Conventional methods and future trends in antimicrobial susceptibility testing

Sickle Cell Disease and Antimicrobial Resistance: A Systematic Review and Meta-Analysis

Background/Objectives: Antimicrobial resistance (AMR) is increasingly rising due to antimicrobial overuse and misuse. In sickle cell disease (SCD) care, frequent antibiotic use drives the rapid emergence of AMR, threatening treatment options and patient lives. This systematic review synthesizes data on AMR with regard to SCD patients for the first time. Methods: A comprehensive database search for articles published in English was conducted in PubMed, Scopus, ScienceDirect, and Web of Science, with no restriction set for the year of publication. The DerSimonian-Laird method was applied to derive the pooled prevalence, while the Mantel-Haenszel method was used to calculate the pooled odds ratio. Results: A total of 18 eligible studies covering 3220 SCD patients published between 1996 and 2024 were included in this review. The common bacterial pathogens reported in the included studies were Streptococcus pneumoniae (10 studies), Staphylococcus aureus (10 studies), and Escherichia coli (4 studies). For S. aureus, the pooled resistance was highest for penicillins (ampicillin = 100%; penicillin = 93.64%; and amoxicillin = 77.82%) followed by cefuroxime (51.23%). The pooled prevalence of methicillin-resistant S. aureus (MRSA) was 19.30%. SCD patients had 2.89 and 2.47 times higher odds of being colonized or infected with penicillin-resistant and erythromycin-resistant S. aureus strains, respectively. For S. pneumoniae, resistance prevalence was highest for co-trimoxazole (81.1%), followed by penicillin (47.08%). The pooled prevalence of multidrug-resistant (MDR) S. pneumoniae isolates was 32.12%. The majority of the studies included (n = 14, 77.8%) were of moderate quality according to the modified STROBE checklist. Conclusions: This review reveals a high prevalence of AMR with regard to SCD patients. SCD patients have an increased risk of resistance to penicillin and co-trimoxazole across several bacterial pathogens. The limited geographical distribution of the included studies underscores the urgent need for expanded AMR research on the subject, especially in regions with high SCD burden.

In vitro detection of antimicrobial impact, organic acids production and phytochemical screening of Musa acuminata wastes after treatment with fungi

The current study was performed to evaluate the bioactivity of banana wastes against some bacterial and fungal isolates, organic acids production, antioxidant and to screen the phytochemicals were present in Musa acuminate (M. acuminate) wastes. The waste was processed by some microbial species. The organic acids were evaluated in the yield using HPLC. Antioxidant impact of the yield was tested by DPPH assay. Qualitative analysis for phytochemicals were done after each treatment. M. acuminate (Banana) extracts showed moderate effect against the growth of tested microorganisms while this effect became much better after treated with fungal species (Fusarium moniliform; Rhizopus stolonifer; Aspergillus parasiticus; Alternaria alternate; Penicillium expansum and Aspergillus flavus). The MIC ranging from 6.25 to 100 mg/ml, MBC and MFC ranging from 3.125 to 250 mg/ml. Citric acid was the most produced organic acid obtained from banana wastes and highly increased after treatment with fungal isolates used. The antioxidant potential of M. acuminata leaves and pseudostem wastes enhanced after treatment with fungal extracts relative to butylated hydroxytoluene (BHT). Phytochemical screening confirmed the presence of active compounds like glycosides, tannins, saponnins, phenols, steroids and flavonoids in the M. acuminate extracts. The treated banana wastes using fungi could be used as a source of in citric acid production, antioxidant source and other chemical production to be applied in many applications.

Modulation of pulmonary immune functions by the Pseudomonas aeruginosa secondary metabolite pyocyanin

Pseudomonas aeruginosa is a prevalent opportunistic Gram-negative bacterial pathogen. One of its key virulence factors is pyocyanin, a redox-active phenazine secondary metabolite that plays a crucial role in the establishment and persistence of chronic infections. This review provides a synopsis of the mechanisms through which pyocyanin exacerbates pulmonary infections. Pyocyanin induces oxidative stress by generating reactive oxygen and nitrogen species which disrupt essential defense mechanisms in respiratory epithelium. Pyocyanin increases airway barrier permeability and facilitates bacterial invasion. Pyocyanin also impairs mucociliary clearance by damaging ciliary function, resulting in mucus accumulation and airway obstruction. Furthermore, it modulates immune responses by promoting the production of pro-inflammatory cytokines, accelerating neutrophil apoptosis, and inducing excessive neutrophil extracellular trap formation, which exacerbates lung tissue damage. Additionally, pyocyanin disrupts macrophage phagocytic function, hindering the clearance of apoptotic cells and perpetuating inflammation. It also triggers mucus hypersecretion by inactivating the transcription factor FOXA2 and enhancing the IL-4/IL-13-STAT6 and EGFR-AKT/ERK1/2 signaling pathways, leading to goblet cell metaplasia and increased mucin production. Insights into the role of pyocyanin in P. aeruginosa infections may reveal potential therapeutic strategies to alleviate the severity of infections in chronic respiratory diseases including cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD).

Microfluidic Array Enables Rapid Testing of Natural Compounds Against Xylella fastidiosa

The bacterial pathogen Xylella fastidiosa (Xf), which causes several plant diseases with significant economic impacts on agriculture and the environment, remains a challenge to manage due to its wide host range. This study investigated the in vitro antibacterial effects of natural compounds, including Trametes versicolor extract, clove essential oil, and the resistance inducer FossilⓇ, against X. fastidiosa subsp. fastidiosa using an antibacterial susceptibility testing (AST) method based on microfluidic channels. This novel method was compared with the traditional broth macrodilution method to assess its reliability and the potential advantages microfluidics offers. For each substance and test, both the ability to limit planktonic growth (reported as the minimum inhibitory concentration) and the ability to inhibit biofilm formation were evaluated. The results suggest that compared to the macrodilution method, microfluidic channels allow for a more rapid AST execution, use less material, and allow for real-time observation of bacterial behavior under a continuous flow of nutrients and antibacterial substances. All tested products demonstrated high antibacterial efficacy against Xf with the macrodilution method, yielding comparable results with microfluidic AST. These findings highlight the antimicrobial properties of the tested substances and establish the groundwork for applying this new technique to select promising eco-friendly products for potential future field applications in controlling Xf.

