Restriction Endonuclease Analysis Of DNA Research Articles

Prenatal Diagnosis of β-Thalassemias by Amniocentesis: Linkage Analysis Using Multiple Polymorphic Restriction Endonuclease Sites

In order to assess the applicability of multiple restriction endonuclease analyses of amniocyte DNA to the prenatal diagnosis of beta-thalassemias in general, we studied 12 consecutive couples at risk. DNA of both members of the 12 couples and a previous offspring of each was analyzed for the presence of 4 polymorphic restriction endonuclease sites: the Hpa I site 3' to the beta-globin gene, the Hind III site in the G gamma gene, the Hind III site in the A gamma gene, and the Bam HI site 3' to the beta-gene. Linkage disequilibrium between these sites and beta A or beta thal genes was not found, presumably due to the heterogeneity of beta thal genes. However, the high frequency of polymorphism at these sites allowed differentiation of beta A-bearing chromosomes from beta thal or beta S-bearing chromosomes in both members of 6 couples. In these couples, complete prenatal diagnosis by linkage analysis of amniocyte DNA would be possible. In the remaining 6 couples, beta A and beta thal chromosomes could be discriminated in one member. In about 50% of the pregnancies of these couples, exclusion of beta-thalassemia is possible by this analysis. These data suggest that when linkage analysis of polymorphic restriction endonuclease sites is carried out, prenatal diagnosis of beta-thalassemia states can be accomplished by amniocentesis alone in 75% of pregnancies at risk.

Analysis of homology and drug sensitivity of vaginal isolates of 10 patients with recurrent vulvovaginal candidiasis in recurrent episodes

Objective: To detect karyotype homology of vaginal isolates from patients with recurrent vulvovaginal candidiasis (RVVC) in recurrent episodes, and to discuss changes of susceptibility of Candida strains to antifungal drugs with clinical progress. Method: s Ten patients were recruited from Beijing Obstetrics and Gynecology Hospital, Capital Medical University from September 2018 to June 2019, who were firstly diagnosed with RVVC. Vaginal discharges were collected before first treatment and after first relapse. Vaginal strains were isolated, purificated and identificated. Then karyotype of 20 strains isolated from 10 patients were detected by restriction endonuclease analysis of genomic DNA (REAG) using enzyme BssHⅡand pulsed field gel electrophoresis (PFGE) methods, and sensitivity of clinical isolates to 5 antifungal drugs (clostridium, fluconazole, miconazole, itraconazole and nystatin) was also detected using disk diffusion method. Result: s (1) All 20 strains of 10 patients with RVVC were Candida albicans, and their chromosomes were extremely similar after BssHⅡ enzyme digestion. The gene bands of isolated strains from the same patient were completely identical. (2) After clinical medication, the sensitivity of vaginal isolates to azoles was generally decreased, but remained highly sensitive to nystatin, nystatin (first and second clinical isolates: 100% sensitivity and 100% sensitivity)>clotrimazole (100% sensitivity and 90% sensitivity)>fluconazole (80% sensitivity and 70% sensitivity)>itraconazole (60% sensitivity and 50% sensitivity)>miconazole (30% sensitivity and 20% sensitivity). Conclusions: (1) The latency of the same colonized strain in the vagina may be the cause of repeated RVVC episodes. (2) Antifungal agents could selectively induce drug resistance to Candidas, and Candidas show cross-resistance to antifungal agents. Repeated fungal culture and drug sensitivity test in patients with RVVC are very necessary for correct selection of antifungals.

Restriction Enzyme Analysis of Double-Stranded DNA on Pristine Single-Walled Carbon Nanotubes.

