Data-driven, cross-disciplinary collaboration: lessons learned at the largest academic health center in Latin America during the COVID-19 pandemic.

Introduction: The COVID-19 pandemic has prompted global research efforts to reduce infection impact, highlighting the potential of cross-disciplinary collaboration to enhance research quality and efficiency. Methods: At the FMUSP-HC academic health system, we implemented innovative flow management routines for collecting, organizing and analyzing demographic data, COVID-related data and biological materials from over 4,500 patients with confirmed SARS-CoV-2 infection hospitalized from 2020 to 2022. This strategy was mainly planned in three areas: organizing a database with data from the hospitalizations; setting-up a multidisciplinary taskforce to conduct follow-up assessments after discharge; and organizing a biobank. Additionally, a COVID-19 curated collection was created within the institutional digital library of academic papers to map the research output. Results: Over the course of the experience, the possible benefits and challenges of this type of research support approach were identified and discussed, leading to a set of recommended strategies to enhance collaboration within the research institution. Demographic and clinical data from COVID-19 hospitalizations were compiled in a database including adults and a minority of children and adolescents with laboratory confirmed COVID-19, covering 2020-2022, with approximately 350 fields per patient. To date, this database has been used in 16 published studies. Additionally, we assessed 700 adults 6 to 11 months after hospitalization through comprehensive, multidisciplinary in-person evaluations; this database, comprising around 2000 fields per subject, was used in 15 publications. Furthermore, thousands of blood samples collected during the acute phase and follow-up assessments remain stored for future investigations. To date, more than 3,700 aliquots have been used in ongoing research investigating various aspects of COVID-19. Lastly, the mapping of the overall research output revealed that between 2020 and 2022 our academic system produced 1,394 scientific articles on COVID-19. Discussion: Research is a crucial component of an effective epidemic response, and the preparation process should include a well-defined plan for organizing and sharing resources. The initiatives described in the present paper were successful in our aim to foster large-scale research in our institution. Although a single model may not be appropriate for all contexts, cross-disciplinary collaboration and open data sharing should make health research systems more efficient to generate the best evidence.

Paracoccidioidomycosis after eyebrow micropigmentation: Unusual reactivation or a new form of transmission by cutaneous inoculation?

We report a case of unusual paracoccidioidomycosis reactivation after eyebrow micropigmentation in a Brazilian patient. The cutaneous lesion was the only clinical manifestation. Direct cutaneous inoculation in dermal tissues with Paracoccidioides sp. is extremely rare, explaining why paracoccidioidomycosis is not classically considered a cutaneous implantation mycosis.

Cutaneous Naganishia albida (Cryptococcus albidus) infection: a case report and literature review.

Naganishia albida (Cryptococcus albidus) is considered saprophytic fungi, and is rarely reported as a human pathogen. Cutaneous infections caused by non-neoformans cryptococcus are rare. We describe a case of an immunocompetent older male with cutaneous cryptococcosis caused by Naganishia albida following skin trauma, and conduct a literature review in PubMed, Lilacs, and Embase. Only six previous similar reports were found. The seven cases (including ours) were widely distributed geographically (Brazil, the US, the UK, Hungary, South Korea, and Iran), all males, and their ages varied, ranging from 14 to 86 years. Four individuals had underlying skin diseases (Sezary Syndrome, psoriasis, and skin rash without etiology) plus potentially immunosuppressive underlying conditions (diabetes mellitus, kidney transplantation, and the use of etanercept, adalimumab, and methylprednisolone). Cutaneous presentation was polymorphic, with lesions characterized as warts, ulcers, plaques, and even macules. Two patients presented disseminated disease. Serum cryptococcal antigen was negative in six patients, and diagnosis was made by fungal culture in all. There is a lack of data on optimal antifungal treatment and outcomes.

Workload assessment: cross-cultural adaptation, content validity and instrument reliability.

