Biomedical subjects

N H Smith

Publications and source records attributed to N H Smith.

At least 19 recordsLinked to original sources

PubMed1998

Free recombination within Helicobacter pylori.

Sequences of three gene fragments (flaA, flaB, and vacA) from Helicobacter pylori strains isolated from patients in Germany, Canada, and South Africa were analyzed for diversity and for linkage equilibrium by using the Homoplasy Test and compatibility matrices. Horizontal genetic exchange in H. pylori is so frequent that different loci and polymorphisms within each locus are all at linkage equilibrium. These results indicate that H. pylori is panmictic. Comparisons with sequences from Escherichia coli, Neisseria meningitidis, and Drosophila melanogaster showed that recombination in H. pylori was much more frequent than in other species. In contrast, when multiple family members infected with H. pylori were investigated, some strains were indistinguishable at all three loci. Thus, H. pylori is clonal over short time periods after natural transmission.

Alleles↗

PubMed1998

Combination drug therapy for cryptosporidiosis in AIDS.

Aside from effective antiretroviral therapy, there is no consistently effective antiparasitic therapy for cryptosporidiosis in AIDS. The purpose of this study was to assess safety, efficacy, and durability of combination therapy with paromomycin and azithromycin for chronic cryptosporidiosis. Patients with AIDS, chronic cryptosporidiosis, and < 100 CD4 cells/microL were treated with open-label paromomycin (1.0 g twice a day) plus azithromycin (600 mg once a day) for 4 weeks, followed by paromomycin alone for 8 weeks. In 11 patients, median stool frequency decreased from 6.5/day (baseline) to 4.9/day (week 4) and 3.0/day (week 12). Median reductions in 24-h oocyst excretion were 84%, 95%, and >99% at 2, 4, and 12 weeks, respectively. None of the responses were attributable to antiretrovirals. Of 5 survivors at 12-30 months of follow-up, 3 remain asymptomatic off medications, and 2 have chronic, mild diarrhea. Treatment of cryptosporidiosis with azithromycin and paromomycin was associated with significant reduction in oocyst excretion and some clinical improvement.

AIDS-Related Opportunistic Infections↗

PubMed1998

Detecting recombination from gene trees.

In this article, a method is proposed for detecting recombination in the sequences of a gene from a set of closely related organisms. The method, the Homoplasy Test, is appropriate when the sequences are rather similar, differing by 1%-5% of nucleotides. It is effective in detecting relatively frequent recombination between a set of rather similar strains, in contrast to previous methods which detect rare or unique transfers between more distant strains. It is based on the fact that, if there is no recombination and if no repeated mutations have occurred (homoplasy), then the number of polymorphic sites, v, is equal to the number of steps, t, in a most-parsimonious tree. If the number of "apparent homoplasies" in the most-parsimonious tree, h = t-v, is greater than zero, then either homoplasies have occurred by mutation or there has been recombination. An estimate of the distribution of h expected on the null hypothesis of no recombination depends on Se, the "effective site number," defined as follows: if ps is the probability that two independent substitutions in the gene occur at the same site, then Se = 1/ps. Se can be estimated if a suitable outgroup is available. The Homoplasy Test is applied to three bacterial genes and to simulated gene trees with varying amounts of recombination. Methods of estimating the rate, as opposed to the occurrence, of recombination are discussed.

Borrelia↗

PubMed1998

Middle cerebral artery vasculitis and stroke after varicella in a young adult.

Varicella-zoster virus infection has been implicated in a broad range of neurologic complications. In Hispanic immigrants, primary varicella often appears in adolescents and young adults. We describe the case of a 20-year-old Hispanic man with vasculitis and stroke after primary varicella infection. An association between varicella infection and vasculitis is increasingly being described and should be considered in the evaluation of stroke in young adults.

Adult↗

PubMed1997

Cryptosporidiosis in Houston, Texas. A report of 95 cases.

