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J D van Embden

Publications and source records attributed to J D van Embden.

At least 37 records · Page 2Linked to original sources
PubMed1998

Simultaneous detection and strain differentiation of Mycobacterium tuberculosis complex in paraffin wax embedded tissues and in stained microscopic preparations.

AIMS: To detect and differentiate Mycobacterium tuberculosis simultaneously by polymerase chain reaction (PCR) in clinical samples prepared for histopathological analysis and for microscopic detection of acid fast bacteria. METHODS: Paraffin wax embedded tissue samples and Ziehl-Neelsen (ZN) and auramine stained microscopic preparations from culture positive tuberculosis patients were subjected to DNA extraction and amplification by PCR. PCR was performed with primers specific for direct repeats and the product was detected by hybridisation to a set of 43 different oligonucleotides, a procedure designated as "spoligotyping". RESULTS: Mycobacterium tuberculosis complex DNA was detected in all of the 23 paraffin wax embedded tissues analysed. Strain differentiation was possible in 20 of the 23 paraffin wax embedded tissues. Mycobacterium tuberculosis complex DNA was also detected and typed in eight of 10 ZN stained microscopic preparations. The hybridisation patterns obtained from virtually all of these samples were identical to those obtained from DNA extracted from cultures. CONCLUSION: Simultaneous detection and strain differentiation of M. tuberculosis complex bacteria is possible in clinical samples prepared by current methods for microscopic and histopathological analysis, without the need to culture. The methodology described opens the way to rapid disclosure of outbreaks in high risk settings, such as hospitals and prisons, where dissemination of tuberculosis might be very fast as a result of a high prevalence of human immunodeficiency virus infected patients.

Bacterial Typing Techniques↗
PubMed1998

Towards a standardized approach to DNA fingerprinting of Mycobacterium bovis. International Union Against Tuberculosis and Lung Disease, Tuberculosis in Animals Subsection.

The Tuberculosis in Animals Subsection of the International Union Against Tuberculosis and Lung Disease (IUATLD) recently identified a need to standardize the deoxyribonucleic acid (DNA) strain typing of Mycobacterium bovis. The standard method for strain typing of M. tuberculosis isolates cannot be directly extrapolated to M. bovis due to the low copy number of IS6110 identified in the majority of M. bovis strains, particularly from cattle. To improve the resolution of M. bovis strains, alternative methods and additional DNA probes have been investigated. In combination with studies of published literature, laboratories performing M. bovis DNA fingerprinting were surveyed. Results of these surveys allowed us to reach consensus and to make recommendations for DNA typing of M. bovis isolates, which hopefully will lead towards a standardized approach to the DNA fingerprinting of this organism. This approach, in conjunction with conventional epidemiological traceback approaches, should facilitate more accurate and effective investigations into the epidemiology, maintenance and transmission of M. bovis within and between man and domesticated, feral and wild animals, both at a local and a global level.

Algorithms↗
PubMed1998

Molecular epidemiology of tuberculosis in Cuba outside of Havana, July 1994-June 1995: utility of spoligotyping versus IS6110 restriction fragment length polymorphism.

SETTING: Molecular typing has become an important tool for examining the extent of active transmission of tuberculosis. OBJECTIVES: To examine transmission of tuberculosis in Cuba using IS6110 restriction fragment length polymorphism (RFLP) typing and to evaluate the utility of spoligotyping. DESIGN: One hundred and sixty Mycobacterium tuberculosis strains isolated over a one year period in Cuba were subjected to RFLP and spoligotyping. RESULTS: Forty-eight percent of the isolates were found in 19 clusters of strains with identical RFLP patterns. In general, cluster sizes were limited, except for two large institutional outbreaks. Age was strongly inversely correlated to clustering. Most streptomycin-resistant isolates were found in clusters. Fifteen spoligotype clusters comprised 78% of the isolates. Significantly different IS6110 RFLP types subdivided 11 spoligotype clusters, whereas none of the IS6110 clusters were subdivided by spoligotyping. CONCLUSIONS: Considering the short study period, 48% clustering is high, indicating that recent transmission plays an important role in Cuba. Although resistance is still a minor problem, transmission of streptomycin-resistant strains occurs. The high polymorphism observed with IS6110 RFLP indicates that this marker is useful for future molecular epidemiological studies in Cuba. Spoligotyping appeared less suitable for population-based studies.

