Procalcitonin and C-reactive protein to rule out early bacterial coinfection in COVID-19 critically ill patients

Although the prevalence of community-acquired respiratory bacterial coinfection upon hospital admission in patients with coronavirus disease 2019 (COVID-19) has been reported to be < 5%, almost three-quarters of patients received antibiotics. We aim to investigate whether procalcitonin (PCT) or C-reactive protein (CRP) upon admission could be helpful biomarkers to identify bacterial coinfection among patients with COVID-19 pneumonia. Methods: We carried out a multicentre, observational cohort study including consecutive COVID-19 patients admitted to 55 Spanish intensive care units (ICUs). The primary outcome was to explore whether PCT or CRP serum levels upon hospital admission could predict bacterial coinfection among patients with COVID-19 pneumonia. The secondary outcome was the evaluation of their association with mortality. We also conducted subgroups analyses in higher risk profile populations. Results: Between 5 February 2020 and 21 December 2021, 4076 patients were included, 133 (3%) of whom presented bacterial coinfection. PCT and CRP had low area under curve (AUC) scores at the receiver operating characteristic (ROC) curve analysis [0.57 (95% confidence interval (CI) 0.51–0.61) and 0.6 (95% CI, 0.55–0.64), respectively], but high negative predictive values (NPV) [97.5% (95% CI 96.5–98.5) and 98.2% (95% CI 97.5–98.9) for PCT and CRP, respectively]. CRP alone was associated with bacterial coinfection (OR 2, 95% CI 1.25–3.19; p = 0.004). The overall 15, 30 and 90 days mortality had a higher trend in the bacterial coinfection group, but without significant difference. PCT ≥ 0.12 ng/mL was associated with higher 90 days mortality. Conclusion: Our study suggests that measurements of PCT and CRP, alone and at a single time point, are not useful for ruling in or out bacterial coinfection in viral pneumonia by COVID-19

Brewpitopes: a pipeline to refine B-cell epitope predictions during public health emergencies

The application of B-cell epitope identification to develop therapeutic antibodies and vaccine candidates is well established. However, the validation of epitopes is time-consuming and resource-intensive. To alleviate this, in recent years, multiple computational predictors have been developed in the immunoinformatics community. Brewpitopes is a pipeline that curates bioinformatic B-cell epitope predictions obtained by integrating different state-of-the-art tools. We used additional computational predictors to account for subcellular location, glycosylation status, and surface accessibility of the predicted epitopes. The implementation of these sets of rational filters optimizes in vivo antibody recognition properties of the candidate epitopes. To validate Brewpitopes, we performed a proteome-wide analysis of SARS-CoV-2 with a particular focus on S protein and its variants of concern. In the S protein, we obtained a fivefold enrichment in terms of predicted neutralization versus the epitopes identified by individual tools. We analyzed epitope landscape changes caused by mutations in the S protein of new viral variants that were linked to observed immune escape evidence in specific strains. In addition, we identified a set of epitopes with neutralizing potential in four SARS-CoV-2 proteins (R1AB, R1A, AP3A, and ORF9C). These epitopes and antigenic proteins are conserved targets for viral neutralization studies. In summary, Brewpitopes is a powerful pipeline that refines B-cell epitope bioinformatic predictions during public health emergencies in a high-throughput capacity to facilitate the optimization of experimental validation of therapeutic antibodies and candidate vaccines

The evolution of the ventilatory ratio is a prognostic factor in mechanically ventilated COVID-19 ARDS patients

