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IntroductionCOVID-19-associated acute respiratory distress syndrome (CARDS) poses significant challenges in resource-limited settings. This case series explores the role of bronchoscopy and molecular techniques in identifying superimposed infections in CARDS patients during the second wave of the pandemic in Ecuador.MethodsNine critically ill CARDS patients underwent bronchoscopy and molecular testing to detect co-infections and superinfections. Clinical presentations, diagnostic findings, and outcomes were analyzed.ResultsBronchoscopy and molecular techniques identified a range of secondary infections, including multidrug-resistant pathogens such as Acinetobacter baumannii and Klebsiella pneumoniae. The case series highlights the complexities of managing severe COVID-19 cases in resource-constrained environments.DiscussionEarly identification of microorganisms using PCR methods allows for rapid and accurate diagnosis, facilitating targeted management of critically ill CARDS patients. The study underscores the importance of advanced diagnostic tools and adaptable strategies in pandemic situations, particularly in low-resource settings.