The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis

Recent advances in inhibitor development and metabolic targeting in tuberculosis therapy

Despite being a preventable and treatable disease, tuberculosis (TB) remained the second leading infectious cause of death globally in 2022, surpassed only by COVID-19. The death rate from TB is influenced by numerous factors that include antibiotic drug resistance, noncompliance with chemotherapy by patients, concurrent infection with the human immunodeficiency virus, delayed diagnosis, varying effectiveness of the Bacille-Calmette-Guerin vaccine, and other factors. Even with the recent advances in our knowledge of Mycobacterium tuberculosis and the accessibility of advanced genomic tools such as proteomics and microarrays, alongside modern methodologies, the pursuit of next-generation inhibitors targeting distinct or multiple molecular pathways remains essential to combat the increasing antimicrobial resistance. Hence, there is an urgent need to identify and develop new drug targets against TB that have unique mechanisms. Novel therapeutic targets might encompass gene products associated with various aspects of mycobacterial biology, such as transcription, metabolism, cell wall formation, persistence, and pathogenesis. This review focuses on the present state of our knowledge and comprehension regarding various inhibitors targeting key metabolic pathways of M. tuberculosis. The discussion encompasses small molecule, synthetic, peptide, natural product and microbial inhibitors and navigates through promising candidates in different phases of clinical development. Additionally, we explore the crucial enzymes and targets involved in metabolic pathways, highlighting their inhibitors. The metabolic pathways explored include nucleotide synthesis, mycolic acid synthesis, peptidoglycan biosynthesis, and energy metabolism. Furthermore, advancements in genetic approaches like CRISPRi and conditional expression systems are discussed, focusing on their role in elucidating gene essentiality and vulnerability in Mycobacteria.

The l,d-transpeptidation pathway is inhibited by antibiotics of the β-lactam class in Clostridioides difficile

The resistance of Clostridioides difficile to the β-lactam antibiotics cephalosporins, which target the peptidoglycan (PG) assembly, is a leading contributor to the development of C. difficile infections. C. difficile has an original PG structure with a predominance of 3→3 cross-links generated by l,d-transpeptidases (LDTs). C. difficile forms spores and we show that the spore cortex PG contains exclusively 3→3 cross-links. PG and spore cortex of C. difficile cells were largely unaffected by the deletion of the three predicted LDTs, revealing the implication of a new family of LDTs. The d,d-carboxypeptidases producing the essential LDT substrate were inactivated by cephalosporins, resulting in the inhibition of the l,d-transpeptidation pathway. In contrast, the participation of penicillin-binding proteins (PBPs) to PG cross-linking increased in the presence of the antibiotics. Our findings highlight that cephalosporin resistance is not primarily mediated by LDTs and illustrate the plasticity of the PG biosynthesis machinery in C. difficile.

Rationally designed antimicrobial peptides with high selectivity and efficiency against phytopathogenic Ralstonia solanecearum

Ralstonia solanacearum, the causative agent of bacterial wilt, poses a global threat to agriculture, necessitating urgent and sustainable solutions as traditional methods lose efficacy. This study developed WRF-13, a synthetic antimicrobial peptide (AMP) designed to mimic natural AMPs, exhibiting potent antibacterial and anti-biofilm activity with high specificity against R. solanacearum. Mechanistic studies, including microscopy and computational analyses, demonstrated that WRF-13 disrupts the bacterial membrane. WRF-13 remained stable across a wide pH (5-8) and temperature (25-50 °C) range, essential for field applications, and showed no detectable toxicity to mammalian or plant cells at elevated concentrations. Greenhouse trials confirmed its efficacy in reducing bacterial wilt severity up to 65 %, highlighting its potential to protect crops from R. solanacearum infection. Overall, this study highlights WRF-13 as a targeted solution for managing bacterial wilt and advancing sustainable agriculture.

The juxtamembrane domain of StkP is phosphorylated and influences cell division in Streptococcus pneumoniae

Eukaryotic-like membrane Ser/Thr protein kinases play a pivotal role in different aspects of bacterial physiology. In contrast to the diversity of their extracellular domains, their cytoplasmic catalytic domains are highly conserved. However, the function of a long juxtamembrane domain (JMD), which connects the catalytic domain to the transmembrane helix, remains elusive. In this study, we investigated the function of the JMD of the Ser/Thr protein kinase StkP in the cell division of Streptococcus pneumoniae. We observed that the deletion of the JMD affected the ability of StkP to phosphorylate some of its endogenous substrates, thereby resulting in significant cell morphogenesis defects. Furthermore, multiple threonine residues were identified as being phosphorylated in the JMD. To investigate the functional significance of these phosphorylation sites, we conducted an integrative analysis, combining structural biology, proteomics, and bacterial cell imaging. Our results revealed that the phosphorylation of the JMD did not perturb the phosphorylation of StkP substrates. However, we observed that it modulated the timing of StkP localization to the division septum and the dynamics of cell constriction. We further demonstrated that phosphorylation of the JMD facilitated the recruitment of several cell division proteins, suggesting that it is required to assemble the division machinery at the division septum. In conclusion, this study demonstrates that the function of the JMD of StkP is modulated by phosphorylation and is critical for the cell division of S. pneumoniae. These observations may serve as a model for understanding the regulatory function of other bacterial Ser/Thr protein kinases.IMPORTANCEHow bacterial serine/threonine protein kinases are activated remains highly debated. In particular, models rely on the observations made with their eukaryotic counterparts, and only a few studies have investigated the molecular activation mechanism of bacterial serine/threonine protein kinases. This is particularly the case with regard to the juxtamembrane domain (JMD), which is proposed to contribute to kinase activation in numerous eukaryotic kinases. This study demonstrates that the juxtamembrane domain is likely not essential for the activation of the serine/threonine protein kinase StkP of S. pneumoniae. Rather, our findings reveal that it is required for cell division, where its phosphorylation affects the assembly of the division machinery at the division septum. These observations allow us to assign a function to the JMD in StkP-mediated regulation of pneumococcal cell division, thereby providing a new avenue for understanding the contribution of membrane serine/threonine protein kinases in the physiology of other bacteria.

Evaluation of in vitro pharmacodynamic drug interactions of ceftazidime-avibactam with tigecycline in ESBL- and carbapenemase producing Escherichia coli and Klebsiella pneumoniae

BACKGROUND

Combination therapy offers a promising option to enhance efficacy and prevent resistance. A comprehensive and quantitative assessment of the last-resort combination of ceftazidime/avibactam and tigecycline is not available.

OBJECTIVE

This study systematically investigated the pharmacodynamic interaction between ceftazidime/avibactam and tigecycline in clinical and isogenic Escherichia coli and Klebsiella pneumoniae strains harbouring genes that encode various carbapenemases or ESBLs.

METHODS

An adaptive in vitro 'dynamic' checkerboard design and pharmacometric modelling were employed for the evaluation of pharmacodynamic interactions in fifteen bacterial isolates. Additionally, time-kill assays and metabolomic analyses were used to provide mechanistic insights.

RESULTS

Antagonistic drug interactions between ceftazidime/avibactam and tigecycline were identified in the majority of tested strains. Time-kill assays confirmed antagonistic interactions, with tigecycline limiting ceftazidime/avibactam total killing. Metabolomic analyses of mono and combined drug exposure to bacteria revealed matching metabolomes in tigecycline alone and the combination with ceftazidime/avibactam, corroborating the identified antagonism between these drugs.

CONCLUSIONS

Our study reveals that the antagonistic interaction between ceftazidime/avibactam and tigecycline can undermine ceftazidime/avibactam's efficacy, suggesting limited clinical benefit in combining these antibiotics. Therefore, further research is encouraged to explore this and alternative combinations or approaches that may offer better clinical outcomes.

Genomic approach to evaluate the intrinsic antibacterial activity of novel diazabicyclooctanes (zidebactam and nacubactam) against clinical Escherichia coli isolates from diverse clonal lineages in the United Arab Emirates

BACKGROUND

The spiking rise in the prevalence of multidrug-resistant (MDR) pathogens necessitates discovering new antimicrobial agents. This study aims to investigate the intrinsic activity of two novel diazabicyclooctane (DBO) β-lactamase inhibitors, zidebactam and nacubactam, against diverse MDR Escherichia coli isolates from the United Arab Emirates. We aimed to correlate their antibacterial efficacy with the genomic characteristics of the strains.

METHODS

This study investigated 73 E. coli strains and tested them for susceptibility to different antibiotics, including DBOs. PCR screening for carbapenemase and major β-lactamase genes was done. The strains were then grouped according to phenotypic and genotypic profiles. Whole-genome sequencing was employed to characterize the genetic landscape and clonality of selected 32 strains. Additionally, time-kill studies were conducted to confirm the bactericidal activity of DBOs.

