Biomedical subjects

Pierre-Edouard Fournier

Publications and source records attributed to Pierre-Edouard Fournier.

At least 19 recordsLinked to original sources

PubMed2025

Whole Genome Sequencing and Genetic Diversity of Respiratory Viruses Detected in Children With Acute Respiratory Infections: A One-Year Cross-Sectional Study in Senegal.

Acute respiratory infections (ARI) are a health priority, especially in countries with limited resources. They are a major cause of morbidity and mortality, especially among children and the elderly. In Senegal, the endemic circulation of respiratory viruses other than influenza has been demonstrated. However, there is a paucity of data exploring the genetic diversity of these viruses based on whole-genome sequencing. In this study, we present data on the genetic diversity of respiratory viruses in children under 15 years old in Senegal, including an overview of the different pathogens detected. Between November 2022 and November 2023, we collected nasopharyngeal swabs from children seen in curative consultations for symptoms of acute respiratory infections. Of the 156 children included, 73.7% tested positive for at least one pathogen. The most frequently detected virus was rhinovirus (50.0%), followed by influenza B (41.6%) and human parainfluenza virus type 3 (7.6%). Combinations of rhinovirus/influenza B, human parainfluenza virus type 2/human parainfluenza virus type 4, and rhinovirus/influenza B/adenovirus were the most frequently identified. A statistically significant association was detected between some of the viruses detected. A high genetic diversity of respiratory viruses circulating in children was revealed. The strains were phylogenetically close to various strains circulating worldwide, suggesting a global circulation of respiratory viruses. Our study provides the first complete genome sequences of human parainfluenza viruses type 2, 3, 4 and human bocavirus from Senegal and thus contributes to the enrichment of international databases on sequences from Senegal and underlines the importance of sequencing in the dynamics of pathogen circulation.

Humans↗

PubMed2006

Molecular analysis of pericardial fluid: a 7-year experience.

AIMS: Aetiological investigations of pericardial effusion are often negative. We evaluate the interest of systematic analysis of fluid in order to diminish the number of pericarditis classified as idiopathic. METHODS AND RESULTS: We performed a systematic analysis of pericardial fluid and biopsy specimens, using cultures and molecular analyses for the identification of bacteriological, fungal, and viral agents, as well as histopathological examination of 106 pericardial fluid samples. The aetiological diagnosis was determined clinically and by non-invasive procedures in 40 and nine patients, respectively. In the remaining 57 patients, 14 neoplasias and 17 infections were diagnosed. Molecular procedures identified seven viral (Enterovirus, Herpes simplex virus, and Epstein-Barr virus in four, two, and one of the cases, respectively), one fungal (Cryptococcus neoformans), and nine bacterial infections. Four of these bacteria were not diagnosed by culture because of prior antibiotics treatment (Mycobacterium tuberculosis in two cases, Streptococcus pneumoniae in one case, and Actinomyces neuii in one case). The aetiology remained undetermined in 26 patients. CONCLUSION: The systematic use of molecular techniques permitted a significant increase in aetiological diagnoses of punctured pericardial effusions when compared with cultures (39.5 vs. 13.9%, respectively; P<0.01). It is particularly beneficial for patients with a previous antibiotic regimen or suspicion of tuberculosis.

Adolescent↗

PubMed2006

Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens.

The recently sequenced Rickettsia felis genome revealed an unexpected plasmid carrying several genes usually associated with DNA transfer, suggesting that ancestral rickettsiae might have been endowed with a conjugation apparatus. Here we present the genome sequence of Rickettsia bellii, the earliest diverging species of known rickettsiae. The 1,552,076 base pair-long chromosome does not exhibit the colinearity observed between other rickettsia genomes, and encodes a complete set of putative conjugal DNA transfer genes most similar to homologues found in Protochlamydia amoebophila UWE25, an obligate symbiont of amoebae. The genome exhibits many other genes highly similar to homologues in intracellular bacteria of amoebae. We sought and observed sex pili-like cell surface appendages for R. bellii. We also found that R. bellii very efficiently multiplies in the nucleus of eukaryotic cells and survives in the phagocytic amoeba, Acanthamoeba polyphaga. These results suggest that amoeba-like ancestral protozoa could have served as a genetic "melting pot" where the ancestors of rickettsiae and other bacteria promiscuously exchanged genes, eventually leading to their adaptation to the intracellular lifestyle within eukaryotic cells.