COVID-19; Mechanical ventilation; Ventilatory ratioCOVID-19; Respiració assistida; Relació ventilatòriaCOVID-19; Ventilación mecánica; Relación ventilatoriaBackground Mortality due to COVID-19 is high, especially in patients requiring mechanical ventilation. The purpose of the study is to investigate associations between mortality and variables measured during the first three days of mechanical ventilation in patients with COVID-19 intubated at ICU admission. Methods Multicenter, observational, cohort study includes consecutive patients with COVID-19 admitted to 44 Spanish ICUs between February 25 and July 31, 2020, who required intubation at ICU admission and mechanical ventilation for more than three days. We collected demographic and clinical data prior to admission; information about clinical evolution at days 1 and 3 of mechanical ventilation; and outcomes. Results Of the 2,095 patients with COVID-19 admitted to the ICU, 1,118 (53.3%) were intubated at day 1 and remained under mechanical ventilation at day three. From days 1 to 3, PaO2/FiO2 increased from 115.6 [80.0–171.2] to 180.0 [135.4–227.9] mmHg and the ventilatory ratio from 1.73 [1.33–2.25] to 1.96 [1.61–2.40]. In-hospital mortality was 38.7%. A higher increase between ICU admission and day 3 in the ventilatory ratio (OR 1.04 [CI 1.01–1.07], p = 0.030) and creatinine levels (OR 1.05 [CI 1.01–1.09], p = 0.005) and a lower increase in platelet counts (OR 0.96 [CI 0.93–1.00], p = 0.037) were independently associated with a higher risk of death. No association between mortality and the PaO2/FiO2 variation was observed (OR 0.99 [CI 0.95 to 1.02], p = 0.47). Conclusions Higher ventilatory ratio and its increase at day 3 is associated with mortality in patients with COVID-19 receiving mechanical ventilation at ICU admission. No association was found in the PaO2/FiO2 variation.Financial support was provided by the Instituto de Salud Carlos III de Madrid (COV20/00110, ISCIII), Fondo Europeo de Desarrollo Regional (FEDER), "Una manera de hacer Europa", and by the Centro de Investigación Biomedica En Red – Enfermedades Respiratorias (CIBERES). DdGC has received financial support from Instituto de Salud Carlos III (Miguel Servet 2020: CP20/00041), co-funded by European Social Fund (ESF)/”Investing in your future”

The evolution of the ventilatory ratio is a prognostic factor in mechanically ventilated COVID-19 ARDS patients

Background Mortality due to COVID-19 is high, especially in patients requiring mechanical ventilation. The purpose of the study is to investigate associations between mortality and variables measured during the first three days of mechanical ventilation in patients with COVID-19 intubated at ICU admission. Methods Multicenter, observational, cohort study includes consecutive patients with COVID-19 admitted to 44 Spanish ICUs between February 25 and July 31, 2020, who required intubation at ICU admission and mechanical ventilation for more than three days. We collected demographic and clinical data prior to admission; information about clinical evolution at days 1 and 3 of mechanical ventilation; and outcomes. Results Of the 2,095 patients with COVID-19 admitted to the ICU, 1,118 (53.3%) were intubated at day 1 and remained under mechanical ventilation at day three. From days 1 to 3, PaO2/FiO2 increased from 115.6 [80.0–171.2] to 180.0 [135.4–227.9] mmHg and the ventilatory ratio from 1.73 [1.33–2.25] to 1.96 [1.61–2.40]. In-hospital mortality was 38.7%. A higher increase between ICU admission and day 3 in the ventilatory ratio (OR 1.04 [CI 1.01–1.07], p = 0.030) and creatinine levels (OR 1.05 [CI 1.01–1.09], p = 0.005) and a lower increase in platelet counts (OR 0.96 [CI 0.93–1.00], p = 0.037) were independently associated with a higher risk of death. No association between mortality and the PaO2/FiO2 variation was observed (OR 0.99 [CI 0.95 to 1.02], p = 0.47). Conclusions Higher ventilatory ratio and its increase at day 3 is associated with mortality in patients with COVID-19 receiving mechanical ventilation at ICU admission. No association was found in the PaO2/FiO2 variation.Instituto de Salud Carlos III de Madrid COV20/00110, ISCII

Higher frequency of comorbidities in fully vaccinated patients admitted to the ICU due to severe COVID-19: a prospective, multicentre, observational study

