ORCID Profile
0000-0003-4783-6641
Current Organisation
Universidade Estadual de Maringá
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Publisher: Cold Spring Harbor Laboratory
Date: 16-08-2021
DOI: 10.1101/2021.08.16.456539
Abstract: The growth of sequenced bacterial genomes has revolutionized the assessment of microbial ersity. Pseudomonas is a widely erse genus, containing more than 254 species. Although type strains have been employed to estimate Pseudomonas ersity, they represent a small fraction of the genomic ersity at a genus level. We used 10,035 available Pseudomonas genomes, including 210 type strains, to build a genomic distance network to estimate the number of species through community identification. We identified taxonomic inconsistencies with several type strains and found that 25.65% of the Pseudomonas genomes deposited on Genbank are misclassified. The phylogenetic tree using single-copy genes from representative genomes in each species cluster in the distance network revealed at least 14 Pseudomonas groups, including P. alcaligenes group proposed here. We show that Pseudomonas is likely an admixture of different genera and should be further ided. This study provides an overview of Pseudomonas ersity from a network and phylogenomic perspective that may help reduce the propagation of mislabeled Pseudomonas genomes.
Publisher: Cold Spring Harbor Laboratory
Date: 20-10-2022
DOI: 10.1101/2022.10.17.512634
Abstract: Genomic surveillance provides a data source complementary to contact tracing to resolve putative transmission chains. However, the role of within-host ersity in transmission is understudied due to a lack of experimental and clinical datasets that capture within-host ersity in both donors and recipients. Here, we assess the utility of deep-sequenced genomic surveillance within a mouse transmission model where the gastrointestinal pathogen Citrobacter rodentium was controllably spread during co-housing of infected and naïve animals. We observed that within-host variants were maintained over multiple transmission steps until fixation or elimination. We present a model for inferring the likelihood that a given pair of s les are linked by transmission, by comparing the allelic frequency at variant genomic loci . Our data affirm that within-host single nucleotide variants (iSNVs) can repeatedly pass from donor to recipient along the transmission chain, and the mere sharing of iSNVs between different transmission pairs offers limited confidence in identifying a transmission pair. Beyond the presence and absence of within-host variants, we show that differences arising in the relative abundance of iSNVs can infer transmission pairs with high precision. An important component of our approach is that the inference is based solely on sequence data, without incorporating epidemiological or demographic data for context. Our model, which substantially reduces the number of comparisons a contact tracer needs to consider, may enhance the accuracy of contact tracing and other epidemiological processes, including early detection of emerging transmission clusters.
Publisher: Cold Spring Harbor Laboratory
Date: 22-12-2020
DOI: 10.1101/2020.12.22.423983
Abstract: The Pseudomonas putida group comprises strains with biotechnological and clinical relevance. P. alloputida was proposed as a new species and highlighted the misclassification of P. putida . Nevertheless, the population structure of P. alloputida remained unexplored. We retrieved 11,025 Pseudomonas genomes and used P. alloputida Kh7 T to delineate the species. The P. alloputida population structure comprises at least 7 clonal complexes (CCs). Clinical isolates are mainly found in CC4 and acquired resistance genes are present at low frequency in plasmids. Virulence profiles support the potential of CC7 members to outcompete other plant or human pathogens through a type VI secretion system. Finally, we found that horizontal gene transfer had an important role in shaping the ability of P. alloputida to bioremediate aromatic compounds such as toluene. Our results provide the grounds to understand P. alloputida genetic ersity and safety for environmental applications.
Location: Brazil
No related grants have been discovered for Hemanoel Passarelli-Araujo.