Estimating the burden of antimicrobial resistance: a systematic literature review

Self and professional treatment of skin and soft tissue infections among women who inject drugs: Implications for wound care provision to prevent endocarditis

Background:

Skin and soft tissue infections (SSTI) are common among people who inject drugs and can result in severe health consequences, including infective endocarditis. Numerous barriers to accessing care often prevent people who inject drugs from seeking healthcare including past negative healthcare experiences, transportation, and shame around drug use. These barriers can lead some people who inject drugs to self-care instead of seeking formal treatment.

Methods:

We explored the prevalence of SSTIs and associated treatment behaviors among women who inject drugs and sell sex (N = 114). Women reported their drug use and SSTI histories. Those who experienced an SSTI reported if they self-treated their SSTIs and/or sought formal treatment.

Results:

Half (50.0%) experienced at least one SSTI in the past 6 months. SSTIs were more common among those who injected painkillers (24.6% vs 8.8%, p = 0.02) and who had ever been treated for endocarditis (28.1% vs 10.5%, p = 0.02). SSTIs were less common among those who injected multiple times per day (17.9% vs 38.6%, p = 0.01) and always injected with a sterile syringe (19.3% vs 42.1%, p = 0.01). Among those who experienced an SSTI, most (85.7%) reported self-treating, and half (52.6%) sought formal care. The emergency room was the most common source of care (73.3%).

Conclusions:

When experiencing SSTIs, women often opted to self-treat rather than seek formal healthcare. A lack of formal care can lead to infections progressing to serious conditions, like endocarditis. Self-treatment with non-prescribed antibiotics may further result in antibiotic-resistant infections. Low threshold, stigma free, community-based wound care programs are warranted.

Isolation and Characterization of Werneria Chromene and Dihydroxyacidissimol from Burkillanthus malaccensis (Ridl.) Swingle

The secondary metabolites of endemic plants from the Rutaceae family, such as Burkillanthusmalaccensis (Ridl.) Swingle from the rainforest of Malaysia, has not been studied. Burkillanthusmalaccensis (Ridl.) Swingle may produce antibacterial and antibiotic-potentiating secondary metabolites. Hexane, chloroform, and methanol extracts of leaves, bark, wood, pericarps, and endocarps were tested against bacteria by broth microdilution assay and their antibiotic-potentiating activities. Chromatographic separations of hexane extracts of seeds were conducted to investigate effective phytochemicals and their antibacterial activities. Molecular docking studies of werneria chromene and dihydroxyacidissiminol against SARS-CoV-2 virus infection were conducted using AutoDock Vina. The methanol extract of bark inhibited the growth of Staphylococcusaureus, Escherichiacoli, and Pseudomonasaeruginosa with the minimum inhibitory concentration of 250, 500, and 250 µg/mL, respectively. The chloroform extract of endocarps potentiated the activity of imipenem against imipenem-resistant Acinetobacterbaumannii. The hexane extract of seeds increased the sensitivity of P. aeruginosa against ciprofloxacin and levofloxacin. The hexane extract of seeds and chloroform extract of endocarps were chromatographed, yielding werneria chromene and dihydroxyacidissiminol. Werneria chromene was bacteriostatic for P.aeruginosa and P.putida, with MIC/MBC values of 1000 > 1000 µg/mL. Dihydroxyacidissiminol showed the predicted binding energies of −8.1, −7.6, −7.0, and −7.5 kcal/mol with cathepsin L, nsp13 helicase, SARS-CoV-2 main protease, and SARS-CoV-2 spike protein receptor-binding domain S-RBD. Burkillanthusmalaccensis (Ridl.) Swingle can be a potential source of natural products with antibiotic-potentiating activity and that are anti-SARS-CoV-2.

Assessment of Infection Prevention and Control Measures at Points of Entry in Sierra Leone in 2021: A Cross-Sectional Study

Implementing and monitoring infection prevention and control (IPC) measures at immigration points of entry (PoEs) is key to preventing infections, reducing excessive use of antimicrobials, and tackling antimicrobial resistance (AMR). Sierra Leone has been implementing IPC measures at four PoEs (Queen Elizabeth II Quay port, Lungi International Airport, and the Jendema and Gbalamuya ground crossings) since the last Ebola outbreak in 2014-2015. We adapted the World Health Organization IPC Assessment Framework tool to assess these measures and identify any gaps in their components at each PoE through a cross-sectional study in May 2021. IPC measures were Inadequate (0-25%) at Queen Elizabeth II Quay port (21%; 11/53) and Jendema (25%; 13/53) and Basic (26-50%) at Lungi International Airport (40%; 21/53) and Gbalamuya (49%; 26/53). IPC components with the highest scores were: having a referral system (85%; 17/20), cleaning and sanitation (63%; 15/24), and having a screening station (59%; 19/32). The lowest scores (0% each) were reported for the availability of IPC guidelines and monitoring of IPC practices. This was the first study in Sierra Leone highlighting significant gaps in the implementation of IPC measures at PoEs. We call on the AMR multisectoral coordinating committee to enhance IPC measures at all PoEs.

The Use of Antibody-Antibiotic Conjugates to Fight Bacterial Infections

The emergence of antimicrobial resistance (AMR) is rapidly increasing and it is one of the significant twenty-first century’s healthcare challenges. Unfortunately, the development of effective antimicrobial agents is a much slower and complex process compared to the spread of AMR. Consequently, the current options in the treatment of AMR are limited. One of the main alternatives to conventional antibiotics is the use of antibody-antibiotic conjugates (AACs). These innovative bioengineered agents take advantage of the selectivity, favorable pharmacokinetic (PK), and safety of antibodies, allowing the administration of more potent antibiotics with less off-target effects. Although AACs’ development is challenging due to the complexity of the three components, namely, the antibody, the antibiotic, and the linker, some successful examples are currently under clinical studies.

Hydrazone analogues with promising antibacterial profiles: Synthesis, morphology, in vitro and in silico approaches

Emergence of resistance to antibacterial drugs remains an important global threat that necessitates an urgent need for the discovery of alternative drugs. This study was undertaken to synthesize some novel nitroaryl/heteroaryl hydrazone derivatives as potential antibacterial agents. After synthesizing by a simple reaction between quinoline/quinazoline hydrazine and nitroaryl/heteroaryl aldehydes, all the compounds were screened for their antibacterial activities, cytotoxicity, and in silico investigations. The compound, 2-(4-nitrobenzylidene)-1-(quinazolin-4-yl)hydrazine (1b) displayed significant antimicrobial activity against several susceptible and resistant bacteria without any cytotoxicity. Moreover, scanning electron microscopy (SEM) revealed the complete destruction of Staphylococcus aureus and Escherichia coli following exposure to this compound after 2 hours exposure. The in silico studies confirmed the better binding energy of these compounds in comparison with the reference drugs in complex with topoisomerase IV and bacterial ribosomal receptor. Compound 1b can be considered as a promising lead compound for the development of broad-spectrum antibacterial medications after further studies.

Carvacrol Enhances the Antimicrobial Potency of Berberine in Bacillus subtilis

The essential oil carvacrol from oregano displays a wide range of biological activities among which is found the inhibition of efflux pumps. Thus, using carvacrol, the current work undertook the effort to potentiate the antimicrobial activity of berberine, a natural product with limited antimicrobial efficacy due to its efflux. Following the selection of concentrations for the combinatorial treatments, guided by checkerboard microtiter plate assay and growth experiments, ethidium bromide accumulation assay was used to find that 25 μg mL^-1 carvacrol displayed a weak efflux pump inhibitor character in Bacillus subtilis. Scanning electron microscopy images and cellular material leakage assays showed that carvacrol at this concentration neither altered the morphology nor the permeability of the membrane alone but when combined with 75 μg mL^-1 berberine. Among the efflux pumps of different families found in B. subtilis, except for BmrA and Mdr, the increase in the expressional changes was striking, with Blt displaying ~ 4500-fold increase in expression under the combination treatment. Overall, the findings demonstrated that carvacrol potentiated the effect of berberine; however, not only multiple pumps but also different targets may be responsible for the observed activity.

