Regulation of the apoptosis pathway in Rhipicephalus annulatus ticks by the protozoan Babesia bigemina

As carraças são os vetores de agentes patogénicos com maior importância na área veterinária enquanto que em saúde humana aparecem em segundo, atrás dos mosquitos. Estes ectoparasitas hematófagos obrigatórios de vertebrados terrestres são capazes de transmitir um grande número de agentes patogénicos. Diferentes ixodídeos são responsáveis pela transmissão do protozoário Babesia, agente causal de babesiose numa ampla variedade de animais incluindo humanos. A carraça Rhipicephalus annulatus, considerado um dos mais importantes ectoparasitas do gado com grande impacto económico na produção animal, é o principal vetor de Babesia bigemina. O controlo de carraças e agentes patogénicos transmitidos por carraças baseia-se sobretudo no uso de acaricidas. Contudo, a acumulação de resíduos químicos nos animais e produtos derivados de animais, bem como o aparecimento de carraças resistentes aos acaricidas e contaminação ambiental evidenciam a necessidade de desenvolver alternativas económica e ambientalmente seguras como as vacinas. A identificação e caracterização de antigénios com uma função essencial no desenvolvimento da carraça e/ou no “fitness” do parasita ainda estão a limitar o desenvolvimento de vacinas contra carraças e agentes patogénicos transmitidos por carraças. Focar as interações vetor-agente patogénico é uma abordagem que permite a identificação de antigénios de carraça com um possível efeito tanto na carraça como no agente patogénico. Estas interações têm sido ajustadas ao longo de uma coevolução duradoura: os agentes patogénicos invadem o hospedeiro e, as células hospedeiras respondem, forçando os agentes patogénicos a desenvolver novas estratégias moleculares para ultrapassar os seus mecanismos de defesa. Alguns agentes patogénicos transmitidos por carraças parecem ter desenvolvido estratégias para manipular diferentes processos metabólicos, como a apoptose, mecanismo de defesa celular baseado no sacrifício individual em beneficio do tecido ou organismo. Com estas premissas, o principal objetivo deste estudo foi a caracterização da via de apoptose durante a infeção por B. bigemina nas glândulas salivares das carraças, uma barreira que os agentes patogénicos têm de ultrapassar e explorar para serem transmitidos com sucesso ao hospedeiro vertebrado. A informação sobre a regulação da apoptose por agentes patogénicos em carraças é escassa e nula no caso de Babesia spp. Assim, o sistema R. annulatus – B. bigemina foi usado para investigar se o parasita Babesia é capaz de afetar o processo celular de apoptose. Com base num catálogo de sialotranscriptómica previamente obtido, seis genes apoptóticos de carraças foram selecionados para estudos quantitativos de expressão genética. Três genes pró-apoptóticos, DAP3, DAPK1 e VDAC demonstraram estar significativamente diferenciadamente expressos na infeção por B. bigemina. Os três genes anti-apoptóticos AATF, BI-1 e API5 não mostraram expressão diferencial significativa. No geral, os resultados sugerem que a Babesia pode ser capaz de reprimir parte da resposta celular apoptótica promovendo a sua sobrevivência e multiplicação nas células. Contudo, esta ação