Detection of antimicrobial resistance via state-of-the-art technologies versus conventional methods

Antimicrobial resistance (AMR) is recognized as one of the foremost global health challenges, complicating the treatment of infectious diseases and contributing to increased morbidity and mortality rates. Traditionally, microbiological culture and susceptibility testing methods, such as disk diffusion and minimum inhibitory concentration (MIC) assays, have been employed to identify AMR bacteria. However, these conventional techniques are often labor intensive and time consuming and lack the requisite sensitivity for the early detection of resistance. Recent advancements in molecular and genomic technologies-such as next-generation sequencing (NGS), matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), lateral flow immunoassays (LFIAs), PCR-based diagnostic methods, and CRISPR-based diagnostics-have revolutionized the diagnosis of AMR. These innovative approaches provide increased sensitivity, reduced turnaround times, and the ability to identify genetic resistance mechanisms. This review seeks to examine the advantages and disadvantages of both emerging technologies and traditional methods for detecting AMR, emphasizing the potential benefits and limitations inherent to each. By understanding the strengths and limitations of these technologies, stakeholders, including researchers, healthcare professionals, regulatory agencies, health authorities, financial managers, and patients, can make informed decisions aimed at preventing the emergence and dissemination of antibiotic-resistant strains, thereby ultimately increasing patient safety.

Frontiers in superbug management: innovating approaches to combat antimicrobial resistance

Anti-microbial resistance (AMR) is a global health issue causing significant mortality and economic burden. Pharmaceutical companies' discontinuation of research hinders new agents, while MDR pathogens or "superbugs" worsen the problem. Superbugs pose a threat to common infections and medical procedures, exacerbated by limited antibiotic development and rapid antibiotic resistance. The rising tide of antimicrobial resistance threatens to undermine progress in controlling infectious diseases. This review examines the global proliferation of AMR, its underlying mechanisms, and contributing factors. The study explores various methodologies, emphasizing the significance of precise and timely identification of resistant strains. We discuss recent advancements in CRISPR/Cas9, nanoparticle technology, light-based techniques, and AI-powered antibiogram analysis for combating AMR. Traditional methods often fail to effectively combat multidrug-resistant bacteria, as CRISPR-Cas9 technology offers a more effective approach by cutting specific DNA sequences, precision targeting and genome editing. AI-based smartphone applications for antibiogram analysis in resource-limited settings face challenges like internet connectivity, device compatibility, data quality, energy consumption, and algorithmic limitations. Additionally, light-based antimicrobial techniques are increasingly being used to effectively kill antibiotic-resistant microbial species and treat localized infections. This review provides an in-depth overview of AMR covering epidemiology, evolution, mechanisms, infection prevention, control measures, antibiotic access, stewardship, surveillance, challenges and emerging non-antibiotic therapeutic approaches.

Evaluation of the antimicrobial potential of extracts Myrciaria cauliflora in strains of Staphylococcus aureus ATCC and Staphylococcus aureus BLAC

Bacteria of medical interest have increasingly acquired resistance to available antimicrobials over the years. This resistance makes these microorganisms a challenge for conventional medicine treatments, and new research is focusing on herbal medicine to fight these pathogens. The present work aimed to evaluate the cytotoxic activity of Myrciaria cauliflora and Genipa americana extracts, considering an in vitro bacterial inhibition, using a modified antibiogram technique, the extracts were studied in strains of Staphylococcus aureus ATCC 29213 and Staphylococcus aureus BLAC, where inhibition was observed in the two strains studied by the extract. This study observed that the M. cauliflora bark extract has antimicrobial potential when tested in vitro on S. aureus ATCC 29213 and S. aureus BLAC strains, indicating it is a potential herbal medicine for infections by this pathogen.

Green Extraction of Bioactives from Curcuma longa Using Natural Deep Eutectic Solvents: Unlocking Antioxidative, Antimicrobial, Antidiabetic, and Skin Depigmentation Potentials

This study evaluates the efficiency of 20 Natural Deep Eutectic Solvents (NADES) formulations for extracting curcuminoids and other bioactive compounds from turmeric and emphasize their ability to preserve and enhance antioxidant, antimicrobial, antidiabetic, and skin depigmentation effects. The NADES formulations, prepared using choline chloride (ChCl) combined with sugars, carboxylic acids, glycerol, amino acids, urea, polyols, and betaine, were assessed for their extraction efficiency based on the total phenolic content and curcumin concentration. Fourier transform infrared spectroscopy was employed to characterize the synthesized NADES and confirm their chemical composition. Bioactivity evaluations included antioxidant assays (ABTS and DPPH), antidiabetic tests (α-amylase inhibition), antimicrobial assays, and skin depigmentation (tyrosinase inhibition). The results demonstrated that NADES significantly enhanced the extraction efficiency and bioactive properties of turmeric extracts compared to water as a conventional green solvent. NADES 18 (ChCl/1,2-propanediol/water 1:1:1) and NADES 19 (glycerol/betaine/water 1:1:3) exhibited the highest extraction yields, with curcumin concentrations of 30.73 ± 1.96 mg/g and 31.70 ± 2.02 mg/g, respectively, outperforming water (26.91 ± 1.72 mg/g), while NADES 17 (ChCl/1,2-propanediol/water 0.5:3:0.5:5) and NADES 20 (glycerol/lysine/water 1:1:3) exhibited the most potent antioxidant activity. Furthermore, NADES 14 (ChCl/lactic acid/water 1:2:5) demonstrated the strongest tyrosinase inhibition (98.7%), supporting its potential for skin-brightening applications, including notable α-amylase inhibition exceeding 90%. This study aligns with the principles of green chemistry, as NADES are effective and sustainable solvents for natural product extraction. The presenting benefits of improved extraction efficiency and enhanced bioactivities position NADES as a promising and eco-friendly approach for developing efficient bioactive compound extraction methodologies.

