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Biomedical subjects

J D van Embden

Publications and source records attributed to J D van Embden.

At least 19 recordsLinked to original sources
PubMed2001

Variant esp gene as a marker of a distinct genetic lineage of vancomycin-resistant Enterococcus faecium spreading in hospitals.

In the USA, vancomycin-resistant Enterococcus faecium (VREF) is endemic in hospitals, despite lack of carriage among healthy individuals. In Europe, however, hospital outbreaks are rare, but VREF carriage among healthy individuals and livestock is common. We used amplified fragment-length polymorphism analysis to genotype 120 VREF isolates associated with hospital outbreaks and 45 non-epidemic isolates from the USA, Europe, and Australia. We also looked for the esp virulence gene in these isolates and in 98 VREF from animals. A specific E. faecium subpopulation genetically distinct from non-epidemic VREF isolates was found to be the cause of the hospital epidemics in all three continents. This subpopulation contained a variant of the esp gene that was absent in all non-epidemic and animal isolates. Identification of the variant esp gene will be important in guiding infection-control strategies, and the Esp protein could be a new target for antibacterial therapy.

Bacterial Proteins↗
PubMed2001

The effect of age and study duration on the relationship between 'clustering' of DNA fingerprint patterns and the proportion of tuberculosis disease attributable to recent transmission.

Though it is recognized that the extent of 'clustering' of isolates from tuberculosis cases in a given population is related to the amount of disease attributable to recent transmission, the relationship between the two statistics is poorly understood. Given age-dependent risks of disease and the fact that a long study (e.g. spanning several years) is more likely to identify transmission-linked cases than a shorter study, both measures, and thus the relationship between them, probably depend strongly on the ages of the cases ascertained and study duration. The contribution of these factors is explored in this paper using an age-structured model which describes the introduction and transmission of M. tuberculosis strains with different DNA fingerprint patterns in The Netherlands during this century, assuming that the number of individuals contacted by each case varies between cases and that DNA fingerprint patterns change over time through random mutations, as observed in several studies. Model predictions of clustering in different age groups and over different time periods between 1993 and 1997 compare well against those observed. According to the model, the proportion of young cases with onset in a given time period who were 'clustered' underestimated the proportion of disease attributable to recent transmission in this age group (by up to 25% in males); for older individuals, clustering overestimated this proportion. These under- and overestimates decreased and increased respectively as the time period over which the cases were ascertained increased. These results have important implications for the interpretation of estimates of the proportion of disease attributable to recent transmission, based on 'clustering' statistics, as are being derived from studies of the molecular epidemiology of tuberculosis in many populations.

Adolescent↗
PubMed2000

Host specificity of vancomycin-resistant Enterococcus faecium.

Amplified-fragment length polymorphism (AFLP) analysis was used to investigate the genetic relationships among 255 vancomycin-resistant Enterococcus faecium (VREF) strains isolated from hospitalized patients, nonhospitalized persons, and various animal sources. Four major AFLP genogroups (A-D) were discriminated. The strains of each taxon shared >/=65% of the restriction fragments. Most isolates recovered from nonhospitalized persons (75%) were grouped together with all pig isolates in genogroup A. Most isolates from hospitalized patients (84%), a subset of veal calf isolates (25%), and all isolates from cats and dogs clustered in genogroup C. Most isolates from chickens (97%) and turkeys (86%) were grouped in genogroup B, whereas most veal calf isolates (70%) clustered in genogroup D. Therefore, VREF strains are predominantly host-specific, and strains isolated from hospitalized patients are genetically different from the prevailing VREF strains present in the fecal flora of nonhospitalized persons.

Animals↗
PubMed2000

Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria.

The direct repeat region in Mycobacterium tuberculosis complex strains is composed of multiple direct variant repeats (DVRs), each of which is composed of a 36-bp direct repeat (DR) plus a nonrepetitive spacer sequence of similar size. It has been shown previously that clinical isolates show extensive polymorphism in the DR region by the variable presence of DVRs, and this polymorphism has been used in the epidemiology of tuberculosis. In an attempt to better understand the evolutionary scenario leading to polymorphic DR loci and to improve strain differentiation by spoligotyping, we characterized and compared the DNA sequences of the complete DR region and its flanking DNA of M. tuberculosis complex strains. We identified 94 different spacer sequences among 26 M. tuberculosis complex strains. No sequence homology was found between any of these spacers and M. tuberculosis DNA outside of the DR region or with any other known bacterial sequence. Although strains differed extensively in the presence or absence of DVRs, the order of the spacers in the DR locus was found to be well conserved. The data strongly suggest that the polymorphism in clinical isolates is the result of successive deletions of single discrete DVRs or of multiple contiguous DVRs from a primordial DR region containing many more DVRs than seen in present day isolates and that virtually no scrambling of DVRs took place during evolution. Because the majority of the novel spacer sequences identified in this study were confined to isolates of the rare Mycobacterium canettii taxon, the use of the novel spacers in spoligotyping led only to a slight improvement of strain differentiation by spoligotyping.