OBJECTIVES: to adapt, validate the content and assess the reliability of the instrument National Aeronautics and Space Administration - Task Load Index, translated into Brazilian Portuguese. METHODS: a methodological study, divided into five steps: translation; synthesis; back-translation; assessment of the Portuguese version by an expert committee; pre-test and content validity of the final version by health professionals working in inpatient units. The Content Validity Index (CVI) (minimum 0.80) and Cronbach's alpha (minimum 0.70) were calculated. RESULTS: in the first round, in the agreement analysis of the translated version, three items did not reach the minimum CVI value. It was decided to remove the statement. The instrument title and items "performance" and "effort" were changed. There was consensus and approval of the final version in the pre-test step. CONCLUSIONS: the NASA Task Load Index instrument, adapted to Brazilian Portuguese, presents reliability and content validity evidence.

Chlorhexidine susceptibility and Eagle effect in planktonic cells and biofilm of nosocomial isolates.

The aim of this study is to evaluate the chlorhexidine gluconate (CHG) susceptibility in both planktonic cells and biofilm of 32 Gram-negative (Gn) and 6 Gram-positive (Gp) isolates by minimal inhibitory concentration (2-256 µg/mL for Gn and 2-32 µg/mL for Gp), minimal bactericidal concentration (4-256 µg/mL for Gn and 2-32 µg/mL for Gp) in planktonic cells, and minimal biofilm elimination concentration (128 ≥ 16,384 µg/mL in Gn and 32 ≥ 16,384 µg/mL in Gp) in biofilm environment. Our study showed that Gn isolates have higher minimal concentrations than Gp and bacteria in biofilms are more tolerant than planktonic ones. No correlation between MBC or MBEC and biofilm formation was statistically confirmed. The Eagle effect, previously described for antimicrobials and antifungals, was evidenced in this work for CHG, an antiseptic. Besides that, the phenomenon was described in 23/38 isolates (60.5%), raising minimal concentration up to ≥ 16,384 µg/mL. Our study showed that clinical isolates have a high ability to form biofilm allowing them to tolerate CHG concentrations as high as the ones used in clinical practice. Therefore, attention should be given to the occurrence of this phenomenon to avoid false susceptibility results.

Fundamental frequency related parameters in Brazilians with COVID-19.

This study compares fundamental frequency (fo) and fundamental frequency standard deviation (foSD) of COVID-19 patients with the same parameters in the speech of subjects without COVID-19, and verifies whether there is an effect of age and sex in the patient group. Both groups, subjects with and without COVID-19, are formed by Brazilian Portuguese speakers. Speech samples were obtained from 100 patients with mild to severe symptoms of COVID-19, and 100 healthy subjects. A single 31-syllable Portuguese sentence was used as the elicitation material for all subjects. The recordings were divided into four age groups. The acoustic measures were semi-automatically extracted and analyzed by a series of analyses of variance. Patients with COVID-19 present vocal differences in fo-related parameters when compared to healthy subjects, that is, patient voices presented higher fo and foSD with respect to control voices. In addition, for patient voices, there was an age and sex effect on fo SD values. Vocal parameters of women and elderly subjects showed more marked differences in fo-related parameters, indicating that patient voices are higher-pitched and have a higher variation of fo SD. Consequently, fo-related parameters may be tested as vocal biomarkers in the screening of respiratory insufficiency by voice analysis, in patients with severe symptoms of COVID-19.

Risk factors for reduction in adherence to protective measures following coronavirus disease 2019 (COVID-19) vaccination and vaccine perceptions among healthcare workers, in São Paulo, Brazil.

A survey evaluated 2,300 healthcare workers following the first dose of a coronavirus disease 2019 (COVID-19) vaccine in a tertiary-quaternary hospital in São Paulo, Brazil. Adherence to protective measures following vaccination was compared to previous non-work-related behaviors. Younger age, previous COVID-19, and burnout symptoms were associated with reduced adherence to mitigation measures.

Cutaneous Naganishia albida (Cryptococcus albidus) infection: a case report and literature review

ABSTRACT Naganishia albida (Cryptococcus albidus) is considered saprophytic fungi, and is rarely reported as a human pathogen. Cutaneous infections caused by non-neoformans cryptococcus are rare. We describe a case of an immunocompetent older male with cutaneous cryptococcosis caused by Naganishia albida following skin trauma, and conduct a literature review in PubMed, Lilacs, and Embase. Only six previous similar reports were found. The seven cases (including ours) were widely distributed geographically (Brazil, the US, the UK, Hungary, South Korea, and Iran), all males, and their ages varied, ranging from 14 to 86 years. Four individuals had underlying skin diseases (Sezary Syndrome, psoriasis, and skin rash without etiology) plus potentially immunosuppressive underlying conditions (diabetes mellitus, kidney transplantation, and the use of etanercept, adalimumab, and methylprednisolone). Cutaneous presentation was polymorphic, with lesions characterized as warts, ulcers, plaques, and even macules. Two patients presented disseminated disease. Serum cryptococcal antigen was negative in six patients, and diagnosis was made by fungal culture in all. There is a lack of data on optimal antifungal treatment and outcomes.

