The SARS-CoV-2 pandemic has given added impetus for metagenomic testing using nanopore sequencing to progress from a research tool to routine clinical application. A study led by researchers from Guy’s and St. Thomas’ NHS Foundation Trust has shown the potential for clinical metagenomics to become a same-day test for identifying secondary infection in ventilated ICU patients. Getting results in hours rather than days would help to ensure rapid treatment with the correct antibiotic, minimize unnecessary prescriptions, and thus reduce the growing menace of antimicrobial resistance.
‘SARS-CoV-2 has put considerable strain on ICUs’
The researchers point out that the setting of an intensive care unit involves frequent staff-patient contact that imparts a risk of secondary or nosocomial infection. In addition, invasive ventilation may introduce organisms into the lungs and lead to ventilator-acquired pneumonia. This carries a high mortality and is responsible for up to 70% of antimicrobial prescribing, with current guidelines requiring empiric antibiotics pending culture results, which typically takes 2-4 days.
Many of these infection problems worsened during SARS-CoV-2. Expanded critical care capacity raised the risk of nosocomial infections, with attendant increased antimicrobial prescriptions and the threat of antimicrobial resistance. In addition, treatment of COVID-19 patients with steroid therapy potentially exacerbates bacterial or fungal infections.
The researchers, from the National Institute for Health Research (NIHR) Biomedical Research Centre at Guy’s and St. Thomas’ NHS Foundation Trust and King’s College London, in collaboration with the Quadram Institute in Norwich, Oxford Nanopore Technologies, and Viapath, the U.K.’s largest independent pathology service provider, noted that the pandemic thus reinforced “a need for rapid comprehensive diagnostics to improve antimicrobial stewardship and help prevent emergence and transmission of multi-drug-resistant organisms.”
“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 on ICU,” said Professor Jonathan Edgeworth, who led the research team.
“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.”
Proof-of-concept study
The team performed a proof-of-concept study of nanopore metagenomics sequencing – a type of DNA sequencing that allows direct rapid unbiased detection of all organisms present in a clinical sample – on 43 surplus respiratory samples from 34 intubated COVID-19 patients with suspected secondary bacterial or fungal pneumonia. Patients were drawn from seven ICUs at St. Thomas’ Hospital, London over a 9-week period between April 11 and June 15 2020, during the first wave of COVID-19.
Their median age was 52, 70% were male, 47% White, and 44% Black or minority ethnicities. Median length of stay was 32 days and mortality 24%. Samples sent for metagenomic analysis and culture included 10 bronchoalveolar lavages, 6 tracheal aspirates, and 27 non-direct bronchoalveolar lavages.
The study, published in Genome Medicine, showed that an 8-hour metagenomics workflow was 92% sensitive (95% CI, 75% to 99%) and 82% specific (95% CI, 57% to 96%) for bacterial identification, based on culture-positive and culture-negative samples, respectively.
The main Gram-negative bacteria identified were Klebsiella spp. (53%), Citrobacter spp. (15%), and E coli (9%). The main Gram-positive bacteria were S aureus (9%), C striatum (24%) and Enterococcus spp. (12%). In addition, C albicans, other Candida spp. and Aspergillus spp. were cultured from 38%, 15%, and 9% of patients, respectively.
In every case, the initial antibiotics prescribed according to prevailing guideline recommendations would have been modified by metagenomic sequencing demonstrating the presence or absence of β-lactam-resistant genes carried by Enterobacterales.
Next day results of sequencing also detected Aspergillus fumigatus in four samples, with results 100% concordant with quantitative PCR for both the four positive and 39 negative samples. It identified two multi-drug–resistant outbreaks, one involving K pneumoniae ST307 affecting four patients and one a C striatum outbreak involving 14 patients across three ICUs.
Thus, a single sample can provide enough genetic sequence data to compare pathogen genomes with a database and accurately identify patients carrying the same strain, enabling early detection of outbreaks. This is the first time this combined benefit of a single test has been demonstrated, the team say.
Gordon Sanghera, CEO of Oxford Nanopore commented that “rapidly characterizing co-infections for precision prescribing is a vital next step for both COVID-19 patients and respiratory disease in general.”
Dr. Andrew Page of the Quadram Institute said: “We have been working on metagenomics technology for the last 7 years. It is great to see it applied to patient care during the COVID-19 pandemic.”
He said in an interview: “The pandemic has accelerated the transition from using sequencing purely in research labs to using it in the clinic to rapidly provide clinicians with information they can use to improve outcomes for patients.”