parece estar limitada à via intrínseca de apoptose. Estudos futuros podem esclarecer esta questão considerando mais genes de carraças para entender melhor as limitações desta regulação.Ticks are the vectors of pathogens of major importance in the veterinary area whereas in human health they appear in second, behind the mosquitoes. These obligate hematophagous ectoparasites of terrestrial vertebrates are capable of transmitting a large number of pathogens. Different ixodid ticks are responsible for the transmission of the protozoan Babesia, causal agent of babesiosis in a wide variety of animals including humans. The tick Rhipicephalus annulatus, considered one of the most important ectoparasites of cattle with great economic impact on animal production, is the main vector of Babesia bigemina. The control of ticks and tick-borne pathogens (TTBP) is mainly based on the use of acaricides. However, the accumulation of chemical residues in animals and animal products, as well as the appearance of acaricide resistant ticks and environmental contamination evidence the need for the development of cost-effective and environmentally safe alternatives such as vaccines. Identification and characterization of antigens with a key role in the development of tick and/or parasite "fitness" are still limiting the development of anti-TTBP vaccines. Focusing the intricate vector-pathogen interactions is one approach that enables the identification of tick antigens with a potential effect on both tick and pathogen. These interactions have been adjusted through long-lasting coevolution: pathogens invade the host and host cells respond by forcing pathogens to develop new molecular strategies to bypass their defense mechanisms. Some tick-borne pathogens (TBP) appear to have developed strategies for manipulating different metabolic processes, such as apoptosis, a cellular defense mechanism based on individual sacrifice for the benefit of the tissue or organism. With these premises, the main objective of this study was the characterization of the apoptosis pathway during B. bigemina infection in the salivary glands (SG) of ticks, a barrier that pathogens have to overcome and exploit to be successfully transmitted to the vertebrate host. Information regarding apoptosis regulation in ticks by pathogens is scarce and nothing is known in the case of Babesia spp. Thus, herein the system R. annulatus – B. bigemina was used to investigate if Babesia parasite is able to affect the cellular process of apoptosis. Based on a previously obtained sialotranscriptomic catalogue, six tick apoptotic genes were selected for quantitative gene expression studies. Three pro-apoptotic genes DAP3, DAPK1 and VDAC demonstrated to be significantly differentially expressed upon B. bigemina infection. The three anti-apoptotic genes AATF, BI-1 and API5 did not-show a significant differential expression. Overall, the results suggest that Babesia may be able to repress part of the cellular apoptotic response promoting survival and multiplication within cells. However, this action appears to be limited to the intrinsic apoptotic pathway. Future studies may clarify this issue considering more tick genes to better understand the limitations of such regulation