Workload assessment: cross-cultural adaptation, content validity and instrument reliability / Evaluación de la carga de trabajo: adaptación transcultural, validez de contenido y confiabilidad del instrumento / Avaliação da carga de trabalho: adaptação transcultural, validade de conteúdo e confiabilidade de instrumento

ABSTRACT Objectives: to adapt, validate the content and assess the reliability of the instrument National Aeronautics and Space Administration - Task Load Index, translated into Brazilian Portuguese. Methods: a methodological study, divided into five steps: translation; synthesis; back-translation; assessment of the Portuguese version by an expert committee; pre-test and content validity of the final version by health professionals working in inpatient units. The Content Validity Index (CVI) (minimum 0.80) and Cronbach's alpha (minimum 0.70) were calculated. Results: in the first round, in the agreement analysis of the translated version, three items did not reach the minimum CVI value. It was decided to remove the statement. The instrument title and items "performance" and "effort" were changed. There was consensus and approval of the final version in the pre-test step. Conclusions: the NASA Task Load Index instrument, adapted to Brazilian Portuguese, presents reliability and content validity evidence.

RESUMEN Objetivos: adaptar, validar el contenido y evaluar la confiabilidad del instrumento National Aeronautics and Space Administration - Task Load Index , traducido al portugués brasileño. Métodos: estudio metodológico, dividido en cinco etapas: traducción; síntesis; traducción inversa; evaluación de la versión portuguesa por un comité de expertos; pretest y validación de contenido de la versión final por profesionales de la salud que actúan en unidades de hospitalización. Se calculó el Índice de Validez de Contenido (IVC) (mínimo 0,80) y el alfa de Cronbach (mínimo 0,70). Resultados: en la primera ronda, en el análisis de concordancia de la versión traducida, tres ítems no alcanzaron el valor mínimo de IVC. Se decidió eliminar la declaración. Se modificó el título del instrumento y los ítems "desempeño" y "esfuerzo". Hubo consenso y aprobación de la versión final en la etapa de pre-prueba. Conclusiones: el instrumento NASA Task Load Index , adaptado al portugués brasileño, presenta evidencias de confiabilidad y validez de contenido.

RESUMO Objetivos: adaptar, validar o conteúdo e avaliar a confiabilidade do instrumento National Aeronautics and Space Administration - Task Load Index , traduzido para o português brasileiro. Métodos: estudo metodológico, dividido em cinco etapas: tradução; síntese; retrotradução; avaliação da versão em português por comitê de especialistas; pré-teste e validação de conteúdo da versão final por profissionais de saúde atuantes em unidades de internação. Foram calculados o Índice de Validade de Conteúdo (IVC) (mínimo 0,80) e o alfa de Cronbach (mínimo 0,70). Resultados: na primeira rodada, na análise de concordância da versão traduzida, três itens não alcançaram o valor mínimo do IVC. Optou-se pela remoção do enunciado. O título do instrumento e os itens "desempenho" e "esforço" foram alterados. Houve consenso e aprovação da versão final na etapa de pré-teste. Conclusões: o instrumento Índice NASA de carga de tarefa, adaptado para o português brasileiro, apresenta evidências de confiabilidade e validade de conteúdo.

Evaluation of eleven immunochromatographic assays for SARS-CoV-2 detection: investigating the dengue cross-reaction.

