Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana.

Environmental disturbances in the Neotropics (e.g., deforestation, agriculture intensification, urbanization) contribute to an increasing risk of cross-species transmission of microorganisms and to disease outbreaks due to changing ecosystems of reservoir hosts. Although Amazonia encompasses the greatest diversity of reservoir species, the outsized viral population diversity (virome) has yet to be investigated. Here, through a metagenomic approach, we identified 10,991 viral sequences in the saliva and feces of two bat species, Desmodus rotundus (hematophagous), trapped in two different caves surrounded by primary lowland forest, and Molossus molossus (insectivorous), trapped in forest and urban habitats. These sequences are related to 51 viral families known to infect a wide range of hosts (i.e., bacteria, plants, insects and vertebrates). Most viruses detected reflected the diet of bat species, with a high proportion of plant and insect-related viral families for M. molossus and a high proportion of vertebrate-related viral families for D. rotundus, highlighting its influence in shaping the viral diversity of bats. Lastly, we reconstructed the phylogenetic relationships for five vertebrate-related viral families (Nairoviridae, Circoviridae, Retroviridae, Herpesviridae, Papillomaviridae). The results showed highly supported clustering with other viral sequences of the same viral family hosted by other bat species, highlighting the potential association of viral diversity with the host's diet. These findings provide significant insight into viral bat diversity in French Guiana belonging to the Amazonian biome and emphasize that habitats and the host's dietary ecology may drive the viral diversity in the bat communities investigated.

Unraveling the genetic diversity and phylogeny of Leishmania RNA virus 1 strains of infected Leishmania isolates circulating in French Guiana.

INTRODUCTION: Leishmania RNA virus type 1 (LRV1) is an endosymbiont of some Leishmania (Vianna) species in South America. Presence of LRV1 in parasites exacerbates disease severity in animal models and humans, related to a disproportioned innate immune response, and is correlated with drug treatment failures in humans. Although the virus was identified decades ago, its genomic diversity has been overlooked until now. METHODOLOGY/PRINCIPLES FINDINGS: We subjected LRV1 strains from 19 L. (V.) guyanensis and one L. (V.) braziliensis isolates obtained from cutaneous leishmaniasis samples identified throughout French Guiana with next-generation sequencing and de novo sequence assembly. We generated and analyzed 24 unique LRV1 sequences over their full-length coding regions. Multiple alignment of these new sequences revealed variability (0.5%-23.5%) across the entire sequence except for highly conserved motifs within the 5' untranslated region. Phylogenetic analyses showed that viral genomes of L. (V.) guyanensis grouped into five distinct clusters. They further showed a species-dependent clustering between viral genomes of L. (V.) guyanensis and L. (V.) braziliensis, confirming a long-term co-evolutionary history. Noteworthy, we identified cases of multiple LRV1 infections in three of the 20 Leishmania isolates. CONCLUSIONS/SIGNIFICANCE: Here, we present the first-ever estimate of LRV1 genomic diversity that exists in Leishmania (V.) guyanensis parasites. Genetic characterization and phylogenetic analyses of these viruses has shed light on their evolutionary relationships. To our knowledge, this study is also the first to report cases of multiple LRV1 infections in some parasites. Finally, this work has made it possible to develop molecular tools for adequate identification and genotyping of LRV1 strains for diagnostic purposes. Given the suspected worsening role of LRV1 infection in the pathogenesis of human leishmaniasis, these data have a major impact from a clinical viewpoint and for the management of Leishmania-infected patients.

Identification of lymphocytic choriomeningitis mammarenavirus in house mouse (Mus musculus, Rodentia) in French Guiana.

Thirty-seven house mice (Mus musculus, Rodentia) caught in different localities in French Guiana were screened to investigate the presence of lymphocytic choriomeningitis mammarenavirus (LCMV). Two animals trapped in an urban area were found positive, hosting a new strain of LCMV, that we tentatively named LCMV "Comou". The complete sequence was determined using a metagenomic approach. Phylogenetic analyses revealed that this strain is related to genetic lineage I composed of strains inducing severe disease in humans. These results emphasize the need for active surveillance in humans as well as in house mouse populations, which is a rather common rodent in French Guianese cities and settlements.

A vanG-type locus in Clostridium argentinense.

OBJECTIVES: The objective was to study a new vanG-type locus in Clostridium argentinense vanGCar and to determine its impact on glycopeptide susceptibility of the host. METHODS: The whole genome of C. argentinense NCIB 10714 was sequenced using Illumina single-reads sequencing technology. The presence of vanGCar in seven C. argentinense strains was tested by PCR and its expression was tested by quantitative RT-PCR (qRT-PCR). Glycopeptide susceptibility was determined by the Etest procedure. RESULTS: The vanGCar locus contained four genes encoding a carboxypeptidase, a d-alanine:d-serine ligase, a serine transporter and a serine racemase, and was present in the seven C. argentinense studied. An AraC-type transcriptional regulator was found upstream from the genes. C. argentinense NCIB 10714 was susceptible to vancomycin and to teicoplanin. qRT-PCR experiments revealed that vanGCar was not expressed without or with induction by a subinhibitory concentration of vancomycin. CONCLUSIONS: The new vanGCar locus was cryptic in C. argentinense and intrinsic to this species. Emergence of vancomycin resistance in C. argentinense due to decryptification of the vanGCar gene cluster could occur.

