scholarly journals Insights about the epidemiology of Salmonella Typhimurium isolates from different sources in Brazil using comparative genomics

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Amanda Ap. Seribelli ◽  
Patrick da Silva ◽  
Marcelo Ferreira da Cruz ◽  
Fernanda de Almeida ◽  
Miliane R. Frazão ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Efflux Pump ◽  
Single Copy ◽  
Marker Genes ◽  
Pathogenic Potential ◽  
Orthologous Protein ◽  
Regulatory Processes ◽  
Protein Clusters ◽  
Single Cluster ◽  
Different Sources

Abstract Background Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is an important zoonotic agent worldwide. The aim of this work was to compare genetically 117 S. Typhimurium isolated from different sources over 30 years in Brazil using different genomics strategies. Results The majority of the 117 S. Typhimurium strains studied were grouped into a single cluster (≅ 90%) by the core genome multilocus sequence typing and (≅ 77%) by single copy marker genes. The phylogenetic analysis based on single nucleotide polymorphism (SNP) grouped most strains from humans into a single cluster (≅ 93%), while the strains isolated from food and swine were alocated into three clusters. The different orthologous protein clusters found for some S. Typhimurium isolated from humans and food are involved in metabolic and regulatory processes. For 26 isolates from swine the sequence types (ST) 19 and ST1921 were the most prevalent ones, and the ST14, ST64, ST516 and ST639 were also detected. Previous results typed the 91 S. Typhimurium isolates from humans and foods as ST19, ST313, ST1921, ST3343 and ST1649. The main prophages detected were: Gifsy-2 in 79 (67.5%) and Gifsy-1 in 63 (54%) strains. All of the S. Typhimurium isolates contained the acrA, acrB, macA, macB, mdtK, emrA, emrB, emrR and tolC efflux pump genes. Conclusions The phylogenetic trees grouped the majority of the S. Typhimurium isolates from humans into a single cluster suggesting that there is one prevalent subtype in Brazil. Regarding strains isolated from food and swine, the SNPs’ results suggested the circulation of more than one subtype over 30 years in this country. The orthologous protein clusters analysis revealed unique genes in the strains studied mainly related to bacterial metabolism. S. Typhimurium strains from swine showed greater diversity of STs and prophages in comparison to strains isolated from humans and foods. The pathogenic potential of S. Typhimurium strains was corroborated by the presence of exclusive prophages of this serovar involved in its virulence. The high number of resistance genes related to efflux pumps is worrying and may lead to therapeutic failures when clinical treatment is needed.

scholarly journals Insights about the Epidemiology of Salmonella Typhimurium Isolates from different Sources in Brazil using Comparative Genomics

2020 ◽  
Author(s):  
Amanda Seribelli ◽  
Patrick da Silva ◽  
Marcelo da Cruz ◽  
Fernanda de Almeida ◽  
Miliane Frazão ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Efflux Pump ◽  
Phylogenetic Analyses ◽  
Efflux Pumps ◽  
Marker Genes ◽  
Pathogenic Potential ◽  
Orthologous Protein ◽  
Protein Clusters ◽  
Single Cluster ◽  
Different Sources