COVID-19 disease is spread worldwide and diagnostic techniques have been studied in order to contain the pandemic. Immunochromatographic (IC) assays are feasible and a low-cost alternative especially in low and middle-income countries, which lack structure to perform certain diagnostic techniques. Here we evaluate the sensitivity and specificity of eleven different IC tests in 145 serum samples from confirmed cases of COVID-19 using RT-PCR and 100 negative serum samples from blood donors collected in February 2019. We also evaluated the cross-reactivity with dengue using 20 serum samples from patients with confirmed diagnosis for dengue collected in early 2019 through four different tests. We found high sensitivity (92%), specificity (100%) and an almost perfect agreement (Kappa 0.92) of IC assay, especially when we evaluated IgG and IgM combined after 10 days from the onset of symptoms with RT-PCR. However, we detected cross-reactivity between dengue and COVID-19 mainly with IgM antibodies (5 to 20% of cross-reaction) and demonstrated the need for better studies about diagnostic techniques for these diseases.

Brazilian perspective: antimicrobial stewardship in solid organ transplant.

BACKGROUND: The incidence of multidrug resistant organisms (MDROs) infections among solid organ transplant (SOT) patients is very high in Brazil. METHODS: This review will discuss antimicrobial use and resistance in SOT in Brazil, highlighting the main barriers and facilitators for implementation of an antimicrobial stewardship programme (ASP). RESULTS: The most common group of MDROs is carbapenem-resistant Gram-negative bacteria and vancomycin-resistant Enterococcus. Carbapenem-resistant Enterobacterales (CREs) are the most frequent MDROs and have been reported as donor-derived as well. Although ASPs are mandatory in the country, there is a lack of information regarding ASPs in SOT recipients. The main barriers for the implementation of ASPs in Brazilian hospitals are lack of electronic medical records, absence of national guidelines specific to SOT recipients, lack of recommendations on surveillance culture to evaluate colonization and transmission of donor-derived MDROs, limited availability of rapid diagnostic tests, and insufficient pharmacist and clinician time allocated to ASP activities in some SOT centers. CONCLUSIONS: The incidence of MDRO infections caused mainly by VREs and CREs is very high in the country. There is limited data regarding antimicrobial use among SOT recipients in Brazil. The absence of antimicrobial stewardship national guidelines specific to SOT recipients is one of the main barriers for the implementation of ASPs in Brazilian hospitals.

Monkeypox Virus Transmission to Healthcare Worker through Needlestick Injury, Brazil.

We describe monkeypox virus (MPXV) transmission from a patient to a healthcare worker through needlestick injury. A lesion appeared at the inoculation site 5 days after injury. Blood tested MPXV-positive by PCR before symptoms worsened; blood remained MPXV-positive at discharge 19 days after symptom onset. Postexposure prophylaxis could prevent potential MPXV bloodborne transmission.

Mortality over time among COVID-19 patients hospitalized during the first surge of the pandemic: A large cohort study.

BACKGROUND: Capacity strain negatively impacts patient outcome, and the effects of patient surge are a continuous threat during the COVID-19 pandemic. Evaluating changes in mortality over time enables evidence-based resource planning, thus improving patient outcome. Our aim was to describe baseline risk factors associated with mortality among COVID-19 hospitalized patients and to compare mortality rates over time. METHODS: We conducted a retrospective cohort study in the largest referral hospital for COVID-19 patients in Sao Paulo, Brazil. We investigated risk factors associated with mortality during hospitalization. Independent variables included age group, sex, the Charlson Comorbidity Index, admission period according to the stage of the first wave of the epidemic (early, peak, and late), and intubation. RESULTS: We included 2949 consecutive COVID-19 patients. 1895 of them were admitted to the ICU, and 1473 required mechanical ventilation. Median length of stay in the ICU was 10 (IQR 5-17) days. Overall mortality rate was 35%, and the adjusted odds ratios for mortality increased with age, male sex, higher Charlson Comorbidity index, need for mechanical ventilation, and being admitted to the hospital during the wave peak of the epidemic. Being admitted to the hospital during the wave peak was associated with a 33% higher risk of mortality. CONCLUSIONS: In-hospital mortality was independently affected by the epidemic period. The recognition of modifiable operational variables associated with patient outcome highlights the importance of a preparedness plan and institutional protocols that include evidence-based practices and allocation of resources.

Personal protective equipment implementation in healthcare: A scoping review.