The increased length of hospital stay and mortality associated with community-associated infections in Australia

Background

An increasing proportion of antibiotic-resistant infections are community acquired. However, the burden of community-associated infections (CAIs) and the resulting impact due to resistance have not been well described.

Methods

We conducted a multisite, retrospective case–cohort study of all acute care hospital admissions across 134 hospitals in Australia. Patients admitted with a positive culture of 1 of 5 organisms of interest, namely Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and Enterococcus faecium, from January 1, 2012, through December 30, 2016, were included. Data linkage was used to link hospital admissions and pathology data. Patients with a bloodstream infection (BSI), urinary tract infection (UTI), or respiratory tract infection (RTI) were included in the analysis. We compared patients with a resistant and drug-sensitive infection and used regression analyses to derive the difference in length of hospital stay (LOS) and mortality estimates associated with resistance.

Results

No statistically significant impact on hospital LOS for patients with resistant CAIs compared with drug-sensitive CAIs was identified. CAI patients with drug-resistant Enterobacteriaceae (E. coli, K. pneumoniae) BSIs were more likely to die in the hospital than those with drug-sensitive Enterobacteriaceae BSIs (odds ratio [OR], 3.28; 95% CI, 1.40–6.92). CAI patients with drug-resistant P. aeruginosa UTIs were more likely to die in the hospital than those with the drug-sensitive counterpart (OR, 2.43; 95% CI, 1.12–4.85).

Conclusions

The burden of CAI in the hospital is significant, and antibiotic resistance is adding to associated mortality.

Interprofessional Collaboration between ICU Physicians, Staff Nurses, and Hospital Pharmacists Optimizes Antimicrobial Treatment and Improves Quality of Care and Economic Outcome

(1) Background: Antibiotic resistance is a worldwide health threat. The WHO published a global strategic plan in 2001 to contain antimicrobial resistance. In the following year, a workshop identified crucial barriers to the implementation of the strategy, e.g., underdeveloped health infrastructures and the scarcity of valid data as well as a lack of implementation of antibiotic stewardship (ABS) programs in medical curricula. Here, we show that interprofessional learning and education can contribute to the optimization of antibiotic use and preserving antibiotic effectiveness. We have initiated interprofessional rounds on a medical intensive care unit (MICU) with a focus on gastroenterology, hepatology, infectious diseases, endocrinology, and liver transplantation. We integrated ICU physicians, hospital pharmacists, nursing staff, and medical students as well as students of pharmacy to broaden the rather technical concept of ABS with an interprofessional approach to conceptualize awareness and behavioral change in antibiotic prescription and use. Methods: Clinical performance data and consumption figures for antibiotics were analyzed over a 10-year period from 2012 to 2021. The control period covered the years 2012–2014. The intervention period comprised the years 2015–2021, following the implementation of an interprofessional approach to ABS at a MICU of a German university hospital. Data from the hospital pharmacy, hospital administration, and hospital information system were included in the analyses. A specific electronic platform was developed for the optimization of documentation, interprofessional learning, education, and sustainability. The years 2020 and 2021 were analyzed independently due to the SARS-CoV-2 pandemic and the care of numerous COVID-19 patients at the MICU. Results: Implementation of an interprofessional ABS program resulted in the optimization of antibiotic management at the MICU. The suggestions of the hospital pharmacist for optimization can be divided into the following categories (i) indication for and selection of therapy (43.6%), (ii) optimization of dosing (27.6%), (iii) drug interactions (9.4%), (iv) side effects (4.1%), and (v) other pharmacokinetic, pharmacodynamic, and pharmacoeconomic topics (15.3%). These suggestions were discussed among the interprofessional team at the MICU; 86.1% were consequently implemented and the prescription of antibiotics was changed. In addition, further analysis of the intensive care German Diagnosis Related Groups (G-DRGs) showed that the case mix points increased significantly by 31.6% during the period under review. Accordingly, the severity of illness of the patients treated at the ICU as measured by the Simplified Acute Physiology Score (SAPS) II increased by 21.4% and the proportion of mechanically ventilated patients exceeded 50%. Antibiotic spending per case mix point was calculated. While spending was EUR 60.22 per case mix point in 2015, this was reduced by 42.9% to EUR 34.37 per case mix point by 2019, following the implementation of the interprofessional ABS program on the MICU. Through close interprofessional collaboration between physicians, hospital pharmacists, and staff nurses, the consumption of broad-spectrum antibiotics, e.g., carbapenems, was significantly reduced, thus improving patient care. In parallel, the case mix and case mix index increased. Thus, the responsible use of resources and high-performance medicine are not contradictory. In our view, close interprofessional and interdisciplinary collaboration between physicians, pharmacists, and nursing staff will be of outstanding importance in the future to prepare health care professionals for global health care to ensure that the effectiveness of our antibiotics is preserved.

SPiNCAR: A systematic model to evaluate and guide actions for tackling AMR

Background

Italy records very alarming levels antimicrobial resistance (AMR), so a National Action Plan on Antimicrobial resistance (PNCAR) was developed, adopting the AMR European Union’s recommendations based on the results of the ECDC site visit of January 2017. For achieving PNCAR objectives, it is necessary to support and harmonize the implementation of recommendations in all the different healthcare levels (regional authorities and local trusts), so the SPiNCAR project was launched to create a tool for reaching this goal.

Methods

We developed a framework based on a scientific literature and national and international guidelines. Firstly, we identified the major intervention areas for tackling AMR, then, for each area, we built a set of standards, both for regional authorities than for local trusts. Every standard is composed by a set of essential and additional criteria, which refer to a minimum or supplemental performance level respectively. The contents were firstly discussed by the project’s team during face-to-face kick-off meetings, then confirmed with Delphi methodology and finally validated through a pilot study.

Results

The final framework consists of seven different areas that reflect the PNCAR structure: Governance, Surveillance and Monitoring, Appropriate Use of antimicrobials, Healthcare-associated Infections (HAIs) control and prevention, Education and Training, Alliance among Stakeholders, Implementation. The total number of standards for the regional framework was 34 with 264 criteria and for the local version 36 criteria with 279 standards.

Conclusion

The ongoing use of this tool, developed on international evidences and recommendations that were tailored on the Italian specific context, allows monitoring the improvement achieved over time and plan the next steps.

Associations between socio-spatially different urban areas and knowledge, attitudes, practices and antibiotic use: A cross-sectional study in the Ruhr Metropolis, Germany

Inappropriate and excessive antibiotic use fuels the development of antibiotic resistance. Determinants of antibiotic use, including knowledge and attitudes, are manifold and vary on different spatial scales. The objective of this study was to examine the associations between socio-spatially diverse urban areas and knowledge, attitudes, practices and antibiotic use within a metropolitan city. A cross-sectional survey was conducted in the general population in socio-spatially different areas in Dortmund, Germany, in February and March 2020. Three urban areas were chosen to represent diverse socio-spatial contexts (socio-spatially disadvantaged: A, intermediate: B, socio-spatially disadvantaged: C). Participants were selected via simple random sampling. The questionnaire comprised knowledge and attitude statements and questions around antibiotic use and handling practices. Differences between the areas were examined by estimating odds ratios (OR) and corresponding 95% confidence intervals by multiple logistic regression. Overall, 158 participants were included. Participants of Area C showed the lowest proportions of correct knowledge statements, indicated more often attitudes contrary to common recommendations, lower risk awareness and reported more often antibiotic use (C: 40.8%; A: 32.7%; B: 26.5%) and potential mishandling practices (C: 30.4%; A: 9.6%; B: 17.3%). The multiple logistic regression confirmed these differences. Around 42.3% (C), 33.3% (A) and 20.0% (B) of the diseases mentioned for which an antibiotic was used are mainly caused by viral pathogens. A common misconception across all areas was the perception of antibiotic resistance as an individual rather than a universal issue. This study reveals distinct differences between socio-spatially diverse urban areas within a metropolitan city, regarding knowledge, attitudes and practices around antibiotics and ABR. Our findings confirm that enhanced efforts are required to better inform the population about the adequate use and handling of antibiotics. This study emphasizes the need for future interventions to be tailored to the specific local socio-economic context.

Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis

BACKGROUND

Antimicrobial resistance (AMR) poses a major threat to human health around the world. Previous publications have estimated the effect of AMR on incidence, deaths, hospital length of stay, and health-care costs for specific pathogen-drug combinations in select locations. To our knowledge, this study presents the most comprehensive estimates of AMR burden to date.

METHODS

We estimated deaths and disability-adjusted life-years (DALYs) attributable to and associated with bacterial AMR for 23 pathogens and 88 pathogen-drug combinations in 204 countries and territories in 2019. We obtained data from systematic literature reviews, hospital systems, surveillance systems, and other sources, covering 471 million individual records or isolates and 7585 study-location-years. We used predictive statistical modelling to produce estimates of AMR burden for all locations, including for locations with no data. Our approach can be divided into five broad components: number of deaths where infection played a role, proportion of infectious deaths attributable to a given infectious syndrome, proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of a given pathogen resistant to an antibiotic of interest, and the excess risk of death or duration of an infection associated with this resistance. Using these components, we estimated disease burden based on two counterfactuals: deaths attributable to AMR (based on an alternative scenario in which all drug-resistant infections were replaced by drug-susceptible infections), and deaths associated with AMR (based on an alternative scenario in which all drug-resistant infections were replaced by no infection). We generated 95% uncertainty intervals (UIs) for final estimates as the 25th and 975th ordered values across 1000 posterior draws, and models were cross-validated for out-of-sample predictive validity. We present final estimates aggregated to the global and regional level.

FINDINGS

On the basis of our predictive statistical models, there were an estimated 4·95 million (3·62-6·57) deaths associated with bacterial AMR in 2019, including 1·27 million (95% UI 0·911-1·71) deaths attributable to bacterial AMR. At the regional level, we estimated the all-age death rate attributable to resistance to be highest in western sub-Saharan Africa, at 27·3 deaths per 100 000 (20·9-35·3), and lowest in Australasia, at 6·5 deaths (4·3-9·4) per 100 000. Lower respiratory infections accounted for more than 1·5 million deaths associated with resistance in 2019, making it the most burdensome infectious syndrome. The six leading pathogens for deaths associated with resistance (Escherichia coli, followed by Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa) were responsible for 929 000 (660 000-1 270 000) deaths attributable to AMR and 3·57 million (2·62-4·78) deaths associated with AMR in 2019. One pathogen-drug combination, meticillin-resistant S aureus, caused more than 100 000 deaths attributable to AMR in 2019, while six more each caused 50 000-100 000 deaths: multidrug-resistant excluding extensively drug-resistant tuberculosis, third-generation cephalosporin-resistant E coli, carbapenem-resistant A baumannii, fluoroquinolone-resistant E coli, carbapenem-resistant K pneumoniae, and third-generation cephalosporin-resistant K pneumoniae.

INTERPRETATION

To our knowledge, this study provides the first comprehensive assessment of the global burden of AMR, as well as an evaluation of the availability of data. AMR is a leading cause of death around the world, with the highest burdens in low-resource settings. Understanding the burden of AMR and the leading pathogen-drug combinations contributing to it is crucial to making informed and location-specific policy decisions, particularly about infection prevention and control programmes, access to essential antibiotics, and research and development of new vaccines and antibiotics. There are serious data gaps in many low-income settings, emphasising the need to expand microbiology laboratory capacity and data collection systems to improve our understanding of this important human health threat.

FUNDING

Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care using UK aid funding managed by the Fleming Fund.

Point Prevalence Survey of Antibiotic Use across 13 Hospitals in Uganda

Standardized monitoring of antibiotic use underpins the effective implementation of antimicrobial stewardship interventions in combatting antimicrobial resistance (AMR). To date, few studies have assessed antibiotic use in hospitals in Uganda to identify gaps that require intervention. This study applied the World Health Organization’s standardized point prevalence survey methodology to assess antibiotic use in 13 public and private not-for-profit hospitals across the country. Data for 1077 patients and 1387 prescriptions were collected between December 2020 and April 2021 and analyzed to understand the characteristics of antibiotic use and the prevalence of the types of antibiotics to assess compliance with Uganda Clinical Guidelines; and classify antibiotics according to the WHO Access, Watch, and Reserve classification. This study found that 74% of patients were on one or more antibiotics. Compliance with Uganda Clinical Guidelines was low (30%); Watch-classified antibiotics were used to a high degree (44% of prescriptions), mainly driven by the wide use of ceftriaxone, which was the most frequently used antibiotic (37% of prescriptions). The results of this study identify key areas for the improvement of antimicrobial stewardship in Uganda and are important benchmarks for future evaluations.

Disparity in socio-economic status explains the pattern of self-medication of antibiotics in India: understanding from game-theoretic perspective

The emergence of antimicrobial resistance has raised great concern for public health in many lower-income countries including India. Socio-economic determinants like poverty, health expenditure and awareness accelerate this emergence by influencing individuals' attitudes and healthcare practices such as self-medication. This self-medication practice is highly prevalent in many countries, where antibiotics are available without prescriptions. Thus, complex dynamics of drug- resistance driven by economy, human behaviour, and disease epidemiology poses a serious threat to the community, which has been less emphasized in prior studies. Here, we formulate a game-theoretic model of human choices in self-medication integrating economic growth and disease transmission processes. We show that this adaptive behaviour emerges spontaneously in the population through a self-reinforcing process and continual feedback from the economy, resulting in the emergence of resistance as externalities of human choice under resource constraints situations. We identify that the disparity between social-optimum and individual interest in self-medication is primarily driven by the effectiveness of treatment, health awareness and public health interventions. Frequent multiple-peaks of resistant strains are also observed when individuals imitate others more readily and self-medication is more likely. Our model exemplifies that timely public health intervention for financial risk protection, and antibiotic stewardship policies can improve the epidemiological situation and prevent economic collapse.

In silico screening and in vitro validation of phytocompounds as multidrug efflux pump inhibitor against E. coli

Multiple drug resistance (MDR) in bacteria has increased globally in recent times. This has reduced the efficacy of antibiotics and increasing the rate of therapeutic failure. Targeting efflux pump by natural and synthetic compounds is one of the strategies to develop an ideal broad-spectrum resistance-modifying agent. Very few inhibitors of AcrB from natural sources have been reported till date. In the current study, 19 phytocompounds were screened for efflux pump inhibitory activity against AcrB protein of E. coli TG1 using molecular docking studies. The molecular dynamics simulation provided stability the protein (AcrB) and its complex with chlorogenic acid under physiological conditions. Moreover, the detailed molecular insights of the binding were also explored. The Lipinski rule of 5 and the drug-likeness prediction was determined using Swiss ADME server, while toxicity prediction was done using admetSAR and PROTOX-II webservers. Chlorogenic acid showed the highest binding affinity (-9.1 kcal mol^-1) with AcrB protein among all screened phytocompounds. Consequently, all the phytocompounds that accede to Lipinski's rule, demonstrated a high LD50 value indicating that they are non-toxic except the phytocompound reserpine. Chlorogenic acid and capsaicin are filtered out based on the synergy with tetracycline having FIC index of 0.25 and 0.28. The percentage increase of EtBr fluorescence by chlorogenic acid was 36.6% followed by piperine (24.2%). Chlorogenic acid may be a promising efflux pump inhibitor that might be employed in combination therapy with tetracycline against E. coli, based on the above relationship between in silico screening and in vitro positive efflux inhibitory activity.Communicated by Ramaswamy H. Sarma.

Effects of patient education to reduce antibiotic prescribing rates for upper respiratory infections in primary care

BACKGROUND

Antibiotic stewardship programs in primary care are necessary to reduce the estimated 30% of inappropriately written antibiotic prescriptions and reduce the spread of microbial resistance. Most programs focus on educating prescribers, but this intervention focused on educating patients.

OBJECTIVES

To develop and implement an antibiotic stewardship program in a primary care clinic to educate patients with upper respiratory infections (URIs) about antibiotic use and to assess the effectiveness of the program through antibiotic prescribing rates.

