cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14277222.v1
title: Comparative performance of four malaria rapid diagnostic tests, Vikia Malaria Pf/Pan, Meriline-Meriscreen Pf/Pv/Pan, Right Sign Malaria Pf/Pan, and Right Sign Malaria Pf, among febrile patients in Gabon

description: Abstract INTRODUCTION: Rapid diagnostic tests (RDTs) are selected based on their performances. Here, we compared the diagnostic performance of different malaria RDTs. METHODS: Febrile patients were tested for malaria using Vikia Malaria Pf/Pan, Meriline-Meriscreen Pf/Pv/Pan, Right Sign Malaria Pf/Pan, and Right Sign Malaria Pf RDTs at Melen Regional Hospital in Gabon. RESULTS: In total, 120 of 274 tested children (43.8%) had malaria. The sensitivity was &gt; 95% for all RDTs, while the specificity was &gt; 85% for two tests. One test generated invalid tests (8%). CONCLUSIONS: Based on their performances, all tests except one may be recommended for malaria diagnosis.
DOI: 10.6084/m9.figshare.14277224
title: Surveillance of the first cases of COVID-19 in Sergipe using a prospective spatiotemporal analysis: the spatial dispersion and its public health implications

description: Abstract INTRODUCTION: Coronavirus disease 2019 (COVID-19) has become a global public health emergency with lethality ranging from 1% to 5%. This study aimed to identify active high-risk transmission clusters of COVID-19 in Sergipe. METHODS: We performed a prospective space-time analysis using confirmed cases of COVID-19 during the first 7 weeks of the outbreak in Sergipe. RESULTS: The prospective space-time statistic detected "active" and emerging spatio-temporal clusters comprising six municipalities in the south-central region of the state. CONCLUSIONS: The Geographic Information System (GIS) associated with spatio-temporal scan statistics can provide timely support for surveillance and assist in decision-making.
DOI: 10.6084/m9.figshare.14277226
title: Identification of plasmid IncQ1 and NTEKPC-IId harboring bla KPC-2 in isolates from Klebsiella pneumoniae infections in patients from Recife-PE, Brazil

description: Abstract INTRODUCTION: This study investigated the genetic environment of bla KPC-2 in Klebsiella pnemoniae multi-drug resistant clinical isolates. METHODS: Four carbapenemase gene isolates resistant to carbapenems, collected from infected patients from two hospitals in Brazil, were investigated using polymerase chain reaction and plasmid DNA sequencing. RESULTS: The bla KPC-2 gene was located between ISKpn6 and a resolvase tnpR in the non-Tn4401 element (NTEKPC-IId). It was detected on a plasmid belonging to the IncQ1 group. CONCLUSIONS To our knowledge, this is the first report of the presence of the bla KPC-2 gene in the NTEKPC-IId element carried by plasmid IncQ1 from infections in Brazil.
DOI: 10.6084/m9.figshare.14277226.v1
title: Identification of plasmid IncQ1 and NTEKPC-IId harboring bla KPC-2 in isolates from Klebsiella pneumoniae infections in patients from Recife-PE, Brazil

description: Abstract INTRODUCTION: This study investigated the genetic environment of bla KPC-2 in Klebsiella pnemoniae multi-drug resistant clinical isolates. METHODS: Four carbapenemase gene isolates resistant to carbapenems, collected from infected patients from two hospitals in Brazil, were investigated using polymerase chain reaction and plasmid DNA sequencing. RESULTS: The bla KPC-2 gene was located between ISKpn6 and a resolvase tnpR in the non-Tn4401 element (NTEKPC-IId). It was detected on a plasmid belonging to the IncQ1 group. CONCLUSIONS To our knowledge, this is the first report of the presence of the bla KPC-2 gene in the NTEKPC-IId element carried by plasmid IncQ1 from infections in Brazil.
DOI: 10.6084/m9.figshare.14277228
title: Clinical response to antibiotics in indigenous versus non-indigenous children under 5 years old with community-acquired pneumonia in Otavalo, Ecuador

