cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19938466
title: Carbapenem-resistant Acinetobacter baumannii contamination in an intensive care unit

description: Abstract INTRODUCTION: Acinetobacter baumannii is a major pathogen causing infections in intensive care units (ICUs). In this study, we aimed to evaluate the presence of A. baumannii in an ICU environment and gloves from ICU workers and to characterize the antimicrobial resistance of the isolates in comparison with those isolated from ICU patients at the same hospital. METHODS: ICU samples were collected from March to November 2010. Isolates biochemically characterized as Acinetobacter calcoaceticus-Acinetobacter baumannii complex were evaluated by PCR targeting the 16S rDNA and bla OXA-51 genes. Antimicrobial susceptibility was determined using the disk diffusion method, and carbapenem-resistant isolates were also evaluated for the minimum inhibitory concentration of imipenem using broth microdilution. The presence of the bla OXA-23 gene was evaluated in isolates with reduced susceptibility to carbapenems. RESULTS: A. baumannii was detected in 9.5% (84) of the 886 samples collected from the ICU environment, including from furniture, medical devices, and gloves, with bed rails being the most contaminated location (23.8%; 20/84). Multidrug-resistant (MDR) A. baumannii was found in 98.8% (83/84) of non-clinical and 97.8% (45/46) of clinical isolates. Reduced susceptibility to carbapenems was detected in 83.3% (70/84) of non-clinical and 80.4% (37/46) of clinical isolates. All isolates resistant to carbapenems harbored bla OXA-23. CONCLUSIONS: We found a strong similarity between the antimicrobial susceptibility profiles of non-clinical and clinical A. baumannii isolates. Such data highlight the ICU environment as a potential origin for the persistence of MDR A. baumannii, and hence the ICU may be a source of hospital-acquired infections caused by this microorganism.
DOI: 10.21954/ou.rd.19905514.v1
title: UKREDIDDESC corpus

description: Eight datasets comprising text extracted from the UK RED data from data.open.ac.uk, divided into 50-year periods based on the date of the reading experience.
DOI: 10.6084/m9.figshare.19938463
title: Circulating microRNA as a marker for predicting liver disease progression in patients with chronic hepatitis B

description: Abstract INTRODUCTION Hepatitis B virus (HBV) constitutes an important risk factor for cirrhosis and hepatocellular carcinoma (HCC). The link between circulating microRNAs and HBV has been previously reported, although not as a marker of liver disease progression in chronic hepatitis B (CHB). The aim of this study was to characterize miRNA expression profiles between CHB with and without cirrhosis or HCC. METHODS: A total of 12 subjects were recruited in this study. We employed an Affymetrix Gene Chip miRNA 3.0 Array to provide universal miRNA coverage. We compared microRNA expression profiles between CHB with and without cirrhosis/HCC to discover possible prognostic markers associated with the progression of CHB. RESULTS: Our results indicated 8 differently expressed microRNAs, of which miRNA-935, miRNA-342, miRNA-339, miRNA-4508, miRNA-3615, and miRNA-3200 were up-regulated, whereas miRNA-182 and miRNA-4485 were down-regulated in patients with CHB who progressed to cirrhosis/HCC as compared to those without progression. CONCLUSIONS: We demonstrated the differential expression of miRNA-935, miRNA-342, miRNA-339, miRNA-4508, miRNA-3615, miRNA-3200, miRNA-182, and miRNA-4485 between patients with HBV without cirrhosis/HCC and those who had progressed to these more severe conditions. These miRNAs may serve as novel and non-invasive prognostic markers for early detection of CHB-infected patients who are at risk of progression to cirrhosis and/or HCC.
DOI: 10.6084/m9.figshare.19938466.v1
title: Carbapenem-resistant Acinetobacter baumannii contamination in an intensive care unit

