A5050319289- SARS-CoV-2 and COVID-19 Research
- COVID-19 epidemiological studies
- SARS-CoV-2 detection and testing
- Antibiotic Resistance in Bacteria
- Evolution and Genetic Dynamics
- Vaccine Coverage and Hesitancy
- COVID-19 Clinical Research Studies
- Bacterial Identification and Susceptibility Testing
- Bacterial Genetics and Biotechnology
- Biosensors and Analytical Detection
- Urinary Tract Infections Management
- Genomics and Phylogenetic Studies
- Microbial Natural Products and Biosynthesis
- Gut microbiota and health
- Evolutionary Game Theory and Cooperation
- Antibiotics Pharmacokinetics and Efficacy
- Bacterial biofilms and quorum sensing
- Pharmaceutical and Antibiotic Environmental Impacts
- Antimicrobial Resistance in Staphylococcus
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Clostridium difficile and Clostridium perfringens research
- Gene Regulatory Network Analysis
- Bacteriophages and microbial interactions
- Respiratory viral infections research
Technion – Israel Institute of Technology
2013-2024
Hebrew University of Jerusalem
2011
Hadassah
2009
A key aspect of bacterial survival is the ability to evolve while migrating across spatially varying environmental challenges. Laboratory experiments, however, often study evolution in well-mixed systems. Here, we introduce an experimental device, microbial and growth arena (MEGA)–plate, which bacteria spread evolved on a large antibiotic landscape (120 × 60 centimeters) that allowed visual observation mutation selection front. While resistance increased consistently, multiple coexisting...
The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to a current pandemic unprecedented scale. Although diagnostic tests are fundamental the ability detect and respond, overwhelmed healthcare systems already experiencing shortages reagents associated with this test, calling for lean immediately applicable protocol.RNA extracts positive samples were tested presence SARS-CoV-2 using reverse transcription quantitative polymerase chain reaction, alone or in...
The effectiveness of the coronavirus disease 2019 (COVID-19) BNT162b2 vaccine in preventing and reducing viral loads breakthrough infections (BTIs) has been decreasing, concomitantly with rise Delta variant severe acute respiratory syndrome 2 (SARS-CoV-2). However, it is unclear whether observed decreased inherent to or dependent on time from immunization. By analyzing over 16,000 during current, Delta-variant-dominated pandemic wave Israel, we found that BTIs recently fully vaccinated...
Treatment of bacterial infections currently focuses on choosing an antibiotic that matches a pathogen's susceptibility, with less attention paid to the risk even susceptibility-matched treatments can fail as result resistance emerging in response treatment. Combining whole-genome sequencing 1113 pre- and posttreatment isolates machine-learning analysis 140,349 urinary tract 7365 wound infections, we found treatment-induced emergence could be predicted minimized at individual-patient level....
Abstract The recent emergence of SARS-CoV-2 lead to a current pandemic unprecedented levels. Though diagnostic tests are fundamental the ability detect and respond, many health systems already experiencing shortages reagents associated with this test. Here, testing pooling approach for standard RT-qPCR test, we find that single positive sample can be detected even in pools up 32 samples, an estimated false negative rate 10%. Detection samples diluted 64 may also attainable, though require...
Mass vaccination has the potential to curb current COVID-19 pandemic by protecting individuals who have been vaccinated against disease and possibly lowering likelihood of transmission not vaccinated. The high effectiveness widely administered BNT162b vaccine from Pfizer-BioNTech in preventing only but also infection with SARS-CoV-2 suggests a for population-level effect, which is critical eradication. However, this putative effect difficult observe, especially light highly fluctuating...
Vaccinations are considered the major tool to curb current SARS-CoV-2 pandemic. A randomized placebo-controlled trial of Pfizer BNT162b2 vaccine has demonstrated a 95% efficacy in preventing COVID-19 disease. These results now corroborated with statistical analyses real-world vaccination rollouts, but resolving effectiveness across demographic groups and its interaction comorbidities is challenging. Here, applying multivariable logistic regression analysis approach large patient-level...
Abstract Beyond their substantial protection of individual vaccinees, it is hoped that the COVID-19 vaccines would reduce viral load in breakthrough infections thereby further suppress onward transmission. Here, analyzing positive SARS-CoV-2 test results following inoculation with BNT162b2 mRNA vaccine, we find reduced 4-fold for occurring 12-28 days after first dose vaccine. These loads hint to lower infectiousness, contributing vaccine impact on virus spread.
