Antibacterial activity of nonantibiotics is orthogonal to standard antibiotics.

Numerous nonantibiotic drugs have potent antibacterial activity and can adversely affect the human microbiome. The mechanistic underpinning of this toxicity remains largely unknown. We investigated the antibacterial activity of 200 drugs using genetic screens with thousands of barcoded Escherichia coli knockouts. We analyzed 2 million gene-drug interactions underlying drug-specific toxicity. Network-based analysis of drug-drug similarities revealed that antibiotics clustered into modules that are consistent with the mode of action of their established classes, whereas nonantibiotics remained unconnected. Half of the nonantibiotics clustered into separate modules, potentially revealing shared and unexploited targets for new antimicrobials. Analysis of efflux systems revealed that they widely affect antibiotics and nonantibiotics alike, suggesting that the impact of nonantibiotics on antibiotic cross-resistance should be investigated closely in vivo.

An antibiotic preorganized for ribosomal binding overcomes antimicrobial resistance.

We report the design conception, chemical synthesis, and microbiological evaluation of the bridged macrobicyclic antibiotic cresomycin (CRM), which overcomes evolutionarily diverse forms of antimicrobial resistance that render modern antibiotics ineffective. CRM exhibits in vitro and in vivo efficacy against both Gram-positive and Gram-negative bacteria, including multidrug-resistant strains of Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. We show that CRM is highly preorganized for ribosomal binding by determining its density functional theory-calculated, solution-state, solid-state, and (wild-type) ribosome-bound structures, which all align identically within the macrobicyclic subunits. Lastly, we report two additional x-ray crystal structures of CRM in complex with bacterial ribosomes separately modified by the ribosomal RNA methylases, chloramphenicol-florfenicol resistance (Cfr) and erythromycin-resistance ribosomal RNA methylase (Erm), revealing concessive adjustments by the target and antibiotic that permit CRM to maintain binding where other antibiotics fail.

Establishing a synthetic orthogonal replication system enables accelerated evolution in E. coli.

The evolution of new function in living organisms is slow and fundamentally limited by their critical mutation rate. Here, we established a stable orthogonal replication system in Escherichia coli. The orthogonal replicon can carry diverse cargos of at least 16.5 kilobases and is not copied by host polymerases but is selectively copied by an orthogonal DNA polymerase (O-DNAP), which does not copy the genome. We designed mutant O-DNAPs that selectively increase the mutation rate of the orthogonal replicon by two to four orders of magnitude. We demonstrate the utility of our system for accelerated continuous evolution by evolving a 150-fold increase in resistance to tigecycline in 12 days. And, starting from a GFP variant, we evolved a 1000-fold increase in cellular fluorescence in 5 days.

Elimination of blaKPC-2-mediated carbapenem resistance in Escherichia coli by CRISPR-Cas9 system.

OBJECTIVE: The purpose of this study is to re-sensitive bacteria to carbapenemases and reduce the transmission of the blaKPC-2 gene by curing the blaKPC-2-harboring plasmid of carbapenem-resistant using the CRISPR-Cas9 system. METHODS: The single guide RNA (sgRNA) specifically targeted to the blaKPC-2 gene was designed and cloned into plasmid pCas9. The recombinant plasmid pCas9-sgRNA(blaKPC-2) was transformed into Escherichia coli (E.coli) carrying pET24-blaKPC-2. The elimination efficiency in strains was evaluated by polymerase chain reaction (PCR) and quantitative real-time PCR (qPCR). Susceptibility testing was performed by broth microdilution assay and by E-test strips (bioMérieux, France) to detect changes in bacterial drug resistance phenotype after drug resistance plasmid clearance. RESULTS: In the present study, we constructed a specific prokaryotic CRISPR-Cas9 system plasmid targeting cleavage of the blaKPC-2 gene. PCR and qPCR results indicated that prokaryotic CRISPR-Cas9 plasmid transforming drug-resistant bacteria can efficiently clear blaKPC-2-harboring plasmids. In addition, the drug susceptibility test results showed that the bacterial resistance to imipenem was significantly reduced and allowed the resistant model bacteria to restore susceptibility to antibiotics after the blaKPC-2-containing drug-resistant plasmid was specifically cleaved by the CRISPR-Cas system. CONCLUSION: In conclusion, our study demonstrated that the one plasmid-mediated CRISPR-Cas9 system can be used as a novel tool to remove resistance plasmids and re-sensitize the recipient bacteria to antibiotics. This strategy provided a great potential to counteract the ever-worsening spread of the blaKPC-2 gene among bacterial pathogens and laid the foundation for subsequent research using the CRISPR-Cas9 system as adjuvant antibiotic therapy.

