Microbiology Assessments in Critically Ill Patients

Abstract

The prevalence of suspected or proven infections in critically ill patients is high, with a substantial attributable risk to in-hospital mortality. Coordinated guidance and interventions to improve the appropriate microbiological assessment for diagnostic and therapeutic decisions are therefore pivotal. Conventional microbiology follows the paradigm of “best practice” of specimen selection and collection, governed by laboratory processing and standard operating procedures, and informed by the latest developments and trends. In this regard, the preanalytical phase of a microbiological diagnosis is crucial since inadequate sampling may result in the incorrect diagnosis and inappropriate management. In addition, the isolation and detection of contaminants interfere with multiple intensive care unit (ICU) processes, which confound the therapeutic approach to critically ill patients. To facilitate bedside enablement, the microbiology laboratory should provide expedited feedback, reporting, and interpretation of results. Compared with conventional microbiology, novel rapid and panel-based diagnostic strategies have the clear advantages of a rapid turnaround time, the detection of many microorganisms including antimicrobial resistant determinants and thus promise substantial improvements in health care. However, robust data on the clinical evaluation of rapid diagnostic tests in presumed sepsis, sepsis and shock are extremely limited and more rigorous intervention studies, focusing on direct benefits for critically ill patients, are pivotal before widespread adoption of their use through the continuum of ICU stay. Advocating the use of these diagnostics without firmly establishing which patients would benefit most, how to interpret the results, and how to treat according to the results obtained, could in fact be counterproductive with regards to diagnostic “best practice” and antimicrobial stewardship. Thus, for the present, they may supplement but not yet supplant conventional microbiological assessments.

Epidemiology of Gram-negative bacteria during coronavirus disease 2019. What is the real pandemic?

“…Secondly, as the presence of either bacterial co-or -secondary infections is associated with poor outcomes, including increased mortality, the need for rapid diagnostic testing and resistance genotyping, and expedited interpretation thereof, is critical. In a recent review, in which the ability to identify bacterial co-infections was evaluated by BioFire FilmArray in critically ill patients with COVID-19, 33% of specimens were positive vs. 18% utilizing conventional culture, and was associated with a 24À48-h decrease in turnaround time [39,46]. However, the role and impact of culture-independent techniques in the management of concurrent bacterial infections and clear patient-level benefit during the COVID-19 pandemic was not apparent, and requires further studies [39].…”

“…In a recent review, in which the ability to identify bacterial co-infections was evaluated by BioFire FilmArray in critically ill patients with COVID-19, 33% of specimens were positive vs. 18% utilizing conventional culture, and was associated with a 24À48-h decrease in turnaround time [39,46]. However, the role and impact of culture-independent techniques in the management of concurrent bacterial infections and clear patient-level benefit during the COVID-19 pandemic was not apparent, and requires further studies [39].…”

“…One of the major limitations in our current understanding of the impact of COVID-19 relates to additional infections. Whilst they do occur in patients with SARS-CoV-2 infection, whether they represent either true co-infection or secondary/superinfection, remains to be elucidated [39]. Differentiating between them, however, can be onerous and was not clearly delineated in the literature we reviewed [40].…”