First results of the active surveillance of Listeria monocytogenes infections in the Netherlands reveal higher than expected incidence.
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Cluster Analysis↗
Biomedical subjects
A van der Ende
Publications and source records attributed to A van der Ende.
Invasive Listeria monocytogenes infections in the Netherlands, 1995-2003.
In order to add to the limited data available about the incidence of invasive Listeria monocytogenes infection in the Netherlands, two studies were conducted. In the first study, data on hospital patients with listeriosis in the period 1995-2003 were obtained from the National Medical Registration (study 1). In the second study, hospital discharge letters for patients whose Listeria isolates were received by the Netherlands Reference Laboratory for Bacterial Meningitis (NRLBM) in the period 1999-2003 were retrieved (study 2). Serotyping and pulsed-field gel electrophoresis (PFGE) were used to subtype the various strains of Listeria. These reviews revealed 283 hospital patients and 159 patients with Listeria isolates. Discharge letters were received for 107 (67%) patients. The mean annual incidence of listeriosis in both studies was 2.0 per million inhabitants. The main clinical manifestations were meningitis (incidence: 0.9 and 1.0 per million in studies 1 and 2, respectively) and septicaemia (incidence: 0.08 and 1.0 per million, respectively). Listeriosis in pregnancy was rare (incidence: 1.3 and 2.4 per 100,000 pregnancies over 24 weeks of gestation, respectively). Predisposing conditions were present in 47 and 71% of the patients in studies 1 and 2, respectively. The mortality due to listeriosis was 18%. Serotypes 4b, 1/2a, and 1/2b were responsible for 96% of the cases of human listeriosis. Listeriosis is rare in the Netherlands, but its clinical course is severe and the resulting mortality is high. Therefore, the current recommendations for pregnant women to avoid high-risk foods should be continued. These dietary recommendations should also be given to individuals with predisposing conditions, since they, too, are at risk of Listeria infection.
Adult↗
Inclusion proteins of Chlamydiaceae.
Chlamydiaceae are obligate intracellular pathogens with family members among the etiological agents of several human diseases, such as blinding trachoma, sexually transmitted disease (Chlamydia trachomatis) and pneumonia (Chlamydophila pneumoniae, Chlamydophila psittaci). The bacteria replicate intracellularly in a membrane-bound vacuole termed inclusion. The chlamydial inclusion is effectively separated from eukaryotic endocytic pathways. More than two decades ago it was already speculated that Chlamydiae might modify the inclusion membrane through the insertion of chlamydial-derived components. However, because the classical genetic approaches cannot be applied to manipulate these bacteria, it took more than 10 years before definitive proof was obtained that Chlamydiae indeed actively modify the inclusion membrane by the insertion of proteins of chlamydial origin, first observed by Rockey et al. in 1995. This review will focus on the structural and functional aspects of inclusion proteins of Chlamydiaceae, thereby summarizing data obtained by in vitro studies and comparative genomics.
Bacterial Proteins↗
[Increase in the number of invasive Haemophilus influenzae type b infections].
OBJECTIVE: To describe the increase of invasive Haemophilus influenzae type b (Hib) infections in The Netherlands before and after the introduction of Hib vaccination in 1993, and to hypothesise about possible explanations. DESIGN: Descriptive. METHOD: Data on the prevalence of invasive Hib infections, such as meningitis and epiglottitis, during 1990-2004 were obtained from The Netherlands Reference Laboratory for Bacterial Meningitis, which collects Hib isolates from spinal fluid and blood from across the country. RESULTS: The incidence of invasive Hib infections decreased substantially for a few years after 1993. The total number of isolates was at a minimum in 1999 (n = 12) and increased to 49 in 2004. The annual number of patients with vaccine failure was 5 or less during 1995-2001, but was between 10 and 15 from 2002 onwards. A definite explanation for the increase in the incidence of invasive Hib infections cannot be given. Improbable causes are a surveillance artefact, an impaired response to the vaccine due to vaccination-scheme changes or interaction with other vaccines, or selection of Hib variants that are less sensitive to the vaccine-induced immunity. It most likely involves secondary vaccine failure: Hib carriership is decreased by mass vaccination, whereupon natural boosting occurs less frequently later in life. Subsequently, immunity decreases and susceptibility to invasive infection increases. Careful surveillance of invasive Hib infections in The Netherlands remains important.
Bacterial Capsules↗
An acquisition account of genomic islands based on genome signature comparisons.
