scholarly journals Reorganized Genomic Taxonomy of Francisellaceae Enables Design of Robust Environmental PCR Assays for Detection of Francisella tularensis

2021 ◽  
Vol 9 (1) ◽  
pp. 146
Author(s):  
Caroline Öhrman ◽  
Jason W. Sahl ◽  
Andreas Sjödin ◽  
Ingrid Uneklint ◽  
Rebecca Ballard ◽  
...  
Keyword(s):  
Francisella Tularensis ◽  
Environmental Samples ◽  
Multiple Sources ◽  
Phylogenetic Structure ◽  
Specific Pcr ◽  
Comprehensive Collection ◽  
The Family ◽  
Genomic Taxonomy ◽  
Pcr Assays ◽  
Genomic Regions

In recent years, an increasing diversity of species has been recognized within the family Francisellaceae. Unfortunately, novel isolates are sometimes misnamed in initial publications or multiple sources propose different nomenclature for genetically highly similar isolates. Thus, unstructured and occasionally incorrect information can lead to confusion in the scientific community. Historically, detection of Francisella tularensis in environmental samples has been challenging due to the considerable and unknown genetic diversity within the family, which can result in false positive results. We have assembled a comprehensive collection of genome sequences representing most known Francisellaceae species/strains and restructured them according to a taxonomy that is based on phylogenetic structure. From this structured dataset, we identified a small number of genomic regions unique to F. tularensis that are putatively suitable for specific detection of this pathogen in environmental samples. We designed and validated specific PCR assays based on these genetic regions that can be used for the detection of F. tularensis in environmental samples, such as water and air filters.

scholarly journals Genomic Markers for Differentiation of Francisella tularensis subsp. tularensis A.I and A.II Strains

2007 ◽  
Vol 74 (1) ◽  
pp. 336-341 ◽  
Author(s):  
Claudia R. Molins-Schneekloth ◽  
John T. Belisle ◽  
Jeannine M. Petersen
Keyword(s):  
Suppression Subtractive Hybridization ◽  
Francisella Tularensis ◽  
Geographical Location ◽  
Subtractive Hybridization ◽  
Clinical Isolates ◽  
Type B ◽  
Tularensis Subsp ◽  
Genomic Markers ◽  
Pcr Assays ◽  
Genomic Regions

ABSTRACT Tularemia is caused by two subspecies of Francisella tularensis, F. tularensis subsp. tularensis (type A) and F. tularensis subsp. holarctica (type B). F. tularensis subsp. tularensis is further subdivided into two genetically distinct populations (A.I and A.II) that differ with respect to geographical location, anatomical source of recovered isolates, and disease outcome. Using two human clinical isolates, suppression subtractive hybridization was performed to identify 13 genomic regions of difference between A.I and A.II strains. Two PCR assays, one to identify A.I and A.II as well as to discriminate between F. tularensis subsp. holarctica and F. novicida and another specific for A.I, were developed. This is the first report to identify and characterize conserved genomic differences between A.I and A.II.

scholarly journals Genus- and Species-Specific PCR-Based Detection of Dairy Propionibacteria in Environmental Samples by Using Primers Targeted to the Genes Encoding 16S rRNA

1999 ◽  
Vol 65 (9) ◽  
pp. 4241-4244 ◽  
Author(s):  
Franca Rossi ◽  
Sandra Torriani ◽  
Franco Dellaglio
Keyword(s):  
16S Rrna ◽  
Environmental Samples ◽  
Specific Pcr ◽  
Genes Encoding ◽  
Propionibacterium Thoenii ◽  
Pcr Assays ◽  
Dairy Propionibacteria ◽  
Species Specific

ABSTRACT PCR assays with primers targeted to the genes encoding 16S rRNA were developed for detection of dairy propionibacteria.Propionibacterium thoenii specific oligonucleotide PT3 was selected after partial resequencing. Tests allowed the detection of less than 10 cells per reaction from milk and cheese and 102 cells per reaction from forage and soil.

scholarly journals Distribution of the leptospiral immunoglobulin-like (lig) genes in pathogenic Leptospira species and application of ligB to typing leptospiral isolates

