Diagnosis of fasciolosis antibodies in Brazilian cattle through ELISA employing both native and recombinant antigens.

Bovine fasciolosis is a parasitic disease with a global reach. Coprological based on egg detection in fecal samples and liver inspection to evaluate the presence of the parasite is currently the gold standard for diagnosing chronic fasciolosis in cattle. However, these techniques are labor-intensive and ineffective during the acute phase of the disease. Serodiagnosis using native and recombinant antigens has become an interesting alternative in efforts to identify cattle fasciolosis. We evaluated cattle from abattoir (n = 139) and farms (n = 500) through liver inspection and coprological examination, respectively. Our laboratory team optimized and validated enzyme-linked immunosorbent assay tests based on somatic antigen, excretory/secretory proteins, and the recombinant antigen cathepsin L-1 to detect serum antibodies against fasciolosis in cattle. For animals from abattoir, 10 were positive for fasciolosis according to liver inspection. Both FhES and FhrCL-1 presented an area under the receiver operating characteristic (AUROC) curve of 0.80, with a sensitivity of 0.80 (95% CI: 0.46-0.95) and 0.70 (95% CI: 0.38-0.90) and specificity of 0.81 (95% CI: 0.73-0.87) and 0.87 (95% CI: 0.80-0.92), respectively. For those cattle from farms, 28 were positive only for fasciolosis according to coprological examination. In this scenario, FhES gave the best performance, with an AUROC of 0.84, sensitivity of 0.79 (95% CI: 0.60-0.90), and specificity of 0.86 (95% CI: 0.82-0.89). In conclusion, our study highlights the potential of serodiagnosis for accurately screening cattle fasciolosis. The promising sensitivity and specificity values of FhES when compared to liver inspection or coprological examination enhance its importance for cattle fasciolosis diagnosis. IMPORTANCE: The aim of this article was to identify antibodies against fasciolosis in cattle in Brazil. The methodology was reproduced in our laboratory and applied for the first time to the Brazilian cattle herd. The antigens tested can be used as a screening test and thus speed up the diagnosis of bovine fascioliasis.

Serological diagnosis of fasciolosis (Fasciola hepatica) in humans, cattle, and sheep: a meta-analysis.

Fasciola hepatica can cause problems in both animals and humans. Fasciolosis can be diagnosed through the indirect ELISA immunodiagnostic test. Serological diagnosis of Fasciola is based on recombinant antigens secreted by this worm. We used PubMed and Google Scholar databases to review the published literature on 'antigens with immunogenic potential' used in serological tests to identify antibodies against F. hepatica in humans, cattle, and sheep. Studies that investigated diagnostic tests with common reference standards were included in the sensitivity and/or specificity bivariate meta-analysis. In the quality and susceptibility to bias analysis of the 33 included studies, 26 fulfilled at least six (75%) of the eight QUADAS criteria and were considered good-quality papers. We found that most of the studies used native excretory-secretory antigens and recombinant cathepsin in ELISA tests for serological diagnosis of fascioliasis in humans, cattle, and sheep. The meta-analysis revealed that all antigens demonstrated good accuracy. The best results in terms of sensitivity [0.931-2.5% confidence interval (CI) and 0.985-97.5% CI] and specificity (0.959-2.5% CI and 0.997-97.5% CI) were found in human FhES. FhrCL-1, FhES, and FhrSAP-2 antigens gave the best results for the serum diagnosis of human and animal fasciolosis.

Relationship between peripheral ischemic microvascular reserve, persistent hyperlactatemia, and its temporal dynamics in sepsis: a post hoc study.