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≤ 18 years: 69, 48, 23; 85%), older adults (≥ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P < 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men

Mergulho e seleção de habitat de tartarugas-verdes chelonia mydas da África Ocidental

Dissertação de Mestrado apresentada no ISPA – Instituto Universitário para a obtenção de grau de Mestre na especialidade de Biologia Marinha e ConservaçãoA ilha de Poilão, na Guiné-Bissau, alberga uma das seis maiores populações nidificantes de tartarugas-verdes Chelonia mydas do mundo. Face à ausência de conhecimento sobre o comportamento de mergulho das tartarugas desta população, foram colocados transmissores Fast GPS equipados com sensores de profundidade em treze fêmeas nidificantes em 2021. Os movimentos horizontais e as profundidades ocupadas pelos indivíduos foram analisados para três períodos do ciclo de vida – reprodução, migração e alimentação. Durante o período de reprodução, as tartarugas permaneceram próximas a Poilão, onde a média das profundidades máximas de mergulho foi 13,9 m (± 5,0 m). Durante a migração, as tartarugas estabeleceram duas rotas distintas. Nove indivíduos migraram para a Mauritânia e um indivíduo migrou para o Gana. A maioria das rotas foram costeiras, observando-se uma única rota oceânica. A média das profundidades máximas de mergulho durante a migração para a Mauritânia e para o Gana foi 21,8 m (± 13,9 m) e 29,4 m (± 9,5 m), respetivamente. Nas áreas de alimentação, a média das profundidades máximas de mergulho foi 9,9 m (± 5,7 m) na Mauritânia e de 26,1 m (± 9,3 m) no Gana. A ocupação de águas pouco profundas durante o período de reprodução sugere que as tartarugas repousam durante parte do tempo sob estruturas rochosas para contrabalançar a flutuabilidade positiva. As profundidades usadas pelas tartarugas durante as migrações costeiras foram idênticas às usadas por conspecíficos no Mediterrâneo. Na Mauritânia, a ocupação frequente de profundidades para além do limite de crescimento de ervas marinhas e algas marinhas sugere que durante o inverno as tartarugas apresentam atividade alimentar reduzida. Por sua vez, as profundidades usadas no Gana podem sugerir que a tartaruga que frequentou esta zona terá tido uma dieta omnívora. Este estudo, para além de aumentar o conhecimento sobre a ecologia e o comportamento de mergulho das tartarugas-verdes de Poilão, contém dados que podem informar os regulamentos zonais da atividade pesqueira e os regulamentos sobre o uso de artes de pesca, de forma a reduzir as capturas acessórias de tartarugas desta população ao longo da costa oeste africana.Poilão Island, in Guinea-Bissau, hosts a green turtle Chelonia mydas nesting population among the top six worldwide. Due to the lack of knowledge about the diving behaviour of the turtles of this population, Argos linked FastGPS tags equipped with depth sensors were placed in thirteen nesting females in 2021. The horizontal movements and the depths occupied by the turtles were analysed for three periods of the life cycle – breeding, migration and foraging. During the breeding period turtles remained close to Poilão, where the average maximum dive depths was 13.9 m (± 5.0 m). During migration, turtles established two distinct routes. Nine turtles travelled to Mauritania and one travelled to Ghana. Turtles followed coastal routes and a single oceanic route was observed. The average maximum dive depths during the migration to Mauritania and Ghana were 21.8 m (± 13.9 m) and 29.4 m (± 9.5 m), respectively. On foraging grounds, the average maximum dive depths were 9.9 m (± 5.7 m) in Mauritania and 26.1 m (± 9.3 m) in Ghana. The occupation of shallow waters during the breeding season suggests that turtles may rest part of the time under rocky structures to counterbalance positive buoyancy. The depths used by turtles during coastal migrations were identical to those used by conspecifics in the Mediterranean. In Mauritania, the frequent occupation of depths beyond the limits of seagrass and algal growth suggests that during the winter turtles have reduced feeding activity. In turn, the depths used in Ghana may suggest that this particular turtle had an omnivorous diet. This study, in addition to increasing knowledge about the ecology and diving behavior of the green turtles of Poilão, contains data that can inform zonal fishing regulations and regulations on gear-use to reduce bycatch of turtles from this population along the West African coast

Characterisation of microbial attack on archaeological bone

As part of an EU funded project to investigate the factors influencing bone preservation in the archaeological record, more than 250 bones from 41 archaeological sites in five countries spanning four climatic regions were studied for diagenetic alteration. Sites were selected to cover a range of environmental conditions and archaeological contexts. Microscopic and physical (mercury intrusion porosimetry) analyses of these bones revealed that the majority (68%) had suffered microbial attack. Furthermore, significant differences were found between animal and human bone in both the state of preservation and the type of microbial attack present. These differences in preservation might result from differences in early taphonomy of the bones. © 2003 Elsevier Science Ltd. All rights reserved

Respiratory support in patients with severe COVID-19 in the International Severe Acute Respiratory and Emerging Infection (ISARIC) COVID-19 study: a prospective, multinational, observational study

