Dataset Information

Genomic epidemiology of Mycobacterium tuberculosis in Santa Catarina, Southern Brazil.

ABSTRACT: Mycobacterium tuberculosis (M.tb), the pathogen responsible for tuberculosis (TB) poses as the major cause of death among infectious diseases. The knowledge about the molecular diversity of M.tb enables the implementation of more effective surveillance and control measures and, nowadays, Whole Genome Sequencing (WGS) holds the potential to produce high-resolution epidemiological data in a high-throughput manner. Florianópolis, the state capital of Santa Catarina (SC) in south Brazil, shows a high TB incidence (46.0/100,000). Here we carried out a WGS-based evaluation of the M.tb strain diversity, drug-resistance and ongoing transmission in the capital metropolitan region. Resistance to isoniazid, rifampicin, streptomycin was identified respectively in 4.0% (n?=?6), 2.0% (n?=?3) and 1.3% (n?=?2) of the 151 studied strains by WGS. Besides, resistance to pyrazinamide and ethambutol was detected in 0.7% (n?=?1) and reistance to ethionamide and fluoroquinolone (FQ) in 1.3% (n?=?2), while a single (0.7%) multidrug-resistant (MDR) strain was identified. SNP-based typing classified all isolates into M.tb Lineage 4, with high proportion of sublineages LAM (60.3%), T (16.4%) and Haarlem (7.9%). The average core-genome distance between isolates was 420.3 SNPs, with 43.7% of all isolates grouped across 22 genomic clusters thereby showing the presence of important ongoing TB transmission events. Most clusters were geographically distributed across the study setting which highlights the need for an urgent interruption of these large transmission chains. The data conveyed by this study shows the presence of important and uncontrolled TB transmission in the metropolitan area and provides precise data to support TB control measures in this region.

SUBMITTER: Verza M

PROVIDER: S-EPMC7393130 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Genomic epidemiology of Mycobacterium tuberculosis in Santa Catarina, Southern Brazil.

Verza Mirela M Scheffer Mara Cristina MC Salvato Richard Steiner RS Schorner Marcos André MA Barazzetti Fernando Hartmann FH Machado Hanalydia de Melo HM Medeiros Taiane Freitas TF Rovaris Darcita Buerger DB Portugal Isabel I Viveiros Miguel M Perdigão João J Kritski Afrânio A Bazzo Maria Luiza ML

Scientific reports 20200730 1

Mycobacterium tuberculosis (M.tb), the pathogen responsible for tuberculosis (TB) poses as the major cause of death among infectious diseases. The knowledge about the molecular diversity of M.tb enables the implementation of more effective surveillance and control measures and, nowadays, Whole Genome Sequencing (WGS) holds the potential to produce high-resolution epidemiological data in a high-throughput manner. Florianópolis, the state capital of Santa Catarina (SC) in south Brazil, shows a hig ...[more]

PMID: 32732910

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Project description:BackgroundPatients under haemodialysis are considered at high risk to acquire hepatitis B virus (HBV) infection. Since few data are reported from Brazil, our aim was to assess the frequency and risk factors for HBV infection in haemodialysis patients from 22 Dialysis Centres from Santa Catarina State, south of Brazil.MethodsThis study includes 813 patients, 149 haemodialysis workers and 772 healthy controls matched by sex and age. Serum samples were assayed for HBV markers and viraemia was detected by nested PCR. HBV was genotyped by partial S gene sequencing. Univariate and multivariate statistical analyses with stepwise logistic regression analysis were carried out to analyse the relationship between HBV infection and the characteristics of patients and their Dialysis Units.ResultsFrequency of HBV infection was 10.0%, 2.7% and 2.7% among patients, haemodialysis workers and controls, respectively. Amidst patients, the most frequent HBV genotypes were A (30.6%), D (57.1%) and F (12.2%). Univariate analysis showed association between HBV infection and total time in haemodialysis, type of dialysis equipment, hygiene and sterilization of equipment, number of times reusing the dialysis lines and filters, number of patients per care-worker and current HCV infection. The logistic regression model showed that total time in haemodialysis, number of times of reusing the dialysis lines and filters, and number of patients per worker were significantly related to HBV infection.ConclusionsFrequency of HBV infection among haemodialysis patients at Santa Catarina state is very high. The most frequent HBV genotypes were A, D and F. The risk for a patient to become HBV positive increase 1.47 times each month of haemodialysis; 1.96 times if the dialysis unit reuses the lines and filters > or = 10 times compared with haemodialysis units which reuse < 10 times; 3.42 times if the number of patients per worker is more than five. Sequence similarity among the HBV S gene from isolates of different patients pointed out to nosocomial transmission.