description: Abstract INTRODUCTION: Community-acquired pneumonia (CAP) is an important cause of morbidity and mortality worldwide. This study compares the clinical response to antimicrobials between indigenous and non-indigenous Kichwa children under 5 years old with CAP in Otavalo, Ecuador. METHODS: All children with CAP who met the inclusion criteria and were admitted at the San Luis de Otavalo Hospital between March 2017 and June 2018 were evaluated. RESULTS: No significant differences were observed in clinical responses between indigenous and non-indigenous children. CONCLUSIONS: The improved healthcare access of the Otavalo’s Kichwa population may have contributed to the observed clinical response to CAP treatment.
DOI: 10.6084/m9.figshare.11997237
title: Influence of climatic variables on the Aedes aegypti and Culex quinquefasciatus populations in Mato Grosso, Brazil

description: Abstract INTRODUCTION: Aedes aegypti and Culex quinquefasciatus are vector species responsible for the transmission of important arboviruses. METHODS: Adult mosquitoes were collected in the urban areas of four municipalities in Mato Grosso within 1 year. RESULTS: A total of 19,110 mosquitoes were collected. Among them, 16,578 (86,8%) were C. quinquefasciatus (44% female and 56% male); 2,483 (13%), A. (Stegomyia) aegypti (54% female and 46% male); and 49 (0,30%), from the genus Psorophora, Anopheles, Coquilettidia, and Sabethes. A significant correlation was observed between the number of mosquitoes from all species and dew point (female mosquitoes, p = 0.001; male mosquitoes, p = 0.001). CONCLUSIONS: The results of this study may be used as environmental indicators of mosquito populations.
DOI: 10.6084/m9.figshare.14277228.v1
title: Clinical response to antibiotics in indigenous versus non-indigenous children under 5 years old with community-acquired pneumonia in Otavalo, Ecuador

description: Abstract INTRODUCTION: Community-acquired pneumonia (CAP) is an important cause of morbidity and mortality worldwide. This study compares the clinical response to antimicrobials between indigenous and non-indigenous Kichwa children under 5 years old with CAP in Otavalo, Ecuador. METHODS: All children with CAP who met the inclusion criteria and were admitted at the San Luis de Otavalo Hospital between March 2017 and June 2018 were evaluated. RESULTS: No significant differences were observed in clinical responses between indigenous and non-indigenous children. CONCLUSIONS: The improved healthcare access of the Otavalo’s Kichwa population may have contributed to the observed clinical response to CAP treatment.
DOI: 10.6084/m9.figshare.11997237.v1
title: Influence of climatic variables on the Aedes aegypti and Culex quinquefasciatus populations in Mato Grosso, Brazil

description: Abstract INTRODUCTION: Aedes aegypti and Culex quinquefasciatus are vector species responsible for the transmission of important arboviruses. METHODS: Adult mosquitoes were collected in the urban areas of four municipalities in Mato Grosso within 1 year. RESULTS: A total of 19,110 mosquitoes were collected. Among them, 16,578 (86,8%) were C. quinquefasciatus (44% female and 56% male); 2,483 (13%), A. (Stegomyia) aegypti (54% female and 46% male); and 49 (0,30%), from the genus Psorophora, Anopheles, Coquilettidia, and Sabethes. A significant correlation was observed between the number of mosquitoes from all species and dew point (female mosquitoes, p = 0.001; male mosquitoes, p = 0.001). CONCLUSIONS: The results of this study may be used as environmental indicators of mosquito populations.
DOI: 10.6084/m9.figshare.14277231
title: Coronavirus disease and basic sanitation: too early to be worried?