Cluster Analysis↗
PubMed1997

A molecular epidemiological approach to studying the transmission of tuberculosis in Amsterdam.

We conducted a retrospective, population-based study with use of restriction fragment length polymorphism (RFLP) analysis to determine the incidence of and risk factors for clustering of Mycobacterium tuberculosis isolates, indicative of recently transmitted infection, among patients with culture-proven tuberculosis diagnosed between 1 July 1992 and 1 January 1995 in Amsterdam. We found that 214 (47%) of 459 patients were in 53 clusters, probably because of recent transmission of M. tuberculosis among 161 (35%) of these patients. Conventional contact tracing resulted in identification of 5.6% of the 161 patients. Clustering was more frequent among Dutch patients (59.3%) than among foreign ethnic patients (42.1%) (P = .002). The independent risk factor for clustering among Dutch patients was younger age; the independent risk factors among foreign ethnic patients were hard-drug use; alcohol abuse; and country of origin (Surinam or the Netherlands Antilles). These findings suggest the shortcomings of the usual tuberculosis control policies in Amsterdam. We identified several risk factors for clustering, which may guide adjustment of tuberculosis control and contact tracing strategies.

Adult↗
PubMed1997

A novel pathogenic taxon of the Mycobacterium tuberculosis complex, Canetti: characterization of an exceptional isolate from Africa.

In an attempt to characterize an unusual mycobacterial strain isolated from a 2-year-old Somali patient with lymphadenitis, we applied various molecular methods not previously used for the taxonomic classification of mycobacteria. This isolate, designated So93, did not differ from Mycobacterium tuberculosis in the biochemical tests and in its 16S rRNA sequence, but produced smooth and glossy colonies, which is highly exceptional for this species. This smooth phenotype was unstable and switched nonreversibly to a rough colony morphology with a low frequency. The two colony types were equally virulent for the guinea pig, exhibiting characteristic tuberculous disease. Both morphotypes had shorter generation times than the M. tuberculosis reference laboratory strain H37Rv and clinical isolates of M. tuberculosis and Mycobacterium bovis. Furthermore, the So93 isolate differed from all M. tuberculosis complex strains described thus far by having only a single copy of insertion sequence IS1081, an unusual composition of the direct repeat cluster, and a characteristic phenolic glycolipid and lipooligosaccharide. This glycolipid had previously been observed only in a smooth isolate of M. tuberculosis obtained in 1969 by Canetti in France. Analysis of the Canetti strain showed that it shared virtually all genetic properties characteristic of So93, distinguishing these two strains from the known M. tuberculosis complex taxa, M. tuberculosis, Mycobacterium africanum, M. bovis, and Mycobacterium microti. The natural reservoir, host range, and mode of transmission of the group of bacteria described in this paper are presently unknown. This study, partly based on not previously used molecular criteria, supports the idea that the established members within the M. tuberculosis complex and the newly described Canetti grouping should be regarded as a single species, which likely will be designated "M. tuberculosis".

Animals↗
PubMed1997

Identification by spoligotyping of a caprine genotype in Mycobacterium bovis strains causing human tuberculosis.

We have used spoligotyping to characterize 18 Mycobacterium bovis strains isolated from cattle and 23 M. bovis strains isolated from goats. The spoligotypes revealed that caprine strains form a separate and well-differentiated group that we refer to hereafter in this abstract as the caprine genotype. To evaluate the importance of this genotype as a cause of tuberculosis in other animal species, including humans, we applied the spoligotyping method to 112 strains, including to all isolates identified as M. bovis by a Mycobacterial National Reference Laboratory (Majadahonda, Madrid) from 1994 to 1996. Eighty-three of these strains were identified in human isolates. In addition to being identified in three goat isolates and two sheep isolates, the caprine genotype was also found in three isolates causing human tuberculosis. Evidence to support the argument that there is a zoonotic risk of caprine tuberculosis was presented by the identification of the caprine genotype in an isolate from a veterinary worker with a recent history of contact with tuberculous goats.