Background: Up to 30% of hospitalised patients with COVID-19 require advanced respiratory support, including high-flow nasal cannulas (HFNC), non-invasive mechanical ventilation (NIV), or invasive mechanical ventilation (IMV). We aimed to describe the clinical characteristics, outcomes and risk factors for failing non-invasive respiratory support in patients treated with severe COVID-19 during the first two years of the pandemic in high-income countries (HICs) and low middle-income countries (LMICs). Methods: This is a multinational, multicentre, prospective cohort study embedded in the ISARIC-WHO COVID-19 Clinical Characterisation Protocol. Patients with laboratory-confirmed SARS-CoV-2 infection who required hospital admission were recruited prospectively. Patients treated with HFNC, NIV, or IMV within the first 24 h of hospital admission were included in this study. Descriptive statistics, random forest, and logistic regression analyses were used to describe clinical characteristics and compare clinical outcomes among patients treated with the different types of advanced respiratory support. Results: A total of 66,565 patients were included in this study. Overall, 82.6% of patients were treated in HIC, and 40.6% were admitted to the hospital during the first pandemic wave. During the first 24 h after hospital admission, patients in HICs were more frequently treated with HFNC (48.0%), followed by NIV (38.6%) and IMV (13.4%). In contrast, patients admitted in lower- and middle-income countries (LMICs) were less frequently treated with HFNC (16.1%) and the majority received IMV (59.1%). The failure rate of non-invasive respiratory support (i.e. HFNC or NIV) was 15.5%, of which 71.2% were from HIC and 28.8% from LMIC. The variables most strongly associated with non-invasive ventilation failure, defined as progression to IMV, were high leukocyte counts at hospital admission (OR [95%CI]; 5.86 [4.83-7.10]), treatment in an LMIC (OR [95%CI]; 2.04 [1.97-2.11]), and tachypnoea at hospital admission (OR [95%CI]; 1.16 [1.14-1.18]). Patients who failed HFNC/NIV had a higher 28-day fatality ratio (OR [95%CI]; 1.27 [1.25-1.30]). Conclusions: In the present international cohort, the most frequently used advanced respiratory support was the HFNC. However, IMV was used more often in LMIC. Higher leucocyte count, tachypnoea, and treatment in LMIC were risk factors for HFNC/NIV failure. HFNC/NIV failure was related to worse clinical outcomes, such as 28-day mortality. Trial registration This is a prospective observational study; therefore, no health care interventions were applied to participants, and trial registration is not applicable

Respiratory support in patients with severe COVID-19 in the International Severe Acute Respiratory and Emerging Infection (ISARIC) COVID-19 study: a prospective, multinational, observational study

Background: Up to 30% of hospitalised patients with COVID-19 require advanced respiratory support, including high-flow nasal cannulas (HFNC), non-invasive mechanical ventilation (NIV), or invasive mechanical ventilation (IMV). We aimed to describe the clinical characteristics, outcomes and risk factors for failing non-invasive respiratory support in patients treated with severe COVID-19 during the first two years of the pandemic in high-income countries (HICs) and low middle-income countries (LMICs). Methods: This is a multinational, multicentre, prospective cohort study embedded in the ISARIC-WHO COVID-19 Clinical Characterisation Protocol. Patients with laboratory-confirmed SARS-CoV-2 infection who required hospital admission were recruited prospectively. Patients treated with HFNC, NIV, or IMV within the first 24 h of hospital admission were included in this study. Descriptive statistics, random forest, and logistic regression analyses were used to describe clinical characteristics and compare clinical outcomes among patients treated with the different types of advanced respiratory support. Results: A total of 66,565 patients were included in this study. Overall, 82.6% of patients were treated in HIC, and 40.6% were admitted to the hospital during the first pandemic wave. During the first 24 h after hospital admission, patients in HICs were more frequently treated with HFNC (48.0%), followed by NIV (38.6%) and IMV (13.4%). In contrast, patients admitted in lower- and middle-income countries (LMICs) were less frequently treated with HFNC (16.1%) and the majority received IMV (59.1%). The failure rate of non-invasive respiratory support (i.e. HFNC or NIV) was 15.5%, of which 71.2% were from HIC and 28.8% from LMIC. The variables most strongly associated with non-invasive ventilation failure, defined as progression to IMV, were high leukocyte counts at hospital admission (OR [95%CI]; 5.86 [4.83–7.10]), treatment in an LMIC (OR [95%CI]; 2.04 [1.97–2.11]), and tachypnoea at hospital admission (OR [95%CI]; 1.16 [1.14–1.18]). Patients who failed HFNC/NIV had a higher 28-day fatality ratio (OR [95%CI]; 1.27 [1.25–1.30]). Conclusions: In the present international cohort, the most frequently used advanced respiratory support was the HFNC. However, IMV was used more often in LMIC. Higher leucocyte count, tachypnoea, and treatment in LMIC were risk factors for HFNC/NIV failure. HFNC/NIV failure was related to worse clinical outcomes, such as 28-day mortality. Trial registration This is a prospective observational study; therefore, no health care interventions were applied to participants, and trial registration is not applicable