High-resolution landscape of an antibiotic binding site.

Antibiotic binding sites are located in important domains of essential enzymes and have been extensively studied in the context of resistance mutations; however, their study is limited by positive selection. Using multiplex genome engineering1 to overcome this constraint, we generate and characterize a collection of 760 single-residue mutants encompassing the entire rifampicin binding site of Escherichia coli RNA polymerase (RNAP). By genetically mapping drug-enzyme interactions, we identify an alpha helix where mutations considerably enhance or disrupt rifampicin binding. We find mutations in this region that prolong antibiotic binding, converting rifampicin from a bacteriostatic to bactericidal drug by inducing lethal DNA breaks. The latter are replication dependent, indicating that rifampicin kills by causing detrimental transcription-replication conflicts at promoters. We also identify additional binding site mutations that greatly increase the speed of RNAP.Fast RNAP depletes the cell of nucleotides, alters cell sensitivity to different antibiotics and provides a cold growth advantage. Finally, by mapping natural rpoB sequence diversity, we discover that functional rifampicin binding site mutations that alter RNAP properties or confer drug resistance occur frequently in nature.

Self-Enhanced Antibacterial and Antifouling Behavior of Three-Dimensional Porous Cu2O Nanoparticles Functionalized by an Organic-Inorganic Hybrid Matrix.

Cu2O is currently an important protective material for domestic engineering and equipment used to exploit marine resources. Cu+ is considered to have more effective antibacterial and antifouling activities than Cu2+. However, disproportionation of Cu+ in the natural environment leads to its reduced bioavailability and weakened reactivity. Novel and functionalized Cu2O composites could enable efficient and environmentally friendly applications of Cu+. To this end, a series of three-dimensional porous Cu2O nanoparticles (3DNP-Cu2O) functionalized by organic (redox gel, R-Gel)-inorganic (reduced graphene oxide, rGO) hybrids─3DNP-Cu2O/rGOx@R-Gel─at room temperature by immobilization-reduction method was prepared and applied for protection against marine biofouling. 3DNP-Cu2O/rGO1.76@R-Gel includes rGO and R-Gel shape 3D porous Cu2O nanoparticles with diameters ∼177 nm and strong dispersion and antioxidant stability. Compared with commercial Cu2O (Cu2O-0), 3DNP-Cu2O/rGO1.76@R-Gel exhibited an ∼50% higher bactericidal rate, ∼96.22% higher water content, and ∼75% lower adhesion of mussels and barnacles. Moreover, 3DNP-Cu2O/rGOx@R-Gel maintains the same excellent, stable, and long-lasting bactericidal performance as Cu2O-0@R-Gel while reducing the average copper ion release concentration by ∼56 to 76%. This was also confirmed by X-ray diffraction, X-ray photoelectric spectroscopy (XPS), atomic absorption spectroscopy, and antifouling tests. In addition, XPS tests of rGO-Cu2+ and R-Gel-Cu2+, photocurrent tests of 3DNP-Cu2O/rGO1.76@R-Gel, and energy-dispersive spectrometry pictures of bacteria confirm that R-Gel and rGO act as electron donors and transfer substrates driving the reduction of Cu2+ (Cu2+ → Cu+) and the diffusion of Cu+. Thus, a self-growing antibacterial and antifouling system of 3DNP-Cu2O/rGO1.76@R-Gel was achieved. The mechanism of accelerated bacterial inactivation and resistance to mussel and barnacle adhesion by 3DNP-Cu2O/rGO1.76@R-Gel was interpreted. It is shown that rGO and R-Gel are important players in the antibacterial and antifouling system of 3DNP-Cu2O/rGO1.76@R-Gel.