Project description:BackgroundMining activities have environmental impacts due to sediment movement and contamination of areas and may also pose risks to people's food security. In Brazil, the majority of coal mining activities are in the south, in the Santa Catarina carboniferous region. In this region, previously mined areas contaminated with heavy metals frequently occur nearby inhabited zones. Mining is part of the daily lives of local communities, and its environmental impacts are visible in the landscape; however, plants with medicinal and food use from these areas can be still consumed. Heavy metals are contaminants that do not have odor, color, or taste, and are therefore difficult to detect. We aimed to verify whether people use plants from contaminated mine areas, and understand which factors can influence the use of these resources, even from areas visibly impacted.MethodsWe conducted 195 semi-structured interviews with residents from 14 areas nearby abandoned mines in the main municipalities of the Santa Catarina carboniferous region. We asked each interviewee about the length of time they lived in the region, their perception of the quality of the environment, and what plant species were used and for what purpose. We constructed generalized multivariate linear models to verify which variables can affect the group of species mentioned and generalized linear models to verify which variables can affect the total number of citations. We estimated the frequency of citing species collected using the Smith index.ResultsFrom all interviewees, 127 (65%) reported collecting plants for medicinal and food use, directly from contaminated mine areas. Long-term residents, as well as those who noticed more environmental changes (positive and negative), cited more plants used and had more detailed knowledge of plant use in their communities. When asked if they were aware of the possible contamination of mined areas, 85% said they knew about it. However, only 10% associated negative health effects with the use of plant species collected in contaminated mined areas.ConclusionsOur study demonstrates that people living nearby contaminated areas use and consume locally sourced plants, e.g., people know little about the danger of this contamination in their food and the risk of these contaminants to their health. These results also reveal a lack of information about contamination, as well as a lack of actions that include local communities in contaminated area restoration strategies. This situation poses a risk to the food security of the people living nearby former coal mining areas.

Project description:National border areas are special places for the spread of Mycobacterium tuberculosis (MTB). These regions concentrate vulnerable populations and constant population movements. Understanding the dynamics of the transmission of MTB is fundamental to propose control measures and to monitor drug resistance. We conducted a population-based prospective study of tuberculosis (TB) to evaluate molecular characteristics of MTB isolates circulating in Roraima, a state on the border of Venezuela and Guyana. Eighty isolates were genotyped by IS6110-RFLP (restriction fragment length polymorphism), spoligotyping, and 24-locus mycobacterial interspersed repetitive unit-variable number of repeats tandem (MIRU-VNTR). Drug susceptibility tests were performed by using the proportion method and GeneXpert® MTB/RIF (Cepheid, Sunnyvale, CA). Isolates showing a phenotypic resistance profile were submitted to polymerase chain reaction (PCR) and sequencing. Spoligotyping showed 40 distinct patterns with a high prevalence of Latin-American and Mediterranean (LAM), Haarlem (H), and the "ill-defined" T clades. Mycobacterial interspersed repetitive unit -VNTR and IS6110-RFLP showed clustering rates of 21.3% and 30%, respectively. Drug resistance was detected in 11 (15.1%) isolates, and all were found to have primary resistance; among these, six (8.2%) isolates were streptomycin mono-resistant, four (5.4%) isoniazid mono-resistant, and one (1.3%) multidrug resistant. This is the first study on the molecular epidemiology and drug resistance profile of MTB from Roraima. Herein, we describe high diversity of genetic profiles circulating in this region that may be driven by the introduction of new strain types because of large population flow in this region. In summary, our results showed that analyses of these circulating strains can contribute to a better understanding of TB epidemiology in the northern Brazilian border and be useful to establish public health policies on TB prevention.

Dataset Information

Genomic epidemiology of Mycobacterium tuberculosis in Santa Catarina, Southern Brazil.

Publications

Genomic epidemiology of Mycobacterium tuberculosis in Santa Catarina, Southern Brazil.

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