description: Abstract INTRODUCTION: Acinetobacter baumannii is a major pathogen causing infections in intensive care units (ICUs). In this study, we aimed to evaluate the presence of A. baumannii in an ICU environment and gloves from ICU workers and to characterize the antimicrobial resistance of the isolates in comparison with those isolated from ICU patients at the same hospital. METHODS: ICU samples were collected from March to November 2010. Isolates biochemically characterized as Acinetobacter calcoaceticus-Acinetobacter baumannii complex were evaluated by PCR targeting the 16S rDNA and bla OXA-51 genes. Antimicrobial susceptibility was determined using the disk diffusion method, and carbapenem-resistant isolates were also evaluated for the minimum inhibitory concentration of imipenem using broth microdilution. The presence of the bla OXA-23 gene was evaluated in isolates with reduced susceptibility to carbapenems. RESULTS: A. baumannii was detected in 9.5% (84) of the 886 samples collected from the ICU environment, including from furniture, medical devices, and gloves, with bed rails being the most contaminated location (23.8%; 20/84). Multidrug-resistant (MDR) A. baumannii was found in 98.8% (83/84) of non-clinical and 97.8% (45/46) of clinical isolates. Reduced susceptibility to carbapenems was detected in 83.3% (70/84) of non-clinical and 80.4% (37/46) of clinical isolates. All isolates resistant to carbapenems harbored bla OXA-23. CONCLUSIONS: We found a strong similarity between the antimicrobial susceptibility profiles of non-clinical and clinical A. baumannii isolates. Such data highlight the ICU environment as a potential origin for the persistence of MDR A. baumannii, and hence the ICU may be a source of hospital-acquired infections caused by this microorganism.
DOI: 10.6084/m9.figshare.19938469.v1
title: Phenotypic methods for screening carbapenem-resistant Enterobacteriaceae and assessment of their antimicrobial susceptibility profile

description: Abstract INTRODUCTION: In this study, we used phenotypic methods to screen carbapenem-resistant Enterobacteriaceae (CREs) and evaluated their antimicrobial sensitivity profile. METHODS: One hundred and seventy-eight CREs were isolated at a university hospital in south Brazil in a one-year period. Samples were assessed using disk diffusion tests with inhibitors of β-lactamases such as phenylboronic acid (AFB), cloxacillin (CLOXA), and ethylenediaminetetraacetic acid (EDTA). Strains with differences in zone diameters ≥ 5mm for disks supplemented or not were considered producers of carbapenemases. RESULTS: Klebsiella pneumoniae was the most prevalent CRE, which appeared in 80.3% cases (n = 143). Among clinical materials, the rectal swab was responsible for 43.4% of the isolations (n = 62), followed by urine (18.9%; n = 27). Among the CREs identified in this study, the growth of 56.7% (n = 101) isolates, which were putative producers of Klebsiella pneumoniae carbapenemase (KPC), were inhibited by AFB, whereas 7.3% (n = 13) isolates were inhibited by both AFB and CLOXA and were considered as putative producers of plasmid-mediated AmpC; approximately 3.4% (n = 6) were inhibited by EDTA, which possibly produced metallo-β-lactamase. Lastly, 32.6% (n = 58) cases showed negative results for AFB, CLOXA, and EDTA sensitivity, and represented another class of β-lactamases and/or mechanism of resistance. CONCLUSIONS: Phenotypic screening of CREs is important for clinical laboratories that monitor outbreaks of resistant microbes. Phenotypic tests that use carbapenemase inhibitors and enhancers such as AFB, CLOXA, and EDTA are necessary since they are good screening methods for the detection of carbapenemases.
DOI: 10.6084/m9.figshare.19938469
title: Phenotypic methods for screening carbapenem-resistant Enterobacteriaceae and assessment of their antimicrobial susceptibility profile

description: Abstract INTRODUCTION: In this study, we used phenotypic methods to screen carbapenem-resistant Enterobacteriaceae (CREs) and evaluated their antimicrobial sensitivity profile. METHODS: One hundred and seventy-eight CREs were isolated at a university hospital in south Brazil in a one-year period. Samples were assessed using disk diffusion tests with inhibitors of β-lactamases such as phenylboronic acid (AFB), cloxacillin (CLOXA), and ethylenediaminetetraacetic acid (EDTA). Strains with differences in zone diameters ≥ 5mm for disks supplemented or not were considered producers of carbapenemases. RESULTS: Klebsiella pneumoniae was the most prevalent CRE, which appeared in 80.3% cases (n = 143). Among clinical materials, the rectal swab was responsible for 43.4% of the isolations (n = 62), followed by urine (18.9%; n = 27). Among the CREs identified in this study, the growth of 56.7% (n = 101) isolates, which were putative producers of Klebsiella pneumoniae carbapenemase (KPC), were inhibited by AFB, whereas 7.3% (n = 13) isolates were inhibited by both AFB and CLOXA and were considered as putative producers of plasmid-mediated AmpC; approximately 3.4% (n = 6) were inhibited by EDTA, which possibly produced metallo-β-lactamase. Lastly, 32.6% (n = 58) cases showed negative results for AFB, CLOXA, and EDTA sensitivity, and represented another class of β-lactamases and/or mechanism of resistance. CONCLUSIONS: Phenotypic screening of CREs is important for clinical laboratories that monitor outbreaks of resistant microbes. Phenotypic tests that use carbapenemase inhibitors and enhancers such as AFB, CLOXA, and EDTA are necessary since they are good screening methods for the detection of carbapenemases.
DOI: 10.6084/m9.figshare.19938472
title: Group B Streptococcus detection in pregnant women via culture and PCR methods