Animals↗
PubMed1997

Differentiation of Mycobacterium tuberculosis isolates by spoligotyping and IS6110 restriction fragment length polymorphism.

Mycobacterium tuberculosis isolates from 167 patients attending three London hospitals were analyzed by two techniques for strain differentiation. A significant number of isolates that appeared identical with the recently developed spoligotyping system could be distinguished from each other by IS6110 restriction fragment length polymorphism analysis, with the latter technique demonstrating a generally higher level of discrimination. Spoligotyping, on the other hand, was particularly useful for analysis of isolates with low IS6110 copy numbers, and use of the two techniques in tandem provided an optimal approach to the identification of clusters with epidemiological evidence consistent with recent transmission. Spoligotyping can be applied directly to clinical samples by PCR and provides an important tool for the rapid detection of nosocomial transmission of individual strains.

Adolescent↗
PubMed1996

[Transmission of sensitive and resistant strains of Mycobacterium tuberculosis in The Netherlands, 1993-1995, studied by means of DNA fingerprinting].

OBJECTIVE: Determination of the contribution of recent transmission of both sensitive and drug-resistant Mycobacterium tuberculosis strains to the number of tuberculosis cases in the Netherlands. DESIGN: Descriptive study. SETTING: National Institute for Public Health and Environment, Bilthoven, the Netherlands. METHODS: Since 1993 all isolates of M. tuberculosis in the Netherlands are sent to the national reference laboratory for surveillance purposes. The strains with IS6110 DNA fingerprint, isolated from January 1993 to July 1995, were analysed for clustering of DNA patterns (clustering of identical DNA patterns was assumed to represent recent transmission of tuberculosis). A transmission index was calculated from the ratio of the number recently infected tuberculosis patients and the number of source patients. RESULTS: Among 2,217 M. tuberculosis isolates, 1,313 unique DNA fingerprints were observed, while 264 DNA patterns occurred more than once. 904 (41%) DNA fingerprints were part of a cluster of identical fingerprints. The mean cluster size was 3.42. The 232 resistant strains showed significantly less clustering (33% versus 42%, p < 0.02) and a smaller transmission index (0.27 versus 0.42, p < 0.02) compared with sensitive strains. CONCLUSION: Recent transmission contributes to the magnitude of the tuberculosis problem in the Netherlands. The epidemiological situation would, however, lead to gradual elimination of the disease were it not for introduction of tuberculosis from other countries. Transmission of resistant strains is relatively limited. Micro-epidemics caused by resistant M. tuberculosis strains were not observed.

DNA Fingerprinting↗
PubMed1996

Characterization of the catalase-peroxidase gene (katG) and inhA locus in isoniazid-resistant and -susceptible strains of Mycobacterium tuberculosis by automated DNA sequencing: restricted array of mutations associated with drug resistance.

The catalase-peroxidase gene (katG) and a two-gene locus (inhA) containing mutations associated with resistance to isoniazid in Mycobacterium tuberculosis were sequenced in 34 resistant and 12 susceptible strains. Virtually all resistant organisms had amino acid changes in KatG or nucleotide substitutions upstream of inhA. A region of katG encoding two amino acids frequently altered in resistant strains (residues Ser315 and Arg463) and the inhA locus were sequenced in 10 susceptible and 51 isoniazid-resistant isolates from the Netherlands. Most (84%) of the resistant isolates had mutations in katG or the inhA locus or lacked katG. Together, approximately 75% of isoniazid-resistant isolates had replacements at amino acids 315 or 463 in KatG or nucleotide substitutions upstream of inhA. All 16 strains of Mycobacterium bovis and Mycobacterium microti studied had Leu463 rather than Arg463 in KatG, an observation consistent with the hypothesis that Leu463 is the ancestral condition in M. tuberculosis.

