Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “sequence types”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 631 records · Page 35Linked to original sources
PubMed2001

Comparative molecular investigation of Nc5-PCR amplicons from Neospora caninum NC-1 and Hammondia heydorni-Berlin-1996.

The clinical relevance of Neospora caninum as a cyst-forming coccidian parasite is increasingly acknowledged within veterinary medicine, although the pathways of transmission are far from being solved. The parasite is well known for causing diaplacental infections in cows associated with abortion and/or severe damage of the fetus. In addition, it may cause neuromuscular disease in dogs, which thus apparently act as intermediate hosts as well as final hosts. In our previous studies, we have demonstrated that molecular diagnosis of N. caninum infections has a high performance when a highly sensitive polymerase chain reaction (PCR) targeted to the Nc5 region of the parasite is used. The present study indicates that the high sensitivity of the PCR is the consequence of a target dose effect which reflects a high redundancy of Nc5-type sequences within the genome of the parasite. The PCR was shown to amplify a set of DNA molecules exhibiting significant sequence differences. A complex composition of Nc5-type sequences was observed in the parasite isolate N. caninum NC-1 but also in another isolate, designated Hammondia heydorni-Berlin-1996. Investigation of the infection pattern of this parasite in its intermediate and final canine hosts showed it to be indistinguishable from N. caninum NC-1.

Animals↗
PubMed2006

A community outbreak of conjunctivitis caused by nontypeable Streptococcus pneumoniae in Minnesota.

BACKGROUND: The Minnesota Department of Health (MDH) was notified of an outbreak of conjunctivitis in city A with cultures positive for Streptococcus pneumoniae. METHODS: MDH staff contacted clinics and schools in city A and city B regarding conjunctivitis cases, reviewed clinical findings of conjunctivitis cases in city A and collected isolates for subtyping. RESULTS: Between September 1 and December 12, 2003, cities A and B reported 735 conjunctivitis cases. Fifty-one percent of the cases were reported from schools, childcare centers and colleges. Adults were more likely to report itching, burning or swelling of the eye(s); children were more likely to report crusty eyes (P < 0.05). Forty-nine percent of conjunctival cultures (71 of 144) were positive for S. pneumoniae. All isolates were nontypeable by serotyping. Pulsed field gel electrophoresis identified 3 clonal groups with 84% of isolates belonging to one clonal group. Multilocus sequence typing revealed that isolates had the same multilocus sequence type as isolates from a 2002 outbreak at a New England college. CONCLUSIONS: This outbreak was widespread in the community and conjunctivitis clinical presentation varied by age. The predominant strains in this outbreak were related to a pneumococcal strain implicated in prior conjunctivitis outbreaks, suggesting these strains have a predilection for causing conjunctivitis.

Adolescent↗
PubMed2003

Molecular characterization of a strain of group a streptococcus isolated from a patient with a psoas abscess.

We report the first case of a primary group A streptococcus (GAS) psoas abscess in a 31-year-old woman. The psoas abscess was preceded by an episode of acute pharyngitis. The M-protein gene (emm) and streptolysin S structural gene (sagA) were present in the isolate, with no significant amino acid differences from previously described sequences of M1 GAS isolates. Multilocus sequence typing (MLST) showed that the isolate belonged to MLST sequence type (MLST-ST) 28, the predominant MLST-ST associated with invasive disease caused by M1 isolates.

Adult↗
PubMed1996

A computerized method to predict the discriminatory properties for class II sequencing based typing.

