Rapid Methods for Antimicrobial Resistance Diagnostics

Healthcare as a driver, reservoir and amplifier of antimicrobial resistance: opportunities for interventions

Antimicrobial resistance (AMR) is a global health challenge that threatens humans, animals and the environment. Evidence is emerging for a role of healthcare infrastructure, environments and patient pathways in promoting and maintaining AMR via direct and indirect mechanisms. Advances in vaccination and monoclonal antibody therapies together with integrated surveillance, rapid diagnostics, targeted antimicrobial therapy and infection control measures offer opportunities to address healthcare-associated AMR risks more effectively. Additionally, innovations in artificial intelligence, data linkage and intelligent systems can be used to better predict and reduce AMR and improve healthcare resilience. In this Review, we examine the mechanisms by which healthcare functions as a driver, reservoir and amplifier of AMR, contextualized within a One Health framework. We also explore the opportunities and innovative solutions that can be used to combat AMR throughout the patient journey. We provide a perspective on the current evidence for the effectiveness of interventions designed to mitigate healthcare-associated AMR and promote healthcare resilience within high-income and resource-limited settings, as well as the challenges associated with their implementation.

Development of Rapid Disk Diffusion Device Using Laser Speckle Formation Technology for Rapid Antimicrobial Susceptibility Testing

The escalation of antimicrobial resistance (AMR) due to the excessive and inappropriate use of antimicrobials has prompted the urgent need for more rapid and effective antimicrobial susceptibility testing (AST) methods. Conventional AST techniques often take 16-24 h, leading to empirical prescription practices and the potential emergence of AMR. The study aimed to develop a rapid disk diffusion (RDD) method utilizing laser speckle formation (LSF) technology to expedite AST results. The study aimed to evaluate the performance of LSF technology in determining antimicrobial susceptibility. In this study, preclinical and clinical settings were established to compare the LSF technology with conventional disk diffusion (DD) methods to measure the inhibition zones. Preclinical experiments with different bacterial strains demonstrated more than 70% categorical agreement (CA) against most antimicrobials. Further, clinical experiments with multiple strains and antibiotics revealed CA ranging from 40 to 79%, while major and minor discrepancies were observed around 30% and 11%, respectively. These observations revealed high concordance between RDD and DD for multiple antimicrobials in multiple species. The results underscore the potential of RDD-based LSF technology for hastening AST procedures. The current study is marked by a unique equipment setup and analysis approach. Collectively, the suggested laser-based RDD showed greater potential than previously developed comparable methods. The proposed method and design have a higher application potential than formerly developed similar technologies. Together, the study contributes to the ongoing development of rapid AST methods.

New Agents Are Coming, and So Is the Resistance

Antimicrobial resistance is a global threat that requires urgent attention to slow the spread of resistant pathogens. The United States Centers for Disease Control and Prevention (CDC) has emphasized clinician-driven antimicrobial stewardship approaches including the reporting and proper documentation of antimicrobial usage and resistance. Additional efforts have targeted the development of new antimicrobial agents, but narrow profit margins have hindered manufacturers from investing in novel antimicrobials for clinical use and therefore the production of new antibiotics has decreased. In order to combat this, both antimicrobial drug discovery processes and healthcare reimbursement programs must be improved. Without action, this poses a high probability to culminate in a deadly post-antibiotic era. This review will highlight some of the global health challenges faced both today and in the future. Furthermore, the new Infectious Diseases Society of America (IDSA) guidelines for resistant Gram-negative pathogens will be discussed. This includes new antimicrobial agents which have gained or are likely to gain FDA approval. Emphasis will be placed on which human pathogens each of these agents cover, as well as how these new agents could be utilized in clinical practice.

Fourier Transform Infrared Spectroscopy Application for Candida auris Outbreak Typing in a Referral Intensive Care Unit: Phylogenetic Analysis and Clustering Cut-Off Definition

Recently Candida auris has emerged as a multi-resistant fungal pathogen, with a significant clinical impact, and is able to persist for a long time on human skin and hospital environments. It is a critical issue on the WHO fungal priority list and therefore it is fundamental to reinforce hospital surveillance protocols to limit nosocomial outbreaks. The purpose of this study was to apply Fourier transform infrared spectroscopy (FT-IR) to investigate the phylogenetic relationships among isolated strains from a C. auris outbreak at the University Intensive Care Unit of a Tertiary University hospital in Turin (Italy). To calculate a clustering cut-off, intra- and inter-isolate, distance values were analysed. The data showed the presence of a major Alfa cluster and a minor Beta cluster with a defined C. auris clustering cut-off. The results were validated by an external C. auris strain and Principal Component and Linear Discriminant Analyses. The application of FT-IR technology allowed to obtain important information about the phylogenetic relationships between the analysed strains, defining for the first time a "not WGS-based" clustering cut-off with a statistical-mathematical approach. FT-IR could represent a valid alternative to molecular methods for the rapid and cost-saving typing of C. auris strains with important clinical implications.

A Comprehensive Review of Innovative Paradigms in Microbial Detection and Antimicrobial Resistance: Beyond Traditional Cultural Methods

Microbial detection and antimicrobial resistance (AMR) surveillance are critical components of public health efforts to combat infectious diseases and preserve the efficacy of antimicrobial agents. While foundational in microbial identification, traditional cultural methods are often laborious, time-consuming, and limited in their ability to detect AMR markers. In response to these challenges, innovative paradigms have emerged, leveraging advances in molecular biology, genomics, proteomics, nanotechnology, and bioinformatics. This comprehensive review provides an overview of innovative approaches beyond traditional cultural methods for microbial detection and AMR surveillance. Molecular-based techniques such as polymerase chain reaction (PCR) and next-generation sequencing (NGS) offer enhanced sensitivity and specificity, enabling the rapid identification of microbial pathogens and AMR determinants. Mass spectrometry-based methods provide rapid and accurate detection of microbial biomarkers, including matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and biosensor technologies. Nanotechnology approaches, such as nanoparticle-based assays and nanopore sequencing, offer novel platforms for sensitive and label-free detection of pathogens and AMR markers. Embracing these innovative paradigms holds immense promise for improving disease diagnosis, antibiotic stewardship, and AMR containment efforts. However, challenges such as cost, standardization, and integration with existing healthcare systems must be addressed to realize the full potential of these technologies. By fostering interdisciplinary collaboration and innovation, we can strengthen our ability to detect, monitor, and combat AMR, safeguarding public health for generations.

Comprehensive genomic and plasmid characterization of multidrug-resistant bacterial strains by R10.4.1 nanopore sequencing

The escalating prevalence of multidrug-resistant (MDR) bacteria pose a significant public health threat. Understanding the genomic features and deciphering the antibiotic resistance profiles of these pathogens is crucial for development of effective surveillance and treatment strategies. In this study, we employed the R10.4.1 nanopore sequencing technology, specifically through the use of the MinION platform, to analyze eight MDR bacterial strains originating from clinical, ecological and food sources. A single 72-hour sequencing run could yield approximately 12 million reads which covered a total of 34 gigabases (Gbp). The nanopore R10.4.1 data was processed using the Flye assembler, successfully assembling the genomes of eight bacterial strains and their 18 plasmids. Notably, the assemblies generated solely from R10.4.1 nanopore data closely matched those from next-generation sequencing data. Diverse antibiotic resistance patterns and specific resistance genes in the test strains were identified. Hospital strains that exhibited multidrug resistance were found to harbor various resistance genes that encode efflux pumps and extended-spectrum β-lactamases. Environmental and food sources were found to display resistance profiles in a species-specific manner. The composition of structurally complex plasmids in the test strains could also be revealed by analysis of nanopore long reads, which also suggested evidence of horizontal transfer of plasmids between different bacterial species. These findings provide valuable insights into the genetic characteristics of MDR bacteria and demonstrating the practicality of nanopore sequencing technology for detecting of resistance elements in bacterial pathogens.

