Global mortality associated with 33 bacterial pathogens in 2019: a systematic analysis for the Global Burden of Disease Study 2019

POD-like nanozyme constructed from perspective of charge transfer engineering for biosensing of magnetic separation treated Listeria monocytogenes

For foodborne pathogens pose a serious threat to public health, a magnetic separation strategy and a nanozyme-based biosensor are proposed for biosensing of Listeria monocytogenes (L. monocytogenes). In this work, doripenem is selected as a recognized molecule for the modification of magnetic beads to capture L.monocytogenes in food and environmental samples. Furthermore, the POD-like MXene-Hemin-Au is constructed from perspective of charge transfer engineering which provides a vivid example to rational design of nanozymes. Finally, the captured L.monocytogenes is labeled with MXene-Hemin-Au@mAb, forming the sandwich complexes for quantitative determination. The current signals that generated by the complexes exhibit a good linear relationship with a limit of detection of 2.3 × 101 CFU/mL. The biosensor shows a satisfactory applicability in real samples with recoveries of 91.19% to 102.98%. Overall, the biosensor with integrated magnetic separation strategy presents a potential approach for high sensitivity biosensing of foodborne pathogens.

Simultaneous viscoelasticity and sprayability in antimicrobial acetic acid-alginate fluid gels

Acetic acid is a promising alternative to antibiotics for topical applications, particularly burn wounds, however its site specificity and retention are impaired by poor material properties. In this study, acetic acid was investigated as both the gelling agent and antimicrobial active in alginate fluid gels. The formed microstructure was found to be directly dependent on acetic acid concentration, leading to highly tuneable material properties. At clinically relevant concentrations of 2.5-5 % acetic acid, the fluid gels were elastically dominated at rest, with viscosities up to 7 orders of magnitude greater than acetic acid alone. These material properties imparted long term surface retention and microparticle barrier function, not seen with either acetic acid or alginate solutions. Most notably, sprayability was enhanced simultaneously with the increased viscosity and elasticity due to the introduction of a discretised microstructure, leading to a remarkable tenfold increase in spray coverage. Formulation was found not to inhibit antimicrobial activity, despite the less acidic pH, with common burn wound pathogens Staphylococcus aureus and Pseudomonas aeruginosa being equally susceptible to the fluid gels as to acetic acid solutions.

Construction of a one-stop N-doped negatively charged carbon dot nanoplatform with antibacterial and anti-inflammatory dual activities for wound infection based on biocompatibility

The development of bacterial resistance significantly contributes to the persistence of infections. Although previous studies have highlighted the benefits of metal-doped positive carbon nanodots in managing bacterial wound infections, their mechanism of action is relatively simple and they may pose potential hazards to human cells. Therefore, it is essential to develop a one-stop carbon dot nanoplatform that offers high biocompatibility, antibacterial properties, and anti-inflammatory activities for wound infection management. This study explores the antibacterial efficacy, without detectable resistance, and wound-healing potential of nitrogen-doped (N-doped) negatively charged carbon dots (TPP-CDs). These carbon dots are synthesized using tannic acid (TA), polyethylene polyamine, and polyethylene glycol (PEG) as precursors, with a focus on their biocompatibility. Numerous systematic studies have shown that TPP-CDs can effectively destroy bacterial biofilms and deoxyribonucleic acid (DNA), while also inducing oxidative stress, leading to a potent antimicrobial effect. TPP-CDs also demonstrate the ability to scavenge excess free radicals, promote cellular proliferation, and inhibit inflammatory factors, all of which contribute to improved wound healing. TPP-CDs also demonstrate favorable cell imaging capabilities. These findings suggest that N-doped negatively charged TPP-CDs hold significant potential for treating bacterial infections and offer practical insights for their application in the medical field.

Mucosal adjuvanticity and mucosal booster effect of colibactin-depleted probiotic Escherichia coli membrane vesicles

There is a growing interest in development of novel vaccines against respiratory tract infections, due to COVID-19 pandemic. Here, we examined mucosal adjuvanticity and the mucosal booster effect of membrane vesicles (MVs) of a novel probiotic E. coli derivative lacking both flagella and potentially carcinogenic colibactin (ΔflhDΔclbP). ΔflhDΔclbP-derived MVs showed rather strong mucosal adjuvanticity as compared to those of a single flagellar mutant strain (ΔflhD-MVs). In addition, glycoengineered ΔflhDΔclbP-MVs displaying serotype-14 pneumococcal capsular polysaccharide (CPS14+MVs) were well-characterized based on biological and physicochemical parameters. Subcutaneous (SC) and intranasal (IN) booster effects of CPS14+MVs on systemic and mucosal immunity were evaluated in mice that have already been subcutaneously prime-immunized with the same MVs. With a two-dose regimen, an IN boost (SC-IN) elicited stronger IgA responses than homologous prime-boost immunization (SC-SC). With a three-dose regimen, serum IgG levels were comparable among all tested regimens. Homologous immunization (SC-SC-SC) elicited the highest IgM responses among all regimens tested, whereas SC-SC-SC failed to elicit IgA responses in blood and saliva. Furthermore, serum IgA and salivary SIgA levels were increased with an increased number of IN doses administrated. Notably, SC-IN-IN induced not only robust IgG response, but also the highest IgA response in both serum and saliva among the groups. The present findings suggest the potential of a heterologous three-dose administration for building both systemic and mucosal immunity, e.g. an SC-IN-IN vaccine regimen could be beneficial. Another important observation was abundant packaging of colibactin in MVs, suggesting increased applicability of ΔflhDΔclbP-MVs in the context of vaccine safety.

Nanocatalytic medicine enabled next-generation therapeutics for bacterial infections

The rapid rise of antibiotic-resistant strains and the persistence of biofilm-associated infections have significantly challenged global public health. Unfortunately, current clinical high-dose antibiotic regimens and combination therapies often fail to completely eradicate these infections, which can lead to adverse side effects and further drug resistance. Amidst this challenge, however, the burgeoning development in nanotechnology and nanomaterials brings hopes. This review provides a comprehensive summary of recent advancements in nanomaterials for treating bacterial infections. Firstly, the research progress of catalytic therapies in the field of antimicrobials is comprehensively discussed. Thereafter, we systematically discuss the strategies of nanomaterials for anti-bacterial infection therapies, including endogenous response catalytic therapy, exogenous stimulation catalytic therapy, and catalytic immunotherapy, in order to elucidate the mechanism of nanocatalytic anti-infections. Based on the current state of the art, we conclude with insights on the remaining challenges and future prospects in this rapidly emerging field.

Phage probe on RAFT polymer surface for rapid enumeration of E. coli K12

This study presents a simple, fast, and sensitive label-free sensing assay for the precise enumeration of modeled pathogenic Escherichia coli K12 (E. coli K12) bacteria for the first time. The method employs the covalent binding bacteriophage technique on the surface of a reversible addition-fragmentation chain transfer (RAFT) polymer film. The Nyquist plots obtained from electrochemical impedance spectroscopy (EIS) identified the charge transfer resistance Rct was calculated from a suitable electrochemical circuit model through an evaluation of the relevant parameter after the immobilization of the bacteriophage and the binding of specific E. coli K12. The impedimetric biosensor reveals specific and reproducible detection with sensitivity in the linear working range of 104.2-107.0 CFU/mL, a limit of detection (LOD) of 101.3 CFU/mL, and a short response time of 15 min. The SERS response validates the surface roughness and interaction of the SERS-tag with E. coli K12-modified electrodes. Furthermore, the covalently immobilized active phage selectivity was proved against various non-targeting bacterial strains in the presence of targeted E.coli K12 with a result of 94 % specificity and 98 % sensitivity. Therefore, the developed phage-based electrode surface can be used as a disposable, label-free impedimetric biosensor for rapid and real-time monitoring of serum samples.

Adaptations to cationic biocide exposure differentially influence virulence factors and pathogenicity in Pseudomonas aeruginosa

Cationic biocides (CBs), which include quaternary ammonium compounds (QACs), are employed to mitigate the spread of infectious bacteria, but resistance to such surface disinfectants is rising. CB exposure can have profound phenotypic implications that extend beyond allowing microorganisms to persist on surfaces. Pseudomonas aeruginosa is a deadly bacterial pathogen that is intrinsically tolerant to a wide variety of antimicrobials and is commonly spread in healthcare settings. In this study, we pursued resistance selection assays to the QAC benzalkonium chloride and quaternary phosphonium compound P6P-10,10 to assess the phenotypic effects of CB exposure in P. aeruginosa PAO1 and four genetically diverse, drug-resistant clinical isolates. In particular, we sought to examine how CB exposure affects defensive strategies and the virulence-associated "offensive" strategies in P. aeruginosa. We demonstrated that development of resistance to BAC is associated with increased production of virulence-associated pigments and alginate as well as pellicle formation. In an in vivo infection model, CB-resistant PAO1 exhibited a decreased level of virulence compared to wild type, potentially due to an observed fitness cost in these strains. Taken together, these results illustrate the significant consequence CB resistance exerts on the virulence-associated phenotypes of P. aeruginosa.

