MLSTGenomeGenotypesRRNALociVirulenceGene sequencesBacterialEpidemiologicalSpeciesSerotypesNucleotidePFGEGenomicsStrains were classifiedPhylogeneticCapsularMicroarrayPathogenPrevalentIsolates were classifiedAssaysBurkholderiaAnalysisSubtypesSeverityPolymorphismRelatednessStrainColiSalmonellaClustersPlasmidHaemophilusHostsCapsuleIntegronAmplificationGyrAClonal complexFungiInfluenzaeSerogroupsVariabilityInfectionsResults
MLST15
- iron acquisition) by PCR and sequencing and submitted to multilocus sequence typing (MLST). (biomedcentral.com)
- the other isolates did not match any type available in the MLST database. (biomedcentral.com)
- 9 ] proposed multi-locus sequence typing (MLST). (biomedcentral.com)
- These genes were further analyzed by sequencing, and the strains were compared by MLST of seven housekeeping genes ( adk , aroA , deoD , gdhA , g6pD , mdh , and pgi ). (biomedcentral.com)
- Both clades are assigned to ST131 by the Achtman multilocus sequence typing (MLST) system and a screening PCR assay that targets ST131-specific sequence polymorphisms in the mdh and gyrB genes. (umn.edu)
- However, they are classified as separate STs by the Pasteur Institute MLST system, and an ST131 PCR method that targets the O25b rfb region and an ST131-specific polymorphism in pabB detects only the O25b-associated clade. (umn.edu)
- Introduction Multilocus Sequence Typing (MLST) is a molecular typing technique used in microbiology and genetics to classify and differentiate bacterial strains based on their genetic diversity. (medicallabnotes.com)
- The sequence types (STs) were analyzed with multilocus sequence typing (MLST). (biomedcentral.com)
- In all the samples, 50 E. coli strains were isolated and then assigned to serotyping, antimicrobial susceptibility test, detection of antimicrobial resistance genes and the Class 1 integrons, and multilocus sequence typing (MLST). (hindawi.com)
- MLST analysis showed that 32 sequence types (STs) were identified, while ST46 was the predominant genotype among all isolates. (hindawi.com)
- 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)
- Background: A recent report has shown that the phylogenetic origin of Helicobacter pylori based on multi-locus sequence typing (MLST) was significantly associated with the severity of gastritis in Colombia. (unair.ac.id)
- We identify a set of 2,882 core genes clusters based on 73 publicly available Salmonella enterica genomes and evaluate their value as typing targets, comparing whole genome typing and traditional methods such as 16S and MLST. (biomedcentral.com)
- Today, the most widely used typing methods for bacterial genomes include multilocus sequence typing (MLST), pulsed field gel electrophoresis (PFGE), sequencing of 16S rRNA genes, and multilocus variable-number of tandem-repeat analysis (MLVA). (biomedcentral.com)
- Subtyping using a repetitive sequence-based PCR system (DiversiLab) and multilocus sequence typing (MLST) were used to assess the interspecific biodiversity of isolates. (who.int)
Genome22
- This species was the first free-living microorganism to have its entire genome sequenced. (wikipedia.org)
- Here, we provide a step-by-step protocol to (1) identify whether host genome projects contain reads from associated Wolbachia and (2) isolate/retrieve the Wolbachia reads from the rest of the sequenced material. (bvsalud.org)
- Genome sequence analysis of 20 S . ruminantium isolates provided information about the antibiotic resistance, potential virulence, and serological diversity of this species. (biomedcentral.com)
- Therefore, we established an accurate and rapid whole genome sequencing (WGS) based classification and serotyping algorithm and combined it with the detection of resistance genes. (biomedcentral.com)
- Population Analysis of O26 Shiga Toxin-Producing Causing Hemolytic Uremic Syndrome in Italy, 1989-2020, Through Whole Genome Sequencing. (sciensano.be)
- Core genome Multi Locus Sequence Typing grouped ST21 and ST29 strains in three clades each, with each ST29 clade exactly corresponding to one HCPC cluster. (sciensano.be)
- David M. Wagner mostly deals with Microbiology, Virology, Whole genome sequencing, Genome and Burkholderia pseudomallei. (research.com)
- His Whole genome sequencing research is classified as research in Genetics. (research.com)
- N. meningitidis isolates were evaluated for antibiotic susceptibility and characterised by whole genome sequencing. (bmj.com)
- Genetic relationships among the meningococcal carriage isolates were determined using core genome multilocus sequence typing analysis. (bmj.com)
