Biological and genomic characteristics of three novel bacteriophages and a phage-plasmid of Klebsiella pneumoniae.

Bacteriophages have emerged as promising candidates for the treatment of difficult-to-treat bacterial infections. The aim of this study is to isolate and characterize phages infecting carbapenem-resistant and extended-spectrum beta-lactamase producer Klebsiella pneumoniae isolates. Water samples were taken for the isolation of bacteriophages. One-step growth curve, the optimal multiplicity of infection (MOI), thermal and pH stabilities, transmission electron microscopy and whole-genome sequencing of phages were studied. Four phages were isolated and named Klebsiella phage Kpn02, Kpn17, Kpn74, and Kpn13. The optimal MOI and latent periods of phage Kpn02, Kpn17, Kpn74, and Kpn13 were 10, 1, 0.001, and 100 PFU/CFU and 20, 10, 20, and 30 min, respectively. Burst sizes ranged from 811 to 2363. No known antibiotic resistance and virulence genes were identified. No tRNAs were detected except Klebsiella phage Kpn02 which encodes 24 tRNAs. Interestingly, Klebsiella phage Kpn74 was predicted to be a lysogenic phage whose prophage is a linear plasmid molecule with covalently closed ends. Of the Klebsiella-infecting phages presented in current study, virulent phages suggest that they may represent candidate therapeutic agents against MDR K. pneumoniae, based on short latent period, high burst sizes and no known antibiotic resistance and virulence genes in their genomes.

An outbreak analysis of wound infection due to Acinetobacter baumannii in earthquake-trauma patients.

BACKGROUND: Multidrug-resistant Acinetobacter baumannii is still a major contributor to outbreaks and infections health care-associated infections. This study aimed to investigate an outbreak of wound infection due to A baumannii in trauma patients injured in the Kahramanmaras earthquake. METHODS: This retrospective case-control study was conducted on an outbreak of wound infection caused by A. baumannii in trauma patients affected by the February 6 Turkey earthquake. Among the patients who underwent at least one extremity surgery due to earthquake-related crush-trauma injury, patients with wound infection due to A baumannii were included in the case group and without infection were included in the control group. Multivariate analysis and logistic regression were performed to identify risk factors. Environmental cultures were taken to identify the source of the outbreak. Molecular typing by pulsed-field gel electrophoresis was used to confirm the relationships of the wound infection agent A. baumannii strains. RESULTS: A total of 44 patients were included in the case group and 62 patients in the control group. Time under the debris; 22.0 versus 35.7 (odds ratio [OR]:1.02, 95% confidence interval [CI]: 1.00-1.04) and hemodialysis (OR: 6.09, 95% CI: 1.64-22.66) were identified as risk factors for in the multivariate analysis. Performing the first intervention in a fully equipped tertiary hospital was seen as an infection-reducing factor compared to performing it in a field hospital (OR: 0.21, 95% CI: 0.06-0.68). Dressing trolleys and scissors were identified as the source of the outbreak. CONCLUSIONS: After devastating earthquakes, a large number of patients are admitted and require emergency interventions due to life-threatening conditions. Organ failure often develops and requires the use of invasive catheters and procedures. Compliance with infection control measures and clean surgical interventions reduce wound site infections and allow extremities to heal, while problems in adhering to infection control measures can lead to many problems such as outbreaks of gram-negative bacteria. This highlights the importance of infection control measures.

Evaluation of the Lytic Activity of Various Phage Cocktails Against, ESBL-Producer, Non-Producer and Carbapenem-Resistant Escherichia coli Isolates.

Bacteriophages have been proposed as an alternative therapy for the treatment of bacterial infections. This research aims to determine the lytic activity of bacteriophage-cocktails (BC) against carbapenem-resistant (CR-EC), ESBL-producer (EP-EC), and non-producer (NP-EC) E. coli isolates. Related resistance genes in 87 E. coli isolates were screened by PCR. The efficacies of BCs were determined by spot test and lytic zones were evaluated from fully-confluent to opaque. MOIs of the BCs were compared for fully-confluent and opaque lytic zones. BCs were also evaluated in terms of their biophysical characteristics including latency, burst size, pH and temperature stabilities. Among EP-EC, 96.9% of the isolates carry blaCTX-M, 25% of them blaSHV and 15.6% of them carry blaTEM. All CR-EC isolates carried blaOXA-48, but not blaKPC and blaNDM. CR-EC isolates were the least susceptible for the each of four BCs. MOIs for ENKO, SES and INTESTI-phage forming fully-confluent zone in E. coli isolates EC3 (NP-EC), EC8 (EP-EC) and EC27 (NP-EC), respectively were 10, 100 and 1, respectively. MOIs for ENKO, SES and INTESTI opaque zone in EC19 (EP-EC), EC10 (EP-EC), EC1(NP-EC), respectively were 0.01, 0.01, 0.1 PFU/CFU, respectively. The MOI for PYO-phage forming a semi-confluent zone in EC6 (NP-EC) isolate was 1 PFU/CFU. The phages were thermally stable and tolerant to a wide pH range. Comparison of MOIs according to lysis zone characteristics demonstrated that the activities of phages in phage cocktails vary depending on the characteristics of each bacterial host. Supplementary Information: The online version contains supplementary material available at 10.1007/s12088-023-01074-9.