A phase 2, randomized, blinded, dose-finding, controlled clinical trial to evaluate the safety, tolerability, and immunogenicity of a 24-valent pneumococcal conjugate vaccine (VAX-24) in healthy adults 65 years and older

Despite current polysaccharide and conjugate vaccine use, pneumococcal diseases remain prevalent in older adults. VAX-24 is a 24-valent pneumococcal conjugate vaccine (PCV) containing eCRM, a proprietary carrier protein with non-native amino acids (para-azidomethyl-L-phenylalanine) that undergo site-specific conjugation to pneumococcal polysaccharides that have been activated with a small-molecule linker (dibenzocyclooctyne). Site-specific conjugation utilizing click chemistry enables consistent exposure of T-cell epitopes, reduction in carrier protein to pneumococcal polysaccharide ratio, and enhances manufacturing process consistency to improve PCVs by increasing serotype coverage while minimizing carrier suppression. Healthy adults aged 65 or older were randomized in a 1:1:1:1 ratio to receive a single injection of VAX-24 at 1 of 3 dose levels (1.1, 2.2, or a mixed dose of 2.2 or 4.4 mcg) or Prevnar 20® (PCV20) in a phase 2, blinded study. Primary outcome measures were solicited local and systemic events within 7 days post-vaccination, unsolicited adverse events (AEs) within 1 month, and serious AEs, medically attended AEs, or new onset of chronic disease within 6 months of vaccination. Serotype-specific opsonophagocytic activity (OPA) and immunoglobulin G (IgG) were measured pre-vaccination and at 1 month post-vaccination. Of 207 participants enrolled, 200 completed the trial. Safety profiles were comparable across the three VAX-24 doses and PCV20. Robust OPA and IgG immune responses were seen for all 24 serotypes. On average, immune responses to VAX-24 2.2 mcg dose were similar or higher compared to PCV20. In adults ≥ 65 years, VAX-24 had a safety profile similar to PCV20 through six months post-vaccination and induced robust OPA and IgG responses to all 24 serotypes, supporting prior data showing that site-specific conjugation allows for increased serotype coverage with similar or higher immune response vs other PCVs. The outcome of this phase 2 study further supports use of VAX-24 2.2 mcg dose in phase 3 trials. Clinicaltrials.gov: NCT05297578.

Genome sequence of multi-drug-resistant Staphyloccocus aureus isolated from a clinical sample collected in Maroua, Cameroon

Staphylococcus aureus is a major pathogen of public health concern due to its implications in pathologies and its increasing antimicrobial resistance. Here, we present the draft genome of a 2.7-Mbp S. aureus isolate obtained from a pus swab sampled in Cameroon. The GC content of the draft genome is 32%.

Discovery of a family of menaquinone-targeting cyclic lipodepsipeptides for multidrug-resistant Gram-positive pathogens

Menaquinone (MK) in bacterial membrane is an attractive target for the development of novel therapeutic agents. Mining the untapped chemical diversity encoded by Gram-negative bacteria presents an opportunity to identify additional MK-binding antibiotics (MBAs). By MK-binding motif searching of bioinformatically predicted linear non-ribosomal peptides from 14,298 sequenced genomes of 45 underexplored Gram-negative bacterial genera, here we identify a novel MBA structural family, including silvmeb and pseudomeb, using structure prediction-guided chemical synthesis. Both MBAs show rapid bacteriolysis by MK-dependent membrane depolarization to achieve their potent activities against a panel of Gram-positive pathogens. Furthermore, both MBAs are proven to be effective against methicillin-resistant Staphylococcus aureus in a murine peritonitis-sepsis model. Our findings suggest that MBAs are a kind of structurally diverse and still underexplored antibacterial lipodepsipeptide class. The interrogation of underexplored bacterial taxa using synthetic bioinformatic natural product methods is an appealing strategy for discovering novel biomedically relevant agents to confront the crisis of antimicrobial resistance.

Factors Influencing Vaccine Receipt During a 2018 Pediatric Typhoid Conjugate Vaccine Campaign in Navi Mumbai, India

In 2018, the Navi Mumbai Municipal Corporation implemented phase 1 of a public sector typhoid conjugate vaccine campaign in Navi Mumbai, India, targeting all children aged 9 months to 14 years within its administrative boundaries. To assess associations with receipt of vaccine in phase 1, we used generalized estimating equations to calculate estimates of vaccination by child-, household-, and community-level demographics (child education and age; household head education, income, and occupation; community informal settlement percent). Campaign vaccine receipt was most associated with children enrolled in school (odds ratio [OR] = 3.84, 95% CI: 2.18-6.77), the lowest household income tertile when divided into three equal parts (OR = 1.64, 95% CI: 1.43-1.84), and lower community-level socioeconomic status (OR = 1.06, 95% CI: 1.04-1.08 per 10% informal settlement proportion). The campaign was successful in reaching the most underserved populations of its target communities.

Streptococcus pneumoniae epidemiology, pathogenesis and control

Infections caused by Streptococcus pneumoniae (also known as pneumococci) pose a threat to human health. Pneumococcal infections are the most common cause of milder respiratory tract infections, such as otitis and sinusitis, and of more severe diseases, including pneumonia (with or without septicaemia) and meningitis. The introduction of pneumococcal conjugate vaccines in the childhood vaccination programme in many countries has led to a notable decrease of severe invasive pneumococcal disease in vaccinated children. However, infections caused by non-vaccine types have concurrently increased, causing invasive pneumococcal disease in unvaccinated populations (such as older adults), which has hampered the effect of these vaccines. Moreover, emerging antibiotic resistance is threatening effective therapy. Thus, new approaches are needed for the treatment and prevention of pneumococcal infections, and recent advances in the field may pave the way for new strategies. Recently, several important findings have been gained regarding pneumococcal epidemiology, genomics and the effect of the introduction of pneumococcal conjugate vaccines and of the COVID-19 pandemic. Moreover, elucidative pathogenesis studies have shown that the interactions between pneumococcal virulence factors and host receptors may be exploited for new therapies, and new vaccine candidates have been suggested. In this Review, we summarize some recent findings from clinical disease to basic pathogenesis studies that may be of importance for future control strategies.

New resorcylic acid derivatives of Lysimachia tengyuehensis against MRSA and VRE by interfering with bacterial metabolic imbalance

The abuse of antibiotics leads to the rapid spread of bacterial resistance, which seriously threatens human life and health. Now, 8 resorcylic acid derivatives, including 4 new compounds (1-4) were isolated from Lysimachia tengyuehensis by bio-guided isolation, and they inhibited both methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) (MIC = 4-8 μg/mL). Notably, 1 and 2 rapidly killed MRSA and VRE within 40 min without drug resistance in 20 days. Mechanically, they potently disrupted biofilm and cell membrane by interfering with bacterial metabolic imbalance. The structure-activity relationship (SAR) revealed that the lipophilic long carbon chains (C-5/C-6) and hydrophilic hydroxyl/carboxyl groups were essential for the anti-MRSA and VRE bioactivity. Additionally, they effectively recovered MRSA-infected skin wounds and VRE-infected peritoneal in vivo. Resorcylic acid derivatives showed significant anti-MRSA and VRE bioactivity in vitro and in vivo with potential application for the first time.

Rapid and Specific Detection of Bacillus cereus Using Phage Protein-Based Lateral Flow Assays

Rapid and precise diagnostic techniques are essential for identifying foodborne pathogens, including Bacillus cereus (B. cereus), which poses significant challenges to food safety. Traditional detection methods are limited by long incubation times and high costs. In this context, gold nanoparticle (AuNP)-based lateral flow assays (LFAs) are emerging as valuable tools for rapid screening. However, the use of antibodies in LFAs faces challenges, including complex production processes, ethical concerns, or variability. Here, we address these challenges by proposing an innovative approach using bacteriophage-derived proteins for pathogen detection on LFAs. We used the engineered endolysin cell-wall-binding domain (CBD) and distal tail proteins (Dit) from bacteriophages that specifically target B. cereus. The protein-binding properties, essential for the formation of efficient capture and detection biointerfaces in LFAs, were extensively characterized from the microstructural to the LFA device level. Machine-learning models leverage knowledge of the protein sequence to predict advantageous protein orientations on the nitrocellulose membrane and AuNPs. The study of the biointerface binding quantified the degree of attachment of AuNPs to bacteria, providing, for the first time, a microscopic model of the number of AuNPs binding to bacteria. It highlighted the binding of up to one hundred 40 nm AuNPs per bacterium in conditions mimicking LFAs. Eventually, phage proteins were demonstrated as efficient bioreceptors in a straightforward LFA prototype combining the two proteins, providing a rapid colorimetric response within 15 min upon the detection of 105 B. cereus cells. Recombinantly produced phage binding proteins present an opportunity to generate a customizable library of proteins with precise binding capabilities, offering a cost-effective and ethical alternative to antibodies. This study enhances our understanding of phage protein biointerfaces, laying the groundwork for their utilization as efficient bioreceptors in LFAs and rapid point-of-care diagnostic assays, thus potentially strengthening public health measures.