Actins↗

PubMed2006

Sca1, a previously undescribed paralog from autotransporter protein-encoding genes in Rickettsia species.

BACKGROUND: Among the 17 genes encoding autotransporter proteins of the "surface cell antigen" (sca) family in the currently sequenced Rickettsia genomes, ompA, sca5 (ompB) and sca4 (gene D), have been extensively used for identification and phylogenetic purposes for Rickettsia species. However, none of these genes is present in all 20 currently validated Rickettsia species. Of the remaining 14 sca genes, sca1 is the only gene to be present in all nine sequenced Rickettsia genomes. To estimate whether the sca1 gene is present in all Rickettsia species and its usefulness as an identification and phylogenetic tool, we searched for sca1genes in the four published Rickettsia genomes and amplified and sequenced this gene in the remaining 16 validated Rickettsia species. RESULTS: Sca1 is the only one of the 17 rickettsial sca genes present in all 20 Rickettsia species. R. prowazekii and R. canadensis exhibit a split sca1 gene whereas the remaining species have a complete gene. Within the sca1 gene, we identified a 488-bp variable sequence fragment that can be amplified using a pair of conserved primers. Sequences of this fragment are specific for each Rickettsia species. The phylogenetic organization of Rickettsia species inferred from the comparison of sca1 sequences strengthens the classification based on the housekeeping gene gltA and is similar to those obtained from the analyses of ompA, sca5 and sca4, thus suggesting similar evolutionary constraints. We also observed that Sca1 protein sequences have evolved under a dual selection pressure: with the exception of typhus group rickettsiae, the amino-terminal part of the protein that encompasses the predicted passenger domain, has evolved under positive selection in rickettsiae. This suggests that the Sca1 protein interacts with the host. In contrast, the C-terminal portion containing the autotransporter domain has evolved under purifying selection. In addition, sca1 is transcribed in R. conorii, and might therefore be functional in this species. CONCLUSION: The sca1 gene, encoding an autotransporter protein that evolves under dual evolution pressure, is the only sca-family gene to be conserved by all Rickettsia species. As such, it is a valuable identification target for these bacteria, especially because rickettsial isolates can be identified by amplification and sequencing of a discriminatory gene fragment using a single primer pair. It may also be used as a phylogenetic tool. However, its current functional status remains to be determined although it was found expressed in R. conorii.

Antigens, Surface↗

PubMed2006

Mimivirus and the emerging concept of "giant" virus.

The recently discovered Acanthamoeba polyphaga Mimivirus is the largest known DNA virus. Its particle size (750 nm), genome length (1.2 million bp) and large gene repertoire (911 protein coding genes) blur the established boundaries between viruses and parasitic cellular organisms. In addition, the analysis of its genome sequence identified many types of genes never before encountered in a virus, including aminoacyl-tRNA synthetases and other central components of the translation machinery previously thought to be the signature of cellular organisms. In this article, we examine how the finding of such a giant virus might durably influence the way we look at microbial biodiversity, and lead us to revise the classification of microbial domains and life forms. We propose to introduce the word "girus" to recognize the intermediate status of these giant DNA viruses, the genome complexity of which makes them closer to small parasitic prokaryotes than to regular viruses.

Acanthamoeba↗

PubMed2006

Quantitative histological examination of bioprosthetic heart valves.

