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1.
Mem Inst Oswaldo Cruz ; 116: e200517, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33729319

RESUMO

Molecular-typing can help in unraveling epidemiological scenarios and improvement for disease control strategies. A literature review of Mycobacterium tuberculosis transmission in Brazil through genotyping on 56 studies published from 1996-2019 was performed. The clustering rate for mycobacterial interspersed repetitive units - variable tandem repeats (MIRU-VNTR) of 1,613 isolates were: 73%, 33% and 28% based on 12, 15 and 24-loci, respectively; while for RFLP-IS6110 were: 84% among prison population in Rio de Janeiro, 69% among multidrug-resistant isolates in Rio Grande do Sul, and 56.2% in general population in São Paulo. These findings could improve tuberculosis (TB) surveillance and set up a solid basis to build a database of Mycobacterium genomes.


Assuntos
Repetições Minissatélites/genética , Mycobacterium tuberculosis/genética , Polimorfismo de Fragmento de Restrição/genética , Técnicas de Tipagem Bacteriana , Brasil/epidemiologia , Genótipo , Humanos , Epidemiologia Molecular , Mycobacterium tuberculosis/isolamento & purificação , Sequenciamento Completo do Genoma
2.
Braz J Infect Dis ; 25(1): 101043, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33406389

RESUMO

BACKGROUND: Epidemiological studies are important tools to assess the diversity of Brucella isolates and to estimate their epidemiological relationship among isolates from different geographical origins. In this study the MLVA16 (multiple-locus variable number tandem repeat analysis based on 16 loci) was employed to investigate the diversity of Brucella spp. Isolated from humans and animals for epidemiological purposes and to determine the most common Brucella genotypes in Iran. METHODS: We designed a molecular-based study to evaluate the potential reservoirs of human brucellosis. After isolation and identification of 54 Brucella spp human and animal specimens from three regions of Iran, bacterial genomic DNA was extracted MLVA with three panel was used for the genotyping of isolates. The size of PCR products were analyzed and converted to repeat unit numbers using a published allele numbering system and data set was imported into Bionumerics. RESULTS: Three isolates (5.55%) were identified as Brucella abortus and 51 (94.44%) as Brucella melitensis. Two isolates of Brucella abortus were from humans and one from an animal. Thirty-four Brucella melitensis isolates were from humans and 17 from animals. Using MLVA16-genotyping, 54 isolates with genetic similarity coefficient of 80% were divided into 46 genotypes and 22 genotypes were represented by a single isolate, while 4, 2, 1 and 2 genotypes were represented by 2, 3, 4 and 7 isolates, respectively. The most prevalent genotype was represented by 14 isolates. There were two other frequent genotypes each represented by seven isolates, among which only one was restricted to a geographic region. Discriminatory power for each locus was determined in this study and panel 2B shows the high discretionary power [Bruce04 (0.837), Bruce30 (0.806), Bruce 09 (0.787), Bruce 07 (0.772), Bruce16 (0.766)]. CONCLUSION: MLVA16 analysis of 54 Brucella isolates showed high level polymorphism in their genotypes. Only two genotypes, each observed in seven isolates, were related to one another and only one of these genotypes were found in to two separate regions.


Assuntos
Brucella melitensis , Brucelose , Animais , Brucella melitensis/genética , Variação Genética , Genótipo , Humanos , Irã (Geográfico) , Repetições Minissatélites/genética
3.
BMC Infect Dis ; 20(1): 789, 2020 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-33097000

RESUMO

BACKGROUND: People successfully completing treatment for tuberculosis remain at elevated risk for recurrent disease, either from relapse or reinfection. Identifying risk factors for recurrent tuberculosis may help target post-tuberculosis screening and care. METHODS: We enrolled 500 patients with smear-positive pulmonary tuberculosis in South Africa and collected baseline data on demographics, clinical presentation and sputum mycobacterial cultures for 24-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing. We used routinely-collected administrative data to identify recurrent episodes of tuberculosis occurring over a median of six years after successful treatment completion. RESULTS: Of 500 patients initially enrolled, 333 (79%) successfully completed treatment for tuberculosis. During the follow-up period 35 patients with successful treatment (11%) experienced a bacteriologically confirmed tuberculosis recurrence. In our Cox proportional hazards model, a 3+ AFB sputum smear grade was significantly associated with recurrent tuberculosis with a hazard ratio of 3.33 (95% CI 1.44-7.7). The presence of polyclonal M. tuberculosis infection at baseline had a hazard ratio for recurrence of 1.96 (95% CI 0.86-4.48). CONCLUSION: Our results indicate that AFB smear grade is independently associated with tuberculosis recurrence after successful treatment for an initial episode while the association between polyclonal M. tuberculosis infection and increased risk of recurrence appears possible.