RESULTS

Zidebactam demonstrated superior efficacy compared to nacubactam, primarily due to its higher affinity for penicillin-binding protein 2 (PBP2). Notably, zidebactam alone exhibited the most potent in vitro activity, outperforming both traditional β-lactams and novel antibiotics like cefiderocol. DBOs maintained effectiveness against strains harboring various resistance determinants, including NDM-5, OXA-181, CTX-M-15, SHV-12, CMY, and DHA. Genomic analysis revealed multiple mutations in PBP1-3, with PBP2 mutations correlating with DBO susceptibility variations. Importantly, DBOs remained highly effective against isolates with PBP mutations, even those belonging to high-risk clonal lineages (ST167, ST410, ST131). Time-kill studies confirmed the bactericidal activity of DBOs, with only one strain showing reduced susceptibility (MIC: 4 µg/ml).

CONCLUSIONS

This study provides compelling evidence for the potential of DBOs, particularly zidebactam, as novel antibacterial agents. Their unique characteristics and broad-spectrum activity position them as promising candidates for future antibiotic development. While the inclusion of DBO therapies in the antibiotic arsenal could significantly impact MDR pathogen treatment, realizing their full potential requires further research, clinical evaluation, and vigilant monitoring of resistance mechanisms through integrated genomic approaches.

Localization and Single Molecule Dynamics of Bacillus subtilis Penicillin-Binding Proteins Depend on Substrate Availability and Are Affected by Stress Conditions

We have used single molecule tracking to investigate dynamics of four penicillin-binding proteins (PBPs) in Bacillus subtilis to shed light on their possible modes of action. We show that Pbp2a, Pbp3, Pbp4, and Pbp4a, when expressed at very low levels, show at least two distinct states of mobility: a state of slow motion, likely representing molecules involved in cell wall synthesis, and a mode of fast motion, likely representing freely diffusing molecules. Except for Pbp4, all other PBPs showed about 50% molecules in the slow mobility state, suggesting that roughly half of all molecules are engaged in a substrate-bound mode. We observed similar coefficients for the slow mobility state for Pbp4 and Pbp4a on the one hand, and for Pbp2a and Pbp3 on the other hand, indicating possible joint activities, respectively. Upon induction of osmotic stress, Pbp2a and Pbp4a changed from a pattern of localization mostly at the lateral cell membrane to also include localization at the septum, revealing that sites of preferred positioning for these two PBPs can be modified during stress conditions. While Pbp3 became more dynamic after induction of osmotic stress, Pbp4 became more static, showing that PBPs reacted markedly differently to envelope stress conditions. The data suggest that PBPs could take over functions in cell wall synthesis during different stress conditions, increasing the resilience of cell wall homeostasis in different environmental conditions. All PBPs lost their respective localization pattern after the addition of vancomycin or penicillin G, indicating that patterns largely depend on substrate availability. Our findings show that PBPs rapidly alter between non-targeted motion through the cell membrane and capture at sites of active cell wall synthesis, most likely guided by complex formation with other cell wall synthesis enzymes.

Impacts of Naphthenic Acids (NAs) Exposure on Soil Bacterial Community and Antibiotic Resistance Genes (ARGs) Dissemination

Naphthenic acids (NAs) are indigenous and complex components in petroleum. In the context of increasing global energy demand, the increasing extraction of fossil resources leads to increased environmental release of NAs, resulting in various environmental risks. However, the impact of NAs exposure on soil microorganisms remains still unclear. This study constructed a microcosm system to explore bacterial community structure and function, biological risk generation, and the mechanism of antibiotic resistance genes (ARGs) dissemination under NAs exposure. After 28 days of NAs stimulation, the denitrifying bacteria were enriched and the abundance of genes related to nitrogen cycle was up-regulated, enhancing nitrification and denitrification. Meanwhile, NAs stimulated the production of extracellular polymeric substances (EPS) and the accumulation of reactive oxygen species (ROS), as well as activated the glutathione antioxidant system. Furthermore, the cell metabolic, repair, and transfer regulatory pathways were enhanced under NAs exposure. The networks of ARGs with genera and mobile genetic elements (MGEs) indicated that NAs exposure promoted the enrichment of ARGs in hosts, the selective accumulation of MGEs, and the induction of horizontal gene transfer (HGT) of ARGs. This study will provide valuable perspectives of interactions between NAs and its microecological environment, as well as ARGs transfer mechanisms.

Functional redundancy between penicillin-binding proteins during asymmetric cell division in Clostridioides difficile

Peptidoglycan synthesis is an essential driver of bacterial growth and division. The final steps of this crucial process involve the activity of the SEDS family glycosyltransferases that polymerize glycan strands and the class B penicillin-binding protein (bPBP) transpeptidases that cross-link them. While many bacteria encode multiple bPBPs to perform specialized roles during specific cellular processes, some bPBPs can play redundant roles that are important for resistance against certain cell wall stresses. Our understanding of these compensatory mechanisms, however, remains incomplete. Endospore-forming bacteria typically encode multiple bPBPs that drive morphological changes required for sporulation. The sporulation-specific bPBP, SpoVD, is important for synthesizing the asymmetric division septum and spore cortex peptidoglycan during sporulation in the pathogen Clostridioides difficile. Although SpoVD catalytic activity is essential for cortex synthesis, we show that it is unexpectedly dispensable for SpoVD to mediate asymmetric division. The dispensability of SpoVD's catalytic activity requires the presence of its SEDS partner, SpoVE, and is facilitated by another sporulation-induced bPBP, PBP3. Our data further suggest that PBP3 interacts with components of the asymmetric division machinery, including SpoVD. These findings suggest a possible mechanism by which bPBPs can be functionally redundant in diverse bacteria and facilitate antibiotic resistance.

Comparative metabolomic study of twelve Acacia species by UHPLC-q-tof-ESI-MS coupled with chemometrics in correlation with antibacterial activity

Genus Acacia comprises around 1500 species. They are widely used to treat inflammation as well as bacterial and fungal infections as they are enriched in phytochemicals, especially phenolics. The aim of this study was to evaluate the antibacterial activity of leaves' methanolic extracts of twelve Acacia species growing in Egypt against Vibrio parahaemolyticus, Salmonella enterica, Listeria monocytogens, Klebsiella pnemoniae, Bacillus aquimaris, Bacillus subtilis, and Escherichia coli. These species are Acacia nilotica (wild and cultivated), Acacia seyal, Acacia auriculiformis, Acacia saligna, Acacia xanthophloea, Acacia tortilis subsp. raddiana (Gabal Elba and Aswan), Acacia tortilis, Acacia laeta (wild and cultivated), and Acacia albida. Furthermore, to study the metabolomic composition and variation among these species using ultra-high-performance liquid chromatography-electrospray ionization quadrupole time of flight mass spectrometry (UHPLC-q-tof-ESI-MS) coupled with multivariate statistical analysis and correlate it to the antibacterial potential. Results showed that Acacia nilotica (AN) has superior antibacterial activity over the other species. In addition, it exhibited a distinct segregation in Principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA). Full profiling of AN using UHPLC-ESI-q-tof-MS revealed 42 phenolics mainly catechins. It was further subjected to bio-guided fractionation and revealed the presence of methyl gallic acid, gallic acid, catechin gallate, and digallate isomers in its most bioactive fraction. These compounds were identical to the compounds annotated as VIPs and were responsible for the segregation of AN in both PCA and PLS-DA analyses. Hence, this study sheds light on the use of chemometrics as an early tool for the detection of bioactive compounds.

Navigating Antibiotic Resistance in Gram-Negative Bacteria: Current Challenges and Emerging Therapeutic Strategies

The rapid rise of antibiotic resistance poses a severe global health crisis, necessitating new approaches to counter this growing threat. The problem is exacerbated in Gram-negative bacterial pathogens as many antibiotics are unable to enter these cells owing to their unique additional outer membrane barrier. In this review, we discuss the challenges of targeting Gram-negative bacteria, including the complexity of the outer membrane, as well as the presence of efflux pumps and β-lactamases that contribute to resistance. We also review solutions proposed to facilitate the entry and accumulation of antibiotics in Gram-negative bacteria. These involve using existing antibiotics in combination with other inhibitors to attack the bacterial cell synergistically. We also highlight approaches to target Gram-negative pathogens via novel modes of action, providing new strategies to tackle antibiotic resistance.