Graphene Oxide Nanosheets Interact and Interfere with SARS-CoV-2 Surface Proteins and Cell Receptors to Inhibit Infectivity.

Nanotechnology can offer a number of options against coronavirus disease 2019 (COVID-19) acting both extracellularly and intracellularly to the host cells. Here, the aim is to explore graphene oxide (GO), the most studied 2D nanomaterial in biomedical applications, as a nanoscale platform for interaction with SARS-CoV-2. Molecular docking analyses of GO sheets on interaction with three different structures: SARS-CoV-2 viral spike (open state - 6VYB or closed state - 6VXX), ACE2 (1R42), and the ACE2-bound spike complex (6M0J) are performed. GO shows high affinity for the surface of all three structures (6M0J, 6VYB and 6VXX). When binding affinities and involved bonding types are compared, GO interacts more strongly with the spike or ACE2, compared to 6M0J. Infection experiments using infectious viral particles from four different clades as classified by Global Initiative on Sharing all Influenza Data (GISAID), are performed for validation purposes. Thin, biological-grade GO nanoscale (few hundred nanometers in lateral dimension) sheets are able to significantly reduce copies for three different viral clades. This data has demonstrated that GO sheets have the capacity to interact with SARS-CoV-2 surface components and disrupt infectivity even in the presence of any mutations on the viral spike. GO nanosheets are proposed to be further explored as a nanoscale platform for development of antiviral strategies against COVID-19.

2D MXenes with antiviral and immunomodulatory properties: A pilot study against SARS-CoV-2.

Two-dimensional transition metal carbides/carbonitrides known as MXenes are rapidly growing as multimodal nanoplatforms in biomedicine. Here, taking SARS-CoV-2 as a model, we explored the antiviral properties and immune-profile of a large panel of four highly stable and well-characterized MXenes - Ti3C2Tx, Ta4C3T x , Mo2Ti2C3T x and Nb4C3T x . To start with antiviral assessment, we first selected and deeply analyzed four different SARS-CoV-2 genotypes, common in most countries and carrying the wild type or mutated spike protein. When inhibition of the viral infection was tested in vitro with four viral clades, Ti3C2T x in particular, was able to significantly reduce infection only in SARS-CoV-2/clade GR infected Vero E6 cells. This difference in the antiviral activity, among the four viral particles tested, highlights the importance of considering the viral genotypes and mutations while testing antiviral activity of potential drugs and nanomaterials. Among the other MXenes tested, Mo2Ti2C3T x also showed antiviral properties. Proteomic, functional annotation analysis and comparison to the already published SARS-CoV-2 protein interaction map revealed that MXene-treatment exerts specific inhibitory mechanisms. Envisaging future antiviral MXene-based drug nano-formulations and considering the central importance of the immune response to viral infections, the immune impact of MXenes was evaluated on human primary immune cells by flow cytometry and single-cell mass cytometry on 17 distinct immune subpopulations. Moreover, 40 secreted cytokines were analyzed by Luminex technology. MXene immune profiling revealed i) the excellent bio and immune compatibility of the material, as well as the ability of MXene ii) to inhibit monocytes and iii) to reduce the release of pro-inflammatory cytokines, suggesting an anti-inflammatory effect elicited by MXene. We here report a selection of MXenes and viral SARS-CoV-2 genotypes/mutations, a series of the computational, structural and molecular data depicting deeply the SARS-CoV-2 mechanism of inhibition, as well as high dimensional single-cell immune-MXene profiling. Taken together, our results provide a compendium of knowledge for new developments of MXene-based multi-functioning nanosystems as antivirals and immune-modulators.

Evaluation of the diagnostic performance and optimal cutoff value of a fourth-generation ELISA, VIDAS HIV-1/2 Duo Ultra assay, in a low-prevalence country.

In this study, we described the largest analysis to date conducted with VIDAS® HIV Duo Ultra assay. Additionally, we analyzed the diagnostic performance and cutoff values (TV) of HIV Duo Ultra assay and total cost analysis for HIV testing. Of 11,642 enzyme-linked immunosorbent assay (ELISA)-positive samples referred to our center for confirmation, 2000 were positive with HIV Duo Ultra, and of these, 87% were HIV-1 positive and 0.6% were HIV-1 indeterminate with the confirmatory test. Overall, the false-positivity rate was 1.75% for HIV Duo Ultra assay. The sensitivity and specificity were 100% and 99.1%, respectively, when the TV was set at the recommended cutoff value. Even increasing the cutoff value four times, sensitivity and specificity remained high, pointing out that a TV of 0.99 is highly indicative of HIV positivity. Retesting samples with HIV Duo Ultra assay decreased 80% of the confirmatory tests, revealing a significant decrease of 78% in the total costs and reporting time.