OBJECTIVE: To measure the prognostic value of peripheral ischemic microvascular reserve in the context of persistent sepsis-induced hyperlactatemia and measure its influence on the temporal dynamics of lactate and the strength of association between these variables. METHODS: This post hoc analysis of the peripheral perfusion index/postocclusive reactive hyperemia trial, an observational cohort study that enrolled patients with sepsis who persisted with lactate levels ≥ 2mmol/L after fluid resuscitation (with or without shock). Peripheral ischemic microvascular reserve was evaluated using the association of the peripheral perfusion index and postocclusive reactive hyperemia techniques. The cutoff point of ∆ peripheral perfusion index peak values (%) defined the groups with low (≤ 62%) and high peripheral ischemic microvascular reserve (> 62%). RESULTS: A total of 108 consecutive patients with persistent sepsis-induced hyperlactatemia were studied. The high peripheral ischemic microvascular reserve group showed higher 28-day mortality than the low peripheral ischemic microvascular reserve group (p < 0.01). The temporal dynamics of lactate within the first 48 hours showed a rapid decrease in lactate levels in the low peripheral ischemic microvascular reserve group (p < 0.01). However, this result was not reproduced in the linear mixed effects model. A weak correlation between peripheral ischemic microvascular reserve (%) and lactate level (mmol/L) was observed within the first 24 hours (r = 0.23; p < 0.05). CONCLUSION: The prognostic value of high peripheral ischemic microvascular reserve was confirmed in the context of persistent sepsis-induced hyperlactatemia. Although there was a weak positive correlation between peripheral ischemic microvascular reserve value and lactate level within the first 24 hours of sepsis diagnosis, the low peripheral ischemic microvascular reserve group appeared to have a faster decrease in lactate over the 48 hours of follow-up.

Peripheral ischemic reserve in sepsis and septic shock as a new bedside prognostic enrichment tool: A Brazilian cohort study.

Microvascular dysfunctions are associated with poor prognosis in sepsis. However, the potential role of clinical assessment of peripheral ischemic microvascular reserve (PIMR), a parameter that characterizes the variation of peripheral perfusion index (PPI) after brief ischemia of the upper arm, as a tool to detect sepsis-induced microvascular dysfunction and for prognostic enrichment has not been established. To address this gap, this study investigated the association of high PIMR with mortality over time in patients with sepsis and its subgroups (with and without shock) and peripheral perfusion (capillary-refill time). This observational cohort study enrolled consecutive septic patients in four Intensive-care units. After fluid resuscitation, PIMR was evaluated using the oximetry-derived PPI and post-occlusive reactive hyperemia for two consecutive days in septic patients. Two hundred and twenty-six patients were included-117 (52%) in the low PIMR group and 109 (48%) in the high PIMR group. The study revealed differences in mortality between groups on the first day, which was higher in the high PIMR group (RR 1.25; 95% CI 1.00-1.55; p = 0.04) and maintained its prognostic significance after multivariate adjustment. Subsequently, this analysis was made for sepsis subgroups and showed significant differences in mortality only for the septic-shock subgroup, with was higher in the high PIMR group (RR 2.14; 95% CI 1.49-3.08; p = 0.01). The temporal ΔPPI peak values (%) analyses did not demonstrate maintenance of the predictive value over the first 48 h in either group (p > 0.05). A moderate positive correlation (r = 0.41) between ΔPPI peak (%) and capillary-refill time (s) was found within the first 24 hours of diagnosis (p < 0.001). In conclusion, detecting a high PIMR within 24 h appears to be a prognostic marker for mortality in sepsis. Furthermore, its potential as a prognostic enrichment tool seems to occur mainly in septic shock.

Validation of the NAT Chagas IVD Kit for the Detection and Quantification of Trypanosoma cruzi in Blood Samples of Patients with Chagas Disease.

In the absence of validated biomarkers to control the cure of Chagas disease, PCR-based diagnosis is being used as the main tool for an early indication of therapeutic failure. However, since it is considered a technique of complex reproducibility, mainly due to difficulties in establishing accurate controls to guarantee the quality of the reaction, the use of PCR for Chagas disease diagnosis is restricted to specialized centers. In an effort to disseminate the molecular diagnosis of Chagas disease and its applications, new diagnostic kits based on qPCR have been made available in the market in recent years. Here, we show the results of the validation of the NAT Chagas kit (Nucleic Acid Test for Chagas Disease) for the detection and quantification of T. cruzi in blood samples of patients suspected of Chagas disease infection. The kit, composed of a TaqMan duplex reaction targeting the T. cruzi satellite nuclear DNA and an exogenous internal amplification control, presented a reportable range from 104 to 0.5 parasite equivalents/mL and a limit of detection (LOD) of 0.16 parasite equivalents/mL of blood. In addition, the NAT Chagas kit detected T. cruzi belonging to all six discrete typing units (DTUs-TcI to TcVI), similarly to the in-house real-time PCR performed with commercial reagents, which has been selected as the best performance assay in the international consensus for the validation of qPCR for Chagas disease. In the clinical validation presented here, the kit showed 100% sensitivity and 100% specificity when compared to the consensus in-house real-time PCR assay. Thus, the NAT Chagas kit, which is produced entirely in Brazil under the international standards of good manufacturing practices (GMP), appears as an excellent alternative to enable the molecular diagnosis of Chagas disease in public and private diagnostic centers, as well as to facilitate the monitoring of patients under etiological treatment participating in clinical trials.