Discovery of amino acid substitutions in penicillin-binding proteins associated with adaptation to D-Ala-D-Lac in vancomycin-resistant Enterococcus faecalis

The bacterial cell wall, essential for structural integrity, is synthesized with penicillin-binding proteins (PBPs). Vancomycin-resistant enterococci (VRE) evades vancomycin by replacing D-Ala-D-Ala in their cell wall precursors with D-Ala-D-Lac, reducing the drug's effectiveness. However, how PBPs-which typically use D-Ala-D-Ala as a substrate-adapt to recognize D-Ala-D-Lac remains unclear. Here, we performed Sanger sequencing and alignment of PBP genes from both vancomycin-susceptible and -resistant E. faecalis strains to identify mutations, following amplification by PCR. We then applied homology modeling to assess structural impacts of these changes on PBPs and conducted docking studies to investigate ligand-binding interactions. For the first time, we identified specific adaptations in certain VRE PBPs that may facilitate the D-Ala-D-Lac utilization. We found that PBP1B, PBP2A, PBP3 showed changes, while PBP1A, PBP2B and PBP4 remained unchanged. Notably, a threonine-to-asparagine substitution at location 491 in PBP1B leads to a shift in substrate preference from D-Ala-D-Ala to D-Ala-D-Lac. Similar structural changes in PBP3 suggest that the presence of changed and unchanged PBPs within the same classes suggests compensatory interactions, indicating a teamwork among multiple PBPs. These insights into PBPs provide a deeper understanding of D-Ala-D-Lac utilization in VRE, may be used to develop new therapeutic agents to combat vancomycin resistance.

Unveiling the Potential of Tetrahedral DNA Frameworks in Clinical Medicine: Mechanisms, Advances, and Future Perspectives

As deoxyribonucleic acis (DNA) nanotechnology advances, DNA, a fundamental biological macromolecule, has been employed to treat various clinical diseases. Among the advancements in this field, tetrahedral frameworks nucleic acids (tFNAs) have gained significant attention due to their straightforward design, structural simplicity, low cost, and high yield since their introduction by Turberfield in the early 2000s. Due to its stable spatial structure, tFNAs can resist the impact of innate immune responses on DNA and nuclease activity. Meanwhile, structural programmability of tFNAs allows for the development of static tFNA-based nanomaterials through the engineering of functional oligonucleotides or therapeutic molecules and dynamic tFNAs through the attachment of stimuli-responsive DNA apparatuses. This review first summarizes the key merits of tFNAs, including natural biocompatibility, biodegradability, structural stability, unparalleled programmability, functional diversity, and efficient cellular internalization. Based on these strengths, this review comprehensively analyzes applications of tFNAs in different clinical settings, including orthopedics, stomatology, urinary system diseases, liver-related diseases, tumors, infection, neural system diseases, ophthalmic diseases, and immunoprophylaxis. We also discuss the limitations of tFNAs and the challenges encountered in preclinical studies. This review provides new perspectives for future research and valuable guidance for researchers working in this field.

Evaluation of ampicillin plus ceftobiprole combination therapy in treating Enterococcus faecalis infective endocarditis and bloodstream infection

Enterococcus faecalis is responsible for numerous serious infections, and treatment options often include ampicillin combined with an aminoglycoside or dual beta-lactam therapy with ampicillin and a third-generation cephalosporin. The mechanism of dual beta-lactam therapy relies on the saturation of penicillin-binding proteins (PBPs). Ceftobiprole exhibits high affinity binding to nearly all E. faecalis PBPs, thus suggesting its potential utility in the treatment of severe E. faecalis infections. The availability of therapeutic drug monitoring (TDM) for ampicillin and ceftobiprole has prompted the use of this drug combination in our hospital. Due to the time-dependent antimicrobial properties of these antibiotics, an infusion administration longer than indicated was chosen. From January to December 2020, twenty-one patients were admitted to our hospital for severe E. faecalis infections and were treated with this approach. We retrospectively analyzed their clinical characteristics and pharmacological data. Most patients achieved an aggressive PK/PD target (T > 4-8 minimum inhibitory concentration, MIC) when this alternative drug combination regimen was used. Our analysis included the study of E. faecalis biofilm production, as well as the kinetics of bacterial killing of ceftobiprole alone or in combination with ampicillin. Time-kill experiments revealed strong bactericidal activity of ceftobiprole alone at concentrations four times higher than the MIC for some enterococcal strains. In cases where a bactericidal effect of ceftobiprole alone was not evident, synergism with ampicillin and bactericidal activity were demonstrated instead. The prolonged infusion of ceftobiprole, either alone or with ampicillin, emerges as a valuable option for the treatment of severe invasive E. faecalis infections.

Unseen Enemy: Mechanisms of Multidrug Antimicrobial Resistance in Gram-Negative ESKAPE Pathogens

Multidrug antimicrobial resistance (AMR) represents a formidable challenge in the therapy of infectious diseases, triggered by the particularly concerning gram-negative Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. (ESKAPE) pathogens. Designated as a "priority" in 2017, these bacteria continue to pose a significant threat in 2024, particularly during the worldwide SARS-CoV-2 pandemic, where coinfections with ESKAPE members contributed to worsened patient outcomes. The declining effectiveness of current treatments against these pathogens has led to an increased disease burden and an increase in mortality rates globally. This review explores the sophisticated mechanisms driving AMR in gram-negative ESKAPE bacteria, focusing on Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter spp. Key bacterial mechanisms contributing to resistance include limitations in drug uptake, production of antibiotic-degrading enzymes, alterations in drug target sites, and enhanced drug efflux systems. Comprehending these pathways is vital for formulating innovative therapeutic strategies and tackling the ongoing threat posed by these resistant pathogens.

Bacterial and host enzymes modulate the inflammatory response produced by the peptidoglycan of the Lyme disease agent

The spirochete Borrelia burgdorferi causes Lyme disease. In some patients, an excessive, dysregulated proinflammatory immune response can develop in joints leading to persistent arthritis. In such patients, persistence of antigenic B. burgdorferi peptidoglycan (PGBb) fragments within joint tissues may contribute to the immunopathogenesis, even after appropriate antibiotic treatment. In live B. burgdorferi cells, the outer membrane shields the polymeric PGBb sacculus from exposure to the immune system. However, unlike most diderm bacteria, B. burgdorferi releases PGBb turnover products into its environment due to the absence of recycling activity. In this study, we identified the released PGBb fragments using a mass spectrometry-based approach. By characterizing the l,d-carboxypeptidase activity of B. burgdorferi protein BB0605 (renamed DacA), we found that PGBb turnover largely occurs at sites of PGBb synthesis. In parallel, we demonstrated that the lytic transglycosylase activity associated with BB0259 (renamed MltS) releases PGBb fragments with 1,6-anhydro bond on their N-acetylmuramyl residues. Stimulation of human cell lines with various synthetic PGBb fragments revealed that 1,6-anhydromuramyl-containing PGBb fragments are poor inducers of a NOD2-dependent immune response relative to their hydrated counterparts. We also showed that the activity of the human N-acetylmuramyl-l-alanine amidase PGLYRP2, which reduces the immunogenicity of PGBb material, is low in joint (synovial) fluids relative to serum. Altogether, our findings suggest that MltS activity helps B. burgdorferi evade PG-based immune detection by NOD2 during growth despite shedding PGBb fragments and that PGBb-induced immunopathology likely results from host sensing of PGBb material from dead (lysed) spirochetes. Additionally, our results suggest the possibility that natural variation in PGLYRP2 activity may contribute to differences in susceptibility to PG-induced inflammation across tissues and individuals.

Response regulator protein CiaR regulates the transcription of ccn-microRNAs and β-lactam antibiotic resistance conversion of Streptococcus pneumoniae

BACKGROUND

Streptococcus pneumoniae does not produce β-lactamases, and its reduced susceptibility to β-lactam antibiotics is predominantly caused by mutations of penicillin-binding proteins (PBPs). However, mechanisms of non-PBP mutation-related β-lactam antibiotic resistance in pneumococcal strains remain poorly characterized.

METHODS

Susceptibility of S. pneumoniae ATCC49619 and its ciaR gene knockout, complemented, or overexpression mutant (ΔciaR, CΔciaR, or ciaROE) to penicillin, cefotaxime, and imipenem was detected using an E-test. Levels of pneumococcal ciaR-mRNA, 5 ccn-microRNAs, and 6 pbps-mRNAs were determined by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Recombinant CiaR (rCiaR) binding to the promoters of ccn-microRNA genes was confirmed using electrophoresis mobility shift and chromatin immunoprecipitation assays. Sequence matching between the ccn-microRNAs and pbps-mRNAs was analyzed using IntaRNA software.

RESULTS

S. pneumoniae ATCC49619 was sensitive to the 3 β-lactam antibiotics, but overexpression of CiaR, a response regulator protein in 2-component system, caused the increase of MICs against these antibiotics. The ciaROE mutant exhibited the significantly increased transcription of ccn-microRNAs but notably decreased transcription of pbps-mRNAs; conversely, the ΔciaR mutant displayed decreased levels of ccn-microRNAs and increasesed transcription of pbps-mRNAs. rCiaR was able to bind to the promoters of all ccn-microRNA genes in vitro and within cells. The 3 antibiotics at 1/8 minimal inhibitory concentrations caused a significant increase in the ciaR-mRNA and ccn-microRNAs. The mRNA-binding seed sequences in the 5 ccn-microRNAs matched all the promoter-containing sequences of pbps-mRNAs.

