A5047298158- Tuberculosis Research and Epidemiology
- Mycobacterium research and diagnosis
- Evolution and Genetic Dynamics
- Genomics and Phylogenetic Studies
- Antibiotic Resistance in Bacteria
- Evolution and Paleontology Studies
- RNA and protein synthesis mechanisms
- Genetic diversity and population structure
- Species Distribution and Climate Change
- Cancer Genomics and Diagnostics
- vaccines and immunoinformatics approaches
- Vibrio bacteria research studies
- Microbial infections and disease research
- Antibiotic Use and Resistance
- Influenza Virus Research Studies
- Metabolomics and Mass Spectrometry Studies
- Respiratory viral infections research
- Bacillus and Francisella bacterial research
- Vector-borne infectious diseases
- Yersinia bacterium, plague, ectoparasites research
- Biochemical and Molecular Research
- COVID-19 Clinical Research Studies
- Bacteriophages and microbial interactions
- Gut microbiota and health
- Infectious Diseases and Tuberculosis
National Institute of Allergy and Infectious Diseases
2021-2025
National Institutes of Health
2021-2025
Swiss Tropical and Public Health Institute
2017-2023
University of Basel
2017-2021
Lung epithelial and endothelial cell damage defective lung tissue repair contribute to fatal COVID-19.
Large sequence datasets are difficult to visualize and handle. Additionally, they often do not represent a random subset of the natural diversity, but result uncoordinated convenience sampling. Consequently, can suffer from redundancy sampling biases.Here we present Treemmer, simple tool evaluate phylogenetic trees reduce their complexity by eliminating leaves that contribute least tree diversity.Treemmer size with different structures levels while maintaining sub-sample is representative...
Multidrug-resistant tuberculosis (MDR-TB) is among the most frequent causes of death due to antimicrobial resistance. Although only 3% global TB cases are MDR, geographical hotspots with up 40% MDR-TB have been observed in countries former Soviet Union. While quality control and patient-related factors known contributors such hotspots, role pathogen remains unclear. Here we show that country Georgia, a hotspot MDR-TB, MDR Mycobacterium strains lineage 4 (L4) transmit less than their...
Whole-genome sequencing allows rapid detection of drug-resistant Mycobacterium tuberculosis isolates. However, the availability high-quality data linking quantitative phenotypic drug susceptibility testing (DST) and genomic have thus far been limited.
Transition bias, an overabundance of transitions relative to transversions, has been widely reported among studies the rates and spectra spontaneous mutations. However, demonstrating role transition bias in adaptive evolution remains challenging. In particular, it is unclear whether such biases direct bacterial pathogens adapting treatment. We addressed this challenge by analyzing antibiotic-resistance mutations major human pathogen Mycobacterium tuberculosis (MTB). found strong evidence for...
The Lineage 2–Beijing (L2–Beijing) sub-lineage of Mycobacterium tuberculosis has received much attention due to its high virulence, fast disease progression, and association with antibiotic resistance. Despite several reports the recent emergence L2–Beijing in Africa, no study investigated evolutionary history this on continent. In study, we used whole genome sequences 781 L2 clinical strains from 14 geographical regions globally distributed investigate origins onward spread lineage Africa....
<ns3:p><ns3:bold>Background: </ns3:bold>Lineage 1 (L1) and 3 (L3) are two lineages of the<ns3:italic> Mycobacterium tuberculosis</ns3:italic> complex (MTBC) causing tuberculosis (TB) in humans. L1 L3 prevalent around the rim Indian Ocean, region that accounts for most world’s new TB cases. Despite their relevance this region, remain understudied.</ns3:p><ns3:p> <ns3:bold>Methods: </ns3:bold>We analyzed 2,938 2,030 whole genome sequences originating from 69 countries. We reconstructed...
Background: Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC) causing (TB) in humans. L1 L3 prevalent around rim Indian Ocean, region that accounts for most world's new TB cases. Despite their relevance this region, remain understudied. Methods: We analyzed 2,938 2,030 whole genome sequences originating from 69 countries. reconstructed evolutionary history these identified genes under positive selection. Results: found a strongly asymmetric pattern...