Cryptosporidiosis is an important cause of diarrhea. We identified 95 patients with cryptosporidiosis over a 6-year period in our county hospital system, including 9 children and 86 adults infected with the human immunodeficiency virus (HIV). Risk factors included male-to-male sexual practices and Hispanic race. Diarrhea, weight loss, and gastrointestinal complaints were the most common symptoms at presentation. Among the HIV-infected adults, 20 (23%) developed biliary tract disease. Biliary involvement was associated with low CD4 counts. Treatment with paromomycin and antimotility agents was effective in reducing diarrheal symptoms in 54 of 70 (77%) patients with the acquired immunodeficiency syndrome (AIDS), although there was a high rate of relapse. Paromomycin did not prevent the development of biliary disease. Biliary disease responded to cholecystectomy or sphincterotomy with stent placement. Though often a cause of morbidity, cryptosporidiosis was only rarely the cause of death, even among patients with HIV. Cryptosporidiosis continues to be an important medical problem even in developed-countries. Current methods of prevention and treatment are suboptimal.

AIDS-Related Opportunistic Infections↗

PubMed1997

Epidemiology of human immunodeficiency virus infection in Central Americans treated in Harris County, Texas Hospital District facilities.

The prevalence of human immunodeficiency virus (HIV) infection among Central Americans is increasing. The purpose of this study was to describe the epidemiology of HIV infection among local Central American immigrants in the United States. Medical records of HIV-infected Central Americans treated at Harris County Hospital District (HCHD) facilities, the major source of indigent care in Houston, Texas, were retrospectively reviewed. Between January 1, 1990 and February 28, 1995, 18,156 Central Americans were seen at HCHD facilities, of whom 56 (13 females and 43 males) were identified as HIV-infected (0.3% versus 1.3% of all locally treated patients; P < 0.001, by test of binomial proportions). Most were from Honduras (n = 25) or El Salvador (n = 23). The mean age was 28.7 years, the mean CD4+ lymphocyte count at presentation was 173 cells/mm3, and 36 (64%) had acquired immunodeficiency syndrome (AIDS) at presentation. The 13 women (23% versus 22% for all locally treated HIV patients) were disproportionately Honduran (10 of 25 Hondurans versus 3 of 31 other Central Americans; P = 0.011). The HIV risk factors included heterosexuality in 46%, homosexuality in 29%. and a history of injection drug use in 7% (versus 10%, 57%, and 34%, respectively, for all locally treated HIV patients). The 76 diagnosed opportunistic infections (OIs) included a disproportionately greater number of patients with tuberculosis (n = 14, 33% versus 6% of all locally treated AIDS patients), toxoplasmosis (n = 10, 24% versus 7%), and cryptococcal meningitis (n = 9, 21% versus 7%), and a lower number of patients with pneumocystosis (n = 12, 29% versus 43%) and candida esophagitis (n = 2, 5% versus 16%). Central American immigrants infected with HIV present with relatively advanced disease, and the most frequent OIs are diseases for which effective prophylaxis exists. Targeted HIV screening and early intervention in this group are warranted.

AIDS-Related Opportunistic Infections↗

PubMed1996

Synonymous nucleotide divergence: what is "saturation"?

The nucleotide divergence at synonymous third sites between two lineages will increase with time since the latest common ancestor, up to some saturation level. The "null-hypothesis divergence" is defined as the percentage of difference predicted at synonymous third sites, allowing for amino acid composition and codon bias, but assuming that codon bias is the same at all sites occupied by a given amino acid, when equilibrium has been reached between forward and backward substitutions. For two highly expressed genes, gapA and ompA, in the enterobacteria, the estimated values of the null-hypothesis divergence are 39.3 and 38.15%, respectively, compared to estimated values of saturation divergence of 19.0 and 25.4%. A possible explanation for this discrepancy is that different codons for a given amino acid are favored at different sites in the same gene.

Codon↗

PubMed1996

Site-specific codon bias in bacteria.

Sequences of the gapA and ompA genes from 10 genera of enterobacteria have been analyzed. There is strong bias in codon usage, but different synonymous codons are preferred at different sites in the same gene. Site-specific preference for unfavored codons is not confined to the first 100 codons and is usually manifest between two codons utilizing the same tRNA. Statistical analyses, based on conclusions reached in an accompanying paper, show that the use of an unfavored codon at a given site in different genera is not due to common descent and must therefore be caused either by sequence-specific mutation or sequence-specific selection. Reasons are given for thinking that sequence-specific mutation cannot be responsible. We are unable to explain the preference between synonymous codons ending in C or T, but synonymous choice between A and G at third sites is largely explained by avoidance of AG-G (where the hyphen indicates the boundary between codons). We also observed that the preferred codon for proline in Enterobacter cloacea has changed from CCG to CCA.

