Same Day Test Identifies Secondary Infections in COVID-19 Patients

The intensive care unit (ICU) is a dynamic environment with frequent staff-patient contact for invasive monitoring, interventions and personal care that together introduce the risk of secondary or nosocomial infection. When critically ill patients are cared for in the ICU, doctors may take deep samples from their lungs.

Currently samples are often sent to multiple laboratories where different bacterial and fungal cultures are set up alongside other complex molecular tests. Initial results take two to four days to return. SARS-CoV-2 has put considerable strain on ICUs, which has the potential to increase nosocomial infection, antimicrobial treatment and antimicrobial resistance (AMR).

A team of Infectious Diseases specialists led by those at Guy’s and St Thomas’ Hospital (London, UK) processed surplus clinical respiratory samples from 34 ICU COVID-19 patients with suspected secondary infections. Samples processed by the clinical laboratory included respiratory clinical samples (tracheal aspirates, bronchoalveolar lavages (BALs) and non-direct bronchoalveolar lavages (NDLs, a BAL collected without the use of a bronchoscope) for (i) routine microbiological culture for bacterial and fungal pathogens or detection of SARS-CoV-2 by PCR and (ii) sera and BALs for galactomannan (GM) antigen detection when Aspergillus infection was suspected.

Sabouraud agar plates were set up for the detection of Candida spp. and Aspergillus spp. and incubated for five days at 37 °C in aerobic conditions. Bacterial colonies were identified using MALDI-TOF (Bruker, Billerica, MA, USA) except the Aspergillus spp. where microscopy was performed. Clinical metagenomics (CMg) using nanopore sequencing (Oxford Nanopore Technologies, Oxford Science Park, UK) was evaluated in a proof-of-concept study on 43 respiratory samples from 34 intubated patients across seven intensive care units (ICUs) over a 9-week period during the first COVID-19 pandemic wave. Fragment size and quality of metagenomic libraries were analyzed using the TapeStation 4200 automated electrophoresis platform (Agilent Technologies, Santa Clara, CA, USA).

The investigators reported that an 8-hour CMg workflow was 92% sensitive and 82% specific for bacterial identification based on culture-positive and culture-negative samples, respectively. CMg sequencing reported the presence or absence of β-lactam-resistant genes carried by Enterobacterales that would modify the initial guideline-recommended antibiotics in every case. CMg was also 100% concordant with quantitative PCR for detecting Aspergillus fumigatus from four positive and 39 negative samples. Molecular typing using 24-h sequencing data identified multi-drug resistant (MDR)- Klebsiella pneumoniae ST307 outbreak involving four patients and an MDR- Corynebacterium striatum outbreak involving 14 patients across three ICUs.

Jonathan D. Edgeworth, PhD, a Consultant Microbiologist and senior author of the study, said, “As soon as the pandemic started, our scientists realized there would be a benefit to sequencing genomes of all bacteria and fungi causing infection in COVID-19 patients while in the ICU. Within a few weeks we showed it can diagnose secondary infection, target antibiotic treatment and detect outbreaks much earlier than current technologies – all from a single sample.”

The authors concluded that CMg testing provides accurate pathogen detection and antibiotic resistance prediction in a same-day laboratory workflow, with assembled genomes available the next day for genomic surveillance. The provision of this technology in a service setting could fundamentally change the multi-disciplinary team approach to managing ICU infections. The potential to improve the initial targeted treatment and rapidly detect unsuspected outbreaks of MDR-pathogens justifies further expedited clinical assessment of CMg. The study was published on November 17, 2021 in the journal Genome Medicine.

Related Links:
Guys and St Thomas’ Hospital
Bruker
Oxford Nanopore Technologies
Agilent Technologies