Influenza A viruses (IAVs) present major public health threats from annual seasonal epidemics and pandemics adapted to a variety of animals including poultry, pigs, horses. Vaccines that broadly protect against all such IAVs, so-called “universal” influenza vaccines, do not currently exist but are urgently needed. Here, we demonstrated an inactivated, multivalent whole-virus vaccine, delivered intramuscularly or intranasally, was protective challenges with multiple IAV hemagglutinin...
Background/Objectives: Bacterial vaccines were first developed and used in the late 1800s to prevent chicken cholera anthrax. pneumonia widely during 1918 influenza pandemic, despite A/H1N1 virus not yet being identified. Studies showed that bacterial pathogens, including Haemophilus influenzae, Streptococcus pneumoniae, pyogenes, contributed significantly fatal secondary pneumonias pandemic. In this study, we aimed characterize microbial composition of two ampules a mixed vaccine produced...
Whole genome sequencing (WGS) methods provide new possibilities in the field of molecular epidemiology. This is particularly true for monomorphic organisms where discriminatory power traditional (e.g. restriction enzyme length polymorphism typing, multi locus sequence typing etc.) inadequate to elucidate complex disease transmission patterns, as well resolving phylogeny at high resolution on a micro-geographic scale. In this study, we present insights into population structure Francisella...
Antimicrobial resistance (AMR) poses a threat to global health and the economy. Rifampicin-resistant Mycobacterium tuberculosis accounts for third of AMR burden. Gaining upper hand on requires deeper understanding physiology resistance. often results in fitness cost absence drug. Identifying molecular mechanisms underpinning this could help strengthen future treatment regimens. Here, we used collection M. strains that provide an evolutionary phylogenetic snapshot rifampicin subjected them...
Abstract The Lineage 2–Beijing (L2–Beijing) sub-lineage of Mycobacterium tuberculosis has received much attention due to its high virulence, fast disease progression, and association with antibiotic resistance. Despite several reports the recent emergence L2–Beijing in Africa, no study investigated evolutionary history this on continent. In study, we used whole genome sequences 817 L2 clinical strains from 14 geographical regions globally distributed investigate origins onward spread lineage...
Abstract Large sequence datasets are difficult to visualize and handle. Additionally, they often not an adequate representation of the natural diversity, but result uncoordinated convenience sampling. Consequently, can suffer from redundancy sampling biases. Here we present Treemmer, a simple tool evaluate phylogenetic trees reduce their complexity by eliminating leaves that contribute least tree diversity. Treemmer size with different structures levels while maintaining sub-sample is...
Summary Antimicrobial resistance poses a threat to global health and the economy. It is widely accepted that, in absence of antibiotics, drug mutations carry fitness cost. In case rifampicin fast-growing bacteria, this cost stems from reduced transcription rate RNA polymerase resulting slower ribosome biosynthesis. However, relationship does not apply slow-growing Mycobacterium tuberculosis , where true mechanism as well impact compensatory evolution remain unknown. Here we show, using...
Abstract Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC), causing (TB) in humans. L1 L3 endemic to Rim Indian Ocean, region that accounts for most world’s new TB cases. Despite their relevance this region, remain understudied. Here we analyzed 2,938 2,030 whole genome sequences originating from 69 countries. We show South Asia played a central role dispersion these neighboring regions. Moreover, found exhibits signatures local adaptation at esxH...
Abstract Transition bias, an overabundance of transitions relative to transversions, has been widely reported among studies mutations spreading under relaxed selection. However, demonstrating the role transition bias in adaptive evolution remains challenging. We addressed this challenge by analyzing antibiotic-resistance major human pathogen Mycobacterium tuberculosis . found strong evidence for two independently curated datasets comprising 152 and 208 antibiotic resistance mutations. This...
Abstract Whole genome sequencing allows rapid detection of drug-resistant M. tuberculosis isolates. However, high-quality data linking quantitative phenotypic drug susceptibility testing (DST) and genomic have thus far been lacking. We determined resistance profiles 176 genetically diverse clinical isolates from Democratic Republic the Congo, Ivory Coast, Peru, Thailand Switzerland by DST for 11 antituberculous drugs using BD BACTEC MGIT 960 system 7H10 agar dilution to generate a...