Nanoprobes such as single-walled carbon nanotubes (SWCNTs) are capable of label-free detection that benefits from intrinsic and photostable near-infrared fluorescence. Despite the growing number of SWCNT-based applications, uncertainty surrounding the nature of double-stranded DNA (dsDNA) immobilization on pristine SWCNTs has limited their use as optical sensors for probing DNA-protein interactions. To address this limitation, we study enzyme activity on unmodified dsDNA strands immobilized on pristine SWCNTs. Restriction enzyme activity on various dsDNA sequences was used to verify the retention of the dsDNA's native conformation on the nanotube surface and to quantitatively compare the degree of dsDNA accessibility. We report a 2.8-fold enhancement in initial enzyme activity in the presence of surfactants. Förster resonance electron transfer (FRET) analysis attributes this enhancement to increased dsDNA displacement from the SWCNT surface. Furthermore, the accessibility of native dsDNA was found to vary with DNA configuration and the spacing between the restriction site and the nanotube surface, with a minimum spacing of four base pairs (bp) from the anchoring site needed to preserve enzyme activity. Molecular dynamics (MD) simulations verify that the anchored dsDNA remains within the vicinity of the SWCNT, revealing an unprecedented bimodal displacement of the bp nearest to SWCNT surface. Together, these findings illustrate the successful immobilization of native dsDNA on pristine SWCNTs, offering a new near-infrared platform for exploring vital DNA processes.

Genetic and Biological Characterization of Four Nucleopolyhedrovirus Isolates Collected in Mexico for the Control of Spodoptera exigua (Lepidoptera: Noctuidae).

This study describes four multiple nucleocapsid nucleopolyhedrovirus isolates recovered from infected larvae of beet armyworm, Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae), on crops in two different geographical regions of Mexico. Molecular and biological characterization was compared with characterized S. exigua multiple nucleopolyhedrovirus (SeMNPV) isolates from the United States (SeUS1 and SeUS2) and Spain (SeSP2). Restriction endonuclease analysis of viral DNA confirmed that all Mexican isolates were SeMNPV isolates, but molecular differences between the Mexican and the reference isolates were detected using PCR combined with restriction fragment length polymorphism (RFLP). Amplification of the variable region V01 combined with RFLP distinguished the two Mexican isolates, SeSLP6 and SeSIN6. BglII digestions showed that the majority of the isolates contained submolar bands, indicating the presence of genetic heterogeneity. Amplification of the variable regions V04 and V05 distinguished between American and the Spanish isolates. Biological characterization was performed against two laboratory colonies of S. exigua, one from Mexico, and another from Switzerland. Insects from the Mexican colony were less susceptible to infection than insects from Se-Swiss colony. In the Se-Mex colony, SeSP2 was the most pathogenic isolate followed by SeSIN6, although their virulence was similar to most of the isolates tested. In Se-Swiss colony, similar LD50 values were observed for the five isolates, although the virulence was higher for the SeSLP6 isolate, which also had the highest OB (occlusion body) yield. We conclude that the Mexican isolates SeSIN6 and SeSLP6 possess insecticidal traits of value for the development of biopesticides for the control of populations of S. exigua.

Biodiversity of Lactobacillus helveticus bacteriophages isolated from cheese whey starters.

Twenty-one Lactobacillus helveticus bacteriophages, 18 isolated from different cheese whey starters and three from CNRZ collection, were phenotypically and genetically characterised. A biodiversity between phages was evidenced both by host range and molecular (RAPD-PCR) typing. A more detailed characterisation of six phages showed similar structural protein profiles and a relevant genetic biodiversity, as shown by restriction enzyme analysis of total DNA. Latent period, burst time and burst size data evidenced that phages were active and virulent. Overall, data highlighted the biodiversity of Lb. helveticus phages isolated from cheese whey starters, which were confirmed to be one of the most common phage contamination source in dairy factories. More research is required to further unravel the ecological role of Lb. helveticus phages and to evaluate their impact on the dairy fermentation processes where whey starter cultures are used.