Abstract Background: Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is an important zoonotic agent worldwide. In Brazil, there are few published studies that have characterized the possible differences of S. Typhimurium strains isolated from humans, foods and animal by whole genome sequencing (WGS). The aim of this work was to compare genetically 117 S. Typhimurium isolates from different sources from 30 years (1983 to 2013) in Brazil using different genomics strategies, including: phylogenetic analysis; orthologous protein clusters analysis; Multi-locus sequence typing (MLST); prophages and resistance genes screening related to efflux pumps. Results: The majority of the 117 S. Typhimurium strains studied were grouped into a single cluster (≅90%) by the genome core (cgMLST) and (≅77%) by single copy marker genes (ggTree). The different orthologous protein clusters found for some S. Typhimurium strains isolated from humans and food are involved in metabolic and regulatory processes. For 26 S. Typhimurium isolates from swine the sequence type (ST) 19 was the most common, the ST1921 was the second most prevalent and the STs 14, 64, 516 and 639 were also detected. The main prophages detected were: Gifsy-2 in 79 (67.5%) and Gifsy-1 in 63 (54%) S. Typhimurium isolates. All of the S. Typhimurium isolates contained the acrA, acrB, macA, macB, mdtK, emrA, emrB, emrR and tolC efflux pump genes. Conclusions: Phylogenetic analyses grouped the majority of the S. Typhimurium isolates into a single cluster suggesting that there is one prevalent subtype that has successful contaminated human, food and animal sources for 30 years in Brazil. The orthologous protein clusters analysis revealed unique genes in the S. Typhimurium studied mainly related to bacterial metabolism and that may be important in their pathogenicity. S. Typhimurium isolates from swine showed greater diversity of STs and prophages in comparison to S. Typhimurium strains isolated from humans and foods. The pathogenic potential of S. Typhimurium strains was corroborated by the presence of exclusive prophages of this serovar involved in their virulence. The high number of resistance genes related to efflux pumps is worrying and may lead to therapeutic failures when treatment is needed.

scholarly journals Real-Time PCR for Molecular Detection of Zoonotic and Non-Zoonotic Giardia spp. in Wild Rodents

2021 ◽  
Vol 9 (8) ◽  
pp. 1610
Author(s):  
Christian Klotz ◽  
Elke Radam ◽  
Sebastian Rausch ◽  
Petra Gosten-Heinrich ◽  
Toni Aebischer
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Gastrointestinal Disease ◽  
Single Copy ◽  
Marker Genes ◽  
Small Rodent ◽  
Analytical Sensitivity ◽  
Single Copy Gene ◽  
Wild Rodents ◽  
Copy Gene

Giardiasis in humans is a gastrointestinal disease transmitted by the potentially zoonotic Giardia duodenalis genotypes (assemblages) A and B. Small wild rodents such as mice and voles are discussed as potential reservoirs for G. duodenalis but are predominantly populated by the two rodent species Giardia microti and Giardia muris. Currently, the detection of zoonotic and non-zoonotic Giardia species and genotypes in these animals relies on cumbersome PCR and sequencing approaches of genetic marker genes. This hampers the risk assessment of potential zoonotic Giardia transmissions by these animals. Here, we provide a workflow based on newly developed real-time PCR schemes targeting the small ribosomal RNA multi-copy gene locus to distinguish G. muris, G. microti and G. duodenalis infections. For the identification of potentially zoonotic G. duodenalis assemblage types A and B, an established protocol targeting the single-copy gene 4E1-HP was used. The assays were specific for the distinct Giardia species or genotypes and revealed an analytical sensitivity of approximately one or below genome equivalent for the multi-copy gene and of about 10 genome equivalents for the single-copy gene. Retesting a biobank of small rodent samples confirmed the specificity. It further identified the underlying Giardia species in four out of 11 samples that could not be typed before by PCR and sequencing. The newly developed workflow has the potential to facilitate the detection of potentially zoonotic and non-zoonotic Giardia species in wild rodents.

scholarly journals Whole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia

2021 ◽  
Vol 15 (8) ◽  
pp. e0009665
Author(s):  
Shuai Xu ◽  
Zhenpeng Li ◽  
Yuanming Huang ◽  
Lichao Han ◽  
Yanlin Che ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Gene Families ◽  
Single Copy ◽  
Taxonomic Classification ◽  
Genomic Diversity ◽  
Evolutionary Relationships ◽  
Taxonomic Structure ◽  
Pan Genome ◽  
Dipeptidyl Aminopeptidase

Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Our study revealed an open pan-genome for Nocardia containing 265,836 gene families, with about 99.7% of the pan-genome being variable. Horizontal gene transfer appears to have been an important evolutionary driver of genetic diversity shaping the Nocardia genome and may have caused historical taxonomic confusion from other taxa (primarily Rhodococcus, Skermania, Aldersonia, and Mycobacterium). Based on single-copy gene families, we established a high-accuracy phylogenomic approach for Nocardia using 229 genome sequences. Furthermore, we found 28 potentially new species and reclassified 16 strains. Finally, by comparing the topology between a phylogenomic tree and 384 phylogenetic trees (from 384 single-copy genes from the core genome), we identified a novel locus for inferring the phylogeny of this genus. The dapb1 gene, which encodes dipeptidyl aminopeptidase BI, was far superior to commonly used markers for Nocardia and yielded a topology almost identical to that of genome-based phylogeny. In conclusion, the present study provides insights into the genetic diversity, contributes a robust framework for the taxonomic classification, and elucidates the evolutionary relationships of Nocardia. This framework should facilitate the development of rapid tests for the species identification of highly variable species and has given new insight into the behavior of this genus.

scholarly journals GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring

2022 ◽  
Vol 12 ◽  
Author(s):  
Ilona A. Ruhl ◽  
Andriy Sheremet ◽  
Chantel C. Furgason ◽  
Susanne Krause ◽  
Robert M. Bowers ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Hot Spring ◽  
Gc Content ◽  
Gene Copy ◽  
Marker Genes ◽  
Rrna Gene ◽  
Separate Species ◽  
Distinct Subgroup

GAL08 are bacteria belonging to an uncultivated phylogenetic cluster within the phylum Acidobacteria. We detected a natural population of the GAL08 clade in sediment from a pH-neutral hot spring located in British Columbia, Canada. To shed light on the abundance and genomic potential of this clade, we collected and analyzed hot spring sediment samples over a temperature range of 24.2–79.8°C. Illumina sequencing of 16S rRNA gene amplicons and qPCR using a primer set developed specifically to detect the GAL08 16S rRNA gene revealed that absolute and relative abundances of GAL08 peaked at 65°C along three temperature gradients. Analysis of sediment collected over multiple years and locations revealed that the GAL08 group was consistently a dominant clade, comprising up to 29.2% of the microbial community based on relative read abundance and up to 4.7 × 105 16S rRNA gene copy numbers per gram of sediment based on qPCR. Using a medium quality threshold, 25 single amplified genomes (SAGs) representing these bacteria were generated from samples taken at 65 and 77°C, and seven metagenome-assembled genomes (MAGs) were reconstructed from samples collected at 45–77°C. Based on average nucleotide identity (ANI), these SAGs and MAGs represented three separate species, with an estimated average genome size of 3.17 Mb and GC content of 62.8%. Phylogenetic trees constructed from 16S rRNA gene sequences and a set of 56 concatenated phylogenetic marker genes both placed the three GAL08 bacteria as a distinct subgroup of the phylum Acidobacteria, representing a candidate order (Ca. Frugalibacteriales) within the class Blastocatellia. Metabolic reconstructions from genome data predicted a heterotrophic metabolism, with potential capability for aerobic respiration, as well as incomplete denitrification and fermentation. In laboratory cultivation efforts, GAL08 counts based on qPCR declined rapidly under atmospheric levels of oxygen but increased slightly at 1% (v/v) O2, suggesting a microaerophilic lifestyle.

scholarly journals Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data

2019 ◽  
Vol 37 (2) ◽  
pp. 599-603 ◽  
Author(s):  
Li-Gen Wang ◽  
Tommy Tsan-Yuk Lam ◽  
Shuangbin Xu ◽  
Zehan Dai ◽  
Lang Zhou ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
R Package ◽  
External Data ◽  
Input And Output ◽  
Evolutionary Context ◽  
Tree Data ◽  
Downstream Analysis ◽  
Different Sources ◽  
Associated Data

