and erm(B), and quaternary ammonium efflux pump qacEdelta. Bleomycin and colistin resistance genes were detected as ble and pmrB_R256G, respectively. Comprehensive analysis of MDR strains provided by WGS detected variable antimicrobial resistance genes and their precise resistance mechanism. WGS is essential for control and prevention strategies to combat the growing threat of AMR and the implementation of multifaceted interventions are needed.