Modulation of Klebsiella pneumoniae Outer Membrane Vesicle Protein Cargo under Antibiotic Treatment.

Klebsiella pneumoniae is a nosocomial pathogen and an important propagator of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains. Like other Gram-negative bacteria, they secrete outer membrane vesicles (OMVs) that distribute virulence and resistance factors. Here, we subjected a K. pneumoniae-XDR to subinhibitory concentrations of meropenem, amikacin, polymyxin B, and a combination of these agents to evaluate changes in the protein cargo of OMVs through liquid chromatography-tandem mass spectrometry (LC-MS/MS). Genome sequencing of the clinical isolate K. pneumoniae strain HCD1 (KpHCD1) revealed the presence of 41 resistance genes and 159 virulence factors. We identified 64 proteins in KpHCD1-OMVs modulated with different antibiotic treatments involved in processing genetic information, environmental information, cell envelope formation, energy metabolism, and drug resistance. The OMV proteome expression profile suggests that OMVs may be associated with pathogenicity, survival, stress response, and resistance dissemination.

Relationship between peripheral ischemic microvascular reserve, persistent hyperlactatemia, and its temporal dynamics in sepsis: a post hoc study / Relação entre reserva microvascular isquêmica periférica, hiperlactatemia persistente e sua dinâmica temporal na sepse: um estudo post hoc

ABSTRACT Objective: To measure the prognostic value of peripheral ischemic microvascular reserve in the context of persistent sepsis-induced hyperlactatemia and measure its influence on the temporal dynamics of lactate and the strength of association between these variables. Methods: This post hoc analysis of the peripheral perfusion index/postocclusive reactive hyperemia trial, an observational cohort study that enrolled patients with sepsis who persisted with lactate levels ≥ 2mmol/L after fluid resuscitation (with or without shock). Peripheral ischemic microvascular reserve was evaluated using the association of the peripheral perfusion index and postocclusive reactive hyperemia techniques. The cutoff point of ∆ peripheral perfusion index peak values (%) defined the groups with low (≤ 62%) and high peripheral ischemic microvascular reserve (> 62%). Results: A total of 108 consecutive patients with persistent sepsis-induced hyperlactatemia were studied. The high peripheral ischemic microvascular reserve group showed higher 28-day mortality than the low peripheral ischemic microvascular reserve group (p < 0.01). The temporal dynamics of lactate within the first 48 hours showed a rapid decrease in lactate levels in the low peripheral ischemic microvascular reserve group (p < 0.01). However, this result was not reproduced in the linear mixed effects model. A weak correlation between peripheral ischemic microvascular reserve (%) and lactate level (mmol/L) was observed within the first 24 hours (r = 0.23; p < 0.05). Conclusion: The prognostic value of high peripheral ischemic microvascular reserve was confirmed in the context of persistent sepsis-induced hyperlactatemia. Although there was a weak positive correlation between peripheral ischemic microvascular reserve value and lactate level within the first 24 hours of sepsis diagnosis, the low peripheral ischemic microvascular reserve group appeared to have a faster decrease in lactate over the 48 hours of follow-up.

RESUMO Objetivo: Avaliar o valor prognóstico da reserva microvascular isquêmica periférica no contexto da hiperlactatemia persistente induzida pela sepse, determinar sua influência na dinâmica temporal de lactato e analisar a força da associação entre essas variáveis. Métodos: Análise post hoc do estudo de índice de perfusão periférica/hiperemia reativa pós-oclusiva caracterizada por uma coorte observacional que incluiu pacientes com sepse que persistiram com níveis de lactato ≥ 2mmol/L após a ressuscitação volêmica (com ou sem choque). A reserva microvascular isquêmica periférica foi mensurada utilizando-se a associação dos métodos do índice de perfusão periférica e hiperemia reativa pós-oclusiva. O ponto de corte dos valores da ∆ índice de perfusão periférica de pico (%) definiu os grupos com baixa (≤ 62%) e alta (> 62%) reserva microvascular isquêmica periférica. Resultados: Estudaram-se 108 pacientes consecutivos com hiperlactatemia persistente induzida pela sepse. O grupo com alta reserva microvascular isquêmica periférica apresentou maior mortalidade aos 28 dias em relação ao grupo com baixa reserva microvascular isquêmica periférica (p < 0,01). A dinâmica temporal de lactato nas primeiras 48 horas mostrou redução rápida dos níveis de lactato no grupo com baixa reserva microvascular isquêmica periférica (p < 0,01). No entanto, esse resultado não foi reproduzido no modelo de efeitos mistos lineares. Observou-se fraca correlação (%) entre os valores da reserva microvascular isquêmica periférica e níveis de lactato (mmol/L) nas primeiras 24 horas (r = 0,23; p < 0,05). Conclusão: O valor prognóstico da alta reserva microvascular isquêmica periférica foi confirmado no contexto da hiperlactatemia persistente induzida por sepse. Embora tenha sido observada uma baixa correlação positiva entre os valores da reserva microvascular isquêmica periférica e os níveis de lactato nas primeiras 24 horas do diagnóstico de sepse, o grupo com baixa reserva microvascular isquêmica periférica pareceu apresentar redução mais rápida do lactato nas 48 horas de seguimento.

