Subtyping of outbreak-associated isolates using pulsed-field gel electrophoresis (PFGE) revealed two similar but distinct Asc I PFGE patterns. (biomedcentral.com)
High-throughput pyrosequencing of two L. monocytogenes isolates was used to rapidly provide the genome sequence of the primary outbreak strain and to investigate the extent of genetic diversity associated with a change of a single restriction enzyme fragment during PFGE. (biomedcentral.com)
At the Utah Public Health laboratory, I oversee the area of the lab that performs Pulsed-field gel electrophoresis, also known as PFGE. (cdc.gov)
FDA performed pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) on the isolates from mung bean sprouts and environmental samples from Wholesome Soy Products, Inc. to further characterize the Listeria isolates. (cdc.gov)
Genome fingerprinting by pulsed-field gel electrophoresis (PFGE) on Mycobacterium isolates further showed that the isolates represented three strains of M. chelonae although the possibility of one of the strains being clonal with M. immunogenum cannot be excluded. (cdc.gov)
WGS performs the same function as Pulse Field Gel Electrophoresis (PFGE) but can differentiate all strains of foodborne pathogens, no matter what the species. (texas.gov)
DNA "fingerprinting" is performed on Salmonella bacteria isolated from ill people using techniques called pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS). (cdc.gov)
We defined an outbreak case-patient as a person in Ontario with listeriosis symptom onset after November 1, 2015, who had pulsed-field gel electrophoresis (PFGE) pattern combinations LMACI.0015/LMAAI.0024 or LMACI.0015/LMAAI.0069. (cdc.gov)
Also various molecular typing techniques have been used, including pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST), and these assays were considered as efficient techniques in MRSA typing but they are time consuming, expensive, and technically complex [ 8 ]. (hindawi.com)
Pulsed-field gel electrophoresis (PFGE) is a highly discriminative molecular typing technique that is used in epidemiological studies worldwide. (applied-maths.com)
PFGE is based upon the variable migration of large DNA restriction fragments in an electrical field of alternating polarity. (applied-maths.com)
All isolates were typed by pulsed-field gel electrophoresis (PFGE) and subjected to antibiotic susceptibility testing. (puce.edu.ec)
Control measures to alleviate human infections require that food isolates be characterized and this was until recently carried out using Pulsed-Field Gel Electrophoresis (PFGE) and phage typing as the main laboratory subtyping tools for use in demonstrating relatedness of isolates recovered from infected humans and the food source. (intechopen.com)
Pulsed-field gel electrophoresis (PFGE) evaluation labeled the wild deer and boar strains into 4 and three PFGE patterns, respectively. (cellgenetherapy.com)
In this thesis, we reported on a 26-month surveillance study performed in an effort to identify and characterise persistent ST type(s), cultured from four PIF production facilities, using molecular strategies including target-specific polymerase chain reaction (PCR), pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST) and multi-genome microarray. (ucd.ie)
The strain type information provided by GSS was comparable to pulsed field gel electrophoresis (PFGE), the current standard for pathogen typing in foodborne outbreak investigation and response. (rapidmicromethods.com)
To achieve this baseline information, a spatial and traffic-flow map is developed from culture confirmed isolates and Pulsed-Field Gel Electrophoresis (PFGE) and PCR-based serogrouping. (centerforproducesafety.org)
Normally, a process called pulsed-field gel electrophoresis (PFGE) is used to match outbreak isolates, but WGS provides an even clearer distinction of isolates, according to the CDC. (foodpoisoningbulletin.com)
Strains11
This pilot has shown the potential of whole genome sequencing to advance our knowledge base on the types of E.coli O157 strains circulating in the environment in Scotland and how these relate to the strains which are transmitted through the food chain and those which lead to illness in humans. (food.gov.uk)
High-throughput genome sequencing provided a more detailed real-time assessment of genetic traits characteristic of the outbreak strains than could be achieved with routine subtyping methods. (biomedcentral.com)
Whole genome sequences of the Listeria strains isolated from mung bean sprouts produced by Wholesome Soy Products, Inc. and environmental isolates collected at the production facility were found to be highly related to sequences of Listeria strains isolated from five people who became ill from June through August 2014. (cdc.gov)
A total of 219 French patient isolates and environmental strains were compared using a mixed-genome micro-array. (biomedcentral.com)