Establishment and application of a rapid new detection method for antimicrobial susceptibility testing of Klebsiella pneumoniae based on MALDI-TOF MS

The earlier appropriate treatment of Klebsiella pneumoniae infections according to the antimicrobial susceptibility profile based on the minimum inhibitory concentration (MIC) has a great clinical benefit. Our objective was to establish a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based antimicrobial susceptibility test (AST) for K. pneumoniae that produces reliable results within a few hours. Our rapid method is similar to the classical turbidity-based microdilution method. We confirmed, theoretically and experimentally, that MALDI-TOF MS can replace the naked eye in judging the results (MICMS) by "seeing" the bacterial growth in the presence of different concentrations of antibiotics, including determination of the lower limit of bacterial count detection (4 × 105 cfu), the optimal period of incubation (2 h), and bacterial growth curve assay. Based on the study mentioned above, we determined the susceptibility of K. pneumoniae to imipenem. The MICMS and MIC data agreed over 85% (40/46) within 1 dilution range. Susceptibility profiles determined with our rapid method and the reference broth microdilution method were also compared. MICMS resulted in 97.9% (45/46) category agreement, 2.2% minor discrepancies, no major discrepancies, and no very major discrepancies. The summarized category agreement resulted in a kappa coefficient of almost 1 for weighted Cohen's kappa, which could be considered a nearly perfect agreement. It took just 2 h to produce a susceptibility profile with a low failure rate using our new rapid AST method, a work day earlier than the broth microdilution method.IMPORTANCEEmpirical antimicrobial use before antimicrobial susceptibility test (AST) is necessary but risks patient harm and excess costs. It is particularly worrying that the inappropriate use of carbapenems has allowed carbapenem-resistant Klebsiella pneumoniae to become the commonest transmissible carbapenem-resistant Enterobacterales worldwide. Guidelines recommend targeted therapy based on minimum inhibitory concentration results, which directly reflect the effectiveness of antibacterial drugs. The gold standard method of AST relies on visible bacterial growth, causing long turnaround times. Current rapid AST techniques are hampered by factors such as high costs, technological complexities, and limited detection capabilities. We present a novel rapid method and applied to the determination of the susceptibility of K. pneumoniae to imipenem. It took just 2 h to produce a susceptibility profile with a low failure rate, a work day earlier than the standard method. Our method is potentially a faster, more precise, cost-efficient, and user-friendly AST method that can enhance the effectiveness of treatment strategies.

Advances in genotypic antimicrobialresistance testing: a comprehensive review

Antimicrobial resistance (AMR) represents a substantial threat to global public health, complicating the treatment of common infections and leading to prolonged illness and escalated healthcare expenses. To effectively combat AMR, timely and accurate detection is crucial for AMR surveillance and individual-based therapy. Phenotypic antibiotic resistance testing (AST) has long been considered the gold standard in clinical applications, serving as the foundation for clinical AMR diagnosis and optimized therapy. It has significantly contributed to ensuring patients' health and the development of novel antimicrobials. Despite advancements in automated culture-based AST technologies, inherent limitations impede the widespread use of phenotypic AST in AMR surveillance. Genotypic AST technologies offer a promising alternative option, exhibiting advantages of rapidity, high sensitivity, and specificity. With the continuous advancement and expanding applications of genotypic AST technologies, such as microfluidics, mass spectrometry, and high-resolution melting curve analysis, new vigor has been injected into the development and clinical implementation of genotypic AST technologies. In this narrative review, we discuss the principles, applications, and advancements of emerging genotypic AST methods in clinical settings. The comprehensive review aims to highlight the significant scientific potential of emerging genotypic AST technologies in clinical AMR diagnosis, providing insights to enhance existing methods and explore novel approaches.

Clinical and metagenomic predicted antimicrobial resistance in pediatric critically ill patients with infectious diseases in a single center of Zhejiang

BACKGROUND

Antimicrobial resistance (AMR) poses a significant threat to pediatric health; therefore, precise identification of pathogens as well as AMR is imperative. This study aimed at comprehending antibiotic resistance patterns among critically ill children with infectious diseases admitted to pediatric intensive care unit (PICU) and to clarify the impact of drug-resistant bacteria on the prognosis of children.

METHODS

This study retrospectively collected clinical data, identified pathogens and AMR from 113 children's who performed metagenomic next-generation sequencing for pathogen and antibiotic resistance genes identification, and compared the clinical characteristic difference and prognostic effects between children with and without AMR detected.

RESULTS

Based on the presence or absence of AMR test results, the 113 patients were divided into Antimicrobial resistance test positive group (AMRT+, n = 44) and Antimicrobial resistance test negative group (AMRT-, n = 69). Immunocompromised patients (50% vs. 28.99%, P = 0.0242) and patients with underlying diseases (70.45% vs. 40.58%, P = 0.0019) were more likely to develop resistance to antibiotics. Children in the AMRT + group showed significantly increased C-reaction protein, score of pediatric sequential organ failure assessment and pediatric risk of mortality of children and longer hospital stay and ICU stay in the AMRT + group compared to the AMRT+- group (P < 0.05). Detection rate of Gram-negative bacteria was significantly higher in the AMRT + group rather than Gram-positive bacteria (n = 45 vs. 31), in contrast to the AMRT- group (n = 10 vs. 36). Cephalosporins, β-lactams/β-Lactamase inhibitors, carbapenems and sulfonamides emerged as the most common types of drug resistance in children. Resistance rates to these antibiotics exhibited considerable variation across common pathogens, including Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii.

CONCLUSIONS

The development of drug resistance in bacteria will significantly affect the prognosis of patients. The significant differences in drug resistance of common pathogenic bacteria indicate that identification of drug resistance is important for the rational use of antibiotics and patient prognosis.

