Multiplex PCR in the empirical antibiotic treatment of patients with SARS-CoV-2 and bacterial respiratory superinfection

Impact of Multiplex PCR on Diagnosis of Bacterial and Fungal Infections and Choice of Appropriate Antimicrobial Therapy

Multiplex Polymerase Chain Reaction (PCR) has significantly impacted the field of infectious disease diagnostics, offering rapid and precise identification of bacterial and fungal pathogens. Unlike traditional culture methods, which may take days to yield results, multiplex PCR provides diagnostic insights within hours, enabling faster, targeted antimicrobial therapy and reducing the delay in treating critical infections like sepsis. The technique's high sensitivity and broad pathogen coverage make it ideal for both single and polymicrobial infections, improving outcomes across respiratory, bloodstream, and bacterial/fungal infections. However, multiplex PCR is not without challenges; initial high costs and the need for specialized training can limit its adoption, especially in low-resource settings. This review discusses the clinical advantages and limitations of multiplex PCR, highlighting its influence on diagnostic accuracy, antimicrobial stewardship, and the global fight against antimicrobial resistance (AMR). Furthermore, recent innovations in multiplex PCR, such as digital PCR and portable devices, are explored as potential tools for expanding access to rapid diagnostics worldwide.

ADLM Guidance Document on Laboratory Diagnosis of Respiratory Viruses

Respiratory viral infections are among the most frequent infections experienced worldwide. The COVID-19 pandemic has highlighted the need for testing and currently several tests are available for the detection of a wide range of viruses. These tests vary widely in terms of the number of viral pathogens included, viral markers targeted, regulatory status, and turnaround time to results, as well as their analytical and clinical performance. Given these many variables, selection and interpretation of testing requires thoughtful consideration. The current guidance document is the authors' expert opinion based on the preponderance of available evidence to address key questions related to best practices for laboratory diagnosis of respiratory viral infections including who to test, when to test, and what tests to use. An algorithm is proposed to help laboratories decide on the most appropriate tests to use for the diagnosis of respiratory viral infections.

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.