CONCLUSIONS

β-Lactam antibiotics at low concentrations induce non-PBP mutation-related antibiotic resistance conversion of S. pneumoniae by decrease of PBPs through the pathway of CiaR-mediated transcriptional increase of ccn-microRNAs and ccn-microRNA-dependent degradation of pbp-mRNAs.

Phytochemistry, Antibacterial and Antioxidant Activities of Grewia lasiocarpa E. Mey. Ex Harv. Fungal Endophytes: A Computational and Experimental Validation Study

The genus Grewia are well-known for their medicinal properties and are widely used in traditional remedies due to their rich phytochemical composition and potential health benefits. This study isolated and characterized five endophytic fungi from Grewia lasiocarpa E. Mey. Ex Harv. and evaluated their in vitro antibacterial and antioxidant activities. Five [Aspergillus fumigatus (MK243397.1), A. fumigatus (MK243451.1), Penicillium raistrickii (MK243492.1), P. spinulosum (MK243479.1), Meyerozyma guilliermondii (MK243634.1)] of the 22 isolated endophytic fungi had inhibitory activity (62.5-1000 µg/mL) against methicillin-resistant Staphylococcus aureus (MRSA). The antioxidant activities were 66.5% and 98.4% for 2,2-diphenyl-1-picrylhydrazyl (DPPH) and ferric ion reducing antioxidant power (FRAP), respectively. In silico evaluation of the phytochemicals of the extract (containing majorly n-hexadecanoic acid) was performed against penicillin-binding protein 2a (PBP2a) implicated in the broad clinical resistance of MRSA to conventional beta-lactams. Molecular docking and molecular dynamic simulation analyses revealed that the phytosterol constituents of the extract, especially dehydroergosterol (-46.28 kcal/mol), had good stability (4.35 Å) and compactness (35.08 Å) with PBP2a relative to the unbound PBP2a and amoxicillin-PBP2a complex during the 100 ns simulation period, reinforcing them as putative leads that may be developed as viable alternatives to beta-lactams against infections caused by MRSA. However, the prediction that dehydroergosterol lacks oral bioavailability with poor water solubility suggests that it could benefit from structural optimization for improved druggability. Hence, isolating and derivatizing dehydroergosterol for subsequent evaluation against PBP2a in vitro and in vivo is highly recommended.

Comparative genomic study of non-typeable Haemophilus influenzae in children with pneumonia and healthy controls

Non-typeable Haemophilus influenzae (NTHi) is a common pathogen causing respiratory infections, including pneumonia in children, and can also be found in the upper respiratory tracts of asymptomatic individuals. This study examines genomic variations between NTHi strains from healthy children and those from children with acute or chronic community-acquired pneumonia (CAP). Using bacterial genome-wide association studies (bGWAS), we compared these strains to identify key differences. Our analysis revealed that approximately 32% of genes exhibit variations between commensal and pathogenic states. Notably, we identified changes in peptidoglycan biosynthesis pathways and significant virulence factors associated with pneumonia. Furthermore, we observed a significant difference in β-lactam resistance due to PBP3 mutations between the healthy and pneumonia groups, confirmed by the ampicillin susceptibility test and characterized by the mutation pattern D350N, S357N, S385T, L389F. These findings contribute valuable insights into the genomic basis of NTHi pathogenicity and may inform more targeted clinical diagnostics and treatments.

Escherichia coli persisters in biofilm can perform horizontal gene transfer by transformation

Persisters represent a subset of cells that exhibit transient tolerance to antimicrobials. These persisters can withstand sudden exposure to antimicrobials, even as the majority of normal cells perish. In this study, we have demonstrated the capacity of ampicillin-tolerant and alkali-tolerant persisters to execute horizontal gene transfer via in situ transformation within biofilms. Air-solid biofilms, comprising two Escherichia coli populations each with a distinct plasmid, were formed on agar media. They were treated with lethal doses of ampicillin or NaOH for 24 h, followed by a 1-min glass-ball roll. This process led to a high frequency of horizontal plasmid transfer (10-7-10-6 per cell) from dead cells to surviving persisters within the biofilms. Plasmid transfer was DNase-sensitive and also occurred by adding purified plasmid DNA to plasmid-free biofilms, demonstrating a transformation mechanism. This marks the first evidence of persisters' novel ability for horizontal gene transfer, via transformation.

The hit-and-run of cell wall synthesis: LpoB transiently binds and activates PBP1b through a conserved allosteric switch

The peptidoglycan (PG) cell wall is the primary protective layer of bacteria, making the process of PG synthesis a key antibiotic target. Class A penicillin-binding proteins (aPBPs) are a family of conserved and ubiquitous PG synthases that fortify and repair the PG matrix. In gram-negative bacteria, these enzymes are regulated by outer-membrane tethered lipoproteins. However, the molecular mechanism by which lipoproteins coordinate the spatial recruitment and enzymatic activation of aPBPs remains unclear. Here we use single-molecule FRET and single-particle tracking in E. coli to show that a prototypical lipoprotein activator LpoB triggers site-specific PG synthesis by PBP1b through conformational rearrangements. Once synthesis is initiated, LpoB affinity for PBP1b dramatically decreases and it dissociates from the synthesizing enzyme. Our results suggest that transient allosteric coupling between PBP1b and LpoB directs PG synthesis to areas of low peptidoglycan density, while simultaneously facilitating efficient lipoprotein redistribution to other sites in need of fortification.

Advancements of paper-based sensors for antibiotic-resistant bacterial species identification

Evolution of antimicrobial-resistant bacterial species is on a rise. This review aims to explore the diverse range of paper-based platforms designed to identify antimicrobial-resistant bacterial species. It highlights the most important targets used for sensor development and examines the applications of nanosized particles used in paper-based sensors. This review also discusses the advantages, limitations, and applicability of various targets and detection techniques for sensing drug-resistant bacterial species using paper-based platforms.

kinact/KI Value Determination for Penicillin-Binding Proteins in Live Cells

Penicillin-binding proteins (PBPs) are an essential family of bacterial enzymes that are covalently inhibited by the β-lactam class of antibiotics. PBP inhibition disrupts peptidoglycan biosynthesis, which results in deficient growth and proliferation, and ultimately leads to lysis. IC50 values are often employed as descriptors of enzyme inhibition and inhibitor selectivity, but can be misleading in the study of time-dependent, covalent inhibitors. Due to this disconnect, the second-order rate constant, kinact/KI, is a more appropriate metric of covalent-inhibitor potency. Despite being the gold standard measurement of potency, kinact/KI values are typically obtained from in vitro assays, which limits assay throughput if investigating an enzyme family with multiple homologues (such as the PBPs). Therefore, we developed a whole-cell kinact/KI assay to define inhibitor potency for the PBPs in Streptococcus pneumoniae using the fluorescent, activity-based probe, Bocillin-FL. Our results align with in vitro kinact/KI data and show a comparable relationship to previously established IC50 values. These results support the validity of our in vivo kinact/KI method as a means of obtaining β-lactam potency for a suite of PBPs to enable structure-activity relationship studies.

From Biofilm to Breath: The Role of Lacticaseibacillus paracasei ET-22 Postbiotics in Combating Oral Malodor

Previous studies demonstrated that sufferers with halitosis can be significantly improved with Lacticaseibacillus paracasei ET-22 (ET-22) postbiotics intervention. The objectives of this investigation were to identify the primary components responsible for inhibiting oral malodor. This study demonstrated that cell-free supernatants (CFSs) were more effective in inhibiting production of volatile sulfur compounds (VSCs). Untargeted metabolomics identified CFSs as primarily consisting of organic acids, lipids, peptides, and nucleotides. Among the potential active components, phenyllactic acid (PLA) and peptide GP(Hyp)GAG significantly inhibited microbial-induced VSCs production, with VSC concentrations reduced by 42.7% and 44.6%, respectively. Given the correlation between biofilms and halitosis, microstructural changes in biofilms were examined. PLA suppressed the biomass of the biofilm by 41.7%, while the biofilm thickness was reduced from 202.3 to 70.0 μm. GP(Hyp)GAG intervention reduced the abundance of Fusobacterium nucleatum and Streptococcus mutans within the biofilm, and the expression of biofilm-forming genes FadA and Gtfb were also suppressed by 41.8% and 59.4%. Additionally, the VSC production capacities were reduced due to the decrease in VSC producing bacteria (F. nucleatum, Prevotella intermedia, and Solobacterium moorei) and down-regulation of Cdl and Mgl genes. Collectively, the current study proved that PLA and GP(Hyp)GAG may be the main contributors to halitosis inhibition by ET-22 postbiotics.

