scholarly journals Molecular Approach for the Diagnosis of Blood and Skin Canine Filarioids

2020 ◽  
Vol 8 (11) ◽  
pp. 1671
Author(s):  
Younes Laidoudi ◽  
Samia Bedjaoui ◽  
Hacène Medkour ◽  
Maria Stefania Latrofa ◽  
Abdeslam Mekroud ◽  
...  
Keyword(s):  
Rapid Identification ◽  
The Novel ◽  
Molecular Approach ◽  
Infected Blood ◽  
Multiplex Qpcr ◽  
Cercopithifilaria Bainae ◽  
Acanthocheilonema Reconditum ◽  
Dna Collection ◽  
Canine Filarioids ◽  
Skin Samples

The zoonotic Onchocerca lupi and tick-transmitted filarioids of the genus Cercopithifilaria remain less well known due to the difficulties in accessing to skin samples as target tissues. Here, we proposed a molecular approach reliying on multiplex qPCR assays that allow the rapid identification of filarioids from canine blood, skin, and tick samples. This includes two newly developed duplex qPCR tests, the first one targeting filarial and C. grassii DNA (CanFil-C. grassii). and the second qPCR assay designed for the detection of Cercopithifilaria bainae and Cercopithifilaria sp. II DNAs (C. bainae-C.spII). The third one is a triplex TaqMan cox 1 assay targeting DNA of blood microfilariae (e.g., Dirofilaria immitis, Dirofilaria repens and Acanthocheilonema reconditum). The novel duplex qPCRs developed were validated in silico and by screening of known DNA collection. The qPCR assays were also used for screening the blood and tick samples of 72 dogs from Algeria. This allowed the identification of canine filariasis infection with 100% of specificity and 89.47% and 100% of sensitivity from naturally infected blood and tick samples, respectively. The prevalences of 26.39% for D. immitis and 5.56% for both D. repens and A. reconditum were reported in blood and tick samples. Cercopithifilaria DNAs were detected only in tick samples, with a prevalence of 4.17% and 5.56% for C. bainae and Cercopithifilaria sp. II, respectively. Co-infections were diagnosed in 6.94% and 13.89% of blood and tick samples, respectively. Whereas all samples were negative for C. grassii DNA. The use of engorged ticks instead of blood and skin samples could be an easier option for the surveillance of all canine filarioids herein investigated. The multiplex qPCR assays herein validated were shown to be useful in the detection of filarial co-infections by overcoming sequencing of positive samples.

scholarly journals Detection of Canine Vector-Borne Filariasis and Their Wolbachia Endosymbionts in French Guiana

2020 ◽  
Vol 8 (5) ◽  
pp. 770 ◽  
Author(s):  
Younes Laidoudi ◽  
Jean-Lou Marié ◽  
Djamel Tahir ◽  
Stéphanie Watier-Grillot ◽  
Oleg Mediannikov ◽  
...  
Keyword(s):  
French Guiana ◽  
Virulent Strain ◽  
Sequencing Analysis ◽  
Two Samples ◽  
Cercopithifilaria Bainae ◽  
Canine Heartworm Disease ◽  
Clade C ◽  
Acanthocheilonema Reconditum ◽  
Vector Borne ◽  
Species Specific

In French Guiana, canine heartworm disease is well known, but the diversity of filarial parasites of dogs remains largely unknown. A total of 98 canine blood samples from Cayenne and Kourou were assessed by a blood wet mount preparation, heartworm antigen test and molecular exploration of filarioid and Wolbachia DNAs, followed by a multiplex species-specific qPCR’s identification and a subsequent sequencing analysis. Thereafter, a phylogeny based on maximum likelihood was carried out to facilitate specific identification. Five dogs were microfilaremic. Heartworm antigens were detected in 15 (15.3%) dogs. Of these, six (6.1%) were considered as occult infections as neither microfilariae nor Dirofilaria immitis DNA were detected. The 11 (11.2%) D. immitis isolates corresponded to a low virulent strain. Six of the D. immitis isolates were positive for Wolbachia endosymbionts of D. immitis belonging to the clade C DNA. Acanthocheilonema reconditum DNA was detected in 3 (3.1%) samples. Of these latter, one was found co-infected with the Brugia sp. genotype and the DNA of the clade D of the Wolbachia endosymbiont of Brugia species. This latter was also detected in two filarioid DNA-free samples. Finally, two samples were positive for Cercopithifilaria bainae genotype, which is distinct from those identified in Europe. The present study highlights the urgent need to implement chemoprophylaxis associated with anti-Wolbachia drugs to control these potential zoonoses.

