scholarly journals Molecular Serotyping by Phylogenetic Analyses of a 1498bp Segment of the invA Gene of Salmonella

2021 ◽  
Vol 14 ◽  
pp. 1-14
Author(s):  
Windell L. Rivera ◽  
Rance Derrick Neri Pavon
Keyword(s):  
Phylogenetic Analyses ◽  
Gene Segment ◽  
Virulence Gene ◽  
Molecular Techniques ◽  
Control Measures ◽  
Host Cells ◽  
Gene Marker ◽  
Sequence Alignments ◽  
Inva Gene ◽  
Molecular Serotyping

The current gold standard for Salmonella serotyping is costly, labor-intensive and time-consuming. However, proper identification is key to monitor Salmonella transmission and implementation of necessary control measures. The onset of advanced molecular techniques has lessened resource and labor requirements; however, it still remains complex, unestablished and plagued with insufficiencies. Hence, a simpler serotyping method with sufficient resolution is needed. In this study, the invA virulence gene, associated with Salmonella invasion into host cells and is considered as a marker for Salmonella detection, was amplified and sequenced among isolates from meat samples in Metro Manila, Philippines. This was followed by sequence alignments with reference sequences (Refseqs), oversaturation and model tests, phylogenetic tree analyses and signal detections. Unfortunately, alignment of a 229bp amplified and sequenced invA gene segment with Refseqs generated little to no base variations and consequently provided insufficient phylogenetic resolution for molecular serotyping (0 of the 17 serotypes tested). However, another segment of 1498bp, outside the amplified region, showed considerable base variation in alignment and consequently resolved a maximum of 13 out of 17 (76.47%) serotypes tested, all generated trees considered. These suggest the potential of the invA virulence gene as a single-gene marker for molecular serotyping of Salmonella through phylogenetic analyses.

scholarly journals Respiratory syncytial virus B sequence analysis reveals a novel early genotype

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Juan C. Muñoz-Escalante ◽  
Andreu Comas-García ◽  
Sofía Bernal-Silva ◽  
Daniel E. Noyola
Keyword(s):  
Molecular Markers ◽  
Respiratory Syncytial Virus ◽  
Maximum Likelihood ◽  
Respiratory Infections ◽  
Phylogenetic Analyses ◽  
Detection Methods ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Individual Gene ◽  
Syncytial Virus

AbstractRespiratory syncytial virus (RSV) is a major cause of respiratory infections and is classified in two main groups, RSV-A and RSV-B, with multiple genotypes within each of them. For RSV-B, more than 30 genotypes have been described, without consensus on their definition. The lack of genotype assignation criteria has a direct impact on viral evolution understanding, development of viral detection methods as well as vaccines design. Here we analyzed the totality of complete RSV-B G gene ectodomain sequences published in GenBank until September 2018 (n = 2190) including 478 complete genome sequences using maximum likelihood and Bayesian phylogenetic analyses, as well as intergenotypic and intragenotypic distance matrices, in order to generate a systematic genotype assignation. Individual RSV-B genes were also assessed using maximum likelihood phylogenetic analyses and multiple sequence alignments were used to identify molecular markers associated to specific genotypes. Analyses of the complete G gene ectodomain region, sequences clustering patterns, and the presence of molecular markers of each individual gene indicate that the 37 previously described genotypes can be classified into fifteen distinct genotypes: BA, BA-C, BA-CC, CB1-THB, GB1-GB4, GB6, JAB1-NZB2, SAB1, SAB2, SAB4, URU2 and a novel early circulating genotype characterized in the present study and designated GB0.