Genetic and biological characterisation of a novel Plutella xylostella granulovirus, PlxyGV-SA

Plutella xylostella granulovirus (PlxyGV) has been isolated from insect populations in many countries and is considered a potential biopesticide for sustainable control of P. xylostella (L.) (Lepidoptera: Plutellidae). Several PlxyGV isolates have been genetically characterised, and the full genome sequence of PlxyGV-Japan is available for comparison with novel isolates. A South African PlxyGV was recently recovered from an overcrowded laboratory P. xylostella colony and identified as a genetically distinct isolate by sequencing of the granulin gene and restriction endonuclease (REN) analysis of genomic DNA. In this report, PlxyGV-SA was further characterised by PCR amplification and sequencing of egt, lef-8 and lef-9 genes, and several amino acid substitutions were observed. The PstI REN profile of PlxyGV-SA was different from that of PlxyGV-Japan in terms of band size and number, thereby confirming its novel genetic identity. Surface dose bioassays showed that PlxyGV-SA is pathogenic to neonate but not late instar larvae at the same and higher virus doses, indicating that a biopesticide should be targeted at early larval stages in the field.

Structural Basis for Inactivation of Giardia lamblia Carbamate Kinase by Disulfiram

Carbamate kinase from Giardia lamblia is an essential enzyme for the survival of the organism. The enzyme catalyzes the final step in the arginine dihydrolase pathway converting ADP and carbamoyl phosphate to ATP and carbamate. We previously reported that disulfiram, a drug used to treat chronic alcoholism, inhibits G. lamblia CK and kills G. lamblia trophozoites in vitro at submicromolar IC50 values. Here, we examine the structural basis for G. lamblia CK inhibition of disulfiram and its analog, thiram, their activities against both metronidazole-susceptible and metronidazole-resistant G. lamblia isolates, and their efficacy in a mouse model of giardiasis. The crystal structure of G. lamblia CK soaked with disulfiram revealed that the compound thiocarbamoylated Cys-242, a residue located at the edge of the active site. The modified Cys-242 prevents a conformational transition of a loop adjacent to the ADP/ATP binding site, which is required for the stacking of Tyr-245 side chain against the adenine moiety, an interaction seen in the structure of G. lamblia CK in complex with AMP-PNP. Mass spectrometry coupled with trypsin digestion confirmed the selective covalent thiocarbamoylation of Cys-242 in solution. The Giardia viability studies in the metronidazole-resistant strain and the G. lamblia CK irreversible inactivation mechanism show that the thiuram compounds can circumvent the resistance mechanism that renders metronidazole ineffectiveness in drug resistance cases of giardiasis. Together, the studies suggest that G. lamblia CK is an attractive drug target for development of novel antigiardial therapies and that disulfiram, an FDA-approved drug, is a promising candidate for drug repurposing.

Medium-sized tandem repeats represent an abundant component of the Drosophila virilis genome

BackgroundPreviously, we developed a simple method for carrying out a restriction enzyme analysis of eukaryotic DNA in silico, based on the known DNA sequences of the genomes. This method allows the user to calculate lengths of all DNA fragments that are formed after a whole genome is digested at the theoretical recognition sites of a given restriction enzyme. A comparison of the observed peaks in distribution diagrams with the results from DNA cleavage using several restriction enzymes performed in vitro have shown good correspondence between the theoretical and experimental data in several cases. Here, we applied this approach to the annotated genome of Drosophila virilis which is extremely rich in various repeats.ResultsHere we explored the combined approach to perform the restriction analysis of D. virilis DNA. This approach enabled to reveal three abundant medium-sized tandem repeats within the D. virilis genome. While the 225 bp repeats were revealed previously in intergenic non-transcribed spacers between ribosomal genes of D. virilis, two other families comprised of 154 bp and 172 bp repeats were not described. Tandem Repeats Finder search demonstrated that 154 bp and 172 bp units are organized in multiple clusters in the genome of D. virilis. Characteristically, only 154 bp repeats derived from Helitron transposon are transcribed.ConclusionUsing in silico digestion in combination with conventional restriction analysis and sequencing of repeated DNA fragments enabled us to isolate and characterize three highly abundant families of medium-sized repeats present in the D. virilis genome. These repeats comprise a significant portion of the genome and may have important roles in genome function and structural integrity. Therefore, we demonstrated an approach which makes possible to investigate in detail the gross arrangement and expression of medium-sized repeats basing on sequencing data even in the case of incompletely assembled and/or annotated genomes.

