The Challenge of Overcoming Antibiotic Resistance in Carbapenem-Resistant Gram-Negative Bacteria: "Attack on Titan"

Evaluation of the quickmic system in the rapid diagnosis of Gram-negative bacilli bacteremia

Rapid microbiological diagnosis of the antibiotic susceptibility of Gram-negative bacilli is a priority in clinical microbiology, especially in cases of bacteremia. The rapid advancement of antimicrobial resistance proposes a challenge for empirical antibiotic therapy and shows the need for fast antibiotic susceptibility diagnostics to guide treatments. The QuickMIC System (Gradientech AB, Uppsala, Sweden) is a recently developed rapid diagnostic tool for antibiotic susceptibility testing. Our study evaluates a rapid phenotypic system (QuickMIC) that provides information on the susceptibility of 12 antibiotics against Escherichia coli, Klebsiella spp., Pseudomonas aeruginosa, Acinetobacter baumannii, Enterobacter cloacae, Proteus spp., Citrobacter spp., and Serratia marcescens. A total of 816 antibiotic/microorganism combinations were tested, resulting in eight discrepancies. The concordance between the antibiotics offered by QuickMIC and reference methods (MicroScan WalkAway plus system, Beckman Coulter; Etest (BioMerieux microdilution system (Bruker); Real-time PCR (GeneXpert, Cepheid); and immunochromatography (Biotech) was 99.02%. Time elapsed to obtain a valid minimal inhibitory concentration (MIC) was between 2 and 4 h. The QuickMIC system allows for the early adjustment of antibiotic treatment in these infections. Given the existing limitations of currently available rapid methods, its clinical utility is particularly relevant in the management of P. aeruginosa infections and AmpC-producing Enterobacterales. The use of rapid methods can help diversify antibiotic use and reduce carbapenem consumption.

IMPORTANCE

The rapid diagnosis of antibiotic sensitivity in Gram-negative bacilli is of paramount importance in clinical microbiology, particularly in cases of bacteremia. The escalating challenge of antimicrobial resistance underscores the need for expeditious antibiotic susceptibility diagnostics to guide empirical antibiotic therapy effectively. In light of this, we present our study that evaluates the QuickMIC System, a recently developed rapid diagnostic antibiogram. QuickMIC System, offers a novel approach to phenotypic testing, providing information on the activity of 12 antibiotics against key pathogens, including Escherichia coli, Klebsiella spp., Pseudomonas aeruginosa, Acinetobacter baumannii, Enterobacter cloacae, Proteus spp., Citrobacter spp., and Serratia marcescens. Our investigation involved testing a total of 816 antibiotic/microorganism combinations. The study demonstrated an impressive 99.02% concordance between the QuickMIC System and the reference methods, with only eight discrepancies observed. The time to actionable minimum inhibitory concentration (MIC) ranged between 2 and 4 h, highlighting the system's efficiency in providing rapid results.

Molecular epidemiology and carbapenem resistance mechanisms of Pseudomonas aeruginosa isolated from a hospital in Fujian, China

The worldwide spread of Pseudomonas aeruginosa, especially carbapenem-resistant P. aeruginosa (CRPA), poses a serious threat to global public health. In this research, we collected and studied the clinical prevalence, molecular epidemiology, and resistance mechanisms of CRPA in Fujian, China. Among 167 non-duplicated P. aeruginosa isolates collected during 2019-2021, strains from respiratory specimens and wound secretions of older males in the intensive care unit dominated. Ninety-eight isolates (58.7 %) were resistant to at least one tested antibiotic, among which 70 strains were carbapenem-resistant. Moleclar typing of the CRPA isolates revealed they were highly divergent, belonging to 46 different sequence types. It is noteworthy that two previously reported high risk clones, ST1971 specific to China and the globally prevalent ST357, were found. Several carbapenem resistance-related characteristics were also explored in 70 CRPA isolates. Firstly, carbapenemase was phenotypically positive in 22.9 % of CRPA, genetically predominant by metallo-β-lactamase (MBL) and co-carrige of different carbapenemase genes. Then, mutations of the carbapenem-specific porins oprD and opdP were commonly observed, with frequencies of 97.1% and 100.0%, respectively. Furthermore, the biofilm formation and relative transcription levels of 8 multidrug efflux pump genes were also found to be increased in 48.6 % and 72.9 % of CRPA isolates compared to the reference strain PAO1. These findings will help fill the data gaps in molecular characteristics of CRPA on the southeastern coast of China and emphasize the urgent need for data-based specific stewardship for antipseudomonal practices to prevent the dissemination of CRPA.