scholarly journals SARS2020: an integrated platform for identification of novel coronavirus by a consensus sequence-function model

2020 ◽  
Author(s):  
Dachuan Zhang ◽  
Tong Zhang ◽  
Sheng Liu ◽  
Dandan Sun ◽  
Shaozhen Ding ◽  
...  
Keyword(s):  
Biological Function ◽  
Consensus Sequence ◽  
Rapid Identification ◽  
Data Driven ◽  
Supplementary Information ◽  
Respiratory Syndrome Virus ◽  
The Novel ◽  
Function Model ◽  
Catalytic Function ◽  
Novel Coronavirus

Abstract Motivation The 2019 novel coronavirus outbreak has significantly affected global health and society. Thus, predicting biological function from pathogen sequence is crucial and urgently needed. However, little work has been conducted to identify viruses by the enzymes that they encode, and which are key to pathogen propagation. Results We built a comprehensive scientific resource, SARS2020, which integrates coronavirus-related research, genomic sequences and results of anti-viral drug trials. In addition, we built a consensus sequence-catalytic function model from which we identified the novel coronavirus as encoding the same proteinase as the severe acute respiratory syndrome virus. This data-driven sequence-based strategy will enable rapid identification of agents responsible for future epidemics. Availabilityand implementation SARS2020 is available at http://design.rxnfinder.org/sars2020/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Old concepts, new molecules and current approaches applied to the bacterial nucleotide signalling field

2016 ◽  
Vol 371 (1707) ◽  
pp. 20150503 ◽  
Author(s):  
Angelika Gründling ◽  
Vincent T. Lee
Keyword(s):  
Mass Spectrometry ◽  
Rapid Identification ◽  
Screening Methods ◽  
Bacterial Cells ◽  
The Novel ◽  
Specific Receptor ◽  
Receptor Proteins ◽  
The Past ◽  
Genome Wide ◽  
Cellular Pathways

Signalling nucleotides are key molecules that help bacteria to rapidly coordinate cellular pathways and adapt to changes in their environment. During the past 10 years, the nucleotide signalling field has seen much excitement, as several new signalling nucleotides have been discovered in both eukaryotic and bacterial cells. The fields have since advanced quickly, aided by the development of important tools such as the synthesis of modified nucleotides, which, combined with sensitive mass spectrometry methods, allowed for the rapid identification of specific receptor proteins along with other novel genome-wide screening methods. In this review, we describe the principle concepts of nucleotide signalling networks and summarize the recent work that led to the discovery of the novel signalling nucleotides. We also highlight current approaches applied to the research in the field as well as resources and methodological advances aiding in a rapid identification of nucleotide-specific receptor proteins. This article is part of the themed issue ‘The new bacteriology’.

scholarly journals Frequency Analysis Techniques for Identification of Viral Genetic Data

mBio ◽  
2010 ◽  
Vol 1 (3) ◽  
Author(s):  
Vladimir Trifonov ◽  
Raul Rabadan
Keyword(s):  
High Throughput ◽  
Frequency Analysis ◽  
Genetic Relationships ◽  
Genetic Material ◽  
Genetic Data ◽  
Rapid Identification ◽  
The Novel ◽  
Sequencing Technologies ◽  
Analysis Technique ◽  
Low Costs