The prognostic value of peripheral ischemic microvascular reserve in sepsis is not related to calcitonin gene-related peptide or substance P. / O valor prognóstico da reserva microvascular isquêmica periférica na sepse não está vinculado ao peptídeo relacionado ao gene da calcitonina ou à substância P.

OBJECTIVE: To evaluate the mechanisms attributed to the prognostic value of peripheral ischemic microvascular reserve in patients with sepsis. METHODS: This observational cohort study enrolled 46 consecutive septic patients in the intensive care unit between November 2020 and October 2021. After fluid resuscitation, the peripheral ischemic microvascular reserve was evaluated using the association of postocclusion reactive hyperemia with the peripheral perfusion index. Additionally, peripheral venous blood samples were used to evaluate the neuropeptide calcitonin gene-related peptide and substance P levels in the upper limb before and immediately after postocclusion reactive hyperemia. RESULTS: There was no statistically significant correlation (p > 0.05) between basal values (pg/mL) or variations from neuropeptide levels (%) and the peripheral ischemic microvascular reserve (%). CONCLUSION: Although calcitonin gene-related peptide and substance P may have a prognostic role in sepsis, these neuropeptides do not appear to contribute to peripheral ischemic microvascular reserve.

OBJETIVO: Avaliar possíveis mecanismos atribuídos ao valor prognóstico da reserva microvascular isquêmica periférica em pacientes com sepse. MÉTODOS: Este estudo de coorte observacional incluiu 46 pacientes consecutivos com sepse em uma unidade de terapia intensiva entre novembro de 2020 e outubro de 2021. Após a ressuscitação volêmica com fluidos, avaliou-se a reserva microvascular isquêmica periférica mediante a associação dos testes hiperemia reativa pós-oclusão e índice de perfusão periférica. Adicionalmente, amostras de sangue venoso periférico foram coletadas para avaliar os níveis dos neuropeptídeos substância P e peptídeo relacionado ao gene da calcitonina no membro superior do paciente antes e imediatamente após o teste de hiperemia reativa pós-oclusão. RESULTADOS: Não houve correlação estatisticamente significativa (p > 0,05) entre os valores basais ou variações dos níveis de neuropeptídeos e a reserva microvascular isquêmica periférica. CONCLUSÃO: Embora o peptídeo relacionado ao gene da calcitonina e a substância P possam desempenhar papel prognóstico na sepse, esses neuropeptídeos não parecem contribuir para a reserva microvascular isquêmica periférica.

O valor prognóstico da reserva microvascular isquêmica periférica na sepse não está vinculado ao peptídeo relacionado ao gene da calcitonina ou à substância P / The prognostic value of peripheral ischemic microvascular reserve in sepsis is not related to calcitonin gene-related peptide or substance P

RESUMO Objetivo: Avaliar possíveis mecanismos atribuídos ao valor prognóstico da reserva microvascular isquêmica periférica em pacientes com sepse. Métodos: Este estudo de coorte observacional incluiu 46 pacientes consecutivos com sepse em uma unidade de terapia intensiva entre novembro de 2020 e outubro de 2021. Após a ressuscitação volêmica com fluidos, avaliou-se a reserva microvascular isquêmica periférica mediante a associação dos testes hiperemia reativa pós-oclusão e índice de perfusão periférica. Adicionalmente, amostras de sangue venoso periférico foram coletadas para avaliar os níveis dos neuropeptídeos substância P e peptídeo relacionado ao gene da calcitonina no membro superior do paciente antes e imediatamente após o teste de hiperemia reativa pós-oclusão. Resultados: Não houve correlação estatisticamente significativa (p > 0,05) entre os valores basais ou variações dos níveis de neuropeptídeos e a reserva microvascular isquêmica periférica. Conclusão: Embora o peptídeo relacionado ao gene da calcitonina e a substância P possam desempenhar papel prognóstico na sepse, esses neuropeptídeos não parecem contribuir para a reserva microvascular isquêmica periférica.