Assessing antimicrobial resistance profiles of Salmonella enterica in the pork production system

Introduction. Salmonella enterica is a significant enteric pathogen affecting human and livestock health. Pork production is a common source of Salmonella contamination, with emerging multidrug resistance (MDR) posing a global health threat.Gap statement. Salmonella contamination and antimicrobial resistance (AMR) profiles in the pig production chain are underreported.Aim. To investigate the prevalence of S. enterica in the pig production chain and characterise their AMR profiles.Methodology. We collected 485 samples from pig farms, a standard pig abattoir and retail markets in Patthalung and Songkhla provinces in southern Thailand. Antimicrobial susceptibility testing was performed on these samples, and AMR profiles were determined.Results. S. enterica was detected in 68.67% of farm samples, 45.95% of abattoir samples and 50.67% of retail market samples. Analysis of 264 isolates, representing 18 serotypes, identified S. enterica serotype Rissen as the most prevalent. The predominant resistance phenotypes included ampicillin (AMP, 91.29%), tetracycline (TET, 88.26%) and streptomycin (STR, 84.47%). Over 80% of isolates showed resistance to three or more antimicrobial classes, indicating MDR. The AMP-STR-TET resistance pattern was found in nearly 70% of all MDR isolates across the production chain.Conclusions. The high prevalence of MDR is consistent with extensive antimicrobial use in the livestock sector. The presence of extensively resistant S. enterica highlights the urgent need for antimicrobial stewardship. Strengthening preventive strategies and control measures is crucial to mitigate the risk of MDR Salmonella spreading from farm to fork.

Epidemiological pattern and genomic insights into multidrug-resistant ST491 Acinetobacter baumannii BD20 isolated from an infected wound in Bangladesh: Concerning co-occurrence of three classes of beta lactamase genes

OBJECTIVE

Multidrug-resistant (MDR) Acinetobacter baumannii is a major issue within healthcare facilities in Bangladesh due to its frequent association with hospital-acquired infections. In this study we report on a carbapenem-resistant draft genome sequence of an A. baumannii BD20 sample isolated from an infected wound in Bangladesh.

METHODS

A. baumannii BD20 was isolated from an infected burn wound. Whole-genome sequencing was carried out and annotated using PGAP and Prokka. Sequence type, antimicrobial resistance genes, virulence factor genes, and metal resistance genes were investigated. Core genome multilocus sequence typing-based phylogenomic analysis between A. baumannii BD20 and 213 A. baumannii strains retrieved from the NCBI GenBank database was performed using the BacWGSTdb 2.0 server.

RESULTS

A. baumannii BD20 (MLST 491) was resistant to all the antibiotics tested, except for colistin and polymyxin B. Along with many other antibiotic resistance genes, the isolate harbored three classes of beta lactamase-producing genes: blaGES-11 (class A), blaOXA-69 (class D), blaADC-10 (class C), and blaADC-11 (class C). Additionally, the strain carried several virulence genes and metal resistance determinants, which may contribute to its increased virulence. Core genome MLST-based phylogenomic analysis revealed that A. baumannii BD20 was closely related to another ST491 strain isolated from Singapore.

CONCLUSIONS

The findings of this study underscore the growing challenge of MDR A. baumannii, emphasizing the need for vigilant surveillance and infection-control measures in healthcare settings in order to address these emerging threats effectively.

Hospital and municipal wastewater as a source of carbapenem-resistant Acinetobacter baumannii and Pseudomonas aeruginosa in the environment: a review

The increase in the prevalence of carbapenem-resistant Gram-negative bacteria, in particular Acinetobacter baumannii (CRAB) and Pseudomonas aeruginosa (CRPA), poses a serious threat for public health worldwide. This article reviews the alarming data on the prevalence of infections caused by CRAB and CRPA pathogens and their presence in hospital and municipal wastewater, and it highlights the environmental impact of antibiotic resistance. The article describes the key role of antibiotic resistance genes (ARGs) in the acquisition of carbapenem resistance and sheds light on bacterial resistance mechanisms. The main emphasis was placed on the transfer of ARGs not only in the clinical setting, but also in the environment, including water, soil, and food. The aim of this review was to expand our understanding of the global health risks associated with CRAB and CRPA in hospital and municipal wastewater and to analyze the spread of these micropollutants in the environment. A review of the literature published in the last decade will direct research on carbapenem-resistant pathogens, support the implementation of effective preventive measures and interventions, and contribute to the development of improved strategies for managing this problem.