description: Abstract INTRODUCTION: Considering that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been detected in feces, this study aimed to verify a possible relationship between basic sanitation indices and coronavirus disease (COVID-19) numbers/rates. METHODS: Data of COVID-19 cases registered in Brazil until May 28, 2020, and independent variables associated with basic sanitation were analyzed. RESULTS: A significant correlation between the number of cases and sewage treatment index/population density was observed. In addition, COVID-19 incidence and mortality rates were significantly associated with the total water service index and lethality rate was significantly associated with the sewage treatment index. CONCLUSIONS: Precarious basic sanitation infrastructure may potentially increase the SARS-CoV-2 transmission in Brazil.
DOI: 10.6084/m9.figshare.14277231.v1
title: Coronavirus disease and basic sanitation: too early to be worried?

description: Abstract INTRODUCTION: Considering that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been detected in feces, this study aimed to verify a possible relationship between basic sanitation indices and coronavirus disease (COVID-19) numbers/rates. METHODS: Data of COVID-19 cases registered in Brazil until May 28, 2020, and independent variables associated with basic sanitation were analyzed. RESULTS: A significant correlation between the number of cases and sewage treatment index/population density was observed. In addition, COVID-19 incidence and mortality rates were significantly associated with the total water service index and lethality rate was significantly associated with the sewage treatment index. CONCLUSIONS: Precarious basic sanitation infrastructure may potentially increase the SARS-CoV-2 transmission in Brazil.
DOI: 10.6084/m9.figshare.14277233
title: Transmission and prevalence of drug-resistant tuberculosis in a Brazilian setting under a directly observed therapy short-course strategy

description: Abstract INTRODUCTION: We aimed to estimate the prevalence and transmission of drug-resistant tuberculosis in a high-burden Brazilian setting under directly observed therapy short-course strategy. METHODS: Isolates of culture-confirmed pulmonary tuberculosis patients from Guarulhos, Brazil, diagnosed in October 2007-2011 were subjected to drug susceptibility and IS6110-restriction fragment length polymorphism testing. RESULTS: The overall resistance prevalence was 11.5% and the multi-drug resistance rate was 4.2%. Twenty-six (43.3%) of 60 drug-resistant isolates were clustered. Epidemiological relationships were identified in 11 (42.3%) patients; 30.8% of the cases were transmitted in households. CONCLUSIONS: Drug-resistant tuberculosis was relatively low and transmitted in households and the community.
DOI: 10.6084/m9.figshare.14277233.v1
title: Transmission and prevalence of drug-resistant tuberculosis in a Brazilian setting under a directly observed therapy short-course strategy

description: Abstract INTRODUCTION: We aimed to estimate the prevalence and transmission of drug-resistant tuberculosis in a high-burden Brazilian setting under directly observed therapy short-course strategy. METHODS: Isolates of culture-confirmed pulmonary tuberculosis patients from Guarulhos, Brazil, diagnosed in October 2007-2011 were subjected to drug susceptibility and IS6110-restriction fragment length polymorphism testing. RESULTS: The overall resistance prevalence was 11.5% and the multi-drug resistance rate was 4.2%. Twenty-six (43.3%) of 60 drug-resistant isolates were clustered. Epidemiological relationships were identified in 11 (42.3%) patients; 30.8% of the cases were transmitted in households. CONCLUSIONS: Drug-resistant tuberculosis was relatively low and transmitted in households and the community.
DOI: 10.6084/m9.figshare.14277237
title: Is it time to talk about the end of social distancing? A joinpoint analysis of COVID-19 time series in Brazilian capitals

description: Abstract INTRODUCTION: Monitoring coronavirus disease (COVID-19)-related infections and deaths in Brazil is controversial, with increasing pressure to ease social distance measures. However, no evidence of a sustained, widespread fall in cases exists. METHODS We used segmented (joinpoint) regression analysis to describe the behavior of COVID-19 infections in Brazilian capital cities. RESULTS All capitals showed an exponential or a near-exponential increase in cases through May. A decline in reported cases was subsequently noted in 20 cities but was only significant for 8 (29.6%) and was followed in two by a renewed increase. CONCLUSIONS Caution is warranted when considering the relaxation of restrictions.
DOI: 10.6084/m9.figshare.14277237.v1
title: Is it time to talk about the end of social distancing? A joinpoint analysis of COVID-19 time series in Brazilian capitals