ABSTRACT Objective: To evaluate the mechanisms attributed to the prognostic value of peripheral ischemic microvascular reserve in patients with sepsis. Methods: This observational cohort study enrolled 46 consecutive septic patients in the intensive care unit between November 2020 and October 2021. After fluid resuscitation, the peripheral ischemic microvascular reserve was evaluated using the association of postocclusion reactive hyperemia with the peripheral perfusion index. Additionally, peripheral venous blood samples were used to evaluate the neuropeptide calcitonin gene-related peptide and substance P levels in the upper limb before and immediately after postocclusion reactive hyperemia Results: There was no statistically significant correlation (p > 0.05) between basal values (pg/mL) or variations from neuropeptide levels (%) and the peripheral ischemic microvascular reserve (%). Conclusion: Although calcitonin gene-related peptide and substance P may have a prognostic role in sepsis, these neuropeptides do not appear to contribute to peripheral ischemic microvascular reserve.

Multiplex qPCR assay to determine Leishmania infantum load in Lutzomyia longipalpis sandfly samples.

The study aimed to develop a multiplex qPCR to detect Leishmania infantum load in different sandfly sample settings using Leishmania kDNA and sandfly vacuolar ATPase (VATP) subunit C as internal control gene. The amplification of Lutzomyia longipalpis VATP gene was evaluated together with Leishmania infantum kDNA in a multiplex reaction. The concentration of VATP gene oligonucleotides was adjusted until no statistically significant difference was observed between all multiplex standard curves and singleplex curves, that is, only kDNA amplification. Limit of detection (LoD) was measured using a probit model and a cut-off defined by receiver operating characteristic analysis. Limit of quantification (LoQ) was assessed by a linear model using the coefficient of variation threshold of 25%. After assuring VATP gene amplification, its primer-probe concentrations were best at 100 nM/10 nM, respectively. The cut-off Cq value for L. infantum kDNA was defined as 35.46 with 100% of sensitivity and specificity. A total of 95% LoD was determined to be of 0.162 parasites while LoQ was 5.858. Our VATP/kDNA multiplex qPCR assay shows that it can be used to evaluate both DNA integrity and determine L. infantum load in L. longipalpis even for low yielded samples, that is, individual midguts.

Development, verification, and validation of an RT-qPCR-based protocol for Yellow Fever diagnosis.

INTRODUCTION: Yellow fever (YF) is a public health threat with frequent outbreaks in tropical and subtropical areas, despite the existence of a safe and effective vaccine. The diagnosis of acute infection of the etiologic agent relies mainly on real-time reverse transcription-polymerase chain reaction (RT-qPCR)-based assays. OBJECTIVES: The aim of this study was to evaluate and compare this novel protocol for yellow fever virus (YFV) diagnosis against assays developed in-house by reference laboratories for arboviruses. METHODS: We developed a novel molecular protocol for the detection of YFV that includes an Internal Control to validate the reaction and an External Control to monitor the RNA extraction efficiency. RESULTS AND DISCUSSION: Our assay detects one viral genome per reaction and displays no cross-reactions with dengue (1-4), Zika, or Chikungunya viruses. This novel assay yielded 95% of agreement with the reference method recommended by the Pan American Health Organization when analyzing 204 clinical samples and cultured viruses, these samples were analyzed in 3 different diagnosis centers for arboviruses in Brazil. The data suggest the use of the proposed multiplex assay protocol to do routine tests in a clinical laboratory. This product adds higher specificity and sensitivity in addition to reduced cost per test due to hands-on time and reagent spending.

Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak.