METHODS

Using materials from the Centers for Disease Control and Prevention (CDC) Be Antibiotics Aware program, posters on antibiotic use were placed in the exam rooms, graphic interchange formats (GIFs) and memes were displayed on exam room monitors, patient-provider discussions on antibiotic use were held, and written information for symptom management of URIs was provided. Retrospective chart reviews were conducted to assess antibiotic prescribing rates by four prescribers in a primary care clinic for September and October 2020 and compared to the same time period for 2019.

RESULTS

The rate of total antibiotic prescriptions decreased by 12.6% (P = 0.044) and the rate of repeat consultation antibiotic prescriptions decreased by 12.2% (P = 0.007), whereas the rate of antibiotics prescribed at the time of the visit remained unchanged (P = 0.937). All providers had decreased rates of antibiotic prescribing after the intervention.

CONCLUSION

Results of this study indicate that providing education about antibiotics to patients in need of treatment for URIs may reduce the rate of antibiotics prescribed in primary care; however, further research is warranted.

Risk Factors for Multidrug-Resistant Gram-Negative Bacteria Carriage upon Admission to the Intensive Care Unit

Multidrug-resistant Gram-negative bacteria (MDR-GNB) are microorganisms that have acquired resistance to extended-spectrum antibacterials and constitute an emerging threat to public health. Although carriers are an important source of transmission in healthcare settings, data about risk factors for MDR-GNB carriage are limited. Therefore, we aimed to identify risk factors for MDR-GNB carriage upon intensive care unit (ICU) admission and to optimise screening strategies. We conducted a case–control study. Admissions of adult patients to the ICU of a 1000-bed hospital during a year were included. We collected sociodemographic, clinical and microbiological data and performed a multivariate logistic regression model. A total of 1342 patients resulted in 1476 episodes of ICU admission, 91 (6.2%) of whom harboured MDR-GNB (38.5% women; median age 63.9 years). The most frequently isolated pathogens were Escherichia coli (57%) and Klebsiella pneumoniae (16%). The most frequent resistance mechanism was production of extended-spectrum beta lactamases. MDR-GNB carriage was associated to liver cirrhosis (OR 6.54, 95% CI 2.17–19.17), previous MDR-GNB carriage (OR 5.34, 1.55–16.60), digestive surgery (OR 2.83, 1.29–5.89) and length of hospital stay (OR 1.01 per day, 1.00–1.03). Several risk factors for MDR-GNB carriage upon admission to a high-risk setting were identified; the main comorbidity was liver cirrhosis.

Characterization and in vitro testing of newly isolated lytic bacteriophages for the biocontrol of Pseudomonas aeruginosa

Aim: Two lytic phages were isolated using P. aeruginosa DSM19880 as host and fully characterized. Materials & methods: Phages were characterized physicochemically, biologically and genomically. Results & conclusion: Host range analysis revealed that the phages also infect some multidrug-resistant (MDR) P. aeruginosa clinical isolates. Increasing MOI from 1 to 1000 significantly increased phage efficiency and retarded bacteria regrowth, but phage ph0034 (reduction of 7.5 log CFU/ml) was more effective than phage ph0031 (reduction of 5.1 log CFU/ml) after 24 h. Both phages belong to Myoviridae family. Genome sequencing of phages ph0031 and ph0034 showed that they do not carry toxin, virulence, antibiotic resistance and integrase genes. The results obtained are highly relevant in the actual context of bacterial resistance to antibiotics.

Antibiotic resistance and phylogenetic profiling of Escherichia coli from dairy farm soils; organic versus conventional systems

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First known comparison of antimicrobial resistance traits in E. coli strains from new zealand farms practicing organic and conventional husbandry.

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Potential extended spectrum β-lactamase producing strains isolated from dairy farm environments.

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Organic dairy farms tended to harbour fewer resistant isolates than those recovered from conventionally farmed counterparts.

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Evidence for anthroponotic transmission of resistant strains of human origin to farm environments.

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Implications for the spread of antimicrobial resistance traits from farm environments discussed.

The prevalence and spread of antimicrobial resistance (AMR) as a result of the persistent use and/or abuse of antimicrobials is a key health problem for health authorities and governments worldwide. A study of contrasting farming systems such as organic versus conventional dairy farming may help to authenticate some factors that may contribute to the prevalence and spread of AMR in their soils. A case study was conducted in organic and conventional dairy farms in the South Canterbury region of New Zealand.

A total of 814 dairy farm soil E. coli (DfSEC) isolates recovered over two years were studied. Isolates were recovered from each of two farms practicing organic, and another two practicing conventional husbandries. The E. coli isolates were examined for their antimicrobial resistance (AMR) against cefoxitin, cefpodoxime, chloramphenicol, ciprofloxacin, gentamicin, meropenem, nalidixic acid, and tetracycline. Phylogenetic relationships were assessed using an established multiplex PCR method. The AMR results indicated 3.7% of the DfSEC isolates were resistant to at least one of the eight selected antimicrobials. Of the resistant isolates, DfSEC from the organic dairy farms showed a lower prevalence of resistance to the antimicrobials tested, compared to their counterparts from the conventional farms. Phylogenetic analysis placed the majority (73.7%) of isolates recovered in group B1, itself dominated by isolates of bovine origin. The tendency for higher rates of resistance among strains from conventional farming may be important for future decision-making around farming practices Current husbandry practices may contribute to the prevalence and spread of AMR in the industry.

Prevalence and Antimicrobial Resistance of Enterococcus Species: A Retrospective Cohort Study in Italy

Antimicrobial resistance represents one of the main threats to healthy ecosystems. In recent years, among the multidrug-resistant microorganisms responsible for nosocomial infections, the Enterococcus species have received much attention. Indeed, Enterococcus have peculiar skills in their ability to acquire resistance genes and to cause severe diseases, such as endocarditis. This study showed the prevalence and antimicrobial resistance rate of Enterococcus spp. isolated from clinical samples, from January 2015 to December 2019 at the University Hospital "San Giovanni di Dio e Ruggi d'Aragona" in Salerno, Italy. A total of 3236 isolates of Enterococcus faecalis (82.2%) and Enterococcus faecium (17.8%) were collected from urine cultures, blood cultures, catheters, respiratory tract, and other samples. Bacterial identification and antibiotic susceptibility were performed with VITEK 2. E. faecium showed a high resistance rate against ampicillin (84.5%), ampicillin/sulbactam (82.7%), and imipenem (86.7%), while E. faecalis showed the highest resistance rate against gentamicin and streptomycin high level, but both were highly sensitive to such antibiotics as tigecycline and vancomycin. Studies of surveillance are an important tool to detect changes in the resistance profiles of the main pathogens. These antimicrobial susceptibility patterns are necessary to improve the empirical treatment guideline of infections.

Antibiotic consumption at community pharmacies: A multicenter repeated prevalence surveillance using WHO methodology

Background:

Antibiotics are losing their effectiveness because of the rapid emergence of resistant bacteria. Unnecessary antimicrobial use increases antimicrobial resistance (AMR). There are currently no published data on antibiotic consumption in Pakistan at the community level. This is a concern given high levels of self-purchasing of antibiotics in Pakistan and variable knowledge regarding antibiotics and AMR among physicians and pharmacists.

Objective:

The objective of this repeated prevalence survey was to assess the pattern of antibiotic consumption data among different community pharmacies to provide a baseline for developing future pertinent initiatives.

Methods:

A multicenter repeated prevalence survey conducted among community pharmacies in Lahore, a metropolitan city with a population of approximately 10 million people, from October to December 2017 using the World Health Organization (WHO) methodology for a global program on surveillance of antimicrobial consumption.

Results:

The total number of defined daily doses (DDDs) dispensed per patient ranged from 0.1 to 50.0. In most cases, two DDDs per patient were dispensed from pharmacies. Co-amoxiclav was the most commonly dispensed antibiotic with a total number of DDDs at 1018.15. Co-amoxiclav was followed by ciprofloxacin with a total number of 486.6 DDDs and azithromycin with a total number of 472.66 DDDs. The least consumed antibiotics were cefadroxil, cefotaxime, amikacin, and ofloxacin, with overall consumption highest in December.