- Analysis of average nucleotide identity and genome-to-genome distances, which have recently been proposed as reliable substitutes for classical DNA-DNA hybridization, further confirmed that these isolates should be classified as representatives of a novel species. (nih.gov)
- Technological advances in high throughput genome sequencing are making whole genome sequencing (WGS) available as a routine tool for bacterial typing. (biomedcentral.com)
- Genomic variation within the core genome is useful for investigating molecular evolution and providing candidate genes for bacterial genome typing. (biomedcentral.com)
- The price and time for whole genome sequencing will soon be in the same range as the traditional typing methods mentioned above. (biomedcentral.com)
- Currently there are more than a hundred bacterial species for which sufficient genomic data are available to estimate the species core-genome (that is, there are at least three genomes sequenced from the same species) [ 14 ]. (biomedcentral.com)
- Its genome sequence has an average mol% G+C content of 64.34%, which is considerably lower than that of other Burkholderia species. (edu.au)
- Comparisons with publicly available whole genome sequences demonstrated that strain TSV85, an Australian water isolate, also represents the same species and therefore, to date, B. singularis has been recovered from human or environmental samples on three continents. (edu.au)
- Furthermore, average nucleotide identity (ANI) estimation, single nucleotide polymorphism (SNP), and core gene multilocus sequence typing (cgMLST) were applied to characterize the molecular profile of isolates based on whole genome sequencing. (biomedcentral.com)
- However, the use of modern molecular techniques such as PCR and whole-genome sequencing is on the rise. (biomedcentral.com)
- To assess whether there are genetic markers associated with host tropism we comparatively analyzed whole-genome sequences of 61 C. psittaci strains, 47 of which carrying a 7.6-kbp plasmid. (biomedcentral.com)
- Following clean-up, reassembly and polishing of poorly assembled genomes from public databases, phylogenetic analyses using C. psittaci whole-genome sequence alignment revealed four major clades within this species. (biomedcentral.com)
- With the rapid development of high-throughput biological experiment technology, especially the development of gene chips and next-generation sequencing technology, gene expression data in the whole genome has exploded, and the method of network biology is used to analyze high-throughput gene expression data. (cd-genomics.com)
Genotypes7
- In our previous study, genotypes of MRSA isolates from keratitis cases were classified into ST5 or ST764 lineage by multi-locus sequence typing. (elsevierpure.com)
- However, the ruminant S. suis and S. ruminantium isolates from diseased animals were classified into diverse genotypes rather than belonging to certain clonal groups. (biomedcentral.com)
- Sixty-six strains, with one exception, were classified as hpEurope irrespective of the cagA and vacA genotypes, and type of disease. (unair.ac.id)
- 140 southern sea otters represent Type II or Type X strains, or variants of these genotypes. (frontiersin.org)
- The genotypes of H. pylori virulence factors were determined by polymerase chain reaction (PCR)-based sequencing. (biomedcentral.com)
- We found that clade membership correlates with typing schemes based on SNP types, ompA genotypes, multilocus sequence types as well as plasticity zone (PZ) structure and host preference. (biomedcentral.com)
- The ESBL genotypes were determined by polymerase chain reaction (PCR) using the bla(SHV), bla(TEM), and bla(CTX-M) gene sequences. (who.int)
RRNA5
- This was inferred from sequence analysis of rrs (16S rRNA) and other genetic loci and suggests that they belong to a novel species. (nih.gov)
- The genus has been divided into different groups based on 16S rRNA gene sequence similarity. (biomedcentral.com)
- The present study was taken up to explore 16S rRNA gene sequence to develop methods that can be used for preliminary identification and can supplement the existing methods for identification of clinically-relevant isolates of the genus Streptococcus . (biomedcentral.com)
- The markers generated exploring 16S rRNA gene sequences provided useful tool that can be further used for identification of different species of the genus Streptococcus . (biomedcentral.com)