BACKGROUND: The histological features that characterize infective endocarditis in bioprosthetic valves are not accurately defined. Moreover, bioprosthetic valves may have a noninfective, degenerative evolution associated with calcifications, vegetation-like lesions, and inflammatory infiltrates. Such histological findings may be misdiagnosed as infective endocarditis. METHODS: Pathologic analysis of inflamed bioprosthetic valve tissues was conducted retrospectively for 21 patients who underwent surgical removal of a bioprosthetic valve because of suspected infective endocarditis and for 67 patients who underwent surgical removal of a bioprosthetic valve because of noninfective dysfunction. To better define the histological criteria for infective endocarditis, we used quantitative image analysis to compare these 2 groups of patients with respect to vegetations, calcifications, and patterns of inflammation. RESULTS: Histologically, infective endocarditis in patients with bioprostheses was characterized by demonstration of microorganisms, vegetations, and neutrophil-rich, inflammatory infiltrates. Valve tissue specimens from patients whose bioprosthetic valves were removed because of noninfective complications showed, in 30% of cases, inflammatory infiltrates mainly composed of macrophages and lymphocytes. Inflammatory adherent thrombi that can occur to the surface of noninfective degenerative bioprostheses are differentiated because their vegetations have macrophage-rich content. A neutrophil surface area with a cutoff value of > or =1.5% of the total valve tissue surface area is highly specific (94%) for infective endocarditis. CONCLUSIONS: When no microorganisms are detected and vegetations are not found in bioprosthetic valve tissues during the histological examination, a neutrophil-rich inflammation might better define the term "active endocarditis" in the Duke criteria and would allow differentiation between infective endocarditis and inflammatory, noninfective valve processes in patients with bioprosthetic valves.

Adult↗

PubMed2006

Comparative genomics of multidrug resistance in Acinetobacter baumannii.

Acinetobacter baumannii is a species of nonfermentative gram-negative bacteria commonly found in water and soil. This organism was susceptible to most antibiotics in the 1970s. It has now become a major cause of hospital-acquired infections worldwide due to its remarkable propensity to rapidly acquire resistance determinants to a wide range of antibacterial agents. Here we use a comparative genomic approach to identify the complete repertoire of resistance genes exhibited by the multidrug-resistant A. baumannii strain AYE, which is epidemic in France, as well as to investigate the mechanisms of their acquisition by comparison with the fully susceptible A. baumannii strain SDF, which is associated with human body lice. The assembly of the whole shotgun genome sequences of the strains AYE and SDF gave an estimated size of 3.9 and 3.2 Mb, respectively. A. baumannii strain AYE exhibits an 86-kb genomic region termed a resistance island--the largest identified to date--in which 45 resistance genes are clustered. At the homologous location, the SDF strain exhibits a 20 kb-genomic island flanked by transposases but devoid of resistance markers. Such a switching genomic structure might be a hotspot that could explain the rapid acquisition of resistance markers under antimicrobial pressure. Sequence similarity and phylogenetic analyses confirm that most of the resistance genes found in the A. baumannii strain AYE have been recently acquired from bacteria of the genera Pseudomonas, Salmonella, or Escherichia. This study also resulted in the discovery of 19 new putative resistance genes. Whole-genome sequencing appears to be a fast and efficient approach to the exhaustive identification of resistance genes in epidemic infectious agents of clinical significance.

Acinetobacter Infections↗

PubMed2006

Sub-acute neuropathy in patients with African tick bite fever.

African tick bite fever (ATBF) caused by Rickettsia africae is an emerging health problem in travellers to sub-Saharan Africa. We here present 6 patients with evidence of long-lasting sub-acute neuropathy following ATBF contracted during safari trips to southern Africa. Three patients developed radiating pain, paresthaesia and/or motor weakness of extremities, 2 had hemi-facial pain and paresthaesia, and 1 developed unilateral sensorineural hearing loss. When evaluated 3-26 months after symptom onset, cerebrospinal fluid samples from 5 patients were negative for R. africae PCR and serology, but revealed elevated protein content in 3 and mild pleocytosis in 1 case. Despite extensive investigations, no plausible alternative causes of neuropathy could be identified. Treatment with doxycycline in 2 patients had no clinical effect. Given the current increase of international safari tourism to sub-Saharan Africa, more cases of sub-acute neuropathy following ATBF may well be encountered in Europe and elsewhere in the y to come.

