Patrick Basset

Patrick Basset
Lausanne University Hospital | CHUV · Centre universitaire romand de médecine légale

PhD

About

86
Publications
5,211
Reads
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1,352
Citations
Additional affiliations
March 2013 - present
Lausanne University Hospital
Position
  • Certifying Scientist
February 2008 - February 2013
Lausanne University Hospital
May 2006 - July 2007
The University of Arizona
Description
  • Swiss National Science Foundation junior Post-doc
Education
October 2000 - February 2006
University of Lausanne
Field of study
  • Population Genetics
October 1995 - February 2000
University of Lausanne
Field of study
  • Biology

Publications

Publications (86)
Article
Full-text available
The detection of body fluids (e.g., blood, saliva or semen) provides information that is important both for the investigation and for the choice of the analytical protocols. Because of their sensitivity, specificity, as well as their simplicity of use, immunochromatographic tests are widely applied. These tests target different body fluids and gene...
Article
Full-text available
Chemical and staining methods, immunochromatography, spectroscopy, RNA expression or methylation patterns, do not allow to determine the nature of the biological material with certainty. However, to our knowledge, there are few forensic scientists that assess the value of such test results using a probabilistic approach. This is surprising as it wo...
Article
The identification of victims of a disaster (DVI) requires the collaboration of different specialists. Within a DVI context, DNA analyses often play an important role. Consequently, forensic genetic laboratories should be prepared to cope with DVI situations, as this can involve large-scale DNA profile comparisons. Six forensic genetic laboratories...
Article
Cambridge Core - Cell Biology and Developmental Biology - Shrews, Chromosomes and Speciation - edited by Jeremy B. Searle
Chapter
Shrews, Chromosomes and Speciation - edited by Jeremy B. Searle February 2019
Chapter
Shrews, Chromosomes and Speciation - edited by Jeremy B. Searle February 2019
Article
DNA contamination incidents are one of the most frequent sources of error in forensic genetics and can have serious consequences. It is therefore essential to take measures to prevent these events and to monitor the real impact of contamination minimization procedures. In this study, we review and compare the number of contamination events detected...
Chapter
Methicillin-resistant Staphylococcus aureus (MRSA) were first isolated in 1961, soon after the introduction of methicillin for therapeutic treatments. Since then, the rate of MRSA isolates among S. aureus has continuously increased to reach 60% in some healthcare institutions. The resistance to methicillin is conferred by the acquisition of the mec...
Article
In Switzerland, the DNA profiles of police officers collecting crime scene traces as well as forensic genetic laboratories employees are stored in the staff index of the national DNA database to detect potential contaminations. Our study aimed at making a national inventory of contaminations to better understand their origin and to make recommendat...
Article
Background: Pseudomonas aeruginosa is a leading cause of healthcare-associated infections in the intensive care unit (ICU). Aim: To investigate an unexplained increase in the incidence of P. aeruginosa recovered from clinical samples in the ICU over a two-year period. Methods: After unsuccessful epidemiological investigation by conventional to...
Poster
Background: From 2010 to 2012, an increase in P. aeruginosa incidence was observed in the ICUs at the University Hospital of Lausanne. A total of 689 isolates from 254 patients were typed using Double Locus Sequence Typing (DLST), and subsequently grouped into 46 DLST clusters. Cluster DLST 1-18 affected the highest number of patients (24 out of 25...
Article
Full-text available
Whole-genome sequencing (WGS) of 228 isolates was used to elucidate the origin and dynamics of a long-term outbreak of methicillin-resistant Staphylococcus aureus (MRSA) sequence type 228 (ST228) SCC mec I that involved 1,600 patients in a tertiary care hospital between 2008 and 2012. Combining of the sequence data with detailed metadata on patient...
Article
Full-text available
Despite the development of novel typing methods based on whole genome sequencing, most laboratories still rely on classical molecular methods for outbreak investigation or surveillance. Reference methods for Clostridium difficile include ribotyping and pulsed-field gel electrophoresis, which are band-comparing methods often difficult to establish a...
Data
Supplemental methods (infection control policy for MRSA, microbiology and molecular typing, whole genome sequencing) and supplemental results (SNPs distribution of SNPs across genes, figure of the incidence of ST228 MRSA patients in different wards). Download
Article
Full-text available
Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of both hospital- and community-acquired infections worldwide. However, data about the molecular epidemiology of MRSA in North Africa are still scarce. All MRSA isolates recovered between January 2006 and July 2011 from one Algerian hospital were genetically and phenotypically char...
Article
Although the molecular typing of Pseudomonas aeruginosa is important to understand the local epidemiology of this opportunistic pathogen, it remains challenging. Our aim was to develop a simple typing method based on the sequencing of two highly variable loci. Single-strand sequencing of three highly variable loci (ms172, ms217, and oprD) was perfo...
Article
We conducted a molecular study of MRSA isolated in Swiss hospitals, including the first five consecutive isolates recovered from blood cultures and the first ten isolates recovered from other sites in newly identified carriers. Among 73 MRSA isolates, 44 different double locus sequence typing (DLST) types and 32 spa types were observed. Most isolat...