Fabrication of smart nanogel based on carrageenan and green coffee extract as a long-term antifouling agent to improve biofilm prevention in food production

This study investigates the extract of the bioactive compounds from green coffee extract (GCE) and the loading of two different concentrations of GCE (1% and 2%) onto carrageenan nanogels (CAR NGs) to compare their antibacterial and antibiofilm effects with unloaded nanogels (NGs). The bioactive compounds of GCE were characterized using GC-MS analysis. The GCE1 and GCE2 were successfully deposited onto the surface of CAR NGs. The antibacterial and antibiofilm potential of prepared NGs were conducted against some foodborne pathogens (E. coli O157, Salmonella enterica, Staphylococcus aureus, and Listeria monocytogenes). The results of GC-MS analysis indicated that there were identified 16 bioactive compounds in GCE, including caffeine (36.27%), Dodemorph (9.04%), and D-Glycero-d-ido-heptose (2.44%), contributing to its antimicrobial properties. The antibacterial coatings demonstrated a notable antimicrobial effect, showing zone of inhibition (ZOI) diameters of up to 37 mm for GCE2 loaded CAR NGs. The minimum inhibitory concentration (MIC) values for GCE2 loaded CAR NGs were 80 ppm for E. coli O157, and 120 ppm for S. enterica, S. aureus, and L. monocytogenes, achieving complete bacterial inactivation within 10-15 min of exposure. Both GCE1 and GCE2 loaded CAR NGs significantly reduced biofilm cell densities on stainless steel (SS) materials for E. coli O157, S. enterica, S. aureus, and L. monocytogenes, with reductions ranging from 60% to 95%. Specifically, biofilm densities were reduced by up to 95% for E. coli O157, 89% for S. enterica, 85% for S. aureus, and 80% for L. monocytogenes. Results of the toxicity evaluation indicated that the NGs were non-toxic and biocompatible, with predicted EC50 values proved their biocompatibility and safety. These results recommended that GCE loaded CAR NGs are promising as natural antimicrobial agents for enhancing food safety and extending shelf life. Further, the study concluded that incorporating GCE into CAR NGs is an effective strategy for developing sustainable antimicrobial coatings for the food industry and manufacturing.

Low-cost, real-time detection of bacterial growth via diffraction-based sensing

The emergence of antibacterial resistance impacts healthcare networks globally, with mortality rates and linked burdens of infection disproportionately affecting the developing world. Rapid alternatives to antibiotic susceptibility testing (AST) allow for swifter, more effective treatment, though they are limited in use in low-resource settings due to significant cost barriers. Herein we demonstrate a simple, cost-effective diffraction sensing-based approach for rapidly detecting bacterial growth (a precursor to AST). Diffraction gratings (1D, lined) directly comprised of our test bacteria (Escherichia coli DH5α) were produced using soft agar-based gel templates designed to direct bacterial attachment and produce a near-zero background signal. The diffraction spot intensities from the live bacterial gratings were monitored in growth and no growth (ampicillin) conditions at room temperature, using a simple fixed laser and photodetector setup. Growth-induced differences in signal were observed within 10-20 minutes, highlighting the sensitivity of this approach and its potential to be adapted as a rapid and accessible AST alternative.

A Decade of Antimicrobial Resistance in Human and Animal Campylobacter spp. Isolates

Objectives: Campylobacter spp. remain a leading cause of bacterial gastroenteritis worldwide, with resistance to antibiotics posing significant challenges to treatment and public health. This study examines profiles in antimicrobial resistance (AMR) for Campylobacter isolates from human and animal sources over the past decade. Methods: We conducted a comprehensive review of resistance data from studies spanning ten years, analyzing profiles in resistance to key antibiotics, ciprofloxacin (CIP), tetracycline (TET), erythromycin (ERY), chloramphenicol (CHL), and gentamicin (GEN). Data were collated from various regions to assess global and regional patterns of resistance. Results: The analysis reveals a concerning trend of increasing resistance patterns, particularly to CIP and TET, across multiple regions. While resistance to CHL and GEN remains relatively low, the high prevalence of CIP resistance has significantly compromised treatment options for campylobacteriosis. Discrepancies in resistance patterns were observed between human and animal isolates, with variations across different continents and countries. Notably, resistance to ERY and CHL showed regional variability, reflecting potential differences in antimicrobial usage and management practices. Conclusions: The findings underscore the ongoing challenge of AMR in Campylobacter, highlighting the need for continued surveillance and research. The rising resistance prevalence, coupled with discrepancies in resistance patterns between human and animal isolates, emphasize the importance of a One Health approach to address AMR. Enhanced monitoring, novel treatment strategies, and global cooperation are crucial for mitigating the impact of resistance and ensuring the effective management of Campylobacter-related infections.

Phenotypic and genotypic perspectives on detection methods for bacterial antimicrobial resistance in a One Health context: research progress and prospects

The widespread spread of bacterial antimicrobial resistance (AMR) and multidrug-resistant bacteria poses a significant threat to global public health. Traditional methods for detecting bacterial AMR are simple, reproducible, and intuitive, requiring long time incubation and high labor intensity. To quickly identify and detect bacterial AMR is urgent for clinical treatment to reduce mortality rate, and many new methods and technologies were required to be developed. This review summarizes the current phenotypic and genotypic detection methods for bacterial AMR. Phenotypic detection methods mainly include antimicrobial susceptibility tests, while genotypic detection methods have higher sensitivity and specificity and can detect known or even unknown drug resistance genes. However, most of the current tests are either genotypic or phenotypic and rarely combined. Combining the advantages of phenotypic and genotypic methods, combined with the joint application of multiple rapid detection methods may be the trend for future AMR testing. Driven by rapid diagnostic technology, big data analysis, and artificial intelligence, detection methods of bacterial AMR are expected to constantly develop and innovate. Adopting rational detection methods and scientific data analysis can better address the challenges of bacterial AMR and ensure human health and social well-being.