Assuntos
Antituberculosos/uso terapêutico , Mycobacterium tuberculosis/genética , Escarro/microbiologia , Tuberculose Pulmonar/tratamento farmacológico , Tuberculose Pulmonar/epidemiologia , Adulto , Feminino , Seguimentos , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Repetições Minissatélites/genética , Recidiva , Fatores de Risco , África do Sul/epidemiologia , Resultado do Tratamento , Tuberculose Pulmonar/diagnóstico , Tuberculose Pulmonar/microbiologia , Adulto Jovem
4.
BMC Infect Dis ; 20(1): 750, 2020 Oct 13.
Artigo em Inglês | MEDLINE | ID: mdl-33050903

RESUMO

BACKGROUND: Tuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC). Mapping the genetic diversity of MTBC in high TB burden country like Ethiopia is important to understand principles of the disease transmission and to strengthen the regional TB control program. The aim of this study was to investigate the genetic diversity of Mycobacterium tuberculosis complex (MTBC) isolates circulating in the South Omo, southern Ethiopia. METHODS: MTBC isolates (N = 156) were genetically analyzed using spacer oligotyping (spoligotyping) and mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing. Major lineages and lineages were identified using MTBC databases. Logistic regression was used to correlate patient characteristics with strain clustering. RESULTS: The study identified Euro-American (EA), East-African-Indian (EAI), Indo-Oceanic (IO), Lineage_7/Aethiops vertus, Mycobacterium bovis and Mycobacterium africanum major lineages in proportions of 67.3% (105/156), 22.4% (35/156), 6.4% (10/156), 1.9% (3/156), 1.3% (2/156) and 0.6% (1/156), respectively. Lineages identified were Delhi/CAS 23.9% (37/155), Ethiopia_2 20.6% (32/155), Haarlem 14.2% (22/155), URAL 14.2%(22/155), Ethiopia_3 8.4% (13/155), TUR 6.5% (10/155), Lineage_7/Aethiops vertus 1.9% (3/155), Bovis 1.3% (2/155), LAM 1.3% (2/155), EAI 0.6% (1/155), X 0.6% (1/155) and Ethiopia H37Rv-like strain 0.6% (1/155). Of the genotyped isolates 5.8% (9/155) remained unassigned. The recent transmission index (RTI) was 3.9%. Orphan strains compared to shared types (AOR: 0.09, 95% CI: 0.04-0.25) were associated with reduced odds of clustering. The dominant TB lineage in pastoral areas was EAI and in non-pastoral areas was EA. CONCLUSION: The epidemiological data, highly diverse MTBC strains and a low RTI in South Omo, provide information contributing to the TB Control Program of the country.


Assuntos
Variação Genética , Mycobacterium bovis/genética , Mycobacterium tuberculosis/genética , Tuberculose Pulmonar/epidemiologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Alelos , Etiópia/epidemiologia , Feminino , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Repetições Minissatélites/genética , Epidemiologia Molecular , Reação em Cadeia da Polimerase Multiplex , Mycobacterium bovis/isolamento & purificação , Mycobacterium tuberculosis/isolamento & purificação , Escarro/microbiologia , Tuberculose Pulmonar/microbiologia , Adulto Jovem
5.
Zhonghua Liu Xing Bing Xue Za Zhi ; 41(8): 1341-1344, 2020 Aug 10.
Artigo em Chinês | MEDLINE | ID: mdl-32867447

RESUMO

Objective: To understand the molecular characteristics and correlation among isolated strains of Brucella melitensis (BM) so as to improve the strategies on prevention and control of the disease in Jiangxi province. Methods: A total of 25 strains of BM isolated from human in 17 counties of Jiangxi province were analyzed by multiple locus variable-number tandem repeat analysis (MLVA) method. Results: A total of 25 strains of BM were classified into 24 independent genotypes with similarities between 67.00% and 100.00% and Simpson index between 0.000 and 0.773. There were 3 genotypes in MLVA8, including 60.00% (15/25) as 42 genotype, 32.00% (8/25) as 43 genotype, and 8.00% (2/25) as 63 genotype, respectively. There were 7 genotypes in MLVA11 identified, with 116 genotype and 125 genotype the main genotypes, accounting for 56.00% (14/25) of all the identified strains. Conclusions: Genes from all the 25 strains of BM that isolated from human being were with high genetic diversities, and various, genotypes. However, no obvious epidemiological correlation was noticed among these strains, indicating the complexity of the source of infection on Brucella in Jiangxi province.


Assuntos
Brucella melitensis/genética , Brucelose/microbiologia , Brucella melitensis/isolamento & purificação , Brucelose/epidemiologia , China/epidemiologia , Genótipo , Humanos , Repetições Minissatélites/genética , Epidemiologia Molecular
6.
PLoS Genet ; 16(8): e1008981, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32745133

RESUMO

Tribbles homolog 3 (TRIB3) is pseudokinase involved in intracellular regulatory processes and has been implicated in several diseases. In this article, we report that human TRIB3 promoter contains a 33-bp variable number tandem repeat (VNTR) and characterize the heterogeneity and function of this genetic element. Analysis of human populations around the world uncovered the existence of alleles ranging from 1 to 5 copies of the repeat, with 2-, 3- and 5-copy alleles being the most common but displaying considerable geographical differences in frequency. The repeated sequence overlaps a C/EBP-ATF transcriptional regulatory element and is highly conserved, but not repeated, in various mammalian species, including great apes. The repeat is however evident in Neanderthal and Denisovan genomes. Reporter plasmid experiments in human cell culture reveal that an increased copy number of the TRIB3 promoter 33-bp repeat results in increased transcriptional activity. In line with this, analysis of whole genome sequencing and RNA-Seq data from human cohorts demonstrates that the copy number of TRIB3 promoter 33-bp repeats is positively correlated with TRIB3 mRNA expression level in many tissues throughout the body. Moreover, the copy number of the TRIB3 33-bp repeat appears to be linked to known TRIB3 eQTL SNPs as well as TRIB3 SNPs reported in genetic association studies. Taken together, the results indicate that the promoter 33-bp VNTR constitutes a causal variant for TRIB3 expression variation between individuals and could underlie the results of SNP-based genetic studies.