BACKGROUND: We report a genomic surveillance of SARS-CoV-2 lineages circulating in Paraná, southern Brazil, from March 2020 to April 2021. Our analysis, based on 333 genomes, revealed that the first variants detected in the state of Paraná in March 2020 were the B.1.1.33 and B.1.1.28 variants. The variants B.1.1.28 and B.1.1.33 were predominant throughout 2020 until the introduction of the variant P.2 in August 2020 and a variant of concern (VOC), Gamma (P.1), in January 2021. The VOC Gamma, a ramification of the B.1.1.28 lineage first detected in Manaus (northern Brazil), has grown rapidly since December 2020 and was thought to be responsible for the deadly second wave of COVID-19 throughout Brazil. METHODS: The 333 genomic sequences of SARS-CoV-2 from March 2020 to April 2021 were generated as part of the genomic surveillance carried out by Fiocruz in Brazil Genomahcov Fiocruz. SARS-CoV-2 sequencing was performed using representative samples from all geographic areas of Paraná. Phylogenetic analyses were performed using the 333 genomes also included other SARS-CoV-2 genomes from the state of Paraná and other states in Brazil that were deposited in the GISAID. In addition, the time-scaled phylogenetic tree was constructed with up to 3 random sequences of the Gamma variant from each state in Brazil in each month of 2021. In this analysis we also added the sequences identified as the B.1.1.28 lineage of the Amazonas state and and the Gamma-like-II (P.1-like-II) lineage identified in different regions of Brazil. RESULTS: Phylogenetic analyses of the SARS-CoV-2 genomes that were previously classified as the VOC Gamma lineage by WHO/PANGO showed that some genomes from February to April 2021 branched in a monophyletic clade and that these samples grouped together with genomes recently described with the lineage Gamma-like-II. Additionally, a new mutation (E661D) in the spike (S) protein has been identified in nearly 10% of the genomes classified as the VOC Gamma from Paraná in March and April 2021.Finally, we analyzed the correlation between the lineage and the Gamma variant frequency, age group (patients younger or older than 60 years old) and the clinical data of 86 cases from the state of Paraná. CONCLUSIONS: Our results provided a reliable picture of the evolution of the SARS-CoV-2 pandemic in the state of Paraná characterized by the dominance of the Gamma strain, as well as a high frequencies of the Gamma-like-II lineage and the S:E661D mutation. Epidemiological and genomic surveillance efforts should be continued to unveil the biological relevance of the novel mutations detected in the VOC Gamma in Paraná.

A low-cost PCR instrument for molecular disease diagnostics based on customized printed circuit board heaters.

This article describes the fabrication of a low-cost Polymerase Chain Reaction (PCR) instrument to detect diseases. In order to reduce the instrument price and simplify construction we developed an alternative fabrication process, transforming conventional printed circuit boards (PCB) in heating elements, avoiding the use of aluminum heating/cooling blocks and Peltier devices. To cool down the reaction a simple computer fan was used. The vial holder was fabricated using two double side PCB boards assembled in a sandwich-like configuration. The bottom PCB has a resistance of 0.9 Ω used to heat the reaction mix, while the top layer has a resistance of 1.1 Ω to heat the vial body, preventing vapor condensation. The top board was maintained at ~ 110 ± 1 °C during all cycles. The final device was able to heat and cool down the reaction at rates of ~ 2.0 °C/s, a rate comparable to commercial thermocyclers. An SMD NTC thermistor was used as temperature sensors, and a PID (proportional-integral-derivative) control algorithm was implemented to acquire and precisely control the temperature. We also discuss how the instrument is calibrated. The device was tested successfully for the amplification of T. pallidum (Syphilis) bacterial DNA and Zika virus RNA samples, showing similar performance to a commercial PCR instrument.

Colorimetric RT-LAMP SARS-CoV-2 diagnostic sensitivity relies on color interpretation and viral load.

The use of RT-LAMP (reverse transcriptase-loop mediated isothermal amplification) has been considered as a promising point-of-care method to diagnose COVID-19. In this manuscript we show that the RT-LAMP reaction has a sensitivity of only 200 RNA virus copies, with a color change from pink to yellow occurring in 100% of the 62 clinical samples tested positive by RT-qPCR. We also demonstrated that this reaction is 100% specific for SARS-CoV-2 after testing 57 clinical samples infected with dozens of different respiratory viruses and 74 individuals without any viral infection. Although the majority of manuscripts recently published using this technique describe only the presence of two-color states (pink = negative and yellow = positive), we verified by naked-eye and absorbance measurements that there is an evident third color cluster (orange), in general related to positive samples with low viral loads, but which cannot be defined as positive or negative by the naked eye. Orange colors should be repeated or tested by RT-qPCR to avoid a false diagnostic. RT-LAMP is therefore very reliable for samples with a RT-qPCR Ct < 30 being as sensitive and specific as a RT-qPCR test. All reactions were performed in 30 min at 65 °C. The use of reaction time longer than 30 min is also not recommended since nonspecific amplifications may cause false positives.