BACKGROUND: Adherence to infection prevention and control (IPC) measures, including the proper use of protective personal equipment (PPE), in health care is complex and is influenced by many factors. Isolated interventions do not have the potential to achieve optimal PPE adherence and appropriate provision, leading to incomplete PPE implementation. OBJECTIVE: To map PPE implementation in health care with a focus on its barriers and facilitators. METHODS: A scoping review was conducted across 14 electronic databases using the Joanna Briggs Institute methodology. RESULTS: Seventy-four papers were included in the review. Findings were analyzed and synthesized into categories to match the Consolidated Framework for Implementation Research domains. The content was then synthesized into barriers for PPE implementation and interventions to address them. The main barriers were discomfort in clinical work; shortage, supply and logistics problems; inadequacies in facilities infrastructure, weakness in policies and communication procedures; and health workers' (HW) psychological issues and lack of preparedness. Implementation interventions reported were related to HW wellbeing assurance; work reorganization; IPC protocols; adoption of strategies to improve communication and HW training; and adoption of structural and organizational changes to improve PPE adherence. CONCLUSIONS: PPE implementation, which is critical IPC programs, involves multilevel transdisciplinary complexity. It relies on the development of context-driven implementation strategies to inform and harmonize IPC policy in collaboration with local and international health bodies.

Performance of NEWS, qSOFA, and SIRS Scores for Assessing Mortality, Early Bacterial Infection, and Admission to ICU in COVID-19 Patients in the Emergency Department.

SARS-CoV-2 infection has a wide spectrum of presentations, from asymptomatic to pneumonia and sepsis. Risk scores have been used as triggers for protocols that combine several interventions for early management of sepsis. This study tested the accuracy of the score SIRS, qSOFA, and NEWS in predicting outcomes, including mortality and bacterial infection, in patients admitted to the emergency department (ED) during the COVID-19 pandemic. We described 2,473 cases of COVID-19 admitted to the ED of the largest referral hospital for severe COVID-19 in Brazil during the pandemic. SIRS, qSOFA and NEWS scores showed a poor performance as prognostic scores. However, NEWS score had a high sensitivity to predict in-hospital death (0.851), early bacterial infection (0.851), and ICU admission (0.868), suggesting that it may be a good screening tool for severe cases of COVID-19, despite its low specificity.

Adherence to non-pharmacological preventive measures among healthcare workers in a middle-income country during the first year of the COVID-19 pandemic: Hospital and community setting.

This study assessed, using a self-reported questionnaire, the adherence to PPE (mask, gowns, and gloves) at the workplace, as well as to non-pharmacological preventive measures (NPPM) (physical distance defined as hardly ever and/or never approaches other people within 1.5 meters, social isolation as leaving home less than once a week, hand hygiene was defined as performing hand hygiene ≥ 6 times per period, and adherence to the use of a mask outside of the workplace was defined as on all outings and hardly ever and/or never removes the mask) outside of the workplace among 1,296 health care workers (HCWs), including if NPPM adherence was associated with COVID-19 in HCWs. High adherence to PPE was independently associated with younger age, professional category, work in an area of direct patient assistance; use of public transportation, or adherence to NPPM outside of the workplace.

Phenotypic and genotypic characteristics of a carbapenem-resistant Serratia marcescens cohort and outbreak: describing an opportunistic pathogen.

Serratia marcescens is an emerging opportunistic pathogen with high genetic diversity. This article describes the microbiological characteristics of isolates and the risk factors for infections caused by carbapenem-resistant S. marcescens. A retrospective study of patients colonized (n=43) and infected (n=20) with carbapenem-resistant S. marcescens over a 3-year period was conducted. Polymerase chain reaction for carbapenemase genes and molecular typing of all available strains was performed. Forty-two isolates were analysed, including three environmental samples identified during an outbreak. Thirty-five carbapenem-resistant S. marcescens carried blaKPC-2, one isolate was blaNDM-positive and four isolates carried blaOXA-101. The genomes were grouped into three clusters with 100% bootstrap; three patterns of mutations on ompC and ompF were found. The strains carried virulence genes related to invasion and haemolysis, and the environmental strains presented fewer mutations on the virulence genes than the clinical strains. Multi-variate analysis showed that previous use of polymyxin (P=0.008) was an independent risk factor for carbapenem-resistant S. marcescens infection. This study highlighted that blaKPC-2 in association with ompC or ompF mutation was the most common mechanism of resistance in the study hospital, and that previous use of polymyxin was an independent risk factor for carbapenem-resistant S. marcescens. There was a predominant clone, including the environmental isolates, suggesting that cross-transmission was involved in the dissemination of this pathogen.