The BNT162b2 COVID-19 vaccine has been shown to reduce viral load of breakthrough infections (BTIs), an important factor affecting infectiousness. This viral-load protective effect waning with time post the second and later restored a booster shot. It is currently unclear though for how long this regained effectiveness lasts. Analyzing Ct values SARS-CoV-2 qRT-PCR tests over 22,000 during Delta-variant-dominant period in Israel, we find that reduction significantly declines within months...
Abstract Antibiotic-sensitive and -resistant bacteria coexist in natural environments with low, if detectable, antibiotic concentrations. Except possibly around localized sources, where resistance can provide a strong advantage, bacterial fitness is dominated by stresses unaffected to the antibiotic. How do such mixed heterogeneous conditions influence selective advantage or disadvantage of resistance? Here we find that sub-inhibitory levels tetracyclines potentiate selection for against...
Abstract The incidence of beta-lactam resistance among clinical isolates is a major health concern. A key method to study the emergence antibiotic adaptive laboratory evolution. However, in case ampicillin, bacteria evolved settings do not recapitulate clinical-like levels, hindering efforts identify evolutionary paths and their dependency on genetic background. Here, we used Microbial Evolution Growth Arena (MEGA) plate select ampicillin-resistant Escherichia coli mutants with varying...
Abstract Beta-lactamase inhibitors are increasingly used to counteract antibiotic resistance mediated by beta-lactamase enzymes. These compete with the beta-lactam for same binding site on beta-lactamase, thus generating an evolutionary tradeoff: mutations that increase enzyme’s activity tend also its susceptibility inhibitor. Here, we investigate how common and accessible mutants escape this adaptive tradeoff. Screening a deep mutant library of bla ampC gene Escherichia coli , identified...
In experimental evolution, scientists evolve organisms in the lab, typically by challenging them to new environmental conditions. How best a desired trait? Should challenge be applied abruptly, gradually, periodically, sporadically? one apply chemical mutagenesis, and do strains with high innate mutation rate faster? What are ideal population sizes of evolving populations? There endless strategies, beyond those that can exposed individual labs. We therefore arranged community challenge,...
Abstract Programmed chromosomal inversions allow bacteria to generate intra-population genotypic and functional heterogeneity, a bet-hedging strategy important in changing environments. Some programmed modify coding sequences, producing different alleles several gene families, most notably specificity-determining genes such as Type I restriction-modification systems, where systematic searches revealed cross phylum abundance. Yet, broad, gene-independent, search for gene-altering has been...
Abstract The BNT162b2 vaccine showed high real-life effectiveness both at preventing disease and in reducing viral loads of breakthrough infections, but coincidental with the rise Delta-variant SARS-CoV2, these protective effects have been decreasing, prompting a third, booster, inoculation. Here, analyzing over 11,000 infections during current wave Israel, we find that even though this is dominated by Delta-variant, recently vaccinated patients, still within 2 months post their second...
Abstract Widespread, frequent testing is essential for curbing the ongoing COVID-19 pandemic. Because its simplicity makes it ideal widely distributed, high throughput testing, RT-LAMP provides an attractive alternative to RT-qPCR. However, most protocols require purification of RNA, a complex and low-throughput bottleneck that has often been subject reagent supply shortages. Here, we report optimized RT-LAMP-based SARS-CoV-2 diagnostic protocol saliva swab samples. In replace RNA with...
Abstract Mass vaccination has the potential to curb current COVID-19 pandemic by protecting vaccinees from disease and possibly lowering chance of transmission unvaccinated individuals. The high effectiveness widely-administered BNT162b vaccine in preventing not only but also infection suggests a for population-level effect, critical eradication. However, this putative effect is difficult observe, especially light highly fluctuating spatio-temporal epidemic dynamics. Here, analyzing records...
Abstract Members of the yeast family PUF proteins bind unique subsets mRNA targets that encode with common functions. They therefore became a paradigm for post-transcriptional gene control. To provide new insights into roles seemingly redundant Puf1 and Puf2 members, we monitored growth rates their deletions under many different stress conditions. A differential effect was observed at high CaCl 2 concentrations, whereby puf1Δ affected much more than puf2Δ , inhibition exacerbated in...