Assuntos
Proteínas de Ciclo Celular/genética , Heterogeneidade Genética , Genética Populacional , Repetições Minissatélites/genética , Proteínas Serina-Treonina Quinases/antagonistas & inibidores , Proteínas Repressoras/genética , Estônia/epidemiologia , Feminino , Regulação da Expressão Gênica/genética , Genótipo , Humanos , Masculino , Regiões Promotoras Genéticas , Proteínas Serina-Treonina Quinases/genética , RNA-Seq , Sequenciamento Completo do Genoma
7.
Am J Hum Genet ; 107(3): 445-460, 2020 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-32750315

RESUMO

Tandem repeats are proposed to contribute to human-specific traits, and more than 40 tandem repeat expansions are known to cause neurological disease. Here, we characterize a human-specific 69 bp variable number tandem repeat (VNTR) in the last intron of WDR7, which exhibits striking variability in both copy number and nucleotide composition, as revealed by long-read sequencing. In addition, greater repeat copy number is significantly enriched in three independent cohorts of individuals with sporadic amyotrophic lateral sclerosis (ALS). Each unit of the repeat forms a stem-loop structure with the potential to produce microRNAs, and the repeat RNA can aggregate when expressed in cells. We leveraged its remarkable sequence variability to align the repeat in 288 samples and uncover its mechanism of expansion. We found that the repeat expands in the 3'-5' direction, in groups of repeat units divisible by two. The expansion patterns we observed were consistent with duplication events, and a replication error called template switching. We also observed that the VNTR is expanded in both Denisovan and Neanderthal genomes but is fixed at one copy or fewer in non-human primates. Evaluating the repeat in 1000 Genomes Project samples reveals that some repeat segments are solely present or absent in certain geographic populations. The large size of the repeat unit in this VNTR, along with our multiplexed sequencing strategy, provides an unprecedented opportunity to study mechanisms of repeat expansion, and a framework for evaluating the roles of VNTRs in human evolution and disease.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal/genética , Esclerose Amiotrófica Lateral/genética , Evolução Molecular , Sequências de Repetição em Tandem/genética , Idoso , Doença de Alzheimer/genética , Doença de Alzheimer/patologia , Esclerose Amiotrófica Lateral/patologia , Expansão das Repetições de DNA/genética , Feminino , Regulação da Expressão Gênica/genética , Humanos , Masculino , Repetições Minissatélites/genética , Fenótipo , Especificidade da Espécie
8.
Braz J Psychiatry ; 42(6): 630-637, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32491038

RESUMO

OBJECTIVE: Studies to reduce the heterogeneity of attention-deficit/hyperactivity disorder (ADHD) have increased interest in the concept of sluggish cognitive tempo (SCT). The aim of this study was to investigate if the prevalence of two variable-number tandem repeats (VNTRs) located within the 3'-untranslated region of the DAT1 gene and in exon 3 of the dopamine D4 receptor (DRD4) gene differ among four groups (31 subjects with SCT but no ADHD, 146 individuals with ADHD but no SCT, 67 subjects with SCT + ADHD, and 92 healthy controls). METHODS: We compared the sociodemographic profiles, neurocognitive domains, and prevalence of two VNTRs in SCT and ADHD subjects versus typically developing (TD) controls. RESULTS: The SCT without ADHD group had a higher proportion of females and lower parental educational attainment. Subjects in this group performed worse on neuropsychological tests, except for psychomotor speed and commission errors, compared to controls. However, the ADHD without SCT group performed significantly worse on all neuropsychological domains than controls. We found that 4R homozygosity for the DRD4 gene was most prevalent in the ADHD without SCT group. The SCT without ADHD group had the highest 7R allele frequency, differing significantly from the ADHD without SCT group. CONCLUSION: The 7R allele of DRD4 gene was found to be significantly more prevalent in SCT cases than in ADHD cases. No substantial neuropsychological differences were found between SCT and ADHD subjects.