Multifunctional nanofibrous mats: toward antibacterial and anti-inflammatory applications, and visual bacterial diagnosis.

In most circumstances, wounds face the challenges of bacterial invasions and inappropriate inflammatory responses when they lack proper wound management. Endowing dressings with both antibacterial and anti-inflammatory functions is a compelling strategy for resolving the above issues. However, seizing the right moment to change the dressings and providing satisfactory management of wounds are still urgently required. Herein, an antibacterial and anti-inflammatory nanofibrous mat is proposed by encapsulating antibiotic gentamicin sulfate (GS) and anti-inflammatory drug ibuprofen (IB) into nanofibers via a coaxial electrospinning technique and is further decorated with Prussian blue nanocrystals (PBNCs) to enhance anti-inflammatory activity and, more importantly, to monitor bacterial infections and guide dressing changes in a timely manner. Such a nanofibrous mat releases most of the therapeutic drugs within 120 min and reveals excellent antibacterial activity and anti-inflammatory ability. Specifically, it can destroy both Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli), as well as conspicuously reduce the production of reactive oxygen species (ROS) and the expression of pro-inflammatory cytokines in macrophages. In addition, the nanofibrous mat can be used for point-of-use diagnosis of living bacteria relying on the naked eye or color analysis, which exhibits the potential of monitoring wound infection and guiding dressing changes promptly. This finding demonstrates the theranostic applications of multifunctional nanofibrous mats in wound healing.

Extended-spectrum ß-lactamase-producing E. coli from retail meat and workers: genetic diversity, virulotyping, pathotyping and the antimicrobial effect of silver nanoparticles.

BACKGROUND: The spread of extended-spectrum ß-lactamases (ESBL) producing E. coli from food animals and the environment to humans has become a significant public health concern. The objectives of this study were to determine the occurrence, pathotypes, virulotypes, genotypes, and antimicrobial resistance patterns of ESBL-producing E. coli in retail meat samples and workers in retail meat shops in Egypt and to evaluate the bactericidal efficacy of silver nanoparticles (AgNPs-H2O2) against multidrug resistant (MDR) ESBL-producing E. coli. RESULTS: A total of 250 retail meat samples and 100 human worker samples (hand swabs and stool) were examined for the presence of ESBL- producing E. coli. Duck meat and workers' hand swabs were the highest proportion of ESBL- producing E. coli isolates (81.1%), followed by camel meat (61.5%). Pathotyping revealed that the isolates belonged to groups A and B1. Virulotyping showed that the most prevalent virulence gene was Shiga toxin 2 (stx2) associated gene (36.9%), while none of the isolates harbored stx1 gene. Genotyping of the identified isolates from human and meat sources by REP-PCR showed 100% similarity within the same cluster between human and meat isolates. All isolates were classified as MDR with an average multiple antibiotic resistance (MAR) index of 0.7. AgNPs-H2O2 at concentrations of 0.625, 1.25, 2.5 and 5 µg/mL showed complete bacterial growth inhibition. CONCLUSIONS: Virulent MDR ESBL-producing E. coli were identified in retail meat products in Egypt, posing significant public health threats. Regular monitoring of ESBL-producing E. coli frequency and antimicrobial resistance profile in retail meat products is crucial to enhance their safety. AgNPs-H2O2 is a promising alternative for treating MDR ESBL-producing E. coli infections and reducing antimicrobial resistance risks.

DNA binding peptide CF-14 enhances bactericidal efficacy of eugenol/carvacrol nanoparticles to Escherichia coli.

To evaluate the bactericidal action of antimicrobial peptide CF-14, Eugenol (EU) and carvacrol (CAR) nanoparticles (NPs) less than 200 nm were surface-modified with CF14, gaining approximately 200 nm of EU-CF and CAR-CF NPs with swollen morphology. EU-CF and CAR-CF NPs were bactericidal to E. coli at dosage of 0.09% and 0.07% (v/v), respectively; while they were just bacteriostatic to Staphylococcus aureus at 0.10% and 0.08% (v/v). Spectral variations in bacterial carbohydrates (1185-900 cm-1), lipids (3000-2800 cm-1) and DNA (1500-1185 cm-1) were obvious as evident from Fourier transform infrared spectroscopy (FTIR). A higher percentage of membrane damaged (non-revivable) E. coli than S. aureus was found, which indicated electrostatic interactions between Gram-negative E. coli with cationic CF conjugated NPs leading to DNA disintegration. Interestingly, EU-CF and CAR-CF NPs inhibited E. coli growth in orange juice without impacting flavour compounds.