Direct detection of microorganisms in sonicated orthopedic devices after in vitro biofilm production and different processing conditions.

BACKGROUND: The gold standard for microbial detection in prosthetic joint infections is the multiple culture of the peri-prosthetic tissue. The fluid cultures after sonication can improve the recovery of the microorganisms. OBJECTIVE: The aim of this study was to evaluate the sonication technique with a plastic bag and the effect of refrigeration on microorganism detection with conventional culturing, MALDI-TOF MS and qPCR assay on an orthopedic screw model. METHODS: We produced biofilms of Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans on orthopedic screws, which were stored under different conditions and temperatures before sonication. After sonication, the mass spectrometry by MALDI-TOF, qPCR and culture protocols was performed using the sonicated fluid, for detecting the microorganisms involved in the biofilm. RESULTS: The bacterial bioburden decreased by approximately one log after the refrigeration period, in the screws containing P. aeruginosa and S. aureus biofilms. All the microorganisms involved in the screw biofilms were detected with MALDI-TOF and qPCR. Significant reductions in CFU counts occurred only in groups stored in the plastic bag, indicating that changes in temperature and humidity may favor cell death. However, this variation is not important for this model as it did not affect the detection owing to the high counts obtained. CONCLUSION: Microbial identification by MALDI-TOF in sonicated fluid is feasible. With qPCR, there were no differences between the detection in the screws processed immediately or after refrigeration. It is necessary to consider whether or not the refrigeration period would affect microbial recovery in an explanted prosthesis.

Assessment of clinical and epidemiological characteristics of patients with and without sepsis in intensive care units of a tertiary hospital.

OBJECTIVE: To describe the clinical and epidemiological features of patients with and without sepsis at critical care units of a public hospital. METHODS: A cross-sectional study was carried out from May 2012 to April 2013. Clinical and laboratory data of patients with and without sepsis in the intensive care units were reviewed of medical records. RESULTS: We evaluated 466 patients, 58% were men, median age was 40 years, and 146 (31%) of them were diagnosed with sepsis. The overall mortality was 20% being significantly higher for patients with sepsis (39%). The factors associated with intensive care unit mortality were the presence of sepsis (OR: 6.1, 95%CI: 3.7-10.5), age (OR: 3.6, 95%CI: 1.4-7.2), and length of hospital stay (OR: 0.96, 95%CI: 0.94-0.98). Pulmonary (49%) and intra-abdominal (20%) infections were most commonly identified sites, and coagulase-negative staphylococci and enteric Gram negative bacilli the most frequent (66%) pathogens isolated. CONCLUSION: Although the impact of sepsis on mortality is related to patients' clinical and epidemiological characteristics, a critical evaluation of these data is important since they will allow the direct implementation of local policies for managing this serious public health problem.

Assessment of clinical and epidemiological characteristics of patients with and without sepsis in intensive care units of a tertiary hospital / Avaliação das características clínicas e epidemiológicas de pacientes com e sem sepse nas unidades de terapia intensiva de um hospital terciário

ABSTRACT Objective To describe the clinical and epidemiological features of patients with and without sepsis at critical care units of a public hospital. Methods A cross-sectional study was carried out from May 2012 to April 2013. Clinical and laboratory data of patients with and without sepsis in the intensive care units were reviewed of medical records. Results We evaluated 466 patients, 58% were men, median age was 40 years, and 146 (31%) of them were diagnosed with sepsis. The overall mortality was 20% being significantly higher for patients with sepsis (39%). The factors associated with intensive care unit mortality were the presence of sepsis (OR: 6.1, 95%CI: 3.7-10.5), age (OR: 3.6, 95%CI: 1.4-7.2), and length of hospital stay (OR: 0.96, 95%CI: 0.94-0.98). Pulmonary (49%) and intra-abdominal (20%) infections were most commonly identified sites, and coagulase-negative staphylococci and enteric Gram negative bacilli the most frequent (66%) pathogens isolated. Conclusion Although the impact of sepsis on mortality is related to patients' clinical and epidemiological characteristics, a critical evaluation of these data is important since they will allow the direct implementation of local policies for managing this serious public health problem.