Assuntos
Transtorno do Deficit de Atenção com Hiperatividade , Transtorno do Deficit de Atenção com Hiperatividade/diagnóstico , Transtorno do Deficit de Atenção com Hiperatividade/genética , Cognição , Feminino , Genótipo , Humanos , Repetições Minissatélites/genética , Receptores de Dopamina D4/genética
9.
J Appl Microbiol ; 129(5): 1193-1206, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32426861

RESUMO

AIMS: Development of a novel hierarchical Mycobacterium avium subsp. paratuberculosis (MAP) typing approach and characterization of MAP field cultures in Central Germany. METHODS AND RESULTS: By combining single nucleotide polymorphisms (SNPs) and mycobacterial interspersed repetitive unit-variable number tandem repeat, we developed a highly discriminating and phylogenetically accurate hierarchical MAP typing approach. Moreover, a novel stepwise workflow was employed to reduce the number of SNP reactions required making the typing approach more affordable. MAP field cultures (n = 142) from dairy herds in Central Germany were classified as cattle type and showed a high level of heterogeneity. Intra-herd multiple genotypes were evident in (13-25%) of the investigated herds. CONCLUSIONS: The hierarchical MAP typing approach proved to be useful in fine discrimination between MAP cultures within limited geographical regions. This could potentially be used in unravelling MAP transmission chains in the respective regions. The observed heterogeneity in some herds is assumed to be due to either multiple introductions through inter-herd trade or intra-herd evolution over time. SIGNIFICANCE AND IMPACT OF THE STUDY: Future MAP epidemiological studies will benefit from the advantages of the novel hierarchical typing approach. The SNP number reduction approach employed here could be extrapolated for other analogous pathogens.


Assuntos
Técnicas de Tipagem Bacteriana/veterinária , Doenças dos Bovinos/microbiologia , Mycobacterium avium subsp. paratuberculosis/classificação , Mycobacterium avium subsp. paratuberculosis/isolamento & purificação , Paratuberculose/microbiologia , Animais , Técnicas de Tipagem Bacteriana/métodos , Bovinos , Doenças dos Bovinos/epidemiologia , DNA Bacteriano/genética , Genótipo , Alemanha/epidemiologia , Repetições Minissatélites/genética , Mycobacterium avium subsp. paratuberculosis/genética , Paratuberculose/epidemiologia , Filogenia , Polimorfismo de Nucleotídeo Único/genética
10.
Nature ; 582(7812): 426-431, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32461690

RESUMO

Sex chromosomes in males of most eutherian mammals share only a small homologous segment, the pseudoautosomal region (PAR), in which the formation of double-strand breaks (DSBs), pairing and crossing over must occur for correct meiotic segregation1,2. How cells ensure that recombination occurs in the PAR is unknown. Here we present a dynamic ultrastructure of the PAR and identify controlling cis- and trans-acting factors that make the PAR the hottest segment for DSB formation in the male mouse genome. Before break formation, multiple DSB-promoting factors hyperaccumulate in the PAR, its chromosome axes elongate and the sister chromatids separate. These processes are linked to heterochromatic mo-2 minisatellite arrays, and require MEI4 and ANKRD31 proteins but not the axis components REC8 or HORMAD1. We propose that the repetitive DNA sequence of the PAR confers unique chromatin and higher-order structures that are crucial for recombination. Chromosome synapsis triggers collapse of the elongated PAR structure and, notably, oocytes can be reprogrammed to exhibit spermatocyte-like levels of DSBs in the PAR simply by delaying or preventing synapsis. Thus, the sexually dimorphic behaviour of the PAR is in part a result of kinetic differences between the sexes in a race between the maturation of the PAR structure, formation of DSBs and completion of pairing and synapsis. Our findings establish a mechanistic paradigm for the recombination of sex chromosomes during meiosis.


Assuntos
Quebras de DNA de Cadeia Dupla , Meiose , Regiões Pseudoautossômicas/genética , Regiões Pseudoautossômicas/metabolismo , Animais , Proteínas de Ciclo Celular/metabolismo , Montagem e Desmontagem da Cromatina , Pareamento Cromossômico/genética , Proteínas de Ligação a DNA , Feminino , Heterocromatina/genética , Heterocromatina/metabolismo , Heterocromatina/ultraestrutura , Cinética , Masculino , Meiose/genética , Camundongos , Repetições Minissatélites/genética , Oócitos/metabolismo , Recombinação Genética/genética , Caracteres Sexuais , Troca de Cromátide Irmã , Espermatócitos/metabolismo , Ubiquitina-Proteína Ligases/metabolismo
11.
Epidemiol Mikrobiol Imunol ; 69(1): 20-28, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32326712

RESUMO

AIM: To determine clonal characteristics of Streptococcus pneumoniae (S. pneumoniae) strains causing invasive pneumococcal disease (IPD) in the Czech Republic (CR) in 2017. Clonal assignment of strains was performed in the National Reference Laboratory for Streptococcal Infections (NRL) by the routinely used method, multilocus sequence typing (MLST), and a newly introduced method, multiple-locus variable number tandem repeat analysis (MLVA). MATERIAL AND METHOD: The study strains were 87 isolates of S. pneumoniae selected from those referred to the NRL within the IPD surveillance programme from all over the CR in 2017. The study set covers S. pneumoniae isolates of both pneumococcal 13-valent conjugate vaccine serotypes (1, 4, and 9V) and non-vaccine serotypes (8, 9N, and 22F) widely spread in the CR. The study methods were MLST, the standard method used worldwide for the characterisation of pneumococcal isolates based on sequencing of a set of gene regions, and MLVA, which allows to characterise isolates based on the number of tandem repeats in intergenic regions. RESULTS: MLST revealed and confirmed a high level of clonal homogeneity of S. pneumoniae isolates of serotypes 1, 9N, 9V, and 22F and a considerable genetic variability of serotype 4 and 8 isolates. There was a general correlation between the MLST and MLVA clonal complex assignments. In comparison with MLST, MLVA has superior clonal discriminatory power. Isolates with the newly determined MLVA profiles should be assigned to new MLVA types (MT). Nevertheless, the new web support of the MLVA scheme for S. pneumoniae is less relevant as it does not provide services comparable to those available from the web support for MLST characterisation. CONCLUSIONS: MLST continues to be the standard method for clonal characterisation of S. pneumoniae isolates from IPD for the purposes of both national and international surveillance. MLST characteristics of isolates are helpful in the study of clonal variability conducted by both national and transnational public health protection authorities. MLVA is not routinely used but can serve as a complementary method for rapid identification of clonal relatedness between isolates, e.g. those from local outbreaks. It is more suitable for the detection of emergence and spread of a virulent clonal variant.