Predictive Modeling of Phenotypic Antimicrobial Susceptibility of Selected Beta-Lactam Antimicrobials from Beta-Lactamase Resistance Genes

The outcome of bacterial infection management relies on prompt diagnosis and effective treatment, but conventional antimicrobial susceptibility testing can be slow and labor-intensive. Therefore, this study aims to predict phenotypic antimicrobial susceptibility of selected beta-lactam antimicrobials in the bacteria of the family Enterobacteriaceae from different beta-lactamase resistance genotypes. Using human datasets extracted from the Antimicrobial Testing Leadership and Surveillance (ATLAS) program conducted by Pfizer and retail meat datasets from the National Antimicrobial Resistance Monitoring System for Enteric Bacteria (NARMS), we used a robust or weighted least square multivariable linear regression modeling framework to explore the relationship between antimicrobial susceptibility data of beta-lactam antimicrobials and different types of beta-lactamase resistance genes. In humans, in the presence of the blaCTX-M-1, blaCTX-M-2, blaCTX-M-8/25, and blaCTX-M-9 groups, MICs of cephalosporins significantly increased by values between 0.34-3.07 μg/mL, however, the MICs of carbapenem significantly decreased by values between 0.81-0.87 μg/mL. In the presence of carbapenemase genes (blaKPC, blaNDM, blaIMP, and blaVIM), the MICs of cephalosporin antimicrobials significantly increased by values between 1.06-5.77 μg/mL, while the MICs of carbapenem antimicrobials significantly increased by values between 5.39-67.38 μg/mL. In retail meat, MIC of ceftriaxone increased significantly in the presence of blaCMY-2, blaCTX-M-1, blaCTX-M-55, blaCTX-M-65, and blaSHV-2 by 55.16 μg/mL, 222.70 μg/mL, 250.81 μg/mL, 204.89 μg/mL, and 31.51 μg/mL respectively. MIC of cefoxitin increased significantly in the presence of blaCTX-M-65 and blaTEM-1 by 1.57 μg/mL and 1.04 μg/mL respectively. In the presence of blaCMY-2, MIC of cefoxitin increased by an average of 8.66 μg/mL over 17 years. Compared to E. coli isolates, MIC of cefoxitin in Salmonella enterica isolates decreased significantly by 0.67 μg/mL. On the other hand, MIC of ceftiofur increased in the presence of blaCTX-M-1, blaCTX-M-65, blaSHV-2, and blaTEM-1 by 8.82 μg/mL, 9.11 μg/mL, 8.18 μg/mL, and 1.04 μg/mL respectively. In the presence of blaCMY-2, MIC of ceftiofur increased by an average of 10.20 μg/mL over 14 years. The ability to predict antimicrobial susceptibility of beta-lactam antimicrobials directly from beta-lactamase resistance genes may help reduce the reliance on routine phenotypic testing with higher turnaround times in diagnostic, therapeutic, and surveillance of antimicrobial-resistant bacteria of the family Enterobacteriaceae.

Evaluation of three protocols for direct susceptibility testing for gram negative-Enterobacteriaceae from patient samples in Uganda with SMS reporting

In Uganda, the challenge of generating and timely reporting essential antimicrobial resistance (AMR) data has led to overreliance on empirical antibiotic therapy, exacerbating the AMR crisis. To address this issue, this study aimed to adapt a one-step AMR testing protocol alongside an SMS (Short Message Service) result relay system (SRRS), with the potential to reduce the turnaround time for AMR testing and result communication from 4 days or more to 1 day in Ugandan clinical microbiology laboratories. Out of the 377 samples examined, 54 isolates were obtained. Notably, E. coli (61%) and K. pneumoniae (33%) were the most frequently identified, majority testing positive for ESBL. Evaluation of three AMR testing protocols revealed varying sensitivity and specificity, with Protocol A (ChromID ESBL-based) demonstrating high sensitivity (100%) but no calculable specificity, Protocol B (ceftazidime-based) showing high sensitivity (100%) and relatively low specificity (7.1%), and Protocol C (cefotaxime-based) exhibiting high sensitivity (97.8%) but no calculable specificity. ESBL positivity strongly correlated with resistance to specific antibiotics, including cefotaxime, ampicillin, and aztreonam (100%), cefuroxime (96%), ceftriaxone (93%), and trimethoprim sulfamethoxazole (87%). The potential of integrating an SRRS underscored the crucial role this could have in enabling efficient healthcare communication in AMR management. This study underscores the substantial potential of the tested protocols for accurately detecting ESBL production in clinical samples, potentially, providing a critical foundation for predicting and reporting AMR patterns. Although considerations related to specificity warrant careful assessment before widespread clinical adoption.

Antimicrobial susceptibility testing using infrared attenuated total reflection (IR-ATR) spectroscopy to monitor metabolic activity

Fast and accurate detection of antimicrobial resistance in pathogens remains a challenge, and with the increase in antimicrobial resistance due to mis- and overuse of antibiotics, it has become an urgent public health problem. We demonstrate how infrared attenuated total reflection (IR-ATR) can be used as a simple method for assessment of bacterial susceptibility to antibiotics. This is achieved by monitoring the metabolic activities of bacterial cells via nutrient consumption and using this as an indicator of bacterial viability. Principal component analysis of the obtained spectra provides a tool for fast and simple discrimination of antimicrobial resistance in the acquired data. We demonstrate this concept using four bacterial strains and four different antibiotics, showing that the change in glucose concentration in the growth medium after 2 h, as monitored by IR-ATR, can be used as a spectroscopic diagnostic technique, to reduce detection time and to improve quality in the assessment of antimicrobial resistance in pathogens.

Microwell-enhanced optical rapid antibiotic susceptibility testing of single bacteria

Bacteria that are resistant to antibiotics present an increasing burden on healthcare. To address this emerging crisis, novel rapid antibiotic susceptibility testing (AST) methods are eagerly needed. Here, we present an optical AST technique that can determine the bacterial viability within 1 h down to a resolution of single bacteria. The method is based on measuring intensity fluctuations of a reflected laser focused on a bacterium in reflective microwells. Using numerical simulations, we show that both refraction and absorption of light by the bacterium contribute to the observed signal. By administering antibiotics that kill the bacteria, we show that the variance of the detected fluctuations vanishes within 1 h, indicating the potential of this technique for rapid sensing of bacterial antibiotic susceptibility. We envisage the use of this method for massively parallelizable AST tests and fast detection of drug-resistant pathogens.

Origin of Antibiotics and Antibiotic Resistance, and Their Impacts on Drug Development: A Narrative Review

Antibiotics have revolutionized medicine, saving countless lives since their discovery in the early 20th century. However, the origin of antibiotics is now overshadowed by the alarming rise in antibiotic resistance. This global crisis stems from the relentless adaptability of microorganisms, driven by misuse and overuse of antibiotics. This article explores the origin of antibiotics and the subsequent emergence of antibiotic resistance. It delves into the mechanisms employed by bacteria to develop resistance, highlighting the dire consequences of drug resistance, including compromised patient care, increased mortality rates, and escalating healthcare costs. The article elucidates the latest strategies against drug-resistant microorganisms, encompassing innovative approaches such as phage therapy, CRISPR-Cas9 technology, and the exploration of natural compounds. Moreover, it examines the profound impact of antibiotic resistance on drug development, rendering the pursuit of new antibiotics economically challenging. The limitations and challenges in developing novel antibiotics are discussed, along with hurdles in the regulatory process that hinder progress in this critical field. Proposals for modifying the regulatory process to facilitate antibiotic development are presented. The withdrawal of major pharmaceutical firms from antibiotic research is examined, along with potential strategies to re-engage their interest. The article also outlines initiatives to overcome economic challenges and incentivize antibiotic development, emphasizing international collaborations and partnerships. Finally, the article sheds light on government-led initiatives against antibiotic resistance, with a specific focus on the Middle East. It discusses the proactive measures taken by governments in the region, such as Saudi Arabia and the United Arab Emirates, to combat this global threat. In the face of antibiotic resistance, a multifaceted approach is imperative. This article provides valuable insights into the complex landscape of antibiotic development, regulatory challenges, and collaborative efforts required to ensure a future where antibiotics remain effective tools in safeguarding public health.

Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology

Recent advancements in sequencing technology and data analytics have led to a transformative era in pathogen detection and typing. These developments not only expedite the process, but also render it more cost-effective. Genomic analyses of infectious diseases are swiftly becoming the standard for pathogen analysis and control. Additionally, national surveillance systems can derive substantial benefits from genomic data, as they offer profound insights into pathogen epidemiology and the emergence of antimicrobial-resistant strains. Antimicrobial resistance (AMR) is a pressing global public health issue. While clinical laboratories have traditionally relied on culture-based antimicrobial susceptibility testing, the integration of genomic data into AMR analysis holds immense promise. Genomic-based AMR data can furnish swift, consistent, and highly accurate predictions of resistance phenotypes for specific strains or populations, all while contributing invaluable insights for surveillance. Moreover, genome sequencing assumes a pivotal role in the investigation of hospital outbreaks. It aids in the identification of infection sources, unveils genetic connections among isolates, and informs strategies for infection control. The One Health initiative, with its focus on the intricate interconnectedness of humans, animals, and the environment, seeks to develop comprehensive approaches for disease surveillance, control, and prevention. When integrated with epidemiological data from surveillance systems, genomic data can forecast the expansion of bacterial populations and species transmissions. Consequently, this provides profound insights into the evolution and genetic relationships of AMR in pathogens, hosts, and the environment.

A Systematic Review of In Vitro Studies Using Microchip Platforms for Identifying Periodontopathogens from the Red Complex

Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola, collectively recognized as periodontopathogens within the red complex, have been extensively studied in clinical samples collected from individuals with periodontitis. A lab-on-a-chip (LOC) is a miniature mechanism that integrates various laboratory operations onto a single microchip or a small-scale platform. This systematic review evaluates the application of LOC technology in identifying microorganisms from the red complex. This study adhered to PRISMA recommendations, and the review process encompassed several databases. In the electronic search, a total of 58 reports were found, and ultimately, 10 studies were considered relevant for inclusion. All these studies described effective, rapid, and reliable LOC systems for detecting and amplifying P. gingivalis, T. forsythia, and T. denticola. Compared to traditional methods, the LOC approach demonstrated minimal reagent requirements. Additionally, the results indicated that the amplification process took approximately 2 to 8 min, while detection could be completed in as little as 2 min and 40 s, resulting in a total experimental duration of around 11 min. Integrating miniaturization, speed, accuracy, and automation within microchip platforms makes them promising tools for detecting and amplifying microorganisms associated with the red complex in periodontal diseases.

Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria

Antibiotic resistance is a global public health concern, posing a significant threat to the effectiveness of antibiotics in treating bacterial infections. The accurate and timely detection of antibiotic-resistant bacteria is crucial for implementing appropriate treatment strategies and preventing the spread of resistant strains. This manuscript provides an overview of the current and emerging technologies used for the detection of antibiotic-resistant bacteria. We discuss traditional culture-based methods, molecular techniques, and innovative approaches, highlighting their advantages, limitations, and potential future applications. By understanding the strengths and limitations of these technologies, researchers and healthcare professionals can make informed decisions in combating antibiotic resistance and improving patient outcomes.

Ten golden rules for optimal antibiotic use in hospital settings: the WARNING call to action

Antibiotics are recognized widely for their benefits when used appropriately. However, they are often used inappropriately despite the importance of responsible use within good clinical practice. Effective antibiotic treatment is an essential component of universal healthcare, and it is a global responsibility to ensure appropriate use. Currently, pharmaceutical companies have little incentive to develop new antibiotics due to scientific, regulatory, and financial barriers, further emphasizing the importance of appropriate antibiotic use. To address this issue, the Global Alliance for Infections in Surgery established an international multidisciplinary task force of 295 experts from 115 countries with different backgrounds. The task force developed a position statement called WARNING (Worldwide Antimicrobial Resistance National/International Network Group) aimed at raising awareness of antimicrobial resistance and improving antibiotic prescribing practices worldwide. The statement outlined is 10 axioms, or "golden rules," for the appropriate use of antibiotics that all healthcare workers should consistently adhere in clinical practice.

A Novel and Quantitative Detection Assay (effluxR) for Identifying Efflux-Associated Resistance Genes Using Multiplex Digital PCR in Clinical Isolates of Pseudomonas aeruginosa

The rise of multidrug resistance of Pseudomonas aeruginosa highlights an increased need for selective and precise antimicrobial treatment. Drug efflux pumps are one of the major mechanisms of antimicrobial resistance found in many bacteria, including P. aeruginosa. Detection of efflux genes using a polymerase chain reaction (PCR)-based system would enable resistance detection and aid clinical decision making. Therefore, we aimed to develop and optimize a novel method herein referred to as "effluxR detection assay" using multiplex digital PCR (mdPCR) for detection of mex efflux pump genes in P. aeruginosa strains. The annealing/extension temperatures and gDNA concentrations were optimized to amplify mexB, mexD, and mexY using the multiplex quantitative PCR (mqPCR) system. We established the optimal mqPCR conditions for the assay (Ta of 59 °C with gDNA concentrations at or above 0.5 ng/µL). Using these conditions, we were able to successfully detect the presence of these genes in a quantity-dependent manner. The limit of detection for mex genes using the effluxR detection assay with mdPCR was 0.001 ng/µL (7.04-34.81 copies/µL). Moreover, using blind sample testing, we show that effluxR detection assay had 100% sensitivity and specificity for detecting mex genes in P. aeruginosa. In conclusion, the effluxR detection assay, using mdPCR, is able to identify the presence of multiple mex genes in P. aeruginosa that may aid clinical laboratory decisions and further epidemiological studies.

Applications of Lab on a Chip in Antimicrobial Susceptibility of Staphylococcus aureus: A Systematic Review

Background and Objectives: Staphylococcus aureus is a prevalent bacterium capable of inducing various infections, including skin and soft tissue infections, bloodstream infections, pneumonia, and surgical site infections. The emergence of antimicrobial resistance in S. aureus, particularly methicillin-resistant S. aureus, has raised substantial concerns within global healthcare settings. Prior to antibiotic prescription, the ideal approach is antimicrobial susceptibility testing (AST); however, this is frequently perceived as excessively complex and time-intensive. Lab-on-a-chip (LOC) technology holds promise in addressing these challenges and advancing fundamental microbiological research while also aiding in the development of therapeutic strategies. This systematic review aims to evaluate the potential utility of LOC for AST of S. aureus. Materials and Methods: This study adhered to the PRISMA guidelines. Various databases, including SCOPUS, PubMed/MEDLINE, SCIELO, and LILACS, in addition to gray literature sources, were employed in the review process. Results: Sixteen studies were included in this systematic review. All these studies detailed the effectiveness, rapidity, and predictability of LOC systems for assessing S. aureus susceptibility to various antibiotics. When comparing the LOC approach to traditional manual methods, it was evident that LOC requires a minimal quantity of reagents. Furthermore, most studies reported that the entire LOC procedure took 10 min to 7 h, with results being equally accurate as those obtained through traditional AST protocols. Conclusions: The potential application of LOC for AST of S. aureus is emphasized by its ability to provide rapid access to minimum inhibitory concentration data, which can substantially aid in selecting the most suitable antibiotics and dosages for treating challenging infections caused by this microorganism. Moreover, the rapid AST facilitated by LOC holds promise for enhancing the appropriateness and efficacy of therapy in clinical settings.

