Isolates sequenced. Medical search. Frequent questions

Understanding the evolution of Leptospira especially as related to the clinical pathogenesis of leptospirosis is facilitated by systematic comparative genomic analysis of human-infecting isolates. (nih.gov)
The sensitivity of ODELAM allows us to detect different resistance states in individual clinical isolates. (seattlechildrens.org)
To investigate whether MinION-only sequencing is sufficient for identification, genome sequencing and downstream analysis in resource-limited settings, we sequenced the genomes of fourteen clinical isolates suspected to be Neisseria gonorrhoeae from Nairobi, Kenya. (nanoporetech.com)
The workflow for genome identification followed in the study, assembly and analysis could be used for any clinical isolate. (nanoporetech.com)
The distribution of these traits was assessed within further clinical, environmental and food isolates associated with the outbreak, and this comparison indicated that three distinct, but highly related strains may have been involved in this nationwide outbreak. (biomedcentral.com)
Given the widespread occurrence of L. monocytogenes , subtyping of clinical and food isolates is required to establish epidemiologic links during routine surveillance, outbreak investigations, and for source tracking. (biomedcentral.com)
A total of 110 clinical isolates of A. baumannii , collected in a recent 2-year period, were tested for carbapenem antibiotic susceptibility, followed by a molecular analysis of carbapenemase genes. (frontiersin.org)
Whole-genome sequencing potentially represents a single, rapid and cost-effective approach to defining resistance mechanisms and predicting phenotype, and strain type, for both clinical and epidemiological purposes. (ox.ac.uk)
This retrospective study aimed to determine the efficacy of whole genome-based antimicrobial resistance prediction in clinical isolates of Escherichia coli and Klebsiella pneumoniae.Seventy-four E. coli and 69 K. pneumoniae bacteraemia isolates from Oxfordshire, UK, were sequenced (Illumina HiSeq 2000). (ox.ac.uk)
The multilocus sequence typing scheme used previously for phylogenetic analysis of Escherichia coli was applied to 107 clinical isolates of Shigella flexneri. (uea.ac.uk)
A full list of clinical S. flexneri isolates subjected to MLST analysis in this study and a phylogenetic tree generated by the neighbour-joining method for S. flexneri are available as supplementary material with the online version of this paper. (uea.ac.uk)
The aims were to study the clinical presentation of patients with EfsB with focus on the risk of recurrent infection and IE, identify potential improvements of the management, and to investigate whether E. faecalis isolates from different episodes in the same patient were identical. (lu.se)
All nucleic acid in the clinical sample is sequenced and the resulting data is analysed by experienced bioinformaticians. (folkhalsomyndigheten.se)
Metagenomic sequencing engables a thorough mapping of the genetic material in the clinical sample, providing a broader understanding of the microbiological profile. (folkhalsomyndigheten.se)
The result of of metagenomic sequencing is the outcome of a collaborative effort between bioinformaticians and clinical microbiologists, where the clinical interpretation confirms and complements the technical analysis. (folkhalsomyndigheten.se)
16S sequencing is performed to determine which bacterial species are present in a clinical sample or isolate. (folkhalsomyndigheten.se)
The basis of the GENSAM project is the joint national management of clinical microbial sequencing data. (folkhalsomyndigheten.se)

Whole genome sequencing and phylogenetic analysis of six SARS-CoV-2 strains isolated during COVID-19 pandemic in Tunisia, North Africa. (pasteur.fr)

The Public Health Agency's Next Generation Sequencing (NGS) platform performs massive parallel sequencing of DNA and RNA. (folkhalsomyndigheten.se)

The system, software and consumables will initially be sold to research organizations, pharmaceutical companies and diagnostic companies that will sequence large regions of genomic DNA, including whole genomes, at costs several orders of magnitude below current levels. (scienceopen.com)
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)
Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. (ox.ac.uk)
Genomic sequence and phylogenetic analyses showed that it was highly homologous with the North American H5N2 viruses and all eight genes of this virus belonged to the North American gene lineage. (bvsalud.org)

Our revolutionary sequencing technologies combine the completeness of long reads with the accuracy of short reads to provide the most comprehensive view of genomes, transcriptomes, and epigenomes. (pacb.com)
CoV-2 highly positive samples detected during the early phase of the outbreak.Full genomes sequences of six Tunisian SARS-CoV-2 strains were obtained from imported and locally transmission cases during the COVID-19 outbreak. (pasteur.fr)