Application of Electrospun Nanofiber-Based Electrochemical Sensors in Food Safety

Food safety significantly impacts public health and social welfare. Recently, issues such as heavy metal ions, drug residues, food additives, and microbial contamination in food have become increasingly prominent. Electrochemical sensing technology, known for its low cost, simplicity, rapid response, high sensitivity, and excellent selectivity, has been crucial in food safety detection. Electrospun nanofibers, with their high specific surface area, superior mechanical properties, and design flexibility, offer new insights and technical platforms for developing electrochemical sensors. This study introduces the fundamental principles, classifications, and detection mechanisms of electrochemical sensors, along with the principles and classifications of electrospinning technology. The applications of electrospun nanofiber-based electrochemical sensors in food safety detection over the past five years are detailed, and the limitations and future research prospects are discussed. Continuous innovation and optimization are expected to make electrospun nanofiber-based electrochemical sensors a key technology in rapid food safety detection, providing valuable references for expanding their application and advancing food safety detection methods.

Aetiologies of bacterial tick-borne febrile illnesses in humans in Africa: diagnostic limitations and the need for improvement

Tick-borne febrile illnesses caused by pathogens like Anaplasma spp., Bartonella spp., Borrelia spp., Ehrlichia spp., Coxiella burnetii, Francisella tularensis, and Rickettsia spp., are significant health concerns in Africa. The epidemiological occurrence of these pathogens is closely linked to the habitats of their vectors, prevalent in rural and semi-urban areas where humans and livestock coexist. The overlapping clinical presentations, non-specific symptoms, and limited access to commercially available in vitro diagnostics in resource-limited settings exacerbate the complexity of accurate diagnoses. This review aimed to systematically extract and analyze existing literature on tick-borne febrile illnesses in Africa, highlighting the diagnostic challenges and presenting an up-to-date overview of the most relevant pathogens affecting human populations. A comprehensive literature search from January 1990 to June 2024 using databases like PubMed, Cochrane Library, Science Direct, EMBASE, and Google Scholar yielded 13,420 articles, of which 70 met the inclusion criteria. Anaplasma spp. were reported in Morocco, Egypt, and South Africa; Francisella spp. in Kenya and Ethiopia; Ehrlichia spp. in Cameroon; Bartonella spp. in Senegal, Namibia, South Africa, and Ethiopia; Borrelia spp. in Senegal, Gabon, Tanzania, and Ethiopia; Coxiella burnetii in 10 countries including Senegal, Mali, and South Africa; and Rickettsia spp. in 14 countries including Senegal, Algeria, and Uganda. Data were analyzed using a fixed-effect model in R version 4.0.1 and visualized on an African map using Tableau version 2022.2. This review highlights the urgent need for improved diagnostics to better manage and control tick-borne febrile illnesses in Africa.

Hospital mortality and length of stay associated with Enterobacterales positive blood cultures: a multicenter analysis

Delayed time to antimicrobial susceptibility results can impact patients' outcomes. Our study evaluated the impact of susceptibility turnaround time (TAT) and inadequate empiric antibacterial therapy (IET) in patients with bloodstream infections (BSI) caused by Enterobacterales (ENT) species on in-hospital mortality and length of stay (LOS). This retrospective, multicenter investigation which included 29,570 blood ENT-positive admissions across 161 US healthcare facilities evaluated the association between antimicrobial susceptibility testing (AST) TAT, carbapenem susceptibility, and empiric therapy on post-BSI in-hospital mortality and LOS following an ENT BSI event in adult patients. After adjusting for outcomes covariates, post-BSI in-hospital mortality was significantly higher for patients in the IET vs adequate empiric therapy (AET) group [odds ratio (OR): 1.61 (95% CI: 1.32, 1.98); P < 0.0001], and when AST TAT was >63 h [OR:1.48 (95% CI: 1.16, 1.90); P = 0.0017]. Patients with carbapenem non-susceptible (carb-NS) ENT BSI had significantly higher LOS (16.6 days, 95% CI: 15.6, 17.8) compared to carbapenem susceptible (carb-S, 12.2 days, 95% CI: 11.8, 12.6), (P < 0.0001). Extended AST TAT was significantly associated with longer LOS for TAT of 57-65 h and >65 h (P = 0.005 and P< 0.0001, respectively) compared to TAT ≤42 h (reference). Inadequate empiric therapy (IET), carb-NS, and delayed AST TAT are significantly associated with adverse hospital outcomes in ENT BSI. Workflows that accelerate AST TAT for ENT BSIs and facilitate timely and adequate therapy may reduce post-BSI in-hospital mortality rate and LOS.IMPORTANCEFor patients diagnosed with bloodstream infections (BSI) caused by Enterobacterales (ENT), delayed time to antimicrobial susceptibility (AST) results can significantly impact in-hospital mortality and hospital length of stay. However, this relationship between time elapsed from blood culture collection to AST results has only been assessed, to date, in a limited number of publications. Our study focuses on this important gap using retrospective data from 29,570 blood ENT-positive admissions across 161 healthcare facilities in the US as we believe that a thorough understanding of the dynamic between AST turnaround time, adequacy of empiric therapy, post-BSI event mortality, and hospital length of stay will help guide effective clinical management and optimize outcomes of patients with ENT infections.

Identifying antibiotic-resistant strains via cell sorting and elastic-light-scatter phenotyping

The proliferation and dissemination of antimicrobial-resistant bacteria is an increasingly global challenge and is attributed mainly to the excessive or improper use of antibiotics. Currently, the gold-standard phenotypic methodology for detecting resistant strains is agar plating, which is a time-consuming process that involves multiple subculturing steps. Genotypic analysis techniques are fast, but they require pure starting samples and cannot differentiate between viable and non-viable organisms. Thus, there is a need to develop a better method to identify and prevent the spread of antimicrobial resistance. This work presents a novel method for detecting and identifying antibiotic-resistant strains by combining a cell sorter for bacterial detection and an elastic-light-scattering method for bacterial classification. The cell sorter was equipped with safety mechanisms for handling pathogenic organisms and enabled precise placement of individual bacteria onto an agar plate. The patterning was performed on an antibiotic-gradient plate, where the growth of colonies in sections with high antibiotic concentrations confirmed the presence of a resistant strain. The antibiotic-gradient plate was also tested with an elastic-light-scattering device where each colony's unique colony scatter pattern was recorded and classified using machine learning for rapid identification of bacteria. Sorting and patterning bacteria on an antibiotic-gradient plate using a cell sorter reduced the number of subculturing steps and allowed direct qualitative binary detection of resistant strains. Elastic-light-scattering technology is a rapid, label-free, and non-destructive method that permits instantaneous classification of pathogenic strains based on the unique bacterial colony scatter pattern. KEY POINTS: • Individual bacteria cells are placed on gradient agar plates by a cell sorter • Laser-light scatter patterns are used to recognize antibiotic-resistant organisms • Scatter patterns formed by colonies correspond to AMR-associated phenotypes.