Assuntos
Repetições Minissatélites , Tipagem de Sequências Multilocus , Infecções Pneumocócicas , Streptococcus pneumoniae , República Tcheca , Humanos , Repetições Minissatélites/genética , Infecções Pneumocócicas/microbiologia , Streptococcus pneumoniae/classificação , Streptococcus pneumoniae/genética
12.
Biochemistry ; 59(12): 1261-1272, 2020 03 31.
Artigo em Inglês | MEDLINE | ID: mdl-32191439

RESUMO

We investigate herein the interaction between nucleolin (NCL) and a set of G4 sequences derived from the CEB25 human minisatellite that adopt a parallel topology while differing in the length of the central loop (from nine nucleotides to one nucleotide). It is revealed that NCL strongly binds to long-loop (five to nine nucleotides) G4 while interacting weakly with the shorter variants (loop with fewer than three nucleotides). Photo-cross-linking experiments using 5-bromo-2'-deoxyuridine (BrU)-modified sequences further confirmed the loop-length dependency, thereby indicating that the WT-CEB25-L191 (nine-nucleotide loop) is the best G4 substrate. Quantitative proteomic analysis (LC-MS/MS) of the product(s) obtained by photo-cross-linking NCL to this sequence enabled the identification of one contact site corresponding to a 15-amino acid fragment located in helix α2 of RNA binding domain 2 (RBD2), which sheds light on the role of this structural element in G4-loop recognition. Then, the ability of a panel of benchmark G4 ligands to prevent the NCL-G4 interaction was explored. It was found that only the most potent ligand PhenDC3 can inhibit NCL binding, thereby suggesting that the terminal guanine quartet is also a strong determinant of G4 recognition, putatively through interaction with the RGG domain. This study describes the molecular mechanism by which NCL recognizes G4-containing long loops and leads to the proposal of a model implying a concerted action of RBD2 and RGG domains to achieve specific G4 recognition via a dual loop-quartet interaction.


Assuntos
Quadruplex G , Repetições Minissatélites/genética , Fosfoproteínas/metabolismo , Proteínas de Ligação a RNA/metabolismo , Sítios de Ligação , Bromodesoxiuridina/química , Cromatografia Líquida de Alta Pressão , Reagentes para Ligações Cruzadas/química , Modelos Moleculares , Conformação de Ácido Nucleico/efeitos dos fármacos , Fosfoproteínas/química , Conformação Proteica em alfa-Hélice , Domínios e Motivos de Interação entre Proteínas , Proteômica , Motivo de Reconhecimento de RNA , Proteínas de Ligação a RNA/química , Espectrometria de Massas em Tandem
13.
Transbound Emerg Dis ; 67 Suppl 1: 99-107, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32174038

RESUMO

Theileria parva is a tick-transmitted apicomplexan protozoan parasite that infects lymphocytes of cattle and African Cape buffalo (Syncerus caffer), causing a frequently fatal disease of cattle in eastern, central and southern Africa. A live vaccination procedure, known as infection and treatment method (ITM), the most frequently used version of which comprises the Muguga, Serengeti-transformed and Kiambu 5 stocks of T. parva, delivered as a trivalent cocktail, is generally effective. However, it does not always induce 100% protection against heterologous parasite challenge. Knowledge of the genetic diversity of T. parva in target cattle populations is therefore important prior to extensive vaccine deployment. This study investigated the extent of genetic diversity within T. parva field isolates derived from Ankole (Bos taurus) cattle in south-western Uganda using 14 variable number tandem repeat (VNTR) satellite loci and the sequences of two antigen-encoding genes that are targets of CD8+T-cell responses induced by ITM, designated Tp1 and Tp2. The findings revealed a T. parva prevalence of 51% confirming endemicity of the parasite in south-western Uganda. Cattle-derived T. parva VNTR genotypes revealed a high degree of polymorphism. However, all of the T. parva Tp1 and Tp2 alleles identified in this study have been reported previously, indicating that they are widespread geographically in East Africa and highly conserved.