Antimicrobial Resistance Studies Using Raman Spectroscopy on Clinically Relevant Bacterial Strains

There has been a steep rise in the emergence of antibiotic-resistant bacteria in the past few years. A timely diagnosis can help in initiating appropriate antibiotic therapy. However, conventional techniques for diagnosing antibiotic resistance are time-consuming and labor-intensive. Therefore, we investigated the potential of Raman spectroscopy as a rapid surveillance technology for tracking the emergence of antibiotic resistance. In this study, we used Raman spectroscopy to differentiate clinical isolates of antibiotic-resistant and -sensitive bacteria of Escherichia coli, Acinetobacter baumannii, and Enterobacter species. The spectra were collected with or without exposure to various antibiotics (ciprofloxacin, gentamicin, meropenem, and nitrofurantoin), each having a distinct mechanism of action. Ciprofloxacin- and meropenem-treated sensitive strains showed a decrease in the intensity of Raman bands associated with DNA (667, 724, 785, 1378, 1480, and 1575 cm^-1) and proteins (640 and 1662 cm^-1), coupled with an increase in the intensity of lipid bands (891, 960, and 1445 cm^-1). Gentamicin- and nitrofurantoin-treated sensitive strains showed an increase in the intensity of nucleic acid bands (668, 724, 780, 810, 1378, 1480, and 1575 cm^-1) while a decrease in the intensity of protein bands (640, 1003, 1606, and 1662 cm^-1) and the lipid band (1445 cm^-1). The Raman spectral changes observed in the antibiotic-resistant strains were opposite to that of antibiotic-sensitive strains. The Raman spectral data correlated well with the antimicrobial susceptibility test results. The Raman spectral dataset was used for partial least-squares (PLS) analysis to validate the biomarkers obtained from the univariate analysis. Overall, this study showcases the potential of Raman spectroscopy for detecting antibiotic-resistant and -sensitive bacteria.

3D Printed Materials for Combating Antimicrobial Resistance

Three-dimensional (3D) printing is a rapidly growing technology with a significant capacity for translational applications in both biology and medicine. 3D-printed living and non-living materials are being widely tested as a potential replacement for conventional solutions for testing and combating antimicrobial resistance (AMR). The precise control of cells and their microenvironment, while simulating the complexity and dynamics of an in vivo environment, provides an excellent opportunity to advance the modeling and treatment of challenging infections and other health conditions. 3D-printing models the complicated niches of microbes and host-pathogen interactions, and most importantly, how microbes develop resistance to antibiotics. In addition, 3D-printed materials can be applied to testing and delivering antibiotics. Here, we provide an overview of 3D printed materials and biosystems and their biomedical applications, focusing on ever increasing AMR. Recent applications of 3D printing to alleviate the impact of AMR, including developed bioprinted systems, targeted bacterial infections, and tested antibiotics are presented.

Circular Health: exploiting the SDG roadmap to fight AMR

Circular Health is a novel approach to address complex health issues that is based on the expansion of the One Health Paradigm. Circular health recognizes the need for a multidisciplinary convergence effort to complement the biomedical dimension of health. Antimicrobial resistance (AMR) is one of the greatest global concerns for public health that is likely on the rise, given the extensive use of antibiotics during the early Covid-19 years. Prior to the Covid-19 pandemic, an expert group chaired by Jim O'Neill published "The Review on Antimicrobial Resistance", which contains a final report and recommendations on how to tackle AMR. The report, for the first time, considers AMR from a multi-perspective viewpoint highlighting how it cannot be successfully addressed unless there is a converging approach encompassing many dimensions of the problem. In this perspective, we propose to include the recommendations from that seminal report and other more recent reviews which include the lessons learnt from the Covid-19 pandemic, into the operational framework of the sustainable development goals (SDGs). AMR represents a perfect case study to explore how the SDG roadmap has the potential of becoming the driving force and implementation tool to address complex health issues by pursuing the optimization of resources and actions via a convergent and multi-stakeholder approach. The implementation of health-related policies through the whole spectrum of the SDGs could be both a novel and a well-established framework to inform multi-dimensional policies for more sustainable health in the future.

Ten simple rules for the sharing of bacterial genotype-Phenotype data on antimicrobial resistance

The increasing availability of high-throughput sequencing (frequently termed next-generation sequencing (NGS)) data has created opportunities to gain deeper insights into the mechanisms of a number of diseases and is already impacting many areas of medicine and public health. The area of infectious diseases stands somewhat apart from other human diseases insofar as the relevant genomic data comes from the microbes rather than their human hosts. A particular concern about the threat of antimicrobial resistance (AMR) has driven the collection and reporting of large-scale datasets containing information from microbial genomes together with antimicrobial susceptibility test (AST) results. Unfortunately, the lack of clear standards or guiding principles for the reporting of such data is hampering the field's advancement. We therefore present our recommendations for the publication and sharing of genotype and phenotype data on AMR, in the form of 10 simple rules. The adoption of these recommendations will enhance AMR data interoperability and help enable its large-scale analyses using computational biology tools, including mathematical modelling and machine learning. We hope that these rules can shed light on often overlooked but nonetheless very necessary aspects of AMR data sharing and enhance the field's ability to address the problems of understanding AMR mechanisms, tracking their emergence and spread in populations, and predicting microbial susceptibility to antimicrobials for diagnostic purposes.

Current molecular approach for diagnosis of MRSA: a meta-narrative review

Introduction:

Detection and diagnosis of methicillin-resistant Staphylococcus aureus (MRSA) are important in ensuring a correct and effective treatment, further reducing its spread. A wide range of molecular approaches has been used for the diagnosis of antimicrobial resistance (AMR) in MRSA. This review aims to study and appraise widely used molecular diagnostic methods for detecting MRSA.

Methods:

This meta-narrative review was performed by searching PubMed using the following search terms: (molecular diagnosis) AND (antimicrobial resistance) AND (methicillin-resistant Staphylococcus aureus). Studies using molecular diagnostic techniques for the detection of MRSA were included, while non-English language, duplicates and non-article studies were excluded. After reviewing the libraries and a further manual search, 20 studies were included in this article. RAMESES publication standard for narrative reviews was used for this synthesis.

Results:

A total of 20 full papers were reviewed and appraised in this synthesis, consisting of PCR technique (n = 7), deoxyribonucleic acid (DNA) Microarray (n = 1), DNA sequencing (n = 2), Xpert MRSA/SA BC assay (n = 2), matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) (n = 2), MLST (n = 4), SCCmec typing (n = 1) and GENECUBE (n = 1).

Discussion:

Different diagnostic methods used to diagnose MRSA have been studied in this review. This study concludes that PCR has been extensively used due to its higher sensitivity and cost-effectiveness in the past five years

The Development of Technology to Prevent, Diagnose, and Manage Antimicrobial Resistance in Healthcare-Associated Infections

There is a growing risk of antimicrobial resistance (AMR) having an adverse effect on the healthcare system, which results in higher healthcare costs, failed treatments and a higher death rate. A quick diagnostic test that can spot infections resistant to antibiotics is essential for antimicrobial stewardship so physicians and other healthcare professionals can begin treatment as soon as possible. Since the development of antibiotics in the last two decades, traditional, standard antimicrobial treatments have failed to treat healthcare-associated infections (HAIs). These results have led to the development of a variety of cutting-edge alternative methods to combat multidrug-resistant pathogens in healthcare settings. Here, we provide an overview of AMR as well as the technologies being developed to prevent, diagnose, and control healthcare-associated infections (HAIs). As a result of better cleaning and hygiene practices, resistance to bacteria can be reduced, and new, quick, and accurate instruments for diagnosing HAIs must be developed. In addition, we need to explore new therapeutic approaches to combat diseases caused by resistant bacteria. In conclusion, current infection control technologies will be crucial to managing multidrug-resistant infections effectively. As a result of vaccination, antibiotic usage will decrease and new resistance mechanisms will not develop.

Primary exploring the value of metagenomic next-generation sequencing in detecting pathogenic bacteria of cholangitis with biliary atresia after Kasai operation

PURPOSE

To evaluate the value of metagenomic next-generation sequencing (mNGS) in detecting pathogenic bacteria of cholangitis for patients with biliary atresia after Kasai operation.