Flexible Curcumin-Loaded Zn-MOF Hydrogel for Long-Term Drug Release and Antibacterial Activities.

Management of chronic inflammation and wounds has always been a key issue in the pharmaceutical and healthcare sectors. Curcumin (CCM) is an active ingredient extracted from turmeric rhizomes with antioxidant, anti-inflammatory, and antibacterial activities, thus showing significant effectiveness toward wound healing. However, its shortcomings, such as poor water solubility, poor chemical stability, and fast metabolic rate, limit its bioavailability and long-term use. In this context, hydrogels appear to be a versatile matrix for carrying and stabilizing drugs due to their biomimetic structure, soft porous microarchitecture, and favorable biomechanical properties. The drug loading/releasing efficiencies can also be controlled via using highly crystalline and porous metal-organic frameworks (MOFs). Herein, a flexible hydrogel composed of a sodium alginate (SA) matrix and CCM-loaded MOFs was constructed for long-term drug release and antibacterial activity. The morphology and physicochemical properties of composite hydrogels were analyzed by scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), ultraviolet-visible spectroscopy (UV-Vis), Raman spectroscopy, and mechanical property tests. The results showed that the composite hydrogel was highly twistable and bendable to comply with human skin mechanically. The as-prepared hydrogel could capture efficient CCM for slow drug release and effectively kill bacteria. Therefore, such composite hydrogel is expected to provide a new management system for chronic wound dressings.

Do Pathogenic Escherichia coli Isolated from Gallus gallus in South Africa Carry Co-Resistance Toward Colistin and Carbapenem Antimicrobials?

Colistin and carbapenems are critically important antimicrobials often used as a last resort to manage multidrug-resistant bacterial infections in humans. With limited alternatives, resistance to these antimicrobials is of concern as organisms could potentially spread horizontally rendering treatments ineffective. The aim of this study was to investigate co-resistance to colistin and carbapenems among Escherichia coli isolated from poultry in South Africa. Forty-six E. coli strains obtained from clinical cases of breeder and broiler chickens were used. In addition to other antibiotics, all the isolates were tested against colistin and carbapenems using broth microdilution. Multiplex polymerase chain reactions were used to investigate the presence of colistin (mcr-1 to 5) and carbapenem (blaOXA-48, blaNDM-1, and blaVIM) resistance genes. Isolates exhibiting colistin resistance (>2 µg/mL) underwent a whole-genome sequencing analysis. Resistance to colistin (10.9%) and cefepime (6.5%) was noted with all colistin-resistant strains harboring the mcr-1 gene. None of the E. coli isolates were resistant to carbapenems nor carried the other resistant genes (mcr-2 to 5, blaOXA-48, blaNDM-1, and blaVIM). The mcr-1-positive strains belonged to sequence types ST117 and ST156 and carried virulence genes ompA, aslA, fdeC, fimH, iroN, iutA, tsh, pic, ast A and set 1A/1B. In conclusion, clinical E. coli strains from chickens in this study possessed mobile resistance genes for colistin and several other clinically relevant antimicrobials but not carbapenems. Additionally, they belonged to sequence types in addition to carrying virulence factors often associated with human extraintestinal pathogenic E. coli infections. Thus, the potential risk of transmitting these strains to humans cannot be underestimated especially if sick birds are dispatched into the thriving poorly regulated Cornish hen industry. The need for routine veterinary surveillance and monitoring of antimicrobial resistance, antimicrobial use and the importance of strengthening regulations guiding the informal poultry sector remains important.

Protective effect of plantaricin bio-LP1 bacteriocin on multidrug-resistance Escherichia Coli infection by alleviate the inflammation and modulate of gut-microbiota in BALB/c mice model.