FARPA-based tube array coupled with quick DNA extraction enables ultra-fast bedside detection of antibiotic-resistant pathogens

Rapid and accurate detection of pathogens and antimicrobial-resistant (AMR) genes of the pathogens are crucial for the clinical diagnosis and effective treatment of infectious diseases. However, the time-consuming steps of conventional culture-based methods inhibit the precise and early application of anti-infection therapy. For the prompt treatment of pathogen-infected patients, we have proposed a novel tube array strategy based on our previously reported FARPA (FEN1-aided recombinase polymerase amplification) principle for the ultra-fast detection of antibiotic-resistant pathogens on site. The entire process from "sample to result" can be completed in 25 min by combining quick DNA extraction from a urine sample with FARPA to avoid the usually complicated DNA extraction step. Furthermore, a 36-tube array made from commercial 384-well titre plates was efficiently introduced to perform FARPA in a portable analyser, achieving an increase in the loading sample throughput (from several to several tens), which is quite suitable for the point-of-care testing (POCT) of multiple pathogens and multiple samples. Finally, we tested 92 urine samples to verify the performance of our proposed method. The sensitivities for the detection of E. coli, K. pneumoniae, E. faecium, and E. faecalis were 92.7%, 93.8%, 100% and 88.9%, respectively. The specificities for the detection of the four pathogens were 100%. Consequently, our rapid, low-cost and user-friendly POCT method holds great potential for guiding the rational use of antibiotics and reducing bacterial resistance.

A capillary-based centrifugal indicator equipped with in situ pathogenic bacteria culture for fast antimicrobial susceptibility testing

Antimicrobial resistance has become a major global health threat due to the misuse and overuse of antibiotics. Rapid, affordable, and high-efficiency antimicrobial susceptibility testing (AST) is among the effective means to solve this problem. Herein, we developed a capillary-based centrifugal indicator (CBCI) equipped with an in situ culture of pathogenic bacteria for fast AST. The bacterial incubation and growth were performed by macro-incubation, which seamlessly integrated the capillary indicator. Through simple centrifugation, all the bacterial cells were confined at the nanoliter-level capillary column. The packed capillary column height could linearly reflect the bacterial count, and the minimum inhibitory concentration (MIC) was determined based on the difference in the column height between the drug-added groups and the control group. The AST results could easily be determined by the naked eye or smartphone imaging. Thus, the CBCI realized the combination of macro-bacterial incubation and early micro assessment, which accelerated the phenotypic AST without complex microscopic counting or fluorescent labelling. The whole operation process was simple and easy to use. AST results could be determined for E. coli ATCC strains within 3.5 h, and the output results for clinical samples were consistent with the hospital reports. We expect this AST platform to become a useful tool in limiting antimicrobial resistance, especially in remote/resource-limited areas or in underdeveloped countries.

A Comprehensive Review on Biofilms in Otorhinolaryngology: Understanding the Pathogenesis, Diagnosis, and Treatment Strategies

Biofilms, structured communities of microorganisms encased in a self-produced matrix, pose significant challenges in otorhinolaryngology due to their role in chronic and recurrent infections affecting the ear, nose, and throat (ENT) region. This review provides an overview of biofilms, emphasizing their formation, pathogenesis, diagnosis, and treatment strategies in otorhinolaryngological disorders. Biofilms are pivotal in chronic rhinosinusitis (CRS), otitis media, laryngopharyngeal reflux (LPR), and tonsillitis, contributing to treatment resistance and disease recurrence. Current diagnostic techniques, including imaging modalities, microbiological cultures, and molecular techniques, are discussed, alongside emerging technologies. Treatment strategies, ranging from conventional antibiotics to alternative therapies, such as biofilm disruptors, phage therapy, and immunomodulation, are evaluated in terms of their efficacy and potential clinical applications. The review underscores the significance of understanding biofilms in otorhinolaryngology and highlights the need for tailored approaches to diagnosis and management to improve patient outcomes.

Bacterial Infections in Intensive Care Units: Epidemiological and Microbiological Aspects

Intensive care units constitute a critical setting for the management of infections. The patients' fragilities and spread of multidrug-resistant microorganisms lead to relevant difficulties in the patients' care. Recent epidemiological surveys documented the Gram-negative bacteria supremacy among intensive care unit (ICU) infection aetiologies, accounting for numerous multidrug-resistant isolates. Regarding this specific setting, clinical microbiology support holds a crucial role in the definition of diagnostic algorithms. Eventually, the complete patient evaluation requires integrating local epidemiological knowledge into the best practice and the standardization of antimicrobial stewardship programs. Clinical laboratories usually receive respiratory tract and blood samples from ICU patients, which express a significant predisposition to severe infections. Therefore, conventional or rapid diagnostic workflows should be modified depending on patients' urgency and preliminary colonization data. Additionally, it is essential to complete each microbiological report with rapid phenotypic minimum inhibitory concentration (MIC) values and information about resistance markers. Microbiologists also help in the eventual integration of ultimate genome analysis techniques into complicated diagnostic workflows. Herein, we want to emphasize the role of the microbiologist in the decisional process of critical patient management.