description: Abstract INTRODUCTION: Monitoring coronavirus disease (COVID-19)-related infections and deaths in Brazil is controversial, with increasing pressure to ease social distance measures. However, no evidence of a sustained, widespread fall in cases exists. METHODS We used segmented (joinpoint) regression analysis to describe the behavior of COVID-19 infections in Brazilian capital cities. RESULTS All capitals showed an exponential or a near-exponential increase in cases through May. A decline in reported cases was subsequently noted in 20 cities but was only significant for 8 (29.6%) and was followed in two by a renewed increase. CONCLUSIONS Caution is warranted when considering the relaxation of restrictions.
DOI: 10.6084/m9.figshare.14277235.v1
title: Comparison of Inflammatory Markers between Adult and Pediatric Brucellosis Patients

description: Abstract INTRODUCTION: This study aimed to evaluate and compare with healthy control subjects the levels of indirect inflammatory markers such as mean platelet volume (MPV), platelet to lymphocyte ratio (PLR), and neutrophil to lymphocyte ratio (NLR) in adults and children with brucellosis. METHODS: White blood cell, neutrophil, lymphocyte, and platelet counts, and C-reactive protein (CRP) levels were retrospectively recorded for all participants. RESULTS: NLR and neutrophil counts were significantly higher in adult patients compared to those in pediatric patients. CONCLUSIONS: Indirect inflammatory markers such as NLR, PLR, MPV, red distribution width, and CRP levels may be helpful for follow-up of brucellosis.
DOI: 10.6084/m9.figshare.11997228
title: First report of Rhodnius montenegrensis (Hemiptera, Reduviidae, Triatominae) in Amazonas, Brazil

description: Abstract INTRODUCTION: Triatomines are hematophagous insects of epidemiological importance because they are vectors of Chagas disease. We present here the first report of Rhodnius montenegrensis in Amazonas, Brazil. METHODS: Triatomines were collected from Attalea butyracea palm trees in the municipality of Guajará. RESULTS: Two adult female R. montenegrensis specimens were identified. CONCLUSIONS: The present study confirms that the number of triatomine species within the Amazon has increased from 10 to 11, and the number of Brazilian states with R. montenegrensis has increased from two to three.
DOI: 10.6084/m9.figshare.11997228.v1
title: First report of Rhodnius montenegrensis (Hemiptera, Reduviidae, Triatominae) in Amazonas, Brazil

description: Abstract INTRODUCTION: Triatomines are hematophagous insects of epidemiological importance because they are vectors of Chagas disease. We present here the first report of Rhodnius montenegrensis in Amazonas, Brazil. METHODS: Triatomines were collected from Attalea butyracea palm trees in the municipality of Guajará. RESULTS: Two adult female R. montenegrensis specimens were identified. CONCLUSIONS: The present study confirms that the number of triatomine species within the Amazon has increased from 10 to 11, and the number of Brazilian states with R. montenegrensis has increased from two to three.
DOI: 10.6084/m9.figshare.14277240
title: Genomic surveillance of the Chikungunya Virus (CHIKV) in Northeast Brazil after the first outbreak in 2014