Bacterial Outer Membrane Proteins↗

PubMed1996

Risk factors for HIV in pregnant women.

Worldwide, the number of childbearing women infected with the human immunodeficiency virus (HIV) is rising. Early intervention can improve care for these women and reduce HIV transmission to their children. However, for intervention strategies to be effective, childbearing women at risk must be identified. HIV prevalence and risk factors vary widely from one region to another, and strategies for HIV testing must be tailored to local conditions. In this review, published data on HIV risk factors in pregnant women are presented by region, and implications for regional strategies for HIV testing in pregnant women are discussed.

Africa↗

PubMed1995

Sequence evolution of the porB gene of Neisseria gonorrhoeae and Neisseria meningitidis: evidence of positive Darwinian selection.

Protein 1 (PI) is a major porin of Neisseria gonorrhoeae and Neisseria meningitidis and is encoded by a single locus, porB. Alleles of the porB locus of N. gonorrhoeae are assigned to two homology groups, PI(A) and PI(B), on the basis of immunological and structural similarity. In a like manner, alleles of the porB locus of the closely related bacterium, N. meningitidis, are allocated into class 2 and class 3 homology groups. An individual strain of N. gonorrhoeae or N. meningitidis expresses either one or other of these porin homology groups but never both, and the antigenic reactions of these highly diverse outer membrane proteins form part of the N. gonorrhoeae and N. meningitidis serotyping schemes. A comparison of the number of synonymous and nonsynonymous substitutions per site between the two most divergent alleles of each of these four groups of porB alleles shows that PI(A) alleles have accumulated significantly more nonsynonymous substitutions per site than synonymous substitutions. In contrast the distribution of synonymous and nonsynonymous substitutions between alleles of class 2 and class 3 porins are not significantly different from random. We localize the regions of the PI(A) alleles with an excess of amino acid changes to the surface-exposed loops of these outer membrane proteins and suggest that positive Darwinian selection for diversity, driven by the human immune system, can most easily explain the allelic polymorphism and the pattern of synonymous and nonsynonymous substitutions.

Alleles↗

PubMed1995

Interspecies recombination in nature: a meningococcus that has acquired a gonococcal PIB porin.

A vaginal isolate of Neisseria has been reported to resemble Neisseria meningitidis in biochemical characteristics but to react with serological reagents that are specific to the PI porin from Neisseria gonorrhoeae. We have confirmed that this isolate has the biochemical attributes of a meningococcus and have shown that it clusters among meningococcal isolates on a dendrogram based on isoenzyme variation within housekeeping enzymes from populations of N. meningitidis and N. gonorrhoeae. Furthermore, the sequences of the fbp and adk genes were typical of those of N. meningitidis and were distinct from those of N. gonorrhoeae. However, the porB gene was very similar to the por genes of N. gonorrhoeae isolates that express the PIB class of outer-membrane porin (differing from one gonococcal por allele at only a single nucleotide site), and was clearly distinct from the porB genes of N. meningitidis. The isolate therefore appears to be a typical meningococcus, except that its porB gene has been replaced with the por gene from a gonococcus.

Adenylate Kinase↗

PubMed1993

How clonal are bacteria?

Data from multilocus enzyme electrophoresis of bacterial populations were analyzed using a statistical test designed to detect associations between genes at different loci. Some species (e.g., Salmonella) were found to be clonal at all levels of analysis. At the other extreme, Neisseria gonorrhoeae is panmictic, with random association between loci. Two intermediate types of population structure were also found. Neisseria meningitidis displays what we have called an "epidemic" structure. There is significant association between loci, but this arises only because of the recent, explosive, increase in particular electrophoretic types; when this effect is eliminated the population is found to be effectively panmictic. In contrast, linkage disequilibrium in a population of Rhizobium meliloti exists because the sample consisted of two genetically isolated divisions, often fixed for different alleles: within each division association between loci was almost random. The method of analysis is appropriate whenever there is doubt about the extent of genetic recombination between members of a population. To illustrate this we analyzed data on protozoan parasites and again found panmictic, epidemic, and clonal population structures.

Animals↗

PubMed1993

Evolutionary origin and radiation of the avian-adapted non-motile salmonellae.