Multipad agarose plate: a rapid and high-throughput approach for antibiotic susceptibility testing

We describe a phenotypic antibiotic susceptibility testing (AST) method that can provide an eightfold speed-up in turnaround time compared with the current clinical standard by leveraging advances in microscopy and single-cell imaging. A newly developed growth plate containing 96 agarose pads, termed the multipad agarose plate (MAP), can be assembled at low cost. Pads can be prepared with dilution series of antibiotics. Bacteria are seeded on the pads and automatically imaged using brightfield microscopy, with a fully automated segmentation pipeline quantifying microcolony formation and growth rate. Using a test set of nine antibiotics with very different targets, we demonstrate that accurate minimum inhibitory concentration (MIC) measurements can be performed based on the growth rate of microcolonies within 3 h of incubation with the antibiotic when started from exponential phase. Faster, reliable and high-throughput methods for AST, such as MAP, could improve patient care by expediting treatment initiation and alleviating the burden of antimicrobial resistance.

Fabrication of silver nanoparticles loaded acacia gum/chitosan nanogel to coat the pipe surface for sustainable inhibiting microbial adhesion and biofilm growth in water distribution systems

Biofilm formation on the inner surfaces of pipes poses significant threats to water distribution systems, increasing maintenance costs and public health risks. To address this immense issue, we synthesized a nanogel formulation comprising acacia gum (AG) and chitosan (Cs), loaded with varying concentrations of silver nanoparticles (AgNPs), for using as an antimicrobial coating material. AgNPs were synthesized using AG as a reducing and stabilizing agent, exhibiting absorbance at 414 nm. The preparation of AgNPs was proved using TEM. Bactericidal efficacy was assessed against E. coli, Klebsiella pneumoniae, Enterococcus faecalis, and Bacillus subtilis. Using the dipping coating method, two pipe materials (polypropylene (PP) and ductile iron (DI)) were successfully coated. Notably, AgNPs2@AGCsNG nanogel exhibited potent antibacterial action against a wide range of pathogenic bacteria. Toxicity tests confirmed nanogel safety, suggesting broad applications. High EC50% values underscored their non-toxic nature. This research proposes an effective strategy for biofilm prevention in water systems, offering excellent antibacterial properties and biocompatibility. AG and Cs nanogels loaded with AgNPs promise to enhance water quality, reduce maintenance prices, and protect human public health in water distribution networks.

Comprehensive Review of Urinary Tract Infections in Renal Transplant Recipients: Clinical Insights and Management Strategies

Urinary tract infections (UTIs) pose a significant challenge in the care of renal transplant recipients. This comprehensive review explores this population's multifaceted landscape of UTIs, emphasizing the importance of early diagnosis and tailored management strategies. Renal transplant recipients face an elevated risk of UTIs due to immunosuppression, altered urinary tract anatomy, and complex comorbidities. Complications of UTIs can lead to graft dysfunction and systemic illness, underscoring the need for effective management. The emergence of multidrug-resistant uropathogens adds complexity to treatment, highlighting the importance of targeted antibiotic therapy. Antibiotics are the most commonly prescribed drugs for UTIs, with nitrofurantoin, fosfomycin, amoxicillin, and amoxicillin-clavulanate potassium being some of the commonly used antibiotics. However, the emergence of multidrug-resistant uropathogens has led to the exploration of alternative treatments, such as bacteriophage therapy, as a potential alternative against multidrug-resistant uropathogenic bacteria. Analgesics such as phenazopyridine can be prescribed to relieve discomfort associated with UTIs. Estrogen therapy has also been suggested as a potential treatment option for UTIs, particularly in postmenopausal women. Trimethoprim-sulfamethoxazole or trimethoprim is recommended as first-line therapy for uncomplicated UTIs. The choice of drug and therapy for UTIs depends on the severity of the infection, the causative organism, and the presence of antibiotic resistance. Preventive measures encompass pre-transplant evaluation, perioperative strategies, post-transplant follow-up, and vaccination. A multidisciplinary approach involving transplant specialists, infectious disease experts, pharmacists, and patient engagement is vital for successful care. The future of UTI management lies in ongoing research, exploring personalized medicine, novel therapies, and innovative prevention strategies. By implementing these strategies and advancing research, healthcare providers can improve graft and patient survival, enhancing the quality of care for renal transplant recipients.

Agreement of methods to assess antimicrobial susceptibility using Escherichia coli isolates as target models

Antimicrobial susceptibility tests (AST) conducted in vitro offer a range of methods to assess the antimicrobial resistance (AMR) of microorganisms. Escherichia coli, a widely distributed bacterium, is closely linked to the issue of AMR. In this way, the present study aimed to assess the agreement among different in vitro AST methods, including disk diffusion in agar, broth dilution, and agar dilution method. A total of 100 E. coli isolates were analyzed for their resistance levels against six antibiotics: amoxicillin, ceftiofur, ciprofloxacin, chloramphenicol, tetracycline, and sulfamethoxazole + trimethoprim, using the aforementioned AST methods. Standard breakpoint values were employed to classify isolates as resistant, intermediate, or susceptible, and comparisons among the AST methods were conducted by McNemar's test (P < .05). The obtained data demonstrated equivalence among the AST methods, highlighting the reliability of these standardized classical methodologies. This standardization aids in preventing the inappropriate use of antimicrobials and the dissemination of antimicrobial-resistant microorganisms.

Predicting Salmonella MIC and Deciphering Genomic Determinants of Antibiotic Resistance and Susceptibility

Salmonella spp., a leading cause of foodborne illness, is a formidable global menace due to escalating antimicrobial resistance (AMR). The evaluation of minimum inhibitory concentration (MIC) for antimicrobials is critical for characterizing AMR. The current whole genome sequencing (WGS)-based approaches for predicting MIC are hindered by both computational and feature identification constraints. We propose an innovative methodology called the "Genome Feature Extractor Pipeline" that integrates traditional machine learning (random forest, RF) with deep learning models (multilayer perceptron (MLP) and DeepLift) for WGS-based MIC prediction. We used a dataset from the National Antimicrobial Resistance Monitoring System (NARMS), comprising 4500 assembled genomes of nontyphoidal Salmonella, each annotated with MIC metadata for 15 antibiotics. Our pipeline involves the batch downloading of annotated genomes, the determination of feature importance using RF, Gini-index-based selection of crucial 10-mers, and their expansion to 20-mers. This is followed by an MLP network, with four hidden layers of 1024 neurons each, to predict MIC values. Using DeepLift, key 20-mers and associated genes influencing MIC are identified. The 10 most significant 20-mers for each antibiotic are listed, showcasing our ability to discern genomic features affecting Salmonella MIC prediction with enhanced precision. The methodology replaces binary indicators with k-mer counts, offering a more nuanced analysis. The combination of RF and MLP addresses the limitations of the existing WGS approach, providing a robust and efficient method for predicting MIC values in Salmonella that could potentially be applied to other pathogens.