A fully integrated wireless microfluidic immunosensing system for portable monitoring of Staphylococcus aureus

The advanced devices that function fully without the need for external accessories are regarded as a pinnacle goal in the design and construction of modern ones. Staphylococcus aureus (S. aureus), a prominent human pathogen, is responsible for causing a wide variety of infections and chronic diseases. Herein, we present the first instance of a fully integrated wireless microfluidic immunosensing system (FIWMIS) capable of conducting point-of-care S. aureus monitoring in real samples of S. aureus-spiked commercial purified drinking water and S. aureus-spiked watermelon juice. The development of the proposed FIWMIS became a reality by conquering significant engineering hurdles in seamlessly integrating a microfluidic unit for liquid sample transport without the need of an external pump, an immunosensing unit for S. aureus monitoring, and an electronic control unit for signal conversion and wireless transmission. Such full integration culminated in a FIWMIS that upholds its pump-free, wireless, and low-cost characteristics for portable monitoring of S. aureus.

Global prevalence and characteristics of infections and clinical outcomes in hospitalised patients with cirrhosis: a prospective cohort study for the CLEARED Consortium

BACKGROUND

Infections have a poor prognosis in inpatients with cirrhosis. We aimed to determine regional variations in infections and their association with clinical outcomes in a global cohort of inpatients with cirrhosis.

METHODS

In this prospective cohort study initiated by the CLEARED Consortium, we enrolled adults (aged >18 years) with cirrhosis who were non-electively admitted to 98 hospitals from 26 countries or regions across six continents between Nov 5, 2021, and Dec 10, 2022. Data at admission, during hospitalisation, and for 30 days after discharge were collected through patient reports and chart reviews. Collected data included demographics; country and country income level per World Bank classifications (high-income countries [HICs], upper-middle-income countries [UMICs], and low-income or lower-middle-income countries [L-LMICs]); comorbidities; characteristics related to cirrhosis and the infections, including types, culture results, and drug resistance profile; antibiotic use; and disease course while hospitalised and for 30 days post-discharge. The primary outcome was in-hospital death or hospice referral in those with versus those without an admission infection (defined by the presence of infection on or within 48 h of admission). Multivariable log-binomial regression for in-hospital death or hospice referral was performed to identify risk factors.

FINDINGS

Of 4550 patients screened, 4238 patients (mean age 56·1 years [SD 13·3]; 2711 [64·0%] male and 1527 [36·0%] female) with complete data were enrolled. 1351 (31·9%) had admission infections. A higher proportion of patients in L-LMICs had infections (318 [41·7%] of 762 vs 444 [58·3%] without infection) than in UMICs (588 [30·6%] of 1922 vs 1334 [69·4%]) or HICs (445 [28·6%] of 1554 vs 1109 [71·4%]). Patients with admission infections had worse severity of cirrhosis and were more likely to have had an infection or been hospitalised in the preceding 6 months. The most common specific infection types were spontaneous bacterial peritonitis (391 [28·9%] of 1351), pneumonia (233 [17·2%]), and urinary tract infections (193 [14·3%]). 549 (40·6%) patients were culture-positive for bacterial or fungal infections, with the lowest culture-positive rates in Africa and mainland China. Most of the isolated organisms were Gram-negative (345 [63%] of 549), then Gram-positive (157 [29%]), and then fungi or mixed (47 [9%]), with Escherichia coli, Klebsiella pneumoniae, and Enterococcus spp being the top three isolated pathogens. The overall rate of drug resistance was 40% (220 of 549 with positive cultures), being highest in UMICs. The most used empirical antimicrobials were third-generation cephalosporins (453 [37%] of 1241), followed by the broad-spectrum β-lactams and β-lactamase inhibitors (289 [23%]). De-escalation was observed in 62 (20%) of 304 patients who had their antibiotics changed. Patients with versus without admission infections had a higher rate of in-hospital death or hospice transfer (299 [22·1%] of 1351 vs 232 [8·0%] of 2887; p<0·0001), a result replicated in multivariable analysis (adjusted risk ratio 1·75 [95% CI 1·42-2·06]; p<0·0001). Older age, self-reported female gender, not being in a HIC, lactulose use, and higher MELD-Na score were also associated with in-hospital death or hospice transfer on multivariable analysis.

INTERPRETATION

In the CLEARED Consortium cohort of inpatients with cirrhosis, the rates and types of infections, causative organisms, and culture-positivity varied substantially across regions, and infections were associated with a higher mortality risk. Culture positivity, which guides appropriate antibiotic use, was low. Taking a global perspective, considering regional variations in infections, drug resistance, and resources, could help to alleviate disparities in burden and outcomes.

FUNDING

US Department of Veterans Affairs, the Richmond Institute for Veterans Research, the National Natural Science Foundation of China, Shanghai Rising-Star Program, the National Council for Scientific and Technological Development of Brazil, and Shanghai Municipal Key Clinical Specialty.

Rhein-loaded chitosan nanoparticles for treatment of MRSA-infected wound

The multi-drug resistance of methicillin-resistant Staphylococcus aureus (MRSA) and complex wound microenvironment challenge the repair of MRSA infected wound. Herein, in this study, α-tocopherol modified glycol chitosan (TG) nanoparticles encapsulated with phytochemical rhein (Rhein@TG NPs) were prepared for comprehensive anti-infection and promotion of MRSA infected wound healing. Rhein@TG NPs could not only specifically release rhein in the infection site in response to low pH and lipase of infectious microenvironment, but also up-regulated M1 macrophage polarization in the infection stage, thus achieving synergistically bacterial elimination with low possibility of developing resistance. Additionally, the NPs reduced the levels of pro-inflammatory factors in the post-infection stage, scavenged the ROS, promoted cell migration and angiogenesis, which significantly improved the microenvironment of infected wound healing. Therefore, this antibiotic-free NPs enabling anti-infection and promotion of wound healing provides a new and long-term strategy for the treatment of MRSA infected wound.

Exploring uncatalogued genetic variation in antimicrobial resistance gene families in Escherichia coli: an observational analysis

BACKGROUND

Antimicrobial resistance (AMR) in Escherichia coli is a global problem associated with substantial morbidity and mortality. AMR-associated genes are typically annotated based on similarity to variants in a curated reference database, with the implicit assumption that uncatalogued genetic variation within these is phenotypically unimportant. In this study, we evaluated the performance of the AMRFinder tool and, subsequently, the potential for discovering new AMR-associated gene families and characterising variation within existing ones to improve genotype-to-susceptibility phenotype predictions in E coli.

METHODS

In this cross-sectional study of international genome sequence data, we assembled a global dataset of 9001 E coli sequences from five publicly available data collections predominantly deriving from human bloodstream infections from: Norway, Oxfordshire (UK), Thailand, the UK, and Sweden. 8555 of these sequences had linked antibiotic susceptibility data. Raw reads were assembled using Shovill and AMR genes (relevant to amoxicillin-clavulanic acid, ampicillin, ceftriaxone, ciprofloxacin, gentamicin, piperacillin-tazobactam, and trimethoprim) extracted using the National Center for Biotechnology Information AMRFinder tool (using both default and strict [100%] coverage and identity filters). We assessed the predictive value of the presence of these genes for predicting resistance or susceptibility against US Food and Drug Administration thresholds for major and very major errors. Mash was used to calculate the similarity between extracted genes using Jaccard distances. We empirically reclustered extracted gene sequences into AMR-associated gene families (≥70% match) and antibiotic-resistance genes (ARGs; 100% match) and categorised these according to their frequency in the dataset. Accumulation curves were simulated and correlations between gene frequency in the Oxfordshire and other datasets calculated using the Spearman coefficient. Firth regression was used to model the association between the presence of blaTEM-1 variants and amoxicillin-clavulanic acid or piperacillin-tazobactam resistance, adjusted for the presence of other relevant ARGs.