The whole-genome sequences of L. monocytogenes strains in these samples were compared to those found in the 5 ill people. (pritzkerlaw.com)
In an early 2022 publication of Nature Scientific Data , 1,484 genomes from Listeria monocytogenes strains collected in 19 European countries were compiled in one dataset, providing the most accurate pangenome of the species to date. (biomerieux.com)
The K. pneumoniae BHKPC93 and BHKPC104 strains were selected for whole genome sequencing (WGS) based on their pulsed-field gel electrophoresis profile. (qxmd.com)
Entire-genome sequence (WGS) evaluation indicated that each one the strains carried mdfA, a drug resistance gene for macrolide antibiotics, and in addition pathogenicity-related genes much like these within the Sakai pressure. (cellgenetherapy.com)
PathoGenetix, Inc., a commercial-stage developer of an automated system for rapid bacterial identification, has announced new research demonstrating the use of Genome Sequence Scanning™ (GSS™) technology to confirm and identify pathogenic Salmonella strains in enriched spinach samples in less than five hours. (rapidmicromethods.com)
Whole-genome sequencing (WGS) tests show Listeria strains found in Roos cheese are highly related to those isolated from ill patients, according to an update from the Centers for Disease Control and Prevention (CDC). (foodpoisoningbulletin.com)
Isolates11
The aim of this project was to use Whole Genome Sequencing (WGS) to increase our understanding of the evolution and epidemiology of E. coli O157 isolates from Scotland. (food.gov.uk)
The availability of whole genome information enables a number of methods to be applied that can be used to characterise the particular isolate and to determine the genetic relatedness of isolates. (food.gov.uk)
This project is a pilot which has used genome sequence on a selection of isolates primarily from the Grampian Region of Scotland. (food.gov.uk)
In total, 148 isolates were whole genome sequenced using an Illumina HiSeq sequencer. (food.gov.uk)
Notably, these two isolates were found to harbor a 50 kbp putative mobile genomic island encoding translocation and efflux functions that has not been observed in other Listeria genomes. (biomedcentral.com)
We make a fingerprint of the DNA, of the whole genome, that we can then put into our database and we can compare it with other isolates. (genomeweb.com)
BKC-1-positive isolates were typed using pulsed-field gel electrophoresis and multi-locus sequence typing. (cardiff.ac.uk)
Some isolates were submitted to full genomic characterization by whole-genome sequencing (Illumina MiSeq and MinIon), and in-vivo virulence studies using the Galleria mellonella model. (cardiff.ac.uk)
Salmonella isolates were analysed with pulse-field gel electrophoresis and whole-genome sequencing. (cambridge.org)
The tools have now given way to whole genome sequencing which provides a full and comprehensive genetic attributes of an organism and a very attractive and superior tool for defining an isolate and for inferring genetic relatedness among isolates. (intechopen.com)
Because GSS isolates and scans microbial DNA directly from a mixed culture and does not require a pure culture isolate, it greatly reduces the time, complexity, skill and cost required by other molecular and whole genome identification approaches. (rapidmicromethods.com)
Sequence16
They were able to sequence the whole genome and confirm that the bacteria did not carry genetic markers for antibiotic resistance or evidence of genetic engineering in only 8.5 hours. (cdc.gov)
Thus, the increase in genome size seems to be due to an A. oryzae lineage-specific acquisition of sequence, rather than loss of sequence in A. nidulans and A. fumigatus . (nature.com)
This suggests that the genome size differences are largely due to sequence acquisition in A. oryzae . (nature.com)
Kelly Oakeson] Well, whole genome sequence data provides a very high-resolution tool for everything from identifying what types of microbes or viruses you might have in any given sample to determining antimicrobial resistance and identifying clusters of related microbes in the case of a foodborne illness outbreak. (cdc.gov)
If all goes as planned, in the third quarter of 2011, OpGen will launch the system for whole-genome sequence assembly and finishing for research on larger organisms, such as plants and animals, including humans, CEO Doug White told GenomeWeb Daily News . (genomeweb.com)
It and BGI, OpGen said, had already used the technology to complete a study based on human genome data to successfully close gaps in existing sequence folds. (genomeweb.com)
Applications for the technology include strain typing and whole-genome sequence assembly. (genomeweb.com)
For whole-genome sequence assembly and finishing, the Optical Mapping System is complementary to existing second- and forthcoming third-generation sequencing technologies, he said, in that it can provide a complete genome scaffold for contig alignment and orientation. (genomeweb.com)
