Phylogenetic relationships of Ots TSA spacer domains.

<p>All the ATs from each of three spacer domains S-VDI, S-VDII/III and S-VDIII of Indian and South Korean TSA were used for constructing individual Neighbor-Joining phylogenetic trees using their amino acid sequences. The TSA country of origin, the AT type and number of samples with that AT domain type are indicated for each unique AT type for each data set (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0196240#pone.0196240.s006" target="_blank">S3 Table</a>) (e.g., India-24-18). The pairs of identical 12 AT present in both India and South Korea TSAs are highlighted with red circles. Only the nodes with ≥70 bootstrap values are shown (1000 bootstraps). The bracket values show the scale for amino acid differences for each domain.</p

Properties of peptides exhibiting HBA from Indian and South Korean TSAs.

<p>A) The mean binding affinity score was calculated from the binding affinity (score) of each predicted 15 aa peptides (sliding window approach) from ATs present in multiple strains with six prevalent HLA types studied from each country. A total of 7 and 5 ATs in S-VDI, 11 and 8 ATs in S-VDII/III and 13 and 8 ATs in S-VDIII were present in multiple Ots TSA sample sequences from India (blue) and South Korea (red), respectively. The overlapping 7 identical ATs present in multiple Ots strains from both India (blue dash lines) and Korea (red dash lines) TSA spacer domains are also shown. B) The range and the median average binding affinities of the peptides predicted from three spacer domains. C) Comparison of unique HBA TCEs from Indian and South Korean TSAs.</p

Complexity of type-specific 56 kDa antigen CD4 T-cell epitopes of <i>Orientia tsutsugamushi</i> strains causing scrub typhus in India

<div><p><i>Orientia tsutsugamushi</i> (Ots) is an obligate, intracellular, mite-transmitted human pathogen which causes scrub typhus. Understanding the diversity of Ots antigens is essential for designing specific diagnostic assays and efficient vaccines. The protective immunodominant type-specific 56 kDa antigen (TSA) of Ots varies locally and across its geographic distribution. TSA contains four hypervariable domains. We bioinformatically analyzed 345 partial sequences of TSA available from India, most of which contain only the three variable domains (VDI-III) and three spacer conserved domains (SVDI, SVDII/III, SVDIII). The total number (152) of antigenic types (amino acid variants) varied from 14–36 in the six domains of TSA that we studied. Notably, 55% (787/1435) of the predicted CD4 T-cell epitopes (TCEs) from all the six domains had high binding affinities (HBA) to at least one of the prevalent Indian human leukocyte antigen (HLA) alleles. A surprisingly high proportion (61%) of such TCEs were from spacer domains; indeed 100% of the CD4 TCEs in the SVDI were HBA. TSA sequences from India had more antigenic types (AT) than TSA from Korea. Overall, >90% of predicted CD4 TCEs from spacer domains were predicted to have HBA against one or more prevalent HLA types from Indian, Korean, Asia-Pacific region or global population data sets, while only <50% of CD4 TCEs in variable domains exhibited such HBA. The phylogenetically and immunologically important amino acids in the conserved spacer domains were identified. Our results suggest that the conserved spacer domains are predicted to be functionally more important than previously appreciated in immune responses to Ots infections. Changes occurring at the TCE level of TSA may contribute to the wide range of pathogenicity of Ots in humans and mouse models. CD4 T-cell functional experiments are needed to assess the immunological significance of these HBA spacer domains and their role in clearance of Ots from Indian patients.</p></div

Prevalent HLA-DRB1 alleles in different geographical regions and domain prevalence of Indian 15-amino acid TSA peptides with predicted high binding affinities.

<p>A) Top six most prevalent HLA-DRB1 alleles identified in populations in India, South Korea, Asia-Pacific region and global (<a href="http://allelefrequencies.net/" target="_blank">http://allelefrequencies.net/</a>), which were used to predict the binding affinity of all predicted 15 aa peptides from each AT from six domains of Indian TSA. B) The distribution of HBA T-cell epitopes predicted from Indian TSA antigenic types in each TSA domain. For each domain, the first set of bars shows the total number of predicted unique peptides and the number of these peptides identified with HBA to at-least one prevalent Indian HLA allele. Both the total number of predicted peptides and the peptides with HBA were further classified based on their presence in AT detected in single (SS) or multiple strains (MS) (bar pairs 2 and 3, respectively). C) Distribution (percentages) of peptides (15 aa) with HBAs from ATs identified in single (SS-uniquely present) and multiple (MS-shared sequences ≥2) Ots strains.The peptides present in both single and multiple strain sequences are highlighted in orange, the HBA peptides in SS and MS types are highlighted in purple and green, respectively.</p

Proportion of peptides with HBA (CD4 TCEs) from the six domains of TSA from India and South Korea.

<p>The bar diagrams show that the proportion of predicted HBA peptides from all ATs from each of six domains from A) India TSA and B) South Korea TSA. Six prevalent HLA-DRB1 alleles from four different population sets (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0196240#pone.0196240.g002" target="_blank">Fig 2A</a>) were used to identify the CD4 TSA TCEs with HBA.</p

Selected morphological and biological differences between human head and body lice.

<p>Selected morphological and biological differences between human head and body lice.</p

Therapeutic options for the treatment of pediculosis.

1<p>Permethrin is also used for impregnation of clothing for its arthropod repellent properties and as an agricultural pesticide.</p>2<p>Indicate information reported about pediculicidal (numerator) and ovicidal (denominator) activity of the insecticide. According to the report of the American Academy of Pediatrics, none of the currently available pediculicides is 100% ovicidal <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003724#ppat.1003724-Frankowski1" target="_blank">[38]</a>.</p>3<p>Partial ovicidal activity of permethrin has been reported <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003724#ppat.1003724-Durand1" target="_blank">[41]</a>.</p>4<p>At baseline, 38% of body lice collected from homeless were resistant to permethrin <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003724#ppat.1003724-Drali2" target="_blank">[43]</a>.</p>5<p>Possibility of occurrence of ivermectin resistance in body lice has been demonstrated in laboratory settings <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003724#ppat.1003724-Yoon1" target="_blank">[44]</a>.</p

Multivariate analysis of the effect of sex and life stage on the relatedness of <i>Amblyomma americanum</i> bacterial communities.

<p>Tick DNAs from the archival collection (n = 27) were older, collected in a different geographical region, and processed using different protocols than tick DNAs from the Georgia collection (n = 104).</p><p>*Corrected for multiple comparisons using Holm’s method; α  = 0.05.</p

Bacterial operational taxonomic unit (OTU) sequence abundance detected in tick samples.

<p>OTUs present in greater than one third of all tick samples were considered broadly distributed. OTUs present at a mean abundance ≥1% of the community (i.e. 10 sequences) were considered locally abundant. Sequence abundance values are slightly offset to reveal overlapping OTUs.</p

Significance of co-infection patterns between selected operational taxonomic units (OTUs).

<p>Only data from the Georgia tick DNA sample collection is shown. The upper triangle represents <i>p</i>-values of positive associations (codetection in the same sample) between OTUs and the lower triangle the <i>p</i>-values of negative associations. Black cells were not evaluated due to low expected co-occurrence (<1) between the OTUs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102130#pone.0102130-Veech1" target="_blank">[49]</a>.</p