ABSTRACT Environmental metagenomic samples and samples obtained as an attempt to identify a pathogen associated with the emergence of a novel infectious disease are important sources of novel microorganisms. The low costs and high throughput of sequencing technologies are expected to allow for the genetic material in those samples to be sequenced and the genomes of the novel microorganisms to be identified by alignment to those in a database of known genomes. Yet, for various biological and technical reasons, such alignment might not always be possible. We investigate a frequency analysis technique which on one hand allows for the identification of genetic material without relying on alignment and on the other hand makes possible the discovery of nonoverlapping contigs from the same organism. The technique is based on obtaining signatures of the genetic data and defining a distance/similarity measure between signatures. More precisely, the signatures of the genetic data are the frequencies of k-mers occurring in them, with k being a natural number. We considered an entropy-based distance between signatures, similar to the Kullback-Leibler distance in information theory, and investigated its ability to categorize negative-sense single-stranded RNA (ssRNA) viral genetic data. Our conclusion is that in this viral context, the technique provides a viable way of discovering genetic relationships without relying on alignment. We envision that our approach will be applicable to other microbial genetic contexts, e.g., other types of viruses, and will be an important tool in the discovery of novel microorganisms. IMPORTANCE Multiple factors contribute to the emergence of novel infectious diseases. Implementation of effective measures against such diseases relies on the rapid identification of novel pathogens. Another important source of novel microorganisms is environmental metagenomic samples. The low costs and high throughput of sequencing technologies provide a method for the identification of novel microorganisms by sequence alignment. There are several obstacles to this method, as follows: our knowledge of biology is biased by an anthropomorphic view, microbial genomic material could be a minuscule fraction of the sample, the sequencing and enrichment technologies can be a source of errors and biases, and finally, microbes have high diversity and high evolutionary rates. As a result, novel microorganisms could have very low genetic similarity to already known genomes, and the identification by alignment could be computationally prohibitive. We investigate a frequency analysis technique which allows for the identification of novel genetic material without relying on alignment.

scholarly journals Multiplex PCR for the Identification of Pathogenic Listeria in Flammulina velutipes Plant Based on Novel Specific Targets Revealed by Pan-Genome Analysis

2021 ◽  
Vol 11 ◽  
Author(s):  
Fan Li ◽  
Qinghua Ye ◽  
Moutong Chen ◽  
Jumei Zhang ◽  
Liang Xue ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Genome Analysis ◽  
Detection Limits ◽  
Rapid Identification ◽  
Flammulina Velutipes ◽  
The Novel ◽  
Production Environment ◽  
Pan Genome ◽  
Listeria Ivanovii ◽  
Mpcr Assay

Listeria spp. is an important foodborne disease agent, often found in the fresh mushroom (Flammulina velutipes) and its production environment. The aim of this study was to develop multiplex PCR for rapid identification of Listeria monocytogenes and Listeria ivanovii, and nonpathogenic Listeria in F. velutipes plants. Pan-genome analysis was first used to identify five novel Listeria-specific targets: one for the Listeria genus, one for L. monocytogenes, and three for L. ivanovii. Primers for the novel targets were highly specific in individual reactions. The detection limits were 103–104 CFU/mL, meeting the requirements of molecular detection. A mPCR assay for the identification of pathogenic Listeria, with primers targeting the novel genes specific for Listeria genus (LMOSLCC2755_0944), L. monocytogenes (LMOSLCC2755_0090), and L. ivanovii (queT_1) was then designed. The assay specificity was robustly verified by analyzing nonpathogenic Listeria and non-Listeria spp. strains. The determined detection limits were 2.0 × 103 CFU/mL for L. monocytogenes and 3.4 × 103 CFU/mL for L. ivanovii, for pure culture analysis. Further, the assay detected 7.6 × 104 to 7.6 × 100 CFU/10 g of pathogenic Listeria spiked into F. velutipes samples following 4–12 h enrichment. The assay feasibility was evaluated by comparing with a traditional culture-based method, by analyzing 129 samples collected from different F. velutipes plants. The prevalence of Listeria spp. and L. monocytogenes was 58.1% and 41.1%, respectively. The calculated κ factors for Listeria spp., L. monocytogenes, and L. ivanovii were 0.97, 0.97, and 1, respectively. The results of the novel mPCR assay were highly consistent with those of the culture-based method. The new assay thus will allow rapid, specific, and accurate detection and monitoring of pathogenic Listeria in food and its production environment.

scholarly journals Detection of Cercopithifilaria bainae infection in shelter dogs and ticks in Oklahoma, USA