Until recently, however, functional analysis of the DED fungi was hampered by the lack of protocols for efficient gene knockout and by the unavailability of a full genome sequence. (sisef.it)
FDA is spearheading an international effort to build a network of laboratories that can sequence the genomes of foodborne pathogens and then upload the genomic sequence of the pathogen and the geographic location from which the pathogen was gathered into a publicly accessible database. (texas.gov)
For this study, we applied four different whole genome sequencing (WGS)-based subtyping methods: high quality single-nucleotide polymorphism (hqSNP) analysis, whole genome multilocus sequence typing using either all loci [wgMLST (all loci)] and only chromosome-associated loci [wgMLST (chrom)], and core genome multilocus sequence typing (cgMLST) to a dataset of isolate sequences from 9 well-characterized Salmonella outbreaks. (cdc.gov)
82‐40 was finished in 2006 exposing that 90% of the genome constitutes coding sequence (GenBank Accession quantity "type":"entrez-nucleotide" attrs :"text":"NC_008599″ term_id :"118474057″ term_text :"NC_008599″NC_008599). (researchensemble.com)
In this study the complete genome sequence of one such isolate found to persist in a PIF production facility, denoted as C. sakazakii SP291, along with its phenotypic characteristics were reported. (ucd.ie)
When compared with C. sakazakii ATCC® BAA-894, which is also of PIF origin, the annotated genome sequence identified two interesting functional categories, comprising of genes related to the bacterial stress response along with resistance to antimicrobial and toxic compounds. (ucd.ie)
repetitive sequence elements in the members had been in contact with bacterial genome have shown con- patients for several hours. (who.int)
Listeria2
The use of whole-genome sequencing is also increasing the speed of detection of even small Listeria foodborne outbreaks. (cdc.gov)
It was only around twenty years ago that the first genome of Listeria monocytogenes strain EGDe as published in a "Science" paper, after a five-year European project involving several research institutes around Europe. (biomerieux.com)
Sequencing21
Sequencing of the A. oryzae genome was accomplished using the whole-genome shotgun (WGS) approach. (nature.com)
This study confirms that the latest generation of DNA sequencing technologies can be applied during high priority public health events, and laboratories need to prepare for this inevitability and assess how to properly analyze and interpret whole genome sequences in the context of molecular epidemiology. (biomedcentral.com)
Sarah Gregory] Today, I'm talking with Dr. Kelly Oakeson about bioinformatics and genome sequencing in a public health lab. (cdc.gov)
Although limited information is available about the specific sprout products that ill people consumed, the whole genome sequencing findings, together with the sprout consumption history of two patients and inspection findings at the firm, suggest that these illnesses could be related to products from Wholesome Soy Products, Inc. (cdc.gov)
Through CDC's Advanced Molecular Detection initiative , whole genome sequencing of pathogens is already changing infectious disease surveillance and outbreak investigations. (cdc.gov)
As cited in Richards' paper , a recent outbreak investigation of human immunodeficiency virus (HIV) in Indiana showed how genome sequencing can help us understand origin and transmission patterns. (cdc.gov)
Genome sequencing is now poised to transform PulseNet , the major foodborne outbreak detection system, which until recently relied on pulsed-field gel electrophoresis. (cdc.gov)
Genome sequencing is also being integrated in international PulseNet activities. (cdc.gov)
One of the best tools in helping to detect outbreaks is Whole Genome Sequencing (WGS) which can more accurately identify the "fingerprint" of a pathogen serovar than its predecessor Pulsed Field Gel Electrophoresis (PGFE) and therefore identify more outbreaks and identify them more quickly. (foodpoisoningbulletin.com)
The scientific knowledge and capacity in the field of genomic sequencing has been continuously developed during the last two decades. (biomerieux.com)
Studies were conducted using phenotypic (susceptibility testing to carbapenems ± efflux pump inhibitors (EPIs)) and molecular (determining expression levels of efflux operon with regulatory-gene and whole genome sequencing (WGS)) methods. (bvsalud.org)
Whole-genome sequencing (WGS) and hybrid assembly were performed, using data generated on the Illumina and Nanopore platforms. (bvsalud.org)
Whole-genome sequencing was performed on 96 MRSA representatives. (puce.edu.ec)
This Special Issue will aim at combining One Health approaches with OMIC techniques such as whole genome sequencing, shotgun metagenomics, amplicon sequencing or transcriptomics. (onehealthinitiative.com)