Severe COVID-19 disease requiring ICU admission is possible in the fully vaccinated population, especially in those with immunocompromised status and other comorbidities. Interventions to improve vaccine response might be necessary in this population.Peer ReviewedArticle signat per 23 autors/es: Anna Motos, Alexandre López-Gavín, Jordi Riera, Adrián Ceccato, Laia Fernández-Barat, Jesús F. Bermejo-Martin, Ricard Ferrer, David de Gonzalo-Calvo, Rosario Menéndez, Raquel Pérez-Arnal, Dario García-Gasulla, Alejandro Rodriguez, Oscar Peñuelas, José Ángel Lorente, Raquel Almansa, Albert Gabarrus, Judith Marin-Corral, Pilar Ricart, Ferran Roche-Campo, Susana Sancho Chinesta, Lorenzo Socias, Ferran Barbé, Antoni Torres on behalf of the CIBERESUCICOVID Project (COV20/00110, ISCIII).Postprint (published version

Clinical Factors Associated with a Shorter or Longer Course of Antibiotic Treatment in Patients with Exacerbations of Bronchiectasis: A Prospective Cohort Study

Background: Bronchiectasis exacerbations are often treated with prolonged antibiotic use, even though there is limited evidence for this approach. We therefore aimed to investigate the baseline clinical and microbiological findings associated with long courses of antibiotic treatment in exacerbated bronchiectasis patients. Methods: This was a bi-centric prospective observational study of bronchiectasis exacerbated adults. We compared groups receiving short (≤14 days) and long (15-21 days) courses of antibiotic treatment. Results: We enrolled 191 patients (mean age 72 (63, 79) years; 108 (56.5%) females), of whom 132 (69%) and 59 (31%) received short and long courses of antibiotics, respectively. Multivariable logistic regression of the baseline variables showed that long-term oxygen therapy (LTOT), moderate-severe exacerbations, and microbiological isolation of Pseudomonas aeruginosa were associated with long courses of antibiotic therapy. When we excluded patients with a diagnosis of community-acquired pneumonia (n = 49), in the model we found that an etiology of P. aeruginosa remained as factor associated with longer antibiotic treatment, with a moderate and a severe FACED score and the presence of arrhythmia as comorbidity at baseline. Conclusions: Decisions about the duration of antibiotic therapy should be guided by clinical and microbiological assessments of patients with infective exacerbations

Systemic Inflammation during and after Bronchiectasis Exacerbations: Impact of Pseudomonas aeruginosa

Bronchiectasis is a chronic structural disease associated with exacerbations that provoke systemic inflammation. We aimed to evaluate the systemic acute proinflammatory cytokine and its biomarker profiles during and after exacerbations and its relationship with the severity of episode, microbiological findings, and the bronchiectasis severity index. This prospective observational study compared exacerbation and stable groups. Cytokine (interleukins (IL)-17a, IL-1β, IL-6, IL 8; tumor necrosis factor-alpha (α)) and high-sensitivity C-reactive protein (hsCRP) levels were determined by multiplex analysis on days 1, 5, 30, and 60 in the exacerbation group and on day 1 in the stable group. We recruited 165 patients with exacerbations, of which 93 were severe (hospitalized). Proinflammatory systemic IL-17a, IL-1β, IL-8, and tumor necrosis factor-α levels increased similarly on days 1 and 5 in severe and non-severe episodes, but on day 30, IL-17a, IL-8, and IL-6 levels were only increased for severe exacerbations. The highest IL-17a level occurred in patients with chronic plus the acute isolation of Pseudomonas aeruginosa. At 30 days, severe exacerbations were independently associated with higher levels of IL-17 (Odds ratio (OR) 4.58), IL-6 (OR 4.89), IL-8 (OR 3.08), and hsCRP (OR 6.7), adjusted for age, the bronchiectasis severity index, and treatment duration. Exacerbations in patients with chronic P. aeruginosa infection were associated with an increase in IL-17 and IL-6 at 30 days (ORs 7.47 and 3.44, respectively). Severe exacerbations elicit a higher systemic proinflammatory response that is sustained to day 30. Patients with chronic P. aeruginosa infection had impaired IL-17a reduction. IL-17a could be a useful target for measuring systemic inflammation

