Identification of a predominant genotype of Mycobacterium tuberculosis in Brazilian indigenous population.

After nearly a century of vaccination and six decades of drug therapy, tuberculosis (TB) kills more people annually than any other infectious disease. Substantial challenges to disease eradication remain among vulnerable and underserved populations. The Guarani-Kaiowá people are an indigenous population in Paraguay and the Brazilian state of Mato Grosso do Sul. This community, marginalized in Brazilian society, experiences severe poverty. Like other South American indigenous populations, their TB prevalence is high, but the disease has remained largely unstudied in their communities. Herein, Mycobacterium tuberculosis isolates from local clinics were whole genome sequenced, and a population genetic framework was generated. Phylogenetics show M. tuberculosis isolates in the Guarani-Kaiowá people cluster away from selected reference strains, suggesting divergence. Most cluster in a single group, further characterized as M. tuberculosis sublineage 4.3.3. Closer analysis of SNPs showed numerous variants across the genome, including in drug resistance-associated genes, and with many unique changes fixed in each group. We report that local M. tuberculosis strains have acquired unique polymorphisms in the Guarani-Kaiowá people, and drug resistance characterization is urgently needed to inform public health to ensure proper care and avoid further evolution and spread of drug-resistant TB.

Identification of a predominant genotype of Mycobacterium tuberculosis in Brazilian indigenous population

After nearly a century of vaccination and six decades of drug therapy, tuberculosis (TB) kills more people annually than any other infectious disease. Substantial challenges to disease eradication remain among vulnerable and underserved populations. The Guarani-Kaiowá people are an indigenous population in Paraguay and the Brazilian state of Mato Grosso do Sul. This community, marginalized in Brazilian society, experiences severe poverty. Like other South American indigenous populations, their TB prevalence is high, but the disease has remained largely unstudied in their communities. Herein, Mycobacterium tuberculosis isolates from local clinics were whole genome sequenced, and a population genetic framework was generated. Phylogenetics show M. tuberculosis isolates in the Guarani-Kaiowá people cluster away from selected reference strains, suggesting divergence. Most cluster in a single group, further characterized as M. tuberculosis sublineage 4.3.3. Closer analysis of SNPs showed numerous variants across the genome, including in drug resistance-associated genes, and with many unique changes fixed in each group. We report that local M. tuberculosis strains have acquired unique polymorphisms in the Guarani-Kaiowá people, and drug resistance characterization is urgently needed to inform public health to ensure proper care and avoid further evolution and spread of drug-resistant TB

Prevalence, associated factors, outcomes and transmission of extensively drug-resistant tuberculosis among multidrug-resistant tuberculosis patients in São Paulo, Brazil: a cross-sectional study.

OBJECTIVES: To describe the prevalence, associated factors, treatment outcomes and transmission of extensively drug-resistant (XDR) tuberculosis (TB) in the state of São Paulo, Brazil, for 2011 to 2013. METHODS: Drug susceptibility testing to first- and second-line drugs was performed by BACTEC MGIT 960 and molecular typing, by IS6110 restriction fragment length polymorphism. Clinical, epidemiologic and demographic data were obtained from surveillance information systems for TB. Patients were divided into three groups: multidrug resistant (MDR) TB (resistance to at least isoniazid and rifampicin), pre-XDR-TB (MDR-TB resistant to a fluoroquinolone or to at least one of the second-line injectable drugs) and XDR-TB (MDR-TB resistant to a fluoroquinolone and to at least one of the second-line injectables). RESULTS: Among the 313 MDR-TB patients identified, the prevalence of XDR-TB and pre-XDR-TB was 10.2% (n = 32) and 19.2% (n = 60), respectively. Compared to MDR-TB patients, XDR-TB patients were more likely to be female (odds ratio (OR) = 2.74, 95% confidence interval (CI), 1.29-5.83), have a history of TB (OR = 5.16; 95% CI, 1.52-17.51) and present higher death rates (OR= 3.74; 95% CI 1.70-8.25). XDR-TB transmission was observed in households, between neighbours and between a patient and a healthcare worker in a hospital. CONCLUSIONS: The prevalence of XDR-TB in the state of São Paulo is close to that estimated globally. Most of the XDR-TB patients were treated previously for TB and presented the lowest successful outcome rates. Because transmission of XDR-TB occurred, it is important that timely diagnosis of drug resistance is performed.