Penicillin binding proteins-based immunoassay for the selective and quantitative determination of beta-lactam antibiotics

An immunoassay method based on penicillin-binding protein (PBP) was developed for the quantitative determination of 10 kinds of beta-lactam antibiotics (BLAs). First, two kinds of PBPs, which are named PBP1a and PBP2x, were expressed and purified, and they were characterized by SDS-PAGE and western blotting analysis. Then, the binding activity of PBP1a and PBP2x to template BLAs, cefquinome (CEFQ) and ampicillin (AMP), was determined. The effect of the buffer solution system, e.g., pH, ion concentration, and organic solvent, on the immune interaction efficiency between PBPs and BLAs was also evaluated. In the end, the PBP-based immunoassay method was developed and validated for the detection of 10 kinds of BLAs. Under optimal conditions, PBPs exhibited high binding affinity to BLAs. In addition, this method showed a high sensitivity for the detection of 10 kinds of BLAs with the limits of detection from 0.21 to 9.12 ng/mL, which are much lower than their corresponding maximum residual limit of European Union (4-100 ng/mL). Moreover, the developed PBP-immunoassay was employed for BLA detection from milk samples, and satisfactory recoveries (68.9-101.3 %) were obtained.

Boronic acid inhibitors of penicillin-binding protein 1b: serine and lysine labelling agents

Penicillin-binding proteins (PBPs) contribute to bacterial cell wall biosynthesis and are targets of antibacterial agents. Here, we investigated PBP1b inhibition by boronic acid derivatives. Chemical starting points were identified by structure-based virtual screening and aliphatic boronic acids were selected for further investigations. Structure-activity relationship studies focusing on the branching of the boron-connecting carbon and quantum mechanical/molecular mechanical simulations showed that reaction barrier free energies are compatible with fast reversible covalent binding and small or missing reaction free energies limit the inhibitory activity of the investigated boronic acid derivatives. Therefore, covalent labelling of the lysine residue of the catalytic dyad was also investigated. Compounds with a carbonyl warhead and an appropriately positioned boronic acid moiety were shown to inhibit and covalently label PBP1b. Reversible covalent labelling of the catalytic lysine by imine formation and the stabilisation of the imine by dative N-B bond is a new strategy for PBP1b inhibition.

The fall of the mycobacterial cell wall: interrogating peptidoglycan synthesis for novel anti-TB agents

Tuberculosis (TB) caused by Mycobacterium tuberculosis has been a threat to human health for thousands of years and still leads to millions of deaths each year. TB is a disease that is refractory to treatment, partially due to its capacity for in-host persistence. The cell wall of mycobacteria, rich in mycolic acid, is broadly associated with bacterial persistence together with antimicrobial and immunological resistance. Enzymes for the biosynthesis of bacterial peptidoglycan, an essential component of the cell wall, have been addressed and considered as appealing drug targets in pathogens. Significant effort has been dedicated to finding inhibitors that hinder peptidoglycan biosynthesis, many with demonstrated enzymatic inhibition in vitro being published. One family of critical biosynthetic enzymes are the Mur enzymes, with many enzyme specific inhibitors having been reported. However, a lesser developed strategy which may have positive clinical implications is to take advantage of the common structural and catalytic characteristics among Mur enzymes and to allow simultaneous, multiple Mur inhibition, and avert the development of drug resistance. M. tuberculosis relies on these essential Mur enzymes, with the best-known subset being Mur ligases, but also utilizes unique functions of atypical transpeptidases resulting in peptidoglycan peptide cross-linking beneficial to the bacteria's capacity for chronic persistence in humans. A systematic review is now needed, with an emphasis on M. tuberculosis. The urgent development of novel anti-TB agents to counter rapidly developing drug resistance requires a revisit of the literature, past successes and failures, in an attempt to reveal liabilities in critical cellular functions and drive innovation.

PBP4 is required for serum-induced cell wall thickening and antibiotic tolerance in Staphylococcus aureus

The bacterial pathogen Staphylococcus aureus responds to the host environment by synthesizing a thick peptidoglycan cell wall, which protects the bacterium from membrane-targeting antimicrobials and the immune response. However, the proteins required for this response were previously unknown. Here, we demonstrate by three independent approaches that the penicillin-binding protein PBP4 is crucial for serum-induced cell wall thickening. First, mutants lacking various non-essential cell wall synthesis enzymes were tested, revealing that a mutant lacking pbp4 was unable to generate a thick cell wall in serum. This resulted in reduced serum-induced tolerance of the pbp4 mutant toward the last resort antibiotic daptomycin relative to wild-type cells. Second, we found that serum-induced cell wall thickening occurred in each of a panel of 134 clinical bacteremia isolates, except for one strain with a naturally occurring mutation that results in an S140R substitution in the active site of PBP4. Finally, inhibition of PBP4 with cefoxitin prevented serum-induced cell wall thickening and the resulting antibiotic tolerance in the USA300 strain and clinical MRSA isolates. Together, this provides a rationale for combining daptomycin with cefoxitin, a PBP4 inhibitor, to potentially improve treatment outcomes for patients with invasive MRSA infections.

A magnetic epitope-imprinted microsphere used for selective separation and rapid detection of SHV-type β-lactamases in bacteria: a novel strategy of antimicrobial resistance detection

BACKGROUND

The production of β-lactamases is the most prevalent resistance mechanism for β-lactam antibiotics in Gram-negative bacteria. Presently, over 4900 β-lactamases have been discovered, and they are categorized into hundreds of families. In each enzyme family, amino acid substitutions result in subtle changes to enzyme hydrolysis profiles; in contrast, certain conserved sequences retained by all of the family members can serve as important markers for enzyme family identification.

RESULTS

The SHV family was chosen as the study object. First, a unique 10-mer peptide was identified as SHV family's epitope by an approach of protein fingerprint analysis. Then, an SHV-specific magnetic epitope-imprinted gel polymer (MEI-GP) was prepared by an epitope surface imprinting technique, and its sorption behavior and recognition mechanism for template epitope and SHV were both elaborated. Finally, the MEI-GP was successfully applied to selectively extract SHV from bacteria, and the extracted SHV was submitted to MALDI-TOF MS for specific determination. By following this strategy, other β-lactamase families can also be specifically detected. According to the molecular weight displayed in mass spectra, the kind of β-lactamase and its associated hydrolysis profile on β-lactams can be easily identified. Based on this, an initial drug option scheme can be quickly formulated for antimicrobial therapy. From protein extraction to medication guidance reporting, the mean time to detection (MTTD) was less than 2 h, which is much faster than conventional phenotype-based methods (at least 16-20 h) and gene-based techniques (usually about 8 h).

CONCLUSIONS

This enzyme-specific detection strategy combined the specificity of epitope imprinting with the sensitivity of mass spectrometry, enabling β-lactamase to be selectively extracted from bacteria and clearly presented in mass spectra. Compared with other drug resistance detection methods, this technique has good specificity, high sensitivity (≤ 15 mg of bacteria), a short MTTD (less than 2 h), and simple operation, and therefore has a broad application prospect in clinical medicine.

Dual β-lactams for the treatment of Mycobacterium abscessus: a review of the evidence and a call to act against an antibiotic nightmare

Mycobacterium abscessus complex is a group of rapidly growing non-tuberculous mycobacteria (NTM), increasingly emerging as opportunistic pathogens. Current treatment options for these microorganisms are limited and associated with a high rate of treatment failure, toxicity and recurrence. In search of new therapeutic strategies, interest has grown in dual β-lactam (DBL) therapy, as research recently discovered that M. abscessus cell wall synthesis is mainly regulated by two types of enzymes (d,d-transpeptidases and l,d-transpeptidases) differently susceptible to inhibition by distinct β-lactams. In vitro studies testing several DBL combinations have shown synergy in extracellular broth cultures as well as in the intracellular setting: cefoxitin/imipenem, ceftaroline/imipenem, ceftazidime/ceftaroline and ceftazidime/imipenem. The addition of specific β-lactamase inhibitors (BLIs) targeting M. abscessus β-lactamase did not significantly enhance the activity of DBL combinations. However, in vivo data are lacking. We reviewed the literature on DBL/DBL-BLI-based therapies for M. abscessus infections to raise greater attention on this promising yet overlooked treatment option and to guide future preclinical and clinical studies.

Reassessing the substrate specificities of the major Staphylococcus aureus peptidoglycan hydrolases lysostaphin and LytM

Orchestrated action of peptidoglycan (PG) synthetases and hydrolases is vital for bacterial growth and viability. Although the function of several PG synthetases and hydrolases is well understood, the function, regulation, and mechanism of action of PG hydrolases characterised as lysostaphin-like endopeptidases have remained elusive. Many of these M23 family members can hydrolyse glycyl-glycine peptide bonds and show lytic activity against Staphylococcus aureus whose PG contains a pentaglycine bridge, but their exact substrate specificity and hydrolysed bonds are still vaguely determined. In this work, we have employed NMR spectroscopy to study both the substrate specificity and the bond cleavage of the bactericide lysostaphin and the S. aureus PG hydrolase LytM. Yet, we provide substrate-level evidence for the functional role of these enzymes. Indeed, our results show that the substrate specificities of these structurally highly homologous enzymes are similar, but unlike observed earlier both LytM and lysostaphin prefer the D-Ala-Gly cross-linked part of mature peptidoglycan. However, we show that while lysostaphin is genuinely a glycyl-glycine hydrolase, LytM can also act as a D-alanyl-glycine endopeptidase.