2009 ◽  
Vol 58 (9) ◽  
pp. 1173-1181 ◽  
Author(s):  
Gustavo M. Cerqueira ◽  
Alan J. A. McBride ◽  
Mathieu Picardeau ◽  
Samuel G. Ribeiro ◽  
Ângela N. Moreira ◽  
...  
Keyword(s):  
Clinical Isolates ◽  
Pathogenic Leptospira ◽  
Reliable Identification ◽  
Specific Pcr ◽  
The Family ◽  
Leptospira Species

The family of leptospiral immunoglobulin-like (lig) genes comprises ligA, ligB and ligC. This study used PCR to demonstrate the presence of lig genes among serovars from a collection of leptospiral strains and clinical isolates. Whilst ligA and ligC appeared to be present in a limited number of pathogenic serovars, the ligB gene was distributed ubiquitously among all pathogenic strains. None of the lig genes were detected among intermediate or saprophytic Leptospira species. It was also shown that, similar to the previously characterized secY gene, a short specific PCR fragment of ligB could be used to correctly identify pathogenic Leptospira species. These findings demonstrate that ligB is widely present among pathogenic strains and may be useful for their reliable identification and classification.

scholarly journals CRISPR Is an Optimal Target for the Design of Specific PCR Assays for Salmonella enterica Serotypes Typhi and Paratyphi A

2014 ◽  
Vol 8 (1) ◽  
pp. e2671 ◽  
Author(s):  
Laetitia Fabre ◽  
Simon Le Hello ◽  
Chrystelle Roux ◽  
Sylvie Issenhuth-Jeanjean ◽  
François-Xavier Weill
Keyword(s):  
Salmonella Enterica ◽  
Specific Pcr ◽  
Optimal Target ◽  
Pcr Assays

scholarly journals Tick-borne pathogens in Ixodidae ticks collected from privately-owned dogs in Italy: a country-wide molecular survey

2020 ◽  
Author(s):  
Stefania Zanet ◽  
Elena Battisti ◽  
Paola Pepe ◽  
Lavinia Ciuca ◽  
Liliana Colombo ◽  
...  
Keyword(s):  
Borrelia Burgdorferi ◽  
Urban Areas ◽  
Borrelia Burgdorferi Sensu Lato ◽  
Specific Pcr ◽  
The Family ◽  
Borrelia Burgdorferi S.L ◽  
Privately Owned ◽  
Prevalent Species ◽  
Minimum Infection Rate ◽  
Theileria Spp

Abstract Background Ticks and tick-borne diseases are increasingly recognized as a cause of disease in dogs worldwide. The epidemiology of ticks and tick-transmitted protozoa and bacteria has changed due to the spread of ticks to urban and peri-urban areas and the movement of infected animals, posing new risks for animals and humans. This countrywide study reports information on distribution and prevalence of pathogens in ticks collected from privately-owned dogs in Italy. We analyzed 2681 Ixodidae ticks, collected from 1454 pet dogs from Italy. Specific PCR protocols were used to detect i) Piroplasms of the genera Babesia and Theileria , ii) Gram-negative cocci of the family Anaplasmataceae and iii) Borrelia burgdorferi sensu lato. Sequencing of positive amplicons allowed for species identification. Results Babesia / Theileria spp. DNA was detected in 435 homogeneous tick-pools (Minimum Infection Rate (MIR) = 27.6%; 95% confidence interval (CI) = 25.4-29.8%) with higher prevalence in Ixodes ricinus and Rhipicephalus sanguneus group. The zoonotic B. venatorum was the most prevalent species (MIR = 7.5%; 95% CI = 6.3-9.0%). Anaplasma and Ehrlichia species were detected in 165 tick-pools (MIR = 10.5%; 95% CI = 9.3-11.8%) and specifically, A. phagocytophilum was identified with MIR = 5.1% (95% CI = 4.1-6.3%). Borrelia burgdorferi s.l. and B. afzelii were detected with MIR = 0.4% (95% CI = 0.2-0.8%) and MIR = 0.3% (95% CI 0.1-0.7%) respectively. Conclusions Zoonotic pathogens B. venatorum and A. phagocytophilum were the most frequently detected in ticks collected from privately-owned dogs which might be used as markers of pathogens presence and distribution.

