Spatio-temporal patterns of tuberculosis incidence in Ribeirão Preto, State of São Paulo, southeast Brazil, and their relationship with social vulnerability: a Bayesian analysis

INTRODUCTION: The purpose of this ecological study was to evaluate the urban spatial and temporal distribution of tuberculosis (TB) in Ribeirão Preto, State of São Paulo, southeast Brazil, between 2006 and 2009 and to evaluate its relationship with factors of social vulnerability such as income and education level. METHODS: We evaluated data from TBWeb, an electronic notification system for TB cases. Measures of social vulnerability were obtained from the SEADE Foundation, and information about the number of inhabitants, education and income of the households were obtained from Brazilian Institute of Geography and Statistics. Statistical analyses were conducted by a Bayesian regression model assuming a Poisson distribution for the observed new cases of TB in each area. A conditional autoregressive structure was used for the spatial covariance structure. RESULTS: The Bayesian model confirmed the spatial heterogeneity of TB distribution in Ribeirão Preto, identifying areas with elevated risk and the effects of social vulnerability on the disease. We demonstrated that the rate of TB was correlated with the measures of income, education and social vulnerability. However, we observed areas with low vulnerability and high education and income, but with high estimated TB rates. CONCLUSIONS: The study identified areas with different risks for TB, given that the public health system deals with the characteristics of each region individually and prioritizes those that present a higher propensity to risk of TB. Complex relationships may exist between TB incidence and a wide range of environmental and intrinsic factors, which need to be studied in future research.

Bayesian genetic parameters for body weight and survival of Nile tilapia farmed in Brazil

The objective of this study was to estimate genetic parameters for survival and weight of Nile tilapia (Oreochromis niloticus), farmed in cages and ponds in Brazil, and to predict genetic gain under different scenarios. Survival was recorded as a binary response (dead or alive), during harvest time in the 2008 grow-out period. Genetic parameters were estimated using a Bayesian mixed linear-threshold animal model via Gibbs sampling. The breeding population consisted of 2,912 individual fish, which were analyzed together with the pedigree of 5,394 fish. The heritabilities estimates, with 95% posterior credible intervals, for tagging weight, harvest weight and survival were 0.17 (0.09-0.27), 0.21 (0.12-0.32) and 0.32 (0.22-0.44), respectively. Credible intervals show a 95% probability that the true genetic correlations were in a favourable direction. The selection for weight has a positive impact on survival. Estimated genetic gain was high when selecting for harvest weight (5.07%), and indirect gain for tagging weight (2.17%) and survival (2.03%) were also considerable.

Spatial patterns of leprosy in a hyperendemic state in Northern Brazil, 2001-2012

ABSTRACT OBJECTIVE To describe the spatial patterns of leprosy in the Brazilian state of Tocantins. METHODS This study was based on morbidity data obtained from the Sistema de Informações de Agravos de Notificação (SINAN – Brazilian Notifiable Diseases Information System), of the Ministry of Health. All new leprosy cases in individuals residing in the state of Tocantins, between 2001 and 2012, were included. In addition to the description of general disease indicators, a descriptive spatial analysis, empirical Bayesian analysis and spatial dependence analysis were performed by means of global and local Moran’s indexes. RESULTS A total of 14,542 new cases were recorded during the period under study. Based on the annual case detection rate, 77.0% of the municipalities were classified as hyperendemic (> 40 cases/100,000 inhabitants). Regarding the annual case detection rate in < 15 years-olds, 65.4% of the municipalities were hyperendemic (10.0 to 19.9 cases/100,000 inhabitants); 26.6% had a detection rate of grade 2 disability cases between 5.0 and 9.9 cases/100,000 inhabitants. There was a geographical overlap of clusters of municipalities with high detection rates in hyperendemic areas. Clusters with high disease risk (global Moran’s index: 0.51; p < 0.001), ongoing transmission (0.47; p < 0.001) and late diagnosis (0.44; p < 0.001) were identified mainly in the central-north and southwestern regions of Tocantins. CONCLUSIONS We identified high-risk clusters for transmission and late diagnosis of leprosy in the Brazilian state of Tocantins. Surveillance and control measures should be prioritized in these high-risk municipalities.