Conclusion:

The study indicated high antibiotic usage among community pharmacies in Lahore, Pakistan particularly broad-spectrum antibiotics, which were mostly dispensed inappropriately. The National action plan of Pakistan on AMR should be implemented by policymakers including restrictions on the dispensing of antimicrobials.

Understanding the social drivers of antibiotic use during COVID-19 in Bangladesh: Implications for reduction of antimicrobial resistance

Antimicrobial resistance (AMR) is a global public health crisis that is now impacted by the COVID-19 pandemic. Little is known how COVID-19 risks influence people to consume antibiotics, particularly in contexts like Bangladesh where these pharmaceuticals can be purchased without a prescription. This paper identifies the social drivers of antibiotics use among home-based patients who have tested positive with SARS-CoV-2 or have COVID-19-like symptoms. Using qualitative telephone interviews, the research was conducted in two Bangladesh cities with 40 participants who reported that they had tested positive for coronavirus (n = 20) or had COVID-19-like symptoms (n = 20). Our analysis identified five themes in antibiotic use narratives: antibiotics as 'big' medicine; managing anxiety; dealing with social repercussions of COVID-19 infection; lack of access to COVID-19 testing and healthcare services; and informal sources of treatment advice. Antibiotics were seen to solve physical and social aspects of COVID-19 infection, with urgent ramifications for AMR in Bangladesh and more general implications for global efforts to mitigate AMR.

Is antibiotic prophylaxis still mandatory for transperineal prostate biopsy? Results of a comparative study

Introduction and objectives

This study aimed to assess the incidence of urinary tract infections (UTIs) after transperineal prostate biopsy (TP-PB) comparing patients who underwent antibiotic prophylaxis (AP) with patients who had no prophylaxis.

Materials and methods

This prospective, double-center trial was conducted between August and December 2020. Patient candidates to PB were included with 1:1 allocation to case (Group A-no AP) and control group (Group B-standard AP). All TP-PBs were performed in an outpatient setting under local anesthesia. Data collected 2 weeks after the procedure included incidence of UTIs or bacteriuria, evaluated with a urine culture (UC), main symptoms, and complications related to TP-PBs.

Results

A total of 200 patients were included (100 patients in each group). The mean age was 66.2 ± 7.7 in Group A and 67.4 ± 8 years in Group B (P = 0.134). Mean prostate volume was 65.5 ± 26.7 vs. 51 ± 24.6 cc (P < 0.001), number of biopsy cores was 17.8 ± 2.4 vs. 14.9 ± 0.8 (P < 0.001), and PSA value was 15.9 ± 28.1 vs. 13.3 ± 22.3 ng/ml (P = 0.017). Overall PCa detection rate was 55% vs. 59% (P = 0.567). Postoperative UTI occurred in one patient in Group A vs. zero in Group B. Asymptomatic bacteriuria was present in 3 vs. 5 patients (P = 0.470) and was not treated with antibiotics. Postoperative hematuria was observed in 13 patients vs. 29 (P < 0.05), and acute urinary retention was observed in one patient in each group.

Conclusions

The incidence of bacteriuria and UTIs in TP-PBs is not related to AP. Therefore, AP could be discontinued in TP-PB candidates without the risk of increasing UTI-related complications.

First Global Report of Plasmid-Mediated mcr-1 and Extended-Spectrum Beta-Lactamase-Producing Escherichia coli from Sheep in Portugal

Resistances to extended-spectrum cephalosporins (ESC) and colistin are One Health issues since genes encoding these resistances can be transmitted between all sectors of the One Health concept, i.e., human, animal, and the environment. Among food-producing animals, sheep farming has long been overlooked. To fill in this knowledge gap, we looked for ESC- and colistin resistance in 21 faecal samples collected from sheep in one farm in the south of Portugal. ESC-resistant isolates were selected on MacConkey agar plates supplemented with cefotaxime. Susceptibility testing was performed by the disk-diffusion method according to CLSI, while colistin MIC was determined by broth microdilution. ESC- and colistin-resistance genes were identified by PCR, and the clonality of all isolates was assessed by XbaI-PFGE. The replicon content was determined by PCR according to the PCR-based replicon typing (PBRT) scheme. Sixty-two non-duplicate ESC-resistant E. coli isolates were identified, which all presented an extended-spectrum beta-lactamase (ESBL) phenotype, mostly due to the presence of CTX-M genes. One CTX-M-1-producing E. coli was concomitantly colistin-resistant and presented the plasmid-mediated mcr-1 gene. Nearly all isolates showed associated resistances to non-beta-lactam antibiotics, which could act as co-selectors, even in the absence of beta-lactam use. The results showed a high proportion of ESBL-producing E. coli in sheep faeces. Their dissemination was very dynamic, with the spread of successful clones between animals, but also a large diversity of clones and plasmids, sometimes residing in the same animal. This study highlights the need for global surveillance in all food-producing sectors, in order to avoid the dissemination of genes conferring resistance to last-resort antibiotics in human medicine.

A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes

Antimicrobial resistance (AMR) is a major global health threat that affects millions of people each year. Funding agencies worldwide and the global research community have expended considerable capital and effort tracking the evolution and spread of AMR by isolating and sequencing bacterial strains and performing antimicrobial susceptibility testing (AST). For the last several years, we have been capturing these efforts by curating data from the literature and data resources and building a set of assembled bacterial genome sequences that are paired with laboratory-derived AST data. This collection currently contains AST data for over 67 000 genomes encompassing approximately 40 genera and over 100 species. In this paper, we describe the characteristics of this collection, highlighting areas where sampling is comparatively deep or shallow, and showing areas where attention is needed from the research community to improve sampling and tracking efforts. In addition to using the data to track the evolution and spread of AMR, it also serves as a useful starting point for building machine learning models for predicting AMR phenotypes. We demonstrate this by describing two machine learning models that are built from the entire dataset to show where the predictive power is comparatively high or low. This AMR metadata collection is freely available and maintained on the Bacterial and Viral Bioinformatics Center (BV-BRC) FTP site ftp://ftp.bvbrc.org/RELEASE_NOTES/PATRIC_genomes_AMR.txt.

Impact of an empiric antimicrobial therapy manual on antimicrobial usage and multidrug resistant organism trends in a large Italian teaching hospital

Aim

To evaluate the changes in antimicrobial consumption and multidrug-resistant microorganism trends after introducing an empiric antimicrobial therapy manual to support antimicrobial stewardship.

Methods

A 4-year prospective interventional study assessed the effect of introducing an empiric antimicrobial therapy manual in medical and surgical wards during two periods: pre-intervention period (January 2015–May 2017) and post-intervention period (June 2017–December 2019). Outcomes included microorganism trends of bloodstream infections (BSI) for Klebsiella pneumoniae carbapenemase-producing bacteria (KPC), extended spectrum beta-lactamase ESBL-E. coli, meticillin-resistant Staphylococcus aureus (MRSA) and Candida albicans. Also, Clostridioides difficile infection (CDI) episodes were included. Rates were normalised per 1000 patient-days (PD). Antimicrobial consumption was assessed as defined daily dose (DDD)/1000 PD in interrupted time series analysis.

Results

In medical wards, we observed a significant decrease in the consumption of piperacillin-tazobactam and a decrease in the trends of tigecycline and vancomycin consumption. In surgical wards, there was a significant decrease in consumption of fluoroquinolones and piperacillin-tazobactam. This decrease was maintained in trend for all the antimicrobials but was significant for tigecycline only. In medical wards, there was a significant reduction of MRSA and C. albicans. In surgical wards, we observed a decrease in MRSA, ESBL-E. coli, C. albicans and CDI. KPC cases decreased by 22.5% in medical wards and 74.3% in surgical wards.

Conclusion

The results suggest that a persuasive educational approach to antimicrobial stewardship, with the introduction of an empiric antimicrobial manual and continuous education, resulted in reductions in both antimicrobial use and healthcare-associated BSI caused by multidrug-resistant organisms. More studies with longer follow up are needed to investigate the effect of antimicrobial stewardship on clinical outcomes.