Animals↗
PubMed1999

Detection of Borrelia burgdorferi sensu stricto by reverse line blot in the joints of Dutch patients with Lyme arthritis.

OBJECTIVE: To analyze the presence of Borrelia burgdorferi sensu lato in synovial samples from the knee joint of patients with Lyme arthritis by polymerase chain reaction, and to differentiate the species by reverse line blot (RLB). METHODS: Synovial fluid (SF) and synovial tissue (ST) samples were obtained from patients with Lyme arthritis (n = 4) and from patients with various other forms of arthritis (n = 9). DNA extracted from synovial samples was amplified by using, as a target, the spacer region between the 5S and 23S ribosomal RNA genes of B. burgdorferi sensu lato. Subsequently, 4 species-specific DNA probes were used in the RLB for specific hybridization. RESULTS: DNA from B. burgdorferi sensu stricto DNA was detected in the SF and ST from 3 patients with Lyme arthritis. B. burgdorferi sensu lato DNA was not detected in the synovial samples from 9 control patients. CONCLUSION: The relationship between different species of B. burgdorferi sensu lato and arthritis can be studied using direct analysis of extracted DNA from joint samples. This method can be used to study the association between particular clinical manifestations of Lyme disease and different species of B. burgdorferi sensu lato.

Adolescent↗
PubMed1999

Molecular epidemiology of tuberculosis in the Netherlands: a nationwide study from 1993 through 1997.

To disclose risk factors for active tuberculosis transmission in the Netherlands, restriction fragment length polymorphism (RFLP) patterns of 78% of the Mycobacterium tuberculosis isolates, from the period 1993-1997, were analyzed. Of the respective 4266 cases, 46% were found in clusters of isolates with identical RFLPs, and 35% were attributed to active transmission. The clustering percentage increased strongly with the number of isolates; taking this into account, fewer cases were clustered than has been reported in other studies. Contact investigations in the five largest clusters of 23-47 patients suggested epidemiological linkage between cases. Of patients identified through contact tracing, 91% were clustered. Demographic risk factors for active transmission of tuberculosis included male sex, urban residence, Dutch and Surinamese nationality, and long-term residence in the Netherlands. Human immunodeficiency virus infection was not an independent risk factor for active transmission. Isoniazid-resistant strains were relatively less frequently clustered, suggesting that these generated fewer secondary cases.

Adult↗
PubMed1999

Analysis of rate of change of IS6110 RFLP patterns of Mycobacterium tuberculosis based on serial patient isolates.

The rate of change of IS6110 restriction fragment length polymorphism (RFLP) patterns of Mycobacterium tuberculosis was determined in serial isolates from 544 patients. In 25 patients (4.6%), the RFLP patterns of the follow-up isolates differed from the initial isolates. Patients with different follow-up strains were less likely to cluster with patients whose strains had indistinguishable RFLP patterns. Changes in RFLP patterns were more common for persons with extrapulmonary disease and for those who had both pulmonary and extrapulmonary isolates. Based on serial isolates spanning for the most part <3 months, the half-life was extrapolated to be 3.2 years (95% confidence interval, 2.1-5.0). The main implication of this study is that the rate of change of IS6110-based RFLP of M. tuberculosis supports the use of IS6110 typing in epidemiologic studies of recent transmission of tuberculosis.

Adult↗
PubMed1999

Detection of mycobacteria in joint samples from patients with arthritis using a genus-specific polymerase chain reaction and sequence analysis.