Investigating the Effectiveness of Ceragenins against Acinetobacter baumannii to Develop New Antimicrobial and Anti-Adhesive Strategies

A growing body of experimental data indicates that ceragenins (CSAs), which mimic the physicochemical properties of the host's cationic antimicrobial peptide, hold promise for the development of a new group of broad-spectrum antimicrobials. Here, using a set of in vivo experiments, we assessed the potential of ceragenins in the eradication of an important etiological agent of nosocomial infections, Acinetobacter baumannii. Assessment of the bactericidal effect of ceragenins CSA-13, CSA-44, and CSA-131 on clinical isolates of A. baumannii (n = 65) and their effectiveness against bacterial cells embedded in the biofilm matrix after biofilm growth on abiotic surfaces showed a strong bactericidal effect of the tested molecules regardless of bacterial growth pattern. AFM assessment of bacterial cell topography, bacterial cell stiffness, and adhesion showed significant membrane breakdown and rheological changes, indicating the ability of ceragenins to target surface structures of A. baumannii cells. In the cell culture of A549 lung epithelial cells, ceragenin CSA-13 had the ability to inhibit bacterial adhesion to host cells, suggesting that it interferes with the mechanism of bacterial cell invasion. These findings highlight the potential of ceragenins as therapeutic agents in the development of antimicrobial strategies against bacterial infections caused by A. baumannii.

AMPActiPred: A three-stage framework for predicting antibacterial peptides and activity levels with deep forest

The emergence and spread of antibiotic-resistant bacteria pose a significant public health threat, necessitating the exploration of alternative antibacterial strategies. Antibacterial peptide (ABP) is a kind of antimicrobial peptide (AMP) that has the potential ability to fight against bacteria infection, offering a promising avenue for developing novel therapeutic interventions. This study introduces AMPActiPred, a three-stage computational framework designed to identify ABPs, characterize their activity against diverse bacterial species, and predict their activity levels. AMPActiPred employed multiple effective peptide descriptors to effectively capture the compositional features and physicochemical properties of peptides. AMPActiPred utilized deep forest architecture, a cascading architecture similar to deep neural networks, capable of effectively processing and exploring original features to enhance predictive performance. In the first stage, AMPActiPred focuses on ABP identification, achieving an Accuracy of 87.6% and an MCC of 0.742 on an elaborate dataset, demonstrating state-of-the-art performance. In the second stage, AMPActiPred achieved an average GMean at 82.8% in identifying ABPs targeting 10 bacterial species, indicating AMPActiPred can achieve balanced predictions regarding the functional activity of ABP across this set of species. In the third stage, AMPActiPred demonstrates robust predictive capabilities for ABP activity levels with an average PCC of 0.722. Furthermore, AMPActiPred exhibits excellent interpretability, elucidating crucial features associated with antibacterial activity. AMPActiPred is the first computational framework capable of predicting targets and activity levels of ABPs. Finally, to facilitate the utilization of AMPActiPred, we have established a user-friendly web interface deployed at https://awi.cuhk.edu.cn/∼AMPActiPred/.

The potential of Spirulina platensis to substitute antibiotics in Japanese quail diets: impacts on growth, carcass traits, antioxidant status, blood biochemical parameters, and cecal microorganisms

The development of antibiotic-resistant microorganisms prompted the investigation of possible antibiotic substitutes. As a result, the purpose of the current study is to assess the effect of dietary Spirulina platensis extract as an antibiotic alternative on Japanese quail (Coturnix japonica) growth, antioxidant status, blood parameters, and cecal microorganisms. There was a total of 150 Japanese quails used in this study, divided equally among 5 experimental groups (10 birds per group with 3 replicates): group 1 (G1) received a basal diet without any S. platensis extract, group 2 (G2) received a basal diet supplemented with 1 mL S. platensis extract/kg, group 3 (G3) received a basal diet supplemented with 2 mL S. platensis extract/kg, group 4 (G4) received a basal diet supplemented with 3 mL S. platensis extract/kg, and group 5 (G5) received a basal diet supplemented with 4 mL S. platensis extract/kg from d 7 until d 35. The results showed that compared to the control birds in G1, Japanese quail supplemented with 4 mL of S. platensis extract/kg of diet (G5) had significantly better live body weight, body weight gain, feed intake, feed conversion ratio, digestive enzymes, blood parameters, liver and kidney functions, lipid profile, antioxidant profile, immunological parameters, and cecal microorganism's count. There were no significant changes in the percentage of carcasses, liver, and total giblets among all the 5 groups. Only gizzard percentage showed a significant increase in G2 compared to birds in G1. In addition, intestinal pH showed a significant drop in G2 and G5 compared to birds in G1. After cooking the quail meat, the juiciness and tenderness increased as S. platensis extract levels increased, whereas aroma and taste declined slightly as S. platensis extract levels increased. Furthermore, when a high concentration of S. platensis extract was used, the lightness of the meat reduced while its redness and yellowness increased. The disk diffusion assay showed that S. platensis extract had significant antibacterial activity against Staphylococcus aureus, Listeria monocytogenes, Campylobacter jejuni, and Salmonella typhi, with inhibition zones ranging from 16 to 42 mm. This activity may be attributable to the volatile chemicals in S. platensis extract, of which Geosmin and 2-methylisoborneol are the primary components. In the diet of Japanese quails, it is possible to draw the conclusion that the extract of S. platensis can be utilized as a feed additive and as an alternative to antibiotics.