Effects of mefloquine use on Plasmodium vivax multidrug resistance.

Numerous studies have indicated a strong association between amplification of the multidrug resistance-1 gene and in vivo and in vitro mefloquine resistance of Plasmodium falciparum. Although falciparum infection usually is not treated with mefloquine, incorrect diagnosis, high frequency of undetected mixed infections, or relapses of P. vivax infection triggered by P. falciparum infections expose non-P. falciparum parasites to mefloquine. To assess the consequences of such unintentional treatments on P. vivax, we studied variations in number of Pvmdr-1 (PlasmoDB accession no. PVX_080100, NCBI reference sequence NC_009915.1) copies worldwide in 607 samples collected in areas with different histories of mefloquine use from residents and from travelers returning to France. Number of Pvmdr-1 copies correlated with drug use history. Treatment against P. falciparum exerts substantial collateral pressure against sympatric P. vivax, jeopardizing future use of mefloquine against P. vivax. A drug policy is needed that takes into consideration all co-endemic species of malaria parasites.

Candida albicans is not always the preferential yeast colonizing humans: a study in Wayampi Amerindians.

In industrialized countries Candida albicans is considered the predominant commensal yeast of the human intestine, with approximately 40% prevalence in healthy adults. We discovered a highly original colonization pattern that challenges this current perception by studying in a 4- year interval a cohort of 151 Amerindians living in a remote community (French Guiana), and animals from their environment. The prevalence of C. albicans was persistently low (3% and 7% of yeast carriers). By contrast, Candida krusei and Saccharomyces cerevisiae were detected in over 30% of carriers. We showed that C. krusei and S. cerevisiae carriage was of food or environmental origin, whereas C. albicans carriage was associated with specific risk factors (being female and living in a crowded household). We also showed using whole-genome sequence comparison that C. albicans strains can persist in the intestinal tract of a healthy individual over a 4-year period.

Discordant temporal evolution of Pfcrt and Pfmdr1 genotypes and Plasmodium falciparum in vitro drug susceptibility to 4-aminoquinolines after drug policy change in French Guiana.

Analysis of the evolution of drug target genes under changing drug policy is needed to assist monitoring of Plasmodium falciparum drug resistance in the field. Here we genotype Pfcrt and Pfdmr1 of 700 isolates collected in French Guiana from 2000 (5 years after withdrawal of chloroquine) to 2008, i.e., the period when the artemether-lumefantrine combination was progressively introduced and mefloquine was abandoned. Gene sequencing showed fixation of the 7G8-type Pfcrt SMVNT resistance haplotype and near fixation of the NYCDY Pfdmr1 haplotype. Pfdmr1 gene copy number correlated with 50% inhibitory concentrations of mefloquine and halofantrine (r = 0.64 and 0.47, respectively, n = 547); its temporal changes paralleled changes in in vitro mefloquine susceptibility. However, the molecular parameters studied did not account for the regained in vitro susceptibility to chloroquine and showed a poor correlation with susceptibility to artemether, lumefantrine, or quinine. Identification of novel markers of resistance to these antimalarials is needed in this South American area.

High prevalence and fixation of Plasmodium vivax dhfr/dhps mutations related to sulfadoxine/pyrimethamine resistance in French Guiana.

Plasmodium vivax isolates from French Guiana were studied for the presence of mutations associated with sulfadoxine/pyrimethamine (SP) drug resistance. Ninety-six blood samples were collected from 2000 to 2005 from symptomatic malaria patients. SP drug resistance was predicted by determining point mutations in the dihydrofolate reductase (pvdhfr) and dihydropteroate synthase (pvdhps) genes. All samples showed mutant genotypes in both genes with a prevalence > 90% for the 58R, 117N, 382C, and 383G. A new mutation (116G) in pvdhfr was found at a frequency of 3.3%. Six different pvdhfr/dhps multilocus genotypes were observed with the predominance of the quintuple mutant-type 58R/117N/173L-382C/383G (59.3%). No significant differences were observed between the prevalence of haplotypes and the year of collection. Our results indicate that, in this area, the fixation of SP drug-resistant parasites in the P. vivax population is stable.

Sequence analysis of Plasmodium falciparum cytochrome b in multiple geographic sites.