Assuntos
Antígenos de Protozoários/genética , Búfalos/parasitologia , Doenças dos Bovinos/parasitologia , Repetições Minissatélites/genética , Vacinas Protozoárias/imunologia , Theileria parva/genética , Theileriose/parasitologia , Alelos , Animais , Linfócitos T CD8-Positivos/imunologia , Linfócitos T CD8-Positivos/parasitologia , Bovinos , Doenças dos Bovinos/epidemiologia , Doenças dos Bovinos/prevenção & controle , Feminino , Variação Genética , Genótipo , Masculino , Polimorfismo Genético/genética , Theileria parva/imunologia , Theileriose/epidemiologia , Theileriose/prevenção & controle , Carrapatos/parasitologia , Uganda/epidemiologia , Vacinas Atenuadas/imunologia
14.
Transbound Emerg Dis ; 67 Suppl 1: 56-67, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32174044

RESUMO

The infection and treatment (ITM) live vaccination method for control of Theileria parva infection in cattle is increasingly being adopted, particularly in Maasai pastoralist systems. Several studies indicate positive impacts on human livelihoods. Importantly, the first detailed protocol for live vaccine production at scale has recently been published. However, quality control and delivery issues constrain vaccination sustainability and deployment. There is evidence that the distribution of T. parva is spreading from endemic areas in East Africa, North into Southern Sudan and West into Cameroon, probably as a result of anthropogenic movement of cattle. It has also recently been demonstrated that in Kenya, T. parva derived from cape buffalo can 'breakthrough' the immunity induced by ITM. However, in Tanzania, breakthrough has not been reported in areas where cattle co-graze with buffalo. It has been confirmed that buffalo in northern Uganda national parks are not infected with T. parva and R. appendiculatus appears to be absent, raising issues regarding vector distribution. Recently, there have been multiple field population genetic studies using variable number tandem repeat (VNTR) sequences and sequencing of antigen genes encoding targets of CD8+ T-cell responses. The VNTR markers generally reveal high levels of diversity. The antigen gene sequences present within the trivalent Muguga cocktail are relatively conserved among cattle transmissible T. parva populations. By contrast, greater genetic diversity is present in antigen genes from T. parva of buffalo origin. There is also evidence from several studies for transmission of components of stocks present within the Muguga cocktail, into field ticks and cattle following induction of a carrier state by immunization. In the short term, this may increase live vaccine effectiveness, through a more homogeneous challenge, but the long-term consequences are unknown.


Assuntos
Antígenos de Protozoários/imunologia , Búfalos/parasitologia , Doenças dos Bovinos/prevenção & controle , Vacinas Protozoárias/imunologia , Theileria parva/imunologia , Theileriose/prevenção & controle , Vacinação/veterinária , África/epidemiologia , Animais , Linfócitos T CD8-Positivos/imunologia , Linfócitos T CD8-Positivos/parasitologia , Portador Sadio , Bovinos , Doenças dos Bovinos/epidemiologia , Doenças dos Bovinos/parasitologia , Doenças dos Bovinos/terapia , Reservatórios de Doenças/parasitologia , Variação Genética , Genética Populacional , Repetições Minissatélites/genética , Epidemiologia Molecular , Theileria parva/genética , Theileriose/epidemiologia , Theileriose/parasitologia , Theileriose/terapia , Carrapatos/parasitologia , Vacinas Atenuadas/imunologia
15.
Mol Biol Rep ; 47(3): 1681-1689, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31939062

RESUMO

Mixed (polyclonal) infections are one of the main problems in tuberculosis (TB) management. The best available method for detecting polyclonal infections in TB is mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). According to multiple studies, MIRU-VNTR method can be applied to detect TB-related polyclonal infections in sputum samples or cultures. Setup of MIRU-VNTR on smear slides can be an efficient approach, regardless of the limitations of cultures and sputum samples in many laboratories. The present study aimed at investigating the diagnostic potential of MIRU-VNTR on smear slides in detecting mixed infections. Ziehl-Neelsen-stained microscopic slides were prepared from 14 clinical specimens. For amplifying 24 MIRU-VNTR loci, PCR assay was performed on the smear slides, clinical specimens, and cultures. Based on the 24-locus MIRU-VNTR analysis, polyclonal infections were reported in 42.85% of smear slides, while the corresponding rate was estimated at 57.1% (8/14) in the clinical samples. In the corresponding cultures, the rate of mixed infection was 7.14% (1/14). Use of smear slides can be a safe option for transferring clinical specimens between environmental and reference laboratories. Considering their significant impact on TB treatment, it is essential to diagnose mixed infections in low-resource countries with a high prevalence of mixed infections. The present findings show that direct MIRU-VNTR on smear slides can be conveniently used for the detection of mixed infections.


Assuntos
DNA Bacteriano/genética , Repetições Minissatélites/genética , Mycobacterium tuberculosis/genética , Tuberculose/diagnóstico , DNA Bacteriano/isolamento & purificação , Genótipo , Técnicas de Genotipagem/instrumentação , Técnicas de Genotipagem/métodos , Humanos , Mycobacterium tuberculosis/fisiologia , Reação em Cadeia da Polimerase , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Tuberculose/microbiologia
16.
PLoS One ; 15(1): e0227875, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31931511