BACKGROUND: Recent analyses of prokaryotic genome sequences have demonstrated the important force horizontal gene transfer constitutes in genome evolution. Horizontally acquired sequences are detectable by, among others, their dinucleotide composition (genome signature) dissimilarity with the host genome. Genomic islands (GIs) comprise important and interesting horizontally transferred sequences, but information about acquisition events or relatedness between GIs is scarce. In Vibrio vulnificus CMCP6, 10 and 11 GIs have previously been identified in the sequenced chromosomes I and II, respectively. We assessed the compositional similarity and putative acquisition account of these GIs using the genome signature. For this analysis we developed a new algorithm, available as a web application. RESULTS: Of 21 GIs, VvI-1 and VvI-10 of chromosome I have similar genome signatures, and while artificially divided due to a linear annotation, they are adjacent on the circular chromosome and therefore comprise one GI. Similarly, GIs VvI-3 and VvI-4 of chromosome I together with the region between these two islands are compositionally similar, suggesting that they form one GI (making a total of 19 GIs in chromosome I + chromosome II). Cluster analysis assigned the 19 GIs to 11 different branches above our conservative threshold. This suggests a limited number of compositionally similar donors or intragenomic dispersion of ancestral acquisitions. Furthermore, 2 GIs of chromosome II cluster with chromosome I, while none of the 19 GIs group with chromosome II, suggesting an unidirectional dispersal of large anomalous gene clusters from chromosome I to chromosome II. CONCLUSION: From the results, we infer 10 compositionally dissimilar donors for 19 GIs in the V. vulnificus CMCP6 genome, including chromosome I donating to chromosome II. This suggests multiple transfer events from individual donor types or from donors with similar genome signatures. Applied to other prokaryotes, this approach may elucidate the acquisition account in their genome sequences, and facilitate donor identification of GIs.
Algorithms↗
Direct detection of methylation in genomic DNA.
The identification of methylated sites on bacterial genomic DNA would be a useful tool to study the major roles of DNA methylation in prokaryotes: distinction of self and nonself DNA, direction of post-replicative mismatch repair, control of DNA replication and cell cycle, and regulation of gene expression. Three types of methylated nucleobases are known: N6-methyladenine, 5-methylcytosine and N4-methylcytosine. The aim of this study was to develop a method to detect all three types of DNA methylation in complete genomic DNA. It was previously shown that N6-methyladenine and 5-methylcytosine in plasmid and viral DNA can be detected by intersequence trace comparison of methylated and unmethylated DNA. We extended this method to include N4-methylcytosine detection in both in vitro and in vivo methylated DNA. Furthermore, application of intersequence trace comparison was extended to bacterial genomic DNA. Finally, we present evidence that intrasequence comparison suffices to detect methylated sites in genomic DNA. In conclusion, we present a method to detect all three natural types of DNA methylation in bacterial genomic DNA. This provides the possibility to define the complete methylome of any prokaryote.
5-Methylcytosine↗
Deltarho-web, an online tool to assess composition similarity of individual nucleic acid sequences.
SUMMARY: Although whole-genome sequences have been analysed for the presence of anomalous DNA, no dedicated application is currently available to analyse the composition of individual sequence entries, for instance those derived by experimental techniques, such as subtractive hybridization. Since genomic dinucleotide frequency values are conserved between related species, a representative genome sequence can often be found to score for anomalous sequence composition for many of these putative horizontally transferred sequences. We developed the application deltarho-web, which enables the determination of the differences between the dinucleotide composition of an input sequence and that of a selected genome in a size-dependent manner. A feature allowing batch comparisons is included as well. In addition, deltarho-web allows the analysis of the dinucleotide composition of complete genomes. This provides complementary information for the identification of large anomalous gene clusters.
Algorithms↗
Default taxonomy and the genomics era.
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Classification↗
[The effect of Helicobacter pylori eradication on chronic use of acid-suppressant medication by patients in general practice; a randomised, double-blind study].
