A5005615210- Tuberculosis Research and Epidemiology
- Mycobacterium research and diagnosis
- Infectious Diseases and Tuberculosis
- Genomics and Phylogenetic Studies
- Diagnosis and treatment of tuberculosis
- Cancer Immunotherapy and Biomarkers
- Infrared Thermography in Medicine
- Genetic Neurodegenerative Diseases
- vaccines and immunoinformatics approaches
- thermodynamics and calorimetric analyses
- RNA and protein synthesis mechanisms
- Immunotherapy and Immune Responses
- Evolution and Genetic Dynamics
- Genetic diversity and population structure
- Thermography and Photoacoustic Techniques
- Advanced Breast Cancer Therapies
- Reproductive tract infections research
- Amyotrophic Lateral Sclerosis Research
- BRCA gene mutations in cancer
- Fecal contamination and water quality
- Genetic and Environmental Crop Studies
- Advanced biosensing and bioanalysis techniques
- Exercise and Physiological Responses
- Bacteriophages and microbial interactions
- Cancer therapeutics and mechanisms
Pacific Biosciences (United States)
2022-2023
University of Basel
2011-2019
Swiss Tropical and Public Health Institute
2011-2019
University of Bern
2016
Institute of Social and Preventive Medicine
2016
Swiss Federal Institute of Aquatic Science and Technology
2010
Fribourg Development Agency
2005
University Hospital of Basel
1986
Novartis (Switzerland)
1985
High-throughput DNA sequencing produces vast amounts of data, with millions short reads that usually have to be mapped a reference genome or newly assembled. Both reference-based mapping and de novo assembly are computationally intensive, generating large intermediary data files, thus require bioinformatics skills often lacking in the laboratories producing data. Moreover, many research practical applications microbiology only small fraction whole We developed KvarQ, new tool directly scans...
There is increasing evidence that strain variation in Mycobacterium tuberculosis complex (MTBC) might influence the outcome of infection and disease. To assess genotype-phenotype associations, phylogenetically robust molecular markers appropriate genotyping tools are required. Most current methods for MTBC based on mobile or repetitive DNA elements. Because these elements prone to convergent evolution, corresponding techniques suboptimal phylogenetic studies classification. By contrast,...
ABSTRACT Immigrants from regions with a high incidence of tuberculosis (TB) are risk group for TB in low-incidence countries such as Switzerland. In previous analysis nationwide collection 520 Mycobacterium isolates 2000 to 2008, we identified 35 clusters comprising 90 patients based on standard genotyping (24-locus mycobacterial interspersed repetitive-unit–variable-number tandem-repeat [MIRU-VNTR] typing and spoligotyping). Here, used whole-genome sequencing (WGS) revisit these...
The degree to which a water sample can potentially support the growth of human pathogens was evaluated. For this purpose, pathogen potential (PGP) bioassay developed based on principles conventional assimilable organic carbon (AOC) determination, but using pure cultures selected pathogenic bacteria (Escherichia coli O157, Vibrio cholerae, or Pseudomonas aeruginosa) as inoculum. We evaluated 19 samples collected after different treatment steps from two drinking production plants and...
Background. Whole-genome sequencing (WGS) is increasingly used in molecular-epidemiological investigations of bacterial pathogens, despite cost- and time-intensive analyses. We combined strain-specific single-nucleotide polymorphism (SNP) typing targeted WGS to investigate a tuberculosis cluster spanning 21 years Bern, Switzerland. Methods. On the basis genome sequences 3 historical outbreak Mycobacterium isolates, we developed SNP-typing assay identify further cases. screened 1642 patient...
The phylogeographic population structure of Mycobacterium tuberculosis suggests local adaptation to sympatric human populations. We hypothesized that HIV infection, which induces immunodeficiency, will alter the relationship between M. and its host. To test this hypothesis, we performed a nine-year nation-wide molecular-epidemiological study HIV–infected HIV–negative patients with (TB) 2000 2008 in Switzerland. analyzed 518 TB whom 112 (21.6%) were 233 (45.0%) born Europe. found among...
Mycobacterium africanum is a member of the tuberculosis complex (MTBC) and an important cause human in West Africa that rarely observed elsewhere. Here we genotyped 613 MTBC clinical isolates from Ghana, searched for associations between different phylogenetic lineages patient variables. We found 17.1% (105/613) belonged to M. africanum, with remaining belonging sensu stricto. No bovis was identified this sample. significantly more common patients Ewe ethnic group (adjusted odds ratio: 3.02;...