Diabetes increases the risk of recent-transmission tuberculosis in household contacts in São Paulo, Brazil.

SETTING: A cohort of household contacts of tuberculosis (TB) index cases from four public health clinics in São Paulo, Brazil. OBJECTIVE: To measure the association between diabetes mellitus (DM) among household contacts and recent-transmission TB (RT TB). DESIGN: Index TB cases (n = 263) identified from 2001 to 2002 in São Paulo, whose household contacts (n = 1383) were monitored for active TB until December 2010. RESULTS: From 2001 to 2010, there were 29 cases of RT TB among household contacts (cumulative incidence 2.1%, 95%CI 1.4-2.9). DM in household contacts was associated with RT TB (OR 3.96, 95%CI 1.33-11.79) even after adjustment for human immunodeficiency virus (HIV) status, smoking and alcohol use (adjusted OR [aOR] 3.21, 95%CI 1.01-10.19). HIV infection was also associated with RT TB (OR 6.40, 95%CI 1.40-29.40; aOR 4.81, 95%CI 0.96-24.18). Household contact DM was not associated with non-RT TB (OR 1.27, 95%CI 0.30-5.40). The time to diagnosis of TB was shorter in household contacts with and without DM (P = 0.035) and in household contacts with and without HIV (P = 0.0002). CONCLUSION: Household contact DM was associated with an increased risk of RT TB in a cohort in Brazil, lending support to the active screening of household contacts with DM for TB in Brazil.

Genetic and morphological diversity in populations of Nucella lapillus (L.; neogastropoda) in response to tributyltin contamination.

During the past three decades, North Atlantic populations of dogwhelks have been severely reduced in numbers, due to imposex and female sterility caused by TBT. We examined the relationship between the known history of female sterility and the present genetic diversity (measured by five allozyme-loci) and phenotypic variance (measured by nine quantitative characters) in six populations of Nucella lapillus along the coast of Norway. The environment of one of the populations was severely polluted with a vas deferens sequence index (VDSI) of 4.31, resulting in 24% sterile females. The environment of four of the other five populations was moderately polluted (VDSI 3.31-3.97, 0-1.6% sterile females), while the last population was unpolluted (VDSI 0.02, 0% sterile females). The six populations did not differ significantly with respect to genetic diversity. However, the population from the most polluted area had greater phenotypic variation in shell size, compared to all other populations. The results indicate that although TBT has had severe local negative effects on N. lapillus populations, it has not caused a reduction in long-term adaptive potential.

Immunogenicity of a 23-valent pneumococcal polysaccharide vaccine in Brazilian elderly.

Serum antibodies specific for the capsular polysaccharides of Streptococcus pneumoniae provide protection against invasive pneumococcal infection. In Brazil, this vaccine has been used for people over 65 years with clinical risk to develop pneumococcal infection since 1999. We evaluated the immune response of 102 elderly subjects (75.5% females and 24.5% males) with a mean age of 71 years, and 19 young healthy adults (63.2% females and 36.8% males) with a mean age of 27 years. The elderly study group consisted of outpatients who received follow-up care in the Geriatric Department of General Hospital, Faculty of Medicine, University of São Paulo. None had acute illness at the time of vaccination. Both groups were immunized with one intra-deltoid injection with 0.5 ml of a 23-valent pneumococcal polysaccharide vaccine. The total IgG specific antibody concentrations to capsular polysaccharides 1, 3, 5, 6B, 8, and 14 were determined against pre- and 1-month post-vaccination sera. All samples were analyzed according to the second-generation pneumococcal polysaccharide ELISA protocol. We observed that the pneumococcal polysaccharide vaccine evoked consistent antibody increase for serotypes 1, 5, 6B, 8, and 14 (geometric mean concentration increase of 2.46 in the elderly and 2.84 in the young adults). Otherwise, we observed no increase in antibody concentration for serotype 3 in both groups.