2020 ◽  
Author(s):  
Megan W. Lineberry ◽  
Kellee D. Sundstrom ◽  
Susan E. Little ◽  
Erin M. Stayton ◽  
Kelly E. Allen
Keyword(s):  
Dna Sequences ◽  
Rhipicephalus Sanguineus ◽  
Skin Lesions ◽  
12S Rrna ◽  
Rrna Gene ◽  
Positive Skin ◽  
Cercopithifilaria Bainae ◽  
The Usa ◽  
Shelter Dogs ◽  
Skin Samples

Abstract Background Cercopithifilaria bainae is a filarioid nematode of dogs. Infection with the parasite was not reported in the USA until 2017, when a dog with skin lesions in Florida was diagnosed. Brown dog ticks, Rhipicephalus sanguineus sensu lato, are the purported tick vectors, and are widespread in the USA. Therefore, C. bainae is likely present in additional states. Here, we tested dogs and ticks in Oklahoma for evidence of C. bainae infection. Methods Dermal punch biopsies were opportunistically collected from municipal shelter and client-owned dogs. Multiple skin samples collected from interscapular and head regions were tested by saline sedimentation to recover live microfilariae for morphometric identification and by PCR to amplify a 330 bp region of the filarioid 12S rRNA gene. Also, ticks observed on surveyed dogs were collected, identified to species level, and tested for filarioid DNA. Results A total of 496 saline sedimentations were performed on 230 shelter and 20 client-owned dogs. Cercopithifilaria bainae infections were identified in 2.6% (6/230) of shelter dogs by morphometry of microfilariae in sedimentations and/or amplification of DNA from skin. DNA sequences amplified from PCR positive skin samples were 99–100% identical to C. bainae reported in Italy. All skin samples from client-owned dogs were negative for filarioid infection by saline sedimentation and PCR. A total of 112 ticks, comprised of four species, were collected. Two of 72 R. sanguineus s.l., both engorged females found attached to a C. bainae infected dog, harbored C. bainae DNA (99–100% identity). One attached R. sanguineus s.l. male on the same dog harbored filarioid DNA sequence which was difficult to interpret at numerous base-pair locations, but was closest in identity (~80%) to C. bainae . Conclusions The distribution of C. bainae is more widespread than previously known. Here, we document C. bainae infections in dogs and DNA in brown dog ticks in Oklahoma for the first time. As brown dog ticks are commonly found throughout the USA, veterinarians in this region should consider C. bainae infection as a differential diagnosis in canine patients with dermatitis or polyarthritis.

scholarly journals How Times Have Changed! A Cornucopia of Antigens for Membranous Nephropathy

2021 ◽  
Vol 12 ◽  
Author(s):  
Tiffany N. Caza ◽  
Laith F. Al-Rabadi ◽  
Laurence H. Beck
Keyword(s):  
Membranous Nephropathy ◽  
Rapid Identification ◽  
Target Antigen ◽  
The Novel ◽  
Podocyte Injury ◽  
Phospholipase A2 Receptor ◽  
Major Target ◽  
Immune Complex Formation

The identification of the major target antigen phospholipase A2 receptor (PLA2R) in the majority of primary (idiopathic) cases of membranous nephropathy (MN) has been followed by the rapid identification of numerous minor antigens that appear to define phenotypically distinct forms of disease. This article serves to review all the known antigens that have been shown to localize to subepithelial deposits in MN, as well as the distinctive characteristics associated with each subtype of MN. We will also shed light on the novel proteomic approaches that have allowed identification of the most recent antigens. The paradigm of an antigen normally expressed on the podocyte cell surface leading to in-situ immune complex formation, complement activation, and subsequent podocyte injury will be discussed and challenged in light of the current repertoire of multiple MN antigens. Since disease phenotypes associated with each individual target antigens can often blur the distinction between primary and secondary disease, we encourage the use of antigen-based classification of membranous nephropathy.

