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J H Hauman

Publications and source records attributed to J H Hauman.

8 recordsLinked to original sources
PubMed2001

Molecular evolution of Mycobacterium tuberculosis: phylogenetic reconstruction of clonal expansion.

SETTING: M. tuberculosis isolates were collected from patients attending health clinics in a high incidence urban community and in a low incidence rural setting in South Africa. OBJECTIVE: To reconstruct the evolutionary history of a group of closely related M. tuberculosis isolates using IS6110, DRr and MTB484(1) restriction fragment length polymorphism (RFLP) data. DESIGN: Mycobacterium tuberculosis isolates containing an average of ten IS6110 elements, with a similarity index of > or = 65% were genotypically classified by DNA fingerprinting using the IS6110 derived probes IS-3' and IS-5', as well as the DRr and MTB484(1) probes, in combination with PvuII or Hinfl endonuclease digestion. These RFLP data were subjected to phylogenetic analysis using both genetic distance and parsimony algorithms. RESULTS: Phylogenetic analysis predicted the existence of two independently evolving lineages, possibly evolving from a common ancestral strain. The topology of the phylogenetic tree was supported by comprehensive bootstrapping and the specific partitioning of DNA methylation phenotypes. The observed difference in the branch lengths of the two lineages may suggest differential evolutionary rates. Isolates collected from different geographical regions demonstrate independent evolution, suggesting that it is highly unlikely that strains have been recently transmitted between the two regions. The number of evolutionary events identified in this strain family differs significantly from that of previously characterized strain families, implying that evolutionary rate may be strain family dependent. CONCLUSION: Based on this analysis we propose that the algorithm used to calculate recent epidemiological events should be revised to incorporate the evolutionary characteristics of individual strain families, thereby enhancing the accuracy of molecular epidemiological calculations.

Algorithms↗
PubMed1999

Rapid genomic diversification of Helicobacter pylori.

Helicobacter pylori was cultured from antrum and corpus gastric biopsies from 65 patients originating from two separate groups: (i) a geographically linked group and (ii) a geographically nonlinked group. Genomic DNA was recovered from the clinical isolates and subjected to restriction fragment length polymorphism (RFLP) analysis after digestion with DraI. Southern blots were probed with the oligonucleotide (GTG)5, the riboprobe pKK3535, and the cagA gene probe pMC3. (GTG)5 and cagA DNA fingerprints and ribopatterns suggested that most of the patients were infected with their own unique strain; however, some were infected with multiple strains. Minor genomic differences were detected in many antrum/corpus sample pairs (clonal variants), suggesting rapid evolutionary change in domains detected by (GTG)5. The high degree of genomic diversity detected by (GTG)5 may reflect structural versatility of these domains. The genomic diversity indicates that infection by H. pylori in a defined community does not appear to be limited to certain RFLP types.

Adolescent↗
PubMed1999

Impact of social interactions in the community on the transmission of tuberculosis in a high incidence area.

BACKGROUND: Tuberculosis (TB) is transmitted by close contact with an infectious person. It is assumed that close contact occurs amongst household members and that contact outside the house is "causal" and does not play a major role in the transmission of TB. METHODS: This study was conducted in an impoverished area with a high incidence of TB and a low HIV seropositive prevalence. Thirty three households with 84 TB patients were identified between February 1993 and April 1996 and the transmission of TB was studied by combining Mycobacterium tuberculosis fingerprinting with in depth sociological interviews. RESULTS: Forty two strain genotypes were identified in the 84 patients. In 15 households all the patients had identical strains, in nine households all the patients had different strains, and in nine households some patients had identical strains and one had a different strain. In 26 houses at least one patient had a strain which formed part of a larger community cluster and in 12 of these households the patient(s) had contact with a community member who had the identical strain. In 58% of the cases the contact took place while drinking in social groups. CONCLUSION: In high incidence areas contact outside the household may be important for the transmission of TB. This contact often takes place during recreation which, in the case of this study of impoverished people, consisted of drinking in social groups. Social interaction patterns should be studied and understood for effective implementation of control strategies.

Disease Transmission, Infectious↗
PubMed1997

Oligonucleotide (GTG)5 as an epidemiological tool in the study of nontuberculous mycobacteria.

Analysis of restriction fragment length polymorphisms in the genome of Mycobacterium tuberculosis (DNA fingerprinting) has proved to be a useful epidemiological tool in the study of tuberculosis within populations or communities. However, to date, no similar method has been developed to study the epidemiology of nontuberculous mycobacteria (NTM). In this communication, we report that a simple oligonucleotide repeat, (GTG)5, can be used to accurately genotype all species and strains of NTM tested. We suggest that this technology is an easily applied and accurate tool which can be used for the study of the epidemiology of NTM.

DNA Fingerprinting↗
PubMed1996

Genotyping of Mycobacterium tuberculosis with additional markers enhances accuracy in epidemiological studies.

Two highly polymorphic Mycobacterium tuberculosis genomic domains, characterized by hybridization to the oligonucleotide (GTG)5, were identified as potential DNA fingerprinting probes. These domains were cloned [pMTB484(1) and pMTB484(2K4), respectively] and shown to be useful for genotype analysis by Southern blotting. These probes were used to genotype geographically linked strains of M. tuberculosis previously shown to have identical IS6110 fingerprints. Subsequent DNA fingerprints generated with MTB484(1) and MTB484(2K4) showed a high degree of polymorphism, allowing subclassification of IS6110-defined clusters into composites of smaller clusters and unique strains. Correlation of the molecular data with patient interviews and clinical records confirmed the sensitivity of these probes, as contacts were established only within subclusters. These findings demonstrate the requirement for multiple probes to accurately classify M. tuberculosis strains, even those with high copy numbers of IS6110. The enhanced accuracy of strain typing should, in turn, further our understanding of the epidemiology of tuberculosis.

Bacterial Typing Techniques↗
PubMed1982

Plasmid R394 is a cointegrate.

Plasmids R394a and R394b which cointegrate to form R394 are described. They have molecular masses of 102 +/- 4 and 11.0 +/- 0.4 MDal, belong to the T and N incompatibility groups and confer resistance to kanamycin and ampicillin, respectively. R394a is self transmissible and mobilizes R394b, which is non-self transmissible. These findings clarify anomalies in the behaviour of R394 and support suggestions based on the properties of variant phages derived from R394.

Conjugation, Genetic↗