COVID-19 and secondary infections
The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to present a major healthcare burden globally, with over 170,000,000 confirmed cases and 3,500,000 deaths worldwide [1]. Coronavirus Disease 2019 (COVID-19) has a spectrum of severity, and while the vast majority of cases result in a minor self-limiting illness, approximately 5% of patients will become critically unwell with severe respiratory failure which can progress to sepsis and multiple organ failure [2, 3]. Despite recent advances in treatment strategies, the mortality rate for COVID-19 patients admitted to the intensive care unit (ICU) in Scotland remains high at around 35% [4, 5].
The incidence of secondary infections in hospitalised patients with COVID-19 appears relatively low with rates between 6 and 15% [6,7,8]. However the rates are significantly higher in critically ill patients and carry a mortality rate of around 50% [8,9,10]. The clinical features of COVID-19 such as pyrexia, cough and dyspnoea are non-specific and are also observed in bacterial pneumonia [11]. It can therefore be difficult to make a diagnosis of secondary infection by clinical means [12]. Biomarkers such as lactate, C-reactive protein (CRP) and procalcitonin have a well-established role in identifying septic patients who are at risk of further deterioration, but as of yet a specific biomarker to detect the presence of a secondary infection remains elusive [13,14,15]. As such, liberal use of broad spectrum antibiotics has been observed in critically ill COVID-19 patients [2]. The World Health Organisation (WHO) and the Surviving Sepsis Campaign both recommend initiating empirical antibiotics for all severe cases of COVID-19 [12, 16], whereas the National Institutes of Health (NIH) and the National Institute for Health and Care Excellence (NICE) suggest only starting antibiotics when there is a clear clinical suspicion of a secondary infection [17, 18]. Early initiation of antibiotic therapy has been shown to reduce mortality in bacterial sepsis [19], however unnecessary use of broad spectrum antibiotics increases the risk of side effects and promotes antimicrobial resistance [20]. Prompt diagnosis of a secondary infection and identification of the causative pathogen is therefore important in optimal management. Microbiological cultures can guide antimicrobial therapy, but these are time-consuming, and have a low sensitivity [21]. Alternative diagnostic strategies to improve sensitivity and provide rapid specificity would therefore be valuable.
All infections have the potential to cause major disruption to physiological processes, potentially leading to a degree of metabolic dysfunction [22, 23]. This can lead to alteration of the normal serum metabolome (all low molecular weight metabolites less than 1 kDa circulating in the bloodstream at a given point in time) [24]. The physiological response to an infection can result in depletion of certain important nutrients, while simultaneously causing accumulation of other toxic by-products [23]. As such, variation in the composition of the metabolome can be indicative of pathological processes occurring further upstream [24].
Metabolomics
Metabolomics is a discipline which is gaining much traction as a potential diagnostic tool. Metabolomic analysis using techniques such as liquid chromatography–mass spectrometry (LC–MS) can be used to provide a metabolic profile of a patient. This acts as a ‘snapshot’ of the patient’s metabolome, providing a description of the metabolic state of a patient as a result of both genetic contributions and environmental factors [24].
Metabolomics has been investigated for aiding diagnosis of a wide variety of diseases, however in recent years particular focus has been given to its use in identifying biomarkers for infections and sepsis, with several candidate metabolites showing promise. Derangement of fatty acid metabolism has been observed during a septic response, with increased levels of acylcarnitines in septic patients compared with non-septic controls, as well as lower levels of lysophosphatidylcholines in septic shock patients who responded poorly to initial therapy [25,26,27,28]. Animal and human studies have shown that changes in levels of tricarboxylic acid cycle intermediates can occur in response to infection. Derangement of concentrations of citrate, malate and succinate have been observed, particularly in response to gram positive infections including Staph. aureus and Strep. Pneumoniae [29,30,31]. Increases in protein catabolism and amino acid degradation have also been reported during a septic inflammatory response. Multiple studies have shown depletion of the essential amino acid tryptophan leading to a detectable accumulation of the toxic metabolite kynurenine [25, 32, 33]. The biogenic amine trimethylamine-N-oxide (TMAO) has also shown promise as a biomarker of infection. Gut microflora metabolise quaternary ammonium compounds such as betaine and choline to trimethylamine (TMA), which is then converted to TMAO in the liver. TMAO levels are thus indirectly dependant on a functioning gut microbiome [34, 35].
The wide range of possibilities in terms of site of infection, organism type and physiological response means that the resulting metabolic changes will vary from patient to patient. As a result, a single biomarker is unlikely to be sufficient to diagnose a secondary infection. Consideration of groups, or panels of metabolites may be more sensitive for diagnosing secondary infections than individual biomarkers [36]. Moreover, different types of infections may produce a unique signature metabolic profile, thus potentially making identification of the specific organism possible [37].
Study rationale
In critically ill patients with COVID-19, examination of metabolic profiles may permit characterisation of novel biomarkers. These could permit detection of specific underlying infective organisms more rapidly than traditional culture methods. This would allow for earlier initiation of targeted antibiotic therapy, potentially improving outcomes in critically ill patients with COVID-19.
Aim
The primary aim of this study is to ascertain the diagnostic capability of metabolomics for identifying secondary infections in critically ill patients with COVID-19 compared with routinely collected markers of infection.
Secondary objectives will compare profiles between the following subgroups:
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Bacterial and fungal infections
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Gram positive and gram-negative infections
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Healthy controls and COVID-19
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Survivors and non-survivors
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Patients with and without septic shock
This study aims to determine the potential diagnostic capability of metabolomics in diagnosing secondary infections in critically ill patients with COVID-19. We hypothesise that metabolomic profiling of patients with COVID-19 may permit identification of those with secondary infections. As such it is hoped that metabolomic profiling may provide additional perspectives on the underlying pathogen, thus aiding targeted antimicrobial therapy.