Staphylococcus aureus membrane vesicles: an evolving story

Staphylococcus aureus is an important bacterial pathogen that causes a wide variety of human diseases in community and hospital settings. S. aureus employs a diverse array of virulence factors, both surface-associated and secreted, to promote colonization, infection, and immune evasion. Over the past decade, a growing body of research has shown that S. aureus generates extracellular membrane vesicles (MVs) that package a variety of bacterial components, many of which are virulence factors. In this review, we summarize recent advances in our understanding of S. aureus MVs and highlight their biogenesis, cargo, and potential role in the pathogenesis of staphylococcal infections. Lastly, we present some emerging questions in the field.

Peptidoglycan Endopeptidase PBP7 Facilitates the Recruitment of FtsN to the Divisome and Promotes Peptidoglycan Synthesis in Escherichia coli

Escherichia coli has many periplasmic hydrolases to degrade and modify peptidoglycan (PG). However, the redundancy of eight PG endopeptidases makes it challenging to define specific roles to individual enzymes. Therefore, the cellular role of PBP7 (encoded by pbpG) is not clearly defined. In this work, we show that PBP7 localizes in the lateral cell envelope and at midcell. The C-terminal α-helix of PBP7 is crucial for midcell localization but not for its activity, which is dispensable for this localization. Additionally, midcell localization of PBP7 relies on the assembly of FtsZ up to FtsN in the divisome, and on the activity of PBP3. PBP7 was found to affect the assembly timing of FtsZ and FtsN in the divisome. The absence of PBP7 slows down the assembly of FtsN at midcell. The ΔpbpG mutant exhibited a weaker incorporation of the fluorescent D-amino acid HADA, reporting on transpeptidase activity, compared to wild-type cells. This could indicate reduced PG synthesis at the septum of the ΔpbpG strain, explaining the slower accumulation of FtsN and suggesting that endopeptidase-mediated PG cleavage may be a rate-limiting step for septal PG synthesis.

In-vitro antibacterial and antibiofilm activities and in-silico analysis of a potent cyclic peptide from a novel Streptomyces sp. strain RG-5 against antibiotic-resistant and biofilm-forming pathogenic bacteria

The proliferation of multidrug-resistant and biofilm-forming pathogenic bacteria poses a serious threat to public health. The limited effectiveness of current antibiotics motivates the search for new antibacterial compounds. In this study, a novel strain, RG-5, was isolated from desert soil. This strain exhibited potent antibacterial and antibiofilm properties against multidrug-resistant and biofilm-forming pathogenic bacteria. Through phenotypical characterizations, 16S rRNA gene sequence and phylogenetic analysis, the strain was identified as Streptomyces pratensis with 99.8% similarity. The active compound, RG5-1, was extracted, purified by reverse phase silica column HPLC, identified by ESI-MS spectrometry, and confirmed by 1H and 13C NMR analysis as 2,5-Piperazinedione, 3,6-bis(2-methylpropyl), belonging to cyclic peptides. This compound showed interesting minimum inhibitory concentrations (MICs) of 04 to 15 µg/mL and minimum biofilm inhibitory concentrations (MBICs 50%) of ½ MIC against the tested bacteria. Its molecular mechanism of action was elucidated through a molecular docking study against five drug-protein targets. The results demonstrated that the compound RG5-1 has a strong affinity and interaction patterns with glucosamine-6-phosphate synthase at - 6.0 kcal/mol compared to reference inhibitor (- 5.4 kcal/mol), medium with penicillin-binding protein 1a (- 6.1 kcal/mol), and LasR regulator protein of quorum sensing (- 5.4 kcal/mol), confirming its antibacterial and antibiofilm activities. The compound exhibited minimal toxicity and favorable physicochemical and pharmacological properties. This is the first report that describes its production from Streptomyces, its activities against biofilm-forming and multidrug-resistant bacteria, and its mechanism of action. These findings indicate that 2,5-piperazinedione, 3,6-bis(2-methylpropyl) has the potential to be a promising lead compound in the treatment of antibiotic-resistant and biofilm-forming pathogens.

DivIVA controls the dynamics of septum splitting and cell elongation in Streptococcus pneumoniae

Bacterial shape and division rely on the dynamics of cell wall assembly, which involves regulated synthesis and cleavage of the peptidoglycan. In ovococci, these processes are coordinated within an annular mid-cell region with nanometric dimensions. More precisely, the cross-wall synthesized by the divisome is split to generate a lateral wall, whose expansion is insured by the insertion of the so-called peripheral peptidoglycan by the elongasome. Septum cleavage and peripheral peptidoglycan synthesis are, thus, crucial remodeling events for ovococcal cell division and elongation. The structural DivIVA protein has long been known as a major regulator of these processes, but its mode of action remains unknown. Here, we integrate click chemistry-based peptidoglycan labeling, direct stochastic optical reconstruction microscopy, and in silico modeling, as well as epifluorescence and stimulated emission depletion microscopy to investigate the role of DivIVA in Streptococcus pneumoniae cell morphogenesis. Our work reveals two distinct phases of peptidoglycan remodeling during the cell cycle that are differentially controlled by DivIVA. In particular, we show that DivIVA ensures homogeneous septum cleavage and peripheral peptidoglycan synthesis around the division site and their maintenance throughout the cell cycle. Our data additionally suggest that DivIVA impacts the contribution of the elongasome and class A penicillin-binding proteins to cell elongation. We also report the position of DivIVA on either side of the septum, consistent with its known affinity for negatively curved membranes. Finally, we take the opportunity provided by these new observations to propose hypotheses for the mechanism of action of this key morphogenetic protein.IMPORTANCEThis study sheds light on fundamental processes governing bacterial growth and division, using integrated click chemistry, advanced microscopy, and computational modeling approaches. It addresses cell wall synthesis mechanisms in the opportunistic human pathogen Streptococcus pneumoniae, responsible for a range of illnesses (otitis, pneumonia, meningitis, septicemia) and for one million deaths every year worldwide. This bacterium belongs to the morphological group of ovococci, which includes many streptococcal and enterococcal pathogens. In this study, we have dissected the function of DivIVA, which is a structural protein involved in cell division, morphogenesis, and chromosome partitioning in Gram-positive bacteria. This work unveils the role of DivIVA in the orchestration of cell division and elongation along the pneumococcal cell cycle. It not only enhances our understanding of how ovoid bacteria proliferate but also offers the opportunity to consider how DivIVA might serve as a scaffold and sensor for particular membrane regions, thereby participating in various cell cycle processes.

Fully closed conformation of penicillin-binding protein revealed by structure of PBP2 from Acinetobacter baumannii

Penicillin-binding protein 2 (PBP2), a vital protein involved in bacterial cell-wall synthesis, serves a target for β-lactam antibiotics. Acinetobacter baumannii is a pathogen notorious for multidrug resistance; therefore, exploration of PBPs is pivotal in the development of new antimicrobial strategies. In this study, the tertiary structure of PBP2 from A. baumannii (abPBP2) was elucidated using X-ray crystallography. The structural analysis demonstrated notable movement in the head domain, potentially critical for its glycosyltransferase function, suggesting that abPBP2 assumes a fully closed conformation. Our findings offer valuable information for developing novel antimicrobial agents targeting abPBP2 that are applicable in combating multidrug-resistant infections.

Synthesis of designed new 1,3,4-oxadiazole functionalized pyrano [2,3-f] chromene derivatives and their antimicrobial activities

Diethyl 2-(((4-methyl-2-oxo-2H-chromen-7-yl)oxy)methylene)malonate (2) was synthesized from coumarin 1 and diethyl ethoxymethylene malonate in ethanol, followed by cyclization in diphenyl ether to give chromene-9-carboxylate (3). Sugar hydrazones 5a-c were formed by reacting hydrazide 4 with D-galactose, D-mannose, and D-xylose, then acetylated to per-O-acetyl derivatives 6a-c. Heating 5a-c with acetic anhydride at 100 °C gave oxadiazolines 7a-c. Compound 8, obtained by refluxing 4 with carbon disulfide, was alkylated to 9 or reacted to give 10. Further reactions yielded acetoxy derivative 13 and hydroxy derivative 14. Compounds 17a-e and 18a-e were synthesized using thiomorpholinophenyl ureido/thioureido-s-triazine. These compounds were characterized and evaluated for antibacterial activity against Gram (+ve) bacteria (B. subtilis, S. aureus) and Gram (-ve) bacteria (E. coli, P. aeruginosa) in addition to yeast-like fungi (C. albicans). Compounds 11, 13, 15, 16, 17c-e, and 18a-e showed the highest antibacterial activity. Molecular docking was performed to study their binding with transpeptidases.