METHODS

This study retrospectively analyzed patients of biliary atresia with cholangitis after Kasai operation who were admitted to Xi'an Children's Hospital from July 2019 to December 2021. Both blood culture and mNGS were carried out in all of these patients. We compared the detection rate of pathogenic bacteria, pathogenic bacteria spectrum, test time, inflammatory indicators and liver function. All the patients were followed up for 0.5-3 years to evaluate the onset of cholangitis and the survival status of autologous liver.

RESULTS

This study included total of 30 cholangitis occurred in 25 patients. There were significant differences in the detection rate of pathogenic bacteria [23.3 vs.73.3%, P < 0.05] and the test time [120 (114.5-120) vs.16 (16-21) h, P < 0.001] between the blood culture and mNGS. These two methods showed significant statistical differences in comparing inflammatory indicators (CRP, PCT) and liver function (TB, DB, GGT) before and after anti-infection. Four kinds of bacteria were detected by blood cultures and ten kinds of bacteria were detected by mNGS. Cholangitis occurred 3 times in one case (4%) and twice in three cases (12%). Autologous liver survived in 17 cases (68%).

CONCLUSION

Comparing with traditional blood culture, mNGS is more efficient, convenient and accurate in the detection of pathogens. It provides a new method for accurately detecting pathogenic bacteria of cholangitis after Kasai operation.

Recent Developments in Electrochemical Sensors for the Detection of Antibiotic-Resistant Bacteria

The development of efficient point-of-care (POC) diagnostic tools for detecting infectious diseases caused by destructive pathogens plays an important role in clinical and environmental monitoring. Nevertheless, evolving complex and inconsistent antibiotic-resistant species mire their drug efficacy. In this regard, substantial effort has been expended to develop electrochemical sensors, which have gained significant interest for advancing POC testing with rapid and accurate detection of resistant bacteria at a low cost compared to conventional phenotype methods. This review concentrates on the recent developments in electrochemical sensing techniques that have been applied to assess the diverse latent antibiotic resistances of pathogenic bacteria. It deliberates the prominence of biorecognition probes and tailor-made nanomaterials used in electrochemical antibiotic susceptibility testing (AST). In addition, the bimodal functional efficacy of nanomaterials that can serve as potential transducer electrodes and the antimicrobial agent was investigated to meet the current requirements in designing sensor module development. In the final section, we discuss the challenges with contemporary AST sensor techniques and extend the key ideas to meet the demands of the next POC electrochemical sensors and antibiotic design modules in the healthcare sector.

Combating the menace of antimicrobial resistance in Africa: a review on stewardship, surveillance and diagnostic strategies

The emergence of antibiotic-resistant pathogens has threatened not only our ability to deal with common infectious diseases but also the management of life-threatening complications. Antimicrobial resistance (AMR) remains a significant threat in both industrialized and developing countries alike. In Africa, though, poor clinical care, indiscriminate antibiotic use, lack of robust AMR surveillance programs, lack of proper regulations and the burden of communicable diseases are factors aggravating the problem of AMR. In order to effectively address the challenge of AMR, antimicrobial stewardship programs, solid AMR surveillance systems to monitor the trend of resistance, as well as robust, affordable and rapid diagnostic tools which generate data that informs decision-making, have been demonstrated to be effective. However, we have identified a significant knowledge gap in the area of the application of fast and affordable diagnostic tools, surveillance, and stewardship programs in Africa. Therefore, we set out to provide up-to-date information in these areas. We discussed available hospital-based stewardship initiatives in addition to the role of governmental and non-governmental organizations. Finally, we have reviewed the application of various phenotypic and molecular AMR detection tools in both research and routine laboratory settings in Africa, deployment challenges and the efficiency of these methods.

Rapid pathogen identification and phenotypic antimicrobial susceptibility directly from urine specimens

Implementing effective antimicrobial therapy close to the onset of infection lowers morbidity and mortality and attenuates the spread of antimicrobial resistance. Current antimicrobial susceptibility testing (AST) methods, however, require several days to determine optimal therapies. We present technology and an automated platform that identify (ID) Urinary Tract Infection pathogens in 45 min and provide phenotypic AST results in less than 5 h from urine specimens without colony isolation. The ID and AST tests count cells fluorescently labeled with specific rRNA probes using non-magnified digital imaging. The ID test detected five pathogens at ≤ 7,000 CFU/mL and had a linear range of ~ 4 orders of magnitude. For contrived specimens, AST tests gave 93.1% categorical agreement with 1.3% Very Major Errors (VME), 0.3% Major Errors (ME), and 6.3% minor Errors (mE) compared to the broth microdilution (BMD) reference method. For clinical specimens, the ID test had 98.6% agreement and the AST test had 92.3% categorical agreement with 4.2% mE, 3.4% ME and 4.0% VME compared to BMD. Data presented demonstrates that direct-from-specimen AST tests can accurately determine antimicrobial susceptibility/resistance for each pathogen in a specimen containing two pathogens. The method is robust to urine matrix effects and off-target commensal and contaminating bacteria.

Antimicrobial Treatment of Pseudomonas aeruginosa Severe Sepsis

Pseudomonas aeruginosa is a pathogen often encountered in a healthcare setting. It has consistently ranked among the most frequent pathogens seen in nosocomial infections, particularly bloodstream and respiratory tract infections. Aside from having intrinsic resistance to many antibiotics, it rapidly acquires resistance to novel agents. Given the high mortality of pseudomonal infections generally, and pseudomonal sepsis particularly, and with the rise of resistant strains, treatment can be very challenging for the clinician. In this paper, we will review the latest evidence for the optimal treatment of P. aeruginosa sepsis caused by susceptible as well as multidrug-resistant strains including the difficult to treat pathogens. We will also discuss the mode of drug infusion, indications for combination therapy, along with the proper dosing and duration of treatment for various conditions with a brief discussion of the use of non-antimicrobial agents.

Attitude, Opinions, and Working Preferences Survey among Pet Practitioners Relating to Antimicrobials in India

The indiscriminate usage and overuse of antimicrobials in pets or companion animals are underlying causes of antimicrobial resistance (AMR). Despite the multi-faceted global challenge presented by antimicrobial resistance, very few studies have appraised pet practitioners’ factors, such as written policy on antimicrobials, dose rate prescribed, use of critically important antimicrobials, and antimicrobial prescription in clean surgical procedures, which can contribute to AMR. In the present study, an online cross-sectional survey among randomly selected pet practitioners (n = 104) of various Indian provinces and union territories was conducted using a questionnaire comprising 33 closed-ended questions on different parameters, viz., the dosage regimen and level of compliance towards guidelines of the World Health Organization (WHO), other relevant veterinary associations, and their opinion while prescribing antimicrobials. Almost every practitioner of the 104 respondents had revealed the difficulties with owner compliance; i.e., incomplete course of the antibiotics, inappropriate follow-ups, and improper care of the sick animals. The majority of practitioners (95%) reported self-prescription of antimicrobials by the owner before presenting the pet(s) to the veterinary clinic, whereas more than half of the respondents (64%) revealed unavailability of antibiogram facilities. Furthermore, a large number (76%) of practitioners stated empirical treatment based on their experience as the main criteria for antimicrobial choice in the absence of timely results from the laboratory. Although non-necessitated use of antimicrobials in clean surgical procedures has been claimed, surprisingly, the majority of pet practitioners (97%) reported their use to reduce the post-operative complications. The use of the highest priority, critically important antimicrobials (HPCIA) listed by the WHO for humans, particularly quinolones and third-generation cephalosporin, also has been reported for different infections. The treatment durations were nearly as per the recommended guidelines issued by the Danish Small Animal Veterinary Association (DSAVA) for different ailments. Analysis using chi-square tests exhibited a significant correlation between less experienced veterinarians (less than 5 years) and prescription of antimicrobials restricted for critically important infections in human medicine. However, there seems to be no association between the experience of the practitioner and the further studied parameters, namely, antimicrobial regimen prescription, weighing the animals before prescription, dose rate calculation, and antimicrobial selection and use after clean surgical operations. The findings suggest periodic awareness campaigns among practitioners regarding the implementation of the official guidelines, the need for systematic surveillance of AMR, awareness among pet owners about antimicrobial resistance, and the importance of rational use of antimicrobials on their pets.

