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Candidemia is a growing problem in hospitals all over the world. Despite advances in the medical support of critically ill patients, candidiasis leads to prolonged hospitalization, and has a crude mortality rate around 50%. We conducted a multicenter surveillance study in 16 hospitals distributed across five regions of Brazil to assess the incidence, species distribution, antifungal susceptibility, and risk factors for bloodstream infections due to Candida species. From June 2007 to March 2010, we studied a total of 2,563 nosocomial bloodstream infection (nBSI) episodes. Candida spp. was the 7th most prevalent agent. Most of the patients were male, with a median age of 56 years. A total of 64 patients (46.7%) were in the ICU when candidemia occurred. Malignancies were the most common underlying condition (32%). The crude mortality rate of candidemia during the hospital admission was 72.2%. Non-albicans species of Candida accounted for 65.7% of the 137 yeast isolates. C. albicans (34.3%), Candida parapsilosis (24.1%), Candida tropicalis (15.3%) and Candida glabrata (10.2%) were the most prevalent species. Only 47 out of 137 Candida isolates were sent to the reference laboratory for antifungal susceptibility testing. All C. albicans, C. tropicalis and C. parapsilosis isolates were susceptible to the 5 antifungal drugs tested. Among 11 C. glabrata isolates, 36% were resistant to fluconazole, and 64% SDD. All of them were susceptible to anidulafungin and amphotericin B. We observed that C. glabrata is emerging as a major player among non-albicans Candida spp. and fluconazole resistance was primarily confined to C. glabrata and C. krusei strains. Candida resistance to echinocandins and amphotericin B remains rare in Brazil. Mortality rates remain increasingly higher than that observed in the Northern Hemisphere countries, emphasizing the need for improving local practices of clinical management of candidemia, including early diagnosis, source control and precise antifungal therapy.

Background Since its beginning, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been a challenge for clinical and molecular diagnostics, because it has been caused by a novel viral agent. Whole-genome sequencing assisted in the characterization and classification of SARS-CoV-2, and it is an essential tool to genomic surveillance aiming to identify potentials hot spots that could impact on vaccine immune response and on virus diagnosis. We describe two cases of failure at the N2 target of the RT-PCR test Xpert® Xpress SARS-CoV-2. Methods Total nucleic acid from the Nasopharyngeal (NP) and oropharyngeal (OP) swab samples and cell supernatant isolates were obtained. RNA samples were submitted to random amplification. Raw sequencing data were subjected to sequence quality controls, removal of human contaminants by aligning against the HG19 reference genome, taxonomic identification of other pathogens and genome recovery through assembly and manual curation. RT-PCR test Xpert® Xpress SARS-CoV-2 was used for molecular diagnosis of SARS-CoV-2 infection, samples were tested in duplicates. Results We identified 27 samples positive for SARS-CoV-2 with a nucleocapsid (N) gene drop out on Cepheid Xpert® Xpress SARS-CoV-2 assay. Sequencing of 2 of 27 samples revealed a single common mutation in the N gene C29197T, potentially involved in the failed detection of N target. Conclusions This study highlights the importance of genomic data to update molecular tests and vaccines.

Background Healthcare-associated infections caused by Klebsiella pneumoniae isolates are increasing and few effective antibiotics are currently available to treat patients. We observed decreased carbapenem susceptibility among K. pneumoniae isolated from patients at a tertiary private hospital that showed a phenotype compatible with carbapenemase production although this group of enzymes was not detected in any sample. The aim of this study was to describe the epidemiology and clinical outcomes associated with carbapenem-resistant K. pneumoniae and to determine the antimicrobial resistance mechanisms. Methods Risk factors associated with carbapenem-resistant K. pneumoniae infections were investigated by a matched case–control study from January 2006 through August 2008. A cohort study was also performed to evaluate the association between carbapenem resistance and in-hospital mortality. Bacterial identification and antimicrobial susceptibility were determined by Vitek 2 and Etest. Carbapenemase activity was detected using spectrophotometric assays. Production of beta-lactamases and alterations in genes encoding K. pneumoniae outer membrane proteins, OmpK35 and OmpK36, were analyzed by PCR and DNA sequencing, as well as SDS-Page. Genetic relatedness of carbapenem resistant isolates was evaluated by Pulsed Field Gel Electrophoresis. Results Sixty patients were included (20 cases and 40 controls) in the study. Mortality was higher for patients with carbapenem-resistant K. pneumoniae infections compared with those with carbapenem-susceptible K. pneumoniae (50.0% vs 25.7%). The length of central venous catheter use was independently associated with carbapenem resistance in the multivariable analysis. All strains, except one, carried bla CTX-M-2, an extended-spectrum betalactamase gene. In addition, a single isolate also possessed bla GES-1. Genes encoding plasmid-mediated AmpC beta-lactamases or carbapenemases (KPC, metallo-betalactamases or OXA-carbapenemases) were not detected. Conclusions The K. pneumoniae multidrug-resistant organisms were associated with significant mortality. The mechanisms associated with decreased K. pneumoniae carbapenem susceptibility were likely due to the presence of cephalosporinases coupled with porin alterations, which resulted from the presence of the insertion sequences in the outer membrane encoding genes.

