Comparative genomics and phylogenomics of hemotrophic mycoplasmas

Hemotrophic mycoplasmas (hemoplasmas) are a group of animal pathogens of the Mollicutes class. Recently, the genomes of 8 hemoplasmas have been completely sequenced. The aim of this study was to gain a better understanding of their genomic features and relationship to other Mycoplasma species. The genome structure and dynamics of hemoplasmas were analyzed by evaluating gene synteny, adaptive evolution of paralogous gene families (PGF) and horizontal gene transfer (HGT). The Mollicutes class was then phylogenetically analyzed by constructing a distance matrix of the 16S rRNA genes and a phylogenetic tree with 32 conserved, concatenated proteins. Our results suggest that the hemoplasmas have dynamic genomes. The genome size variation (from 547 to 1,545 genes) indicates substantial gene gain/loss throughout evolution. Poorly conserved gene syntenies among hemoplasmas, positional shuffling of paralogous genes between strains, HGT, and codons under positive selection in PGFs were also observed. When compared to other Mollicutes species, the hemoplasmas experienced further metabolic reduction, and the 16S rRNA gene distance matrix of the available mollicutes suggests that these organisms presently constitute the most divergent clade within its class. Our phylogenetic tree of concatenated proteins showed some differences when compared to the 16S rRNA gene tree, but non-mycoplasma organisms, such as Ureaplasma spp. and Mesoplasma spp., continue to branch within Mycoplasma clades. In conclusion, while the hemoplasmas experienced further metabolic shrinkage through gene loss, PGFs with positively selected codons are likely beneficial to these species. Phylogeny of the mollicutes based on 16S rRNA genes or concatenated proteins do not obey the current taxonomy. The metabolism and genetic diversity of the mollicutes, the presence of HGT, and lack of standard for genus circumscription are likely to hinder attempts to classify these organisms based on phylogenetic analyses.Morris Animal Foundation, D10FE-004Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)CAPES-Fulbright Programa, ID 167307/

Dengue Virus Type 4 Phylogenetics in Brazil 2011: Looking beyond the Veil

Dengue Fever and Dengue Hemorrhagic Fever are diseases affecting approximately 100 million people/year and are a major concern in developing countries. In the present study, the phylogenetic relationship of six strains of the first autochthonous cases of DENV-4 infection occurred in Sao Paulo State, Parana State and Rio Grande do Sul State, Brazil, 2011 were studied. Nucleotide sequences of the envelope gene were determined and compared with sequences representative of the genotypes I, II, III and Sylvatic for DEN4 retrieved from GenBank. We employed a Bayesian phylogenetic approach to reconstruct the phylogenetic relationships of Brazilian DENV-4 and we estimated evolutionary rates and dates of divergence for DENV-4 found in Brazil in 2011. All samples sequenced in this study were located in Genotype II. The studied strains are monophyletic and our data suggest that they have been evolving separately for at least 4 to 6 years. Our data suggest that the virus might have been present in the region for some time, without being noticed by Health Surveillance Services due to a low level of circulation and a higher prevalence of DENV-1 and DENV- 2

Invasion of Ureaplasma diversum in bovine spermatozoids

<p>Abstract</p> <p>Background</p> <p><it>Ureaplasma diversum </it>has been associated with infertility in cows. In bulls, this mollicute colonizes the prepuce and distal portion of the urethra and may infect sperm cells. The aim of this study is to analyze <it>in vitro </it>interaction of <it>U. diversum </it>isolates and ATCC strains with bovine spermatozoids. The interactions were observed by confocal microscopy and the gentamycin internalization assay.</p> <p>Findings</p> <p><it>U. diversum </it>were able to adhere to and invade spermatozoids after 30 min of infection. The gentamicin resistance assay confirmed the intracellularity and survival of <it>U. diversum </it>in bovine spermatozoids.</p> <p>Conclusions</p> <p>The intracellular nature of bovine ureaplasma identifies a new difficulty to control the reproductive of these animals.</p

Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 – 2018

São Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paulo, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby helping to evaluate the risk of YFV spillover to humans. Data from infected NHPs can give more accurate insights into YFV spread than when using data from human cases alone. To contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in São Paulo, we generated and analysed virus genomic data and epizootic case data from NHPs in São Paulo. We report the occurrence of three spatiotemporally distinct phases of the outbreak in São Paulo prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in São Paulo, mostly sampled from NHPs between October 2016 and January 2018. Although we observe substantial heterogeneity in lineage dispersal velocities between phylogenetic branches, continuous phylogeographic analyses of generated YFV genomes suggest that YFV lineages spread in São Paulo at a mean rate of approximately 1km per day during all phases of the outbreak. Viral lineages from the first epizootic phase in northern São Paulo subsequently dispersed towards the south of the state to cause the second and third epizootic phases there. This alters our understanding of how YFV was introduced into the densely populated south of São Paulo state. Our results shed light on the sylvatic transmission of YFV in highly fragmented forested regions in São Paulo state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species

Syntenic maps of hemoplasma genomes.

<p>Plots were generated using comparative genomics suite CoGe SynMap and Sybil tool. In the SynMap analysis, each dot represents a matching gene pair. A) y-axis: <i>M. suis</i> Illinois, x-axis: <i>M. suis</i> KI3806; arrow indicates a 39,820 nt insertion in <i>M. suis</i> strain Illinois B) y-axis: <i>M. haemofelis</i> Langford1, x-axis: <i>M. haemofelis Ohio2</i> C) <i>M. haemocanis</i> Illinois x-axis: <i>M. haemofelis</i> Ohio2 D) y-axis: ‘<i>Candidatus</i> M. haemominutum’ Birmingham1, x-axis: <i>M. suis</i> Illinois E) y-axis: ‘<i>Candidatus</i> M. haemolamae’ Purdue, x-axis: ‘<i>Candidatus</i> M. haemominutum’ Birmingham1 F) y-axis: ‘<i>Candidatus</i> M. haemolamae’ Purdue, x-axis: <i>M. suis</i> Illinois G) y-axis: <i>M. wenyonii</i> Massachussets, x-axis: ‘<i>Candidatus</i> M. haemominutum’ Birmingham1 H) y-axis: <i>M. wenyonii</i> Massachussets, x-axis: <i>M. suis</i> Illinois. Other comparisons, which show less conserved synteny, are not shown for simplicity. Arrows indicate expansion of paralog gene families (PGF) as numbered in <i>M. haemofelis</i> Ohio2 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091445#pone.0091445-Santos1" target="_blank">[11]</a>. Circles indicate blocks of synteny. Sybil map used <i>M. haemocanis</i> as a reference genome. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091445#s2" target="_blank">Materials and Methods</a>.</p

Cluster of orthologous groups (COG) analysis of <i>Mollicutes</i> species.

<p>A) Functional categories comparison of the COGs of <i>Mollicutes</i> and hemoplasmas. B) COGs of <i>Mollicutes</i> (n = 108) and its phylogenetic clades (MYCO: Mycoplasma clade; MYCO-URO: Mycoplasma-Ureaplasma clade; MYCOIDES: Mycoides-Entomoplasmataceae cluster; PHYTO: Phytoplasma clade. Phylogenetic groups were defined as described by Volokhov et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091445#pone.0091445-Volokhov1" target="_blank">[62]</a>. The hemoplasmas are part of the Mycoplasma-Ureaplasma clade). X-axis indicate the number of COGs.</p

Putative gene candidates with phylogenetic support for HGT.

1<p>Two similar proteins annotated as hypoxanthine phosphoribosyltranferase are observed in <i>M. haemofelis</i> and <i>M. haemocanis</i> (MHF_0096, 0098 and MHC_00425, 00435; 24–26% identity, 475 to 498 amino acids long). It is possible that MHF_0096 and MHC_00425 are the <i>Mollicutes</i>-related genes and were not horizontally transferred; while MHF_0098 and MHC_00435, homologs to WEN_00280, were horizontally acquired, as demonstrated for WEN_00280.</p>2<p>Three copies of this gene were observed in <i>M. haemofelis</i> (Ohio2 and Langford1) and 4 copies were observed in <i>M. haemocanis</i>; only the genes listed were associated with HGT.</p>3<p>There are two copies of this gene in <i>M. haemofelis</i> and <i>M. haemocanis</i>; therefore, there is possibility of gene duplication and the results should be evaluated with caution.</p