Adult↗

PubMed2006

Estimation of prokaryote genomic DNA G+C content by sequencing universally conserved genes.

Determination of the DNA G+C content of prokaryotic genomes using traditional methods is time-consuming and results may vary from laboratory to laboratory, depending on the technique used. We explored the possibility of extrapolating the genomic DNA G+C content of prokaryotes from gene sequences. For this, 127 universally conserved genes were studied from 50 prokaryotic genomes in the Clusters of Orthologous Groups database. Of these, 57 genes were present as a single copy in the genomes of 157 different prokaryote species available in GenBank. There was a strong correlation [coefficient of determination (r2) >95 %] between the DNA G+C contents of 20 genes and their corresponding genomes. For each of the 157 prokaryotic genomes studied, the DNA G+C content of the 20 genes was used to determine a 'calculated' genome DNA G+C content (CGC) and this value was compared with the 'real' genome DNA G+C content (RGC). In order to select the most suitable gene for the determination of CGC values, we compared the r2 and median mol% difference between CGC and RGC as well as the sensitivity of each gene to provide CGC values for prokaryotic genomes that differ by less than 5 mol% from their RGC. The highly conserved ftsY gene (median size 1144 nucleotides), a vertically inherited member of the GTPase superfamily, showed the highest r2 value of 0.98, the smallest median mol% difference between CGC and RGC of 1.06 and a sensitivity of 100 %. Using ftsY DNA G+C content values, the CGC values of 100 genomes not included in the calculation of r2 differed by less than 5 mol% from their RGC values. These data suggest that the genomic DNA G+C content of prokaryotes may be estimated easily and reliably from the ftsY gene sequence.

Bacteria↗

PubMed2006

Rickettsia tamurae sp. nov., isolated from Amblyomma testudinarium ticks.

Rickettsia sp. strain AT-1(T) was isolated from Amblyomma testudinarium ticks in Japan in 1993. Comparative analysis of sequences obtained from 16S rRNA, gltA, ompA, ompB and sca4 gene fragments demonstrated those from AT-1(T) to be markedly different from those of other members of the spotted fever group. Using mouse serotyping, it was also observed that Rickettsia sp. strain AT-1(T) was different from other Rickettsia species with validly published names. Such genotypic and phenotypic characteristics warrant its classification as a representative of a novel species, for which the name Rickettsia tamurae sp. nov. is proposed, with the type strain AT-1(T) (=CSUR R1(T)).

Bacterial Outer Membrane Proteins↗

PubMed2006

Rickettsia asiatica sp. nov., isolated in Japan.

The characterization of a novel Rickettsia species, first isolated from Ixodes ovatus ticks in Japan in 1993, is described for which the name Rickettsia asiatica sp. nov. is proposed. Using multilocus sequence comparison, five rickettsial isolates from I. ovatus collected at various locations in Japan were found to be identical but belonged to a novel species. Serotyping also demonstrated this rickettsia to be distinct from previously described Rickettsia species. The type strain of Rickettsia asiatica sp. nov. is IO-1(T) (=CSUR R2(T)). Following discussions held at the meeting of the International Committee on Systematics of Prokaryotes (ICSP) and its Judicial Commission (JC) in San Francisco, 2005, and in anticipation of the published minutes of the JC and ICSP, a committee consisting of the chairman of the ICSP, the chairman of the Judicial Commission of the ICSP and the Editor of the IJSEM has granted an exception in this case to the Rule governing the deposit of type material in two different collections in two different countries.

Animals↗

PubMed2006

Multispacer typing to study the genotypic distribution of Bartonella henselae populations.