ICU-acquired pneumonia is associated with poor health post-COVID-19 syndrome

Some patients previously presenting with COVID-19 have been reported to develop persistent COVID-19 symptoms. While this information has been adequately recognised and extensively published with respect to non-critically ill patients, less is known about the incidence and factors associated with the characteristics of persistent COVID-19. On the other hand, these patients very often have intensive care unit-acquired pneumonia (ICUAP). A second infectious hit after COVID increases the length of ICU stay and mechanical ventilation and could have an influence on poor health post-COVID 19 syndrome in ICU-discharged patients. Methods: This prospective, multicentre, and observational study was carrid out across 40 selected ICUs in Spain. Consecutive patients with COVID-19 requiring ICU admission were recruited and evaluated three months after hospital discharge. Results: A total of 1255 ICU patients were scheduled to be followed up at 3 months; however, the final cohort comprised 991 (78.9%) patients. A total of 315 patients developed ICUAP (97% of them had ventilated ICUAP). Patients requiring invasive mechanical ventilation had more persistent post-COVID-19 symptoms than those who did not require mechanical ventilation. Female sex, duration of ICU stay, development of ICUAP, and ARDS were independent factors for persistent poor health post-COVID-19. Conclusions: Persistent post-COVID-19 symptoms occurred in more than two-thirds of patients. Female sex, duration of ICU stay, development of ICUAP, and ARDS all comprised independent factors for persistent poor health post-COVID-19. Prevention of ICUAP could have beneficial effects in poor health post-COVID-19.Financial support was provided by the Instituto Carlos III de Madrid (COV20/00110, ISCIII) and by the Centro de Investigación Biomedica En Red—Enfermedades Respiratorias (CIBERES). DdGC has received financial support from Instituto de Salud Carlos III (Miguel Servet 2020: CP20/00041), co-funded by European Social Fund (ESF)/ “Investing in your future”Peer ReviewedArticle signat per 53 autors/es: Ignacio Martin-Loeches (1,2,3), Anna Motos (1,3), Rosario Menéndez (1,4), Albert Gabarrús (1,4), Jessica González (5,6), Laia Fernández-Barat (1,3), Adrián Ceccato (1,3), Raquel Pérez-Arnal (7), Dario García-Gasulla (7), Ricard Ferrer (1,8), Jordi Riera (1,8), José Ángel Lorente (1,9), Óscar Peñuelas (1,9), Jesús F. Bermejo-Martin (1,10,11), David de Gonzalo-Calvo (5,6), Alejandro Rodríguez (12), Ferran Barbé (5,6), Luciano Aguilera (13), Rosario Amaya-Villar (14), Carme Barberà (15), José Barberán (16), Aaron Blandino Ortiz (17), Elena Bustamante-Munguira (18), Jesús Caballero (19), Cristina Carbajales (20), Nieves Carbonell (21),Mercedes Catalán-González (22), Cristóbal Galbán (23), Víctor D. Gumucio-Sanguino (24), Maria del Carmen de la Torre (25), Emili Díaz (26), Elena Gallego (27), José Luis García Garmendia (28), José Garnacho-Montero (29), José M. Gómez (30), Ruth Noemí Jorge García (31), Ana Loza-Vázquez (32), Judith Marín-Corral (33), Amalia Martínez de la Gándara (34), Ignacio Martínez Varela (35), Juan Lopez Messa (36), Guillermo M. Albaiceta (37,38), Mariana Andrea Novo (39), Yhivian Peñasco (40), Pilar Ricart (41), Luis Urrelo-Cerrón (42), Angel Sánchez-Miralles (43), Susana Sancho Chinesta (44), Lorenzo Socias (45), Jordi Solé-Violan (1,46), Luis Tamayo Lomas (47), Pablo Vidal (48) and Antoni Torres (1,3)*, on behalf of CIBERESUCICOVID Project (COV20/00110 and ISCIII) // (1) CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (2) Pulmonary Department, Hospital Clinic, Universitat de Barcelona, IDIBAPS, 08036 Barcelona, Spain; (3) Department of Intensive Care Medicine, St. James’s Hospital, Multidisciplinary Intensive Care Research Organization (MICRO), James’s Street, D08 NHY1 Dublin, Ireland; (4) Pulmonary Department, University and Polytechnic Hospital La Fe, 46026 Valencia, Spain; (5) Translational Research in Respiratory Medicine Group (TRRM), Lleida Biomedical Research Institute (IRBLleida), 25198 