Rapid and accurate detection of escherichia coli and klebsiella pneumoniae strains susceptible/resistant to cotrimoxazole through evaluation of cell elongation

Trimethoprim-sulfamethoxazole is a well-known antibiotic that inhibits folic acid synthesis, a topic of renewed interest. Since resistant strains are increasingly more common, an early and accurate discrimination of susceptibility may assure confident therapy. Two morphological assays were performed in Escherichia coli (n = 50; 27 non-susceptible) and Klebsiella pneumoniae (n = 52; 18 non-susceptible). First, the strains were incubated with the CLSI breakpoint of cotrimoxazole for 150 min, which induced cell lengthening in the susceptible strains. Second, the bacteria were incubated with mitomycin C (MMC) (0.5 mg/L) for 120 min to induce a SOS-linked cell enlargement higher than that obtained by cotrimoxazole alone. When cotrimoxazole was added 30 min before MMC, the inhibition of folic acid synthesis in the susceptible strain resulted in the suppression of MMC-induced extra elongation. In the non-susceptible strains, folic acid synthesis continued despite the antibiotic, so that the MMC-induced extra cell lengthening could not be impeded. Whereas the first assay resulted in five false negatives and four false positives of resistance, the results of the second assay matched those of the conventional antibiogram. This simple morphological procedure is performed in 2 h and 45 min and may allow a rapid selection of useful and relatively inexpensive therapy, thereby preserving the newer broad-spectrum antibiotics

Breaking antimicrobial resistance by disrupting extracytoplasmic protein folding

Antimicrobial resistance in Gram-negative bacteria is one of the greatest threats to global health. New antibacterial strategies are urgently needed, and the development of antibiotic adjuvants that either neutralize resistance proteins or compromise the integrity of the cell envelope is of ever-growing interest. Most available adjuvants are only effective against specific resistance proteins. Here we demonstrate that disruption of cell envelope protein homeostasis simultaneously compromises several classes of resistance determinants. In particular, we find that impairing DsbA-mediated disulfide bond formation incapacitates diverse β-lactamases and destabilizes mobile colistin resistance enzymes. Furthermore, we show that chemical inhibition of DsbA sensitizes multidrug-resistant clinical isolates to existing antibiotics and that the absence of DsbA, in combination with antibiotic treatment, substantially increases the survival of Galleria mellonella larvae infected with multidrug-resistant Pseudomonas aeruginosa. This work lays the foundation for the development of novel antibiotic adjuvants that function as broad-acting resistance breakers.British Society for Antimicrobial Chemotherapy BSAC-2018-0095NC3Rs NC/V001582/1Biological Sciences Research Council BB/V007823/1Academy of Medical Sciences SBF006\104

The FIELDS Instrument Suite for Solar Probe Plus: Measuring the Coronal Plasma and Magnetic Field, Plasma Waves and Turbulence, and Radio Signatures of Solar Transients.

NASA's Solar Probe Plus (SPP) mission will make the first in situ measurements of the solar corona and the birthplace of the solar wind. The FIELDS instrument suite on SPP will make direct measurements of electric and magnetic fields, the properties of in situ plasma waves, electron density and temperature profiles, and interplanetary radio emissions, amongst other things. Here, we describe the scientific objectives targeted by the SPP/FIELDS instrument, the instrument design itself, and the instrument concept of operations and planned data products

Genetic abnormalities as diagnostic and prognostic markers in B cell lymphomas: role of new molecular technologies in personalized medicine for extranodal diffuse large B cell lymphoma (EN-DLBCL) and follicular lymphoma (FL)

A plethora of molecular biomarkers are available nowadays in the field of cancer research. However, it is crucial to understand when and how they can be integrated into the clinical setting, translating experimental results from bench to bedside, with the aim of improving patients\u2019 care. We decided to investigate the role of some of these biomarkers in two subtypes of non-Hodgkin lymphoma which still represent a challenge for both researchers and clinicians. We started from diffuse large B cell lymphomas (DLBCLs), investigating a multicentric series of primary extranodal DLBCLs. Overall, data analysis provided strong evidence that the distribution of immunophenotypic, cytogenetic and survival characteristics is site-dependent. We next moved to follicular lymphoma (FL). The translocation (14;18), leading to BCL2 protein overexpression, is considered the genetic hallmark of FL. We tested the incidence of BCL2 negative FLs in a series of Italian patients from the Insubric region, concluding that BCL2 rearrangement in FL is not as frequent as generally reported and that the genetic landscape of FL is more complex than previously thought. What we learned is that even within an individual clinical entity, there is considerable heterogeneity with respect to genetic alterations, expression of commonly assayed markers and, most important, outcome. The personalized approach acknowledges this complexity and gives us tools for the continuous improvement of patients\u2019 care