Background Dengue virus infection (DVI) is a prevalent and potentially fatal viral disease associated with coagulopathy. So far, the coagulation profile of DVI patients with thrombocytopenia has not been assessed through a viscoelastic test such as rotational thromboelastometry. We aimed to describe the prevalence and characteristics of coagulation abnormalities in dengue fever outpatients with thrombocytopenia, addressed by both rotational thromboelastometry and conventional coagulation tests. Methods This was a cross-sectional study conducted between April 6 th and May 5 th 2015 in São Paulo, Brazil during a dengue outbreak. Thromboelastometry (ROTEM®) and the conventional coagulation tests prothrombin time (PT), international normalized ratio (INR), activated partial thromboplastin time (aPTT), thrombin time (TT), platelet count and fibrinogen levels were performed in 53 patients with DVI and thrombocytopenia. Results Despite a median interquartile range (IQR) platelet count of 77 (63–88) x 10 9 /L in DVI patients, conventional coagulation tests and plasma fibrinogen levels were within the normal range. Subjects demonstrated hypocoagulability in 71.7% (38/53) in INTEM and 54.7% (29/53) in EXTEM DVI patients. FIBTEM analyses detected only 5.7% (3/53) with hypocoagulability among this population. The median (IQR) clotting time (CT), clot formation time (CFT) and maximum clot firmness (MCF) on INTEM were, respectively, 177 (160–207) sec, 144 (108–178) sec and 48 (42–52) mm. On EXTEM, median (IQR) CT, CFT and MCF were, respectively, 69 (65–78) sec, 148 (126–198) sec and 49 (44–55) mm. Median (IQR) MCF on FIBTEM was 15 (13–18) mm. Conclusion Thromboelastometry impairment is highly prevalent in DVI patients with thrombocytopenia, particularly in INTEM and EXTEM analyses, while standard coagulation tests are normal in this setting. Clinical implications remain to be established.

Methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of healthcare-associated infections. Isolates of MRSA not belonging to the Brazilian Epidemic Clone (BEC) are colonizing and infecting patients at the hospital. These include strains carrying SCCmec type II , not previously described in the city of São Paulo, showing a trend to a MRSA genetic diversity.

Acute kidney injury (AKI) after hematopoietic stem cell transplantation (HSCT) is associated with high mortality rates. To determine the incidence and risk factors associated with AKI in patients undergoing HSCT during the infusion period, patients admitted for HSCT from 2012 to 2015 were studied. AKI was classified according to the KDIGO (Kidney Disease Improving Global Outcomes) criteria. We analyzed the main comorbidities, underlying conditions, types of transplant, preparative regimens, and use of potentially nephrotoxic drugs as risk factors for AKI. Among the 180 patients (median age 53 years), 69 (36.5%) developed AKI (23 KDIGO 1, 28 KDIGO 2, and 18 KDIGO 3), 49 (50.0%) undergoing allogeneic and 20 (22.3%) autologous transplantation, and 18 (9.4%) required dialysis. The main comorbidities were hypertension (38; 19.8%), and diabetes (19; 9.9%). The median pre-transplant creatinine was 0.7 mg/dl. Twenty-one patients died (10.9%). The risk factors for AKI in allogeneic HSCT were as follows: baseline estimated glomerular filtration rate (eGFR) (RR 1.12 (1.02–1.22), p = 0.019), use of vasopressors (RR 3.72 (2.20–6.29), p < 0.001), and use of methotrexate (RR 1.83 (1.08–3.11), p = 0.025). Male gender (RR 5.91 (1.65–21.16), p = 0.006), baseline eGFR (RR 1.22 (1.04–1.43), p = 0.011), and use of aminoglycosides (RR 3.92 (1.06–14.44), p = 0.041) were the risk factors for AKI associated with autologous HSCT. During hospitalization for HSCT, AKI was a common problem. The use of a low dose of methotrexate to prevent graft versus host disease was associated with its occurrence.