Determinants of the use of health care services: multilevel analysis in the Metropolitan Region of Sao Paulo

OBJECTIVE To evaluate the individual and contextual determinants of the use of health care services in the metropolitan region of Sao Paulo.METHODS Data from the Sao Paulo Megacity study – the Brazilian version of the World Mental Health Survey multicenter study – were used. A total of 3,588 adults living in 69 neighborhoods in the metropolitan region of Sao Paulo, SP, Southeastern Brazil, including 38 municipalities and 31 neighboring districts, were selected using multistratified sampling of the non-institutionalized population. Multilevel Bayesian logistic models were adjusted to identify the individual and contextual determinants of the use of health care services in the past 12 months and presence of a regular physician for routine care.RESULTS The contextual characteristics of the place of residence (income inequality, violence, and median income) showed no significant correlation (p > 0.05) with the use of health care services or with the presence of a regular physician for routine care. The only exception was the negative correlation between living in areas with high income inequality and presence of a regular physician (OR: 0.77; 95%CI 0.60;0.99) after controlling for individual characteristics. The study revealed a strong and consistent correlation between individual characteristics (mainly education and possession of health insurance), use of health care services, and presence of a regular physician. Presence of chronic and mental illnesses was strongly correlated with the use of health care services in the past year (regardless of the individual characteristics) but not with the presence of a regular physician.CONCLUSIONS Individual characteristics including higher education and possession of health insurance were important determinants of the use of health care services in the metropolitan area of Sao Paulo. A better understanding of these determinants is essential for the development of public policies that promote equitable use of health care services.

Molecular analysis of the dengue virus type 1 and 2 in Brazil based on sequences of the genomic envelope-nonstructural protein 1 junction region

The genomic sequences of the Envelope-Non-Structural protein 1 junction region (E/NS1) of 84 DEN-1 and 22 DEN-2 isolates from Brazil were determined. Most of these strains were isolated in the period from 1995 to 2001 in endemic and regions of recent dengue transmission in São Paulo State. Sequence data for DEN-1 and DEN-2 utilized in phylogenetic and split decomposition analyses also include sequences deposited in GenBank from different regions of Brazil and of the world. Phylogenetic analyses were done using both maximum likelihood and Bayesian approaches. Results for both DEN-1 and DEN-2 data are ambiguous, and support for most tree bipartitions are generally poor, suggesting that E/NS1 region does not contain enough information for recovering phylogenetic relationships among DEN-1 and DEN-2 sequences used in this study. The network graph generated in the split decomposition analysis of DEN-1 does not show evidence of grouping sequences according to country, region and clades. While the network for DEN-2 also shows ambiguities among DEN-2 sequences, it suggests that Brazilian sequences may belong to distinct subtypes of genotype III.

Use of Poisson spatiotemporal regression models for the Brazilian Amazon Forest: malaria count data

INTRODUCTION: Malaria is a serious problem in the Brazilian Amazon region, and the detection of possible risk factors could be of great interest for public health authorities. The objective of this article was to investigate the association between environmental variables and the yearly registers of malaria in the Amazon region using Bayesian spatiotemporal methods. METHODS: We used Poisson spatiotemporal regression models to analyze the Brazilian Amazon forest malaria count for the period from 1999 to 2008. In this study, we included some covariates that could be important in the yearly prediction of malaria, such as deforestation rate. We obtained the inferences using a Bayesian approach and Markov Chain Monte Carlo (MCMC) methods to simulate samples for the joint posterior distribution of interest. The discrimination of different models was also discussed. RESULTS: The model proposed here suggests that deforestation rate, the number of inhabitants per km², and the human development index (HDI) are important in the prediction of malaria cases. CONCLUSIONS: It is possible to conclude that human development, population growth, deforestation, and their associated ecological alterations are conducive to increasing malaria risk. We conclude that the use of Poisson regression models that capture the spatial and temporal effects under the Bayesian paradigm is a good strategy for modeling malaria counts.

Spatial analysis of new cases of leprosy in the State of Espírito Santo, Brazil, between 2004 and 2009

INTRODUCTION: Leprosy in Brazil is a public health issue, and there are many regions in the State of Espírito Santo with high endemic incidence levels of leprosy, characterizing this state as a priority for leprosy programs. The aim of this study was to determine the spatial distribution of coefficients of new cases of leprosy in the State of Espírito Santo, Brazil. METHODS: We conducted a descriptive and ecologic study based on the spatial distribution of leprosy in the State of Espírito Santo between 2004 and 2009. Data were gathered from the available records of the Espírito Santo State Health Secretary. The global and local Bayesian empirical methods were used to produce an estimate of leprosy risk, smoothing the fluctuation effects of the detection coefficients. RESULTS: The study resulted in a coefficient adjustment of new cases in 10 towns that changed their classification, among which, 2 went from low to medium, 4 from medium to high, 3 from high to very high, and 1 from very high to hyper-endemic. An average variation of 1.02, fluctuating between 0 and 12.39 cases/100,000 inhabitants, was found in a comparative calculation between the Local Ebest value and the average coefficient of new leprosy cases in the State of Espírito Santo. CONCLUSIONS: The spatial analysis of leprosy favors the establishment of control strategies with a better cost-benefit relationship since it reveals specific and priority regions, thereby enabling the development of actions that can interfere in the transmission chain.