Antibiotic resistance in plant growth promoting bacteria: A comprehensive review and future perspectives to mitigate potential gene invasion risks

Plant growth-promoting bacteria (PGPB) are endowed with several attributes that can be beneficial for host plants. They opened myriad doors toward green technology approach to reduce the use of chemical inputs, improve soil fertility, and promote plants’ health. However, many of these PGPB harbor antibiotic resistance genes (ARGs). Less attention has been given to multi-resistant bacterial bioinoculants which may transfer their ARGs to native soil microbial communities and other environmental reservoirs including animals, waters, and humans. Therefore, large-scale inoculation of crops by ARGs-harboring bacteria could worsen the evolution and dissemination of antibiotic resistance and aggravate the negative impacts on such ecosystem and ultimately public health. Their introduction into the soil could serve as ARGs invasion which may inter into the food chain. In this review, we underscore the antibiotic resistance of plant-associated bacteria, criticize the lack of consideration for this phenomenon in the screening and application processes, and provide some recommendations as well as a regulation framework relating to the development of bacteria-based biofertilizers to aid maximizing their value and applications in crop improvement while reducing the risks of ARGs invasion.

Research progress on detection techniques for point-of-care testing of foodborne pathogens

The global burden of foodborne disease is enormous and foodborne pathogens are the leading cause of human illnesses. The detection of foodborne pathogenic bacteria has become a research hotspot in recent years. Rapid detection methods based on immunoassay, molecular biology, microfluidic chip, metabolism, biosensor, and mass spectrometry have developed rapidly and become the main methods for the detection of foodborne pathogens. This study reviewed a variety of rapid detection methods in recent years. The research advances are introduced based on the above technical methods for the rapid detection of foodborne pathogenic bacteria. The study also discusses the limitations of existing methods and their advantages and future development direction, to form an overall understanding of the detection methods, and for point-of-care testing (POCT) applications to accurately and rapidly diagnose and control diseases.

Antimicrobial susceptibility testing for Gram positive cocci towards vancomycin using scanning electron microscopy

The rapid detection of resistant bacteria has become a challenge for microbiologists worldwide. Numerous pathogens that cause nosocomial infections are still being treated empirically and have developed resistance mechanisms against key antibiotics. Thus, one of the challenges for researchers has been to develop rapid antimicrobial susceptibility testing (AST) to detect resistant isolates, ensuring better antibiotic stewardship. In this study, we established a proof-of-concept for a new strategy of phenotypic AST on Gram-positive cocci towards vancomycin using scanning electron microscopy (SEM). Our study evaluated the profiling of Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus after brief incubation with vancomycin. Sixteen isolates were analysed aiming to detect ultrastructural modifications at set timepoints, comparing bacteria with and without vancomycin. After optimising slides preparation and micrographs acquisition, two analytical strategies were used. The high magnification micrographs served to analyse the division of cocci based on the ratio of septa, along with the bacterial size. Susceptible strains with vancomycin showed a reduced septa percentage and the average surface area was consequently double that of the controls. The resistant bacteria revealed multiple septa occurring at advanced timepoints. Low magnification micrographs made it possible to quantify the pixels at different timepoints, confirming the profiling of cocci towards vancomycin. This new phenotypic AST strategy proved to be a promising tool to discriminate between resistant and susceptible cocci within an hour of contact with vancomycin. The analysis strategies applied here would potentially allow the creation of artificial intelligence algorithms for septa detection and bacterial quantification, subsequently creating a rapid automated SEM-AST assay.

Rapid Identification and Classification of Pathogens That Produce Carbapenemases and Cephalosporinases with a Colorimetric Paper-Based Multisensor

Infections caused by bacteria that produce β-lactamases (BLs) are a major problem in hospital settings. The phenotypic detection of these bacterial strains requires culturing samples prior to analysis. This procedure may take up to 72 h, and therefore it cannot be used to guide the administration of the first antibiotic regimen. Here, we propose a multisensor for identifying pathogens bearing different types of β-lactamases above the infectious dose threshold within 90 min that does not require culturing samples. Instead, bacterial cells are preconcentrated in the cellulose scaffold of a paper-based multisensor. Then, 12 assays are performed in parallel to identify whether the pathogens produce carbapenemases and/or cephalosporinases, including metallo-β-lactamases, extended-spectrum β-lactamases (ESBLs), and AmpC enzymes. The multisensor generates an array of colored spots that can be quantified with image processing software and whose interpretation leads to the detection of the different enzymes depending on their specificity toward the hydrolysis of certain antibiotics, and/or their pattern of inhibition or cofactor activation. The test was validated for the diagnosis of urinary tract infections. The inexpensive paper platform along with the uncomplicated colorimetric readout makes the proposed prototypes promising for developing fully automated platforms for streamlined clinical diagnosis.

Nanotechnology Approaches for Rapid Detection and Theranostics of Antimicrobial Resistant Bacterial Infections

As declared by WHO, antimicrobial resistance (AMR) is a high priority issue with a pressing need to develop impactful technologies to curb it. The rampant and inappropriate use of antibiotics due to the lack of adequate and timely diagnosis is a leading cause behind AMR evolution. Unfortunately, populations with poor economic status and those residing in densely populated areas are the most affected ones, frequently leading to emergence of AMR pathogens. Classical approaches for AMR diagnostics like phenotypic methods, biochemical assays, and molecular techniques are cumbersome and resource-intensive and involve a long turnaround time to yield confirmatory results. In contrast, recent emergence of nanotechnology-assisted approaches helps to overcome challenges in classical approaches and offer simpler, more sensitive, faster, and more affordable solutions for AMR diagnostics. Nanomaterial platforms (metallic, quantum-dot, carbon-based, upconversion, etc.), nanoparticle-based rapid point-of-care platforms, nano-biosensors (optical, mechanical, electrochemical), microfluidic-assisted devices, and importantly, nanotheranostic devices for diagnostics with treatment of AMR infections are examples of rapidly growing nanotechnology approaches used for AMR management. This review comprehensively summarizes the past 10 years of research progress on nanotechnology approaches for AMR diagnostics and for estimating antimicrobial susceptibility against commonly used antibiotics. This review also highlights several bottlenecks in nanotechnology approaches that need to be addressed prior to considering their translation to clinics.

Recent Advances in the Use of Molecular Methods for the Diagnosis of Bacterial Infections

Infections caused by bacteria have a major impact on public health-related morbidity and mortality. Despite major advances in the prevention and treatment of bacterial infections, the latter continue to represent a significant economic and social burden worldwide. The WHO compiled a list of six highly virulent multidrug-resistant bacteria named ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) responsible for life-threatening diseases. Taken together with Clostridioides difficile, Escherichia coli, Campylobacter spp., (C. jejuni and C. coli), Legionella spp., Salmonella spp., and Neisseria gonorrhoeae, all of these microorganisms are the leading causes of nosocomial infections. The rapid and accurate detection of these pathogens is not only important for the early initiation of appropriate antibiotic therapy, but also for resolving outbreaks and minimizing subsequent antimicrobial resistance. The need for ever-improving molecular diagnostic techniques is also of fundamental importance for improving epidemiological surveillance of bacterial infections. In this review, we aim to discuss the recent advances on the use of molecular techniques based on genomic and proteomic approaches for the diagnosis of bacterial infections. The advantages and limitations of each of the techniques considered are also discussed.