Stable neutralizing antibody levels 6 months after mild and severe COVID-19 episodes

Background. Understanding mid-term kinetics of immunity to SARS-CoV-2 is the cornerstone for public health control of the pandemic and vaccine development. However, current evidence is rather based on limited measurements, losing sight of the temporal pattern of these changes. Methods. We conducted a longitudinal analysis on a prospective cohort of COVID-19 patients followed up for >6 months. Neutralizing activity was evaluated using HIV reporter pseudoviruses expressing SARS-CoV-2 S protein. IgG antibody titer was evaluated by ELISA against the S2 subunit, the receptor binding domain (RBD), and the nucleoprotein (NP). Statistical analyses were carried out using mixed-effects models. Findings. We found that individuals with mild or asymptomatic infection experienced an insignificant decay in neutralizing activity, which persisted 6 months after symptom onset or diagnosis. Hospitalized individuals showed higher neutralizing titers, which decreased following a 2-phase pattern, with an initial rapid decline that significantly slowed after day 80. Despite this initial decay, neutralizing activity at 6 months remained higher among hospitalized individuals compared to mild symptomatic. The slow decline in neutralizing activity at mid-term contrasted with the steep slope of anti-RBD, S2, or NP antibody titers, all of them showing a constant decline over the follow-up period. Conclusions. Our results reinforce the hypothesis that the quality of the neutralizing immune response against SARS-CoV-2 evolves over the post-convalescent stage.info:eu-repo/semantics/acceptedVersio

Genetic abnormalities as diagnostic and prognostic markers in B cell lymphomas: role of new molecular technologies in personalized medicine for extranodal diffuse large B cell lymphoma (EN-DLBCL) and follicular lymphoma (FL)

A plethora of molecular biomarkers are available nowadays in the field of cancer research. However, it is crucial to understand when and how they can be integrated into the clinical setting, translating experimental results from bench to bedside, with the aim of improving patients’ care. We decided to investigate the role of some of these biomarkers in two subtypes of non-Hodgkin lymphoma which still represent a challenge for both researchers and clinicians. We started from diffuse large B cell lymphomas (DLBCLs), investigating a multicentric series of primary extranodal DLBCLs. Overall, data analysis provided strong evidence that the distribution of immunophenotypic, cytogenetic and survival characteristics is site-dependent. We next moved to follicular lymphoma (FL). The translocation (14;18), leading to BCL2 protein overexpression, is considered the genetic hallmark of FL. We tested the incidence of BCL2 negative FLs in a series of Italian patients from the Insubric region, concluding that BCL2 rearrangement in FL is not as frequent as generally reported and that the genetic landscape of FL is more complex than previously thought. What we learned is that even within an individual clinical entity, there is considerable heterogeneity with respect to genetic alterations, expression of commonly assayed markers and, most important, outcome. The personalized approach acknowledges this complexity and gives us tools for the continuous improvement of patients’ care