Abstract Phylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different analyses in a comparative study. The treeio package is designed to connect phylogenetic tree input and output. It supports extracting phylogenetic trees as well as the outputs of commonly used analytical software. It can link external data to phylogenies and merge tree data obtained from different sources, enabling analyses of phylogeny-associated data from different disciplines in an evolutionary context. Treeio also supports export of a phylogenetic tree with heterogeneous-associated data to a single tree file, including BEAST compatible NEXUS and jtree formats; these facilitate data sharing as well as file format conversion for downstream analysis. The treeio package is designed to work with the tidytree and ggtree packages. Tree data can be processed using the tidy interface with tidytree and visualized by ggtree. The treeio package is released within the Bioconductor and rOpenSci projects. It is available at https://www.bioconductor.org/packages/treeio/.

Molecular characterisation of CGMS, maintainer and inbred lines and diversity analysis in pigeonpea [Cajanus cajan (L.) Millsp.]

2015 ◽  
Vol 38 (6) ◽  
Author(s):  
K. Indira Petchiammal ◽  
A. R. Muthiah ◽  
P. Jayamani
Keyword(s):  
Molecular Diversity ◽  
Molecular Genetic ◽  
Inbred Lines ◽  
Polymorphic Markers ◽  
Molecular Genetic Diversity ◽  
Ssr Primers ◽  
Parental Material ◽  
The Mean ◽  
Single Cluster ◽  
Different Sources

The present study was initiated with forty microsatellite markers for studying the molecular genetic diversity in 28 pigeonpea genotypes (6 CGMS lines of A<sub>1</sub>, A<sub>2</sub> and A<sub>4</sub> sources, their maintainer lines and 16 inbred lines) utilised as the parental material for the synthesis of F<sub>1</sub> hybrids. The level of polymorphism was too low and only 45 per cent markers were polymorphic. A total of 65 alleles were produced and the number of alleles produced ranged from two to six. The mean PIC value of 40 SSR primers was 0.147 and the primer CcM2977 produced the highest PIC value of 0.787 followed by CcM1770 (0.565). The primers <italic>viz.</italic>, CcM0039 and CcM2463 were polymorphic between CGMS and inbred lines and the primer CcM2977 was polymorphic among the different sources of CGMS lines. The UPGMA clustering and Neighbour-joining analyses grouped all the CGMS lines and respective maintainer lines in a single cluster and the inbred lines as two separate clusters. Among the inbred lines ICPL 11966, ICPL11947 and ICPL11950 were distinctly grouped in one cluster and other 13 inbred lines were clustered separately. Polymorphic markers <italic>viz.</italic>,CcM2977 and CcM1770 were used to confirm the hybrids of the crosses <italic>viz.</italic>, ICPA 2043 x LRG 41 and ICPA 2043 x IC 33725. The present study revealed that SSR markers are highly informative for exploiting the molecular diversity prevailing among the parental lines and could be utilized for further pigeonpea improvement at genomic level.

scholarly journals Control ofgdhRExpression inNeisseria gonorrhoeaevia Autoregulation and a Master Repressor (MtrR) of a Drug Efflux Pump Operon

mBio ◽  
2017 ◽  
Vol 8 (2) ◽  
Author(s):  
Corinne E. Rouquette-Loughlin ◽  
Yaramah M. Zalucki ◽  
Vijaya L. Dhulipala ◽  
Jacqueline T. Balthazar ◽  
Raúl G. Doyle ◽  
...  
Keyword(s):  
Dna Binding ◽  
Transcriptional Control ◽  
Efflux Pump ◽  
Human Pathogens ◽  
Genital Tract Infection ◽  
Transmitted Infection ◽  
Innate Defense ◽  
Regulatory Processes ◽  
Transcriptional Regulatory ◽  
Conserved Genes