FINDINGS

The performance of the AMRFinder database for genotype-to-phenotype predictions using strict 100% identity and coverage thresholds did not meet US Food and Drug Administration thresholds for any of the seven antibiotics evaluated. Relaxing filters to default settings improved sensitivity with a specificity cost. For all antibiotics, most explainable resistance was associated with the presence of a small number of genes. There was a proportion of resistance that could not be explained by known ARGs; this ranged from 75·1% for amoxicillin-clavulanic acid to 3·4% for ciprofloxacin. Only 18 199 (51·5%) of the 35 343 ARGs detected had a 100% identity and coverage match in the AMRFinder database. After empirically reclassifying genes at 100% nucleotide sequence identity, we identified 1042 unique ARGs, of which 126 (12·1%) were present ten times or more, 313 (30·0%) were present between two and nine times, and 603 (57·9%) were present only once. Simulated accumulation curves revealed that discovery of new (100% match) ARGs present more than once in the dataset plateaued relatively quickly, whereas new singleton ARGs were discovered even after many thousands of isolates had been included. We identified a strong correlation (Spearman coefficient 0·76 [95% CI 0·73-0·80], p<0·0001) between the number of times an ARG was observed in Oxfordshire and the number of times it was seen internationally, with ARGs that were observed six times in Oxfordshire always being found elsewhere. Finally, using the example of blaTEM-1, we showed that uncatalogued variation, including synonymous variation, is associated with potentially important phenotypic differences; for example, two common, uncatalogued blaTEM-1 alleles with only synonymous mutations compared with the known reference were associated with reduced resistance to amoxicillin-clavulanic acid (adjusted odds ratio 0·58 [95% CI 0·35-0·95], p=0·031) and piperacillin-tazobactam (0·50 [95% CI 0·29-0·82], p=0·005).

INTERPRETATION

We highlight substantial uncatalogued genetic variation with respect to known ARGs, although a relatively small proportion of these alleles are repeatedly observed in a large international dataset suggesting strong selection pressures. The current approach of using fuzzy matching for ARG detection, ignoring the unknown effects of uncatalogued variation, is unlikely to be acceptable for future clinical deployment. The association of synonymous mutations with potentially important phenotypic differences suggests that relying solely on amino acid-based gene detection to predict resistance is unlikely to be sufficient. Finally, the inability to explain all resistance using existing knowledge highlights the importance of new target gene discovery.

FUNDING

National Institute for Health and Care Research, Wellcome, and UK Medical Research Council.

The complement system: A key player in the host response to infections

Infections are one of the most significant healthcare and economic burdens across the world as underscored by the recent coronavirus pandemic. Moreover, with the increasing incidence of antimicrobial resistance, there is an urgent need to better understand host-pathogen interactions to design effective treatment strategies. The complement system is a key arsenal of the host defense response to pathogens and bridges both innate and adaptive immunity. However, in the contest between pathogens and host defense mechanisms, the host is not always victorious. Pathogens have evolved several approaches, including co-opting the host complement regulators to evade complement-mediated killing. Furthermore, deficiencies in the complement proteins, both genetic and therapeutic, can lead to an inefficient complement-mediated pathogen eradication, rendering the host more susceptible to certain infections. On the other hand, overwhelming infection can provoke fulminant complement activation with uncontrolled inflammation and potentially fatal tissue and organ damage. This review presents an overview of critical aspects of the complement-pathogen interactions during infection and discusses perspectives on designing therapies to mitigate complement dysfunction and limit tissue injury.

Non-invasive Streptococcus pneumoniae infections are associated with different serotypes than invasive infections, Belgium, 2020 to 2023

BackgroundDespite widely implemented pneumococcal vaccination programmes, Streptococcus pneumoniae remains a global risk for human health. Streptococcus pneumoniae can cause invasive (IPD) or non-invasive pneumococcal disease (NIPD). Surveillance is mainly focusing on IPD, assessing the full impact of pneumococcal vaccination programmes on pneumococcal disease is challenging.AimWe aimed to prospectively investigate serotype distribution and antimicrobial resistance (AMR) of S. pneumoniae isolates from patients with NIPD and compare with data on IPD isolates and with a 2007-2008 dataset on NIPD.MethodsBetween September 2020 and April 2023, we collected isolates and patient data from patients with NIPD from 23 clinical laboratories in Belgium. Capsular typing was performed by a validated Fourier-Transform Infrared spectroscopic method, and AMR was assessed with broth microdilution, using the European Committee on Antimicrobial Susceptibility Testing (EUCAST) clinical breakpoints.ResultsWe received S. pneumoniae isolates from 1,008 patients with lower respiratory tract infections (n = 760), otitis media (n = 190) and sinusitis (n = 58). Serotype 3 was the most prevalent serotype among the NIPD isolates. Serotypes not included in the 20-valent pneumococcal conjugate vaccine (PCV20) were significantly more common among the NIPD than among the IPD isolates. Antimicrobial resistance levels were significantly higher among the NIPD isolates (n = 539; 2020-2022) compared with the IPD isolates (n = 2,344; 2021-2022). Resistance to several β-lactam antimicrobials had increased significantly compared with 15 years before.ConclusionsThe NIPD isolates were strongly associated with non-vaccine serotypes and with increased AMR levels. This underlines the importance of continued NIPD surveillance for informed policy making on vaccination programmes.

M proteins of group A Streptococcus bind hyaluronic acid via arginine-arginine/serine-arginine motifs

Tissue injury, including extracellular matrix (ECM) degradation, is a hallmark of group A Streptococcus (GAS) skin infection and is partially mediated by M proteins which possess lectin-like properties. Hyaluronic acid is a glycosaminoglycan enriched in the cutaneous ECM, yet an interaction with M proteins has yet to be explored. This study revealed that hyaluronic acid binding was conserved across phylogenetically diverse M proteins, mediated by RR/SR motifs predominantly localized in the C repeat region. Keratinocyte wound healing was decreased through the recruitment of hyaluronic acid by M proteins in an M type-specific manner. GAS strains 5448 (M1 serotype) and ALAB49 (M53 serotype) also bound hyaluronic acid via M proteins, but hyaluronic acid could increase bacterial adherence independently of M proteins. The identification of host-pathogen mechanisms that affect ECM composition and cell repair responses may facilitate the development of nonantibiotic therapeutics that arrest GAS disease progression in the skin.

Differential expression of small RNAs in biofilm-producing clinical methicillin-susceptible Staphylococcus aureus recovered from human urine

Bacterial small RNAs (sRNAs) play crucial roles in coordinating gene regulatory networks in various physiological processes, including biofilm formation. In this study, RNA sequencing was performed on biofilm (n = 4) and planktonic (n = 4) cells harvested at 10 h (pre-stationary phase of biofilm development) to identify biofilm-associated sRNAs in human methicillin-susceptible Staphylococcus aureus (MSSA) recovered from urine isolate. A total of 56 highly expressed sRNAs were identified with 15 overlapping sRNA genes (srn_9348, sprD, sRNA205, sRNA288, srn_2467, Sau-25, srn_2468, sRNA260, sRNA200, RsaE, sRNA397, Teg55, Teg60, RsaX05 and Teg140). Further validation through RT-qPCR analysis of nine sRNAs revealed that srn_9348 and sRNA260 were significantly expressed in the biofilm cells of urine sample. Both sRNAs were predicted to interact with mRNA genes including intracellular adhesin A (icaA) and host factor protein (hfq) involved in biofilm formation via cis-acting and trans-acting using CopraRNA analysis. Therefore, both sRNAs merit further investigations via reverse genetic approaches to elucidate their mechanism of translational regulation. In summary, the transcriptomic analysis conducted in this study offers new insights into the potential regulatory roles of sRNAs in MSSA biofilm development within the urinary environment.

A breath of fresh air: Perspectives on inhaled nutrients and bacteria to improve human health

We propose that the human respiratory system and olfactory pathways sequester airborne nutrients (vitamins, fatty acids and trace minerals) that are beneficial for health, which we term 'aeronutrients'. In addition, airborne bacteria, termed 'aeromicrobes', have the potential for positive health effects by improving species diversity in the microbiotas of the respiratory and gastrointestinal tracts. These concepts have implications for people living in urban areas or those who have limited access to nature, such as astronauts exposed for long periods to highly filtered air which may be depleted of aeronutrients and aeromicrobes. The possibility that fresh air contributes to human nutrition and health may stimulate a re-evaluation of guidelines pertaining to nutrition and access to natural environments, and will open new avenues of scientific enquiry.