description: Abstract INTRODUCTION: We performed an epidemiological surveillance of the Chikungunya (CHIKV) lineages in Bahia after the 2014 East/Central/South African (ECSA) genotype outbreak. METHODS: Reverse-transcription polymerase chain reaction (RT-PCR), viral isolation, and phylogenetic analyses were conducted on serum samples from 605 patients with CHIKV-like symptoms during 2014-2018. RESULTS: Of the 605 samples, 167 were CHIKV-positive. Viral isolation was achieved for 20 samples; their phylogenetic analysis (E2 protein) revealed the presence of ECSA lineage and reinforced the phylogenetic relationship between ECSA and Indian Ocean lineages. CONCLUSIONS: The genomic surveillance of CHIKV showed that only ECSA lineage circulated in Bahia since the 2014 outbreak.
DOI: 10.6084/m9.figshare.14277240.v1
title: Genomic surveillance of the Chikungunya Virus (CHIKV) in Northeast Brazil after the first outbreak in 2014

description: Abstract INTRODUCTION: We performed an epidemiological surveillance of the Chikungunya (CHIKV) lineages in Bahia after the 2014 East/Central/South African (ECSA) genotype outbreak. METHODS: Reverse-transcription polymerase chain reaction (RT-PCR), viral isolation, and phylogenetic analyses were conducted on serum samples from 605 patients with CHIKV-like symptoms during 2014-2018. RESULTS: Of the 605 samples, 167 were CHIKV-positive. Viral isolation was achieved for 20 samples; their phylogenetic analysis (E2 protein) revealed the presence of ECSA lineage and reinforced the phylogenetic relationship between ECSA and Indian Ocean lineages. CONCLUSIONS: The genomic surveillance of CHIKV showed that only ECSA lineage circulated in Bahia since the 2014 outbreak.
DOI: 10.6084/m9.figshare.14277242
title: Short-term forecasting of daily COVID-19 cases in Brazil by using the Holt’s model

description: Abstract: INTRODUCTION: We evaluated the performance of the Holt’s model to forecast the daily COVID-19 reported cases in Brazil and three Brazilian states. METHODS: We chose the date of the first COVID-19 case to April 25, 2020, as the training period, and April 26 to May 3, 2020, as the test period. RESULTS: The Holt’s model performed well in forecasting the cases in Brazil and in São Paulo and Minas Gerais states, but the forecasts were underestimated in Rio de Janeiro state. Conclusions: The Holt’s model can be an adequate short-term forecasting method if their assumptions are adequately verified and validated by experts.
DOI: 10.6084/m9.figshare.14277242.v1
title: Short-term forecasting of daily COVID-19 cases in Brazil by using the Holt’s model

description: Abstract: INTRODUCTION: We evaluated the performance of the Holt’s model to forecast the daily COVID-19 reported cases in Brazil and three Brazilian states. METHODS: We chose the date of the first COVID-19 case to April 25, 2020, as the training period, and April 26 to May 3, 2020, as the test period. RESULTS: The Holt’s model performed well in forecasting the cases in Brazil and in São Paulo and Minas Gerais states, but the forecasts were underestimated in Rio de Janeiro state. Conclusions: The Holt’s model can be an adequate short-term forecasting method if their assumptions are adequately verified and validated by experts.
DOI: 10.6084/m9.figshare.14277243
title: Infections and antimicrobial resistance in an adult intensive care unit in a Brazilian hospital and the influence of drug resistance on the thirty-day mortality among patients with bloodstream infections

description: Abstract INTRODUCTION: The present study aimed to determine the incidence of health care-associated infections (HCAIs) and identify the main resistant microorganisms in intensive care unit (ICU) patients in a Brazilian university hospital. METHODS: A retrospective cohort study was conducted in a Brazilian teaching hospital between 2012 and 2014. RESULTS: Overall, 81.2% of the infections were acquired in the ICU. The most common resistant pathogenic phenotypes in all-site and bloodstream infections were oxacillin-resistant coagulase-negative staphylococci and carbapenem-resistant Acinetobacter spp. (89.9% and 87.4%; 80.6% and 70.0%), respectively. CONCLUSIONS: There is an urgent need to focus on HCAIs in ICUs in Brazil.
DOI: 10.6084/m9.figshare.14277245.v1
title: A Retrospective Survey of Rodent-borne Viruses in Rural Populations of Brazilian Amazon