Thrombotic and hemorrhagic complications of COVID-19 in adults hospitalized in high-income countries compared with those in adults hospitalized in low- and middle-income countries in an international registry

Background: COVID-19 has been associated with a broad range of thromboembolic, ischemic, and hemorrhagic complications (coagulopathy complications). Most studies have focused on patients with severe disease from high-income countries (HICs). Objectives: The main aims were to compare the frequency of coagulopathy complications in developing countries (low- and middle-income countries [LMICs]) with those in HICs, delineate the frequency across a range of treatment levels, and determine associations with in-hospital mortality. Methods: Adult patients enrolled in an observational, multinational registry, the International Severe Acute Respiratory and Emerging Infections COVID-19 study, between January 1, 2020, and September 15, 2021, met inclusion criteria, including admission to a hospital for laboratory-confirmed, acute COVID-19 and data on complications and survival. The advanced-treatment cohort received care, such as admission to the intensive care unit, mechanical ventilation, or inotropes or vasopressors; the basic-treatment cohort did not receive any of these interventions. Results: The study population included 495,682 patients from 52 countries, with 63% from LMICs and 85% in the basic treatment cohort. The frequency of coagulopathy complications was higher in HICs (0.76%-3.4%) than in LMICs (0.09%-1.22%). Complications were more frequent in the advanced-treatment cohort than in the basic-treatment cohort. Coagulopathy complications were associated with increased in-hospital mortality (odds ratio, 1.58; 95% CI, 1.52-1.64). The increased mortality associated with these complications was higher in LMICs (58.5%) than in HICs (35.4%). After controlling for coagulopathy complications, treatment intensity, and multiple other factors, the mortality was higher among patients in LMICs than among patients in HICs (odds ratio, 1.45; 95% CI, 1.39-1.51). Conclusion: In a large, international registry of patients hospitalized for COVID-19, coagulopathy complications were more frequent in HICs than in LMICs (developing countries). Increased mortality associated with coagulopathy complications was of a greater magnitude among patients in LMICs. Additional research is needed regarding timely diagnosis of and intervention for coagulation derangements associated with COVID-19, particularly for limited-resource settings

Association of Country Income Level With the Characteristics and Outcomes of Critically Ill Patients Hospitalized With Acute Kidney Injury and COVID-19

Introduction: Acute kidney injury (AKI) has been identified as one of the most common and significant problems in hospitalized patients with COVID-19. However, studies examining the relationship between COVID-19 and AKI in low- and low-middle income countries (LLMIC) are lacking. Given that AKI is known to carry a higher mortality rate in these countries, it is important to understand differences in this population. Methods: This prospective, observational study examines the AKI incidence and characteristics of 32,210 patients with COVID-19 from 49 countries across all income levels who were admitted to an intensive care unit during their hospital stay. Results: Among patients with COVID-19 admitted to the intensive care unit, AKI incidence was highest in patients in LLMIC, followed by patients in upper-middle income countries (UMIC) and high-income countries (HIC) (53%, 38%, and 30%, respectively), whereas dialysis rates were lowest among patients with AKI from LLMIC and highest among those from HIC (27% vs. 45%). Patients with AKI in LLMIC had the largest proportion of community-acquired AKI (CA-AKI) and highest rate of in-hospital death (79% vs. 54% in HIC and 66% in UMIC). The association between AKI, being from LLMIC and in-hospital death persisted even after adjusting for disease severity. Conclusions: AKI is a particularly devastating complication of COVID-19 among patients from poorer nations where the gaps in accessibility and quality of healthcare delivery have a major impact on patient outcomes

At-admission prediction of mortality and pulmonary embolism in an international cohort of hospitalised patients with COVID-19 using statistical and machine learning methods