BACKGROUND: The antimalarial drug atovaquone specifically targets Plasmodium falciparum cytochrome b (Pfcytb), a mitochondrial gene with uniparental inheritance. Cases of resistance to atovaquone associated with mutant Pfcytb have been reported, justifying efforts to better document the natural polymorphism of this gene. To this end, a large molecular survey was conducted in several malaria endemic areas where atovaquone was not yet in regular use. METHODS: The polymorphism of the Pfcytb was analysed by direct sequencing of PCR products corresponding to the full length coding region. Sequence was generated for 671 isolates originating from three continents: Africa (Senegal, Ivory Coast, Central African Republic and Madagascar), Asia (Cambodia) and South America (French Guiana). RESULTS: Overall, 11 polymorphic sites were observed, of which eight were novel mutations. There was a large disparity in the geographic distribution of the mutants. All isolates from Senegal, Central African Republic and Madagascar displayed a Camp/3D7 wild type Pfcytb sequence, as did most samples originating from Cambodia and Ivory Coast. One synonymous (t759a at codon V253V) and two non-synonymous (t553g and a581g at codons F185V and H194R, respectively) singletons were detected in Ivory Coast. Likewise, two synonymous (a126t and c793t at codons -T42T and L265L, respectively) singletons were observed in Cambodia. In contrast, seven mutated sites, affecting seven codons and defining four mutant haplotypes were observed in French Guiana. The wild type allele was observed in only 14% of the French Guiana isolates. The synonymous c688t mutation at position L230L was highly prevalent; the most frequent allele was the c688t single mutant, observed in 84% of the isolates. The other alleles were singletons (a126t/a165c, a4g/a20t/a1024c and a20t/t341c/c688t corresponding to T42T/S55S, N2D/N71I/I342L, N71I/L114S/L230L, respectively" please replace with ' corresponding to T42T/S55S, N2D/N71I/I342L and N71I/L114S/L230L, respectively). The codon 268 polymorphisms associated with atovaquone resistance were not observed in the panel the isolates studied. Overall, the wild type PfCYTb protein isoform was highly predominant in all study areas, including French Guiana, suggesting stringent functional constraints. CONCLUSION: These data along with previously identified Pfcytb field polymorphisms indicate a clustering of molecular signatures, suggesting different ancestral types in South America and other continents. The absence of mutations associated with most atovaquone-proguanil clinical failures indicates that the atovaquone-proguanil association is an interesting treatment option in the study areas.

Crotoxin, half-century of investigations on a phospholipase A2 neurotoxin

La crotoxina, el mayor componente tóxico del veneno de serpiente cascabel sudamericana Crotalus durissus terrificus, es una fosolipasa A2 neurotóxica que ejerce su acción bloqueando la transmisión neuromuscular. Actúa primariamente alterando la liberación de acetilcolina de las terminales nerviosas mediante un mecanismo todavía no elucidado. Actúa también en membranas postsinápticas estabilizando el receptor de acetilcolina en una configuración inactiva semejante al estado de desensibilización. La crotoxina comprende dos subnuidades distintas: una fosoflipasa A2 básica y débilmente tóxica (componente B) y una acídica y no tóxica (componente A) que no posee actividad enzimática. La subunidad de fosfolipasa A2 se une en forma inespecífica y no saturable a membranas biológicas, mientras que en presencia delo componente A interacciona solamente con un limitado número de sitios de unión de alta afinidad presentes en membranas sinápticas pero no en eritrocitos. Experimentos de unión realizados con vesículas fosfolipídicas unilamelares de diferente composición indicaron que algunos de los fosfolípidos cargados negativamente, como los mono y difosfoinositósidos, podrían ser parte del sitio aceptor de crotoxina. La crotoxina es en realidad una mexcla de diversas isoformas de estructura peptídica similar pero no idéntica. Estas isoformas difieren levemente en su actividad enzimática y farmacológica. Estudios realizados con anticuerpos policonales preparados contra ambas subunidades anticomponente B (Fab) inhiben la actividad fosfolipasa A2 y neutralizan la potencia letal, lo que sugiere que los sitios tóxicos y catalíticos de la crotoxina están relacionados (AU)

Crotoxin, half-century of investigations on a phospholipase A2 neurotoxin

La crotoxina, el mayor componente tóxico del veneno de serpiente cascabel sudamericana Crotalus durissus terrificus, es una fosolipasa A2 neurotóxica que ejerce su acción bloqueando la transmisión neuromuscular. Actúa primariamente alterando la liberación de acetilcolina de las terminales nerviosas mediante un mecanismo todavía no elucidado. Actúa también en membranas postsinápticas estabilizando el receptor de acetilcolina en una configuración inactiva semejante al estado de desensibilización. La crotoxina comprende dos subnuidades distintas: una fosoflipasa A2 básica y débilmente tóxica (componente B) y una acídica y no tóxica (componente A) que no posee actividad enzimática. La subunidad de fosfolipasa A2 se une en forma inespecífica y no saturable a membranas biológicas, mientras que en presencia delo componente A interacciona solamente con un limitado número de sitios de unión de alta afinidad presentes en membranas sinápticas pero no en eritrocitos. Experimentos de unión realizados con vesículas fosfolipídicas unilamelares de diferente composición indicaron que algunos de los fosfolípidos cargados negativamente, como los mono y difosfoinositósidos, podrían ser parte del sitio aceptor de crotoxina. La crotoxina es en realidad una mexcla de diversas isoformas de estructura peptídica similar pero no idéntica. Estas isoformas difieren levemente en su actividad enzimática y farmacológica. Estudios realizados con anticuerpos policonales preparados contra ambas subunidades anticomponente B (Fab) inhiben la actividad fosfolipasa A2 y neutralizan la potencia letal, lo que sugiere que los sitios tóxicos y catalíticos de la crotoxina están relacionados