RESUMO

In Italy anthrax is an endemic disease, with a few outbreaks occurring almost every year. We surveyed 234 B. anthracis strains from animals (n = 196), humans (n = 3) and the environment (n = 35) isolated during Italian outbreaks in the years 1972-2018. Despite the considerable genetic homogeneity of B. anthracis, the strains were effectively differentiated using canonical single nucleotide polymorphisms (CanSNPs) assay and multiple-locus variable-number tandem repeat analysis (MLVA). The phylogenetic identity was determined through the characterization of 14 CanSNPs. In addition, a subsequent 31-loci MLVA assay was also used to further discriminate B. anthracis genotypes into subgroups. The analysis of 14 CanSNPs allowed for the identification of four main lineages: A.Br.011/009, A.Br.008/011 (respectively belonging to A.Br.008/009 sublineage, also known Trans-Eurasian or TEA group), A.Br.005/006 and B.Br.CNEVA. A.Br.011/009, the most common subgroup of lineage A, is the major genotype of B. anthracis in Italy. The MLVA analysis revealed the presence of 55 different genotypes in Italy. Most of the genotypes are genetically very similar, supporting the hypothesis that all strains evolved from a local common ancestral strain, except for two genotypes representing the branch A.Br.005/006 and B.Br.CNEVA. The genotyping analysis applied in this study remains a very valuable tool for studying the diversity, evolution, and molecular epidemiology of B. anthracis.


Assuntos
Antraz/genética , Bacillus anthracis/genética , Epidemiologia Molecular , Filogenia , Animais , Antraz/epidemiologia , Antraz/microbiologia , Bacillus anthracis/classificação , Bacillus anthracis/patogenicidade , Genoma Bacteriano/genética , Genótipo , Humanos , Itália/epidemiologia , Repetições Minissatélites/genética , Polimorfismo de Nucleotídeo Único/genética
17.
Cancer Lett ; 470: 43-53, 2020 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-31790763

RESUMO

The complexity and continuous evolution of cancer make the design of novel strategies of treatment a constant challenge in biomedicine. Moreover, most of cancer treatments are still not tumor-specific and provoke high systemic toxicity. Herein we have developed a novel selective nanodevice to eliminate tumor cells while leaving healthy ones intact. To achieve this objective, a polyplex carrier, comprising an elastin like-recombinamer covalently conjugated to an aptamer and complexed with therapeutic DNA, was tested. This carrier forms a double-lock multifunctional device due to specific binding to a tumor cell marker and the selective expression of therapeutic DNA inside human breast-cancer cells. Due to the stability provided by ELRs, the homogeneous population of polyplexes obtained showed selective toxicity against cancer cells in in vitro and in vivo assay. Inhibition of tumor progression was detected early being very significant at the end point, with a dose-dependent reduction in tumor mass. Histological studies revealed a specific reduction in tumor parenchyma and in specific tumor cell markers. These results represent an important step toward the rational development of an efficient, safe and more specialized gene-delivery device for tumor therapy.


Assuntos
Neoplasias da Mama/terapia , Genes Transgênicos Suicidas/genética , Terapia Genética/métodos , Vetores Genéticos/administração & dosagem , Mucina-1/genética , Animais , Aptâmeros de Nucleotídeos/genética , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Sobrevivência Celular/genética , Progressão da Doença , Elastina/genética , Feminino , Técnicas de Transferência de Genes , Vetores Genéticos/efeitos adversos , Vetores Genéticos/genética , Células Hep G2 , Humanos , Células MCF-7 , Camundongos , Repetições Minissatélites/genética , Mucina-1/metabolismo , Nanopartículas/administração & dosagem , Nanopartículas/efeitos adversos , Carga Tumoral/genética , Ensaios Antitumorais Modelo de Xenoenxerto
18.
Gene ; 733: 144267, 2020 Apr 05.
Artigo em Inglês | MEDLINE | ID: mdl-31809838

RESUMO

Genetic variations in the dopamine D4 receptor (DRD4) gene and the serotonin transporter (SLC6A4) gene are involved in the aetiology of substance abuse disorder (SUD). The main aim of this study is to evaluate the genetic association of DRD4 (48 bp-VNTR) and SLC6A4 (rs25531 and 5-HTTLPR VNTR) gene polymorphisms with SUD susceptibility among the Jordanian Arab population. This study included 500 SUD patients and 500 healthy matched controls. The VNTR Genetic polymorphisms of DRD4 and SLC6A4 genes were genotyped using conventional polymerase chain reaction (PCR). While, the rs25531 SNP was genotyped using PCR-restriction fragment length polymorphism (PCR-RFLP) technique. The genetic association was analysed using different statistical analyses including chi-square, Fisher exact test and one way ANOVA test. The DRD4 exon III VNTR polymorphism was associated with SUD significantly in case of alleles 4, 7 and genotype 7/7 (P = 0.004, 0.0005 and 0.01, respectively). While, there was no genetic association between the 5-HTTLPR (LL, LS, SS), rs25331 (AA, AG, GG) and tri-allelic (SASA, LASG, LASA, LALG, LALA) genotypes (P = 0.26, 0.71 and 0.52, respectively) and SUD. Moreover, using multinomial regression analysis, the homozygous 7/7 and 2/2 VNTR genotypes of DRD4 gene were nominally significantly associated with a lower risk of addiction (OR = 0.285 with P = 0.003 and OR = 0.447 with P = 0.031, respectively) after adjusting for other covariates. Our findings showed that 4 and 7 repeats and the genotype 7/7 of DRD4 exon III VNTRs polymorphism are involved in the aetiology of SUD among Jordanian population in compared to the 5-HTTLPR polymorphisms.