Article
We report the first case of meticillin-resistant Staphylococcus aureus (MRSA) with the mecC gene in a patient in western Switzerland. After this first identification, a polymerase chain reaction protocol was established to investigate the occurrence of this new mecC gene in the population of this region. Enrichment broths were investigated from 106...
Article
Full-text available
Staphylococcus aureus is recognized as one of the major human pathogens and is by far one of the most common nosocomial organisms. The genetic basis for the emergence of highly epidemic strains remains mysterious. Studying the microevolution of the different clones of S. aureus is essential for identifying the forces driving pathogen emergence and...
Data
Likelihood Mapping Analysis for the core genomes with and without the strain N315. Phylogenetic noise was calculated using likelihood mapping analysis as implemented in TREE-PUZZLE [32]. A. Partitioning of the triangle in the seven basins of attraction (see [33] for details). Three basins correspond to fully resolved topologies (A1 A2 and A3), one...
Data
Neighbor-nets for the core genomes with and without the strain N315. Neighbor-nets for the core genomes with (A) and without (B) the strain N315 were inferred using uncorrected p-distances. P-values are shown for the PHI test for recombination, where the alpha value is p = 0.001. (DOCX)
Article
We investigated sex specificities in the evolutionary processes shaping Y chromosome, autosomes, and mitochondrial DNA patterns of genetic structure in the Valais shrew (Sorex antinorii), a mountain dwelling species with a hierarchical distribution. Both hierarchical analyses of variance and isolation-by-distance analyses revealed patterns of popul...
Article
Full-text available
The aim of the present study was to investigate the genetic structure of the Valais shrew (Sorex antinorii) by a combined phylogeographical and landscape genetic approach, and thereby to infer the locations of glacial refugia and establish the influence of geographical barriers. We sequenced part of the mitochondrial cytochrome b (cyt b) gene of 17...
Article
Chromosomal rearrangements are proposed to promote genetic differentiation between chromosomally differentiated taxa and therefore promote speciation. Due to their remarkable karyotypic polymorphism, the shrews of the Sorex araneus group were used to investigate the impact of chromosomal rearrangements on gene flow. Five intraspecific chromosomal h...
Article
Full-text available
The utility of sequencing a second highly variable locus in addition to the spa gene (e.g., double-locus sequence typing [DLST]) was investigated to overcome limitations of a Staphylococcus aureus single-locus typing method. Although adding a second locus seemed to increase discriminatory power, it was not sufficient to definitively infer evolution...
Chapter
This chapter deals with the challenges in hospitals presented by the widespread occurrence of Methicillin-Resistant Staphylococcus aureus (MRSA), especially with the recent emergence of strains with intermediate susceptibility to glycopeptides and of community-acquired MRSA. Staphylococcus aureus is a Gram-positive bacterium which typically resides...
Article
Clin Microbiol Infect 2012; 18: E31–E33 The nose is the anatomical site usually recommended for methicillin-resistant Staphylococcus aureus (MRSA) screening. Other sites are also recommended, but are more controversial. We showed that the sensitivities of MRSA detection from nasal swabs alone were 48% and 62% by culture or by rapid PCR test, respec...
Article
In the early stages of reproductive isolation, genomic regions of reduced recombination are expected to show greater levels of differentiation, either because gene flow between species is reduced in these regions or because the effects of selection at linked sites within species are enhanced in these regions. Here, we study the patterns of DNA sequ...
Article
According to molecular epidemiology theory, two isolates belong to the same chain of transmission if they are similar according to a highly discriminatory molecular typing method. This has been demonstrated in outbreaks, but is rarely studied in endemic situations. Person-to-person transmission cannot be established when isolates of meticillin-resi...
Article
Full-text available
Although MRSA outbreaks might have significant consequences on patients and/or health care resources, few data are available about the microevolution of a strain during a single outbreak. In this study, our aim was to characterize the variability of accessory genes among isolates recovered during a local MRSA outbreak.
Article
Full-text available
The incidence of vancomycin-resistant enterococci (VRE) remains sporadic in Switzerland. We report an unprecedented VRE (E.faecium van B) outbreak in a 900-bed tertiary care hospital and describe its molecular epidemiology.
Article
Full-text available
During a 9-month period, 217 patients were newly diagnosed as methicillin-resistant Staphylococcus aureus (MRSA) carriers by using a commercial rapid PCR-based test (GeneXpert). However, no MRSA was recovered by culturing the second swab in 61 of these patients. Further analyses showed that 28 (12.9%) of the patients harbored S. aureus isolates wit...
Article
Full-text available
Recent population genetic studies suggest that staphylococcal cassette chromosome mec (SCCmec) was acquired much more frequently than previously thought. In the present study, we aimed to investigate the diversity of SCCmec elements in a local methicillin-resistant Staphylococcus aureus (MRSA) population. Each MRSA isolate (one per patient) recover...
Article
The population structure of Staphylococcus aureus is generally described as highly clonal and is consequently subdivided into several clonal complexes (CCs). Recent data suggested that recombination might occur more frequently within than among CCs. To test this hypothesis as well as to understand how genetic diversity is created in S. aureus, we a...