The rapid spread of multidrug-resistant pathogens with the low efficacy of common antibiotics for humans and animals in its clinical therapeutics are a global health concern. Therefore, there is a need to develop new treatment strategies to control them clinically. The study aimed to evaluate the effects of Plantaricin Bio-LP1 bacteriocin produced from Lactiplantibacillus plantarum NWAFU-BIO-BS29 to alleviate the inflammation caused by multidrug-resistance Escherichia Coli (MDR-E. coli) infection in BALB/c mice-model. The focus was given on aspects linked to the mechanism of the immune response. Results indicated that Bio-LP1 had highly promising effects on partially ameliorating MDR-E. coli infection by reducing the inflammatory response through inhibiting the overexpression of proinflammatory-cytokines such as secretion of tumor necrosis factor (TNF-α) and interleukin (IL-6 and IL-ß) and strongly regulated theTLR4 signaling-pathway. Additionally, avoided the villous destruct, colon length shortening, loss of intestinal barrier integrity, and increased disease activity index. Furthermore, significantly increased the relative abundance of beneficial-intestinal-bacteria including Ligilactobacillus, Enterorhabdus, Pervotellaceae, etc. Finally, improved the intestinal mucosal barrier to alleviate the pathological damages and promote the production of short-chain fatty acids (SCFAs) a source of energy for the proliferation. In conclusion, plantaricin Bio-LP1 bacteriocin can be considered a safe alternative to antibiotics against MDR-E. coli-induced intestinal inflammation.

Monomer and Oligomer Transition of Zinc Phthalocyanine Is Key for Photobleaching in Photodynamic Therapy.

Photodynamic therapy (PDT) is recognized as a powerful method to inactivate cells. However, the photosensitizer (PS), a key component of PDT, has suffered from undesired photobleaching. Photobleaching reduces reactive oxygen species (ROS) yields, leading to the compromise of and even the loss of the photodynamic effect of the PS. Therefore, much effort has been devoted to minimizing photobleaching in order to ensure that there is no loss of photodynamic efficacy. Here, we report that a type of PS aggregate showed neither photobleaching nor photodynamic action. Upon direct contact with bacteria, the PS aggregate was found to fall apart into PS monomers and thus possessed photodynamic inactivation against bacteria. Interestingly, the disassembly of the bound PS aggregate in the presence of bacteria was intensified by illumination, generating more PS monomers and leading to an enhanced antibacterial photodynamic effect. This demonstrated that on a bacterial surface, the PS aggregate photo-inactivated bacteria via PS monomer during irradiation, where the photodynamic efficiency was retained without photobleaching. Further mechanistic studies showed that PS monomers disrupted bacterial membranes and affected the expression of genes related to cell wall synthesis, bacterial membrane integrity, and oxidative stress. The results obtained here are applicable to other types of PSs in PDT.

"Three-in-one" platform based on Fe-CDs nanozyme for dual-mode/dual-target detection and NIR-assisted bacterial killing.

As nanozymes, carbon dots (CDs) have attracted increasing attention due to their remarkable properties. Besides general enzyme activity, their photoluminescence and photothermal properties have been explored rarely, whereas their synergistic effects might produce CDs-based nanozymes of high performance. Here, iron-doped CDs (Fe-CDs) with tunable fluorescence and enhanced peroxidase-like activity were designed to develop a novel "three-in-one" multifunctional platform to provide dual-mode/dual-target detection and near infrared (NIR)-assisted antibacterial ability. This proposed strategy for a H2O2 test exhibited a wide linear relationship with a low limit of detection (LOD) of 0.16 µM (colorimetric) and 0.14 µM (ratiometric fluorescent). Furthermore, due to the nature of cholesterol being oxidized to H2O2 by cholesterol oxidase, sensitive and selective detection of cholesterol was realized, and the LOD was 0.42 µM (colorimetric) and 0.27 µM (ratiometric fluorescent), surpassing that reported previously. This result suggested that Fe-CDs could be used for dual-mode quantification of large family of H2O2-producing metabolites, thereby paving the way for developing multi-mode sensing strategies based on nanozymes. Moreover, this platform showed synergistic effects for antibacterial application, indicating great prospects for bacterial killing as well as wound disinfection and healing. Hence, this platform could contribute to the construction of multifunctional CDs with high performance.