Further studies are required to determine the utility of real-time sequencing in outbreak investigations, diagnosis and management of infections, especially in resource-limited settings. (nanoporetech.com)
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)
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)
Accordingly, additional subtyping methods are required to better characterize outbreak isolates. (biomedcentral.com)
Draft Genome Sequence of a Neisseria meningitidis Serogroup C Isolate of Sequence Type 11 Linked to an Outbreak among Men Who Have Sex with Men. (pasteur.fr)
Here, we report the genome sequence of N. meningitidis strain LNP27256, an isolate of sequence type 11 linked to a recent outbreak among men who have sex with men in Europe. (pasteur.fr)
Of the 14 cases among persons with HIV in 2022 that were not related to the outbreak primarily among MSM, nine were caused by a single strain of N. meningitidis serogroup Y clonal complex CC174 sequence type ST-1466. (medscape.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)

Complete genome sequence of Pseudomonas aeruginosa K34-7, a carbapenem-resistant isolate of the high-risk sequence type 233. (pacb.com)

Genetic relatedness of the isolates was characterized by multilocus sequence typing. (frontiersin.org)
In the final analysis step of MLST, the relatedness of isolates are made by comparing allelic profiles. (wikipedia.org)
The relatedness of isolates is displayed as a dendrogram constructed using the matrix of pairwise differences between their allelic profiles, eBURST or a minimum spanning tree (MST). (wikipedia.org)
Alternatively, the relatedness of isolates can also be analysed with MultiLocus Sequence Analysis (MLSA). (wikipedia.org)

The phylogenetic analysis of the strain was based on 16S rRNA gene sequencing and showed that Paenibacillus sp. (asm.org)
The morphology of an isolated bacterial strain was found to be rod type, and the bacterium was identified as Lactobacillaceae species based on the GenBank database, through a phylogenetic analysis using the 16S rRNA sequence. (springeropen.com)

The aim of this preliminary study was to better understand the molecular epidemiology and genetic variability of SARS-CoV-2 viruses circulating in Tunisia and worldwide.Whole genome sequencing was performed using NGS approach on six SARS. (pasteur.fr)

citation needed] Despite MLST providing high discriminatory power, the accumulation of nucleotide changes in housekeeping genes is a relatively slow process and the allelic profile of a bacterial isolate is sufficiently stable over time for the method to be ideal for global epidemiology. (wikipedia.org)
The method uses an internal control sequence (spike) which is amplified and sequenced simultaneously with the sample to facilitate the assessment of the bacterial content and to detect amplification-inhibiting factors in the sample that may lead to a negative result. (folkhalsomyndigheten.se)
For contact tracing or inquiries related to antibiotic resistance, whole genome sequencing (WGS) of bacterial isolates is offered. (folkhalsomyndigheten.se)

FusA allele sequencing revealed that 49/52 strains were Cronobacter sakazakii, while the remaining 3 strains were Escherichia coli, Enterobacter cloacae, and Franconibacter helveticus . (biomedcentral.com)
DNA sequencing of 3423 bp throughout seven housekeeping genes identified eight new allele types and ten new sequence types among the isolates. (uea.ac.uk)
In the data analysis step, all unique sequences are assigned allele numbers and combined into an allelic profile and assigned a sequence type (ST). If new alleles and STs are found, they are stored in the database after verification. (wikipedia.org)
The large number of potential alleles at each of the loci provides the ability to distinguish billions of different allelic profiles, and a strain with the most common allele at each locus would only be expected to occur by chance approximately once in 10,000 isolates. (wikipedia.org)

At least 120 mutations in the PAFAH1B1 gene have been found to cause isolated lissencephaly sequence (ILS). (medlineplus.gov)
PAFAH1B1 gene mutations that occur in all of the body's cells (germline mutations) usually cause isolated lissencephaly sequence (described above). (medlineplus.gov)

By sequencing the entire genome, a comprehensive understanding of the genetic composition is obtained. (folkhalsomyndigheten.se)
The entire genome has been sequenced. (medscape.com)

Here, we report the draft genome sequence of a multidrug-resistant A. baumannii (ST15/CC15) isolated in 2009 from the state of Espírito Santo (Southeast Brazil). (fiocruz.br)