Article
Many species contain genetic lineages that are phylogenetically intermixed with those of other species. In the Sorex araneus group, previous results based on mtDNA and Y chromosome sequence data showed an incongruent position of Sorex granarius within this group. In this study, we explored the relationship between species within the S. araneus grou...
Article
Clin Microbiol Infect 2010; 16: 1289–1296 Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial infections worldwide. To differentiate reliably among S. aureus isolates, we recently developed double locus sequence typing (DLST) based on the analysis of partial sequences of clfB and spa genes. In the present study, we eva...
Conference Paper
Background: The widespread use of intranasal mupirocin (Mup) ointment for the decolonization of methicillin-resistant Staphylococcus aureus (MRSA) prompted concerns about Mup resistance. Low-level resistance (LLR) is the result of mutations in native tRNA synthetase (IleS), whereas high-level resistance (HLR) is due to the presence of mupA gene on...
Article
Full-text available
Ninety-six clinical isolates of Staphylococcus aureus from Nigeria were characterized phenotypically and genetically. Twelve multidrug-resistant methicillin (meticillin)-resistant S. aureus (MRSA) isolates carrying a new staphylococcal cassette chromosome mec element and a high proportion of Panton-Valentine leukocidin (PVL)-positive methicillin-su...
Article
To reliably differentiate among Staphylococcus aureus isolates we recently developed the Double Locus Sequence Typing (DLST) based on the analysis of partial sequences of clfB and spa genes. This method is highly discriminatory and gives unambiguous definition of types. The highly clonal population structure of S. aureus suggests that isolates with...
Article
Full-text available
Most hybrid zones have existed for hundreds or thousands of years but have generally been observed for only a short time period. Studies extending over periods long enough to track evolutionary changes in the zones or assess the ultimate outcome of hybridization are scarce. Here, we describe the evolution over time of the level of genetic isolation...
Article
Patterns of genetic differentiation among taxa at early stages of divergence provide an opportunity to make inferences about the history of speciation. Here, we conduct a survey of DNA-sequence polymorphism and divergence at loci on the autosomes, X chromosome, Y chromosome and mitochondrial DNA in samples of Mus domesticus, M. musculus and M. cast...
Article
Using one male-inherited, one female-inherited and eight biparentally inherited markers, we investigate the population genetic structure of the Valais shrew (Sorex antinorii) in the Swiss Alps. Bayesian analysis on autosomal microsatellites suggests a clear genetic differentiation between two groups of populations. This geographically based structu...
Article
In hybrid zones, endogenous counter-selection of hybrids is usually first expressed as reduced fertility or viability in hybrids of the heterogametic sex, a mechanism known as Haldane's rule. This phenomenon often leads to a differential of gene flow between sex-linked markers. Here, we address the possibility of a differential gene flow for Y chro...
Article
Robertsonian (Rb) fusions received large theoretical support for their role in speciation, but empirical evidence is often lacking. Here, we address the role of Rb rearrangements on the genetic differentiation of the karyotypically diversified group of shrews, Sorex araneus. We compared genetic structure between 'rearranged' and 'common' chromosome...
Article
Full-text available
The species of the common shrew (Sorex araneus) group are morphologically very similar, but have undergone a spectacular chromosomal evolution. We investigate here the evolutionary history of the Sorex araneus group distributed in western Europe. In particular, we clarify the position of a difficult species, S. granarius, using sex-specific (mtDNA...
Article
Full-text available
Individuals sampled in hybrid zones are usually analysed according to their sampling locality, morphology, behaviour or karyotype. But the increasing availability of genetic information more and more favours its use for individual sorting purposes and numerous assignment methods based on the genetic composition of individuals have been developed. T...
Article
The species and races of the shrews of the Sorex araneus group exhibit a broad range of chromosomal polymorphisms. European taxa of this group are parapatric and form contact or hybrid zones that span an extraordinary variety of situations, ranging from absolute genetic isolation to almost free gene flow. This variety seems to depend for a large pa...
Article
Abstract The species and races of the shrews of the Sorex araneus group exhibit a broad range of chromosomal polymorphisms. European taxa of this group are parapatric and form contact or hybrid zones that span an extraordinary variety of situations, ranging from absolute genetic isolation to almost free gene flow. This variety seems to depend for a...
Article
The species of the common shrew (Sorex araneus) group are morphologically very similar but exhibit high levels of karyotypic variation. Here we used genetic variation at 10 microsatellite markers in a data set of 212 individuals mostly sampled in the western Alps and composed of five karyotypic taxa (Sorex coronatus, Sorex antinorii and the S. aran...
Article
Full-text available
The extremely high rate of karyotypic evolution that characterizes the shrews of the Sorex araneus group makes this group an exceptionally interesting model for population genetics and evolutionary studies. Here, we attempted to map 46 microsatellite markers at the chromosome arm level using flow-sorted chromosomes from three karyotypically differe...