Predictive values according to estimated prevalence before (top) and after (bottom) threshold optimization.

<p>Predictive values according to estimated prevalence before (top) and after (bottom) threshold optimization.</p

Sensivities and 95% confidence intervals of the 3 serological assays according to genomospecies.

<p>Sensivities and 95% confidence intervals of the 3 serological assays according to genomospecies.</p

Comparative <i>Highlighter</i> analyses of <i>env</i> diversity in a donor-recipient HIV-1 transmission pair.

<p>(A) Recipient#1 shows evidence of infection with a single virus. (B) Donor#1 was the chronically infected partner of recipient#1. The same reference amplicon, a V3 RNA sequence from recipient plasma, was used to depict the viral diversity in both individuals.</p

Characteritics of the 8 donors.

¶<p>Results based on the declaration of the recipient.</p><p>EIA-RI test = enzyme-linked immunosorbent assay for recent infection <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069144#pone.0069144-Barin1" target="_blank">[29]</a>, PBMC = peripheral blood mononuclear cells; Het = heterosexual; MSM = man having sex with men; HBV = hepatits B virus; HBsAg = HBV surface antigen; HBsAb = HBV surface antibodies; HBcAb = HBV core antibodies; HCV = hepatitis C virus; n.d. = not done; n.a. = data not available; und = undetectable.</p

Evolutionary relationships between the HIV-1 <i>env</i> genes in the eight donor/recipient pairs.

<p>The evolutionary history was inferred using the Neighbor-Joining method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069144#pone.0069144-Boeras1" target="_blank">[38]</a>. The optimal tree with the sum of branch length = 2.01912678 is shown. The tree is drawn to scale, with branch length in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Maximum Composite Likelihood method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069144#pone.0069144-Whitney1" target="_blank">[39]</a> and the unit is the number of base substitutions per site. Codon positions included were 1^st+2^nd+3^rd+noncoding. All positions containing gaps and missing data were eliminated from the dataset. There were a total of 230 positions in the final dataset. Phylogenetic analyses were conducted in MEGA4 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069144#pone.0069144-Redd1" target="_blank">[40]</a>. For each recipient, viruses isolated from PBMC-derived DNA (•) and plasma RNA (○) are represented, with a different color for each donor/recipient pair. Asterisks indicate branches with bootstrap values greater than 98%.</p

Characteritics of the 8 recipients.

*<p>In the 6 months preceding PHI diagnosis.</p>§<p>Urethritis, rectitis, genital herpes infection, vulvo-vaginal candidosis, condyloma and/or syphilis.</p><p>PBMC = peripheral blood mononuclear cells; Het = heterosexual; MSM = man having sex with men; HBV = hepatits B virus; HBsAg = HBV surface antigen; HBsAb = HBV surface antibodies; HBcAb = HBV core antibodies; HCV = hepatitis C virus; n.d. = not done; und = undetectable.</p

Serovar Diversity of Pathogenic <em>Leptospira</em> Circulating in the French West Indies

<div><p>Background</p><p>Leptospirosis is one of the most important neglected tropical bacterial diseases in Latin America and the Caribbean. However, very little is known about the circulating etiological agents of leptospirosis in this region. In this study, we describe the serological and molecular features of leptospires isolated from 104 leptospirosis patients in Guadeloupe (n = 85) and Martinique (n = 19) and six rats captured in Guadeloupe, between 2004 and 2012.</p> <p>Methods and Findings</p><p>Strains were studied by serogrouping, PFGE, MLVA, and sequencing 16SrRNA and <i>secY</i>. DNA extracts from blood samples collected from 36 patients in Martinique were also used for molecular typing of leptospires via PCR. Phylogenetic analyses revealed thirteen different genotypes clustered into five main clades that corresponded to the species: <i>L. interrogans</i>, <i>L. kirschneri</i>, <i>L. borgpetersenii</i>, <i>L. noguchi</i>, and <i>L. santarosai</i>. We also identified <i>L. kmetyi</i> in at least two patients with acute leptospirosis. This is the first time, to our knowledge, that this species has been identified in humans. The most prevalent genotypes were associated with <i>L. interrogans</i> serovars Icterohaemorrhagiae and Copenhageni, <i>L. kirschneri</i> serovar Bogvere, and <i>L. borgpetersenii</i> serovar Arborea. We were unable to identify nine strains at the serovar level and comparison of genotyping results to the MLST database revealed new <i>secY</i> alleles.</p> <p>Conclusions</p><p>The overall serovar distribution in the French West Indies was unique compared to the neighboring islands. Typing of leptospiral isolates also suggested the existence of previously undescribed serovars.</p> </div

Phylogenetic relationships of leptospirosis isolates based on <i>secY</i> sequences.

<p>The tree was drawn using the UPGMA (unweighted pair group method with arithmetic average) algorithm. The species and genotype are indicated. Circle sizes correspond to the numbers of strains of each genotype. Isolates from Martinique are highlighted by a red background.</p

Identification of Leptospira DNA from acute-blood samples.

<p>NA: non applicable.</p><p>Ictero: Icterohaemorragiae.</p>a<p>: Partial sequencing of the 5′ variable region of the 16S rRNA gene of 201102111 and 201103362 showed 99% (277/279 nucleotides) with the reference strain of <i>L. kmetyi</i>.</p>b<p>: Partial sequencing of the 5′ variable region of the 16S rRNA gene of 201102109 showed identities to both <i>L. kmetyi</i> (273/279 nucleotides) and <i>L. kirschneri</i> (272/279 nucleotides).</p>c<p>: size in bp of the PCR products for VNTR4, VNTR7, and VNTR10.</p>d<p>: serovars Icterohaemorragiae and Copenhageni cannot be distinguished by molecular methods.</p

Representative PFGE patterns of NotI-digested genomic DNA from isolates from Martinique and Guadeloupe.

<p>The genotype is indicated for each clinical isolate, and reference strains for serovars Panama, Icterohaemorragiae, Tbaquite, Bogvere, Beye, Szwajizak, Trinidad, Gorgas, Caribe, Ballum, Castellonis, Arborea, Sulzeae, Navet, Atchafalaya, Rama, Darien, Chagres, Bravo, Nicaragua, Bajan, Peruviana, and Atlantae. The molecular weight size marker is bacteriophage lambda DNA concatemers of 50 kb.</p