OBJECTIVE: Mycobacteria have been implicated in the pathogenesis of various forms of arthritis. The aim of this study was to examine the diagnostic potential of molecular biological techniques as well as to investigate the pathogenetic role of mycobacteria in chronic arthritis. PATIENTS AND METHODS: DNA, extracted from synovial fluid and synovial tissue samples from patients with mycobacterial septic arthritis (n = 2), seronegative spondyloarthropathies (SpA) (n = 18), undifferentiated arthritis (UA) (n = 21) and rheumatoid arthritis (RA) (n = 40), was analysed using a mycobacterial genus-specific polymerase chain reaction (PCR) applied to amplify mycobacterial DNA. Subsequently, automated sequencing was performed for speciation. Samples from patients with either non-mycobacterial septic arthritis, osteoarthritis (OA), crystal arthritis or joint trauma served as negative controls (n = 19). RESULTS: Mycobacterium tuberculosis complex and Mycobacterium marinum were detected in the two patients with mycobacterial septic arthritis. The other species identified were Mycobacterium hodleri (in one RA patient), Mycobacterium smegmatis (in one OA patient and two RA patients) and Mycobacterium austroafricanum (in one crystal arthritis patient). All other samples were negative. CONCLUSIONS: The results suggest that the mycobacterial genus-specific PCR applied on DNA extracts isolated directly from joint samples may be employed as an additional diagnostic tool in the case of clinical suspicion of a mycobacterial infection. No evidence was obtained for a pathogenetic role of mycobacteria in SpA, UA or RA.

Adolescent↗
PubMed1999

Molecular diversity and evolutionary relationships of Tn1546-like elements in enterococci from humans and animals.

We report on a detailed study on the molecular diversity and evolutionary relationships of Tn1546-like elements in vancomycin-resistant enterococci (VRE) from humans and animals. Restriction fragment length polymorphism (RFLP) analysis of the VanA transposon of 97 VRE revealed seven different Tn1546 types. Subsequent sequencing of the complete VanA transposons of 13 VRE isolates representing the seven RFLP types followed by sequencing of the identified polymorphic regions in 84 other VanA transposons resulted in the identification of 22 different Tn1546 derivatives. Differences between the Tn1546 types included point mutations in orf1, vanS, vanA, vanX, and vanY. Moreover, insertions of an IS1216V-IS3-like element in orf1, of IS1251 in the vanS-vanH intergenic region, and of IS1216V in the vanX-vanY intergenic region were found. The presence of insertion sequence elements was often associated with deletions in Tn1546. Identical Tn1546 types were found among isolates from humans and farm animals in The Netherlands, suggesting the sharing of a common vancomycin resistance gene pool. Application of the genetic analysis of Tn1546 to VRE isolates causing infections in Hospitals in Oxford, United Kingdom, and Chicago, Ill., suggested the possibility of the horizontal transmission of the vancomycin resistance transposon. The genetic diversity in Tn1546 combined with epidemiological data suggest that the DNA polymorphism among Tn1546 variants can successfully be exploited for the tracing of the routes of transmission of vancomycin resistance genes.

Animals↗
PubMed1999

Comparison of methods based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis complex strains: interlaboratory study of discriminatory power and reproducibility.

In this study, the currently known typing methods for Mycobacterium tuberculosis isolates were evaluated with regard to reproducibility, discrimination, and specificity. Therefore, 90 M. tuberculosis complex strains, originating from 38 countries, were tested in five restriction fragment length polymorphism (RFLP) typing methods and in seven PCR-based assays. In all methods, one or more repetitive DNA elements were targeted. The strain typing and the DNA fingerprint analysis were performed in the laboratory most experienced in the respective method. To examine intralaboratory reproducibility, blinded duplicate samples were included. The specificities of the various methods were tested by inclusion of 10 non-M. tuberculosis complex strains. All five RFLP typing methods were highly reproducible. The reliability of the PCR-based methods was highest for the mixed-linker PCR, followed by variable numbers of tandem repeat (VNTR) typing and spoligotyping. In contrast, the double repetitive element PCR (DRE-PCR), IS6110 inverse PCR, IS6110 ampliprinting, and arbitrarily primed PCR (APPCR) typing were found to be poorly reproducible. The 90 strains were best discriminated by IS6110 RFLP typing, yielding 84 different banding patterns, followed by mixed-linker PCR (81 patterns), APPCR (71 patterns), RFLP using the polymorphic GC-rich sequence as a probe (70 patterns), DRE-PCR (63 patterns), spoligotyping (61 patterns), and VNTR typing (56 patterns). We conclude that for epidemiological investigations, strain differentiation by IS6110 RFLP or mixed-linker PCR are the methods of choice. A strong association was found between the results of different genetic markers, indicating a clonal population structure of M. tuberculosis strains. Several separate genotype families within the M. tuberculosis complex could be recognized on the basis of the genetic markers used.