The new subtyping test, which exploited whole genome sequencing data, displays the attributes of an ideal subtyping test: high discrimination, low cost, rapid, highly reproducible and epidemiological concordance. (intechopen.com)
This study examined the added value of whole genome sequencing (WGS) for investigating a non-point source outbreak of Salmonella ser. (who.int)
2 Whole genome sequencing (WGS) is a high-resolution typing method that can help foodborne disease investigators distinguish outbreak cases from non-outbreak cases. (who.int)
Whole genome sequencing can be used in Salmonella outbreak investigations for rapid prediction of antimicrobial resistance and can link cases to each other and to possible sources of infection. (barfblog.com)
Conjugation experiment and whole-genome sequencing were performed for further analysis.Results: Strain AeBJ009 was isolated from hospital sewage and identified as A. towneri. (archive.org)
More detailed sub-typing and diversity analysis will be conducted by future Whole Genome Sequencing with an external partner. (centerforproducesafety.org)
Polymerase Chain Re2
Shigatoxin typing was performed by in silico (computer-based) Polymerase Chain Reaction (PCR) and phylogenetic analysis (analysis of the evolution of genetic structure over time) was based on core genome single nucleotide polymorphisms. (food.gov.uk)
In addition, these findings provide further support for models in which conflicts between different genes in genomes can drive the process of speciation. (elifesciences.org)
Here we show that the 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans 5 and Aspergillus fumigatus 6 . (nature.com)
The 37-Mb genome was predicted to contain a total of 12,074 genes encoding proteins with a length greater than 100 amino acid residues (see Methods). (nature.com)
The ongoing annotation of these genomes should spark a new wave of interest in the DED pathosystem, as it should lead to the formal identification of genes modulating parasitic fitness. (sisef.it)
We have used the techniques of linkage analysis and pulsed field gel electrophoresis to determine the proximity of these two antithetically regulated genes in this conserved linkage group. (arizona.edu)
Analysis of this region by pulsed field gel electrophoresis showed that the genes for TSHB and NGFB are located less than 310 kb apart in man and 220 kb in the mouse. (arizona.edu)
Methods: Aberrantly expressed m6A regulator genes were screened in The Cancer Genome Atlas (TCGA) MIBC cohort (n = 408) and validated using fresh-frozen and formalin-fixed paraffin-embedded (FFPE) specimens collected during this study. (bvsalud.org)
The strategy was developed to compare the variations in complex genomes as well as to obtain clones of those differentiating genes (Lisitsyn and Wigler 1993 Before the availability of the genome sequences RDA was applied to reveal genes distinctively or predominantly present in just one subspecies (Gorkiewicz ssp. (researchensemble.com)
To determine the distribution and organization of the amino acid biosynthetic genes on the genome of this β-proteobacterium, various auxotrophic mutations were isolated using a Tn5 derivative that was convenient not only for the determination of its insertion site on the genome map but also for the structural analysis of the flanking regions. (elsevierpure.com)
Southern hybridization analysis, allelic exchange mutagenesis of ATCC 17616, and complementation tests demonstrated that all of the genes examined were functional and existed as a single copy within the genome. (elsevierpure.com)
Five Salmonella genome sequences, representing a broad host range serotype (Typhimurium), two host restricted serotypes (Typhi [two genomes] and Paratyphi) and one host adapted serotype (Choleraesuis) were used to identify core genomegenes that show evidence for recombination and positive selection. (biomedcentral.com)
Overall, 3323 orthologous genes were identified in all 5 Salmonella genomes analyzed. (biomedcentral.com)
Our data show that, among the four serotypes analyzed, (i) less than 10% of Salmonella genes in the core genome show evidence for homologous recombination, (ii) a number of Salmonella genes are under positive selection, including genes that appear to contribute to virulence, and (iii) branch specific positive selection contributes to the evolution of host restricted Salmonella serotypes. (biomedcentral.com)
Sequences3
In 2013, the genome sequences of O. ulmi and O. novo-ulmi were publicly released. (sisef.it)
Access to both genome sequences provides the resources for detailed analysis of physiology as well as subspecies‐specific adaptations and will stimulate efforts to identify mechanisms contributing to pathogen-host relationships and virulence. (researchensemble.com)
has been identified as the 2nd most consensus (ERIC) sequences which · 60 environmental samples were tak- frequent organism causing ventilator- are common to Gram-negative enteric en throughout the ICU, including associated pneumonia, the 4th most bacteria [11,12]. (who.int)