description: Abstract INTRODUCTION: The Amazon tropical rainforest has the most dense and diverse ecosystem worldwide. A few studies have addressed rodent-borne diseases as potential hazards to humans in this region. METHODS: A retrospective survey was conducted using enzyme-linked immunosorbent assay for detecting mammarenavirus and orthohantavirus antibodies in 206 samples collected from rural settlers of the Brazilian Western Amazonian region. RESULTS: Six (2.91%) individuals in the age group of 16 to 36 years were found to possess antibodies against mammarenavirus. CONCLUSION: Evidence of previous exposure to mammarenavirus in the rural population points to its silent circulation in this region.
DOI: 10.6084/m9.figshare.14277235
title: Comparison of Inflammatory Markers between Adult and Pediatric Brucellosis Patients

description: Abstract INTRODUCTION: This study aimed to evaluate and compare with healthy control subjects the levels of indirect inflammatory markers such as mean platelet volume (MPV), platelet to lymphocyte ratio (PLR), and neutrophil to lymphocyte ratio (NLR) in adults and children with brucellosis. METHODS: White blood cell, neutrophil, lymphocyte, and platelet counts, and C-reactive protein (CRP) levels were retrospectively recorded for all participants. RESULTS: NLR and neutrophil counts were significantly higher in adult patients compared to those in pediatric patients. CONCLUSIONS: Indirect inflammatory markers such as NLR, PLR, MPV, red distribution width, and CRP levels may be helpful for follow-up of brucellosis.
DOI: 10.6084/m9.figshare.14277248
title: Cost-utility analysis of interferon-free treatments for patients with early-stage genotype 1 hepatitis C virus in Brazil

description: Abstract INTRODUCTION We conducted a cost-utility analysis of available interferon-free treatments for patients with early-stage genotype 1 chronic hepatitis C based on a Brazilian public health system perspective. METHODS A Markov model was derived using a cohort of stage F0-F2 patients treated as recommended by the Brazilian national guidelines. RESULTS: Glecaprevir plus pibrentasvir was superior to all other treatments, followed by sofosbuvir plus velpatasvir. Sofosbuvir plus daclatasvir was identified as the least cost-effective option. CONCLUSIONS: The above findings were confirmed via probabilistic sensitivity analysis and the tested scenarios.
DOI: 10.6084/m9.figshare.14277248.v1
title: Cost-utility analysis of interferon-free treatments for patients with early-stage genotype 1 hepatitis C virus in Brazil

description: Abstract INTRODUCTION We conducted a cost-utility analysis of available interferon-free treatments for patients with early-stage genotype 1 chronic hepatitis C based on a Brazilian public health system perspective. METHODS A Markov model was derived using a cohort of stage F0-F2 patients treated as recommended by the Brazilian national guidelines. RESULTS: Glecaprevir plus pibrentasvir was superior to all other treatments, followed by sofosbuvir plus velpatasvir. Sofosbuvir plus daclatasvir was identified as the least cost-effective option. CONCLUSIONS: The above findings were confirmed via probabilistic sensitivity analysis and the tested scenarios.
DOI: 10.6084/m9.figshare.14277245
title: A Retrospective Survey of Rodent-borne Viruses in Rural Populations of Brazilian Amazon

description: Abstract INTRODUCTION: The Amazon tropical rainforest has the most dense and diverse ecosystem worldwide. A few studies have addressed rodent-borne diseases as potential hazards to humans in this region. METHODS: A retrospective survey was conducted using enzyme-linked immunosorbent assay for detecting mammarenavirus and orthohantavirus antibodies in 206 samples collected from rural settlers of the Brazilian Western Amazonian region. RESULTS: Six (2.91%) individuals in the age group of 16 to 36 years were found to possess antibodies against mammarenavirus. CONCLUSION: Evidence of previous exposure to mammarenavirus in the rural population points to its silent circulation in this region.