This study re-analyzed, using multi-locus sequence typing (MLST) and whole genome sequence with single nucleotide polymorphism analysis (WGS-SNP), 52 strains which had been identified as Enterobacter sakazakii as according to the convention at the time of isolation. (biomedcentral.com)
Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci, using DNA sequences of internal fragments of multiple housekeeping genes to characterize isolates of microbial species. (wikipedia.org)
MLST directly measures the DNA sequence variations in a set of housekeeping genes and characterizes strains by their unique allelic profiles. (wikipedia.org)
The principle of MLST is simple: the technique involves PCR amplification followed by DNA sequencing. (wikipedia.org)
The workflow of MLST involves: 1) data collection, 2) data analysis and 3) multilocus sequence analysis. (wikipedia.org)

We determined the complete nucleotide sequence of the 16S rRNA from a new bacterium collected from the surfaces of women's hands. (springeropen.com)
In the data collection step, definitive identification of variation is obtained by nucleotide sequence determination of gene fragments. (wikipedia.org)

Sequencing of S. macedonicus ACA-DC 198 genome was performed using a combination of 454 GS-FLX pyrosequencing and HiSeq 2000 Illumina sequencing. (edulll.gr)

Sequence-specific, single primer amplification and detection of PCR products for identification of hepatitis viruses. (cdc.gov)
In contrast to metagenomic detection of unknown pathogens which sequences all available genetic material, 16S sequencing specifically targets the small ribosomal subunit. (folkhalsomyndigheten.se)
The HBV sequence was then labeled for its utilization as a probe in the HBV DNA detection in serum of patients with HBsAg positive, with no evident physical symptoms of the disease. (bvsalud.org)

Whole genome sequencing can also provide insights into the specific genes or mutations that may be linked to antibiotic resistance. (folkhalsomyndigheten.se)

Fourteen diploid sequence types (DSTs) including six new DSTs were determined. (springer.com)

Nanopore sequencing offers advantages in all areas of research. (nanoporetech.com)
Oxford Nanopore whole genome sequencing of Juniperus communis. (nih.gov)

Most of these CRAB isolates (77.62%) were classified as clone complex 92 (CC92), and sequence type (ST) 92 was the most prevalent STs, followed by ST195, ST136, ST843, and ST75. (frontiersin.org)
Clone C2220, 9031 nt in length, was derived by long PCR amplification of proviral DNA from virus cultured on primary peripheral blood mononuclear cells, and contains all but 74 nt of the unique sequence information of the HIV-1 genome. (pitt.edu)
This clone resembles HIV-1 isolates of subtypes A, B, and D in its genome organization with one notable exception: the core promoter contains not two, but three potential binding sites for the transcription factor NF-kB. (pitt.edu)

A 30.43-Mb draft genome sequence with 10,355 predicted protein-coding genes was produced for the ascomycete fungus Exophiala mesophila strain CCFEE 6314, a black yeast isolated from Antarctic cryptoendolithic communities. (escholarship.org)
We present an annotated F. proliferatum draft genome sequence, totaling 45.8 Mb in size, assembled into 597 contigs, with a predicted 15,418 genes. (wur.nl)
For each of these housekeeping genes, the different sequences are assigned as alleles and the alleles at the loci provide an allelic profile. (wikipedia.org)
This does not use the assigned alleles, but instead concatenates the sequences of the gene fragments of the housekeeping genes and uses this concatenated sequence to determine phylogenetic relationships. (wikipedia.org)
The full HA and NA genes of 16 H1N1-positive samples obtained in our study and 21 published HA sequences and 20 published NA sequences from Jordanian viruses that were available on online gene databases were analysed. (who.int)

Here, we report the draft genome sequences of three Listeria monocytogenes isolates from fresh leaves collected in Nigeria, belonging to sequence types ST5 and ST155 (sublineages SL5 and SL155, respectively). (nottingham.ac.uk)

Closely related viruses have been isolated from Ixodes ticks in Europe (see the image below). (medscape.com)

In some PCR reactions multiple sequences have identical nucleotide sequences, for example if five PCR products have identical sequences a 5 will be found in this column. (cdc.gov)
Reported sequences were non-identical with 0.1% nucleotide divergence rate and clustered into 6 different clades with worldwide sequences. (pasteur.fr)
Based on the results of a homology search, the isolated strain was 99 % identical to Lactobacillus paracasei , so it was designated Lactobacillus paracasei HS-05 and was registered in the Korea Culture Center of Microorganisms (KCCM) database as [KCCM11349P]. (springeropen.com)
In 28 of 31 patients with two or more EfsB episodes, isolates with identical sequence type were found. (lu.se)
Episodes of EfsB in patients later diagnosed with IE showed features of IE already during the first episodes, were not adequately evaluated, are due to identical isolates, and most likely represent true relapses. (lu.se)