An analysis of the spatiotemporal distribution of American cutaneous leishmaniasis in counties located along road and railway corridors in the State of Maranhao, Brazil

Introduction The incidence of American cutaneous leishmaniasis (ACL) is increasing in Latin America, especially in Brazil, where 256,587 cases were confirmed in the last decade. Methods This study used a Bayesian model to examine the spatial and temporal distribution of ACL cases between 2000 and 2009 in 61 counties of State of Maranhão located along the three main road and railway corridors. Results During the study period, 13,818 cases of ACL were recorded. There was a significant decrease in the incidence of ACL in the ten study years. The recorded incidence rate ranged from 7.36 to 241.45 per 100,000 inhabitants. The relative risk increased in 77% of the counties, decreased in 18% and was maintained in only five counties. Conclusions Although there was a decreased incidence of the disease, ACL was present in all of the examined municipalities, thus maintaining the risk of contracting this illness.

Spatial distribution of leprosy in areas of risk in Vitoria, State of Espirito Santo, Brazil, 2005 to 2009

Introduction Leprosy remains a relevant public health issue in Brazil. The objective of this study was to analyze the spatial distribution of new cases of leprosy and to detect areas with higher risks of disease in the City of Vitória. Methods The study was ecologically based on the spatial distribution of leprosy in the City of Vitória, State of Espírito Santo between 2005 and 2009. The data sources used came from the available records of the State Health Secretary of Espírito Santo. A global and local empirical Bayesian method was used in the spatial analysis to produce a leprosy risk estimation, and the fluctuation effect was smoothed from the detection coefficients. Results The study used thematic maps to illustrate that leprosy is distributed heterogeneously between the neighborhoods and that it is possible to identify areas with high risk of disease. The Pearson correlation coefficient of 0.926 (p = 0.001) for the Local Method indicated highly correlated coefficients. The Moran index was calculated to evaluate correlations between the incidences of adjoining districts. Conclusions We identified the spatial contexts in which there were the highest incidence rates of leprosy in Vitória during the studied period. The results contribute to the knowledge of the spatial distribution of leprosy in the City of Vitória, which can help establish more cost-effective control strategies because they indicate specific regions and priority planning activities that can interfere with the transmission chain.

Temporal, spatial and spatiotemporal analysis of the occurrence of visceral leishmaniasis in humans in the City of Birigui, State of São Paulo, from 1999 to 2012

Introduction In 1999, Birigui and Araçatuba were the first municipalities in the State of São Paulo to present autochthonous cases of visceral leishmaniasis in humans (VLH). The aim of this study was to describe the temporal, spatial and spatiotemporal behaviors of VLH in Birigui. Methods Secondary data were obtained from the Notifiable Diseases Information System from 1999 to 2012. The incidence, mortality and case fatality rates by sex and age were calculated. The cases of VLH were geocoded and grouped according to census tracts. Local empirical Bayesian incidence rates were calculated. The existence of spatial and spatiotemporal clusters was investigated using SaTScan software. Results There were 156 confirmed cases of autochthonous VLH. The incidence rate was higher in the 0-4-year-old children, and the mortality and case fatality rates were higher in people aged 60 years and older. The peaks of incidence occurred in 2006 and 2011. The Bayesian rates identified the presence of VLH in all of the census tracts in the municipality; however, spatial and spatiotemporal clusters were found in the central area of the municipality. Conclusions Birigui, located in the Araçatuba region, has recently experienced increasing numbers of VLH cases; this increase is contrary to the behavior observed over the entire region, which has shown a decreasing trend in the number of VLH cases. The observations that the highest incidence is in children 0-4 years old and the highest mortality is in people 60 years and older are in agreement with the expected patterns of VLH.

Spatial and spatiotemporal occurrence of human visceral leishmaniasis in Adamantina, State of São Paulo, Brazil

Abstract: INTRODUCTION : Several municipalities of the Western region of the State of São Paulo have been affected by human visceral leishmaniasis (HVL), including the City of Adamantina, where the first autochthonous cases occurred in 2004. Therefore, this study aimed to describe the spatial and spatiotemporal occurrence of HVL in Adamantina. METHODS : Secondary data regarding the occurrence of HVL in Adamantina between 2004 and 2011 were used. Incidence, mortality, and case fatality rates were calculated. We used local empirical Bayesian incidence rates to represent the occurrence of the disease in the census sector of the city. The existence of spatial and spatiotemporal clusters of cases was evaluated using scan statistics. In situ observation was performed to assess the socioeconomic and environmental characteristics of the areas with medium and high incidences. RESULTS : Adamantina reported cases in 70% of its census sectors. No differences were observed between sexes. The group aged 0-4 years presented the highest incidence and mortality rates, and the group aged 40-59 years presented the highest fatality rate. We detected a spatiotemporal cluster, which coincided with the commencement of the endemic in the city. CONCLUSIONS : The individuals most affected by the disease were children. The disease was present in areas with better and worse socioeconomic conditions. The use of spatial analysis techniques was important to achieve the study objectives.