- 16S rRNA gene sequencing has proved to be one of the most powerful tools for the classification of microorganisms [ 38 ] and has been used for identification of clinically relevant microbes [ 39 , 40 ]. (biomedcentral.com)
Loci1
- Multilocus sequence typing at 13 loci revealed that all were infected with the same strain of T. gondii , previously characterized as an atypical and rare genotype in North America (TgCgCa1, or COUG). (frontiersin.org)
Virulence5
- A novel O26 STEC clone belonging to Sequence Type ( ST ) 29 and harboring , and plasmid-borne genes has emerged and spread in Europe since the mid-1990s, while another ST29 clone positive for and lacking plasmid-borne virulence genes was recently described as emerging in France. (sciensano.be)
- Virulence and antimicrobial resistance genes, sequence type, and cluster analysis were investigated using WGS data. (biomedcentral.com)
- In the present study, 1,074 ExPEC isolates were classified by phylogenetic group and possession of 67 other traits, including virulence-associated genes and plasmid replicon types. (unboundmedicine.com)
- The pneumococcus capsule consists of a complex polysaccharide that determines serologic type and contributes to virulence and pathogenicity. (msdmanuals.com)
- Virulence varies somewhat within serologic types because of genetic diversity. (msdmanuals.com)
Gene sequences1
- Based on the differences in their capsular gene sequences, serotype "6E" was assigned to this group in a subsequent study [ 8 ]. (biomedcentral.com)
Bacterial5
- Nowadays, the production of full Wolbachia genomes does not require the physical isolation of the bacterial strains from their respective hosts, and the bacterium is often sequenced as a by-catch of host genomic projects. (bvsalud.org)
- However, plasmid fitness effects in wild-type bacterial hosts remain largely unexplored. (nature.com)
- In this study, we provide a detailed characterisation of the distribution of plasmid fitness effects in wild-type bacterial hosts. (nature.com)
- Bacterial meningitis can be caused by several types of bacteria including Streptococcus pneumonia or Neisseria meningitidis ( N.meningitidis ). (biomedcentral.com)
- Rapid and reliable sub-typing of bacterial pathogens is important for identification of outbreaks and monitoring of trends in order to establish population structure and to study the evolution among bacterial genomes especially within and between the outbreak strains. (biomedcentral.com)
Epidemiological1
- The strains were classified as susceptible or resistant based on epidemiological cut-off values (ECOFFs, www.eucast.org , accessed on 3 November 2022) recommended by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). (biomedcentral.com)
Species4
- The complete sequence of gyrA gene from 77 strains are reported in this study and analyzed in the context of publicly available sequences from N. meningitidis of other CCs as well as other Neisseria species. (biomedcentral.com)
- Some clusters contain sequences from other Neisseria species. (biomedcentral.com)
- B. singularis can be differentiated from other Burkholderia species by multilocus sequence analysis, MALDI-TOF mass spectrometry and a distinctive biochemical profile that includes the absence of nitrate reduction, a mucoid appearance on Columbia sheep blood agar, and a slowly positive oxidase reaction. (edu.au)
- Partial TRI14 sequences from 9 out of 12 species were determined for the first time. (actanaturae.ru)
Serotypes2
- So far, more than 90 pneumococcal serotypes, classified into 46 groups, have been identified. (biomedcentral.com)
- 90 different pneumococcal serotypes have been identified based on their reaction with type-specific antisera. (msdmanuals.com)
Nucleotide2
- An ST is characterized by a different sequence nucleotide for at least one of the 7 reference genes. (biomedcentral.com)
- For the most variable core genes, the variance in amino acid sequences is higher than for the corresponding nucleotide sequences, suggesting that there is a positive selection towards mutations leading to amino acid changes. (biomedcentral.com)
PFGE1
- The PFGE and SE-AFLP were able to type all isolates and, although they presented a slight tendency to cluster according to state and year of isolation, it was also evident the grouping of different herds in the same PFGE subtype and the existence of isolates originated from the same herd classified into distinct subtypes. (omicsdi.org)
Genomics1