Meningococcal disease cases are reported through the National Notifiable Diseases Surveillance System, with additional epidemiologic information and isolates obtained through Enhanced Meningococcal Disease Surveillance. (medscape.com)

Genetic and biological characterization of tick-borne were serologically diagnosed, demonstrating that humans encephalitis virus isolated from wild rodents in southern Hokkaido, Japan in 2008. (cdc.gov)
In this study, we report the isolation, identification, characterization and the whole nuclear genome and mitogenome sequence of the endophyte R. mucilaginosa RIT389 isolated from Distemonanthus benthamianus, a plant known for its anti-fungal and antibacterial properties and commonly used as chewing sticks. (peerj.com)

1 denotes unique sequences. (cdc.gov)

The sequences were are associated with high morbidity and submitted to GenBank under accession mortality ( 1 ). (who.int)

C. albicans is predominantly diploid and displays high degree of genetic diversity across isolates, notably variations in the distribution of heterozygous polymorphisms along the genome. (springer.com)

2006. Sequencing for quasispecies analysis was done using the method described by Ramachandran et al. (cdc.gov)
0 denotes a consensus sequence with no quasispecies analysis. (cdc.gov)
Our offering includes DNA sequencing, as well as RNA and gene expression analysis and future technology for analysing proteins. (nanoporetech.com)
She is interested in developing pipelines for genomics data analysis, and has also worked on structural biology and the protein sequence-structure-function relationship. (nanoporetech.com)
The WGS-SNP analysis demonstrated that indistinguishable Cronobacter strains within a sequence type can be unrelated, and may originate from multiple sources. (biomedcentral.com)
The use of WGS-SNP analysis to distinguishing of strains within a sequence type has important relevance for tracing the source of outbreaks due to Cronobacter spp. (biomedcentral.com)
Cluster analysis revealed that isolates grouped into 8 clades. (springer.com)
Also, an analysis is performed by means of statistical and artificial neural network methods from which it is concluded that the folding properties can be predicted to a certain degree given the binary numbers characterizing the sequences. (lu.se)
Sequence variations between different bacteria provide a unique identity, and the analysis of these sequence enables taxonomic placement. (folkhalsomyndigheten.se)
It is a platform and database for the automated analysis of whole genome sequencing data. (folkhalsomyndigheten.se)
HA and NA sequences each in the analysis. (who.int)

Most of the Utah isolates clustered within GPSC31 in a USA-specific clade with the most recent common ancestor estimated between 1958 and 1981. (ox.ac.uk)

Draft Genome Sequence of the Growth-Promoting Endophyte Paenibacillus sp. (asm.org)
High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM 19883(T)) isolated from a Chironomus sp. (doe.gov)
Draft Genome Sequence of the Symbiotic Frankia sp. (scienceopen.com)
Here, we report the 5.3-Mbp draft genome sequence of Frankia sp. (scienceopen.com)
Draft Genome Sequence of Leifsonia sp. (northumbria.ac.uk)
We report here the draft genome sequence of Leifsonia sp. (northumbria.ac.uk)
The current study describes the draft genome of strain 1961 BR-RJ/09, isolated from the urine of a hospitalized patient from Brazil. (fiocruz.br)
We report the draft genome sequence of Lactobacillus crispatus CIP 104459, isolated from a human vaginal swab. (hal.science)
This draft genome consists of 1,993,673 bp, with 36.8% G+C content and 2,024 predicted protein-encoding sequences. (hal.science)

The predominant sequence type was ST13 (65.3%, 32/49) which had been isolated from dairy products imported from 6 countries. (biomedcentral.com)
Here we report the complete genome sequence of an extensively drug-resistant, Verona integron-encoded metallo-ß-lactamase-expressing isolate belonging to the high-risk sequence type 233. (pacb.com)
Salminen, MO and Johansson, B and Sönnerborg, A and Ayehunie, S and Gotte, D and Leinikki, P and Burke, DS and McCutchan, FE (1996) Full-length sequence of an Ethiopian human immunodeficiency virus type 1 (HIV-1) isolate of genetic subtype C. AIDS Research and Human Retroviruses, 12 (14). (pitt.edu)

In this study, multilocus sequence typing was used to characterise the genetic diversity and population structure of 24 avian origin C. albicans isolates collected from different birds with candidiasis and compared to human isolates. (springer.com)