scholarly journals Mining multiple sources of historical data: The example of a standardized dataset of medieval monasteries and convents in France

2019 ◽  
Vol 2 ◽  
pp. 1-7
Author(s):  
Adam Mertel ◽  
David Zbíral
Keyword(s):  
Data Mining ◽  
Spatial Patterns ◽  
Data Model ◽  
Computational Analysis ◽  
Historical Data ◽  
Model Data ◽  
Multiple Sources ◽  
The Public ◽  
Comprehensive Collection ◽  
Online Databases

<p><strong>Abstract.</strong> In this paper, we present a dataset of medieval monasteries and convents on the territory of today’s France and discuss the workflow of its integration. Spatial historical data are usually dispersed and stored in various forms &amp;ndash; encyclopedias and catalogues, websites, online databases, and printed maps. In order to cope with this heterogeneity and proceed to computational analysis, we have devised a method that includes the creation of a data model, data mining from sources, data transformation, geocoding, editing, and conflicts solving.</p><p> The resulting dataset is probably the most comprehensive collection of records on medieval monasteries within the borders of today’s France. It can be used for understanding the spatial patterns of medieval Christian monasticism and the implantation of the official Church infrastructure, as well as the relation between this official infrastructure and phenomena covered in other datasets. We open this dataset, as well as scripts for mining, to the public (https://github.com/adammertel/dissinet.monasteries) and provide a map tool to visualize, filter, and download the records (http://hde.geogr.muni.cz/monasteries).</p>

scholarly journals Genomic epidemiology and strain taxonomy of Corynebacterium diphtheriae

2021 ◽  
Author(s):  
Julien Guglielmini ◽  
Melanie Hennart ◽  
Edgar Badell ◽  
Julie Toubiana ◽  
Alexis Criscuolo ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Corynebacterium Diphtheriae ◽  
Phylogenetic Structure ◽  
Genomic Epidemiology ◽  
Short Timescale ◽  
Genomic Taxonomy ◽  
Sporadic Cases ◽  
Small Clusters ◽  
Genome Scale ◽  
Analytical Approaches

Background Corynebacterium diphtheriae is highly transmissible and can cause large diphtheria outbreaks where vaccination coverage is insufficient. Sporadic cases or small clusters are observed in high-vaccination settings. The phylogeography and short timescale evolution of C. diphtheriae are not well understood, in part due to a lack of harmonized analytical approaches of genomic surveillance and strain tracking. Methods We combined 1,305 genes with highly reproducible allele calls into a core genome multilocus sequence typing (cgMLST) scheme. We analyzed cgMLST genes diversity among 602 isolates from sporadic clinical cases, small clusters or large outbreaks. We defined sublineages based on the phylogenetic structure within C. diphtheriae and strains based on the highest number of cgMLST mismatches within documented outbreaks. We performed time-scaled phylogenetic analyses of major sublineages. Results The cgMLST scheme showed high allele call rate in C. diphtheriae and the closely related species C. belfantii and C. rouxii . We demonstrate its utility to delineate epidemiological case clusters and outbreaks using a 25 mismatches threshold, and reveal a number of cryptic transmission chains, most of which are geographically restricted to one or a few adjacent countries. Subcultures of the vaccine strain PW8 differed by up to 20 cgMLST mismatches. Phylogenetic analyses revealed short timescale evolutionary gain or loss of the diphtheria toxin and biovar-associated genes. We devised a genomic taxonomy of strains and deeper sublineages (defined using a 500 cgMLST mismatches threshold), currently comprising 151 sublineages, only a few of which are geographically widespread based on current sampling. The cgMLST genotyping tool and nomenclature was made publicly accessible at https://bigsdb.pasteur.fr/diphtheria . Conclusions Standardized genome-scale strain genotyping will help tracing transmission and geographic spread of C. diphtheriae . The unified genomic taxonomy of C. diphtheriae strains provides a common language for studies into the ecology, evolution and virulence heterogeneity among C. diphtheriae sublineages.

Sign in / Sign up

Export Citation Format

Share Document