- For gene interaction network analysis, if you don't have the raw data, CD Genomics relies on years of sequencing experience to provide you with sequencing services, including next-generation sequencing and microarray services. (cd-genomics.com)
Strains were classified1
- Encapsulated strains were classified on the basis of their distinct capsular antigens. (wikipedia.org)
Phylogenetic2
- Phylogenetic inference supported the presence of two functional variants of each FeSOD type across the T. cruzi strains. (biomedcentral.com)
- Also, 58% belonged to the ST95 multilocus sequence typing group, and over 90% of them were assigned to the B2 phylogenetic group typical of human ExPEC strains. (unboundmedicine.com)
Capsular1
- Pasteurella multocida capsular type A ( P. multocida type A) is one of the most common agents associated with bronchopneumonia in pigs [ 1 ]. (biomedcentral.com)
Microarray2
- 2016 Learn How to Analyze Microarray and Next Generation Sequencing Data with Partek Software at Imperial College London, UK. (plymouth.ac.uk)
- For gene interaction network analysis, the raw input data can be next-generation sequencing data or microarray data. (cd-genomics.com)
Pathogen2
- Escherichia coli sequence type 131(ST131), a widely disseminated multidrug-resistant extraintestinal pathogen, typically exhibits serotype O25b:H4. (umn.edu)
- Recently, H. influenzae was classified by the WHO as priority pathogen due to the wide spread of ampicillin resistant strains. (biomedcentral.com)
Prevalent2
- 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)
- EPIYT sequences were more prevalent than EPIYA sequences (P = 0.01) in the EPIYA-B motif of all types of cagA. (biomedcentral.com)
Isolates were classified1
- The Y. enterocolitica isolates were classified into 54 sequence types (STs) and 125 cgMLST types (CTs), with 4/O:3 being the dominant bioserotype in Ningxia. (biomedcentral.com)
Assays1
- Evaluating LAMP assays for detection of phytoplasmas classified in different ribosomal groups. (plymouth.ac.uk)
Burkholderia1
- David M. Wagner has researched Burkholderia pseudomallei in several fields, including Gene mutation, Melioidosis, Multilocus sequence typing and Burkholderia. (research.com)
Analysis7
- DNA sequence analysis of the 3′-end of the Coagulase ( coa ) gene revealed heterogeneity in the 81 bp tandem repeats region that encoding repeated 27-amino-acid sequences in the C-terminal region. (hindawi.com)
- Multilocus sequence typing analysis identified 29 sequence types belonging to 12 clonal complexes. (bmj.com)
- The new isolates formed a distinct clade, which was most closely related to Leptospira borgpetersenii, in multilocus sequence analysis using concatenated sequences of the genes rpoB, recA, fusA, gyrB, leuS and sucA. (nih.gov)
- The dogs were classified into different carriage groups on the basis of the analysis of nine samples collected over a period of six months. (biomedcentral.com)
- Their comparative analysis demonstrated a relatively high level of intraspecific variability in F. graminearum and F. sporotrichioides, but no correlation between the sequence polymorphism and the geographic origin of the strains or their chemotype was found. (actanaturae.ru)
- Gene co-expression is a type of analysis method that uses a large amount of gene expression data to construct correlations between genes, thereby mining gene functions. (cd-genomics.com)
- PCR (polymerase chain reaction) technique has achieved increased importance for post-mortem DNA analysis in forensic cases 8 because of the millions of copies amplified from one specific sequence of DNA. (bvsalud.org)
Subtypes1
- The aim of this study was to use coa gene polymorphism to identify MRSA subtypes isolated from nasal carriers in Minia governorate, Upper Egypt, evaluate the efficiency of these typing methods in discriminating variable strains, and compare these subtypes with antibiotypes. (hindawi.com)
Severity1
- Histological severity of the gastric mucosa was classified into 4 grades, according to the updated Sydney system. (biomedcentral.com)
Polymorphism1
- The intra- and interspecific polymorphism of partial sequences of the translation elongation factor 1 alpha (TEF1α) gene and two genes from the trichothecene cluster TRI5 and TRI14 was studied. (actanaturae.ru)
Relatedness1
- Genetic relatedness of the isolates was characterized by multilocus sequence typing. (frontiersin.org)
Strain3
- nov. is proposed, with 200901116(T) ( = CIP 110703(T) = DSM 28999(T)) as the type strain. (nih.gov)
- The type strain is LMG 28154T (=CCUG 65685T). (edu.au)