ABSTRACTThe MtrCDE efflux pump ofNeisseria gonorrhoeaecontributes to gonococcal resistance to a number of antibiotics used previously or currently in treatment of gonorrhea, as well as to host-derived antimicrobials that participate in innate defense. Overexpression of the MtrCDE efflux pump increases gonococcal survival and fitness during experimental lower genital tract infection of female mice. Transcription ofmtrCDEcan be repressed by the DNA-binding protein MtrR, which also acts as a global regulator of genes involved in important metabolic, physiologic, or regulatory processes. Here, we investigated whether a gene downstream ofmtrCDE, previously annotatedgdhRinNeisseria meningitidis, is a target for regulation by MtrR. In meningococci, GdhR serves as a regulator of genes involved in glucose catabolism, amino acid transport, and biosynthesis, includinggdhA, which encodes anl-glutamate dehydrogenase and is located next togdhRbut is transcriptionally divergent. We report here that inN. gonorrhoeae, expression ofgdhRis subject to autoregulation by GdhR and direct repression by MtrR. Importantly, loss of GdhR significantly increased gonococcal fitness compared to a complemented mutant strain during experimental murine infection. Interestingly, loss of GdhR did not influence expression ofgdhA, as reported for meningococci. This variance is most likely due to differences in promoter localization and utilization between gonococci and meningococci. We propose that transcriptional control of gonococcal genes through the action of MtrR and GdhR contributes to fitness ofN. gonorrhoeaeduring infection.IMPORTANCEThe pathogenicNeisseriaspecies are strict human pathogens that can cause a sexually transmitted infection (N. gonorrhoeae) or meningitis or fulminant septicemia (N. meningitidis). Although they share considerable genetic information, little attention has been directed to comparing transcriptional regulatory systems that modulate expression of their conserved genes. We hypothesized that transcriptional regulatory differences exist between these two pathogens, and we used thegdhlocus as a model to test this idea. For this purpose, we studied two conserved genes (gdhRandgdhA) within the locus. Despite general conservation of thegdhlocus in gonococci and meningococci, differences exist in noncoding sequences that correspond to promoter elements or potential sites for interacting with DNA-binding proteins, such as GdhR and MtrR. Our results indicate that implications drawn from studying regulation of conserved genes in one pathogen are not necessarily translatable to a genetically related pathogen.

scholarly journals A Tree of Human Gut Bacterial Species and its Applications to Metagenomics and Metaproteomics Data Analysis

2020 ◽  
Author(s):  
Moses Stamboulian ◽  
Thomas G. Doak ◽  
Yuzhen Ye
Keyword(s):  
Gut Microbiome ◽  
Phylogenetic Trees ◽  
Bacterial Species ◽  
Taxonomic Composition ◽  
Marker Genes ◽  
Missing Information ◽  
Human Gut ◽  
Taxonomic Profiling ◽  
Tree Building ◽  
The Impact

Abstract1BackgroundRecent advances in genome and metagenome sequencing have dramatically enriched the collection of genomes of bacterial species related to human health and diseases. In metagenomic studies phylogenetic trees are commonly used to depict, describe, and compare the bacterial members of the community under study. The most accurate tree-building algorithms now use large sets of marker genes taken from across genomes. However, many of the current bacterial genomes were assembled from metagenomic datasets (i.e., metagenome assembled genomes, MAGs), and often contain missing information. It is therefore important to study how well the phylogeny approach performs on such genomes. Further, phylogeny methods are not perfect and it is important to know how reliable an inferred tree is.ResultsHere we examined the impact of incompleteness of the genomes on the tree reconstruction, and we showed that phylogeny approaches including RAxML (which handles missing data explicitly) and FastTree generally performed well on simulated collection of 400 genomes with missing information. As RAxML is computationally prohibitive for the much larger collections of gut genomes, we chose FastTree to build a unified tree of human-gut associated bacterial species (referred to as gut tree), including more than 3000 genomes, most of which are incomplete. We developed two downstream applications of the gut tree: peptide-centric analysis of metaproteomics datasets; and taxonomic characterization of metagenomic sequences. In both applications, the gut tree provided the basis for quantification of species composition at various taxonomic resolutions.ConclusionsThe gut tree presented in this study provides a useful framework for taxonomic profiling of human gut microbiome. Including MAGs in the tree provides more comprehensive representation of microbial species diversity associated with human gut, important for studying the taxonomic composition of gut microbiome.Availability and ImplementationThe tree construction pipeline and downstream applications of the gut tree are freely available at https://github.com/mgtools/guttree.