OBJECTIVE: To study the feasibility of tapering long-term acid-suppressant drugs (ASD) use in chronic dyspeptic patients in relation to Helicobacter pylori eradication. DESIGN: Prospective randomised double-blind study. METHOD: Patients from 54 general-practitioner practices in the Amsterdam area were studied in the period 1 April 1997 - 30 September 1999 after selection on the basis of their use of acid suppressants for a period of at least 8 weeks. After gastroscopy the patients with a peptic ulcer (PUD) and H. pylori were treated with eradication therapy and patients without an ulcer but with H. pylori were randomised for eradication or placebo treatment. After a gradual reduction of acid suppressants over a 3-week period following the intervention, the patients kept a diary for 24 weeks of the quantities of acid suppressants and antacids they used. RESULTS: Of the 1083 patients approached, 434 were prepared to undergo the gastroscopy. Data for the follow-up period were available for 186 of the 227 H. pylori-positive patients. Of them 61% stopped ASD use during follow-up. The mean daily ASD dosage per patient decreased by 85% from 1.85 to 0.27 units (p < 0.05), with minimal antacids use. Of the 75 patients with peptic-ulcer disease 86% stopped ASD use. In patients with functional dyspepsia no difference in ASD use was observed after successful H. pylori eradication or placebo. Patients with mild reflux disease (GERD) used more ASD after H. pylori eradication than after placebo (p < 0.05). CONCLUSION. After H. pylori eradication many patients with PUD stopped ADS use, while GERD patients used more ASD than after placebo. A gradual withdrawal of long-term ASD use, supported by antacids and on-demand use of low-dosage ASD, facilitated reduction of ASD use during 6 months.
Adolescent↗
An in vitro strategy for the selective isolation of anomalous DNA from prokaryotic genomes.
In sequenced genomes of prokaryotes, anomalous DNA (aDNA) can be recognized, among others, by atypical clustering of dinucleotides. We hypothesized that atypical clustering of hexameric endonuclease recognition sites in aDNA allows the specific isolation of anomalous sequences in vitro. Clustering of endonuclease recognition sites in aDNA regions of eight published prokaryotic genome sequences was demonstrated. In silico digestion of the Neisseria meningitidis MC58 genome, using four selected endonucleases, revealed that out of 27 of the small fragments predicted (<5 kb), 21 were located in known genomic islands. Of the 24 calculated fragments (>300 bp and <5 kb), 22 met our criteria for aDNA, i.e. a high dinucleotide dissimilarity and/or aberrant GC content. The four enzymes also allowed the identification of aDNA fragments from the related Z2491 strain. Similarly, the sequenced genomes of three strains of Escherichia coli assessed by in silico digestion using XbaI yielded strain-specific sets of fragments of anomalous composition. In vitro applicability of the method was demonstrated by using adaptor-linked PCR, yielding the predicted fragments from the N.meningitidis MC58 genome. In conclusion, this strategy allows the selective isolation of aDNA from prokaryotic genomes by a simple restriction digest-amplification-cloning-sequencing scheme.
Base Sequence↗
Outbreak of meningococcal disease caused by PorA-deficient meningococci.
An outbreak of 7 cases of group C meningococcal disease occurred during the last week of July and the first week of August 2001 in the southwestern part of The Netherlands. Characterization of the 7 patients' isolates by various typing methods showed that the isolates were identical, except for the expression of PorA. Isolates from 5 patients were PorA deficient. These results show that transmission of PorA-deficient meningococci occurs and that PorA-deficient meningococci can cause invasive disease. PorA-based meningococcal vaccines may provide limited protection.
Adolescent↗
Lack of accuracy of the noninvasive Helicobacter pylori stool antigen test in patients with gastroduodenal ulcer bleeding.
OBJECTIVE: Oral presentation at Digestive Diseases Week, San Francisco, California, May 2002. The antigen-based stool assay has proven to be accurate in diagnosing Helicobacter pylori infection in dyspeptic patients. We evaluated the H. pylori antigen-based stool assay (HpSA) in patients with peptic ulcer bleeding (PUB). METHODS: Thirty-six patients with PUB were endoscoped, and antral and corpus biopsy specimens were taken for rapid urease test (RUT), histology, and culture. The first stool sample after admission was collected for the HpSA test. The gold standard was defined as either positive culture or positive RUT and histology. If only RUT or histology was positive, this was defined as indeterminate. To evaluate cross-reaction with blood constituents, citrated blood samples from 10 healthy volunteers (nine H. pylori serology negative and one H. pylori serology positive) were assessed by the HpSA test. RESULTS: A total of 36 consecutive patients with PUB (21 male) with a mean age of 69.5 yr were included in the study. Using the gold standard, the sensitivity and specificity of the HpSA test were 100% and 52%, respectively. Citrated blood samples of three H. pylori negative and one H. pylori positive volunteer gave a positive result in the HpSA test, suggesting cross-reaction with blood con stituents. CONCLUSIONS: The HpSA test gave a high number of false- positive results in patients with PUB, probably because of blood constituents cross-reacting in the enzyme immunoassay. The HpSA test is not accurate for testing H. pylori infection in patients with PUB.
Adolescent↗
Cross-reactivity of antibodies against PorA after vaccination with a meningococcal B outer membrane vesicle vaccine.