Immunogenicity of a 23-valent pneumococcal polysaccharide vaccine in Brazilian elderly

Serum antibodies specific for the capsular polysaccharides of Streptococcus pneumoniae provide protection against invasive pneumococcal infection. In Brazil, this vaccine has been used for people over 65 years with clinical risk to develop pneumococcal infection since 1999. We evaluated the immune response of 102 elderly subjects (75.5 percent females and 24.5 percent males) with a mean age of 71 years, and 19 young healthy adults (63.2 percent females and 36.8 percent males) with a mean age of 27 years. The elderly study group consisted of outpatients who received follow-up care in the Geriatric Department of General Hospital, Faculty of Medicine, University of São Paulo. None had acute illness at the time of vaccination. Both groups were immunized with one intra-deltoid injection with 0.5 ml of a 23-valent pneumococcal polysaccharide vaccine. The total IgG specific antibody concentrations to capsular polysaccharides 1, 3, 5, 6B, 8, and 14 were determined against pre- and 1-month post-vaccination sera. All samples were analyzed according to the second-generation pneumococcal polysaccharide ELISA protocol. We observed that the pneumococcal polysaccharide vaccine evoked consistent antibody increase for serotypes 1, 5, 6B, 8, and 14 (geometric mean concentration increase of 2.46 in the elderly and 2.84 in the young adults). Otherwise, we observed no increase in antibody concentration for serotype 3 in both groups.

Biomarkers in terrestrial invertebrates for ecotoxicological soil risk assessment.

This review has served to present the most recent information on a selected series of biomarker studies undertaken on soil invertebrates during two extensive European-funded scientific consortia, BIOPRINT and BIOPRINT-II. The goals were to develop and validate methods for the analysis of markers of stress in a range of soil-dwelling organisms. We have discussed the potential and limitations of the following invertebrate biomarkers for soil risk assessment purposes: heat shock proteins, histological and ultrastructural markers, metallothioneins and metal-binding proteins, esterases, lysosomal integrity, and the novel biomarker histidine. The hsp response in soil invertebrates is especially suitable to indicate the effects of exposure to comparatively low concentrations for a range of toxicants and can be regarded as a biomarker of general stress. The application of MTs and other metal-binding proteins as biomarkers for exposure in soil invertebrates has been well described, and new methods are being developed for analyzing MT induction both at the protein and molecular level, and reliable and reproducible methods are now available. (Cd)-MT is well characterized for the springtails and its MT concentration is a useful biomarker for exposure as well as for effect. For snails, (Cd)-MT can accumulate in the midgut gland over extended periods of time and therefore its concentration is a biomarker not only for recent intoxication but also for events of cadmium exposure that snails may have experienced a long time before the measurement took place. Cellular and histological alterations can be regarded as reflecting the "health" state of a cell, which may be a measure for the presence of toxicants. Histopathological work on terrestrial invertebrates, however, is still scarce. Isozymes have been poorly studied in soil invertebrates despite their promising role as potential biomarkers in aquatic organisms. Among the large diversity of isozymes, the most well studied are esterases that are frequently used a biomarkers of exposure to various classes of pesticides. Many other isozymes offer potentials for biomarker research, such as glucosephosphate isomerase and phosphoglucomutase, both enzymes necessary for the glycolytic pathway. The lysosomal system has been identified as a particular target for the toxic effects of xenobiotics, although it has yet a limited application in soil invertebrates. This marker is nonspecific, responding equally sensitively to organic or inorganic contamination; however, if used in combination with an earthworm immnunocompetence assay such as total immunoactivity of the coelomocytes, then it is possible to be more specific as to the likely nature of contamination. Free histidine was positively correlated with increasing copper exposure and total copper burden in earthworms from a semifield study. Histidine may thus act as a biomarker of exposure. The transient responses and confounding factors of biomarkers obscure a proper interpretation of biomarker responses under field conditions. These factors are still very poorly understood and require more study. For risk assessment purposes it is recommended that the aforementioned biomarkers may show promise when included in a suite of biomarkers among different soil invertebrate species. It is recommended that a risk assessment protocol draw upon ranking of biomarker responses on a defined scale. It is also hoped that the problems outlined in this review will aid the direction of future research on soil invertebrate biomarkers.