Rapid Detection of Bacterial Pathogens and Antimicrobial Resistance Genes in Clinical Urine Samples With Urinary Tract Infection by Metagenomic Nanopore Sequencing

Urinary tract infections (UTIs) are among the most common acquired bacterial infections in humans. The current gold standard method for identification of uropathogens in clinical laboratories is cultivation. However, culture-based assays have substantial drawbacks, including long turnaround time and limited culturability of many potential pathogens. Nanopore sequencing technology can overcome these limitations and detect pathogens while also providing reliable predictions of drug susceptibility in clinical samples. Here, we optimized a metagenomic nanopore sequencing (mNPS) test for pathogen detection and identification in urine samples of 76 patients with acute uncomplicated UTIs. We first used twenty of these samples to show that library preparation by the PCR Barcoding Kit (PBK) led to the highest agreement of positive results with gold standard clinical culture tests, and enabled antibiotic resistance detection in downstream analyses. We then compared the detection results of mNPS with those of culture-based diagnostics and found that mNPS sensitivity and specificity of detection were 86.7% [95% confidence interval (CI), 73.5-94.1%] and 96.8% (95% CI, 82.4-99.9%), respectively, indicating that the mNPS method is a valid approach for rapid and specific detection of UTI pathogens. The mNPS results also performed well at predicting antibiotic susceptibility phenotypes. These results demonstrate that our workflow can accurately diagnose UTI-causative pathogens and enable successful prediction of drug-resistant phenotypes within 6 h of sample receipt. Rapid mNPS testing is thus a promising clinical diagnostic tool for infectious diseases, based on clinical urine samples from UTI patients, and shows considerable potential for application in other clinical infections.

Application of Nanopore Sequencing in the Detection of Foodborne Microorganisms

Foodborne pathogens have become the subject of intense interest because of their high incidence and mortality worldwide. In the past few decades, people have developed many methods to solve this challenge. At present, methods such as traditional microbial culture methods, nucleic acid or protein-based pathogen detection methods, and whole-genome analysis are widely used in the detection of pathogenic microorganisms in food. However, these methods are limited by time-consuming, cumbersome operations or high costs. The development of nanopore sequencing technology offers the possibility to address these shortcomings. Nanopore sequencing, a third-generation technology, has the advantages of simple operation, high sensitivity, real-time sequencing, and low turnaround time. It can be widely used in the rapid detection and serotyping of foodborne pathogens. This review article discusses foodborne diseases, the principle of nanopore sequencing technology, the application of nanopore sequencing technology in foodborne pathogens detection, as well as its development prospects.

Changes in Serum Blood Parameters in Farmed Rainbow Trout (Oncorhynchus mykiss) Fed with Diets Supplemented with Waste Derived from Supercritical Fluid Extraction of Sweet Basil (Ocimum basilicum)

The antimicrobial and immunostimulant proprieties of aromatic plant extracts have been widely described, but their effects on serum blood biochemistry in fish have not. For this study, we assessed the changes in serum blood biochemical parameters in rainbow trout fed with a fish diet supplemented with a basil supercritical extract (F1-BEO). Our hypothesis was that treatment and time would be associated with changes in 10 serum blood biochemical parameters. F1-BEO was added to a commercial feed (0.5, 1, 2, 3% w/w). The fish were fed for 30 days, and the blood samples were collected at 2 time points (15 and 30 days). A two-way ANOVA showed a significant effect of treatment, time, and interaction treatment × time on creatinine, urea, total protein, albumin, magnesium, and phosphorus (p < 0.05), a significant effect of both time and interaction treatment × time on cholesterol (CHOL), glutamic oxaloacetic transaminase (GOT), and glutamic pyruvic transaminase (GPT) levels, and a significant effect of time on triglycerides (p < 0.05). While changes in several of the parameters were observed, the levels remained within the normal range for rainbow trout. Notably, after 30 days there was a significant decrease in CHOL in fish treated with 0.5% and 1% w/w F1-BEO (p < 0.05). The statistically non-significant increase in GOT and GPT in the fish fed with F1-BEO up to 3% w/w indicated a positive effect of basil on liver health. Our findings suggest a potential use for basil extracts (for example., F1-BEO) in fish feed to reduce antibiotic use and improve fish welfare.

A review on antimicrobial peptides databases and the computational tools

Antimicrobial Peptides (AMPs) have been considered as potential alternatives for infection therapeutics since antibiotic resistance has been raised as a global problem. The AMPs are a group of natural peptides that play a crucial role in the immune system in various organisms AMPs have features such as a short length and efficiency against microbes. Importantly, they have represented low toxicity in mammals which makes them potential candidates for peptide-based drugs. Nevertheless, the discovery of AMPs is accompanied by several issues which are associated with labour-intensive and time-consuming wet-lab experiments. During the last decades, numerous studies have been conducted on the investigation of AMPs, either natural or synthetic type, and relevant data are recently available in many databases. Through the advancement of computational methods, a great number of AMP data are obtained from publicly accessible databanks, which are valuable resources for mining patterns to design new models for AMP prediction. However, due to the current flaws in assessing computational methods, more interrogations are warranted for accurate evaluation/analysis. Considering the diversity of AMPs and newly reported ones, an improvement in Machine Learning algorithms are crucial. In this review, we aim to provide valuable information about different types of AMPs, their mechanism of action and a landscape of current databases and computational tools as resources to collect AMPs and beneficial tools for the prediction and design of a computational model for new active AMPs.

Study on the value of antibiotic-resistant gene detection in Helicobacter pylori in China

The aim of the present study was to explore the value of detecting antibiotic-resistant genes in Helicobacter pylori (H. pylori) and the association between genotype and antibiotic resistance. Two gastric mucosa samples from each H. pylori-positive patient were collected. Each patient's H. pylori sample was cultured in vitro, and the agar plate dilution method was conducted. In addition, all patient samples were analyzed for the detection of antibiotic resistance-related mutant genes and VacA gene genotypes. The association between VacA genotypes and antibiotic resistance was also determined and the value of mutant gene detection in predicting H. pylori resistance to antibiotics was evaluated. In total, 133 H. pylori-positive patients were enrolled. A total of 22 strains of H. pylori failed to grow in in vitro culture and 25 strains were negative in a H. pylori gene test. Among 108 strains detected by PCR, a total of 39 VacA s1m1 strains, 69 VacA s1m2 strains and no VacA s2 strain were identified. There was no significant association between VacA genotypes and antibiotic resistance. The mutation rates of G616A in the rdxA gene, T87A, G91A, A91G and G91T in the gyrA gene and A2143G and A2142G in the 23S rRNA gene were 32.1, 32.3, 22.6, 12.9, 6.5, 81.8 and 0.0%, respectively. Among these mutant sites, the mutation coincidence rates were as follows, according to the agar plate dilution method: rdxA G616A (81.8%), gyrA G91T (66.7%), gyrA G91A (54.5%), 23 S rRNA A2143G (49.1%), gyrA T87A (45.5%), gyrA A91G (33.3%), penicillin-binding protein 1 (PBP1) C556G (0.0%), PBP1 A562T (0.0%), PBP1 A562G (0.0%) and 16 S rRNA 926-927 (AT-GT) (0.0%). VacA m subtypes were not associated with H. pylori antibiotic resistance. In conclusion, the present findings suggested that the detection of related mutant genes had a clinical application value in predicting the antibiotic resistance of H. pylori, particularly resistance to clarithromycin and levofloxacin.

Hand-powered vacuum-driven microfluidic gradient generator for high-throughput antimicrobial susceptibility testing

The growth of bacterial resistance to antimicrobials is a serious problem attracting much attention nowadays. To prevent the misuse and abuse of antimicrobials, it is important to carry out antibiotic susceptibility testing (AST) before clinical use. However, conventional AST methods are relatively laborious and time-consuming (18-24 h). Here, we present a hand-powered vacuum-driven microfluidic (HVM) device, in which a syringe is used as the only vacuum source for rapid generating concentration gradient of antibiotics in different chambers. The HVM device can be preassembled with various amounts of antibiotics, lyophilized, and stored for ready-to-use. Bacterial samples can be loaded into the HVM device through a simple suction step. With the assistance of Alamar Blue, the AST assay and the minimum inhibitory concentration (MIC) of different antibiotics can be investigated by comparing the growth results of bacteria in different culture chambers. In addition, a parallel HVM device was proposed, in which eight AST assays can be performed simultaneously. The results of MIC of three commonly used antibiotics against E. coli K-12 in our HVM device were consistent with those obtained by traditional method while the detection time was shortened to less than 8 h. We believe that our platform is high-throughput, cost-efficient, easy to use, and suitable for POCT applications.