Accurate identification of alleles or groups of alleles is obtained using DNA techniques for HLA class II typing. In PCR-SSP and PCR-SSO the typing resolution is dependent on the location of the amplification primers and the number of oligonucleotide probes used for hybridization. These primers are developed based upon the known allele sequences. However, the number of published allele sequences increases rapidly. Periodic reconsideration of the discriminatory properties of the methods used is necessary and often leads to the addition of primers, and an increase of ambiguous genotypes. SBT is a high-resolution class II typing method which utilizes the second exon sequence at all positions for typing. Using a generic amplification and sequencing approach, a limited number of ambiguous heterozygotes can be expected. However, the number of ambiguities is dependent on the location of the primers. These ambiguities can be solved by the use of group-specific primers in either the amplification or sequencing reaction. To identify the applicability of a SBT approach with respect to typing resolution, it is important to identify these ambiguities and develop strategies to solve them. We developed software that predicts the ambiguous heterozygotes, and analyzes their sequences for group specific primers, solving these ambiguities. The location of the primers is considered as well as the use of generic vs group-specific amplification or sequencing reactions. Allele sequences of all class II genes, as accepted by the WHO nomenclature committee for factors of the HLA system and submitted to the EMBL/Genbank databases, are analyzed to define the allelic discrimination level of HLA-DQB1, -DQA1, -DFB1, -DPA1, -DRB1, -DRB3, -DRB4, and -DRB5.

Alleles↗
PubMed2001

Using human immunodeficiency virus type 1 sequences to infer historical features of the acquired immune deficiency syndrome epidemic and human immunodeficiency virus evolution.

In earlier work, human immunodeficiency virus type 1 (HIV-1) sequences were analysed to estimate the timing of the ancestral sequence of the main group of HIV-1, the virus that is responsible for the acquired immune deficiency syndrome pandemic, yielding a best estimate of 1931 (95% confidence interval of 1915-1941). That work will be briefly reviewed, outlining how phylogenetic tools were extended to incorporate improved evolutionary models, how the molecular clock model was adapted to incorporate variable periods of latency, and how the approach was validated by correctly estimating the timing of two historically documented dates. The advantages, limitations, and assumptions of the approach will be summarized, with particular consideration of the implications of branch length uncertainty and recombination. We have recently undertaken new phylogenetic analysis of an extremely diverse set of human immunodeficiency virus envelope sequences from the Democratic Republic of the Congo (the DRC, formerly Zaire). This analysis both corroborates and extends the conclusions of our original study. Coalescent methods were used to infer the demographic history of the HIV-1 epidemic in the DRC, and the results suggest an increase in the exponential growth rate of the infected population through time.

Acquired Immunodeficiency Syndrome↗
PubMed2002

PCR designer for restriction analysis of various types of sequence mutation.

Restriction analysis is widely used to detect gene mutations such as insertions, deletions and single nucleotide polymorphisms (SNPs). Although such mutation sites sometimes present some natural restriction sites to differentiate the wild-type and mutant sequences, mismatches are often needed in order to create artificial restriction fragment length polymorphisms (RFLPs). In this report, a computer program is described that screens for suitable restriction enzymes, introducing mismatches where appropriate and when necessary, designs primers using the information of the selected restriction enzymes, their recognition sequence and locations as well as the information about the mismatches if any. The program, supported by a WWW web interface, is intended to be used online.

Amidohydrolases↗
PubMed2006

Defining the sunflower (Helianthus annuus L.) linkage group ends with the Arabidopsis-type telomere sequence repeat-derived markers.

The target region amplification polymorphism (TRAP) marker technique was employed to define sunflower (Helianthus annuus L.) linkage group ends. In combination with eight arbitrary primers, nine fixed primers containing the Arabidopsis-type telomere repeat sequences worked successfully in generating polymorphic markers in the mapping population of 92 F(7) recombinant inbred lines (RIL) derived from the cross RHA 280 x RHA 801. This population was used in the construction of the densest sunflower linkage map of 577 simple sequence repeat (SSR) markers. With 18 sets of PCR reactions, 226 polymorphic TRAP markers were amplified from the two parental lines and 92 RIL. The computer program, Mapmaker, placed 183 markers into the established 17 linkage groups of the SSR map. Although most of the added markers spread across the genome, 32 markers were mapped to the outermost positions of the linkage groups, defining 21 of the 34 linkage group ends of the sunflower linkage map. The telomeric origin of a few of these markers was confirmed by sequence analyses. These telomere-associated markers will provide an accurate assessment of the completeness of a linkage group and a better estimate of the actual genetic lengths. The potential application of the telomere mapping to sunflower improvement is discussed.