Morphological redescription and molecular characterization of Trichodina matsu Basson & Van As, 1994 (Ciliophora, Mobilida, Trichodinidae) infecting Tachysurus fulvidraco (Richardson, 1846) from Chongqing, China

Zootaxa ◽  
2021 ◽  
Vol 4995 (2) ◽  
pp. 334-344
Author(s):  
QIAN ZHOU ◽  
FAHUI TANG ◽  
YUANJUN ZHAO
Keyword(s):  
Phylogenetic Analyses ◽  
Molecular Data ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Similar Species ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Morphological And Molecular Data ◽  
Tachysurus Fulvidraco

During a survey of parasitic ciliates in Chongqing, China, Trichodina matsu Basson & Van As, 1994 was isolated from gills of Tachysurus fulvidraco. Furthermore, the 18S rRNA gene and ITS-5.8S rRNA region of T. matsu were sequenced for the first time and applied for the species identification and comparison with similar species in the present study. Based on the morphological and molecular comparisons, the results indicate that T. matsu is an ectoparasite specific for the Siluriformes catfish. Based on the analyses of genetic distance, multiple sequence alignments, and phylogenetic analyses, no obvious differentiation within populations of T. matsu was found. In addition, the ‘Trichodina hyperparasitis’ (KX904933) in GenBank is a misidentification and appears to be conspecific with T. matsu according to the comparison of morphological and molecular data.  

scholarly journals Clinical, virological and epidemiological characterization of dengue outbreak in Myanmar, 2015

2017 ◽  
Vol 145 (9) ◽  
pp. 1886-1897 ◽  
Author(s):  
A. K. KYAW ◽  
M. M. NGWE TUN ◽  
M. L. MOI ◽  
T. NABESHIMA ◽  
K. T. SOE ◽  
...  
Keyword(s):  
Primary Infection ◽  
Phylogenetic Analyses ◽  
Molecular Techniques ◽  
Severe Dengue ◽  
Envelope Gene ◽  
Mosquito Vector ◽  
Serum Samples ◽  
Denv Serotypes ◽  
Significant Difference ◽  
Study Sites

SUMMARYHospital-based surveillance was conducted at two widely separated regions in Myanmar during the 2015 dengue epidemic. Acute phase serum samples were collected from 332 clinically diagnosed dengue patients during the peak season of dengue cases. Viremia levels were measured by quantitative real-time PCR and plaque assays using FcγRIIA-expressing and non-FcγRIIA-expressing BHK cells to specifically determine the infectious virus particles. By serology and molecular techniques, 280/332 (84·3%) were confirmed as dengue patients. All four serotypes of dengue virus (DENV) were isolated from among 104 laboratory-confirmed patients including two cases infected with two DENV serotypes. High percentage of primary infection was noted among the severe dengue patients. Patients with primary infection or DENV IgM negative demonstrated significantly higher viral loads but there was no significant difference among the severity groups. Viremia levels among dengue patients were notably high for a long period which was assumed to support the spread of the virus by the mosquito vector during epidemic. Phylogenetic analyses of the envelope gene of the epidemic strains revealed close similarity with the strains previously isolated in Myanmar and neighboring countries. DENV-1 dominated the epidemic in 2015 and the serotype (except DENV-3) and genotype distributions were similar in both study sites.

scholarly journals A test statistic to quantify treelikeness in phylogenetics

2021 ◽  
Author(s):  
Caitlin Cherryh ◽  
Bui Quang Minh ◽  
Rob Lanfear
Keyword(s):  
Evolutionary History ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Phylogenetic Network ◽  
Parametric Bootstrap ◽  
Lineage Sorting ◽  
Test Statistic ◽  
Sequence Alignments ◽  
Wide Range ◽  
History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

scholarly journals Investigating diversity, evolution, development and physiology of red algal parasites from New Zealand

2021 ◽  
Author(s):  
◽  
Maren Preuss
Keyword(s):  
Host Species ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Host Cells ◽  
Gene Content ◽  
Infected Host ◽  
Parasite Development ◽  
Future Research ◽  
Mitochondrial Genomes ◽  
Red Algal