Lleida, Spain; (6) Pulmonary Department, Hospital Universitari Arnau de Vilanova and Santa Maria, 25198 Lleida, Spain; (7) Barcelona Supercomputing Centre (BSC), 08034 Barcelona, Spain; (8) Intensive Care Department, Vall d’Hebron Hospital Universitari, SODIR Research Group, Vall d’Hebron Institut de Recerca (VHIR), 08035 Barcelona, Spain; (9) Hospital Universitario de Getafe, 28905 Madrid, Spain; (10) Hospital Universitario Río Hortega de Valladolid, 47012 Valladolid, Spain; (11) Instituto de Investigación Biomédica de Salamanca (IBSAL), Gerencia Regional de Salud de Castilla y León, 47007 Valladolid, Spain; (12) Critical Care Department, Hospital Joan XXIII, 43005 Tarragona, Spain; (13) Anestesia, Reanimación y Terapia del Dolor, Hospital Universitario de Basurto, 48013 Bilbao, Spain; (14) Intensive Care Clinical Unit, Hospital Universitario Virgen de Rocío, 41013 Sevilla, Spain; (15) Hospital Santa Maria, IRBLleida, 25198 Lleida, Spain; (16) Critical Care Department, Hospital Universitario HM Montepríncipe, Universidad San Pablo-CEU, 28660 Madrid, Spain; (17) Servicio de Medicina Intensiva, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (18) Department of Intensive Care Medicine, Hospital Clínico Universitario Valladolid, 47003 Valladolid, Spain; (19) Critical Care Department, Hospital Universitari Arnau de Vilanova, IRBLleida, 25198 Lleida, Spain; (20) Hospital Álvaro Cunqueiro, 36213 Vigo, Spain; (21) Intensive Care Unit, Hospital Clínico y Universitario de Valencia, 46010 Valencia, Spain; (22) Department of Intensive Care Medicine, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain, (23) Department of Medicine, CHUS, Complejo Hospitalario Universitario de Santiago, 15076 Santiago de Compostela, Spain; (24) Department of Intensive Care, Hospital Universitari de Bellvitge, L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (25) Hospital de Mataró de Barcelona, 08301 Mataró, Spain; (26) Department of Medicine, Universitat Autònoma de Barcelona (UAB), Critical Care Department, Corpo-Ració Sanitària Parc Taulí, Sabadell, 08208 Barcelona, Spain; (27) Unidad de Cuidados Intensivos, Hospital San Pedro de Alcántara, 10003 Cáceres, Spain; (28) Intensive Care Unit, Hospital San Juan de Dios del Aljarafe, 41930 Sevilla, Spain; (29) Intensive Care Clinical Unit, Hospital Universitario Virgen Macarena, 41009 Seville, Spain; (30) Hospital General Universitario Gregorio Marañón, 28009 Madrid, Spain; (31) Intensive Care Department, Hospital Nuestra Señora de Gracia, 50009 Zaragoza, Spain; (32) Unidad de Medicina Intensiva, Hospital Universitario Virgen de Valme, 41014 Sevilla, Spain; (33) Critical Care Department, Hospital del Mar-IMIM, 08003 Barcelona, Spain; (34) Department of Intensive Medicine, Hospital Universitario Infanta Leonor, 28031 Madrid, Spain; (35) Critical Care Department, Hospital Universitario Lucus Augusti, 27003 Lugo, Spain; (36) Critical Care Department, Complejo Asistencial Universitario de Palencia, 34005 Palencia, Spain; (37) Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33011 Oviedo, Spain; (38) Instituto de Investigación Sanitaria del Principado de Asturias, Hospital Central de Asturias, 33011 Oviedo, Spain; (39) Servei de Medicina Intensiva, Hospital Universitari Son Espases, Palma de Mallorca, 07120 Illes Balears, Spain; (40) Servicio de Medicina Intensiva, Hospital Universitario Marqués de Valdecilla, 39008 Santander, Spain; (41) Servei de Medicina Intensiva, Hospital Universitari Germans Trias, 08916 Badalona, Spain; (42) Hospital Verge de la Cinta, 08916 Tortosa, Spain; (43) Hospital de Sant Joan d’Alacant, 03550 Alacant, Spain; (44) Servicio de Medicina Intensiva, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (45) Intensive Care Unit, Hospital Son Llàtzer, Palma de Mallorca, 07198 Illes Balears, Spain; (46) Critical Care Department, Hospital Dr. Negrín., 35019 Las Palmas de GC, Spain; (47) Critical Care Department, Hospital Universitario Río Hortega de Valladolid, 47102 Valladolid, Spain; (48) Intensive Care Unit, Complexo Hospitalario Universitario de Ourense, 32005 Ourense, Spain.Postprint (published version