Electronic nose versus VITEK 2 system for the rapid diagnosis of bloodstream infections

Infectious diseases that spread through the bloodstream, known as bloodstream infections (BSIs), are a major global health problem. Positive outcomes for patients with sepsis are typically the result of prompt treatment started after an early diagnosis of BSIs. In this study, we evaluated the capabilities of a portable electronic nose (E-Nose) to detect BSIs with two commonly isolated Gram-negative bacterial species, E. coli and K. pneumonia. One hundred and five blood samples were randomly collected for blood culture examinations using BACTEC and VITEK 2 system, and headspace analysis by an E-Nose from June to December 2021. Classification accuracy of E. coli, K. pneumonia, and negative controls was measured using principal component analysis, area under the receiver operating characteristic curve, sensitivity, and specificity analysis. After incubation for 24 h, cluster plots generated using principal component analysis demonstrated that E-Nose could accurately diagnose the presence of E. coli and K. pneumonia in BACTEC blood culture bottles with a sensitivity and specificity of 100% in just 120 s. The E-Nose method has been shown to be an immediate, precise, and cost-effective alternative to automated blood culture BACTEC and VITEK 2 systems for the fast detection of the causative bacterial pathogens of BSIs in clinical practice. Thus, patients with such Gram-negative bacteremia can have guided empirical antimicrobial therapy on the same day of BSIs diagnosis, which can be lifesaving.

In vitro antimicrobial activity of extracts and essential oils of Cinnamomum, Salvia, and Mentha spp. against foodborne pathogens: A meta-analysis study

Essential oils (EOs) are a class of natural products that exhibit potent antimicrobial properties against a broad spectrum of bacteria. Inhibition diameters (IDs) and minimum inhibitory concentrations (MICs) are the typical measures of antimicrobial activity for extracts and EOs obtained from Cinnamomum, Salvia, and Mentha species. This study used a meta-analytical regression analysis to investigate the correlation between ID and MIC measurements and the variability in antimicrobial susceptibility tests. By utilizing pooled ID models, this study revealed significant differences in foodborne pathogens' susceptibility to extracts, which were dependent on both the plant species and the methodology employed (p < .05). Cassia showed the highest efficacy against Salmonella spp., exhibiting a pooled ID of 26.24 mm, while cinnamon demonstrated the highest efficacy against Bacillus cereus, with a pooled ID of 23.35 mm. Mint extract showed the greatest efficacy against Escherichia coli and Staphylococcus aureus. Interestingly, cinnamon extract demonstrated the lowest effect against Shiga toxin-producing E. coli, with a pooled ID of only 8.07 mm, whereas its EOs were the most effective against this bacterial strain. The study found that plant species influenced the MIC, while the methodology did not affect MIC measurements (p > .05). An inverse correlation between ID and MIC measurements was identified (p < .0001). These findings suggest that extracts and EOs obtained from Cinnamomum, Salvia, and Mentha spp. have the potential to inhibit bacterial growth. The study highlights the importance of considering various factors that may influence ID and MIC measurements when assessing the effectiveness of antimicrobial agents.

Antibiotic Resistance Profiling and Phylogenicity of Uropathogenic Bacteria Isolated from Patients with Urinary Tract Infections

Urinary tract infections (UTIs) are healthcare problems that commonly involve bacterial and, in some rare instances, fungal or viral infections. The irrational prescription and use of antibiotics in UTI treatment have led to an increase in antibiotic resistance. Urine samples (145) were collected from male and female patients from Lower Dir, Khyber Pakhtunkhwa (KP), Pakistan. Biochemical analyses were carried out to identify uropathogens. Molecular analysis for the identification of 16S ribosomal RNA in samples was performed via Sanger sequencing. Evolutionary linkage was determined using Molecular Evolutionary Genetics Analysis-7 (MEGA-7). The study observed significant growth in 52% of the samples (83/145). Gram-negative bacteria were identified in 85.5% of samples, while Gram-positive bacteria were reported in 14.5%. The UTI prevalence was 67.5% in females and 32.5% in males. The most prevalent uropathogenic bacteria were Klebsiella pneumoniae (39.7%, 33/83), followed by Escherichia coli (27.7%, 23/83), Pseudomonas aeruginosa (10.8%, 9/83), Staphylococcus aureus (9.6%, 8/83), Proteus mirabilis (7.2%, 6/83) and Staphylococcus saprophyticus (4.8%, 4/83). Phylogenetic analysis was performed using the neighbor-joining method, further confirming the relation of the isolates in our study with previously reported uropathogenic isolates. Antibiotic susceptibility tests identified K. pneumonia as being sensitive to imipenem (100%) and fosfomycin (78.7%) and resistant to cefuroxime (100%) and ciprofloxacin (94%). Similarly, E. coli showed high susceptibility to imipenem (100%), fosfomycin (78.2%) and nitrofurantoin (78.2%), and resistance to ciprofloxacin (100%) and cefuroxime (100%). Imipenem was identified as the most effective antibiotic, while cefuroxime and ciprofloxacin were the least. The phylogenetic tree analysis indicated that K. pneumoniae, E. coli, P. aeruginosa, S. aureus and P. mirabilis clustered with each other and the reference sequences, indicating high similarity (based on 16S rRNA sequencing). It can be concluded that genetically varied uropathogenic organisms are commonly present within the KP population. Our findings demonstrate the need to optimize antibiotic use in treating UTIs and the prevention of antibiotic resistance in the KP population.