Bacterial Typing Techniques↗
PubMed1999

Estimation of serial interval and incubation period of tuberculosis using DNA fingerprinting.

OBJECTIVE: To determine the frequency distributions of serial interval and incubation period of tuberculosis within 4 years of transmission, and to identify correlates of serial intervals and incubation periods. METHODS: DNA fingerprints were obtained for all isolates from all culture-positive patients notified in The Netherlands from 1993 to 1996. Patient information was obtained from the National Tuberculosis Register. Results from contact investigations were provided by public health services. Source cases and secondary cases of tuberculosis were identified, based on 1) identical DNA fingerprints, and 2) epidemiological confirmation of contact. Under-representation of long intervals were corrected for by weighting cases. RESULTS: A total of 69 source-secondary case couples were identified. The geometric mean serial interval was 29.5 weeks (95% confidence interval [CI] 22.8-38.2 weeks) and the geometric mean incubation period 20.8 weeks (95% CI 15.5-27.8 weeks). Serial intervals and incubation periods tended to increase with age (P > 0.05). Three secondary cases with human immunodeficiency virus infection showed very short incubation periods (P > 0.05). CONCLUSION: Using a new methodology, the distribution of incubation periods of tuberculosis gave results consistent with earlier studies.

Adolescent↗
PubMed1998

Spacer oligotyping of Mycobacterium bovis isolates compared to typing by restriction fragment length polymorphism using PGRS, DR and IS6110 probes.

Ninety-two Mycobacterium bovis isolates from cattle, deer and badgers in Northern Ireland and the Republic of Ireland were genotyped by spacer-oligotyping (spoligotyping) and 67 of these were analysed by restriction fragment length polymorphism (RFLP). RFLP analysis was performed using three DNA probes, PGRS, DR and IS6110. Forty-seven of the M. bovis isolates were from 45 different sources; these were typed using both RFLP and spoligotyping. These 47 isolates could be differentiated into 24 different RFLP types and 15 distinct spoligotypes. Although RFLP was found to be more discriminatory compared to the present spoligotyping technique, spoligotyping was able to differentiate 21 RFLP type 'ACA' isolates into three different patterns. The remaining 45 M. bovis isolates were from a small case study, involving infected cattle, deer and badgers from the same geographic region. All these isolates were analysed by spoligotyping and a selection of 20 isolates were RFLP typed. All the isolates in the case study had the same spoligotype pattern with the exception of one cervine isolate. Similarly all the isolates typed by RFLP had the same pattern. Consequently, the predominant strain in the case study was not host restricted. The consistency between the results obtained using the two techniques indicates the potential value of both techniques for epidemiological studies. Spoligotyping was found to be a much more rapid technique and easier to perform, requiring less sophisticated computer software for strain typing. Spoligotyping results were more readily documented and analysed and the technique was also more suitable than RFLP analysis for large-scale screening studies.

Animals↗
PubMed1998

Analysis of tuberculosis transmission between nationalities in the Netherlands in the period 1993-1995 using DNA fingerprinting.

Immigration from high prevalence areas may contribute to an increased risk of tuberculosis in Europe. This study aimed at quantifying transmission of tuberculosis between and within nationalities among residents of the Netherlands. DNA "fingerprints," on the basis of restriction fragment length polymorphism using marker IS6110, were made of all Mycobacterium tuberculosis isolates in the Netherlands from January 1993 through June 1995. Clusters were defined as groups of patients that had isolates with identical fingerprints. It was assumed that the probability of a patient being the source of a cluster was proportional to the incidence rate of potential sources times the probability that a potential source would give rise to a cluster. The transmission index was defined as the average number of secondary cases of infectious tuberculosis caused directly or indirectly through recent transmission by a single potential source case and was used to estimate the effective reproductive rate associated with recent transmission, ReFAST. Among a total of 623 Dutch tuberculosis cases, 17% (95% confidence interval 9-25%) of cases were attributable to recent transmission from a non-Dutch source. The transmission index varied strongly by nationality, and was highest among the Surinamese (1.3), Moroccan (0.8), and Turkish (0.8) populations; ReFAST was 0.26. Aggregation of tuberculosis cases of given nationalities within clusters was most pronounced among recent immigrants from Somalia and (ex-)Yugoslavia. The authors conclude that differences in transmission between subpopulations can be quantified and may be used to evaluate and direct tuberculosis control.