Characterisation of a new virulent phage isolated from Hainan Island with potential against multidrug-resistant Pseudomonas aeruginosa infections

Multidrug-resistant (MDR) Pseudomonas aeruginosa is a serious life-threatening pathogen. The rise in P. aeruginosa resistance rates has renewed interest in phages as an alternative therapeutic approach for treating bacterial infections. In this study, we investigated the characteristics of the first Pseudomonas phage, vB_PaP_HN01, isolated from Hainan, the only tropical island in China. The lytic rate of this phage against P. aeruginosa reached 64.3 % (27/42). Under the optimal multiplicity of infection (MOI) of 0.1, more than 90 % of phage particles absorb onto the host cell within 10 min, with an eclipse period of around 15 min, and a high titer phage production (1011 PFU/ml) within 90 min was demonstrated. vB_PaP_HN01 maintains a robust titer after 1 h exposure to pH values and temperatures (up to 50 °C). Genome annotation revealed that vB_PaP_HN01 did not contain drug-resistance or lysogeny-associated genes. It can effectively inhibit the formation of biofilms of MDR P. aeruginosa and eliminated aggressive biofilms (removal rate about 70 %). In the in vivo infection models, it was demonstrated that the survival rate and lifespan of Galleria mellonella larvae were increased alongside the injection of vB_PaP_HN01. These data revealed the potential of vB_PaP_HN01 against P. aeruginosa in clinic.

Proteomic approach to identify host cell attachment proteins provides protective Pseudomonas aeruginosa vaccine antigen FtsZ

Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen that causes severe nosocomial infections in susceptible individuals due to the emergence of multidrug-resistant strains. There are no approved vaccines against P. aeruginosa infections nor candidates in active clinical development, highlighting the need for novel candidates and strategies. Using a cell-blot proteomic approach, we reproducibly identified 49 proteins involved in interactions with human lung epithelial cells across four P. aeruginosa strains. Among these were cell division protein FtsZ and outer membrane protein OpmH. Escherichia coli BL21 cells overexpressing recombinant FtsZ or rOpmH showed a 66- and 15-fold increased ability to attach to 16HBE14o- cells, further supporting their involvement in host cell attachment. Both antigens led to proliferation of NK and CD8+ cytotoxic T cells, significant increases in the production of IFN-γ, IL-17A, TNF and IL-4 in immunised mice and elicited strong antigen-specific serological IgG1 and IgG2c responses. Immunisation with FtsZ significantly reduced bacterial burden in the lungs by 1.9-log CFU and dissemination to spleen by 1.8-log CFU. The protective antigen candidate, FtsZ, would not have been identified by traditional approaches relying on either virulence mechanisms or sequence-based predictions, opening new avenues in the development of an anti-P. aeruginosa vaccine.

Bacterial Responses and Material-Cell Interplays With Novel MoAlB@MBene

Developing efficient antibacterial nanomaterials has potential across diverse fields, but it requires a deeper understanding of material-bacteria interactions. In this study, a novel 2D core-shell MoAlB@MBene structure is synthesized using a mild wet-chemical etching approach. The growth of E. coli, S. aureus, and B. subtilis bacteria in the presence of MoAlB@MBene decreased in a concentration-dependent manner, with a prolonged lag phase in the initial 6 h of incubation. Even under dark conditions, MoAlB@MBene triggered the formation of intercellular reactive oxygen species (ROS) and singlet oxygen (1O2) in bacteria, while the bacteria protected themselves by forming biofilm and altering cell morphology. The MoAlB@MBene shows consistent light absorption across the visible range, along with a distinctive UV absorption edge. Two types of band gaps are identified: direct (1.67 eV) and indirect (0.74 eV), which facilitate complex light interactions with MoAlB@MBene. Exposure to simulated white light led to decreased viability rates of E. coli (20.6%), S. aureus (22.9%), and B. subtilis (21.4%). Altogether, the presented study enhances the understanding of bacteria responses in the presence of light-activated 2D nanomaterials.

Application of immunoinformatics to develop a novel and effective multiepitope chimeric vaccine against Variovorax durovernensis

Bloodstream infections pose a significant public health challenge caused by resistant bacteria such as Variovorax durovernensis, a recently reported Gram-negative bacterium, worsening the burden on healthcare systems. The design of a vaccine using chimeric peptides derived from a representative V. durovernensis strain holds significant promise for preventing disease onset. The current study aimed to employ reverse vaccinology (RV) approaches such as the retrieval of V. durovernensis proteomics data, removal of redundant proteins by CD-HIT, filtering of non-homologous proteins to humans and essential proteins, identification of outer membrane (OM) proteins by CELLO and PSORTb. Following these steps immunoinformatic approaches were applied, such as epitope prediction by IEDB, vaccine design using linkers and adjuvant and analysis of antigenicity, allergenicity, safety and stability. Among the 4208 nonredundant proteins, an OmpA family protein (A0A940EKP4) was designated a potential candidate for the development of a multiepitope vaccine construct. Upon analysis of OM protein, six immunodominant (B cell) epitopes were found on the basis of the chimeric construct following the prediction of CTL stands cytotoxic T lymphocyte and HTL stands helper T lymphocyte epitopes. To ensure comprehensive population coverage globally, the CTL and HTL coverage rates were 58.18 % and 46.56 %, respectively, and 77.23 % overall. By utilizing EAAAK, GPGPG, and AAY linkers, Cholera toxin B subunit adjuvants, and appropriate epitopes were smoothly incorporated into a chimeric vaccine effectively triggering both adaptive and innate immune responses. For example, the administered antigen showed a peak in counts on the fifthday post injection and then gradually declined until the fifteenth day. Elevated levels of several antibodies (IgG + IgM > 700,000; IgM > 600,000; IgG1 + IgG2; IgG1 > 500,000) were observed as decreased in the antigen concentration. Molecular dynamics simulations carried out via iMODS revealed strong correlations between residue pairs, highlighting the stability of the docked complex. The designed vaccine has promising potential in eliciting specific immunogenic responses, thereby facilitating future research for vaccine development against V. durovernensis.

Development of erythromycin loaded PLGA nanoparticles for improved drug efficacy and sustained release against bacterial infections and biofilm formation

Bacterial infections are a common cause of sepsis, often leading to high patient mortality. Such infections are challenging to treat due to bacterial resistance to many existing drugs. Erythromycin (Ery) is a macrolide antibiotic used against bacterial infections with reported resistance. Recently, synthetic poly-lactide co-glycolic acid (PLGA) polymer nanoparticles (NPs) have displayed improved drug delivery characteristics and biocompatibility. In this study, PLGA-Ery NPs were synthesized by the o/w emulsion diffusion method, having a particle size of 159 ± 23 nm and displayed 71.89 % of encapsulation efficiency. The PLGA-Ery NPs showed 1.5, 2.1 and 1.5-fold improved MIC and antibacterial efficacy against E. coli, S. aureus, and P. aeruginosa, respectively than the pure drug. As illustrated by scanning electron microscopy, PLGA-Ery NPs caused damage to the bacterial cell walls. Furthermore, a surface coating with PLGA-Ery NPs on a glass surface showed efficient inhibition (>90 %) of the biofilm formation by P. aeruginosa, as determined by fluorescence microscopy and MTT assay. This study demonstrates that PLGA-Ery NPs can increase the efficiency of erythromycin and can suppress the growth and biofilm formation of P. aeruginosa. Such polymeric nanoparticles drug nanoformulations have potential as an antimicrobial and as a surface coating for medical devices.

Molecular insights into the structure and function of the Staphylococcus aureus fatty acid kinase

Gram-positive bacteria utilize a Fatty Acid Kinase (FAK) complex to harvest fatty acids from the environment. This complex consists of the fatty acid kinase, FakA, and an acyl carrier protein, FakB, and is known to impact virulence and disease outcomes. Despite some recent studies, there remains many outstanding questions as to the enzymatic mechanism and structure of FAK . To better address this gap in knowledge, we used a combination of modeling, biochemical, and cell-based approaches to build on prior proposed models and identify critical details of FAK activity. Using bio-layer interferometry, we demonstrated nanomolar affinity between FakA and FakB that also indicates that FakA is dimer when binding FakB. Additionally, targeted mutagenesis of the FakA Middle domain demonstrates it possesses a metal binding pocket that is critical for FakA dimer stability and FAK function in vitro and in vivo. Lastly, we solved structures of the apo and ligand-bound FakA kinase domain to capture the molecular changes in the protein following ATP binding and hydrolysis. Together, these data provide critical insight into the structure and function of the FAK complex which is essential for understanding its mechanism.