Arabidopsis↗
PubMed1997

Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel.

Newly described phylogenetic lineages within the domain Archaea have recently been found to be significant components of marine picoplankton assemblages. To better understand the ecology of these microorganisms, we investigated the relative abundance, distribution, and phylogenetic composition of Archaea in the Santa Barbara Channel. Significant amounts of archaeal rRNA and rDNA (genes coding for rRNA) were detected in all samples analyzed. The relative abundance of archaeal rRNA as measured by quantitative oligonucleotide hybridization experiments was low in surface waters but reached higher values (20 to 30% of prokaryotic rRNA) at depths below 100 m. Probes were developed for the two major groups of marine Archaea detected. rRNA originating from the euryarchaeal group (group II) was most abundant in surface waters, whereas rRNA from the crenarchaeal group (group I) dominated at depth. Clone libraries of PCR-amplified archaeal rRNA genes were constructed with samples from 0 and 200 m deep. Screening of libraries by hybridization with specific oligonucleotide probes, as well as subsequent sequencing of the cloned genes, indicated that virtually all archaeal rDNA clones recovered belonged to one of the two groups. The recovery of cloned rDNA sequence types in depth profiles exhibited the same trends as were observed in quantitative rRNA hybridization experiments. One representative of each of 18 distinct restriction fragment length polymorphism types was partially sequenced. Recovered sequences spanned most of the previously reported phylogenetic diversity detected in planktonic crenarchaeal and euryarchaeal groups. Several rDNA sequences appeared to be harbored in archaeal types which are widely distributed in marine coastal waters. In total, data suggest that marine planktonic crenarchaea and euryarchaea of temperate coastal habitats thrive in different zones of the water column. The relative rRNA abundance of the crenarchaeal group suggests that its members constitute a significant fraction of the prokaryotic biomass in subsurface coastal waters.

Animals↗
PubMed1999

Generation of anti-p53 cytotoxic T lymphocytes from human peripheral blood using autologous dendritic cells.

CTLs recognizing the HLA-A2.1-restricted, wild-type sequence p53 epitopes p53(149-157) and p53(264-272) were generated from CD8-enriched populations of nonadherent peripheral blood lymphocytes (PBLs) obtained from healthy donors. The PBLs were restimulated in vitro with peptide-pulsed granulocyte macrophage colony-stimulating factor- and interleukin (IL)-4-induced autologous dendritic cells in the presence of IL-6 and IL-12 and subsequently cultivated with IL-1alpha, IL-2, IL-4, IL-6, and IL-7. Bulk anti-p53(264-272) CTL populations were generated from PBLs obtained from two of five donors. Both CTL populations were cytotoxic against peptide-pulsed HLA-A2+ target cells, but not against untreated target cells. A CD8+ anti-p53 CTL clone designated p264#2 was isolated from one of the bulk populations. It was found to have an intermediate affinity of approximately 10(-9) M for the epitope and to mediate cytotoxicity against several human tumor cell lines, including the squamous cell carcinoma of the head and neck cell line SCC-9, which is known to present the wild-type sequence p53(264-272) epitope. In addition, CTLs reactive against p53(149-157)-pulsed targets as well as a HLA-A2+ tumor cell line were cloned from a bulk population of antitumor CTLs obtained from one of the five normal PBLs restimulated with this epitope. The results indicate that CTLs recognizing wild-type sequence epitopes can be generated from precursors present in PBLs obtained from some normal individuals using autologous dendritic cells as antigen-presenting cells and suggest that vaccine strategies targeting these epitopes can lead to antitumor CTL generation, thereby emphasizing the therapeutic potential of p53-based cancer vaccines.

Antigens, CD↗
PubMed2026

Multidrug resistance and genomic characteristics of nontypeable Haemophilus influenzae isolates from the respiratory tract of pediatric patients.