Background The collection of blood cultures is an extremely important method in the management of patients with suspected infection. Microbiology laboratories should monitor blood culture collection. Methods Over an 8-month period we developed a prospective, observational study in an adult Intensive Care Unit (ICU). We correlated the mass contained in the blood vials with blood culture positivity and we also verified the relationship between the mass of blood and blood volume collected for the diagnosis of bloodstream infection (BSI), as well as we explored factors predicting positive blood cultures. Results We evaluated 345 patients with sepsis, severe sepsis or septic shock for whom blood culture bottles were collected for the diagnosis of BSI. Of the 55 patients with BSI, 40.0 % had peripheral blood culture collection only. BSIs were classified as nosocomial in 34.5 %. In the multivariate model, the blood culture mass (in grams) remained a significant predictor of positivity, with an odds ratio 1.01 (i.e., for each additional 1 mL of blood collected there was a 1 % increase in positivity; 95 % CI 1.01–1.02, p = 0.001; Nagelkerke R Square [R 2 ] = 0.192). For blood volume collected, the adjusted odds ratio was estimated at 1.02 (95 % CI: 1.01–1.03, p < 0.001; R 2  = 0.199). For each set of collected blood cultures beyond one set, the adjusted odds ratio was estimated to be 1.27 (95 % CI: 1.14–1.41, p < 0.001; R 2  = 0.221). Conclusions Our study was a quality improvement project that showed that microbiology laboratories can use the weight of blood culture bottles to determine if appropriate volume has been collected to improve the diagnosis of BSI.

There are few data regarding microbiological findings from the disaster situation in Haiti. A rapid and accurate diagnosis of infection is necessary for the optimal efficacy of antimicrobial therapy, considering the antimicrobial spectrum and the duration of treatment. Furthermore, understanding the microorganisms and their susceptibility profiles is necessary to implement appropriate infection control policies and to contain the emergence and dissemination of Gram-negative multidrug-resistant pathogens.

Candidemia is a growing problem in hospitals all over the world. Despite advances in the medical support of critically ill patients, candidiasis leads to prolonged hospitalization, and has a crude mortality rate around 50%. We conducted a multicenter surveillance study in 16 hospitals distributed across five regions of Brazil to assess the incidence, species distribution, antifungal susceptibility, and risk factors for bloodstream infections due to Candida species. From June 2007 to March 2010, we studied a total of 2,563 nosocomial bloodstream infection (nBSI) episodes. Candida spp. was the 7th most prevalent agent. Most of the patients were male, with a median age of 56 years. A total of 64 patients (46.7%) were in the ICU when candidemia occurred. Malignancies were the most common underlying condition (32%). The crude mortality rate of candidemia during the hospital admission was 72.2%. Non-albicans species of Candida accounted for 65.7% of the 137 yeast isolates. C. albicans (34.3%), Candida parapsilosis (24.1%), Candida tropicalis (15.3%) and Candida glabrata (10.2%) were the most prevalent species. Only 47 out of 137 Candida isolates were sent to the reference laboratory for antifungal susceptibility testing. All C. albicans, C. tropicalis and C. parapsilosis isolates were susceptible to the 5 antifungal drugs tested. Among 11 C. glabrata isolates, 36% were resistant to fluconazole, and 64% SDD. All of them were susceptible to anidulafungin and amphotericin B. We observed that C. glabrata is emerging as a major player among non-albicans Candida spp. and fluconazole resistance was primarily confined to C. glabrata and C. krusei strains. Candida resistance to echinocandins and amphotericin B remains rare in Brazil. Mortality rates remain increasingly higher than that observed in the Northern Hemisphere countries, emphasizing the need for improving local practices of clinical management of candidemia, including early diagnosis, source control and precise antifungal therapy.

Background Identifying patients with hepatitis C virus (HCV) infection and enhancing the cascade of care are essential for eliminating HCV infection. This study aimed to estimate the prevalence of positive anti-HCV serology in Brasilia, Brazil, and evaluate the efficiency of the cascade of care for HCV-positive individuals. Methods This cross-sectional study analyzed 57,697 rapid screening tests for hepatitis C in individuals aged > 40 years between June 2018 and June 2019. HCV-positive patients were contacted and scheduled to undergo the HCV RNA viral test, genotyping, and transient elastography. Results The prevalence of positive serology was 0.27%. Among 161 patients with positive anti-HCV serology, 124 (77%) were contacted, 109 (67.7%) were tested for HCV RNA viral load, and 69 (42.8%) had positive results. Genotype 1 (75%) was the most prevalent genotype. Among 65 patients (94.2%) who underwent transient elastography, 30 (46.2%) presented with advanced fibrosis. Additionally, of the 161 patients, 55 (34.1%) were referred for treatment, but only 39 (24.2%) complied, with 36 (22.4%) showing sustained virological response. By the end of the study, 16 patients were still awaiting to receive medication. Conclusions The prevalence of HCV-positive patients was low in Brasilia, and the gaps in the cascade of care for these patients were significantly below the targets of HCV infection elimination. This study opens new avenues for eliminating HCV infection and suggests that partnerships with clinical laboratories to conduct anti-HCV tests are a useful strategy to improve HCV diagnosis. Trial registration Research Ethics Committee of the Faculty of Health Sciences of the University of Brasília - UNB (CAAE number 77818317.2.0000.0030 ) and by the Ethics Committee of the Health Science Teaching and Research Foundation - FEPECS/SES/DF (CAAE number 77818317.2.3001.5553 ).