Objective The aim of this study was to use spoligotyping and large sequence polymorphism (LSP) the population structure M. tuberculosis complex (MTBC) isolates. Methods MTBC isolates were identified using standard biochemical procedures, IS6110 PCR, polymorphisms. Isolates further typed spoligotyping, phenotypic drug susceptibility patterns determined by proportion method. Result One hundred sixty-two characterised LSP typing. Of these, 130 (80.25%) as Mycobacterium sensu stricto (MTBss),...
Background Mycobacterium tuberculosis has a global population structure consisting of six main phylogenetic lineages associated with specific geographic regions and human populations. One particular M. genotype known as "Beijing" repeatedly been drug resistance emerging in some parts the world. strains are traditionally defined based on characteristic spoligotyping pattern. We used three alternative genotyping techniques to revisit classification complex (MTBC) exhibiting typical Methods...
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....
Insights into the evolution of non-model organisms are limited by lack reference genomes high accuracy, completeness, and contiguity. Here, we present a chromosome-level, karyotype-validated genome pangenome for barn swallow (Hirundo rustica). We complement these resources with reference-free multialignment other bird most comprehensive catalog genetic markers swallow. identify potentially conserved accelerated genes using estimate genome-wide linkage disequilibrium catalog. use to infer...
ABSTRACT Immigrants from high-burden countries and HIV-coinfected individuals are risk groups for tuberculosis (TB) in with low TB incidence. Therefore, we studied their role transmission of Mycobacterium Switzerland. We included all patients the Swiss HIV Cohort a sample national registry. identified molecular clusters by spoligotyping mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) analysis used weighted logistic regression adjusted age sex to identify...
The fast evolution of pathogenic viruses has allowed for the development phylodynamic approaches that extract information about epidemiological characteristics viral genomes. Thanks to advances in whole genome sequencing, they can be applied slowly evolving bacterial pathogens like Mycobacterium tuberculosis. In this study, we investigate and compare dynamics underlying two M. tuberculosis outbreaks using methods. Specifically, (i) test if outbreak data sets contain enough genetic variation...
HIV significantly affects the immunological environment during tuberculosis coinfection, and therefore may influence selective landscape upon which M. evolves. To test this hypothesis whole genome sequences were determined for 169 South African strains from HIV-1 coinfected uninfected individuals analyzed using two Bayesian codon-model based selection analysis approaches: FUBAR was used to detect persistent positive negative (selection respectively favoring disfavoring nonsynonymous...
Tuberculosis (TB) is a major public health problem in Nepal. Strain variation Mycobacterium tuberculosis may influence the outcome of TB infection and disease. To date, phylogenetic diversity M. Nepal unknown.We analyzed 261 isolates recovered from pulmonary patients recruited between August 2009 2010 lineages were determined by single nucleotide polymorphisms (SNP) typing spoligotyping. Drug resistance was sequencing hot spot regions relevant target genes. Overall, 164 (62.8%) new, 97...
Background Combining different molecular typing methods for Mycobacterium tuberculosis complex (MTBC) can be a powerful tool epidemiology-based investigation of TB. However, the current standard method that provides high discriminatory power such combination, mycobacterial interspersed repetitive units-variable numbers tandem repeats (MIRU-VNTR), is laborious, time-consuming and often too costly many resource-limited laboratories. We aimed to evaluate reduced set loci MIRU-VNTR in...
Zoonotic tuberculosis is a risk for human health, especially when animals are in close contact with humans. Mycobacterium was cultured from several organs, including lung tissue and gastric mucosa, of three captive elephants euthanized Swiss zoo. The presented weight loss, weakness exercise intolerance. Molecular characterization the M. isolates by spoligotyping revealed an identical profile, suggesting single source infection. Multilocus variable-number tandem-repeat analysis (MLVA)...
BACKGROUND High-risk human papillomavirus (HR-HPV) testing has been proposed as a replacement for cytology or an adjunct to primary cervical carcinoma screening. The objective of this study was assess the age-specific prevalence HR-HPV infection and correlation between status cytologic diagnosis. METHODS authors enrolled 7254 women receiving routine screening in cross-sectional that conducted during 12 months. Cervical samples were collected using liquid-based perform both Papanicolaou...