Complex genomes1
We think there's a significant [opportunity] for the microbial market," White said, but, he added, the company targeted less complex genomes for the initial launch of the Argus system for practical reasons. (genomeweb.com)
Strain4
In addition, OpGen's technology "gives you much more distinguishing features and gives you the ability to identify down to the strain in an isolate level," unlike pulsed field gel electrophoresis, which White said is the gold standard method for separating DNA molecules. (genomeweb.com)
Three of the French markers differed from the Dutch markers, one showed considerable overlap and was found in one of the Legionella genomes (Lorraine strain). (biomedcentral.com)
Tenover FC, Arbeit RD, Goering AMP deaminase RV, Mickelsen PA, Murray BE, Persing DH, Swaminathan B: Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. (pkc-inhibitors.com)
Pulsed-field gel electrophoresis and Southern blotting showed that strain AeBJ009 carries three plasmids and that blaNDM-1 is located on the 47kb plasmid pNDM-AeBJ009. (archive.org)
Genomic1
The small genomes of the DED fungi also facilitate genomic analyses. (sisef.it)
Restriction2
OpGen's Optical Mapping Technology is a method of deciphering a genome's architecture by creating high-resolution, ordered, whole-genome restriction maps from single DNA molecules. (genomeweb.com)
And by analyzing the images … we can put them back together and create a whole genome," or, in essence, a whole-genome restriction map, White said. (genomeweb.com)
Analysis4
Phylogenetic analysis of the three aspergilli using the whole-genome data showed that A. nidulans branched off earlier than A. oryzae and A. fumigatus 5 . (nature.com)
The combination of a mixed-genome micro-array and statistical analysis using a Random Forest algorithm has identified virulence markers in a consistent way. (biomedcentral.com)
Despite the considerable information provided by whole genome analysis and development of a phylogenetic tree, the approach does not lend itself to generating a useful nomenclature-based description of SE subtypes. (intechopen.com)
Analysis by pulsed-field gel electrophoresis revealed that 20 out of 23 insertion mutations were distributed on the 3.4-Mb chromosome. (elsevierpure.com)
Methods1
The blue bars at the bottom indicate the regions syntenic with A. fumigatus ( AF ) and A. nidulans ( AN ) genomes (see Methods). (nature.com)
Data1
This important feature makes it possible for labs to exchange and compare electrophoresis data obtained with different conditions or setups. (applied-maths.com)
Species1
Comparison of the three aspergilli species revealed the presence of syntenic blocks and A. oryzae -specific blocks (lacking synteny with A. nidulans and A. fumigatus ) in a mosaic manner throughout the genome of A. oryzae . (nature.com)
Genetic2
We observed discrepancies in allele difference ranges when using wgMLST (all loci), likely caused by inflated genetic variation due to loci found on plasmids and/or other mobile genetic elements in the accessory genome. (cdc.gov)
The process of horizontal gene transfer (HGT) in bacteria drives genetic diversity and development providing also a basis for variance NS-304 (Selexipag) in the virulence repertoire as well as resistance to antibiotics and sponsor defences (Hacker genomes confirmed that ssp. (researchensemble.com)
Humans1
NEW YORK (GenomeWeb News) - As OpGen intensifies the commercialization of its optical mapping technology, it is looking to expand its use to larger genomes, including humans, within the next year, its CEO said. (genomeweb.com)
Successfully1
Genus-specific PCR approach was successfully applied for screening of field MWF samples originating from different industrial users for detection of mycobacteria or pseudomonads including both culturable and nonculturable cells. (cdc.gov)
Organisms1
The expansion in genome size appears to be characteristic of the organisms closely related to A. oryzae , as the estimated genome size of its close relatives A. flavus (W. Nierman, personal communication) and Aspergillus niger 8 is comparable to that of A. oryzae . (nature.com)
Small1
All captured small mammals were dissected in the field and Echinococcus infection was identified by visual examinations. (bvsalud.org)
Study1
Publishing on IntechOpen allows authors to earn citations and find new collaborators, meaning more people see your work not only from your own field of study, but from other related fields too. (intechopen.com)
Public health1
The current set of predictive markers is insufficient to justify its use as a reliable test in the public health field in France. (biomedcentral.com)
Found1
As PhD students, we found it difficult to access the research we needed, so we decided to create a new Open Access publisher that levels the playing field for scientists across the world. (intechopen.com)