Recent Developments in Phenotypic and Molecular Diagnostic Methods for Antimicrobial Resistance Detection in Staphylococcus aureus: A Narrative Review

Staphylococcus aureus is an opportunistic pathogen responsible for a wide range of infections in humans, such as skin and soft tissue infections, pneumonia, food poisoning or sepsis. Historically, S. aureus was able to rapidly adapt to anti-staphylococcal antibiotics and become resistant to several classes of antibiotics. Today, methicillin-resistant S. aureus (MRSA) is a multidrug-resistant pathogen and is one of the most common bacteria responsible for hospital-acquired infections and outbreaks, in community settings as well. The rapid and accurate diagnosis of antimicrobial resistance in S. aureus is crucial to the early initiation of directed antibiotic therapy and to improve clinical outcomes for patients. In this narrative review, I provide an overview of recent phenotypic and molecular diagnostic methods for antimicrobial resistance detection in S. aureus, with a particular focus on MRSA detection. I consider methods for resistance detection in both clinical samples and isolated S. aureus cultures, along with a brief discussion of the advantages and the challenges of implementing such methods in routine diagnostics.

Recent advances in antibiotic resistance diagnosis using SERS: focus on the “Big 5” challenges

SERS for antibiotic resistance diagnosis.

Culture-independent susceptibility determination of E. coli isolated directly from patients’ urine using FTIR and machine-learning

One of the most common human bacterial infections is the urinary tract infection (UTI).

Strengths and caveats of identifying resistance genes from whole genome sequencing data

INTRODUCTION

Antimicrobial resistance (AMR) continues to present major challenges to modern healthcare. Recent advances in whole-genome sequencing (WGS) have made the rapid molecular characterization of AMR a realistic possibility for diagnostic laboratories; yet major barriers to clinical implementation exist.

AREAS COVERED

We describe and compare short- and long-read sequencing platforms, typical components of bioinformatics pipelines, tools for AMR gene detection and the relative merits of read- or assembly-based approaches. The challenges of characterizing mobile genetic elements from genomic data are outlined, as well as the complexities inherent to the prediction of phenotypic resistance from WGS. Practical obstacles to implementation in diagnostic laboratories, the critical role of quality control and external quality assurance, as well as standardized reporting standards are also discussed. Future directions, such as the application of machine-learning and artificial intelligence algorithms, linked to clinically meaningful outcomes, may offer a new paradigm for the clinical application of AMR prediction.

EXPERT OPINION

AMR prediction from WGS data presents an exciting opportunity to advance our capacity to comprehensively characterize infectious pathogens in a rapid manner, ultimately aiming to improve patient outcomes. Collaborative efforts between clinicians, scientists, regulatory bodies and healthcare administrators will be critical to achieve the full promise of this approach.

Shotgun whole genome sequencing of drug-resistance Streptococcus anginosus strain 47S1 isolated from a patient with pharyngitis in Saudi Arabia

BACKGROUND

Streptococcus anginosus is an emergence opportunistic pathogen that colonize the human upper respiratory tract (URT), S. anginosus alongside with S. intermedius and S. constellatus, members of S. anginosus group, are implicated in several human infections. However, our understanding this bacterium to the genotype level with determining the genes associated with pathogenicity and antimicrobial resistance (AMR) is scarce. S. anginosus 47S1 strain was isolated from sore throat infection, the whole genome was characterized and the virulence & AMR genes contributing in pathogenicity were investigated.

METHODOLOGY

The whole genome of 47S1 was sequenced by Illumina sequencing technology. Strain 47S1 genome was de novo assembled with different strategies and annotated via PGAP, PROKKA and RAST pipelines. Identifying the CRISPR-Cass system and prophages sequences was performed using CRISPRloci and PhiSpy tools respectively. Prediction the virulence genes were performed with the VFDB database. AMR genes were detected in silico using NCBI AMRFinderPlus pipeline and CARD database and compared with in vitro AST findings.

RESULTS

β-hemolytic strain 47S1 was identified with conventional microbiology techniques and confirmed by the sequences of 16S rRNA gene. Genome of 47S1 comprised of 1981512 bp. Type I-C CRISPR-Cas system and 4 prophages were detected among the genome of 47S1. Several virulence genes were predicted, most of these genes are found in other pathogenic streptococci, mainly lmb, pavA, htrA/degP, eno, sagA, psaA and cpsI which play a significant role in colonizing, invading host tissues and evade form immune system. In silico AMR findings showed that 47S1 gnome harbors (tetA, tetB &tet32), (aac(6')-I, aadK &aph(3')-IVa), fusC, and PmrA genes that mediated-resistance to tetracyclines, aminoglycosides, fusidic acid, and fluoroquinolone respectively which corresponds with in vitro AST obtained results. In conclusion, WGS is a key approach to predict the virulence and AMR genes, results obtained in this study may contribute for a better understanding of the opportunistic S. anginosus pathogenicity.

Hydrogel Droplet Microarray for Genotyping Antimicrobial Resistance Determinants in Neisseria gonorrhoeae Isolates

A multiplex assay based on a low-density hydrogel microarray was developed to identify genomic substitutions in N. gonorrhoeae that determine resistance to the currently recommended treatment agents ceftriaxone and azithromycin and the previously used drugs penicillin, tetracycline, and ciprofloxacin. The microarray identifies 74 drug resistance determinants in the N. gonorrhoeae penA, ponA, porB, gyrA, parC, rpsJ, mtrR, bla_TEM, tetM, and 23S rRNA genes. The hydrogel elements were formed by automated dispensing of nanoliter-volume droplets followed by UV-induced copolymerization of NH₂-containing oligonucleotides with gel-forming monomers. Polybutylene terephthalate plates without special modifications were used as microarray substrates. Sequences and concentrations of immobilized oligonucleotides, gel composition, and hybridization conditions were carefully selected, and the median discrimination ratio ranged from 2.8 to 29.4, allowing unambiguous identification of single-nucleotide substitutions. The mutation identification results in a control sample of 180 N. gonorrhoeae isolates were completely consistent with the Sanger sequencing results. In total, 648 clinical N. gonorrhoeae isolates obtained in Russia during the last 5 years were analyzed and genotyped using these microarrays. The results allowed us to draw conclusions about the present situation with antimicrobial susceptibility of N. gonorrhoeae in Russia and demonstrated the possibility of using hydrogel microarrays to control the spread of antibiotic resistance.

Preparation and Antimicrobial Activity of Chitosan and Its Derivatives: A Concise Review

Despite the advantages presented by synthetic polymers such as strength and durability, the lack of biodegradability associated with the persistence in the environment for a long time turned the attention of researchers to natural polymers. Being biodegradable, biopolymers proved to be extremely beneficial to the environment. At present, they represent an important class of materials with applications in all economic sectors, but also in medicine. They find applications as absorbers, cosmetics, controlled drug delivery, tissue engineering, etc. Chitosan is one of the natural polymers which raised a strong interest for researchers due to some exceptional properties such as biodegradability, biocompatibility, nontoxicity, non-antigenicity, low-cost and numerous pharmacological properties as antimicrobial, antitumor, antioxidant, antidiabetic, immunoenhancing. In addition to this, the free amino and hydroxyl groups make it susceptible to a series of structural modulations, obtaining some derivatives with different biomedical applications. This review approaches the physico-chemical and pharmacological properties of chitosan and its derivatives, focusing on the antimicrobial potential including mechanism of action, factors that influence the antimicrobial activity and the activity against resistant strains, topics of great interest in the context of the concern raised by the available therapeutic options for infections, especially with resistant strains.