Selection and characterization of spontaneous phage-resistant mutant of Limosilactobacillus fermentum

Phage infection remains a major cause of fermentation failures in the dairy industry. The development of phage-resistant mutants of important fermentation strains is an effective measure used to address phage-related issues. This study employed the secondary culture method to screen for spontaneous phage-resistant mutants from the phage sensitive strain Limosilactobacillus fermentum IMAU32646 (L. fermentum IMAU32646). The phenotypic characteristics, technological attributes, probiotic characterization, adsorption characteristics and mutant genes were investigated. The results showed that the mutant strain displayed a high degree of phage-resistance and stability. The mutant strain produced more lactic acid during fermentation than the sensitive strain, while maintaining identical cell structure and morphologies. The mutant strain exhibited superior tolerance to acid and bile salts compared to the sensitive strain. Furthermore, the adsorption rate of phage LFP01 on the mutant strain was significantly lower than that of the sensitive strain. Following genome re-sequencing analysis showed that adsorption interference and blocked DNA injection were responsible for its phage-resistance. These results may provide a new strategy for avoiding phage contamination and industrial application of phage-resistant strains with good characteristics.

Rapid Emergence of Resistance to Broad-Spectrum Direct Antimicrobial Activity of Avibactam

Avibactam (AVI) is a diazabicyclooctane (DBO) β-lactamase inhibitor used clinically in combination with ceftazidime. At concentrations higher than those typically achieved in vivo, it also has broad-spectrum direct antibacterial activity against Enterobacterales strains, including metallo-β-lactamase-producing isolates, mediated by inhibition of penicillin-binding protein 2 (PBP2). This activity is mechanistically similar to that of more potent novel DBOs (zidebactam, nacubactam) in late clinical development. We found that resistance to AVI emerged readily, with a mutation frequency of 2×10-6 to 8×10-5. Whole genome sequencing of resistant isolates revealed a heterogeneous mutational target that permitted bacterial survival and replication despite PBP2 inhibition, in line with prior studies of PBP2-targeting drugs. While such mutations are believed to act by upregulating the bacterial stringent response, we found a similarly high mutation frequency in bacteria deficient in components of the stringent response, although we observed a different set of mutations in these strains. Although avibactam-resistant strains had increased lag time, suggesting a fitness cost that might render them less problematic in clinical infections, there was no statistically significant difference in growth rates between susceptible and resistant strains. The finding of rapid emergence of resistance to avibactam as the result of a large mutational target has important implications for novel DBOs with potent direct antibacterial activity, which are being developed with the goal of expanding cell wall-active treatment options for multidrug-resistant gram-negative infections but may be vulnerable to treatment-emergent resistance.

Structural basis of Pseudomonas aeruginosa penicillin binding protein 3 inhibition by the siderophore-antibiotic cefiderocol

The breakthrough cephalosporin cefiderocol, approved for clinical use in 2019, has activity against many Gram-negative bacteria. The catechol group of cefiderocol enables it to efficiently enter bacterial cells via the iron/siderophore transport system thereby reducing resistance due to porin channel mutations and efflux pump upregulation. Limited information is reported regarding the binding of cefiderocol to its key proposed target, the transpeptidase penicillin binding protein 3 (PBP3). We report studies on the reaction of cefiderocol and the related cephalosporins ceftazidime and cefepime with Pseudomonas aeruginosa PBP3, including inhibition measurements, protein observed mass spectrometry, and X-ray crystallography. The three cephalosporins form analogous 3-exomethylene products with P. aeruginosa PBP3 following elimination of the C3' side chain. pIC50 and k inact/K i measurements with isolated PBP3 imply ceftazidime and cefiderocol react less efficiently than cefepime and, in particular, meropenem with P. aeruginosa PBP3. Crystal structures inform on conserved and different interactions involved in binding of the three cephalosporins and meropenem to P. aeruginosa PBP3. The results will aid development of cephalosporins with improved PBP3 inhibition properties.

Biochemical and crystallographic studies of L,D-transpeptidase 2 from Mycobacterium tuberculosis with its natural monomer substrate

The essential L,D-transpeptidase of Mycobacterium tuberculosis (LdtMt2) catalyses the formation of 3 → 3 cross-links in cell wall peptidoglycan and is a target for development of antituberculosis therapeutics. Efforts to inhibit LdtMt2 have been hampered by lack of knowledge of how it binds its substrate. To address this gap, we optimised the isolation of natural disaccharide tetrapeptide monomers from the Corynebacterium jeikeium bacterial cell wall through overproduction of the peptidoglycan sacculus. The tetrapeptides were used in binding / turnover assays and biophysical studies on LdtMt2. We determined a crystal structure of wild-type LdtMt2 reacted with its natural substrate, the tetrapeptide monomer of the peptidoglycan layer. This structure shows formation of a thioester linking the catalytic cysteine and the donor substrate, reflecting an intermediate in the transpeptidase reaction; it informs on the mode of entrance of the donor substrate into the LdtMt2 active site. The results will be useful in design of LdtMt2 inhibitors, including those based on substrate binding interactions, a strategy successfully employed for other nucleophilic cysteine enzymes.

Pbp4 provides transpeptidase activity to the FtsW-PbpB peptidoglycan synthase to drive cephalosporin resistance in Enterococcus faecalis

Enterococci exhibit intrinsic resistance to cephalosporins, mediated in part by the class B penicillin-binding protein (bPBP) Pbp4 that exhibits low reactivity toward cephalosporins and thus can continue crosslinking peptidoglycan despite exposure to cephalosporins. bPBPs partner with cognate SEDS (shape, elongation, division, and sporulation) glycosyltransferases to form the core catalytic complex of peptidoglycan synthases that synthesize peptidoglycan at discrete cellular locations, although the SEDS partner for Pbp4 is unknown. SEDS-bPBP peptidoglycan synthases of enterococci have not been studied, but some SEDS-bPBP pairs can be predicted based on sequence similarity. For example, FtsW (SEDS)-PbpB (bPBP) is predicted to form the catalytic core of the peptidoglycan synthase that functions at the division septum (the divisome). However, PbpB is readily inactivated by cephalosporins, raising the question-how could the FtsW-PbpB synthase continue functioning to enable growth in the presence of cephalosporins? In this work, we report that the FtsW-PbpB peptidoglycan synthase is required for cephalosporin resistance of Enterococcus faecalis, despite the fact that PbpB is inactivated by cephalosporins. Moreover, Pbp4 associates with the FtsW-PbpB synthase and the TPase activity of Pbp4 is required to enable growth in the presence of cephalosporins in an FtsW-PbpB-synthase-dependent manner. Overall, our results implicate a model in which Pbp4 directly interacts with the FtsW-PbpB peptidoglycan synthase to provide TPase activity during cephalosporin treatment, thereby maintaining the divisome SEDS-bPBP peptidoglycan synthase in a functional state competent to synthesize crosslinked peptidoglycan. These results suggest that two bPBPs coordinate within the FtsW-PbpB peptidoglycan synthase to drive cephalosporin resistance in E. faecalis.

An overview of sulbactam-durlobactam approval and implications in advancing therapeutics for hospital-acquired and ventilator-associated pneumonia by acinetobacter baumannii-calcoaceticus complex: A narrative review

Purpose

Infections caused by Acinetobacter baumannii, particularly those resistant to antibiotics such as carbapenem, have become a global health crisis with a significant mortality rate. Hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP) resulting from the A. baumannii-calcoaceticus (ABC) complex represent a major clinical challenge. This review aimed to understand the approval process, mechanism of action, therapeutic potential, and future implications of sulbactam-durlobactam therapy (SUL-DUR).

Methods

PubMed, Web of Science, EMBASE, Clinical trials. gov, ICTRP, and CENTRAL were searched for studies on SUL-DUR for the treatment of hospital-acquired pneumonia and ventilator-associated pneumonia. Also, World Health Organization, U.S. Food and Drug Administration, and Centers for Disease Control and Prevention websites were searched for relevant information.

Results

SUL-DUR, marketed as Xacduro, is a novel pharmaceutical combination that functions as a narrow-spectrum parenterally administered antibiotic. Sulbactam acts as a β-lactamase inhibitor, whereas durlobactam protects against degradation by A. baumannii enzymes. A phase 1 trial successfully established the safety and tolerability of SUL-DUR in patients with normal and mild renal impairment. A phase 2 trial demonstrated the safety and tolerability of SUL-DUR in a larger population with urinary tract infections. A phase 3 trial showed that SUL-DUR was non-inferior to colistin in terms of mortality in A. baumannii-related VAP, HAP, and bacteremia.

Conclusion

The combination of sulbactam and durlobactam is a promising treatment option for HAP and VAP caused by ABC complex.