Characterization of a new isolate of Malacosoma neustria nucleopolyhedrovirus (ManeNPV) from Turkey

The lackey moth, Malacosoma neustria (Linnaeus, 1758), a worldwide pest, causes extensive economic losses on particularly hazelnut, Prunus, Quercus, Populus, and Salix trees. In this study, a local nucleopolyhedrovirus (NPV) was isolated from the larvae of M. neustria in the northeast of Turkey. It was named ManeNPV-T2. Electron microscopic observations showed that the polyhedra of the new isolate contain several virions with multiple nucleocapsids packaged within a single viral envelope. Restriction endonuclease analysis of ManeNPV-T2 DNA indicated that it has a different restriction profile compared to the previous Turkish and Latvian isolates. The phylogenetic analysis of the amplified polh sequence of ManeNPV-T2 showed its relation to the other NPVs from Malacosoma species. Mortality values for third instar M. neustria larvae ranged from 48% to 100% according to the concentration of polyhedral occlusion bodies. Based on screening tests, the LD50 value of the new isolate was calculated as 1.34 × 104 occlusion bodies per larvae. Consequently, ManeNPV appears to be a promising microbial control agent for biocontrol of M. neustria.

Overcrowding of false codling moth, Thaumatotibia leucotreta (Meyrick) leads to the isolation of five new Cryptophlebia leucotreta granulovirus (CrleGV-SA) isolates

False codling moth, Thaumatotibia leucotreta (Meyrick) is a serious pest of economic importance to the South African fruit industry. As part of sustainable efforts to control this pest, biological control options that involve the application of baculovirus-based biopesticides such as Cryptogran and Cryptex (both formulated with a South African isolate of Cryptophlebia leucotreta granulovirus, CrleGV-SA) are popularly used by farmers. In order to safeguard the integrity of these biopesticides as well as protect against any future development of resistance in the host, we conducted a study to bioprospect for additional CrleGV isolates as alternatives to existing ones. Using overcrowding as an induction method for latent infection, we recovered five new CrleGV isolates (CrleGV-SA Ado, CrleGV-SA Mbl, CrleGV-SA Cit, CrleGV-SA MixC and CrleGV-SA Nels). Single restriction endonuclease (REN) analysis of viral genomic DNA extracted from purified occlusion bodies showed that isolates differed in their DNA profiles. Partial sequencing of granulin and egt genes from the different isolates and multiple alignments of nucleotide sequences revealed the presence of single nucleotide polymorphisms (SNPs), some of which resulted in amino acid substitutions in the protein sequence. Based on these findings as well as comparisons with other documented CrleGV isolates, we propose two phylogenetic groups for CrleGV-SA isolates recovered in this study.

Polymorphism of the tilapia’s populations using restriction endonuclease analysis of mitochondrial DNA

We analyzed the genetic differentiation among seven populations of the tilapia reared in Vietnam by using restriction fragment length polymorphism (RFLP) of mitochondrial DNA (mtDNA). The PCR products of 12S rRNA from all the above samples were digested with AluI, HinfI, HindIII, PstI, TaqI, BamHI, ClaI, EcoRI, MboI, MspI, RsaI, SacI restriction enzymes. The result showed that eleven enzymes did not cleave and TaqI had identical mono-banded phenotypes. In all samples of populations 16S rRNA, PCR product did not show any restriction sites with twelve above restriction enzymes. The PCR amplification of D-loop gene was digested with AluI, HinfI, MspI, TaqI, AvaII and EcoRI. The enzyme EcoRI did not digested and AluI gave homomorphism. In another enzymes, ten different haplotypes was found, among them the genes types a, e, n could identify the populations R3, R4; the types b, i - to define populations R1, R5, R7; the types d - to determine populations R5; the types k - to specify R1, R5. This field can be developed for practical purpose.