Assuntos
Receptores de Dopamina D4/genética , Proteínas da Membrana Plasmática de Transporte de Serotonina/genética , Transtornos Relacionados ao Uso de Substâncias/genética , Adulto , Alelos , Árabes/genética , Estudos de Casos e Controles , Éxons/genética , Frequência do Gene/genética , Genótipo , Homozigoto , Humanos , Jordânia/epidemiologia , Masculino , Repetições Minissatélites/genética , Polimorfismo Genético/genética , Regiões Promotoras Genéticas/genética , Receptores de Dopamina D4/metabolismo , Proteínas da Membrana Plasmática de Transporte de Serotonina/metabolismo
19.
Transbound Emerg Dis ; 67(2): 834-843, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31661607

RESUMO

Brucellosis is a global pandemic infectious zoonosis. Brucella canis is a rare source of human brucellosis in China, and its public health significance remains under debate. Moreover, data pertaining to the epizootiological characteristics and geographical origin of B. canis on a nationwide scale are limited, and the risk to public safety posed by B. canis infections is unknown. The MLVA (multilocus variable-number tandem repeat analysis) assay can be helpful to analyse epidemiological correlations among Brucella isolates and to track their geographic origins. To accomplish this task, MLVA-16 was used to analyse the epidemiological links of 63 isolates obtained from dogs and humans. Sixty-three B. canis strains were sorted into three large clusters (A, B and C) and 50 different genotypes (GT1-50), and 43 unique genotypes were represented by single isolates, suggesting that these strains had no obvious epidemiological links and that canine brucellosis is predominantly sporadic in China. The other seven shared genotypes (among a total of 20 isolates) were each represented by two to eight isolates, indicating that strains from each shared genotype were epidemiologically correlated. Five of the shared genotypes were from 16 strains obtained from Beijing, indicating that canine brucellosis in Beijing originates from multipoint outbreaks with multiple sources of infection. Based on comprehensive case analysis of clinical B. canis infection, we preliminarily suggest that human B. canis infections are associated with Mycoplasma pneumoniae infection that results in decreased patient immunity. B. canis may have limited epidemiological significance for the healthy population, but it remains a significant threat to the canine breeding industry and to humans who come into close contact with dogs. Based on MLVA-11 data, B. canis strains were clustered into 16 genotypes and divided into five evolutionary branches; these data confirm that this population covers an extensive geographic area and exhibits characteristics of the origin and evolution of co-existing introduced and locally native lineages. We believe this study will contribute to strengthening efforts to prevent and control canine brucellosis and to improve public understanding of the health risks posed by B. canis.


Assuntos
Brucella canis/genética , Brucelose/epidemiologia , Surtos de Doenças/veterinária , Doenças do Cão/epidemiologia , Variação Genética , Alelos , Animais , Brucella canis/isolamento & purificação , Brucelose/diagnóstico , Brucelose/tratamento farmacológico , Brucelose/microbiologia , China/epidemiologia , Doenças do Cão/microbiologia , Cães , Feminino , Genótipo , Técnicas de Genotipagem/veterinária , Geografia , Humanos , Masculino , Pessoa de Meia-Idade , Repetições Minissatélites/genética , Epidemiologia Molecular , Saúde Pública , Zoonoses
20.
PLoS One ; 14(12): e0225848, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31825986

RESUMO

BACKGROUND: Multiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) is widely used by laboratory-based surveillance networks for subtyping pathogens causing foodborne and water-borne disease outbreaks. However, Whole Genome Sequencing (WGS) has recently emerged as the new more powerful reference for pathogen subtyping, making a data conversion method necessary which enables the users to compare the MLVA identified by either method. The MLVAType shiny application was designed to extract MLVA profiles of Vibrio cholerae isolates from WGS data while ensuring backward compatibility with traditional MLVA typing methods. METHODS: To test and validate the MLVAType algorithm, WGS-derived MLVA profiles of nineteen Vibrio cholerae isolates from Democratic Republic of the Congo (n = 9) and Uganda (n = 10) were compared to MLVA profiles generated by an in silico PCR approach and Sanger sequencing, the latter being used as the reference method. RESULTS: Results obtained by Sanger sequencing and MLVAType were totally concordant. However, the latter were affected by censored estimations whose percentage was inversely proportional to the k-mer parameter used during genome assembly. With a k-mer of 127, less than 15% estimation of V. cholerae VNTR was censored. Preventing censored estimation was only achievable when using a longer k-mer size (i.e. 175), which is not proposed in the SPAdes v.3.13.0 software. CONCLUSION: As NGS read lengths and qualities tend to increase with time, one may expect the increase of k-mer size in a near future. Using MLVAType application with a longer k-mer size will then efficiently retrieve MLVA profiles from WGS data while avoiding censored estimation.


Assuntos
Repetições Minissatélites/genética , Vibrio cholerae O1/genética , Sequenciamento Completo do Genoma , Algoritmos , Loci Gênicos , Genoma Bacteriano , Uganda
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