Bartonella henselae, a worldwide fastidious bacterium, has a feline reservoir and is pathogenic for humans. However, the relationship between human and cat isolates of B. henselae, as well as its population dynamics and geographic heterogeneity, is not fully understood, in part because of the absence of appropriate typing methods. Multilocus sequence typing (MLST), the most discriminatory genotyping method for B. henselae, identified seven genotypes and suggested that human isolates arose from a limited number of cat isolates. Herein, we estimated the discriminatory power of multispacer typing (MST) by studying 126 B. henselae cat isolates from various areas of Europe, Asia, and the United States. We identified the nine most variable intergenic spacers conserved by both B. henselae and Bartonella quintana genomes. By comparing the sequences obtained from these nine spacers for each studied isolate, we identified 39 MST genotypes. The distribution of isolates into MST genotypes matched their phylogenetic organization into four clusters. MST showed that European and Asian isolates were different, in contrast with American isolates, but failed to identify pandemic strains. Our study demonstrated that MST is a powerful method for genotyping B. henselae at the strain level and may serve in studying the population dynamics of this bacterium and understanding the relationships between cat and human isolates. Finally, we provide a free-access MST-Rick online software program (http://ifr48.timone.univ-mrs.fr/MST_BHenselae/mst) that investigators may use to compare their own MST sequences to our database.

Animals↗

PubMed2006

Genetic differentiation of Chinese isolates of Rickettsia sibirica by partial ompA gene sequencing and multispacer typing.

Current data on rickettsiae and rickettsial diseases in China remain limited. Using partial ompA gene sequencing and multispacer typing, we identified 15 rickettsial isolates from China. All isolates were found to belong to Rickettsia sibirica subsp. sibirica. Four isolates from Dermacentor sinicus collected in Beijing, China, were fully identical to strain BJ-90, previously demonstrated to belong to R. sibirica subsp. sibirica despite antigenic and genotypic specificities. All 11 remaining isolates were similar to the R. sibirica subsp. sibirica type strain, 246. These were widely distributed in China in humans and different tick species. We emphasize the importance of surveying the distribution of R. sibirica in China.

Animals↗

PubMed2006

Endocarditis caused by Cardiobacterium valvarum.

A fastidious, gram-negative bacterium was isolated from the blood of a 51-year-old man who had acute infectious endocarditis (IE). Characterization of the organism through phenotypic and genotypic analyses revealed the causative role of Cardiobacterium valvarum. This is the third reported case of IE caused by C. valvarum.

Cardiobacterium↗

PubMed2006

Ecology and molecular epidemiology of tick-borne rickettsioses and anaplasmoses with natural foci in Russia and Kazakhstan.

During our more than 20 years of monitoring, we have used epidemiological, field, and experimental methods for characterization of natural foci of tick-borne rickettsioses in Russia. The main results were obtained through genetic methods (PCR sequence) at the Université de la Mediterranée (Marseille, France). We describe considerable heterogeneity of tick-borne alpha(1)-proteobacteria: 16 microorganisms the of the order Rickettsiales were detected in Russia and Kazakhstan. R. sibirica-caused North Asiatic tick-borne rickettsiosis is the main tick-borne rickettsiosis in Russia, with wide distribution in Siberia and the Russian Far East and high epidemic activity of natural foci of different landscape types. Our results show circulation of different pathogenic rickettsiae in the same endemic territories. In the Far East region, R. sibirica subsp. R. sibirica, R. sibirica subsp. BJ-90, and R. heilongjiangensis were detected; in the Altay and Krasnojarsk regions, R. sibirica subsp. R. sibirica and R. heilongjiangensis; and in the Kurgan district of West Siberia, R. sibirica subsp. R. sibirica and R. slovaca. The roles of more than 15 new genotypes of alpha(1)-proteobacteria in infectious disease in Russia and Kazakhstan are in need of further study.

Anaplasma↗

PubMed2006

Far eastern tick-borne rickettsiosis: identification of two new cases and tick vector.