Multilocus enzyme electrophoresis was employed to estimate chromosomal genotypic diversity and relationships among 131 isolates of the non-motile Salmonella biotypes Gallinarum and Pullorum (serotype 1, 9, 12:-:-) that cause fowl typhoid and pullorum disease, respectively. Thirteen electrophoretic types (ETs), marking clones, were distinguished, and construction of a neighbour-joining phylogenetic tree revealed three lineages: one consisted of five ETs of Gallinarum, a second included seven ETs of Pullorum, and a third was represented by a single ET (Ga/Pu 1) that is intermediate between those of the other two lineages in both multilocus enzyme genotype and biochemical properties. Enzyme genotype analysis and comparative nucleotide sequencing of the phase 1 flagellin gene (fliC), the hook-associated protein 1 gene (flgK), and the 6-phosphogluconate dehydrogenase gene (gnd) identified serotype Enteritidis (1, 9, 12:g, m:-) as a close relative of the non-motile salmonellae. In most strains of biotype Gallinarum, the fliC gene is complete, intact and identical in sequence to that of Enteritidis, but isolates of three ETs had a stop codon at position 495. The fliC sequences of the ETs of Pullorum differed from that of Enteritidis in having non-synonymous changes in either two or three codons and a synonymous change in one codon. The sharing of distinctive alleles at three metabolic enzyme loci and a stop codon in flgK indicates that the non-motile salmonellae are monophyletic and that their most recent common ancestor was non-motile. Since diverging from that ancestor, the Pullorum lineage has evolved more rapidly than the Gallinarum and Ga/Pu 1 lineages.

Animals↗

PubMed1992

Molecular evolutionary genetics of the cattle-adapted serovar Salmonella dublin.

An electrophoretic analysis of allelic variation at 24 enzyme loci among 170 isolates of the serovar Salmonella dublin (serotype 1,9,12[Vi]:g,p:-) identified three electrophoretic types (Du 1, Du 3, and Du 4), marking three closely related clones, one of which (Du 1) is globally distributed and was represented by 95% of the randomly selected isolates. All but 1 of 114 nonmotile isolates of serotype 1,9,12:-:- recovered from cattle and swine in the United States were genotypically Du 1. The virulence capsular polysaccharide (Vi antigen) is confined to clone Du 3, which apparently is limited in distribution to France and Great Britain. For all 29 isolates of Du 3, positive signals were detected when genomic DNA was hybridized with a probe specific for the ViaB region, which contains the structurally determinant genes for the Vi antigen; and 23 of these isolates had been serologically typed as Vi positive. In contrast, all 30 isolates of Du 1 tested with the ViaB probe were negative. These findings strongly suggest that the ViaB genes were recently acquired by S. dublin via horizontal transfer and additive recombination. The clones of S. dublin are closely similar to the globally predominant clone (En 1) of Salmonella enteritidis (serotype 1,9,12:g,m:-) in both multilocus enzyme genotype and nucleotide sequence of the fliC gene encoding phase 1 flagellin. Comparative sequencing of fliC has revealed the molecular genetic basis for expression of the p and m flagellar epitopes by which these serovars are distinguished in the Kauffmann-White serological scheme of classification.

Alleles↗

PubMed1991

Molecular genetic basis for complex flagellar antigen expression in a triphasic serovar of Salmonella.

Strains of most Salmonella serovars produce either one (monophasic) or two (diphasic) antigenic forms of flagellin protein, but strains capable of expressing three or more serologically distinct flagellins ("complex" serovars) have occasionally been reported. A molecular genetic analysis of a triphasic strain of the normally diphasic serovar Salmonella rubislaw revealed that it has three flagellin genes, including the normal fliC (phase 1) and fljB (phase 2) chromosomal genes encoding type r and type e,n,x flagellins, respectively, and a third locus (herein designated as flpA) that is located on a large plasmid (pRKS01) and codes for a type d flagellin. The coding sequence of the plasmid-borne gene is similar to that of a phase 1 chromosomal gene, but the sequence of its promoter region is homologous to that of a phase 2 chromosomal gene. The irreversible loss of the ability to express a type d flagellin that occurs when the triphasic strain is grown in the presence of d antiserum is caused by deletion of part or all of the flpA gene. Thus, the molecular basis for the unusual serological reactions of the triphasic strain of S. rubislaw and, by inference, other complex serovars of Salmonella is explained. Plasmids of the type carried by the triphasic strain of S. rubislaw provide a mechanism for the generation of new serovars through the lateral transfer and recombination of flagellin genes.