By September 2022, more than 600 million cases of SARS-CoV-2 infection have been reported globally, resulting in over 6.5 million deaths. COVID-19 mortality risk estimators are often, however, developed with small unrepresentative samples and with methodological limitations. It is highly important to develop predictive tools for pulmonary embolism (PE) in COVID-19 patients as one of the most severe preventable complications of COVID-19. Early recognition can help provide life-saving targeted anti-coagulation therapy right at admission. Using a dataset of more than 800,000 COVID-19 patients from an international cohort, we propose a cost-sensitive gradient-boosted machine learning model that predicts occurrence of PE and death at admission. Logistic regression, Cox proportional hazards models, and Shapley values were used to identify key predictors for PE and death. Our prediction model had a test AUROC of 75.9% and 74.2%, and sensitivities of 67.5% and 72.7% for PE and all-cause mortality respectively on a highly diverse and held-out test set. The PE prediction model was also evaluated on patients in UK and Spain separately with test results of 74.5% AUROC, 63.5% sensitivity and 78.9% AUROC, 95.7% sensitivity. Age, sex, region of admission, comorbidities (chronic cardiac and pulmonary disease, dementia, diabetes, hypertension, cancer, obesity, smoking), and symptoms (any, confusion, chest pain, fatigue, headache, fever, muscle or joint pain, shortness of breath) were the most important clinical predictors at admission. Age, overall presence of symptoms, shortness of breath, and hypertension were found to be key predictors for PE using our extreme gradient boosted model. This analysis based on the, until now, largest global dataset for this set of problems can inform hospital prioritisation policy and guide long term clinical research and decision-making for COVID-19 patients globally. Our machine learning model developed from an international cohort can serve to better regulate hospital risk prioritisation of at-risk patients

Implementation of Recommendations on the Use of Corticosteroids in Severe COVID-19

Importance: Research diversity and representativeness are paramount in building trust, generating valid biomedical knowledge, and possibly in implementing clinical guidelines. Objectives: To compare variations over time and across World Health Organization (WHO) geographic regions of corticosteroid use for treatment of severe COVID-19; secondary objectives were to evaluate the association between the timing of publication of the RECOVERY (Randomised Evaluation of COVID-19 Therapy) trial (June 2020) and the WHO guidelines for corticosteroids (September 2020) and the temporal trends observed in corticosteroid use by region and to describe the geographic distribution of the recruitment in clinical trials that informed the WHO recommendation. Design, setting, and participants: This prospective cohort study of 434 851 patients was conducted between January 31, 2020, and September 2, 2022, in 63 countries worldwide. The data were collected under the auspices of the International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC)-WHO Clinical Characterisation Protocol for Severe Emerging Infections. Analyses were restricted to patients hospitalized for severe COVID-19 (a subset of the ISARIC data set). Exposure: Corticosteroid use as reported to the ISARIC-WHO Clinical Characterisation Protocol for Severe Emerging Infections. Main outcomes and measures: Number and percentage of patients hospitalized with severe COVID-19 who received corticosteroids by time period and by WHO geographic region. Results: Among 434 851 patients with confirmed severe or critical COVID-19 for whom receipt of corticosteroids could be ascertained (median [IQR] age, 61.0 [48.0-74.0] years; 53.0% male), 174 307 (40.1%) received corticosteroids during the study period. Of the participants in clinical trials that informed the guideline, 91.6% were recruited from the United Kingdom. In all regions, corticosteroid use for severe COVID-19 increased, but this increase corresponded to the timing of the RECOVERY trial (time-interruption coefficient 1.0 [95% CI, 0.9-1.2]) and WHO guideline (time-interruption coefficient 1.9 [95% CI, 1.7-2.0]) publications only in Europe. At the end of the study period, corticosteroid use for treatment of severe COVID-19 was highest in the Americas (5421 of 6095 [88.9%]; 95% CI, 87.7-90.2) and lowest in Africa (31 588 of 185 191 [17.1%]; 95% CI, 16.8-17.3). Conclusions and relevance: The results of this cohort study showed that implementation of the guidelines for use of corticosteroids in the treatment of severe COVID-19 varied geographically. Uptake of corticosteroid treatment was lower in regions with limited clinical trial involvement. Improving research diversity and representativeness may facilitate timely knowledge uptake and guideline implementation