Overcoming Drug-resistance in Chronic Myeloid Leukemia

Given the success of first-line treatment in chronic myeloid leukemia (CML), the prevalence of the disease is estimated to increase and more patients are expected to develop resistance to therapy. Thus, even relatively rare point mutations are likely to become more common. In CML, the uncontrollable division of myeloid cells is caused by a reciprocal translocation of chromosomes 9 and 22, resulting in the Philadelphia chromosome. At the meeting point of the two chromosomes, breakpoint cluster region (BCR) and Abelson proto-oncogene 1 (ABL1) fuse together to form the chimeric fusion oncogene BCR-ABL1, the latter of which, the non-receptor tyrosine kinase ABL1, is the driver of the disease. Since the tyrosine kinase inhibitor (TKI) imatinib became available in 2001, the success of first-line therapy has significantly improved the prognosis of CML patients. However, up to 50% of patients with imatinib-refractory disease develop resistance due to point mutations in ABL1, and the most common mutation to emerge is BCR-ABL1 T315I. The broad-range TKI ponatinib is the only approved TKI that inhibits the kinase activity of BCR-ABL1 T315I, but adverse side effects leave patients with this mutation in need of a better, safer, and more effective treatment. The kinase inhibitor axitinib was shown to be selective for BCR-ABL1 T315I, but mutations that emerge as a consequence of axitinib-resistance have yet to be explored. Moreover, patients with the T315I mutation treated with ponatinib have been reported to develop highly drug-resistant mutations in BCR-ABL1 such as T315M and the E255V/T315I compound mutation. The purpose of this study was to identify mutations that enable cells to develop resistance to the kinase inhibitor axitinib and to find new, potential inhibitors for cells expressing the drug-resistant mutations BCR-ABL1 T315I, BCR-ABL1 T315M, and BCR-ABL1 E255V/T315I. To this end, mouse hematopoietic cell lines were constructed prior to determining cell viability in response to inhibitors in combinations and as independent agents. As a novel finding, cells stably expressing T315M were found to exhibit sensitivity to inhibitors of topoisomerase II and mTOR. Moreover, synthetic lethality occurred in these cells in response to the combined treatment of the allosteric inhibitor asciminib and the TKI ponatinib, although not in clinically relevant doses. The highly resistant cells expressing BCR-ABL1 E255V/T315I, like cells expressing T315I and T315M, showed sensitivity to conventional chemotherapy. Notably, however, three SMAC mimetics displayed selectivity to cells expressing BCR-ABL1 E255V/T315I over cells expressing only the single T315I mutation. Considering that CML is expected to become increasingly prevalent, more patients are estimated to develop resistance to therapy. As even relatively rare mutations in BCR-ABL1 become more common, finding an effective treatment for cells expressing these highly resistant mutations takes us one step closer to identifying a safe and effective treatment for CML patients carrying those mutations

Network and Algebraic Topology of Influenza Evolution

Evolution is a force that has molded human existence since its divergence from chimpanzees about 5.4 million years ago. In that same amount of time, an influenza virus, which replicates every six hours, would have undergone an equivalent number of generations over only a hundred years. The fast replication times of influenza, coupled with its high mutation rate, make the virus a perfect model to study real-time evolution at a mega-Darwin scale, more than a million times faster than human evolution. While recent developments in high-throughput sequencing provide an optimal opportunity to dissect their genetic evolution, a concurrent growth in computational tools is necessary to analyze the large influx of complex genomic data. In my thesis, I present novel computational methods to examine different aspects of influenza evolution. I first focus on seasonal influenza, particularly the problems that hamper public health initiatives to combat the virus. I introduce two new approaches: 1. The q2-coefficient, a method of quantifying pathogen surveillance, and 2. FluGraph, a technique that employs network topology to track the spread of seasonal influenza around the world. The second chapter of my thesis examines how mutations and reassortment combine to alter the course of influenza evolution towards pandemic formation. I highlight inherent deficiencies in the current phylogenetic paradigm for analyzing evolution and offer a novel methodology based on algebraic topology that comprehensively reconstructs both vertical and horizontal evolutionary events. I apply this method to viruses, with emphasis on influenza, but foresee broader application to cancer cells, bacteria, eukaryotes, and other taxa

Highly Sensitive and Specific Method for Detection of Clinically Relevant Fusion Genes across Cancer

Gene fusions are strong driver mutations in cancer and can be used as a diagnostic tool to predict different tumour phenotypes and treatments. Several fusion detection algorithms for RNA-Seq data have been developed, but all of them report a consistently high number of false positive events. Therefore, new methods are crucial to accurately identify potential fusions that may be key drivers of oncogenesis. We developed Fusion Validator, a new filtering tool able to discriminate false positive fusion transcripts from real fusions and significantly reduce the number of candidates to assess for experimental validation. Fusion Validator perform a local realignment of reads on each fusion transcript sequence and tries to close the gap around the fusion breakpoint using both a de novo assembly and a seed-extend algorithm. If the algorithm fails to reconstruct the fusion transcript around the breakpoint, the fusion is considered as false positive and is discarded. Additional filtering steps are used to remove fusions with breakpoints mapping on low complexity or homologous regions and to find correct fusion partners for promiscuous gene fusion events. A final ranking score based on fusion annotation is created for each validated event to help distinguish real driver fusions from passengers one. We tested Fusion Validator on simulated datasets of different coverage, read length and breakpoint positions, and on four published breast cancer Cell Lines, highlighting the massive increase in sensisitivity, precision and specificity of our algorithm, in comparison to other fusion-detection software. Using this tool, we successfully detected 97.95% of PCR-validated kinase recurrent fusions in 190 pan cancer samples, removing approximately 79.95% of false positives. Particularly in haematological disorders and childhood sarcomas, gene fusions are critical as diagnostic and prognostic factors. Therefore, development of this novel tool to increase the efficiency of detecting driver fusions is critical in disease detection and treatment