Investigation of a Cluster ofCandida albicansInvasive Candidiasis in a Neonatal Intensive Care Unit by Pulsed-Field Gel Electrophoresis

Nosocomial invasive candidiasis (IC) has emerged as a major problem in neonatal intensive care units (NICUs). We investigated herein the temporal clustering of six cases of neonatal IC due to Candida albicans in an NICU. Eighteen isolates obtained from the six neonates and two isolates from two health care workers (HCWs) working at the same unit and suffering from fingers' onychomycosis were genotyped by electrophoretic karyotyping (EK) and restriction endonuclease analysis of genomic DNA by using Sfi I (PFGE-Sfi I). PFGE-Sfi I was more effective in discriminating between temporally related isolates. It showed that (i) both HCWs had specific strains excluding them as a source of infections in neonates. (ii) Isolates collected from three neonates were identical providing evidence of their clonal origin and the occurrence of a horizontal transmission of C. albicans in the unit. (iii) The three remaining neonates had specific strains confirming that the IC cases were coincidental. (iv) Microevolution occurred in one catheter-related candidemia case. Our results illustrate the relevance of the molecular approach to investigate suspected outbreaks in hospital surveys and the effectiveness of PFGE-Sfi I for typing of epidemiologically related C. albicans isolates.

Microbial Diversity in Zostera Sp. Beds in South-Western Black Sea Region Analyzed by Amplified Ribosomal DNA Restriction Enzyme Analysis (ARDRA)

ABSTRACTRecent declines in sea grass distribution in south-western Black sea coast arise the need of understanding microbial community relationships in sea grass beds that might affect the viability of these plants. Several factors and their impact on bacterial community were investigated, including the presence or absence of vegetation, depth into sediment, and a gradient of eutrophication formed from pollution point-source. Amplified Ribosomal DNA Restriction enzyme Analysis (ARDRA) showed similar community profiles, thus demonstrating no difference in dominant bacterial members in connection with vegetation. Although highly diverse, sediment community showed also stable annual tendency. This suggested no effect of anthropogenic impact on the main characteristics of bottom sediments in the Zostera endangered meadows.

The New LM-PCR/Shifter Method for the Genotyping of Microorganisms Based on the Use of a Class IIS Restriction Enzyme and Ligation-Mediated PCR

This study details and examines a novel ligation-mediated polymerase chain reaction (LM-PCR) method. Named the LM-PCR/Shifter, it relies on the use of a Class IIS restriction enzyme giving restriction fragments with different 4-base, 5' overhangs, this being the Shifter, and the ligation of appropriate oligonucleotide adapters. A sequence of 4-base, 5' overhangs of the adapter and a 4- base sequence of the 3' end of the primer(s) determine a subset of the genomic restriction fragments, which are amplified by PCR. The method permits the differentiation of bacterial species strains on the basis of the different DNA band patterns obtained after electrophoresis in polyacrylamide gels stained with ethidium bromide and visualized in UV light. The usefulness of the LM-PCR/ Shifter method for genotyping is analyzed by a comparison with the restriction endonuclease analysis of chromosomal DNA by the pulsed-field gel electrophoresis (REA-PFGE) and PCR melting profile (PCR MP) methods for isolates of clinical origin. The clustering of the LM-PCR/Shifter fingerprinting data matched those of the REA-PFGE and PCR MP methods. We found that the LM-PCR/Shifter is rapid, and offers good discriminatory power and excellent reproducibility, making it a method that may be effectively applied in epidemiological studies.