scholarly journals The complete chloroplast genome of Limonium tetragonum (Plumbaginaceae) isolated in Korea

2021 ◽  
Vol 51 (3) ◽  
pp. 337-344
Author(s):  
Yongsung KIM ◽  
Hong XI ◽  
Jongsun PARK
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Trees ◽  
Sister Group ◽  
Single Copy ◽  
Nucleotide Polymorphisms ◽  
Large Single Copy ◽  
Single Nucleotide ◽  
Complete Chloroplast Genome ◽  
Cp Genome

The chloroplast genome of Limonium tetragonum (Thunb.) Bullock, a halophytic species, was sequenced to understand genetic differences based on its geographical distribution. The cp genome of L. tetragonum was 154,689 bp long (GC ratio is 37.0%) and has four subregions: 84,572 bp of large single-copy (35.3%) and 12,813 bp of small singlecopy (31.5%) regions were separated by 28,562 bp of inverted repeat (40.9%) regions. It contained 128 genes (83 proteincoding genes, eight rRNAs, and 37 tRNAs). Thirty-five single-nucleotide polymorphisms and 33 INDEL regions (88 bp in length) were identified. Maximum-likelihood and Bayesian inference phylogenetic trees showed that L. tetragonum formed a sister group with L. aureum, which is incongruent with certain previous studies, including a phylogenetic analysis.

scholarly journals Telomere Length De Novo Assembly of all 7 Chromosomes and Mitogenome Sequencing of the Model Entomopathogenic Fungus, Metarhizium Brunneum, by Means of a Novel Assembly Pipeline

2020 ◽  
Author(s):  
Zack Saud ◽  
Alexandra M. Kortsinoglou ◽  
Vassili N. Kouvelis ◽  
Tariq M. Butt
Keyword(s):  
Entomopathogenic Fungus ◽  
De Novo ◽  
Gene Prediction ◽  
Fungal Species ◽  
Orthologous Protein ◽  
Metarhizium Brunneum ◽  
Sequencing Technologies ◽  
Protein Clusters ◽  
Assembly Pipeline ◽  
Generation Sequencing

Abstract More accurate and complete reference genomes have improved understanding of gene function, biology, and evolutionary mechanisms. Hybrid genome assembly approaches leverage benefits of both long, relatively error-prone reads from third-generation sequencing technologies and short, accurate reads from second-generation sequencing technologies, to produce more accurate and contiguous de novo genome assemblies in comparison to using either technology independently. In this study, we present a novel hybrid assembly pipeline that allowed for both mitogenome de novo assembly and telomere length de novo assembly of all 7 chromosomes of the model entomopathogenic fungus, Metarhizium brunneum. The improved assembly allowed for better ab initio gene prediction and a more BUSCO complete proteome set has been generated in comparison to the eight current NCBI reference Metarhizium spp. genomes. Remarkably, we note that including the mitogenome in ab initio gene prediction training improved overall gene prediction. The assembly was further validated by comparing contig assembly agreement across various assemblers, assessing the assembly performance of each tool. Genomic synteny and orthologous protein clusters were compared between Metarhizium brunneum and three other Hypocreales species with complete genomes, identifying core proteins, and listing orthologous protein clusters shared uniquely between the two entomopathogenic fungal species, so as to further facilitate the understanding of molecular mechanisms underpinning fungal-insect pathogenesis. The novel assembly pipeline may be used for other haploid fungal species, facilitating the need to produce high-quality reference fungal genomes, leading to better understanding of fungal genomic evolution, chromosome structuring and gene regulation.

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