The cross-reactivity of PorA-specific antibodies induced by a monovalent P1.7-2,4 (MonoMen) and/or a hexavalent (HexaMen) meningococcal B outer membrane vesicle vaccine (OMV) in toddlers and school children was studied by serum bactericidal assays (SBA). First, isogenic vaccine strains and PorA-identical patient isolates were compared as a target in SBA, to ensure that the vaccine strains are representative for patient isolates. Geometric mean titers (GMTs) in SBA against patient isolates with subtypes P1.5-2,10 and P1.5-1,2-2 after vaccination with HexaMen were generally lower than those against vaccine strains with the same subtype, although the percentage of vaccine responders (> or =4-fold increase in SBA after vaccination) was not affected. Using various P1.7-2,4 patient isolates, GMTs as well as the number of vaccine responders were higher than for the P1.7-2,4 vaccine strain, indicating that the use of the P1.7-2,4 vaccine strain may have underestimated the immunogenicity of this subtype in HexaMen. Secondly, the cross-reactivity of antibodies induced by MonoMen and HexaMen was studied using several patient isolates that differed from the vaccine subtypes by having minor antigenic variants of one variable region (VR), by having a completely different VR or by having a different combination of VRs. MonoMen induced P1.4-specific antibodies that were cross-reactive with P1.4 variants P1.4-1 and P1.4-3. HexaMen induced a broader cross-reactive antibody response against various patient isolates with one VR identical to a vaccine subtype or a combination of VRs included in HexaMen. Cross-reactivity, measured by a fourfold increase in SBA after vaccination, against these strains ranged from 23 to 92% depending on the subtype of the tested strain and was directed against both VR1 and VR2. The extended cross-reactivity of vaccinee sera induced by HexaMen against antigenic variants has important favorable implications for meningococcal B OMV vaccine coverage.
Amino Acid Sequence↗
Evaluation of a novel monoclonal enzyme immunoassay for detection of Helicobacter pylori antigen in stool from children.
BACKGROUND: Reliable non-invasive methods for detection of Helicobacter pylori infection are required to investigate the incidence, transmission, and clearance of infection in childhood. AIM: To evaluate a new monoclonal enzyme immunoassay (EIA) (FemtoLab H pylori Cnx) for detection of H pylori antigen in stool in a large cohort of children compared with invasive diagnostic methods and the (13)C urea breath test. PATIENTS AND METHODS: A total of 302 symptomatic previously untreated children (aged 0.5-18.7 years; 148 girls) were recruited at three centres. H pylori status was defined by results of culture, histology, the rapid urease test, and the (13)C urea breath test. Stool samples were investigated locally by the EIA using two different production lots. According to the manufacturer's recommendations, an optical density (OD) of 0.150 was used as a cut off value. RESULTS: OD values clearly differentiated between the 92 H pylori infected and the 210 non-infected children (median (5th-95th percentiles) 2.729 (0.232->4.000) v 0.021 (0.009-0.075)). Only two false positive and two false negative results occurred, giving a sensitivity, specificity, positive predictive value, and negative predictive value of 98%, 99%, 98%, and 99%, respectively. No significant relation was found between age and OD values in infected or non-infected children. CONCLUSIONS: The monoclonal stool antigen EIA was excellent in diagnosing H pylori infection in symptomatic children. Accuracy was independent of the laboratory, production lot used, or the child's age. Because only 18/116 children <6 years of age were infected with H pylori, further validation of the test is needed in young infected children.
Adolescent↗
Polymorphisms of Helicobacter pylori HP0638 reflect geographic origin and correlate with cagA status.
Since the associations between Helicobacter pylori genotype and disease differ in Asia and the West, we investigated the correlation between HP0638, encoding an outer membrane protein, and potential markers of virulence (cagA, vacA, and iceA). For 109 strains from nine countries, the status of cagA, vacA, and iceA was determined by PCR and/or a line probe assay. We also studied 18 strains from 8 patients (parents and 6 daughters) from a Dutch family and paired strains collected on average 8 years apart from 11 patients. When the HP0638 signal sequences were amplified by PCR and DNA sequence determinations were performed, 89 (96%) of 93 cagA-positive strains had HP0638 in frame, versus none (0%) of 16 cagA-negative strains (P < 0.001). Among strains in which HP0638 was in frame, a six-CT dinucleotide repeat pattern was dominant in Western countries (23 of 33 strains [70%]), while a pattern of three CT repeats with another CT after four T's (3 + 1-CT-repeat pattern) was dominant in East Asia (31 of 46 strains [67%]); however, specific CT repeat patterns did not correlate with clinical outcome. HP0638 phylogenetic trees also showed geographic characters. The HP0638 frame status and CT dinucleotide repeat patterns were identical for 9 of 11 pairs of strains obtained on average 8 years apart from individuals and the 15 strains obtained from the mother and all six daughters. Thus, HP0638 frame status and cagA status are strongly correlated. The CT dinucleotide repeat pattern in the putative HP0638 signal sequence has geographic characters and appears stable in particular patients and families over a period of years. Analysis of HP0638 CT polymorphisms may serve as a new typing system to discriminate H. pylori isolates for epidemiological purposes.