UNLABELLED: Nontypeable Haemophilus influenzae (NTHi) is a common colonizer of the human upper respiratory tract and one of the major pathogens responsible for pediatric respiratory tract infections. Given the increasing severity of its multidrug resistance (MDR), this study comprehensively investigated the genomic characteristics of circulating NTHi isolated from sputum and bronchoalveolar lavage fluid (BALF). A total of 104 H. influenzae isolates (69 from sputum; 35 from BALF) were collected from pediatric patients between January 2024 and January 2025. All isolates underwent whole-genome sequencing and antimicrobial susceptibility testing, followed by core/pan-genome phylogenetic analysis, multilocus sequence typing (MLST), and resistome profiling. Among them, 103 were identified as NTHi. We identified 29 known sequence types (STs) and 10 novel STs, with ST-107 (14.4%), ST-57 (10.6%), and ST-11 (8.7%) being the major circulating lineages. However, core-genome phylogenetic analysis provided a more granular view of the genetic variation within these identical STs. All the isolates showed high resistance to ampicillin (98.1%) and cefuroxime (84.6%). Genomically, the multidrug efflux pump gene hmrM was ubiquitous (100%). Ampicillin resistance was predominantly driven by blaTEM-1 carriage (77.9%), with minor contributions from chromosomal ftsI mutations. Fifteen plasmid replicons were predicted from 25 isolates, which highly coincided with the carriage of blaTEM-1 and other acquired resistance genes. This study demonstrates that MDR in pediatric NTHi is primarily driven by acquired resistance genes and chromosomal mutations, with specific resistant clones persisting and enriching under clinical antibiotic pressures. These findings underscore the importance of continuous high-resolution genomic surveillance in guiding rational antibiotic stewardship. IMPORTANCE: This study highlights the critical importance of high-resolution genomic surveillance in managing pediatric nontypeable Haemophilus influenzae (NTHi) infections. By utilizing whole-genome sequencing, we uncovered the pathogen's highly dynamic population structure and complex multidrug resistance (MDR) mechanisms. Crucially, our findings reveal a strong, non-random coupling between core genomic architectures, virulence factors, and MDR elements, driven by dual environmental and pharmacological pressures. This "virulence-MDR" co-evolutionary trend underscores the persistent clinical threat of locally adapted high-risk clones. These findings provide important insights for guiding rational clinical antibiotic stewardship, optimizing treatment strategies, and improving regional infection control.

Humans↗
PubMed2005

Molecular characterization of methicillin-resistant Staphylococcus aureus strains from pet animals and their relationship to human isolates.

OBJECTIVES: Methicillin-resistant Staphylococcus aureus (MRSA) isolates from pet animals were characterized and compared with human isolates from clonal complexes most prevalent in Central Europe. METHODS: S. aureus isolates were investigated for their in vitro susceptibility to antimicrobial agents by broth microdilution. Resistance genes and the Panton-Valentine leucocidin gene lukF-lukS were identified by PCR. All isolates were characterized by SmaI macrorestriction analysis and spa typing to assess their genomic relationships. Representative isolates were additionally analysed by multilocus sequence typing and PCR-directed SCCmec typing. RESULTS: All pet isolates carried the resistance genes mecA and erm(C) and proved to be resistant to beta-lactams and MLS(B) antibiotics. In addition, all isolates were resistant to fluoroquinolones. None of the pet isolates carried the Panton-Valentine leucocidin gene lukF-lukS. Macrorestriction analysis revealed that the pet MRSA isolates exhibited four closely related SmaI fragment patterns. Moreover, all isolates revealed spa type t032. Further analysis of representatives of the different PFGE types revealed the presence of multilocus sequence type ST22 in combination with a type IV SCCmec element. Thus, molecular typing results were similar for pet strains and human ST22 reference strains. CONCLUSIONS: Based on their strain characteristics, the MRSA isolates from pets investigated in this study closely resembled ST22 MRSA isolates which are widely disseminated in German hospitals. The results of this study indicate that cross-transmission of MRSA between pet animals and humans might have occurred.

Animals↗
PubMed1983

Comparative structure and evolution of goat and sheep satellite I DNAs.