<p>Red algal parasites have evolved independently over a 100 times and grow only on other red algal hosts. Most parasites are closely related to their host based on the similarity of their reproductive structures. Secondary pit connections between red algal parasites and their hosts are used to transfer parasite organelles and nuclei into host cells. Morphological and physiological changes in infected host cells have been observed in some species. Parasite mitochondrial genomes are similar in size and gene content to free-living red algae whereas parasite plastids are highly reduced. Overall, red algal parasites are poorly studied and thus the aim of this study was to increase the general knowledge of parasitic taxa with respect to their diversity, evolutionary origin, development, physiology, and organelle evolution. Investigation of the primary literature showed that most species descriptions of red algal parasites were poor and did not meet the criteria for defining a parasitic relationship. This literature study also revealed a lack of knowledge of many key parasitic processes including early parasite development, host cell “control”, and parasite origin. Many of these poorly studied research areas were addressed in this thesis. Phylogenetic analyses, using a range of markers from all three genomes (cpDNA: rbcL, nDNA: actin, LSU rRNA; mtDNA: cox1), showed different patterns of phylogenetic relationships for the four new red algal parasites and their hosts. The parasites Phycodrys novae-zelandiophila sp. nov. and Vertebrata aterrimophila sp. nov. closest relative is its host species. Cladhymenia oblongifoliophila sp. nov. closest relative is its host species based on nuclear and mitochondrial markers whereas the plastid markers group the parasite with Cladhymenia lyallii, suggesting that the parasite plastid was acquired when previously parasitizing C. lyallii. Judithia parasitica sp. nov. grows on two Blastophyllis species but the parasites’ closest relative is the non-host species Judithia delicatissima. Developmental studies of the parasite Vertebrata aterrimophila, showed a unique developmental structure (“trunk-like” cell) not known in other parasites, plus localised infection vi and few changes in infected host cells. High-throughput-sequencing revealed mitochondrial genomes of similar size, gene content and order in the parasite Pterocladiophila hemisphaerica to its host Pterocladia lucida, and a reduced non-photosynthetic plastid in the parasite. Mitochondrial (mt) and plastid (cp) genome phylogenies placed Pterocladiophila hemisphaerica on long branches, either as sister to Ceramiales (mt) or Gracilariales (cp). Further analyses, filtering non-elevated plastid genes grouped the parasite neither with the Gracilariales (mt) or Gelidiales (cp) on shorter branches but without support. Nuclear phylogeny grouped P. hemisphaerica as sister to the Gelidiales and other red algal orders and was the only phylogenetic relationship with support. Investigations of photosystem II capacity using PAM fluorometry, and quantifying chlorophyll a content in three pigmented parasites, showed different host nutrient dependencies. Rhodophyllis parasitica and Vertebrata aterrimophila are not able to photosynthesize and are fully dependent on host nutrients. Pterocladiophila hemisphaerica is able to photosynthesize independently, even though it has a reduced non-photosynthetic plastid genome, and therefore is only partially dependent on its host. This study advances our current understanding of red algal parasites and highlights many possibilities for future research including genome evolution and understanding parasite diversity.</p>

scholarly journals Perforin-2 Protects Host Cells and Mice by Restricting the Vacuole to Cytosol Transitioning of a Bacterial Pathogen

2016 ◽  
Vol 84 (4) ◽  
pp. 1083-1091 ◽  
Author(s):  
Ryan McCormack ◽  
Wael Bahnan ◽  
Niraj Shrestha ◽  
Justin Boucher ◽  
Marcella Barreto ◽  
...  
Keyword(s):  
Bacterial Pathogen ◽  
Virulence Gene ◽  
Systemic Infection ◽  
Protective Role ◽  
Host Cells ◽  
Content Type ◽  
Virulence Gene Expression ◽  
Membrane Bound ◽  
High Level ◽  
Macpf Domain