Amphibambusa hongheensis sp. nov., a novel bambusicolous ascomycete from Yunnan, China

Phytotaxa ◽  
2021 ◽  
Vol 505 (2) ◽  
pp. 201-212
Author(s):  
HONG-BO JIANG ◽  
SHI-JIE ZHANG ◽  
RUNGTIWA PHOOKAMSAK ◽  
ITTHAYAKORN PROMPUTTHA ◽  
PATTANA KAKUMYAN ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Yunnan Province ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
The Novel ◽  
Molecular Approach ◽  
Mucilaginous Sheath ◽  
Phylogenetic Affinity ◽  
First Time

Amphibambusa hongheensis sp. nov. was collected from dead bamboo culms in Honghe County of Yunnan Province, China. The novel species is introduced based on the morpho-molecular approach. Morphologically, A. hongheensis fits well with Amphibambusa and is characterized by immersed, globose to subglobose ascomata, with protruding carbonaceous papilla, unitunicate, cylindrical to elongate fusiform, subsessile to short pedicellate asci with a J+, subapical ring, and fusiform, hyaline to pale brown, 1-septate ascospores, longitudinally striated, and surrounded by a thick mucilaginous sheath. Phylogenetic analyses of a concatenated ITS-LSU sequence dataset based on maximum-likelihood and Bayesian inference criteria revealed the phylogenetic affinity of A. hongheensis within Cainiaceae (Xylariales, Sordariomycetes). Amphibambusa hongheensis formed an independent subclade sister to A. bambusicola with moderate support (81% ML, 0.96 PP) and clustered with the genus Arecophila in Cainiaceae. Amphibambusa hongheensis is the second species accommodated in Amphibambusa and is reported from Yunnan, China, for the first time. Detailed description, illustration and updated phylogeny are provided.

Detection and prevalence of Cercopithifilaria bainae infection in shelter dogs in Oklahoma, USA

2019 ◽  
Author(s):  
Megan W. Lineberry ◽  
Kellee D. Sundstrom ◽  
Susan E. Little ◽  
Erin M. Stayton ◽  
Kelly E. Allen
Keyword(s):  
Dna Sequences ◽  
Rhipicephalus Sanguineus ◽  
Skin Lesions ◽  
Positive Skin ◽  
Cercopithifilaria Bainae ◽  
Rhipicephalus Sanguineus Sensu Lato ◽  
The Usa ◽  
Shelter Dogs ◽  
Tick Vectors ◽  
Skin Samples

Abstract Background Cercopithifilaria bainae is a filarioid nematode of dogs. Infection with the parasite was not reported in the USA until 2017, when a dog with skin lesions in Florida was diagnosed. Brown dog ticks, Rhipicephalus sanguineus sensu lato, are the purported tick vectors, and are widespread in the USA. Therefore, C. bainae is likely present in additional states. Here, we tested dogs and ticks in Oklahoma for evidence of C. bainae infection.Methods Dermal punch biopsies were opportunistically collected from municipal shelter and client-owned dogs. Multiple skin samples collected from interscapular and head regions were tested by saline sedimentation to recover live microfilariae for morphometric identification and by PCR to amplify a 330 bp region of 12S filarioid rDNA. Also, ticks observed on surveyed dogs were collected, identified to species level, and tested for filarioid DNA.Results A total of 1,521 biopsy samples were collected from 230 shelter and 20 client-owned dogs. Cercopithifilaria bainae infections were identified in 2.6% (6/230) of shelter dogs by morphometry of microfilariae in sedimentations and/or amplification of DNA from skin. DNA sequences amplified from PCR positive skin samples were 99–100% identical to C. bainae reported in Italy. All skin samples from client-owned dogs were negative for filarioid infection by saline sedimentation and PCR. A total of 112 ticks, comprised of four species, were collected. Two of 72 R. sanguineus s.l., both replete females found attached to a C. bainae infected dog, harbored C. bainae DNA (99–100% identity). One attached R. sanguineus s.l. male on the same dog harbored filarioid DNA sequence which was difficult to interpret at numerous base-pair locations, but was closest in identity (~80%) to C. bainae.Conclusions The distribution of C. bainae is more widespread than previously known. Here, we document C. bainae infections in dogs and DNA in brown dog ticks in Oklahoma for the first time. As brown dog ticks are commonly found throughout the USA, veterinarians in this region should consider C. bainae infection as a differential diagnosis in canine patients with dermatitis or polyarthritis.

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