Revisiting the smart metallic nanomaterials: advances in nanotechnology-based antimicrobials

Despite significant advancements in diagnostics and treatments over the years, the problem of antimicrobial drug resistance remains a pressing issue in public health. The reduced effectiveness of existing antimicrobial drugs has prompted efforts to seek alternative treatments for microbial pathogens or develop new drug candidates. Interestingly, nanomaterials are currently gaining global attention as a possible next-generation antibiotics. Nanotechnology holds significant importance, particularly when addressing infections caused by multi-drug-resistant organisms. Alternatively, these biomaterials can also be combined with antibiotics and other potent biomaterials, providing excellent synergistic effects. Over the past two decades, nanoparticles have gained significant attention among research communities. Despite the complexity of some of their synthesis strategies and chemistry, unrelenting efforts have been recorded in synthesizing potent and highly effective nanomaterials using different approaches. With the ongoing advancements in nanotechnology, integrating it into medical procedures presents novel approaches for improving the standard of patient healthcare. Although the field of nanotechnology offers promises, much remains to be learned to overcome the several inherent issues limiting their full translation to clinics. Here, we comprehensively discussed nanotechnology-based materials, focusing exclusively on metallic nanomaterials and highlighting the advances in their synthesis, chemistry, and mechanisms of action against bacterial pathogens. Importantly, we delve into the current challenges and prospects associated with the technology.

Enterobacter cloacae from urinary tract infections: frequency, protein analysis, and antimicrobial resistance

The genus Enterobacter belongs to the ESKAPE group, which includes Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. This group is characterized by the development of resistance to various antibiotics. In recent years, Enterobacter cloacae (E. cloacae) has emerged as a clinically important pathogen responsible for a wide range of healthcare-associated illnesses. Identifying Enterobacter species can be challenging due to their similar phenotypic characteristics. The emergence of multidrug-resistant E. cloacae is also a significant problem in healthcare settings. Therefore, our study aimed to identify and differentiate E. cloacae using Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as a fast and precise proteomic analytical technique. We also tested hospital-acquired E. cloacae isolates that produce Extended-spectrum beta-lactamases (ESBL) against commonly used antibiotics for treating urinary tract infections (UTIs). We used a total of 189 E. cloacae isolates from 2300 urine samples of patients with UTIs in our investigation. We employed culturing techniques, as well as the BD Phoenix™ automated identification system (Becton, Dickinson) and Analytical Profile Index (API) system for the biochemical identification of E. cloacae isolates. We used the MALDI Biotyper (MBT) device for peptide mass fingerprinting analysis of all isolates. We utilized the single peak intensities and Principal Component Analysis (PCA) created by MBT Compass software to discriminate and cluster the E. cloacae isolates. Additionally, we evaluated the sensitivity and resistance of ESBL-E. cloacae isolates using the Kirby Bauer method. Out of the 189 E. cloacae isolates, the BD Phoenix system correctly identified 180 (95.24%) isolates, while the API system correctly identified 165 (87.30%) isolates. However, the MBT accurately identified 185 (98.95%) isolates with a score of 2.00 or higher. PCA positively discriminated the identified E. cloacae isolates into one group, and prominent peaks were noticed between 4230 mass-to-charge ratio (m/z) and 8500 m/z. The ESBL-E. cloacae isolates exhibited a higher degree of resistance to ampicillin, amoxicillin-clavulanate, cephalothin, cefuroxime, and cefoxitin. Several isolates were susceptible to carbapenems (meropenem, imipenem, and ertapenem); however, potential future resistance against carbapenems should be taken into consideration. In conclusion, MALDI-TOF MS is a powerful and precise technology that can be routinely used to recognize and differentiate various pathogens in clinical samples. Additionally, the growing antimicrobial resistance of this bacterium may pose a significant risk to human health.