- Clade 1 represents the most recent lineage comprising 40/61 strains and contains 9/10 of the psittacine strains, including type strain 6BC, and 10/13 of human isolates. (biomedcentral.com)
Coli1
- According to the differences in pathogenicity, E. coli can be classified into commensal E. coli and pathogenic E. coli [ 3 ]. (hindawi.com)
Salmonella1
- We found identical Salmonella sequence types in human, animal, and environmental samples in the same locality, which demonstrates the great potential of the applied tools to trace back outbreak strains. (biomedcentral.com)
Clusters1
- For this, it identifies and clusters co-localized genes encoding proteins of secretion systems using sequence similarity search with Hidden Markov Model (HMM) protein profiles. (bvsalud.org)
Plasmid1
- In this study, we determined the fitness effects of the major antibiotic resistance plasmid pOXA-48_K8 in wild-type, ecologically compatible enterobacterial isolates from the human gut microbiota. (nature.com)
Haemophilus1
- 99% in the United States after introduction of whole-cell pertussis vaccines in the 1940s, this highly contagious respiratory illness has refused to go the way of other vaccine-preventable diseases of childhood, such as polio, Haemophilus influenzae type b infection, and diphtheria. (blogspot.com)
Hosts2
- The FeSOD-A and FeSOD-B genes of 35 T. cruzi strains, belonging to six discrete typing units (Tcl-TcVI), from different hosts and geographical regions were amplified by PCR and sequenced using the Sanger method. (biomedcentral.com)
- These types have different disease patterns in their hosts. (medscape.com)
Capsule3
- H. Influenzae type b, also known as Hib, is the most common form, recognizable by its polyribosyl ribitol phosphate (PRP) capsule, and found mostly in children. (wikipedia.org)
- Some types of H. influenzae contain a polysaccharide capsule around the outer membrane to aid in protection and colonization. (wikipedia.org)
- That study showed that a single codon change in the cps gene, encoding a glycosyl transferase, altered the substrate specificity, caused the biosynthesis of heterogeneous capsule repeating units, and resulted in a new hybrid capsule type. (biomedcentral.com)
Integron1
- In addition, long-read sequencing of one representative XDR ST235 isolate identified an integron carrying multiple resistance genes (including bla VIM-2), with differences in gene composition and synteny from the P. aeruginosa class 1 integrons described previously. (who.int)
Amplification2
- The production of Wolbachia genomic DNA free of contamination from host DNA, as required for Wolbachia-targeted sequencing, was then only possible after the amplification and extraction of a large amount of clonal Wolbachia DNA. (bvsalud.org)
- Out of 58 MRSA isolates 15 coa types were classified, and the amplification products showed multiple bands (1, 2, 3, 4, 5, and 8 bands). (hindawi.com)
GyrA1
Clonal complex1
- Furthermore, the strains that are sharing the sequence of 4 or more genes (identified as a number for convenience) among the 7 genes used to determine STs could be classified into the same clonal complex (CC) [ 3 ]. (biomedcentral.com)
Fungi1
- Depending on the side group structure, trichothecene toxins are divided into four types (A-D), with only types A and B produced by Fusarium fungi. (actanaturae.ru)
Influenzae1
- The recommended form of prevention of the type b form of H. influenzae is a series of the Hib vaccine and boosters, which are most often given under the age of 5, and sometimes in conjunction with other vaccines in the form of the DTaP-IPV/Hib vaccine. (wikipedia.org)
Serogroups1
- 1 ). Invasive meningococcal infections where isolates of serogroups A and W and typing of the isolates are all part of can occur in different clinical forms. (who.int)
Variability1
- His biological study spans a wide range of topics, including Genetic variability and DNA sequencing. (research.com)
Infections1
- RÉSUMÉ L'émergence et la propagation rapide des souches de Klebsiella pneumoniae résistantes aux antibiotiques et porteuses du gène blaKPC codant la production de carbapénèmases ont compliqué la prise en charge des infections des patients. (who.int)
Results2
- Our results suggest that T. cruzi FeSOD types are members of distinct families. (biomedcentral.com)
- For this purpose, corneocytes were collected from five dogs that were classified as persistently colonized (D1 and D2), intermittently colonized (D3 and D4) or non-colonized (D5) on the basis of the results of a previous longitudinal study. (biomedcentral.com)