The satellite I DNAs of domestic goat (Capra hircus) and domestic sheep (Ovis aries) have been studied using molecular hybridisation and restriction enzyme analysis. Both satellite DNAs are composed of repeat units of 820 base pairs in length, but their restriction maps, although similar, differ in certain respects. Thus the majority of sheep satellite I repeat units have two EcoRI sites and one AluI site, whereas the majority of goat satellite I repeat units have one EcoRI site and two AluI sites. The sheep satellite I repeat units with the two EcoRI sites are much more homogeneous than the repeats forming the remainder of the satellite, as judged by the difference in the melting temperatures of native and reassociated molecules. DNAs from species of wild sheep and goats were screened for the presence of these repeat units, and they appear to have been amplified during the radiation of the Ovis genus. Goat satellite I is composed of a single sequence type which has changed through base substitution until the sequence now shows considerable heterogeneity. It is proposed that the major sequence types of these two satellite DNAs were amplified by different saltatory replication events at different times in the evolution of the group.

Animals↗
PubMed1993

Conservation of motifs within the unusually variable polypeptide sequences of type I restriction and modification enzymes.

Type I restriction enzymes comprise three subunits encoded by genes designated hsdR, hsdM, and hsdS; S confers sequence specificity. Three families of enzymes are known and within families, but not between, hsdM and hsdR are conserved. Consequently, interfamily comparisons of M and R sequences focus on regions of putative functional significance, while both inter- and intrafamily comparisons address the origin, nature and role of diversity of type I restriction systems. We have determined the sequence of the hsdR gene for EcoA, thus making available sequences of all three hsd genes of one representative from each family. The predicted R polypeptide sequences share conserved regions with one superfamily of putative helicases, so-called 'DEAD box' proteins; these conserved sequences may be associated with the ATP-dependent translocation of DNA that precedes restriction. We also present hsdM and hsdR sequences for EcoE, a member of the same family as EcoA. The sequences of the M and R genes of EcoA and EcoE are at least as divergent as typical genes from Escherichia coli and Salmonella, perhaps as the result of selection favouring diversity of restriction specificities combined with lateral transfer among different species.

Amino Acid Sequence↗
PubMed2005

Distribution of major genotypes among methicillin-resistant Staphylococcus aureus clones in Asian countries.

To investigate the evolutionary pattern and genotypic characteristics of methicillin-resistant Staphylococcus aureus (MRSA) strains in the Asian region, 74 MRSA strains isolated from 12 Asian countries were analyzed by multilocus sequence typing (MLST) and SCCmec typing. Overall, a total of 16 genotypes based on sequence type and SCCmec types were identified among MRSA strains from Asian countries. Data revealed two major genotypes of MRSA strains in Asia, with unique geographic distributions. By MLST analysis, all strains from Korea and Japan except one belonged to clonal complex 5 (CC5) while most MRSA isolates from other Asian countries belonged to CC239. SCCmec typing showed that most isolates from Korea and Japan were SSmec type II whereas SCCmec type III (or IIIA) was the most common type in strains from other Asian countries. Our data documented a unique geographic distribution and evolutionary pattern of MRSA clones in Asia.

Anti-Bacterial Agents↗
PubMed2002

Molecular variation at the self-incompatibility locus in natural populations of the genera Antirrhinum and Misopates.

The self-incompatibility system of flowering plants is a classic example of extreme allelic polymorphism maintained by frequency-dependent selection. We used primers designed from three published Antirrhinum hispanicum S-allele sequences in PCR reactions with genomic DNA of plants sampled from natural populations of Antirrhinum and Misopates species. Not surprisingly, given the polymorphism of S-alleles, only a minority of individuals yielded PCR products of the expected size. These yielded 35 genomic sequences, of nine different sequence types of which eight are highly similar to the A. hispanicum S-allele sequences, and one to a very similar unpublished Antirrhinum S-like RNase sequence. The sequence types are well separated from the S-RNase sequences from Solanaceae and Rosaceae, and also from most known "S-like" RNase sequences (which encode proteins not involved in self-incompatibility). An association with incompatibility types has so far been established for only one of the putative S-alleles, but we describe evidence that the other sequences are also S-alleles. Variability in these sequences follows the pattern of conserved and hypervariable regions seen in other S-RNases, but no regions have higher replacement than silent diversity, unlike the results in some other species.