Agents Targeting the Bacterial Cell Wall as Tools to Combat Gram-Positive Pathogens

The cell wall is an indispensable element of bacterial cells and a long-known target of many antibiotics. Penicillin, the first discovered beta-lactam antibiotic inhibiting the synthesis of cell walls, was successfully used to cure many bacterial infections. Unfortunately, pathogens eventually developed resistance to it. This started an arms race, and while novel beta-lactams, either natural or (semi)synthetic, were discovered, soon upon their application, bacteria were developing resistance. Currently, we are facing the threat of losing the race since more and more multidrug-resistant (MDR) pathogens are emerging. Therefore, there is an urgent need for developing novel approaches to combat MDR bacteria. The cell wall is a reasonable candidate for a target as it differentiates not only bacterial and human cells but also has a specific composition unique to various groups of bacteria. This ensures the safety and specificity of novel antibacterial agents that target this structure. Due to the shortage of low-molecular-weight candidates for novel antibiotics, attention was focused on peptides and proteins that possess antibacterial activity. Here, we describe proteinaceous agents of various origins that target bacterial cell wall, including bacteriocins and phage and bacterial lysins, as alternatives to classic antibiotic candidates for antimicrobial drugs. Moreover, advancements in protein chemistry and engineering currently allow for the production of stable, specific, and effective drugs. Finally, we introduce the concept of selective targeting of dangerous pathogens, exemplified by staphylococci, by agents specifically disrupting their cell walls.

Approachable Synthetic Methodologies for Second-Generation β-Lactamase Inhibitors: A Review

Some antibiotics that are frequently employed are β-lactams. In light of the hydrolytic process of β-lactamase, found in Gram-negative bacteria, inhibitors of β-lactamase (BLIs) have been produced. Examples of first-generation β-lactamase inhibitors include sulbactam, clavulanic acid, and tazobactam. Many kinds of bacteria immune to inhibitors have appeared, and none cover all the β-lactamase classes. Various methods have been utilized to develop second-generation β-lactamase inhibitors possessing new structures and facilitate the formation of diazabicyclooctane (DBO), cyclic boronate, metallo-, and dual-nature β-lactamase inhibitors. This review describes numerous promising second-generation β-lactamase inhibitors, including vaborbactam, avibactam, and cyclic boronate serine-β-lactamase inhibitors. Furthermore, it covers developments and methods for synthesizing MβL (metallo-β-lactamase inhibitors), which are clinically effective, as well as the various dual-nature-based inhibitors of β-lactamases that have been developed. Several combinations are still only used in preclinical or clinical research, although only a few are currently used in clinics. This review comprises materials on the research progress of BLIs over the last five years. It highlights the ongoing need to produce new and unique BLIs to counter the appearance of multidrug-resistant bacteria. At present, second-generation BLIs represent an efficient and successful strategy.

Identification of a family of peptidoglycan transpeptidases reveals that Clostridioides difficile requires noncanonical cross-links for viability

Most bacteria are surrounded by a cell wall that contains peptidoglycan (PG), a large polymer composed of glycan strands held together by short peptide cross-links. There are two major types of cross-links, termed 4-3 and 3-3 based on the amino acids involved. 4-3 cross-links are created by penicillin-binding proteins, while 3-3 cross-links are created by L,D-transpeptidases (LDTs). In most bacteria, the predominant mode of cross-linking is 4-3, and these cross-links are essential for viability, while 3-3 cross-links comprise only a minor fraction and are not essential. However, in the opportunistic intestinal pathogen Clostridioides difficile, about 70% of the cross-links are 3-3. We show here that 3-3 cross-links and LDTs are essential for viability in C. difficile. We also show that C. difficile has five LDTs, three with a YkuD catalytic domain as in all previously known LDTs and two with a VanW catalytic domain, whose function was until now unknown. The five LDTs exhibit extensive functional redundancy. VanW domain proteins are found in many gram-positive bacteria but scarce in other lineages. We tested seven non-C. difficile VanW domain proteins and confirmed LDT activity in three cases. In summary, our findings uncover a previously unrecognized family of PG cross-linking enzymes, assign a catalytic function to VanW domains, and demonstrate that 3-3 cross-linking is essential for viability in C. difficile, the first time this has been shown in any bacterial species. The essentiality of LDTs in C. difficile makes them potential targets for antibiotics that kill C. difficile selectively.

A Hunt for the Resistance of Haemophilus influnezae to Beta-Lactams

Infections due to Haemophilus influnezae require prompt treatment using beta-lactam antibiotics. We used a collection of 81 isolates obtained between 1940 and 2001 from several countries. Whole genome sequencing showed the high heterogeneity of these isolates but allowed us to track the acquisition of beta-lactamase, which was first detected in 1980. Modifications of the ftsI gene encoding the penicillin-binding protein 3, PBP3, also involved in resistance to beta-lactams, appeared in 1991. These modifications (G490E, A502V, R517H, and N526K) were associated with resistance to amoxicillin that was not relieved by a beta-lactamase inhibitor (clavulanic acid), but the isolates retained susceptibility to third-generation cephalosporins (3GC). The modeling of the PBP3 structure suggested that these modifications may reduce the accessibility to the PBP3 active site. Other modifications appeared in 1998 and were associated with resistance to 3GC (S357N, M377I, S385T, and L389F). Modeling of the PBP3 structure suggested that they lie near the S379xN motif of the active site of PBP3. Overall resistance to amoxicillin was detected among 25 isolates (30.8%) of this collection. Resistance to sulfonamides was predicted by a genomic approach from the sequences of the folP gene (encoding the dihydropteroate synthase) due to difficulties in interpreting phenotypic anti-microbial testing and found in 13 isolates (16.0%). Our data suggest a slower spread of resistance to sulfonamides, which may be used for the treatment of H. influnezae infections. Genomic analysis may help in the prediction of antibiotic resistance, inform structure-function analysis, and guide the optimal use of antibiotics.

Antibacterial characteristics and mechanistic insights of combined tea polyphenols, Nisin, and epsilon-polylysine against feline oral pathogens: a comprehensive transcriptomic and metabolomic analysis

AIMS

This study evaluates the antibacterial characteristics and mechanisms of combined tea polyphenols (TPs), Nisin, and ε-polylysine (PL) against Streptococcus canis, Streptococcus minor, Streptococcus mutans, and Actinomyces oris, common zoonotic pathogens in companion animals.

METHODS AND RESULTS

Pathogenic strains were isolated from feline oral cavities and assessed using minimum inhibitory concentration (MIC) tests, inhibition zone assays, growth kinetics, and biofilm inhibition studies. Among single agents, PL exhibited the lowest MIC values against all four pathogens. TP showed significant resistance against S. minor, and Nisin against S. mutans. The combination treatment (Comb) of TP, Nisin, and PL in a ratio of 13:5:1 demonstrated broad-spectrum antibacterial activity, maintaining low MIC values, forming large inhibition zones, prolonging the bacterial lag phase, reducing growth rates, and inhibiting biofilm formation. RNA sequencing and metabolomic analysis indicated that TP, Nisin, and PL inhibited various membrane-bound carbohydrate-specific transferases through the phosphoenolpyruvate-dependent phosphotransferase system in S. canis, disrupting carbohydrate uptake. They also downregulated glycolysis and the citric acid cycle, inhibiting cellular energy metabolism. Additionally, they modulated the activities of peptidoglycan glycosyltransferases and d-alanyl-d-alanine carboxypeptidase, interfering with peptidoglycan cross-linking and bacterial cell wall stability.

CONCLUSIONS

The Comb therapy significantly enhances antibacterial efficacy by targeting multiple bacterial pathways, offering potential applications in food and pharmaceutical antimicrobials.

An engineered prodrug selectively suppresses β-lactam resistant bacteria in a mixed microbial setting

The rise of β-lactam resistance necessitates new strategies to combat bacterial infections. We purposefully engineered the β-lactam prodrug AcephPT to exploit β-lactamase activity to selectively suppress resistant bacteria producing extended-spectrum-β-lactamases (ESBLs). Selective targeting of resistant bacteria requires avoiding interaction with penicillin-binding proteins, the conventional targets of β-lactam antibiotics, while maintaining recognition by ESBLs to activate AcephPT only in resistant cells. Computational approaches provide a rationale for structural modifications to the prodrug to achieve this biased activity. We show AcephPT selectively suppresses gram-negative ESBL-producing bacteria in clonal populations and in mixed microbial cultures, with effective selectivity for both lab strains and clinical isolates expressing ESBLs. Time-course NMR experiments confirm hydrolytic activation of AcephPT exclusively by ESBL-producing bacteria. In mixed microbial cultures, AcephPT suppresses proliferation of ESBL-producing strains while sustaining growth of β-lactamase-non-producing bacteria, highlighting its potential to combat β-lactam resistance while promoting antimicrobial stewardship.