Random amplified polymorphic DNA markers of the Brassica alboglabra chromosome of a B. campestris-alboglabra addition line.

The alien C-genome chromosome in a Brassica campestris alboglabra monosomic addition line was characterized by random amplified polymorphic DNA (RAPD) analysis. The alien chromosome carried three loci, Ec, Wc and Lap-1C, controlling synthesis of erucic acid, white flower colour and a fast-migrating band of leucine aminopeptidase (Lap-1Cc) respectively. The RAPD analysis revealed 17 markers specific to the alien chromosome. Among 45 offspring plants from the selfed addition line the alien C-chromosome was transmitted to 15 plants, four plants had only parts of this chromosome and the remaining 26 plants did not carry the chromosome.

Genetic variation within and among different cultivars and landraces of Brassica campestris L. and B. oleracea L. based on isozymes.

Genetic variation based on isozymes was studied in 43 landraces and cultivars of Brassica campestris from China, 4 cultivars of B. campestris from Sweden and 1 from India, and 5 cultivars of B. oleracea from Sweden and 1 from China (B. alboglabra). A total of 17 isozyme loci was studied, 10 of these were polymorphic in B. campestris and 6 were polymorphic in B. oleracea. The level of heterozygosity seemed to be reduced in the Swedish cultivars compared to the Chinese landraces and cultivars of B. campestris. The level of heterozygosity in B. oleracea was even lower than that in the Swedish cultivars of B. campestris. A phylogeny of the cultivars and landraces of B. campestris showed that the B. campestris var 'yellow sarson' cultivar, originating from India, deviated significantly from the other cultivars of B. campestris. A phylogeny of the cultivars of B. oleracea confirmed the expectations that the cultivar B. alboglabra was not closely related to the cultivated forms of B. oleracea.

Inheritance of isozymes in Brassica campestris L. and genetic divergence among different species of Brassiceae.

Electrophoretic investigations of Brassica campestris revealed 8 polymorphic loci that had not been described earlier. The inheritance of 7 of them was determined by crosses between different accessions of B. campestris. A phylogeny of B. campestris, B. nigra, B. alboglabra, Sinapis arvensis and S. alba was estimated from the analysis of 15 isozyme loci. The phylogeny showed a close relationship between B. nigra and S. arvensis and a less close relationship between B. campestris and B. oleracea. S. alba was remotely-related to all of the other species.

Genetic differentiation in populations of red deer, Cervus elaphus, in Denmark.

Samples from 282 specimens of red deer (Cervus elaphus L.) representing eleven localities, were collected during two hunting seasons, 1986-87 and 1987-88. Four polymorphic isozymes are investigated, and allelic distributions among the populations within an area or among areas are heterogeneous. The differentiation among the populations may be explained as a result of random genetic drift. A dendrogram reveals that seven of the nine populations from the peninsula of Jutland are closely related.

Genetic polymorphism of esterase in plasma of American mink (Mustela vison L.).

Plasma samples of 412 minks, including 20 families and representing 15 lines, have been investigated by isoelectric focusing for the enzyme esterase (ES). The observed variation of the enzyme may be explained as a result of one locus with at least seven codominant alleles. The segregation of six alleles assumed for the locus in 20 families supports this genetic model. Genetic divergence among the lines is observed and may be due to founder effect and/or selection.

A Brassica campestris-alboglabra addition line and its use for gene mapping, intergenomic gene transfer and generation of trisomics.