A novel frameshift mutation in keratin 16 underlies pachyonychia congenita with focal palmoplantar keratoderma

Funding sources: This work was supported by the National 863 Program of China (2007AA02Z440) and the National Natural Science Foundation of China (81000253 and 30971164). Conflicts of interest: none declared. Madam, Pachyonychia congenita (PC) comprises a group of autosomal dominant genetic disorders that involve ectodermal dysplasia. Historically, two main clinical subtypes of PC have been described, PC‐1 (MIM 167200) and PC‐2 (MIM 167210).1 2–3 PC has been linked to mutations in four keratin genes that are expressed in the epithelia, KRT6A, KRT6B, KRT16 and KRT17.4, 5 Recently, more specific molecular genetic nomenclature has been adopted by the International Pachyonychia Congenita Consortium. In this system, PC‐6a, PC‐6b, PC‐16 and PC‐17 refer to cases with mutation identified in the genes KRT6A, KRT6B, KRT16 and KRT17, respectively. PC‐U designates cases of suspected PC, where either a mutation has not been found or has not been investigated.6, 7 We report a large Chinese pedigree of PC with focal palmoplantar keratoderma. Two‐point linkage analysis and haplotype analysis were carried out to map the disease locus; DNA sequencing and restriction endonuclease analysis were then used to identify the pathogenic mutation.

SERPING1 mutations in 59 families with hereditary angioedema

Hereditary angioedema due to C1 Inhibitor (C1Inh) deficiency (HAE types I and II) is a rare, life-threatening disease causing spontaneous edema of the submucosal layers.A cohort of 127 individuals with symptoms of recurrent familial angioedema from 59 non-related families was studied. All the patients included fulfilled the diagnostic and biochemical criteria of HAE, including low C1Inh function and/or concentration. Genetic studies were carried out by PCR and sequencing of the C1NH locus followed, in the negative cases, by MLPA, long-range PCR and restriction enzyme analysis of genomic DNA to detect potential large rearrangements. Mutations located in consensus splicing sequences or nearby positions were studied by RT-PCR.The study identified 52 different mutations (25 missense, 15 frameshift, 7 splicing defects and 5 large deletions) responsible for the disease in 56 HAE families. In the remaining three families no molecular alteration could be detected. Twenty-seven of the mutations in this cohort are novel and 10 are confirmed de novo cases. The pathologic effect of the 5 splicing defects first reported here was assessed at the RNA and protein levels. Large deletions affecting exons 4 and 7, ranging from approximately 1500 to 2500bp, were partially characterized by their altered restriction patterns upon long-range amplification.These results highlight the heterogeneity of mutations in the C1NH gene causing C1Inh deficiency and HAE. An approach to the molecular effects associated to each of the mutations reported here was made when possible based on the available data of pathological variants of serpins.

Nosocomial outbreak of Blastoschizomyces capitatus associated with contaminated milk in a haematological unit

In July 2002, Blastoschizomyces capitatus was isolated from four neutropenic patients in a haematology unit. Two patients died due to disseminated infection while the other two had oropharyngeal colonisation. Nosocomial acquisition of the fungus was suspected and epidemiological and environmental studies were undertaken. To determine the potential source for the acquisition of the fungus, epidemiological relationships between the patients were investigated. We performed surveillance cultures on all patients and took environmental cultures of air, inanimate surfaces, food samples, blood products and chemotherapy drugs. No direct contact transmission between patients was found and B. capitatus was isolated only in vacuum flasks used for breakfast milk distribution. All isolates were compared by four independent molecular typing methods: pulsed-field gel electrophoresis, genomic DNA restriction endonuclease analysis, randomly amplified polymorphic DNA, and polymerase chain reaction fingerprinting using a single primer specific for one minisatellite or two microsatellite DNAs. Milk vacuum flasks and clinical strains were genetically indistinguishable by all typing techniques. Milk vacuum flasks were withdrawn from all hospital units and no further B. capitatus infection was detected. Our findings suggest that clonal dissemination of a single strain of B. capitatus from vacuum flasks used for milk distribution was responsible for this nosocomial outbreak in the haematological unit.