The host-encoded Perforin-2 (encoded by the macrophage-expressed gene 1,Mpeg1), which possesses a pore-forming MACPF domain, reduces the viability of bacterial pathogens that reside within membrane-bound compartments. Here, it is shown that Perforin-2 also restricts the proliferation of the intracytosolic pathogenListeria monocytogenes. Within a few hours of systemic infection, the massive proliferation ofL. monocytogenesinPerforin-2−/−mice leads to a rapid appearance of acute disease symptoms. We go on to show in culturedPerforin-2−/−cells that the vacuole-to-cytosol transitioning ofL. monocytogenesis greatly accelerated. Unexpectedly, we found that inPerforin-2−/−macrophages,Listeria-containing vacuoles quickly (≤15 min) acidify, and that this was coincident with greater virulence gene expression, likely accounting for the more rapid translocation ofL. monocytogenesto its replicative niche in the cytosol. This hypothesis was supported by our finding that aL. monocytogenesstrain expressing virulence factors at a constitutively high level replicated equally well inPerforin-2+/+andPerforin-2−/−macrophages. Our findings suggest that the protective role of Perforin-2 against listeriosis is based on it limiting the intracellular replication of the pathogen. This cellular activity of Perforin-2 may derive from it regulating the acidification ofListeria-containing vacuoles, thereby depriving the pathogen of favorable intracellular conditions that promote its virulence gene activity.

scholarly journals Molecular Epidemiology and Genome Dynamics of New Delhi Metallo-β-Lactamase-Producing Extraintestinal Pathogenic Escherichia coli Strains from India

2016 ◽  
Vol 60 (11) ◽  
pp. 6795-6805 ◽  
Author(s):  
Amit Ranjan ◽  
Sabiha Shaik ◽  
Agnismita Mondal ◽  
Nishant Nandanwar ◽  
Arif Hussain ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Effective Means ◽  
Genomic Analysis ◽  
Virulence Gene ◽  
Carbapenem Resistance ◽  
Control Measures ◽  
Large Sample Size ◽  
Gene Repertoire ◽  
Content Type ◽  
E Coli

ABSTRACTThe global dissemination and increasing incidence of carbapenem-resistant, Gram-negative organisms have resulted in acute public health concerns. Here, we present a retrospective multicenter study on molecular characterization of metallo-β-lactamase (MBL)-producing clinicalEscherichia coliisolates recovered from extraintestinal infections in two hospitals in Pune, India. We screened a large sample size of 510E. coliisolates for MBL production wherein we profiled their molecular determinants, antimicrobial resistance phenotypes, functional virulence properties, genomic features, and transmission dynamics. Approximately 8% of these isolates were MBL producers, the majority of which were of the NDM-1 (69%) type, followed by NDM-5 (19%), NDM-4 (5.5%), and NDM-7 (5.5%). MBL producers were resistant to all antibiotics tested except for colistin, fosfomycin, and chloramphenicol, which were effective to various extents. Plasmids were found to be an effective means of dissemination of NDM genes and other resistance traits. All MBL producers adhered to and invaded bladder epithelial (T24) cells and demonstrated significant serum resistance. Genomic analysis of MBL-producingE. coliisolates revealed higher resistance but a moderate virulence gene repertoire. A subset of NDM-1-positiveE. coliisolates was identified as dominant sequence type 101 (ST101) while two strains belonging to ST167 and ST405 harbored NDM-5. A majority of MBL-producingE. colistrains revealed unique genotypes, suggesting that they were clonally unrelated. Overall, the coexistence of virulence and carbapenem resistance in clinicalE. coliisolates is of serious concern. Moreover, the emergence of NDM-1 among the globally dominantE. coliST101 isolates warrants stringent surveillance and control measures.

scholarly journals Pediatric Helicobacter pylori Isolates Display Distinct Gene Coding Capacities and Virulence Gene Marker Profiles

2009 ◽  
Vol 47 (6) ◽  
pp. 1680-1688 ◽  
Author(s):  
S. Talarico ◽  
B. D. Gold ◽  
J. Fero ◽  
D. T. Thompson ◽  
J. Guarner ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Virulence Gene ◽  
Gene Marker ◽  
Distinct Gene ◽  
Gene Coding

scholarly journals DNA-Binding Activities of the HilC and HilD Virulence Regulatory Proteins of Salmonella enterica Serovar Typhimurium