Lateral position during severe mono-lateral pneumonia: an experimental study

Patients with mono-lateral pneumonia and severe respiratory failure can be positioned in lateral decubitus, with the healthy lung dependent, to improve ventilation-perfusion coupling. Oxygenation response to this manoeuvre is heterogeneous and derecruitment of dependent lung has not been elucidated. Nine pigs (32.2 ± 1.2 kg) were sedated and mechanically ventilated. Mono-lateral right-sided pneumonia was induced with intrabronchial challenge of Pseudomonas aeruginosa. After 24 h, lungs were recruited and the animals were randomly positioned on right or left side. After 3 h of lateral positioning, the animals were placed supine; another recruitment manoeuvre was performed, and the effects of contralateral decubitus were assessed. Primary outcome was lung ultrasound score (LUS) of the dependent lung after 3-h lateral positioning. LUS of the left non-infected lung worsened while positioned in left-lateral position (from 1.33 ± 1.73 at baseline to 6.78 ± 4.49; p = 0.005). LUS of the right-infected lung improved when placed upward (9.22 ± 2.73 to 6.67 ± 3.24; p = 0.09), but worsened in right-lateral position (7.78 ± 2.86 to 13.33 ± 3.08; p < 0.001). PaO2/FiO2 improved in the left-lateral position (p = 0.005). In an animal model of right-lung pneumonia, left-lateral decubitus improved oxygenation, but collapsed the healthy lung. Right-lateral orientation further collapsed the diseased lung. Our data raise potential clinical concerns for the use of lateral position in mono-lateral pneumonia

Assessment of in vivo versus in vitro biofilm formation of clinical methicillin-resistant Staphylococcus aureus isolates from endotracheal tubes

Our aim was to demonstrate that biofilm formation in a clinical strain of methicillin-resistant Staphylococcus aureus (MRSA) can be enhanced by environment exposure in an endotracheal tube (ETT) and to determine how it is affected by systemic treatment and atmospheric conditions. Second, we aimed to assess biofilm production dynamics after extubation. We prospectively analyzed 70 ETT samples obtained from pigs randomized to be untreated (controls, n = 20), or treated with vancomycin (n = 32) or linezolid (n = 18). A clinical MRSA strain (MRSA-in) was inoculated in pigs to create a pneumonia model, before treating with antibiotics. Tracheally intubated pigs with MRSA severe pneumonia, were mechanically ventilated for 69 ± 16 hours. All MRSA isolates retrieved from ETTs (ETT-MRSA) were tested for their in vitro biofilm production by microtiter plate assay. In vitro biofilm production of MRSA isolates was sequentially studied over the next 8 days post-extubation to assess biofilm capability dynamics over time. All experiments were performed under ambient air (O2) or ambient air supplemented with 5% CO2. We collected 52 ETT-MRSA isolates (placebo N = 19, linezolid N = 11, and vancomycin N = 22) that were clonally identical to the MRSA-in. Among the ETT-MRSA isolates, biofilm production more than doubled after extubation in 40% and 50% under 5% CO2 and O2, respectively. Systemic antibiotic treatment during intubation did not affect this outcome. Under both atmospheric conditions, biofilm production for MRSA-in was at least doubled for 9 ETT-MRSA isolates, and assessment of these showed that biofilm production decreased progressively over a 4-day period after extubation. In conclusion, a weak biofilm producer MRSA strain significantly enhances its biofilm production within an ETT, but it is influenced by the ETT environment rather than by the systemic treatment used during intubation or by the atmospheric conditions used for bacterial growth