Impedimetric Gram-Positive Bacteria Biosensor Using Vancomycin-Coated Silica Nanoparticles with a Gold Nanocluster-Deposited Electrode

We introduce a swift, label-free electrochemical biosensor designed for the precise on-site detection of Gram-positive bacteria via electrochemical impedance spectroscopy. The biosensor was prepared by electroplating the electrode surface with gold nanoclusters (AuNCs) on the gold-interdigitated wave-shaped electrode with a printed circuit board (Au-PCB) electrode, which plays a role in cost-effective and promising lab-on-a-chip microsystems and integrated biosensing systems. This was followed by the application of silica nanoparticle-modified vancomycin (SiNPs-VAN) that binds to Gram-positive bacteria and facilitates their detection on the AuNC-coated surface. The biosensor demonstrated remarkable sensitivity and specificity. It could detect as few as 102 colony-forming units (CFU)/mL of Staphylococcus aureus, 101 CFU/mL of Bacillus cereus, and 102 CFU/mL of Micrococcus luteus within 20 min. Additionally, SiNPs-VAN is also known for its high stability, low cost, and ease of preparation. It is effective in identifying Gram-positive bacteria in water samples across a concentration range of 102-105 CFU/mL and shows selective identification of Gram-positive bacteria with minimal interference from Gram-negative bacteria like Escherichia coli. The ability of the biosensor to quantify Gram-positive bacteria aligns well with the results obtained from the quantitative real-time polymerase chain reaction (qRT-PCR). These findings highlight the potential of electrochemical biosensors for the detection of pathogens and other biological entities, marking a significant advancement in this field.

Potential of training of anti-Staphylococcus aureus therapeutic phages against Staphylococcus epidermidis multidrug-resistant isolates is restricted by inter- and intra-sequence type specificity

Phage therapy appears to be a promising approach to tackle multidrug-resistant bacteria, including staphylococci. However, most anti-staphylococcal phages have been characterized in Staphylococcus aureus, while a limited number of studies investigated phage activity against S. epidermidis. We studied the potential of phage training to extend the host range of two types of anti-S. aureus phages against S. epidermidis isolates. The Appelmans protocol was applied to a mixture of Kayvirus and a mixture of Silviavirus phages repeatedly exposed to seven S. epidermidis strains representative of nosocomial-associated sequence types (ST), including the world-wide disseminated ST2. We observed increased activity only for the Kayvirus mixture against two of these strains (ST2 or ST35). Phage subpopulations isolated from the training mixture using these two strains (five/strain) exhibited different evolved phenotypes, active only against their isolation strain or strains of the same ST. Of note, 16/47 ST2 strains were susceptible to one of the groups of trained phages. A comparative genomic analysis of ancestral and trained phage genomes, conducted to identify potential bacterial determinants of such specific activity, found numerous recombination events between two of the three ancestors. However, a small number of trained phage genes had nucleotide sequence modifications impacting the corresponding protein compared to ancestral phages, two to four of them per phage genome being specific of each group of phage subpopulations exhibiting different host range. The results suggest that anti-S. aureus phages can be adapted to S. epidermidis isolates but with inter- and intra-ST specificity.ImportanceS. epidermidis is increasingly recognized as a threat for public health. Its clinical importance is notably related to multidrug resistance. Phage therapy is one of the most promising alternative therapeutic strategies to antibiotics. Nonetheless, only very few phages active against this bacterial species have been described. In the present study, we showed that phage training can be used to extend the host range of polyvalent Kayvirus phages within the Staphylococcus genera to include S. epidermidis species. In the context of rapid development of phage therapy, in vitro forced adaptation of previously characterized phages could be an appealing alternative to fastidious repeated isolation of new phages to improve the therapeutic potential of a phage collection.

The STING signaling pathways and bacterial infection

As antibiotic-resistant bacteria continue to emerge frequently, bacterial infections have become a significant and pressing challenge to global public health. Innate immunity triggers the activation of host responses by sensing "non-self" components through various pattern recognition receptors (PRRs), serving as the first line of antibacterial defense. Stimulator of interferon genes (STING) is a PRR that binds with cyclic dinucleotides (CDN) to exert effects against bacteria, viruses, and cancer by inducing the production of type I interferon and inflammatory cytokines, and facilitating regulated cell death. Currently, drugs targeting the STING signaling pathway are predominantly applied in the fields of modulating host immune defense against cancer and viral infections, with relatively limited application in treating bacterial infections. Given the significant immunomodulatory functions of STING in the interaction between bacteria and hosts, this review summarizes the research progress on STING signaling pathways and their roles in bacterial infection, as well as the novel functions of STING modulators, aiming to offer insights for the development of antibacterial drugs.

Impact of Nutrient Starvation on Biofilm Formation in Pseudomonas aeruginosa: An Analysis of Growth, Adhesion, and Spatial Distribution

Objectives: This study investigates the impact of nutrient availability on the growth, adhesion, and biofilm formation of Pseudomonas aeruginosa ATCC 27853 under static conditions. Methods: Bacterial behaviour was evaluated in nutrient-rich Luria-Bertani (LB) broth and nutrient-limited M9 media, specifically lacking carbon (M9-C), nitrogen (M9-N), or phosphorus (M9-P). Bacterial adhesion was analysed microscopically during the transition from reversible to irreversible attachment (up to 120 min) and during biofilm production/maturation stages (up to 72 h). Results: Results demonstrated that LB and M9 media supported bacterial growth, whereas nutrient-starved conditions halted growth, with M9-C and M9-N inducing stationary phases and M9-P leading to cell death. Fractal analysis was employed to characterise the spatial distribution and complexity of bacterial adhesion patterns, revealing that nutrient-limited conditions affected both adhesion density and biofilm architecture, particularly in M9-C. In addition, live/dead staining confirmed a higher proportion of dead cells in M9-P over time (at 48 and 72 h). Conclusions: This study highlights how nutrient starvation influences biofilm formation and bacterial dispersion, offering insights into the survival strategies of P. aeruginosa in resource-limited environments. These findings should contribute to a better understanding of biofilm dynamics, with implications for managing biofilm-related infections and industrial biofouling.

Early Oral Antibiotic Switch in Staphylococcus aureus Bacteraemia: The Staphylococcus aureus Network Adaptive Platform (SNAP) Trial Early Oral Switch Protocol

BACKGROUND

Staphylococcus aureus bloodstream infection (bacteremia) is traditionally treated with at least 2 weeks of intravenous (IV) antibiotics in adults, 3-7 days in children, and often longer for those with complicated disease. The current practice of treating S. aureus bacteremia (SAB) with prolonged IV antibiotics (rather than oral antibiotics) is based on historical observational research and expert opinion. Prolonged IV antibiotic therapy has significant disadvantages for patients and healthcare systems, and there is growing interest in whether a switch to oral antibiotics following an initial period of IV therapy is a safe alternative for clinically stable patients.

PROTOCOL

The early oral switch (EOS) domain of the S. aureus Network Adaptive Platform (SNAP) trial will assess early switch to oral antibiotics compared with continued IV treatment in clinically stable patients with SAB. The primary endpoint is 90-day all-cause mortality. Hospitalised SAB patients are assessed at platform day 7 ±2 (uncomplicated SAB) and day 14 ±2 (complicated SAB) to determine their eligibility for randomization to EOS (intervention) or continued IV treatment (current standard of care).

DISCUSSION

Recruitment is occurring in the EOS domain of the SNAP trial. As of August 2023, 21% of all SNAP participants had been randomized to the EOS domain, a total of 264 participants across 77 centers, with an aim to recruit at least 1000 participants. We describe challenges and facilitators to enrolment in this domain to aid those planning similar trials.

Estimating the global and regional burden of lower respiratory infections attributable to leading pathogens and the protective effectiveness of immunization programs

OBJECTIVES

Reducing mortality from infectious diseases is an urgent global public health priority. Streptococcus pneumoniae, H. influenzae, and influenza virus are the three leading causes of lower respiratory infections (LRIs) death worldwide. Our objective was to assess the global burden of LRIs attributable to S. pneumoniae, H. influenzae, and influenza virus and explore the protective effectiveness of immunization programs.

METHODS

Data were retrieved from the Global Burden of Disease Study 2021 and World Health Organization United Nations Children's Fund Estimates of National Immunization Coverage. Locally weighted linear regression and Spearman correlation analysis were used to examine the associations between LRI mortality and vaccination coverage. Mixed-effects regression models were used to estimate the reduction in deaths that would be reduced by pneumococcal conjugate vaccine (PCV) and the H. influenzae type b (Hib) vaccine if all countries realized the Immunization Agenda 2030 (IA2030).

