SARS-CoV-2, the virus that causes COVID-19, is currently a global public health problem, declared a pandemic by the World Health Organization, which today has more than one million deaths in the world, of which , 30,000 approximately belong to Colombia, being the country number 11 with the highest number of deaths. The most common symptoms related to this disease are fever, cough, dyspnea, myalgia, headache, diarrhea and rhinorrhea. COVID-19 is characterized by immune system dysfunction and hyperinflammation causing acute respiratory distress syndrome, macrophage activation, and coagulopathy. The clinical course for SARS-CoV-2 in most cases is mild, but approximately 14% of cases can be severe. In pneumonia caused by SARS-CoV-2, the lung lining is known to alter the composition of the lung microbiome, in addition to lymphocyte damage that can promote the growth of bacteria to initiate bacterial pneumonia, and it is estimated that the prevalence of coinfection / superinfection reaches 50% among deaths from COVID-19. Coinfection between different microorganisms and SARS-CoV-2 is a serious problem in the COVID-19 pandemic, and there is still little information on this.

It is for this reason that the researchs propose to develop this research project that will allow to understand the possible mechanisms associated with the development of bacterial coinfection / superinfection in patients diagnosed with COVID-19, which will allow expanding the panorama of knowledge towards a better and adequate treatment in these patients, as well as detection of biomarkers or clinical phenotypics that may be useful in the diagnosis, based on evidence.

It is important to note that these results are of clinical importance since we will try to identify biomarkers or changes in the lung microbiome that allow doctors to early identify patients at risk of developing coinfection and thus initiate early treatments or preventive measures, which allow the improvement of clinical outcomes in patients. Results will be presented in a timely manner at national and international conferences and in peer-reviewed, indexed, high-impact journals.

This is a prospective, translational (T0-T2), multicenter, observational, cohort study of consecutive patients with a first clinical phase, where the collection of different types of samples (Bronco alveolar lavage, blood, nasopharyngeal swab, secretion orotracheal and rectal swabbing) at the start of mechanical ventilation, on day 3 and before extubation and another stage of molecular analysis in human samples collected where by different types of techniques such as: characterization of the 16S ribosomal unit, ELISA, time PCR real, concentration and cell discrimination techniques, we will characterize the microbiological, immunological and cellular changes that condition the development of coinfection.

Descriptive analytical studies, techniques, and parametric and nonparametric tests will be used to explore diagnostic, microbiological, or subgroup differences, as well as clinical outcomes. Independent predictors and associated hazard ratios with 95% confidence intervals will be reported. A two-tailed p value less than 0.05 will be considered statistically significant.

Inclusion Criteria:

• Patients admitted to the ICU, COVID-19 positive by RT-PCR, who require assisted mechanical ventilation.
• Adult patients over 18 years of age.
• Patients who agree to participate in the study and sign the informed consent form (family members or legal representative).
• Patients in whom the identification of the causative agent of coinfection is attempted within the first 48 hours of hospitalization.

Exclusion Criteria:

• Patient on mechanical ventilation for more than 24 hours without being evaluated for study entry.
• Patient who was treated with antibiotics 7 days prior to hospitalization or time of assessment for the study.
• Pregnant or breastfeeding patients.
• People who belong to population groups with increased vulnerability such as, for example, prison population, minors detained in orphanages or people in street situations.

No research procedure, clinical or paraclinical, or taking of clinical information or biological samples will be performed before the patient or his/her legal representative agrees to participate in the study and signs the informed consent form.

Adult patients admitted to the Intensive Care Unit of the Clínica Universitaria de la Sabana, with a diagnosis of COVID-19 by RT-PCR, who require invasive mechanical ventilation due to respiratory failure as a result of the infection and who approve their participation in the study. It is important to highlight that these patients are sedated and cannot agree to participate in the study; therefore, the patient's relatives or legal representative will be in charge of defining the participation of the relative in the study.

confidentiality agreement