Phylogeny of Thylamys (Didelphimorphia, Didelphidae) species, with special reference to Thylamys karimii

The genus Thylamys Gray, 1843 lives in the central and southern portions of South America inhabiting open and shrub-like vegetation, from prairies to dry forest habitats in contrast to the preference of other Didelphidae genera for more mesic environments. Thylamys is a speciose genus including T. elegans (Waterhouse, 1839), T. macrurus (Olfers, 1818), T. pallidior (Thomas, 1902), T. pusillus (Desmarest, 1804), T. venustus (Thomas, 1902), T. sponsorius (Thomas, 1921), T. cinderella (Thomas, 1902), T. tatei (Handley, 1957), T. karimii (Petter, 1968), and T. velutinus (Wagner, 1842) species. Previous phylogenetic analyses in this genus did not include the Brazilian species T. karimii, which is widely distributed in this country. In this study, phylogenetic analyses were performed to establish the relationships among the Brazilian T. karimii and all other previously analyzed species. We used 402-bp fragments of the mitochondrial cytochrome b gene, and the phylogeny estimates were conducted employing maximum parsimony (MP), maximum likelihood (ML), Bayesian (BY), and neighbor-joining (NJ). The topologies of the trees obtained in the different analyses were all similar and pointed out that T. karimii is the sister taxon of a group constituted of taxa from dry and arid environments named the dryland species. The dryland species consists of T. pusillus, T. pallidior, T. tatei, and T. elegans. The results of this work suggest five species groups in Thylamys. In one of them, T. velutinus and T. kariimi could constitute a sister group forming one Thylamys clade that colonized Brazil.

An ecological and comparative analysis of parasites in juvenile Mugil liza (Pisces, Mugilidae) from two sites in Samborombón bay, Argentina

ABSTRACT Mugil liza Valenciennes, 1836 is an economically important food fish and has been recommended for aquaculture in South America. A total of 278 fishes were collected in the spring and summer of 2009 and 2010. These fish were sorted into sample groups according to their size class. We used Bayesian statistics and 95% credible intervals for each parameter tested were calculated. Fish studied harbored a total of 15 different species of parasites. Diversity of parasite species found on Mugil liza was greatest at the S.R.C. collection site, but evidenced a lower species richness than at A.R. site. The 1st size fishes of both sites evidenced greater parasite diversity than either 2nd or 3rd size fish. Differences observed could be explained by the different use of habitat types at the two sites or differential susceptibility to infection by parasites. The dominance of D. fastigatainfluenced observed results of lower community diversity indexes. New works elucidating different parasite life cycles within juvenile and adults ofM. liza in Argentina, promise to be important for determining the risk of the parasitism by zoonotic metacercariae A. (P.) longa and use of this fish as food and an economic resource, and the possible use of mullet parasites in other promising fields as indicators of biodiversity, and/ or water contamination.

Genetic characterization of St. Louis encephalitis virus isolated from human in São Paulo, Brazil

The molecular characterization of SPH253157, a new strain of St. Louis encephalitis virus (SLEV), isolated in 2004 from the first case of human infection recognized in the state of São Paulo, Brazil, is reported. The patient, presenting a febrile illness without neurological involvement, was hospitalized as a probable case of dengue fever. Genomic RNA was isolated from the supernatant of C6/36 cells infected with acute phase-serum specimen of the patient and the envelope gene was amplified by reverse-transcription-polymerase chain reaction. The complete nucleotide sequence of the envelope gene of this isolate was directly sequenced from the amplified products and compared with other Brazilian and American SLEV strains. Phylogenetic analyses were carried out under maximum likelihood criterion with outgroups both included and excluded. Outgroups comprised four flavivirus of the Japanese encephalitis group. Phylogeny also included Bayesian analysis. The results indicated that the new SLEV isolate belongs to lineage III, being closely related to an Argentinean strain recovered from Culex sp. in 1979. It is concluded that there are at least 3 lineages of SLEV in Brazil.

Molecular evidence that human immunodeficiency virus type 1 dissemination in a small Brazilian city was already taking place in the early 1990s

We recently performed a molecular epidemiology survey of human immunodeficiency virus type 1 (HIV-1) infection in Miracema, a small city in Southeast Brazil, and found multiple monophyletic clusters, consistent with independent introductions and spread of different viral lineages in the city. Here we apply Bayesian coalescent-based methods to the two largest subtype B clusters and estimate that the most recent common ancestors that gave rise to these two transmission chains were in circulation around 1991-1992. The finding that HIV-1 spread in this Brazilian small city was already taking place at a time Aids was considered a problem restricted to large urban centers may have important public health implications.