RESULTS

In 2021, about 30.2% of the 2.18 million LRI-related deaths were attributed to three studied pathogens. From 1990 to 2021, the age-standardized mortality rate of LRIs was attributable to three pathogens decreased by more than half. In 2022, the global vaccination rates for PCV and Hib vaccines were 60.0% and 76.0%, respectively. The LRIs attributable to S. pneumoniae (rs = -0.45, P <0.001) and H. influenzae (rs = -0.47, P <0.001) decreased with the increasing vaccination coverage of PCV and Hib. By 2030, approximately 59.9% and 70.8% of countries worldwide will reach the IA2030 targets of 90% coverage for PCV and Hib, respectively. By that time, the number of deaths from LRIs in children attributable to S. pneumoniae and H. influenzae will decrease by 54.8% and 24.4%, respectively.

CONCLUSIONS

Despite the declines in LRI mortality attributed to respiratory pathogens, substantial deaths still occurred in 2021. To advance toward achieving the IA2030 targets and further mitigate mortality associated with LRIs, intensified efforts by the international community and national health systems are imperative.

Haemophilus influenzae and pneumococci: Co-colonization, interactions, cooperation and competition

Nontypeable Haemophilus influenzae (NTHi) and Streptococcus pneumoniae (pneumococcus) are pathobionts that share common environmental niches within the upper respiratory tract. They can form part of the resident upper airway microbiota, but under certain environmental circumstances become pathogenic and induce disease. In children, both organisms have a considerable impact on the healthcare system, commonly causing acute otitis media and pneumonia. They are also associated with chronic biofilm-mediated respiratory infections, such as persistent middle ear effusions and chronic suppurative otitis media, and in the lower airways with protracted bacterial bronchitis and bronchiectasis. Consequently, both organisms are responsible for large numbers of antibiotic prescriptions and substantial healthcare costs. The complex relationship between NTHi and pneumococcal co-interaction during colonization, infection and biofilm formation is poorly understood and a greater understanding is needed to facilitate development of future therapies, and novel interventions and prevention strategies. Co-infections with both bacteria can result in more severe disease, with disease severity likely mediated by their ability to cooperate in some in vivo niches. However, this relationship is not always straightforward, as under certain conditions, these two bacteria compete rather than cooperate. Current opinion supports developing a vaccine targeting NTHi strains, as well as a combined vaccine targeting both NTHi and pneumococci to decrease the respiratory disease burden in young children. This review summarizes our current knowledge of the interactions between NTHi and pneumococci and speculates on the future directions of research to understand how these bacteria co-exist and how to better prevent and treat NTHi and pneumococcal infection.

Development of Fragment-Based Inhibitors of the Bacterial Deacetylase LpxC with Low Nanomolar Activity

In a fragment-based approach using NMR spectroscopy, benzyloxyacetohydroxamic acid-derived inhibitors of the bacterial deacetylase LpxC bearing a substituent to target the uridine diphosphate-binding site of the enzyme were developed. By appending privileged fragments via a suitable linker, potent LpxC inhibitors with promising antibacterial activities could be obtained, like the one-digit nanomolar LpxC inhibitor (S)-13j [Ki (EcLpxC C63A) = 9.5 nM; Ki (PaLpxC): 5.6 nM]. To rationalize the observed structure-activity relationships, molecular docking and molecular dynamics studies were performed. Initial in vitro absorption-distribution-metabolism-excretion-toxicity (ADMET) studies of the most potent compounds have paved the way for multiparameter optimization of our newly developed isoserine-based amides.

Ultrasensitive Analysis of Escherichia coli O157:H7 Based on Immunomagnetic Separation and Labeled Surface-Enhanced Raman Scattering with Minimized False Positive Identifications

It is a big challenge to monitor pathogens in food with high selectivity. In this study, we reported an ultrasensitive method for Escherichia coli O157:H7 detection based on immunomagnetic separation and labeled surface-enhanced Raman scattering (SERS). The bacterium was identified by heterogeneous recognition elements, monoclonal antibody (mAb), and aptamer. E. coli O157:H7 was separated and enriched by magnetic nanoparticles modified by mAb, and then a plasmonic nanostructure functionalized by aptamers with embedded Raman tags and interior gaps was utilized for further discrimination and detection. The selectivity was enhanced by two binding sites. The higher Raman enhancement was obtained by strong local electromagnetic field oscillation in the gap and the firm embedment of 4-mercaptopyridine (4-Mpy). Optimum experiments created that SERS signals of 4-Mpy at 1010 cm-1 had a good linearity with E. coli O157:H7 at a large range of 10 to 107 CFU/mL with a limit of detection of 2 CFU/mL. This method has great potential for on-site food pathogenic bacterial detection.

Lead-Free Cs2AgBiBr6/TiO2 S-Scheme Heterojunction for Efficient Photocatalytic Antibiotic Rifampicin Degradation

Exploring efficient and stable halide perovskite-based photocatalysts is a great challenge due to the balance between the photocatalytic performance, toxicity, and intrinsic chemical instability of the materials. Here, the environmentally friendly lead-free perovskite Cs2AgBiBr6 confined in the mesoporous TiO2 crystal matrix has been designed to enhance the charge carrier extraction and utilization for efficient photocatalytic rifampicin degradation. The as-prepared Cs2AgBiBr6/TiO2 catalyst was stable in air for over 500 days. An S-scheme heterojunction was formed between the (004) plane of Cs2AgBiBr6 and the (101) plane of TiO2 through the Bi-O-Br bonds. The built-in electric field at the interface efficiently promoted the photoinduced charge separation and carrier extraction. The Cs2AgBiBr6/TiO2-200 showed a 92.83% degradation efficiency of rifampicin within 80 min under simulated sunlight illumination (AM 1.5G 100 mW cm-2). This work offers an effective way for the construction of halide perovskite-based photocatalysts with high photocatalytic performance, good stability, and low toxicity simultaneously.

New insights into the photophysical properties and interaction mechanisms of Janus green blue dye with polyanions and its applications in colorimetric visualization of loop-mediated isothermal amplification and polymerase chain reaction

In this investigation, the photophysical properties and interaction mechanisms of Janus green blue (JGB) dye with polyanions were systematically studied using spectroscopic techniques. The absorption spectral analysis revealed that JGB binds cooperatively to sodium alginate, leading to dye stacking along the polymer chain. The interaction of JGB dye with DNA was characterized by the emergence of a metachromatic peak at 564 nm, indicating the formation of dye aggregates. The analysis of absorption data reveals that JGB dye interacts with DNA at multiple binding sites, including at least one high-affinity site. The AutoDock Vina based blind docking approach was used to analyze the most probable binding location of JGB dye in DNA. By making use of the DNA-induced metachromasia, a colorimetric approach was developed for the visualization of loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR). The LAMP-colorimetric assay, targeting the Streptococcus pneumoniae gene, demonstrated a noticeable colour change with a detection limit of 1 pg μL-1. The practical applicability was validated by detecting S. pneumoniae in artificial urine. In addition to LAMP, we tested the JGB dye based colorimetric assay for applicability in PCR reactions. The colorimetric PCR assay using the metal-responsive transcription factor (MTF-1) gene achieved a detection limit as low as 0.1 pg μL-1. The study highlights the potential of DNA binding metachromic dye to significantly enhance colorimetric assays, offering a robust and sensitive tool for molecular diagnostics.

The epidemiology of gram-negative bacteremia in Lebanon: a study in four hospitals

INTRODUCTION

Gram-negative bacteremia is a life-threatening infection with high morbidity and mortality. Its incidence is rising worldwide, and treatment has become more challenging due to emerging bacterial resistance. Little data is available on the burden and outcome of such infections in Lebanon.

METHODS

We conducted this retrospective study in four Lebanese hospitals. Data on medical conditions and demographics of 2400 patients diagnosed with a bloodstream infection based on a positive blood culture were collected between January 2014 and December 2020.

RESULTS

Most bacteremias were caused by Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii, with the more resistant organisms being hospital-acquired. Third-generation cephalosporin and quinolone resistance was steady throughout the study, but carbapenem resistance increased. Mortality with such infections is high, but carbapenem resistance or infection with Pseudomonas or Acinetobacter species were significant risk factors for poor outcomes.

CONCLUSION

This is the first multi-center study from Lebanon on gram-negative bacteremia, resistance patterns, and factors associated with a poor outcome. More surveillance is needed to provide data to guide empirical treatment for bacteremia in Lebanon.

Can immuno-PCR (IPCR) transform bacterial disease diagnostics?