The appropriateness of ceftriaxone utilization in government hospitals of Eastern Ethiopia: A retrospective evaluation of clinical practice

Introduction:

Drug use evaluation is a method of obtaining information to identify problems related to drug use and if properly developed, a means of correcting the problems. Ceftriaxone is among the most commonly utilized cephalosporins. Owing to a broad spectrum of activity and being used empirically, ceftriaxone has been used inappropriately posing a risk for development of antimicrobial resistance. This study is, therefore, designed to evaluate the appropriateness of ceftriaxone utilization in government hospitals in Harar town.

Methods:

A retrospective cross-sectional study was conducted in four government hospitals of Harar town by reviewing the medical records of 271 patients who received ceftriaxone from 1 January to 31 December 2016. Systematic random sampling was utilized to capture the medical records. Data were entered and analyzed using SPSS version 22.

Results:

From the 271 medical records reviewed majority of patients were from surgical ward (n = 85, 31.4%) followed by gynecology and obstetrics ward (n = 67, 24.7%). Demographically, the majority of the patients were female (n = 142, 52.4%). Patients in the age group of 20–29 years were dominant (n = 98, 36.2%). A total of 71 drugs were co-administered with ceftriaxone, the most common being metronidazole followed by tramadol. Among the co-administered drugs, unfractionated heparin (n = 6), warfarin (n = 5), and enoxaparin (n = 1) were found to have a moderate drug interaction with ceftriaxone. Ceftriaxone was commonly used for post-operative prophylaxis (n = 80, 27.5%) followed by for the management of pneumonia (n = 62, 21.3%). The result of ceftriaxone use evaluation showed that majority (n = 190, 70.1%) were found to be inappropriate. The inappropriate utilization was primarily due to wrong indication (indications for which ceftriaxone was not the primary option) (n = 114, 60.0%) followed by wrong duration (n = 54, 28.4%).

Conclusion:

Ceftriaxone was used inappropriately in more than two-thirds of the patients, with wrong indication and wrong duration contributing the majority. Inappropriate use of antibiotics may potentially lead to the emergence and spread of drug-resistant microorganisms and also ultimately exposes the patient to treatment failure, prolonged hospital stay, and higher cost of therapy.

The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans

Following the advent of industrial-scale antibiotic production in the 1940s,¹ antimicrobial resistance (AMR) has been on the rise and now poses a major global health threat in terms of mortality, morbidity, and economic burden.^2,3 Because AMR can be exchanged between humans, livestock, and wildlife, wild animals can be used as indicators of human-associated AMR contamination of the environment.⁴ However, AMR is a normal function of natural environments and is present in host-associated microbiomes, which makes it challenging to distinguish between anthropogenic and natural sources.^4,5 One way to overcome this difficulty is to use historical samples that span the period from before the mass production of antibiotics to today. We used shotgun metagenomic sequencing of dental calculus, the calcified form of the oral microbial biofilm, to determine the abundance and repertoire of AMR genes in the oral microbiome of Swedish brown bears collected over the last 180 years. Our temporal metagenomics approach allowed us to establish a baseline of natural AMR in the pre-antibiotics era and to quantify a significant increase in total AMR load and diversity of AMR genes that is consistent with patterns of national human antibiotic use. We also demonstrated a significant decrease in total AMR load in bears in the last two decades, which coincides with Swedish strategies to mitigate AMR. Our study suggests that public health policies can be effective in limiting human-associated AMR contamination of the environment and wildlife.

Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning

MOTIVATION

Antimicrobial resistance (AMR) is one of the biggest global problems threatening human and animal health. Rapid and accurate AMR diagnostic methods are thus very urgently needed. However, traditional antimicrobial susceptibility testing (AST) is time-consuming, low throughput and viable only for cultivable bacteria. Machine learning methods may pave the way for automated AMR prediction based on genomic data of the bacteria. However, comparing different machine learning methods for the prediction of AMR based on different encodings and whole-genome sequencing data without previously known knowledge remains to be done.

RESULTS

In this study, we evaluated logistic regression (LR), support vector machine (SVM), random forest (RF) and convolutional neural network (CNN) for the prediction of AMR for the antibiotics ciprofloxacin, cefotaxime, ceftazidime and gentamicin. We could demonstrate that these models can effectively predict AMR with label encoding, one-hot encoding and frequency matrix chaos game representation (FCGR encoding) on whole-genome sequencing data. We trained these models on a large AMR dataset and evaluated them on an independent public dataset. Generally, RFs and CNNs perform better than LR and SVM with AUCs up to 0.96. Furthermore, we were able to identify mutations that are associated with AMR for each antibiotic.

AVAILABILITY AND IMPLEMENTATION

Source code in data preparation and model training are provided at GitHub website (https://github.com/YunxiaoRen/ML-iAMR).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Estimation of the Difference in Colistin Plasma Levels in Critically Ill Patients with Favorable or Unfavorable Clinical Outcomes

In recent decades, antimicrobial resistance (AMR) has led to an increased use of therapeutic alternatives. Among these options, colistin continues to be an option for the treatment of multi-resistant (MDR) Gram-negative bacterial infections. However, due to its high toxicity (nephrotoxicity and neurotoxicity) and narrow therapeutic window, colistin treatment must be utilized carefully. Colistin-treated patients have been observed to have higher mortality due to inadequate therapeutic levels. The objective of this study was to estimate the difference in colistin plasma levels in critically ill patients, and its relationship to favorable or unfavorable clinical outcomes. This prospective observational study was conducted between September 2017 and June 2020 at the Universidad de La Sabana Clinic, in patients who had been treated with colistimethate sodium (CMS) for at least 72 h until day 7 of drug treatment in the critical care unit of a university hospital. There were no statistically significant differences in colistin levels between groups with favorable or unfavorable clinical outcomes (0.16 SD vs. 0.54 SD p-value = 0.167). There was higher mortality in patients with subtherapeutic levels (18% vs. 0%), and additionally, there was a greater rate of renal failure in the group with higher therapeutic levels (50% vs. 20.7%). Due to the loss of power of the study, we were unable to demonstrate a possible difference between colistin levels related to favorable or unfavorable clinical outcomes at day 7. However, we recommend further studies to evaluate the impact of measuring levels in terms of mortality and security.

Antimicrobial resistance: progress and challenges in antibiotic discovery and anti-infective therapy

The alarming rise in the emergence of antimicrobial resistance in human, animal and plant pathogens is challenging global health and food production. Traditional strategies used for antibiotic discovery persistently result in the re‐isolation of known compounds, calling for the need to develop more rational strategies to identify new antibiotics. Additionally, anti‐infective therapy approaches targeting bacterial signalling pathways related to virulence is emerging as an alternative to the use of antibiotics. In this perspective article, we critically analyse approaches aimed at revitalizing the identification of new antibiotics and to advance antivirulence therapies. The development of high‐throughput in vivo, in vitro and in silico platforms, together with the progress in chemical synthesis, analytical chemistry and structural biology, are reviving a research area that is of tremendous relevance for global health.

Surveillance strategies using routine microbiology for antimicrobial resistance in low- and middle-income countries

BACKGROUND

Routine microbiology results are a valuable source of antimicrobial resistance (AMR) surveillance data in low- and middle-income countries (LMICs) as well as in high-income countries. Different approaches and strategies are used to generate AMR surveillance data.

OBJECTIVES

We aimed to review strategies for AMR surveillance using routine microbiology results in LMICs and to highlight areas that need support to generate high-quality AMR data.

SOURCES

We searched PubMed for papers that used routine microbiology to describe the epidemiology of AMR and drug-resistant infections in LMICs. We also included papers that, from our perspective, were critical in highlighting the biases and challenges or employed specific strategies to overcome these in reporting AMR surveillance in LMICs.

CONTENT

Topics covered included strategies of identifying AMR cases (including case-finding based on isolates from routine diagnostic specimens and case-based surveillance of clinical syndromes), of collecting data (including cohort, point-prevalence survey, and case-control), of sampling AMR cases (including lot quality assurance surveys), and of processing and analysing data for AMR surveillance in LMICs.