Amino Acid Sequence↗
PubMed1996

Host-mediated modification of PvuII restriction in Mycobacterium tuberculosis.

Restriction endonuclease PvuII plays a central role in restriction fragment length polymorphism analysis of Mycobacterium tuberculosis complex isolates with IS6110 as a genetic marker. We have investigated the basis for an apparent dichotomy in PvuII restriction fragment pattersn observed among strains of the M. tuberculosis complex. The chromosomal regions of two modified PvuII restriction sites, located upstream of the katG gene and downstream of an IS1081 insertion sequence, were studied in more detail. An identical 10-bp DNA sequence (CAGCTGGAGC) containing a PvuII site was found in both regions, and site-directed mutagenesis analysis revealed that this sequence was a target for modification. Strain-specific modification of PvuII sites was identified in DNA from over 80% of the nearly 800 isolates examined. Furthermore, the proportion of modifying and nonmodifying strains differs significantly from country to country.

Bacterial Proteins↗
PubMed1996

Reliability of nucleic acid amplification for detection of Mycobacterium tuberculosis: an international collaborative quality control study among 30 laboratories.

Nucleic acid amplification to detect Mycobacterium tuberculosis in clinical specimens is increasingly used as a laboratory tool for the diagnosis of tuberculosis. However, the specificity and sensitivity of these tests may be questioned, and no standardized reagents for quality control assessment are available. To estimate the performance of amplification tests for routine diagnosis, we initiated an interlaboratory study involving 30 laboratories in 18 countries. We prepared blinded panels of 20 sputum samples containing no, 100, or 1,000 mycobacterial cells. Each laboratory was asked to detect M. tuberculosis by their routine method of nucleic acid amplification. Only five laboratories correctly identified the presence or absence of mycobacterial DNA in all 20 samples. Seven laboratories detected mycobacterial DNA in all positive samples, and 13 laboratories correctly reported the absence of DNA in the negative samples. Lack of specificity was more of a problem than lack of sensitivity. Reliability was not found to be associated with the use of any particular method. Reliable detection of M. tuberculosis in clinical samples by nucleic acid amplification techniques is possible, but many laboratories do not use adequate quality controls. This study underlines the need for good laboratory practice and reference reagents to monitor the performance of the whole assay, including pretreatment of clinical samples.

Bacterial Typing Techniques↗
PubMed1996

Predominance of two Bartonella henselae variants among cat-scratch disease patients in the Netherlands.

Restriction endonuclease analysis of the PCR-amplified 16S-23S rRNA gene spacer region was used to investigate the prevalence of Bartonella henselae variants in samples from cat-scratch disease (CSD) patients. Analysis of spacer PCR fragments from 27 Bartonella DNA-positive samples from Dutch patients with CSD with AluI revealed two restriction fragment length polymorphism (RFLP) patterns, patterns A and B. Twenty samples yielded B. henselae pattern A, and 7 samples yielded B. henselae pattern B. Three samples from North American patients with CSD were shown to contain B. henselae with RFLP pattern B. To be able to detect and differentiate Bartonella DNA in clinical material more sensitively and faster, two B. henselae PCRs which amplify part of the 16S rRNA gene and which can discriminate between two B. henselae variants were developed. Thirty-two of 41 Bartonella DNA-positive samples from Dutch patients with CSD contained type I B. henselae, 7 samples contained type II B. henselae, and two samples were negative in both type-specific PCRs. Two samples from North American patients with CSD both contained type II B. henselae. A 100% correlation was found between the AluI spacer RFLP pattern and the 16S rRNA PCR type. We have shown that Dutch patients with CSD contain a limited number of B. henselae variants, suggesting that, in contrast to systemic bartonellosis, CSD in immunocompetent patients is caused by a limited number of B. henselae variants.

Bartonella henselae↗
PubMed1996

Identification of a polymorphic nucleotide in oxyR specific for Mycobacterium bovis.