Alleles↗
PubMed2005

On the phylogenetic placement of human T cell leukemia virus type 1 sequences associated with an Andean mummy.

Recently, the putative finding of ancient human T cell leukemia virus type 1 (HTLV-1) long terminal repeat (LTR) DNA sequences in association with a 1500-year-old Chilean mummy has stirred vigorous debate. The debate is based partly on the inherent uncertainties associated with phylogenetic reconstruction when only short sequences of closely related genotypes are available. However, a full analysis of what phylogenetic information is present in the mummy data has not previously been published, leaving open the question of what precisely is the range of admissible interpretation. To fulfill this need, we re-analyzed the mummy data in a new way. We first performed phylogenetic analysis of 188 published LTR DNA sequences from extant strains belonging to the HTLV-1 Cosmopolitan clade, using the method of statistical parsimony which is designed both to optimize phylogenetic resolution among sequences with little evolutionary divergence, and to permit precise mapping of individual sequence mutations onto branches of a divergence network. We then deduced possible phylogenetic positions for the two main categories of published Chilean mummy sequences, based on their published 157-nucleotide LTR sequences. The possible phylogenetic placements for one of the mummy sequence categories are consistent with a modern origin. However, one of these placements for the other mummy sequence category falls very close to the root of the Cosmopolitan clade, consistent with an ancient origin for both this mummy sequence and the Cosmopolitan clade.

Asian People↗
PubMed1999

The role of short sequence repeats in epidemiologic typing.

Short sequence repeats (SSRs), also known as variable number of tandem repeats or micro-satellites, are inherently unstable entities that undergo frequent variation in the number of repeated units through slipped strand mispairing during DNA synthesis. In humans, unit number variability in SSRs has been associated with the occurrence of specific genetic diseases, whereas in micro-organisms SSRs have been elegantly linked to modulation of gene expression. Knowledge of the functional constraints imposed upon the SSRs sheds light on their potential use as molecular clocks for monitoring microbial genome evolution. Although microbial SSR genotypes have been used with increasing frequency for studying the epidemiology and evolution of microbial strains and isolates, such approaches should be used with caution.

Bacteria↗
PubMed2001

The evolution of methicillin resistance in Staphylococcus aureus: similarity of genetic backgrounds in historically early methicillin-susceptible and -resistant isolates and contemporary epidemic clones.

The key genetic component of methicillin resistance, the mecA determinant, is not native to Staphylococcus aureus. Thus, the evolution of methicillin-resistant S. aureus (MRSA) must have begun with the acquisition of the mecA determinant from an unknown heterologous source some time before the first reported appearance of MRSA isolates in clinical specimens in the U.K. and Denmark (in the early 1960s). We compared the genetic backgrounds and phenotypes of a group of methicillin-susceptible S. aureus (MSSA) isolates to the properties of MRSA strains isolated in Denmark and the U.K. during the same time period, and also to the genetic profiles of contemporary epidemic clones of MRSA. All early MRSA isolates resembled a large group of the early MSSA blood isolates in phenotypic and genetic properties, including phage group, antibiotype (resistance to penicillin, streptomycin, and tetracycline), pulsed-field gel electrophoresis pattern, and spaA type and multilocus sequence type, strongly suggesting that the early MSSA examined here represented the progeny of a strain that served as one of the first S. aureus recipients of the methicillin-resistance determinant in Europe. The genetic background of this group of early MSSA isolates was also very similar to that of the widely disseminated contemporary "Iberian clone" of MRSA, suggesting that genetic determinants present in early MSSA and essential for some aspects of the epidemicity and/or virulence of these strains may have been retained by this highly successful contemporary MRSA lineage.

Amino Acid Sequence↗