2002 ◽  
Vol 184 (15) ◽  
pp. 4148-4160 ◽  
Author(s):  
Igor N. Olekhnovich ◽  
Robert J. Kadner
Keyword(s):  
Dna Binding ◽  
Salmonella Enterica ◽  
Mutational Analysis ◽  
Major Effect ◽  
Host Cells ◽  
Sequence Specificity ◽  
Sequence Alignments ◽  
Consensus Sequences ◽  
Serovar Typhimurium

ABSTRACT The HilC and HilD proteins of Salmonella enterica serovar Typhimurium are members of the AraC/XylS family of transcription regulators. They are encoded on Salmonella pathogenicity island 1 (SPI1) and control expression of the hilA gene, which encodes the major transcriptional activator for many genes encoded on SPI1 and elsewhere that contribute to invasion of host cells. Gel electrophoretic shift and DNase footprinting assays revealed that purified HilC and HilD proteins can bind to multiple regions in the hilA and hilC promoters and to a single region in the hilD promoter. Although both HilC and -D proteins can bind to the same DNA regions, they showed different dependencies on the sequence and lengths of their DNA targets. To identify the binding-sequence specificity of HilC and HilD, a series of single base substitutions changing each position in a DNA fragment corresponding to positions −92 to −52 of the hilC promoter was tested for binding to HilC and HilD in a gel shift DNA-binding assay. This mutational analysis in combination with sequence alignments allowed deduction of consensus sequences for binding of both proteins. The consensus sequences overlap but differ so that HilC can bind to both types of sites but HilD only to one. The hilA and hilC promoters contain multiple binding sites of each type, whereas the hilD promoter contains a site that binds HilC but not HilD without additional binding elements. The HilC and HilD proteins had no major effect on transcription from the hilA or hilD promoters using purified proteins in vitro but changed the choice of promoter at hilC. These results are consistent with a model derived from analysis of lacZ fusions stating that HilC and HilD enhance hilA expression by counteracting a repressing activity.

Virulence Gene Pattern of Pasteurella multocida Isolates of Buffalo in Association to Capsule Biosynthesis Genes

2020 ◽  
Author(s):  
N. Sujatha ◽  
K. Lakshmi Kavitha ◽  
K.V. Subramanyam ◽  
T. Srinivasa Rao ◽  
R.N. Ramani Pushpa
Keyword(s):  
Virulence Factors ◽  
Pasteurella Multocida ◽  
Virulence Genes ◽  
Systemic Disease ◽  
Virulence Gene ◽  
Disease Status ◽  
Host Cells ◽  
Wide Range ◽  
Serotype B ◽  
Apparently Healthy

Background: Pasteurella multocida is the causative agent of many economically important diseases in a wide range of hosts. The mechanisms by which these bacteria can invade the mucosa, evade innate immunity and cause systemic disease are slowly being elucidated. Many key virulence factors are yet to be identified, including those required for initial attachment and invasion of host cells and for persistence in a relatively nutrient poor and hostile environment. This has led to intensive research to understand host adaptation mechanisms and virulence factors in order to develop effective vaccines. Methods: The present study was carried out to know the distribution of virulence genes viz., haemoglobin binding proteins (hgbA and hgbB), outer membrane protein (ompH), fimbrial antigen (ptfA), filamentous haemagglutinin (pfhA) and transferrin binding protein (tbpA) by PCR in P. multocida CapA isolates from apparently healthy or carrier animals and CapB isolates from field Haemorrhagic septicemia (HS) cases to monitor the epidemiological associations of virulence genes in Cap A and Cap B isolates.Result: The study revealed that all the six virulence associated genes were present in Cap B isolates. None of the Cap A isolates harboured tbpA and pfhA genes. These two genes were closely related to serotype B causing Haemorrhagic septicemia and were epidemiologically associated with disease status.

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