Clinical outcome from hematopoietic cell transplant patients with bloodstream infection caused by carbapenem-resistant P. aeruginosa and the impact of antimicrobial combination in vitro.

Bloodstream infection (BSI) caused by carbapenem-resistant P. aeruginosa (CRPA) has high mortality in hematopoietic stem cell transplant (HSCT) recipients. We performed MIC, checkerboard, time-kill assay, PFGE, PCR, and whole genome sequence and described the clinical outcome through Epi Info comparing the antimicrobial combination in vitro. Mortality was higher in BSI caused by CRPA carrying the lasB virulence gene. The isolates were 97% resistant to meropenem displaying synergistic effect to 57% in combination with colistin. Seventy-three percent of the isolates harbored blaSPM-1 and Tn4371 and belonged to ST277. The synergistic effect in vitro with meropenem with colistin appeared to be a better therapeutic option.

Evaluation of eleven immunochromatographic assays for SARS-CoV-2 detection: investigating the dengue cross-reaction

ABSTRACT COVID-19 disease is spread worldwide and diagnostic techniques have been studied in order to contain the pandemic. Immunochromatographic (IC) assays are feasible and a low-cost alternative especially in low and middle-income countries, which lack structure to perform certain diagnostic techniques. Here we evaluate the sensitivity and specificity of eleven different IC tests in 145 serum samples from confirmed cases of COVID-19 using RT-PCR and 100 negative serum samples from blood donors collected in February 2019. We also evaluated the cross-reactivity with dengue using 20 serum samples from patients with confirmed diagnosis for dengue collected in early 2019 through four different tests. We found high sensitivity (92%), specificity (100%) and an almost perfect agreement (Kappa 0.92) of IC assay, especially when we evaluated IgG and IgM combined after 10 days from the onset of symptoms with RT-PCR. However, we detected cross-reactivity between dengue and COVID-19 mainly with IgM antibodies (5 to 20% of cross-reaction) and demonstrated the need for better studies about diagnostic techniques for these diseases.

Use and misuse of biomarkers and the role of D-dimer and C-reactive protein in the management of COVID-19: A post-hoc analysis of a prospective cohort study.

OBJECTIVE: Coronavirus disease 2019 (COVID-19) is associated with high mortality among hospitalized patients and incurs high costs. Severe acute respiratory syndrome coronavirus 2 infection can trigger both inflammatory and thrombotic processes, and these complications can lead to a poorer prognosis. This study aimed to evaluate the association and temporal trends of D-dimer and C-reactive protein (CRP) levels with the incidence of venous thromboembolism (VTE), hospital mortality, and costs among inpatients with COVID-19. METHODS: Data were extracted from electronic patient records and laboratory databases. Crude and adjusted associations for age, sex, number of comorbidities, Sequential Organ Failure Assessment score at admission, and D-dimer or CRP logistic regression models were used to evaluate associations. RESULTS: Between March and June 2020, COVID-19 was documented in 3,254 inpatients. The D-dimer level ≥4,000 ng/mL fibrinogen equivalent unit (FEU) mortality odds ratio (OR) was 4.48 (adjusted OR: 1.97). The CRP level ≥220 mg/dL OR for death was 7.73 (adjusted OR: 3.93). The D-dimer level ≥4,000 ng/mL FEU VTE OR was 3.96 (adjusted OR: 3.26). The CRP level ≥220 mg/dL OR for VTE was 2.71 (adjusted OR: 1.92). All these analyses were statistically significant (p<0.001). Stratified hospital costs demonstrated a dose-response pattern. Adjusted D-dimer and CRP levels were associated with higher mortality and doubled hospital costs. In the first week, elevated D-dimer levels predicted VTE occurrence and systemic inflammatory harm, while CRP was a hospital mortality predictor. CONCLUSION: D-dimer and CRP levels were associated with higher hospital mortality and a higher incidence of VTE. D-dimer was more strongly associated with VTE, although its discriminative ability was poor, while CRP was a stronger predictor of hospital mortality. Their use outside the usual indications should not be modified and should be discouraged.