The availability of these sequences will hopefully aid in identifying host-specific determinants variably present within this species. (cdc.gov)

Sequences that differ at even a single nucleotide are assigned as different alleles and no weighting is given to take into account the number of nucleotide differences between alleles, as we cannot distinguish whether differences at multiple nucleotide sites are a result of multiple point mutations or a single recombinational exchange. (wikipedia.org)
Peu de renseignements sont disponibles sur les mutations des virus saisonniers de la grippe A(H1N1)pdm09 et H3N2 en Jordanie. (who.int)
Les mutations individuelles sont décrites en détail. (who.int)

Weakly bound, atomic and molecular, clusters have been the subject of many studies to investigate structures, dynamics and energetics of nano-scale objects, with the goal to understand the evolution of their properties from isolated atoms to the bulk solid. (lu.se)
Organización molecular del complejo II y su rol en la anaerobiosis. (bvsalud.org)

P22 has strong 16S rRNA gene sequence similarity to Paenibacillus humicus (99.5%) ( 7 ). (asm.org)
The laboratory procedure is based on amplifying and sequencing four variable regions of the 16S rRNA gene with two amplicons. (folkhalsomyndigheten.se)

Zebedee, SL & Lamb, RA 1989, ' Nucleotide sequences of influenza A virus RNA segment 7: A comparison of five isolates ', Nucleic acids research , vol. 17, no. 7, pp. 2870. (northwestern.edu)
Complete genome sequence of an H5N2 avian influenza virus isolated from a parrot in southern China. (bvsalud.org)
We report the complete genome sequence of an H5N2 avian influenza virus (AIV) that was first isolated from a parrot in Guangdong in southern China in 2004. (bvsalud.org)

Here, we announce the complete genome sequences of three Leptospira strains that were isolated from blood of humans with undifferentiated fever in Sri Lanka. (nih.gov)
Here, we report the first complete genome sequences of B. hinzii in two isolates recovered from humans. (cdc.gov)

Meenakshi Iyer is a postdoctoral fellow in the 'Indo-Africa dengue sequencing, vaccine design and capacity building' consortium with Prof. Sudhir Krishna at National Centre for Biological Sciences, TIFR, Bengaluru, Karnataka, India. (nanoporetech.com)

In order to establish the course of infection, virulence and pathogenicity, a Paraguayan Trypanosoma cruzi strain isolated from a 12 year old patient in 1989, Balb/c mice were inoculated, and the number of parasites were determined by direct parasitemia (micromethod). (bvsalud.org)

HCV sequence contigs were aligned and edited by hand using DNAstar to construct the final sequence for each isolate. (cdc.gov)

The HCV RNA was isolated and sequenced either to determine the genotype of the isolated virus or to determine the viral quasispecies diversity within an infected individual. (cdc.gov)
It was previously noted that the Centers for Disease Control and Prevention held 451 viral isolates obtained from different continents and countries when smallpox was endemic.2 The current review and the studies reported at the meeting concentrated on some 50 isolates in the Russian collection that were not present in the American collection. (who.int)

Here, we present the complete genome sequence of F. vincentii KCOM 2931. (pacb.com)
Complete genome sequence of Nissabacter sp. (scelse.sg)
The plasmid pSP65 which has cloned the complete HBV sequence, was amplified by transformation of coli (DH5). (bvsalud.org)

A huge set of data is produced during the sequencing and identification process so bioinformatic techniques are used to arrange, manage, analyze and merge all of the biological data. (wikipedia.org)
In epidemiological contact tracing, this technology enables the mapping of infection spread and identification of sources of infection through the comparison of genetic sequences. (folkhalsomyndigheten.se)

Afin de remédier à ce problème et d'étudier les variations génétiques et antigéniques des virus A(H1N1)pdm09 et H3N2, nous avons procédé à des analyses génétiques et phylogénétiques des gènes de l'hémagglutinine (HA) et de la neuraminidase (NA) de ces virus, sur la période 2011-2013 en Jordanie. (who.int)

The sequence will be of importance for identifying differences among extremophiles and mesophiles and cataloguing the global population diversity of this organism. (escholarship.org)
To guarantee the purity of the organism, it must be isolated from its host, i.e. the human who was infected, before being propagated in a pure culture. (djetnews.com)

One CRAB isolate of ST195 harbored plasmid pAB52 from a Chinese patient without travel history. (frontiersin.org)

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20001

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