Automated sequence analysis of a 410-bp region of the axyR gene in 105 Mycobacterium tuberculosis complex isolates identified a polymorphic nucleotide that differentiated Mycobacterium bovis isolates from other complex members. All 29 M. bovis isolates sequenced had an adenine residue at nucleotide 285, whereas all 76 other complex isolates had a guanine residue. PCR-restriction fragment length polymorphism analysis of oxyR with restriction endonuclease AluI in an additional 255 complex isolates from widespread intercontinental sources confirmed and extended the unique association of adenine at position 285 with M. bovis isolates.

Adenosine↗
PubMed1995

Etiology of cat scratch disease: comparison of polymerase chain reaction detection of Bartonella (formerly Rochalimaea) and Afipia felis DNA with serology and skin tests.

To determine the role of Bartonella (formerly Rochalimaea) species and Afipia felis in cat scratch disease (CSD), two polymerase chain reaction (PCR) hybridization assays were developed to detect DNA from these organisms. These assays were applied on 89 pus aspirates from skin test-positive CSD patients (group 1) and on 137 pus and lymph node specimens from CSD suspects (group 2). Bartonella DNA was detected in 96% of the samples from group 1 patients and in 60% of group 2 samples; however, A. felis DNA could not be detected in any clinical samples. These results suggest that CSD is caused by bartonellae and that A. felis does not play a significant role in this zoonosis. A strong correlation between Bartonella PCR positivity and Bartonella henselae antibody titer was found. Comparison of CSD skin test results with those obtained by Bartonella PCR suggests a low sensitivity of the skin test.

Amino Acid Sequence↗
PubMed1995

Predominance of a single genotype of Mycobacterium tuberculosis in countries of east Asia.

Analysis of the population structure of Mycobacterium tuberculosis strains from the People's Republic of China showed that the vast majority belong to a genetically closely related group. These strains shared the majority of their IS6110 DNA-containing restriction fragments, and also, the DNA polymorphism associated with other repetitive DNA elements, like the polymorphic GC-rich sequence and the direct repeat, was very limited. Because the majority of these strains originated from the province of Beijing, we designated this grouping the "Beijing family" of M. tuberculosis strains. Strains of this family were also found to dominate in neighboring countries such as Mongolia, South Korea, and Thailand, whereas a low prevalence of such strains was observed in countries on other continents. These data indicate that strains of the Beijing family recently expanded from a single ancestor which had a selective advantage. It is speculated that long-term Mycobacterium bovis BCG vaccination may be one of the selective forces implicated in the successful spread of the Beijing genotype.

China↗
PubMed1995

DNA fingerprinting and phenotyping of Mycobacterium tuberculosis isolates from human immunodeficiency virus (HIV)-seropositive and HIV-seronegative patients in Tanzania.

With the purpose of determining whether the risk of infection with a particular clone of Mycobacterium tuberculosis is influenced by the human immunodeficiency virus (HIV) status of the host, we analyzed and compared 68 mycobacterial isolates obtained from HIV-seropositive patients with tuberculosis (TB) in Dar es Salaam, Tanzania, with 66 mycobacterial isolates obtained from HIV-seronegative patients with TB in the same geographical region by using both DNA fingerprinting and classical phenotyping methods. One hundred one different IS6110 fingerprinting patterns were observed in the 134 isolates. The level of diversity of the DNA fingerprints observed in the HIV-seropositive group was comparable to the level of the diversity observed in the HIV-seronegative group. Resistance to a single anti-TB drug was found in 8.8% of the tested isolates, and 3.2% of the isolates were resistant to more than one anti-TB drug. The drug susceptibility profiles were not significantly difference between the two groups of isolates compared in the present study. Phenotypic characteristics which classify M. tuberculosis strains as belonging to the Asian subgroup correlated with a low IS6110 copy number per isolate. However, the occurrence of Asian subgroup strains was not associated with the HIV status of the patients. The results of the study suggested an equal risk of infection with a defined M. tuberculosis clone for HIV-seropositive and HIV-seronegative individuals.

AIDS-Related Opportunistic Infections↗