Genetic Diversity among Korean Candida albicans Bloodstream Isolates: Assessment by Multilocus Sequence Typing and Restriction Endonuclease Analysis of Genomic DNA by Use of BssHII

Multilocus sequence typing (MLST) has been successfully applied to the epidemiology of Candida albicans isolates not only within the hospital setting but also in multiple locations nationwide. We performed MLST to investigate the genetic relatedness among bloodstream infection (BSI) isolates of C. albicans recovered from 10 Korean hospitals over a 12-month period. The 156 isolates yielded 112 unique diploid sequence types (DSTs). While 95 DSTs were each derived from a single isolate, 17 DSTs were shared by 61 isolates (39.1%). Interestingly, 111 (71.1%) isolates clustered within previously known clades, and 29 (18.6%) clustered within a new clade that includes strains of Asian origin previously typed as singletons. This MLST study was complemented by restriction endonuclease analysis of genomic DNA using BssHII (REAG-B) in order to evaluate whether strains with identical DSTs and originating from the same hospital corresponded to nosocomial clusters. Importantly, only those isolates with a strong epidemiological relationship showed ≥95% identical REAG-B types. Our results indicate that REAG-B typing can be complementary to MLST but should be limited to the investigation of isolates of identical DSTs and when interhuman transmission is suspected.

Comparison of Strain Typing Results for Clostridium difficile Isolates from North America

Accurate strain typing is critical for understanding the changing epidemiology of Clostridium difficile infections. We typed 350 isolates of toxigenic C. difficile from 2008 to 2009 from seven laboratories in the United States and Canada. Typing was performed by PCR-ribotyping, pulsed-field gel electrophoresis (PFGE), and restriction endonuclease analysis (REA) of whole-cell DNA. The Cepheid Xpert C. difficile test for presumptive identification of 027/NAP1/BI isolates was also tested directly on original stool samples. Of 350 isolates, 244 (70%) were known PCR ribotypes, 224 (68%) were 1 of 8 common REA groups, and 187 (54%) were known PFGE types. Eighty-four isolates typed as 027, NAP1, and BI, and 83 of these were identified as presumptive 027/NAP1/BI by Xpert C. difficile. Eight additional isolates were called presumptive 027/NAP1/BI by Xpert C. difficile, of which three were ribotype 027. Five PCR ribotypes contained multiple REA groups, and three North American pulsed-field (NAP) profiles contained both multiple REA groups and PCR ribotypes. There was modest concordance of results among the three methods for C. difficile strains, including the J strain (ribotype 001 and PFGE NAP2), the toxin A-negative 017 strain (PFGE NAP9 and REA type CF), the 078 animal strain (PFGE NAP7 and REA type BK), and type 106 (PFGE NAP11 and REA type DH). PCR-ribotyping, REA, and PFGE provide different but overlapping patterns of strain clustering. Unlike the other methods, the Xpert C. difficile 027/NAP1/BI assay gave results directly from stool specimens, required only 45 min to complete, but was limited to detection of a single strain type.

Fatal disseminated adenovirus infection in a young adult with systemic lupus erythematosus

Background The use of corticosteroids and other immunosuppressive agents increases the risk of infection in patients with systemic lupus erythematosus (SLE). The role of human adenoviruses (HAdV) in the etiology of acute viral diseases in these patients is not known. Objectives Describe a case of acute fatal disseminated adenovirus infection in an SLE patient receiving immunosuppressive therapy. Study design Case report and detailed viral diagnosis by real time PCR and molecular typing of virus isolates by sequencing of hexon and fiber genes and restriction enzyme analysis of viral DNA. Results HAdV was detected by real time PCR in multiple clinical specimens including respiratory, urine, plasma, synovial fluid, and cerebrospinal fluid. Amplification and sequence analysis of the hexon and fiber genes identified the virus as HAdV-7-like for both coding regions. Adenoviruses isolated from respiratory and urine specimens were identical and corresponded to genome type 7d2 by restriction enzyme analysis of viral DNA. The isolated strain encodes a unique fiber gene with a 6-nucleotide deletion corresponding to amino acid positions 250 and 251 in the knob region and not previously described for closely related genomic variants of HAdV-7. Conclusions Adenovirus detection should be included in the diagnostic testing to determine the infectious etiology of fever and/or respiratory symptoms in SLE patients.