description: Abstract INTRODUCTION: Group B Streptococcus (GBS), a source of neonatal infection, colonizes the gastrointestinal and genitourinary tracts of pregnant women. Routine screening for maternal GBS in late pregnancy and consequent intrapartum antibiotic prophylaxis have reduced the incidence of early-onset GBS neonatal infection. The aim of this study was to evaluate the performance of PCR, compared to culture (gold standard), in GBS colonization screening of pregnant women, and to establish the prevalence of GBS colonization among this population. METHODS: Vaginal introitus and perianal samples were collected from 204 pregnant women, between the 35th and 37th weeks of pregnancy, at the Obstetrics and Gynecology Unit of the University of Caxias do Sul General Hospital between June 2008 and September 2009. All samples were cultured after enrichment in a selective medium and then assayed by culture and PCR methods. RESULTS: The culture and PCR methods yielded detection rates of vaginal/perianal GBS colonization of 22.5% and 26%, respectively (sensitivity 100%; specificity 95.6%; positive and negative predictive values 86.8% and 100%, respectively). A higher prevalence of GBS colonization was detected in the combined vaginal and perianal samples by both culture and PCR assay analyses. CONCLUSIONS: PCR is a faster and more efficient method for GBS screening, allowing for optimal identification of women who should receive intrapartum antibiotic prophylaxis to prevent newborn infection.
DOI: 10.6084/m9.figshare.19938472.v1
title: Group B Streptococcus detection in pregnant women via culture and PCR methods

description: Abstract INTRODUCTION: Group B Streptococcus (GBS), a source of neonatal infection, colonizes the gastrointestinal and genitourinary tracts of pregnant women. Routine screening for maternal GBS in late pregnancy and consequent intrapartum antibiotic prophylaxis have reduced the incidence of early-onset GBS neonatal infection. The aim of this study was to evaluate the performance of PCR, compared to culture (gold standard), in GBS colonization screening of pregnant women, and to establish the prevalence of GBS colonization among this population. METHODS: Vaginal introitus and perianal samples were collected from 204 pregnant women, between the 35th and 37th weeks of pregnancy, at the Obstetrics and Gynecology Unit of the University of Caxias do Sul General Hospital between June 2008 and September 2009. All samples were cultured after enrichment in a selective medium and then assayed by culture and PCR methods. RESULTS: The culture and PCR methods yielded detection rates of vaginal/perianal GBS colonization of 22.5% and 26%, respectively (sensitivity 100%; specificity 95.6%; positive and negative predictive values 86.8% and 100%, respectively). A higher prevalence of GBS colonization was detected in the combined vaginal and perianal samples by both culture and PCR assay analyses. CONCLUSIONS: PCR is a faster and more efficient method for GBS screening, allowing for optimal identification of women who should receive intrapartum antibiotic prophylaxis to prevent newborn infection.
DOI: 10.6084/m9.figshare.19938547
title: Serosurvey of anti- Leptospira sp. and anti- Toxoplasma gondii antibodies in capybaras and collared and white-lipped peccaries

description: Abstract INTRODUCTION: Brazilian native species are reemerging as increasingly free-ranging populations. METHODS: Sera from 31 capybaras (Hydrochoerus hydrochaeris) and 28 peccaries (Pecari tajacu and Tayassu pecari) were tested for anti-Leptospira and anti-Toxoplasma gondii antibodies using microscopic seroagglutination test. RESULTS: Nineteen percent of free-ranging and 10.0% of captive capybaras, along with 31.8% of collared peccaries, were seropositive for T. gondii. None was seropositive for Leptospira sp. CONCLUSIONS: The present findings indicated low risk of disease, particularly among capybaras and white-lipped peccaries; however, active surveillance programs are important for monitoring wildlife health and public health once they are in public parks around cities.
DOI: 10.6084/m9.figshare.19938547.v1
title: Serosurvey of anti- Leptospira sp. and anti- Toxoplasma gondii antibodies in capybaras and collared and white-lipped peccaries