Base Sequence↗

PubMed1991

Reference collection of strains of the Salmonella typhimurium complex from natural populations.

A collection of 72 reference strains of the Salmonella typhimurium complex of clones recovered from a variety of hosts and environmental sources in diverse geographic locations has been established for use in studies of variation in natural populations. Included are strains of the serovars S. typhimurium, S. saintpaul, S. heidelberg, S. paratyphi B (including variety java) and S. muenchen. The strains, which have been characterized by enzyme electrophoresis for allelic variation in 24 chromosomal structural genes and represent 48 distinctive multilocus genotypes (electrophoretic types or ETs), exemplify the full range of genotypic variation in the S. typhimurium complex. Evolutionary genetic relationships among the ETs are indicated in a phylogenetic tree generated by the neighbour-joining method from a matrix of Nei's standard genetic distance.

Alleles↗

PubMed1990

Genetic structure of natural populations of the nitrogen-fixing bacterium Rhizobium meliloti.

The genetic structure of populations of the symbiotic nitrogen-fixing soil bacterium Rhizobium meliloti was examined by analysis of electrophoretically demonstrable allelic variation in 14 metabolic, presumably chromosomal, enzyme genes. A total of 232 strains were examined, most of which were isolated from southwest Asia, where there is an unsurpassed number of indigenous host species for R. meliloti. The collection consisted of 115 isolates recovered from annual species of Medicago in Syria, Turkey, and Jordan; 85 isolates cultured from two perennial species of Medicago (M. sativa [alfalfa] and M. falcata) in northern Pakistan and Nepal; and 32 isolates collected at various localities in North and South America, Europe, South Africa, New Zealand, and Australia, largely from M. sativa. Fifty distinctive multilocus genotypes (electrophoretic types [ETs]) were identified, and cluster analysis revealed two primary phylogenetic divisions separated at a genetic distance of 0.83. By the criterion of genetic differentiation conventionally applied in defining species limits among members of the family Enterobacteriaceae and certain other bacteria, the two primary divisions of R. meliloti represent distinct evolutionary species. Division A included 35 ETs represented by 209 strains from the eastern Mediterranean basin, northern Pakistan, Nepal, and various other localities worldwide. This division contained the nine commercial alfalfa inoculant strains examined. Division B included 15 ETs represented by 23 isolates, 21 of which were isolated from annual medic species growing in previously uninoculated soils in the eastern Mediterranean basin. The two remaining strains in division B, both representing the same ET, were isolated in the United States and Australia.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗

PubMed1990

Genetic population structure, clonal phylogeny, and pathogenicity of Salmonella paratyphi B.

Genetic diversity and relationships among 123 strains of Salmonella paratyphi B (serotype 1,4,[5],12:b:[1,2]) were estimated from an assessment of electrophoretically demonstrable allelic variation at 24 chromosomal enzyme gene loci. Fourteen electrophoretic types, marking clones, were distinguished, the phylogeny of the clonal lineages was reconstructed, and biotype and other phenotypic characters were mapped onto this structure. Most d-tartrate-negative strains are members of an abundant, globally distributed clone (Pb 1) that is polymorphic for many biotype characters (including d-tartrate utilization), bacteriophage type, rRNA pattern, and colicin M and phage ES18 sensitivity. This clone is largely responsible for S. paratyphi B enteric fever in humans. In contrast, d-tartrate-positive strains (formerly known as S. java) occurred in all seven of the clonal lineages identified by population genetic analysis, although most d-tartrate-positive isolates belong to only two clones (Pb 3 and Pb 4), which vary in frequency geographically. Monophasic strains represent four closely related clones forming a distinctive phylogenetic lineage. The Kauffmann hypothesis of convergence in serotype among distantly related cell lineages through recombination (via phage transduction or other means) may account for the considerable genotypic diversity among clones of S. paratyphi B. Pb 4, Pb 6, and Pb 7 are more closely allied with clones of S. typhimurium and S. saintpaul than with other clones of S. paratyphi B. Sensitivity or resistance to colicin M and phage ES18 and the electrophoretic pattern of the rRNA, which were incorporated into a recently proposed scheme for the identification of types of S. paratyphi B, individually or in combination fail to mark clones or other meaningful phylogenetic subdivisions.

Colicins↗