IMPLICATIONS

The various AMR surveillance strategies warrant a thorough understanding of their limitations and potential biases to ensure maximum utilization and interpretation of local routine microbiology data across time and space. For instance, surveillance using case-finding based on results from clinical diagnostic specimens is relatively easy to implement and sustain in LMIC settings, but the estimates of incidence and proportion of AMR is at risk of biases due to underuse of microbiology. Case-based surveillance of clinical syndromes generates informative statistics that can be translated to clinical practices but needs financial and technical support as well as locally tailored trainings to sustain. Innovative AMR surveillance strategies that can easily be implemented and sustained with minimal costs will be useful for improving AMR data availability and quality in LMICs.

Zanthoxylum Species: A Review of Traditional Uses, Phytochemistry and Pharmacology in Relation to Cancer, Infectious Diseases and Sickle Cell Anemia

The health benefits and toxicity of plant products are largely dependent on their secondary metabolite contents. These compounds are biosynthesized by plants as protection mechanisms against environmental factors and infectious agents. This review discusses the traditional uses, phytochemical constituents and health benefits of plant species in genus Zanthoxylum with a focus on cancer, microbial and parasitic infections, and sickle cell disease as reported in articles published from 1970 to 2021 in peer-reviewed journals and indexed in major scientific databases. Generally, Z. species are widely distributed in Asia, America and Africa, where they are used as food and for disease treatment. Several compounds belonging to alkaloids, flavonoids, terpenoids, and lignans, among others have been isolated from Z. species. This review discusses the biological activities reported for the plant species and their phytochemicals, including anticancer, antibacterial, antifungal, antiviral, anti-trypanosomal, antimalarial and anti-sickling properties. The safety profiles and suggestions for conservation of the Z. species were also discussed. Taken together, this review demonstrates that Z. species are rich in a wide range of bioactive phytochemicals with multiple health benefits, but more research is needed towards their practical application in the development of functional foods, nutraceuticals and lead compounds for new drugs.

Microbiome-pathogen interactions drive epidemiological dynamics of antibiotic resistance: A modeling study applied to nosocomial pathogen control

The human microbiome can protect against colonization with pathogenic antibiotic-resistant bacteria (ARB), but its impacts on the spread of antibiotic resistance are poorly understood. We propose a mathematical modeling framework for ARB epidemiology formalizing within-host ARB-microbiome competition, and impacts of antibiotic consumption on microbiome function. Applied to the healthcare setting, we demonstrate a trade-off whereby antibiotics simultaneously clear bacterial pathogens and increase host susceptibility to their colonization, and compare this framework with a traditional strain-based approach. At the population level, microbiome interactions drive ARB incidence, but not resistance rates, reflecting distinct epidemiological relevance of different forces of competition. Simulating a range of public health interventions (contact precautions, antibiotic stewardship, microbiome recovery therapy) and pathogens (Clostridioides difficile, methicillin-resistant Staphylococcus aureus, multidrug-resistant Enterobacteriaceae) highlights how species-specific within-host ecological interactions drive intervention efficacy. We find limited impact of contact precautions for Enterobacteriaceae prevention, and a promising role for microbiome-targeted interventions to limit ARB spread.

A protocol for a systematic literature review of economic evaluation studies of interventions to address antimicrobial resistance

BACKGROUND

Antimicrobial resistance (AMR) is accelerated by the widespread and often indiscriminate use of antimicrobials in humans, animals, and the environment. In 2015, the World Health Organization recognised AMR as one of the top ten global health threats, due to its potential to neutralise humanity's advancements in western medicine by enabling the emergence of new strains of existing pathogens, many of which have no available treatments. Over the past decade, several countries, including those in low- and middle-income contexts, have started implementing interventions to tackle AMR. However, economic evidence regarding the cost-effectiveness of these interventions remains weak. To address this evidence gap, we will conduct a systematic literature review to provide a comprehensive summary on the value for money of different AMR interventions.

METHODS

We aim to conduct a systematic literature review of all available economic evaluations on interventions addressing AMR and will provide a narrative synthesis of our findings. Systematic searches for relevant studies will be performed across all suitable databases as well as in grey literature sources such as unpublished studies, reports, and other relevant documents. All economic evaluation studies will be included as long as they report an economic outcome and have stated that the analysed intervention will reduce antimicrobial resistance or antimicrobial use in the abstract. Those studies reporting clinical endpoints alone will be excluded. Selection for final inclusion and data extraction will be performed by two independent reviewers.

DISCUSSION

The review will be one of the first of its kind, and the most recent, to systematically review literature on the cost-effectiveness of AMR interventions, an important evidence gap in the economics of AMR. The findings will enable policy and decision-makers, particularly in resource-constrained settings, to better use available resources when selecting interventions to address AMR burdens, SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42020190310.

BactoSpin: Novel Technology for Rapid Bacteria Detection and Antibiotic Susceptibility Testing

Inappropriate use of antibiotics is one of the leading causes of the increasing numbers of resistant bacteria strains, resulting in 700,000 deaths worldwide each year. Reducing unnecessary use of antibiotics and choosing the most effective antibiotics instead of broad-spectrum drugs will slow the arms race between germs and humans. Urinary tract infections (UTIs) are among the most common bacterial infections. Currently, accurate diagnosis of UTI requires approximately 48 h from the time of urine sample collection until antibiotic susceptibility test (AST) results. This work presents a rapid bacterial detection device that integrates a centrifuge, microscope, and incubator. Two disposable microfluidic chips were developed. The first chip was designed for bacteria concentration, detection, and medium exchange. A second multi-channel chip was developed for AST. This chip contains superhydrophobic and hydrophilic coatings to ensure liquid separation between the channels without the need for valves. The designed chips supported the detection of E. coli at a concentration as low as 5 × 10³ cells/mL within 5 min and AST in under 2 h. AST was also successfully performed with Klebsiella pneumonia isolated from a human urine sample. In addition, machine-learning-based image recognition was shown to reduce the required time for AST and to provide results within 1 h for E. coli cells. Thus, the BactoSpin device can serve as an efficient and rapid platform for UTI diagnostics and AST.

Compound Prioritization through Meta-Analysis Enhances the Discovery of Antimicrobial Hits against Bacterial Pathogens

The development of informatic tools to improve the identification of novel antimicrobials would significantly reduce the cost and time of drug discovery. We previously screened several plant (Xanthomonas sp., Clavibacter sp., Acidovorax sp., and Erwinia sp.), animal (Avian pathogenic Escherichia coli and Mycoplasma sp.), and human (Salmonella sp. and Campylobacter sp.) pathogens against a pre-selected small molecule library (n = 4182 SM) to identify novel SM (hits) that completely inhibited the bacterial growth or attenuated at least 75% of the virulence (quorum sensing or biofilm). Our meta-analysis of the primary screens (n = 11) using the pre-selected library (approx. 10.2 ± 9.3% hit rate per screen) demonstrated that the antimicrobial activity and spectrum of activity, and type of inhibition (growth versus virulence inhibitors) correlated with several physico-chemical properties (PCP; e.g., molecular weight, molar refraction, Zagreb group indexes, Kiers shape, lipophilicity, and hydrogen bond donors and acceptors). Based on these correlations, we build an in silico model that accurately classified 80.8% of the hits (n = 1676/2073). Therefore, the pre-selected SM library of 4182 SM was narrowed down to 1676 active SM with predictable PCP. Further, 926 hits affected only one species and 1254 hits were active against specific type of pathogens; however, no correlation was detected between PCP and the type of pathogen (29%, 34%, and 46% were specific for animal, human foodborne and plant pathogens, respectively). In conclusion, our in silico model allowed rational identification of SM with potential antimicrobial activity against bacterial pathogens. Therefore, the model developed in this study may facilitate future drug discovery efforts by accelerating the identification of uncharacterized antimicrobial molecules and predict their spectrum of activity.

