Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting.

Whole genome sequencing (WGS) can elucidate Mycobacterium tuberculosis (Mtb) transmission patterns but more data is needed to guide its use in high-burden settings. In a household-based TB transmissibility study in Peru, we identified a large MIRU-VNTR Mtb cluster (148 isolates) with a range of resistance phenotypes, and studied host and bacterial factors contributing to its spread. WGS was performed on 61 of the 148 isolates. We compared transmission link inference using epidemiological or genomic data and estimated the dates of emergence of the cluster and antimicrobial drug resistance (DR) acquisition events by generating a time-calibrated phylogeny. Using a set of 12,032 public Mtb genomes, we determined bacterial factors characterizing this cluster and under positive selection in other Mtb lineages. Four of the 61 isolates were distantly related and the remaining 57 isolates diverged ca. 1968 (95%HPD: 1945-1985). Isoniazid resistance arose once and rifampin resistance emerged subsequently at least three times. Emergence of other DR types occurred as recently as within the last year of sampling. We identified five cluster-defining SNPs potentially contributing to transmissibility. In conclusion, clusters (as defined by MIRU-VNTR typing) may be circulating for decades in a high-burden setting. WGS allows for an enhanced understanding of transmission, drug resistance, and bacterial fitness factors.

Anaplasma marginale: Diversity, Virulence, and Vaccine Landscape through a Genomics Approach.

In order to understand the genetic diversity of A. marginale, several efforts have been made around the world. This rickettsia affects a significant number of ruminants, causing bovine anaplasmosis, so the interest in its virulence and how it is transmitted have drawn interest not only from a molecular point of view but also, recently, some genomics research have been performed to elucidate genes and proteins with potential as antigens. Unfortunately, so far, we still do not have a recombinant anaplasmosis vaccine. In this review, we present a landscape of the multiple approaches carried out from the genomic perspective to generate valuable information that could be used in a holistic way to finally develop an anaplasmosis vaccine. These approaches include the analysis of the genetic diversity of A. marginale and how this affects control measures for the disease. Anaplasmosis vaccine development is also reviewed from the conventional vaccinomics to genome-base vaccinology approach based on proteomics, metabolomics, and transcriptomics analyses reported. The use of these new omics approaches will undoubtedly reveal new targets of interest in the near future, comprising information of potential antigens and the immunogenic effect of A. marginale proteins.

Nonclassically secreted proteins as possible antigens for vaccine development: a reverse vaccinology approach.

Reverse vaccinology strategies have already been applied to a variety of microorganisms and have contributed significantly to vaccine development. However, most of the studies focused on an individual organism or on proteins with signature sequence motifs commonly found in known secreted proteins from bacteria. In this work, we applied a reverse vaccinology strategy based on conservation, virulence, and nonclassically surface exposure criterions to identify potential antigens in two microorganisms with significant degree of genomic plasticity among isolates (Streptococcus pneumoniae and Leptospira spp.), which imposes a major limitation to the production of a multistrain component vaccine. PSORTb 3.0.2 was run to predict the subcellular localization of the proteins. OrthoMCL was run to identify groups of the most conserved proteins between strains. Virulence prediction was done for the most conserved proteins, and SecretomeP was run to predict the nonclassically secreted proteins among the potential virulence factors. Based on the above criteria, we identified 37 proteins conserved between 16 genomes of S. pneumoniae and 12 proteins conserved between 5 leptospiral genomes as potential vaccine candidates.

Caracterização de proteínas de membrana de Leptospira interrogans expressas em Escherichia coli / Characterization of membrane proteins of Leptospira interrogans expressed in Escherichia coli

Leptospirose é uma zoonose altamente disseminada causada por espécies patogênicas do gênero Leptospira. Os roedores são os principais reservatórios da doença nos centros urbanos. Anualmente, são relatados no Brasil cerca de 5.000 casos os quais ocorrem como surtos epidêmicos nas épocas de chuva. O sequenciamento genômico da L. interrogans sorovar Copenhageni e os avanços das análises bioinformáticas permitiram a identificação de novos candidatos vacinais e novos fatores de virulência. Dessa forma, foram selecionadas através de bioinformática seis genes de L. interrogans sorovar Copenhageni LIC 10411, LIC12891, LIC 10827, LIC13305, LIC11469 e LIC11030, os quais foram submetidos a ensaios de conservação do DNA genômico, RNA mensageiro e proteína nativa correspondente em onze sorovares patogênicos prevalentes no Brasil em um saprovar saprofítico de Leptospira...

Leptospirosis is a widespread zoonosis caused by pathogenic species of the genus Leptospira. Rodents are the main reservoirs of the disease in the urban areas. Annually, arround 5,000 cases are reported in Brazil, wich occurs in endemic outbreaks during the rainy season. The genomic sequencing and the advances of bioinformatics analysis allowed the identification of new vaccine candidates and new virulence factors. Therefore, six genes from L. interrogans serovar Copenhageni: LIC 10411, LIC 12891, LIC 10827, LIC 13305, LIC 11469 and LIC11030, were selected through bionformatic tools and subjected to conservation assays employing genomic DNA, mRNA and native protein from eleven pathogenic serovars predominat in Brazil and one saprophytic serovar of Leptospira...