Adolescent↗
PubMed1998

Detection of bacterial DNA in joint samples from patients with undifferentiated arthritis and reactive arthritis, using polymerase chain reaction with universal 16S ribosomal RNA primers.

OBJECTIVE: Bacteria are considered to be important in the pathogenesis of several forms of arthritis. The goal of this study was to apply the 16S ribosomal RNA (rRNA)-polymerase chain reaction method for the detection of bacterial DNA in synovial fluid (SF) and synovial tissue (ST) from inflamed joints. METHODS: Samples from 5 patients with septic arthritis and from 7 with osteoarthritis or arthritis secondary to joint trauma were used as controls. Samples from 6 patients with spondylarthropathy (SpA) and from 20 with undifferentiated arthritis (UA) were analyzed for the presence of bacterial DNA using universal 16S rRNA primers. Automated sequencing and comparative data analysis were performed to identify the species. RESULTS: In the positive control group, the bacterial species cultured from the synovium could be identified in all cases. No bacterial DNA was detected in the SF and ST from patients in the negative control group. In 4 of 6 patients with SpA and 7 of 20 with UA, the analysis of joint samples revealed the presence of bacterial DNA. Sequence analysis indicated the presence of multiple species, which was confirmed by sequencing of cloned products. CONCLUSION: When the the above techniques were used with a stringent regimen, we were able to demonstrate that it is possible to collect and analyze joint samples without contaminating bacterial DNA. The accumulation of phagocytic cells that contain bacterial DNA of various species could play a role in the pathogenesis of both SpA and UA.

Adolescent↗
PubMed1998

Resistance of staphylococci in The Netherlands: surveillance by an electronic network during 1989-1995.

An electronic surveillance network for monitoring antibiotic resistance in The Netherlands has been in operation since 1989. Seven public health laboratories participate and the system covers about 25% of all bacteriological determinations in The Netherlands. This paper reports the results of staphylococci isolated in the period 1989-1995. About 0.3% of the Staphylococcus aureus isolates in the study period were resistant to methicillin. This low percentage may be due to the restrictive use of antibiotics and to strict isolation measures aimed at eradicating methicillin-resistant S. aureus. Low frequencies of resistance among methicillin-resistant S. aureus were found for vancomycin (0%), chloramphenicol (11%), cotrimoxazole (11%), mupirocin (3% low-level resistance) and fusidic acid (7%). Twenty-one percent of the coagulase-negative staphylococci were resistant to methicillin. Low frequencies of resistance among these methicillin-resistant coagulase-negative staphylococci were those to vancomycin (0.4%), nitrofurantoin (2%), doxycycline (20%) and amikacin (20%). Coagulase-negative staphylococci from cerebrospinal fluid, blood and skin were less often resistant to quinolones than isolates from respiratory tract, faeces and urine. A significant increase in resistance of coagulase-negative staphylococci to methicillin, erythromycin, gentamicin and ciprofloxacin was observed in the investigated period but the resistance to doxycycline and co-trimoxazole decreased in the last few years. To confirm the determination of methicillin resistance and coagulase production, a PCR method was developed which detects both the mecA and the coagulase gene. The results of the PCR method correlated well with the methicillin MIC as determined by an agar-dilution method.

Anti-Bacterial Agents↗
PubMed1998

Diagnosis of Mycobacterium microti infections among humans by using novel genetic markers.

As a result of DNA typing of Mycobacterium microti isolates from animals in the United Kingdom and The Netherlands, we diagnosed four human M. microti infections. These are the first M. microti infections among humans to be reported. Three of the patients were immunocompromised and suffered from generalized forms of tuberculosis. The fourth patient was a 34-year-old immunocompetent male with a persistent cough and undefined X-ray abnormalities. Two of the M. microti infections were recognized by their IS6110 restriction fragment length polymorphism (RFLP) patterns, which showed a high degree of similarity with those of M. microti strains isolated from a pig and a ferret in The Netherlands. The two other human M. microti infections were recognized by using the recently developed DNA fingerprinting method, "spoligotyping," directly on clinical material. All M. microti isolates from the United Kingdom and The Netherlands were found to contain an exceptionally short genomic direct repeat region, resulting in identical two-spacer sequence reactions in spoligotyping. In contrast, the highly similar IS6110 RFLP patterns of the vole strains from the United Kingdom differed considerably from the RFLPs of all M. microti strains isolated in The Netherlands, suggesting that geographic isolation led to divergent strains in the United Kingdom and on the continent.

Adult↗