Prevalence of multidrug-resistant and extended-spectrum beta-lactamase-producing Escherichia coli in urban community wastewater

Antibiotic resistance (ABR) and the spread of multidrug-resistant and extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli via wastewater to environmental compartments are of rapidly growing global health concern. Health care facilities, industries and slaughterhouses discharge high loads of ABR bacteria with their wastewater. However, the general community is often the biggest indirect discharger. Yet, research focusing explicitly on this important diffuse source is rather scarce raising questions about variations in the occurrence of ESBL-producing E. coli in wastewater from different communities and over time. Between April 2019 and March 2020, wastewater from three socio-spatially different districts in the Ruhr Metropolis, Germany, and the receiving wastewater treatment plant was sampled monthly and analysed for the occurrence of ESBL-producing E. coli via culture-based methods. Isolates were validated with matrix assisted laser desorption ionization time of flight mass spectrometry and antibiotic resistance profiles were analysed via microdilution. Results were interpreted using the European Committee on Antimicrobial Susceptibility Testing criteria. The German Commission for Hospital Hygiene and Infection Prevention criteria were used for multidrug-resistance categorization. Phenotypic ESBL-producing E. coli could be isolated from every wastewater sample demonstrating that the general community is an important indirect discharger. The socio-spatially disadvantaged area displayed higher absolute loads of ESBL-producing E. coli compared to the other two areas, as well as higher adjusted loads for domestic discharge and inhabitants, particularly during winter, indicating a higher ABR burden. Thirty-two isolates (28.6%) were characterized as multidrug-resistant Gram-negative bacteria (3MRGN). Resistance profiles varied only for those antibiotics, which can be administered in outpatient care. Resistance levels tended to be around 10% lower in the socio-spatially advantaged area. This study shows that spatial and seasonal influences regarding the occurrence of ESBL-producing E. coli in wastewater from socio-spatially different communities are identifiable.

Escherichia coli bloodstream infections in the western interior of British Columbia, Canada: a population-based cohort study

Our population-based study objectives were to describe characteristics and outcomes of Escherichia coli bloodstream infections (BSIs), and to evaluate factors associated with outcomes. We included incident E. coli BSIs from western interior residents (British Columbia, Canada; 04/2010–03/2020). We obtained data including patient demographics, location of onset, infection focus, Charlson comorbidity index (CCI), antimicrobial resistance, 30-day all-cause mortality and length of hospital stay (LOS). Using multivariable logistic regression models fitted with generalised estimating equations, we estimated factors associated with 30-day mortality and long post-infection LOS (>75th percentile). We identified 1080 incident E. coli BSIs in 1009 patients. The crude incidence and 30-day mortality rates were 59.1 BSIs and 6.8 deaths/100 000 person-years, respectively. The 30-day case fatality risk was 11.5%. Compared to community-acquired E. coli BSIs, either healthcare-associated or nosocomial cases had higher odds of 30-day mortality. Older cases, non-urogenital BSI foci and CCI ⩾ 3 had higher odds of 30-day mortality compared to younger cases, urogenital foci and CCI < 3. In patients that survived to discharge, those with extended-spectrum β-lactamase (ESBL)-producing E. coli BSIs, nosocomial BSIs, and CCI ⩾ 3 had higher odds of long post-infection LOS compared to those with non-ESBL-producing, community-acquired and healthcare-associated, and CCI < 3. There is a substantial disease burden from E. coli BSIs.

How can artificial intelligence be used for peptidomics?

INTRODUCTION

Peptidomics is an emerging field of omics sciences using advanced isolation, analysis, and computational techniques that enable qualitative and quantitative analyses of various peptides in biological samples. Peptides can act as useful biomarkers and as therapeutic molecules for diseases.

AREAS COVERED

The use of therapeutic peptides can be predicted quickly and efficiently using data-driven computational methods, particularly artificial intelligence (AI) approach. Various AI approaches are useful for peptide-based drug discovery, such as support vector machine, random forest, extremely randomized trees, and other more recently developed deep learning methods. AI methods are relatively new to the development of peptide-based therapies, but these techniques already become essential tools in protein science by dissecting novel therapeutic peptides and their functions (Figure 1).[Figure: see text].

EXPERT OPINION

Researchers have shown that AI models can facilitate the development of peptidomics and selective peptide therapies in the field of peptide science. Biopeptide prediction is important for the discovery and development of successful peptide-based drugs. Due to their ability to predict therapeutic roles based on sequence details, many AI-dependent prediction tools have been developed (Figure 1).

Bed-days and costs associated with the inpatient burden of healthcare-associated infection in the UK

BACKGROUND

Healthcare-associated infection (HAI) is associated with increased morbidity and mortality resulting in excess costs.

AIM

To investigate the impact of all types of HAI on the inpatient cost of HAI using different approaches.

METHODS

The incidence, types of HAI, and excess length of stay were estimated using data collected as part of the Evaluation of Cost of Nosocomial Infection (ECONI) study. Scottish NHS reference costs were used to estimate unit costs for bed-days. Variable (cash) costs associated with infection prevention and control (IPC) measures and treatment were calculated for each HAI type and overall. The inpatient cost of HAI is presented in terms of bed-days lost, bed-day costs, and cash costs.

FINDINGS

In Scotland 58,010 (95% confidence interval: 41,730-74,840) bed-days were estimated to be lost to HAI during 2018/19, costing £46.4 million (19m-129m). The total annual cost in the UK is estimated to be £774 million (328m-2,192m). Bloodstream infection and pneumonia were the most costly HAI types per case. Cash costs are a small proportion of the total cost of HAI, contributing 2.4% of total costs.

CONCLUSION

Reliable estimates of the cost burden of HAI management are important for assessing the cost-effectiveness of IPC programmes. This unique study presents robust economic data, demonstrating that HAI remains a burden to the UK NHS and bed-days capture the majority of inpatient costs. These findings can be used to inform the economic evaluation and decision analytic modelling of competing IPC programmes at local and national level.

Type 2 diabetes mellitus and antibiotic-resistant infections: a systematic review and meta-analysis

BACKGROUND

Type 2 diabetes mellitus (T2DM) has been associated with infectious diseases; however, whether T2DM is associated with bacterial-resistant infections has not been thoroughly studied. We ascertained whether people with T2DM were more likely to experience resistant infections in comparison to T2DM-free individuals.

METHODS

Systematic review and random-effects meta-analysis. The search was conducted in Medline, Embase and Global Health. We selected observational studies in which the outcome was resistant infections (any site), and the exposure was T2DM. We studied adult subjects who could have been selected from population-based or hospital-based studies. I² was the metric of heterogeneity. We used the Newcastle-Ottawa risk of bias scale.

RESULTS

The search retrieved 3370 reports, 97 were studied in detail and 61 (449 247 subjects) were selected. Studies were mostly cross-sectional or case-control; several infection sites were studied, but mostly urinary tract and respiratory infections. The random-effects meta-analysis revealed that people with T2DM were twofold more likely to have urinary tract (OR=2.42; 95% CI 1.83 to 3.20; I² 19.1%) or respiratory (OR=2.35; 95% CI 1.49 to 3.69; I² 58.1%) resistant infections. Although evidence for other infection sites was heterogeneous, they consistently suggested that T2DM was associated with resistant infections.

CONCLUSIONS

Compelling evidence suggests that people with T2DM are more likely to experience antibiotic-resistant urinary tract and respiratory infections. The evidence for other infection sites was less conclusive but pointed to the same overall conclusion. These results could guide empirical treatment for patients with T2DM and infections.

Antimicrobial resistance and the post antibiotic era: better late than never effort

Introduction: Antimicrobial resistance (AMR) is a multi-layered problem with a calamitous impact on humans, livestock, the environment, and the biosphere. Initiatives and action plan to preclude AMR remain poorly implemented in India.Area covered: This review highlights essential factors contributing to AMR, epidemiology of the resistant bacteria, current treatment options, economic impact, and regulatory efforts initiated by the Indian government to tackle AMR.Expert opinion: Health-care professionals, hospitals, and the general public must understand and cooperatively implement the 'One Health approach,' which entails judicious use of antibiotics in humans, animals, and the environment. Neglecting the AMR problem predicts the expansion of the 'Post-antibiotic era' characterized by drying antibiotic discovery pipelines, overuse of 'Watch' and 'Reserve' groups, coupled with underuse of 'Access' antibiotics, increased daily defined doses, increased healthcare cost, rise in morbidity, mortality, and environmental degradation. The Indian case study elucidates a looming international crisis that demands global attention and commitment for envisaging and implementing locally relevant solutions.