Brassica campestris-alboglabra monosomic addition lines were developed from a trigenomic Brassica hybrid (2 n=3 x=29, AAC) obtained by backcrossing a resynthesized B. napus (2 n=4 x=38, AACC) line to its parental B. campestris (2 n=2 x=20, AA) line. One addition line was characterized genetically with three loci specific for the alien chromosome and cytologically by meiotic analysis. The following results were obtained. (1) The same chromosome in the B. alboglabra (2 n= 2 x=18, CC) genome carried the three loci, E c, W c and Lap-1 C (c), which control the biosynthesis of erucic acid, white flower colour and the faster migrating band of leucine aminopeptidase, respectively. The linear order and possible positions of the three loci were inferred. The meiotic behaviour of the alien chromosome was documented and its transmission frequency was assessed. (2) Intergenomic recombination frequently occurred in the monosomic addition line, resulting in the introgression of one or two loci from the alien chromosome into the B. campestris genome. (3) B. campestris trisomics were found in the progeny of the monosomic addition line. (4) The removal of the other eight C-genome chromosomes from the trigenomic Brassica hybrid led to a dramatic increase in the erucic acid content of the monosomic addition line. (5) No offspring of the trigenomic Brassica hybrid showed evidence of intergenomic recombination and introgression of the W c locus into the B. campestris genome. It is questioned whether such a difference might be due to a possible regulating mechanism for homoeologous chromosome pairing.

Genetic polymorphism of adenosine deaminase and mannose phosphate isomerase in blood of arctic foxes, Alopex lagopus.

Blood samples of 70 foxes, including 10 families, have been investigated by horizontal starch gel electrophoresis for the enzymes adenosine deaminase (ADA) and mannose phosphate isomerase (MPI). The observed variation of the enzymes could be explained as a result of one locus with two codominant alleles and one with three respectively. The segregation in the families of the alleles assumed for the two loci is in accordance with this genetic model. The frequency of the two alleles at the Ada locus is about the same and the slowest anodic migrating allele at the Mpi locus is the most frequent.

Comparative and genetic studies of isozymes in resynthesized and cultivated Brassica napus L., B. campestris L. and B. alboglabra Bailey.

Enzyme electrophoresis was used to compare newly resynthesized Brassica napus with its actual parental diploid species, B. campestris and B. alboglabra. Comparisons were also made with cultivated B. napus. Of the eight enzyme systems assayed, four were monomorphic (hexokinase, malate dehydrogenase, mannose phosphate isomerase and peroxidase), whereas the remaining four were polymorphic (glucosephosphate isomerase, leucine aminopeptidase, phosphoglucomutase and shikimate dehydrogenase), when comparisons were made within or between species. The polymorphic enzyme patterns observed in the newly resynthesized B. napus disclosed that the homoeologous loci contributed by the parental species were expressed in the amphiploid. Analysis of the glucosephosphate isomerase enzyme in a breeding line (Sv 02372) of B. napus indicated that, in this case, the gene originating from B. campestris was switched off whereas that of B. oleracea was expressed. Duplicated enzyme loci were observed in B. campestris and B. alboglabra, thus providing additional evidence to support the hypothesis that these species are actually secondary polyploids derived from an unknown archetype of x=6.

Allozyme variation in rye, Secale cereale L. : 2. Commercial varieties.

Eleven samples of eight European commercial varieties of winter rye were examined at eight polymorphic enzyme loci. Genotype frequencies fitted Hardy-Weinberg expectations at all loci in all samples studied. Of the total genetic diversity recorded at the 8 loci, only 7% was expressed between varieties. Allele frequency differences between varieties were, however, sufficient to allow a characterization of each variety by a specific set of allele frequencies. Using subsets of the original data, it could be demonstrated that all pairs of varieties but one still showed significant allozyme differences, when only 4 loci were screened in samples half the original size of 200 individuals. Even when only one locus was analyzed, all varieties but two were distinguishable, but this "diagnostic" locus was not identical in all pairwise comparisons.