Adult↗
Fit genotypes and escape variants of subgroup III Neisseria meningitidis during three pandemics of epidemic meningitis.
The genetic variability at six polymorphic loci was examined within a global collection of 502 isolates of subgroup III, serogroup A Neisseria meningitidis. Nine "genoclouds" were identified, consisting of genotypes that were isolated repeatedly plus 48 descendent genotypes that were isolated rarely. These genoclouds have caused three pandemic waves of disease since the mid-1960s, the most recent of which was imported from East Asia to Europe and Africa in the mid-1990s. Many of the genotypes are escape variants, resulting from positive selection that we attribute to herd immunity. Despite positive selection, most escape variants are less fit than their parents and are lost because of competition and bottlenecks during spread from country to country. Competition between fit genotypes results in dramatic changes in population composition over short time periods.
Alleles↗
Prevalence of Helicobacter pylori infection in stress-induced gastric mucosal injury.
OBJECTIVE: To determine the role of Helicobacter pylori infection in critically ill patients admitted to the intensive care unit in the formation of gastric and duodenal mucosal injury in these patients. DESIGN AND SETTING: Prospective cohort analysis in an 18-bed mixed medical and surgical closed format ICU in a teaching hospital. PATIENTS: Fifty consecutive patients admitted to the intensive care unit for emergency reasons and requiring mechanical ventilation were included. INTERVENTIONS: H. pylori infection was detected by the laser-assisted ratio analyzer [13C]urea breath test (UBT). Gastric and duodenal mucosal lesions were assessed by upper gastrointestinal endoscopy and classified as minor (up to five erosions or submucosal hemorrhages) or major (more than five erosions or submucosal hemorrhages) mucosal injury. MEASUREMENTS AND MAIN RESULTS: Six patients were not eligible because the UBT could not be processed. Of the 44 eligible patients 22 were H. pylori positive by UBT and 22 H. pylori negative. Either minor or major gastric mucosal injury was found on endoscopy in 66 %. Of the 29 patients with minor mucosal injury 10 (34.5 %) were infected with H. pylori as indicated by positive LARA 13C-UBT. In contrast, of the 15 patients with major mucosal injury 12 (80%) were infected with H. pylori (p = 0.004). H. pylori was the only risk factor significantly associated with major mucosal injury in a multiple regression analysis (p = 0.019). CONCLUSION: The severity of gastric and duodenal mucosal injury in critically ill patients during mechanical ventilation is significantly correlated with the presence of H. pylori infection.
Adult↗
The population structure of Neisseria meningitidis serogroup A fits the predictions for clonality.
The population structure of Neisseria meningitidis is supposedly epidemic according to. The model predicts that linkage disequilibrium in N. meningitidis populations is only temporary and arises due to the outgrowth of highly successful clonal genotypes from an essentially sexual population. These clones should disappear after a few years because of frequent recombination. In contrast, multilocus enzyme electrophoresis (MLEE) data had previously been interpreted as showing that serogroup A meningococci are truly clonal and possess only limited genetic variability (Wang et al., 1992). The two interpretations are contradictory. In order to elucidate the true population structure of serogroup A meningococci, we analyzed data for a representative group of 84 serogroup A isolates obtained by MLEE, random amplified polymorphic DNA (RAPD) and multilocus sequence typing (MLST). Analysis of linkage disequilibrium and bootstrap analyses of cluster analysis showed a strongly structured population with highly significant linkage disequilibrium. This was not due to the overrepresentation of certain genotypes, in contrast to the expectations for an epidemic population. The analyses identify two main clades, within each of which linkage disequilibrium was also highly significant, thus, excluding a cryptic speciation model. These observations support a population structure based on clonal evolution, in which clones are much more stable than expected for epidemic clonality. We propose that serogroup A meningococci may possess a different population structure from other serogroups of Neisseria meningitidis.
Clone Cells↗