description: Abstract INTRODUCTION: Brazilian native species are reemerging as increasingly free-ranging populations. METHODS: Sera from 31 capybaras (Hydrochoerus hydrochaeris) and 28 peccaries (Pecari tajacu and Tayassu pecari) were tested for anti-Leptospira and anti-Toxoplasma gondii antibodies using microscopic seroagglutination test. RESULTS: Nineteen percent of free-ranging and 10.0% of captive capybaras, along with 31.8% of collared peccaries, were seropositive for T. gondii. None was seropositive for Leptospira sp. CONCLUSIONS: The present findings indicated low risk of disease, particularly among capybaras and white-lipped peccaries; however, active surveillance programs are important for monitoring wildlife health and public health once they are in public parks around cities.
DOI: 10.6084/m9.figshare.19938550
title: Wuchereria bancrofti infection in Haitian immigrants and the risk of re-emergence of lymphatic filariasis in the Brazilian Amazon

description: Abstract INTRODUCTION: Lymphatic filariasis (LF) is a public health problem in Haiti. Thus, the emigration of Haitians to Brazil is worrisome because of the risk for LF re-emergence. METHODS: Blood samples of Haitian immigrants, aged ≥18 years, who emigrated to Manaus (Brazilian Amazon), were examined using thick blood smears, membrane blood filtration, and immunochromatography. RESULTS: Of the 244 immigrants evaluated, 1 (0.4%) tested positive for W. bancrofti; 11.5% reported as having received LF treatment in Haiti. CONCLUSIONS: The re-emergence of LF in Manaus is unlikely, due to its low prevalence and low density of microfilaremia among the assessed Haitian immigrants.
DOI: 10.6084/m9.figshare.19938550.v1
title: Wuchereria bancrofti infection in Haitian immigrants and the risk of re-emergence of lymphatic filariasis in the Brazilian Amazon

description: Abstract INTRODUCTION: Lymphatic filariasis (LF) is a public health problem in Haiti. Thus, the emigration of Haitians to Brazil is worrisome because of the risk for LF re-emergence. METHODS: Blood samples of Haitian immigrants, aged ≥18 years, who emigrated to Manaus (Brazilian Amazon), were examined using thick blood smears, membrane blood filtration, and immunochromatography. RESULTS: Of the 244 immigrants evaluated, 1 (0.4%) tested positive for W. bancrofti; 11.5% reported as having received LF treatment in Haiti. CONCLUSIONS: The re-emergence of LF in Manaus is unlikely, due to its low prevalence and low density of microfilaremia among the assessed Haitian immigrants.
DOI: 10.6084/m9.figshare.19938569
title: Chikungunya virus infection with severe neurologic manifestations: report of four fatal cases

description: Abstract Here, we present four patients with confirmed Chikungunya virus infection showing atypical neurologic manifestations and death. This case series includes patients ranging in age from five to 92 years, with or without comorbidities. This report is important, as very few cases in the literature reporting death due to atypical Chikungunya virus infection are available.
DOI: 10.6084/m9.figshare.19938569.v1
title: Chikungunya virus infection with severe neurologic manifestations: report of four fatal cases

description: Abstract Here, we present four patients with confirmed Chikungunya virus infection showing atypical neurologic manifestations and death. This case series includes patients ranging in age from five to 92 years, with or without comorbidities. This report is important, as very few cases in the literature reporting death due to atypical Chikungunya virus infection are available.
DOI: 10.6084/m9.figshare.19938620
title: Distribution of the bla OXA , bla VEB-1 , and bla GES-1 genes and resistance patterns of ESBL-producing Pseudomonas aeruginosa isolated from hospitals in Tehran and Qazvin, Iran

description: Abstract INTRODUCTION: Pseudomonas aeruginosa is one of the most common nosocomial pathogens. The emergence of extended spectrum β-lactamases (ESBLs) has been increasingly reported as a major clinical concern worldwide. The main aim of the present study was to determine the distribution of bla OXA, bla PER-1, bla VEB-1, and bla GES-1 genes among ESBL-producing P. aeruginosa isolated from two distinct provinces in Iran. METHODS: In this study, a total of 75 (27.5%) ESBL-producing isolates were identified from 273 P. aeruginosa isolates collected from patients in Qazvin and Tehran. Phenotypic detection of ESBLs and antimicrobial susceptibility testing were performed according to the Clinical and Laboratory Standards Institute guidelines. PCR and sequencing were employed to detect bla OXA-1, bla OXA, bla GES-1, bla PER-1, and bla VEB-1 genes. Isolate genetic relationships were evaluated by repetitive extragenic palindromic sequence-based PCR (REP-PCR). RESULTS: In total, 59 (78.7%) of the ESBL-producing isolates showed multidrug resistance. The highest rates of susceptibility were observed against colistin (75 isolates, 100%) and polymyxin B (75, 100%) followed by amikacin (44, 58.7%), and piperacillin-tazobactam (40, 53.3%). The bla OXA-1 (37.3%) gene was the most common of the genes investigated, followed by bla OXA-4 (32%), bla GES-1 (16%), and bla VEB-1 (13.3%). REP-PCR identified three different genotypes: types A (89.3%), B (6.7%), and C (4%). CONCLUSIONS: We found a significant presence of bla OXA-1, bla OXA-4, bla GES-1, and bla VEB-1 genes among P. aeruginosa isolates, highlighting the need for suitable infection control strategies to effectively treat patients and prevent the further distribution of these resistant organisms.
DOI: 10.6084/m9.figshare.19938595
title: Chagas disease: review of needs, neglect, and obstacles to treatment access in Latin America