We recently reported the first documented cases of a new rickettsial disease caused by Rickettsia heilongjiangensis in the Russian Far East (Far Eastern tick-borne rickettsiosis). Here we report the amplification of DNA of R. heilongjiangensis from both the skin biopsy of an acutely ill patient and the tick removed from him prior to the disease development. The tick has been identified as Haemaphysalis spp. The clinical picture was that of a spotted fever group rickettsiosis and a seroconversion was noted with R. heilongjiangensis antigen. Screening testing of both species of Haemaphysalis ticks inhabiting Russian Far Eastern regions showed that up to 28.13% of H. concinnae and 4.48% of H. japonica douglasii ticks harbor R. heilongjiangensis. It has been concluded that H. concinnae may serve as the main vector for the transmission of R. heilongjiangensis. H. japonica douglasii ticks harbor several varieties of rickettsiae. DNA of "Candidatus Rickettsia tarasevichiae," previously found in Ixodes persulcatus ticks, was amplified from one male tick. Two sequenced complete gltA genes belong to the novel spotted fever group rickettsial species provisionally called here "Candidatus Rickettsia principis" variants Hjd54 and Hjd61. The rate of infection has been found to be not higher than 1.5%.

Adult↗

PubMed2006

Detection of members of the genera Rickettsia, Anaplasma, and Ehrlichia in ticks collected in the Asiatic part of Russia.

A total of 395 adult ixodid ticks from three genera (Dermacentor, Haemaphysalis, and Ixodes) collected from the Urals to the Far East of Russia were tested by PCR and sequencing for the presence of spotted fever rickettsiae, anaplasmae, and ehrlichiae. Four, pathogens recognized in humans were detected in ticks: Rickettsia sibirica, R. heilongjiangensis, R. helvetica, and Anaplasma phagocytophilum. In addition, rickettsiae and ehrlichiae of unknown pathogenicity were detected, including Rickettsia sp. RpA4, Rickettsia sp. DnS14, Rickettsia sp. DnS28, "Candidatus R. tarasevichiae," a rickettsia closely related to R. helvetica, A. bovis, Ehrlichia muris, "Ehrlichia-like" "Schotti variant," and bacterium "Montezuma." Our findings indicated the distribution of rickettsiae and ehrlichiae in hard ticks in Russia.

Anaplasma↗

PubMed2006

Proposal to create subspecies of Rickettsia sibirica and an emended description of Rickettsia sibirica.

The Rickettsia sibirica species is composed of isolates that are genotypically close but can be classified within two distinct serotypes, that is, R. sibirica sensu stricto and R. sibirica mongolitimonae (incorrectly named R. mongolotimonae). We investigated the possibility of classifying rickettsiae closely related to R. sibirica as R. sibirica subspecies, as proposed by the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. For this, we first estimated the genotypic variability by using multilocus sequence typing (MLST), including the sequencing of five genes, and multispacer typing (MST) using three intergenic spacers, of five isolates and three tick amplicons of R. sibirica sensu stricto and six isolates of R. sibirica mongolotimonae. Then, we selected a representative of each MLST genotype and used mouse serotyping to estimate their degree of taxonomic relatedness. Among the 14 isolates or tick amplicons studied, 2 MLST genotypes were identified: (i) the R. sibirica sensu stricto type; and (ii) the R. sibirica mongolitimonae type. Representatives of the two MLST types were classified within three MST types and into two serotypes. Therefore, as isolates within the R. sibirica species are genotypically homogeneous but show MST genotypic, serotypic, and epidemio-clinical dissimilarities, we propose to modify the nomenclature of the R. sibirica species through the creation of subspecies. We propose the names R. sibirica subsp. sibirica subsp. nov. (type strain = 2-4-6, ATCC VR-541(T)), and R. sibirica subsp. mongolitimonae subsp. nov. (type strain = HA-91, ATCC VR-1526(T)). The description of R. sibirica is emended to accommodate the two subspecies.

Animals↗