Impact on S. aureus and E. coli Membranes of Treatment with Chlorhexidine and Alcohol Solutions: Insights from Molecular Simulations and Nuclear Magnetic Resonance.

Membranes form the first line of defence of bacteria against potentially harmful molecules in the surrounding environment. Understanding the protective properties of these membranes represents an important step towards development of targeted anti-bacterial agents such as sanitizers. Use of propanol, isopropanol and chlorhexidine can significantly decrease the threat imposed by bacteria in the face of growing anti-bacterial resistance via mechanisms that include membrane disruption. Here we have employed molecular dynamics simulations and nuclear magnetic resonance to explore the impact of chlorhexidine and alcohol on the S. aureus cell membrane, as well as the E. coli inner and outer membranes. We identify how sanitizer components partition into these bacterial membranes, and show that chlorhexidine is instrumental in this process.

Sequence-targeted Peptides Divert Functional Bacterial Amyloid Towards Destabilized Aggregates and Reduce Biofilm Formation.

Functional bacterial amyloid provides structural stability in biofilm, making it a promising target for anti-biofilm therapeutics. Fibrils formed by CsgA, the major amyloid component in E. coli are extremely robust and can withstand very harsh conditions. Like other functional amyloids, CsgA contains relatively short aggregation-prone regions (APR) which drive amyloid formation. Here, we demonstrate the use of aggregation-modulating peptides to knock down CsgA protein into aggregates with low stability and altered morphology. Remarkably, these CsgA-peptides also modulate fibrillation of the unrelated functional amyloid protein FapC from Pseudomonas, possibly through recognition of FapC segments with structural and sequence similarity with CsgA. The peptides also reduce the level of biofilm formation in E. coli and P. aeruginosa, demonstrating the potential for selective amyloid targeting to combat bacterial biofilm.

Nutrients mediate caffeine inhibition of Escherichia coli.

The consumption of coffee and other caffeinated drinks is increasingly popular across the globe. In the United States, 90% of adults consume at least one caffeinated beverage a day. While caffeine consumption of up to 400 mg/d is not generally associated with negative effects on human health, the impact of caffeine on the gut microbiome and individual gut microbiota remains unclear. We examined the effect of caffeine on the growth rate of Escherichia coli, a bacterium commonly found in the human gut, when grown aerobically or anaerobically in nutrient-rich or minimal medium. A significant negative correlation was observed between caffeine concentration and growth rate under all conditions, suggesting that caffeine can act as an antimicrobial agent when ingested. Caffeine reduced growth rates significantly more in nutrient-poor, but not in anoxic, conditions. Given the highly variable nutrient and oxygen conditions of the gut, these results suggest a need to further explore caffeine's inhibitory effects on the gut microbiome and its relation to human health.

Evolution of Antibiotic Resistance in Escherichia coli and Klebsiella pneumoniae from Urine Cultures

Objective: Determine the evolution of antibiotic resistance of symptomatic bacteriuria caused by Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) in Granada. Material and Method: A descriptive retrospective study was carried out, including antibiograms of urine cultures in which microorganisms identified as E. coli and K. pneumoniae, were isolated in the Microbiology laboratory of the Hospital Universitario Virgen de las Nieves (Granada, Spain) between January 2016 and June 2021. Results: E. coli was the most frequent isolate (10,048) and its resistance to ampicillin (59.45%) and ticarcillin (59.59%), and the increase to cefepime (15.07%) and amoxicillin-clavulanic acid (17.67%) is noteworthy. K. pneumoniae (2222) is notable for resistance to Fosfomycin (27.91%) and an increase to ciprofloxacin (37.79%) and amoxicillin-clavulanic acid (36.63%). Resistance is generally higher in hospitalized patients, males, and adults. Conclusions: Antibiotic resistance to the studied Enterobacteriaceae is on the rise, requiring empirical treatment targeted to the population area (AU)