description: Abstract After more than one century since its discovery, Chagas disease is still extremely prevalent in 21 Latin American countries. Chagas disease is one of the most concerning public health problems in Latin America; the overall cost of CD treatment is approximately 7 billion United States dollars per year and it has a strong social impact on populations. Little progress has been made regarding the access to diagnosis and treatment at the primary health care level, calling into question the current policies to ensure the right to health and access to essential medications. In this article, diverse dimensions of access to treatment for Chagas disease are reviewed, illustrating the present state of benznidazole medication in relation to global production capacity, costs, and needs. The findings are based on an investigation requested by Médecins Sans Frontières Brazil through a consultancy in 2015, aiming to estimate the current costs of benznidazole production.
DOI: 10.6084/m9.figshare.19938595.v1
title: Chagas disease: review of needs, neglect, and obstacles to treatment access in Latin America

description: Abstract After more than one century since its discovery, Chagas disease is still extremely prevalent in 21 Latin American countries. Chagas disease is one of the most concerning public health problems in Latin America; the overall cost of CD treatment is approximately 7 billion United States dollars per year and it has a strong social impact on populations. Little progress has been made regarding the access to diagnosis and treatment at the primary health care level, calling into question the current policies to ensure the right to health and access to essential medications. In this article, diverse dimensions of access to treatment for Chagas disease are reviewed, illustrating the present state of benznidazole medication in relation to global production capacity, costs, and needs. The findings are based on an investigation requested by Médecins Sans Frontières Brazil through a consultancy in 2015, aiming to estimate the current costs of benznidazole production.
DOI: 10.6084/m9.figshare.19938620.v1
title: Distribution of the bla OXA , bla VEB-1 , and bla GES-1 genes and resistance patterns of ESBL-producing Pseudomonas aeruginosa isolated from hospitals in Tehran and Qazvin, Iran

description: Abstract INTRODUCTION: Pseudomonas aeruginosa is one of the most common nosocomial pathogens. The emergence of extended spectrum β-lactamases (ESBLs) has been increasingly reported as a major clinical concern worldwide. The main aim of the present study was to determine the distribution of bla OXA, bla PER-1, bla VEB-1, and bla GES-1 genes among ESBL-producing P. aeruginosa isolated from two distinct provinces in Iran. METHODS: In this study, a total of 75 (27.5%) ESBL-producing isolates were identified from 273 P. aeruginosa isolates collected from patients in Qazvin and Tehran. Phenotypic detection of ESBLs and antimicrobial susceptibility testing were performed according to the Clinical and Laboratory Standards Institute guidelines. PCR and sequencing were employed to detect bla OXA-1, bla OXA, bla GES-1, bla PER-1, and bla VEB-1 genes. Isolate genetic relationships were evaluated by repetitive extragenic palindromic sequence-based PCR (REP-PCR). RESULTS: In total, 59 (78.7%) of the ESBL-producing isolates showed multidrug resistance. The highest rates of susceptibility were observed against colistin (75 isolates, 100%) and polymyxin B (75, 100%) followed by amikacin (44, 58.7%), and piperacillin-tazobactam (40, 53.3%). The bla OXA-1 (37.3%) gene was the most common of the genes investigated, followed by bla OXA-4 (32%), bla GES-1 (16%), and bla VEB-1 (13.3%). REP-PCR identified three different genotypes: types A (89.3%), B (6.7%), and C (4%). CONCLUSIONS: We found a significant presence of bla OXA-1, bla OXA-4, bla GES-1, and bla VEB-1 genes among P. aeruginosa isolates, highlighting the need for suitable infection control strategies to effectively treat patients and prevent the further distribution of these resistant organisms.