INTRODUCTION

Approximately 15 million deaths occur globally each year due to infectious diseases. Timely diagnosis is crucial in promoting cure and preventing disease transmission. Currently, molecular diagnostics have replaced many conventional diagnostic tools due to their inherent limitations. However, the full potential of Immuno Polymerase Chain Reaction (IPCR) remains largely untapped.

AREAS COVERED

This review focuses on the use of IPCR in the diagnosis of different bacterial diseases, highlighting its advantages over traditional methods.

EXPERT OPINION

Early and accurate diagnosis of infectious diseases is crucial because it enhances treatment effectiveness, reduces morbidity and mortality, helps identify potential causes of sepsis earlier, and reduces the risk of unknowingly spreading the disease to others. IPCR in turn has shown promise for the early diagnosis of bacterial diseases as an alternative to conventional culture-based or serological diagnostic assays leading to delayed diagnosis and treatment. IPCR has the potential to revolutionize the diagnostic field due to its increased sensitivity and specificity. Although efforts are needed to reduce the time of the assay and to reduce background noise, IPCR can be combined with other platforms like lateral flow assay/biosensors/automation to improve its use as a point-of-care assay, especially in resource-limited settings.

Enhanced Staphylococcus aureus protection by uncoupling of the α-toxin-ADAM10 interaction during murine neonatal vaccination

Staphylococcus aureus remains a leading global cause of bacterial infection-associated mortality and has eluded prior vaccine development efforts. S. aureus α-toxin (Hla) is an essential virulence factor in disease, impairing the T cell response to infection. The anti-Hla antibody response is a correlate of human protective immunity. Here we observe that this response is limited early in human life and design a vaccine strategy to elicit immune protection against Hla in a neonatal mice. By targeted disruption of the interaction of Hla with its receptor ADAM10, we identify a vaccine antigen (HlaH35L/R66C/E70C, HlaHRE) that elicits an ~100-fold increase in the neutralizing anti-Hla response. Immunization with HlaHRE enhances the T follicular helper (TFH) cell response to S. aureus infection, correlating with the magnitude of the neutralizing anti-toxin response and disease protection. Furthermore, maternal HlaHRE immunization confers protection to offspring. Together, these findings illuminate a path for S. aureus vaccine development at the maternal-infant interface.

Retrospective validation study of a machine learning-based software for empirical and organism-targeted antibiotic therapy selection

Errors in antibiotic prescriptions are frequent, often resulting from the inadequate coverage of the infection-causative microorganism. The efficacy of iAST, a machine-learning-based software offering empirical and organism-targeted antibiotic recommendations, was assessed. The study was conducted in a 12-hospital Spanish institution. After model fine-tuning with 27,531 historical antibiograms, 325 consecutive patients with acute infections were selected for retrospective validation. The primary endpoint was comparing each of the top three of iAST's antibiotic recommendations' success rates (confirmed by antibiogram results) with the antibiotic prescribed by the physicians. Secondary endpoints included examining the same hypothesis within specific study population subgroups and assessing antibiotic stewardship by comparing the percentage of antibiotics recommended that belonged to different World Health Organization AWaRe groups within each arm of the study. All of iAST first three recommendations were non-inferior to doctor prescription in the primary endpoint analysis population as well as the secondary endpoint. The overall success rate of doctors' empirical treatment was 68.93%, while that of the first three iAST options was 91.06% (P < 0.001), 90.63% (P < 0.001), and 91.06% (P < 001), respectively. For organism-targeted therapy, the doctor's overall success rate was 84.16%, and that of the first three ranked iAST options was 97.83% (P < 0.001), 94.09% (P < 0.001), and 91.30% (P < 0.001), respectively. In empirical therapy, compared to physician prescriptions, iAST demonstrated a greater propensity to recommend access antibiotics, fewer watch antibiotics, and higher reserve antibiotics. In organism-targeted therapy, iAST advised a higher utilization of access antibiotics. The present study demonstrates iAST accuracy in predicting antibiotic susceptibility, showcasing its potential to promote effective antibiotic stewardship.

CLINICAL TRIALS

This study is registered with ClinicalTrials.gov as NCT06174519.

Bi- and tricyclic diterpenoids: landmarks from a decade (2013-2023) in search of leads against infectious diseases

Covering: 2013 to 2023In an era where antimicrobial resistance severely threatens our ability to treat infections, the discovery of new drugs that belong to different chemical classes and/or bear original modes of action is urgently needed. In this case, diterpenoids comprise a productive field with a proven track record in providing new anti-infectives to tackle bacterial infections and malaria. This review highlights the potential of both naturally occurring and semi-synthetic bi- and tricyclic diterpenoids to become leads in search of new drugs to treat infections caused by bacteria, fungi, viruses and protozoan parasites. The literature from the last decade (2013-2023) is covered, focusing on naturally occurring and semi-synthetic bicyclic (labdanes and labdane-type) and tricyclic (all classes) diterpenoids, detailing their relevant biological activities in the context of infection, which are explained through structure-activity relationships.

A path forward for Staphylococcus aureus vaccine development

The pursuit of a vaccine to quell Staphylococcus aureus disease has been unfruitful. In this Viewpoint, we explore the biological linkage between microbial niche acquisition and host immunity as a basis to guide future vaccine efforts.

High-throughput fluorescence sensing array based on tetraphenylethylene derivatives for detecting and distinguishing pathogenic microbes

Infections induced by pathogenic microorganisms will bring negative effects such as diseases that damage health and result in heavy economic burden. Therefore, it is very important to detect and identify the pathogens in time. Moreover, traditional clinical diagnosis or food testing often faces the problem of dealing with a large number of samples. Here, we designed a high-throughput fluorescent sensor array based on the different binding ability of five tetraphenylethylene derivatives (TPEs) with various side chains to different kinds of pathogenic microbes, which is used to detect and distinguish various species, so as to realize rapid mass diagnosis, and hopefully provide guidance for further determination of microbial infections and clinical treatment.

The two-component sensor factor envZ influences antibiotic resistance and virulence in the evolutionary dynamics of multidrug-resistant Salmonella enteritidis causing multisite invasive infections

OBJECTIVES

To assess the impact of mutations in the two-component sensor envZ on antibiotic resistance and virulence in the evolutionary dynamics of MDR Salmonella enteritidis (S. enteritidis).

METHODS

Five S. enteritidis isolates obtained from a patient with multisite invasive infections were analysed. Analysis of antibiotic resistance genes, virulence genes and SNP was performed through WGS. RNA sequencing, quantitative RT-PCR, virulence testing in a Galleria mellonella (G. mellonella) infection model and in vitro cell experiments were used to examine the effects of envZ mutations.

RESULTS

WGS revealed identical resistance and virulence genes on an IncFIB(S)/IncFII(S)/IncX1 fusion plasmid in all strains. The faecal strains harboured envZ mutations, reducing outer membrane protein ompD and ompF transcriptional level. Virulence testing demonstrated elevated virulence in envZ mutant strains. In vitro experiments revealed increased adhesion, invasion and phagocytosis resistance in envZ mutants, along with reduced biofilm formation and growth rates.

CONCLUSIONS

These findings highlight novel genetic locations on envZ influencing antibiotic resistance and virulence in clinical S. enteritidis strains. envZ mutations impact antibiotic resistance by down-regulating ompD and ompF expression and enhance virulence, contributing to multisite infections with increased fitness costs.

Antibiotic tolerance among clinical isolates: mechanisms, detection, prevalence, and significance

SUMMARYAntibiotic treatment failures in the absence of resistance are not uncommon. Recently, attention has grown around the phenomenon of antibiotic tolerance, an underappreciated contributor to recalcitrant infections first detected in the 1970s. Tolerance describes the ability of a bacterial population to survive transient exposure to an otherwise lethal concentration of antibiotic without exhibiting resistance. With advances in genomics, we are gaining a better understanding of the molecular mechanisms behind tolerance, and several studies have sought to examine the clinical prevalence of tolerance. Attempts have also been made to assess the clinical significance of tolerance through in vivo infection models and prospective/retrospective clinical studies. Here, we review the data available on the molecular mechanisms, detection, prevalence, and clinical significance of genotypic tolerance that span ~50 years. We discuss the need for standardized methodology and interpretation criteria for tolerance detection and the impact that methodological inconsistencies have on our ability to accurately assess the scale of the problem. In terms of the clinical significance of tolerance, studies suggest that tolerance contributes to worse outcomes for patients (e.g., higher mortality, prolonged hospitalization), but historical data from animal models are varied. Furthermore, we lack the necessary information to effectively treat tolerant infections. Overall, while the tolerance field is gaining much-needed traction, the underlying clinical significance of tolerance that underpins all tolerance research is still far from clear and requires attention.