RESUMO Objetivo Descrever as características clínicas e epidemiológicas de pacientes com sepse e sem sepse em unidades de cuidados intensivos de um hospital público. Métodos Estudo transversal realizado de maio de 2012 a abril de 2013. Os dados clínicos e laboratoriais de pacientes com sepse e sem sepse das unidades de terapia intensiva foram revisados a partir dos prontuários médicos. Resultados Avaliamos 466 pacientes, 58% homens, mediana de idade 40 anos; sendo 146 (31%) diagnosticados com sepse. A mortalidade global foi 20%, e significativamente maior para pacientes com sepse (39%). Os fatores associados à mortalidade em unidade de terapia intensiva foram a presença de sepse (OR: 6,1, IC95%: 3,7-10,5), idade (OR: 3,6, IC95%: 1,4-7,2) e tempo de internação (OR: 0,96, IC95%: 0,94-0,98). As infecções pulmonares (49%) e intra-abdominais (20%) foram os focos mais comumente identificados, e os estafilococos coagulase-negativa e bacilos entéricos Gram-negativos foram os patógenos isolados mais frequentes (66%). Conclusão Embora o impacto da sepse sobre a mortalidade esteja relacionado às características clínicas e epidemiológicas dos pacientes, uma avaliação crítica desses dados é importante, pois permitirá a implementação direta de políticas locais para gerenciar este grave problema de saúde pública.

Conventional culture method and qPCR using 16S rDNA for tissue bank: a comparison using a model of cardiac tissue contamination.

Real-time polymerase chain reaction (qPCR) using 16S rDNA is an alternative to conventional culture-based tests. The aim of this study was to compare the conventional culture method with qPCR using 16S rDNA in a model of cardiac tissue contamination. Samples of cardiac tissue for artificial contamination with Escherichia coli and control samples were submitted for DNA extraction, which was conducted by selective and alkaline lysis and purification steps. A standard curve for 16S rDNA was constructed to determine the efficiency and analytical sensitivity of the assay in concentrations from 106 to 102 c.f.u. ml-1 using TaqMan Master Mix. 16S rDNA was detected in all contaminated samples; however, it was not detected in the the final washing step solution of the sample with a bioburden of 102 c.f.u. ml-1. Using qPCR is a potential alternative to conventional culture for microbiological safety testing of allograft tissues for biobanking, reducing the time and labour input required.

Evidence for the association of the human regulatory protein Ki-1/57 with the translational machinery.

Ki-1/57 is a cytoplasmic and nuclear protein of 57 kDa first identified in malignant cells from Hodgkin's lymphoma. Based on yeast-two hybrid protein interaction we found out that Ki-1/57 interacts with adaptor protein RACK1 (receptor of activated kinase 1), CIRP (cold-inducible RNA-binding protein), RPL38 (ribosomal protein L38) and FXR1 (fragile X mental retardation-related protein 1). Since these proteins are involved in the regulation of translation we suspected that Ki-1/57 may have a role in it. We show by immunoprecipitation the association of Ki-1/57 with FMRP. Confocal microscopy revealed that Ki-1/57 colocalizes with FMRP/FXR1/2 to stress granules. Furthermore Ki-1/57 cosediments with free ribosomal particles and enhances translation, when tethered to a reporter mRNA, suggesting that Ki-1/57 may be involved in translational regulation.

Identification of novel temperature-regulated genes in the human pathogen Cryptococcus neoformans using representational difference analysis.

Cryptococcus neoformans is a basidiomycetous fungus and an opportunistic human pathogen that causes infections in both immunocompromised and immunocompetent hosts. The ability to survive and proliferate at the human body temperature is an essential virulence attribute of this microorganism. Representational difference analysis (RDA) was used to profile gene expression in C. neoformans grown at 37 degrees C or 25 degrees C. Contig assembly of 300 high-quality sequenced cDNAs and comparison analysis to the GenBank database led to the identification of transcripts that may be critical for both pathogen-host interactions and responses to either low or high temperature growth. Gene products involved in cell wall integrity, stress response, filamentation, oxidative metabolism, protein targeting and fatty acids metabolism were induced at 37 degrees C. In addition, genes related to chromatin silencing and phospholipid transport were upregulated at 25 degrees C. Therefore, our RDA analysis, comparing saprophytic and host temperature conditions, revealed new genes with potential involvement in C. neoformans virulence.