The significance of monitoring respiratory sample cultures and polymerase chain reaction tests for detecting bacterial pathogens in severely and critically ill patients with COVID-19

Background: Bacterial superinfection is one of the most common and potentially lethal complications in severely and critically ill patients with COVID-19.

Objectives: To determine the colonisation time frame and the spectrum of potential bacterial pathogens in respiratory samples from patients with severe and critical COVID-19, using routine culture and polymerase chain reaction (PCR) tests.

Methods: A prospective observational study was conducted on patients aged ≥18 years with confirmed severe and critical COVID-19 who were admitted to or transferred to the intensive care unit (ICU). Respiratory samples were collected for microbial culture and PCR testing within the first 2 days after ICU admission/transfer, between days 3 and 6, and after 7 days of ICU stay.

Results: A total of 82 patients, with a median (interquartile range) age of 74.5 (67.3 - 81.0) years and a median Charlson comorbidity index of 4 (3 - 5), were enrolled in the study. Colonisation with any pathogen was observed in 67% of patients, after a median of 4 (2 - 6) days in the ICU. On days 0 - 2 of the ICU stay, micro-organisms were detected in 18% of patients, with Klebsiella pneumoniae (without acquired antibiotic resistance) and methicillin-susceptible Staphylococcus aureus being most frequently identified. Later, A. baumannii and carbapenem-resistant K. pneumoniae became the predominant micro-organisms, identified in nearly half of the patients. In 74% of the samples, the results of microbial culture and PCR tests were identical. In 17%, PCR revealed bacterial pathogens not identified by culture.

Conclusion: Our study confirms that colonisation of the respiratory tract occurs early in the course of ICU stay. Superinfections are predominantly caused by multidrug-resistant Gram-negative bacteria.

Study synopsis: What the study adds. This real-world study provides valuable insights into the significance of microbiological monitoring of critically ill COVID-19 patients. It confirms that bacterial colonisation of the respiratory tract occurs early in the course of ICU stay, with nosocomial superinfections caused predominantly by multidrug-resistant Gram-negative pathogens. Polymerase chain reaction (PCR) testing can assist in ruling out colonisation and in early detection of potential bacterial superinfections.Implications of the findings. Bacterial superinfections present a major challenge in critically ill COVID-19 patients, owing to their high prevalence and mortality rates. Their early detection, determination of causative agents, and antibiotic susceptibility profiling are therefore of paramont importance. PCR testing of clinical specimens appears to be a valuable supplement to respiratory culture, enhancing the precision of diagnosis of lower respiratory tract infections.