Molecular diagnostics for invasive lung infections in children

There is a strong motivation for increasing the speed and accuracy of microbiological diagnosis of invasive bacterial infections. This is driven by the increasing problem of antimicrobial resistance and the need to deploy definitive therapy to improve outcomes. Over the past decades there have been huge advances in rapid diagnostic technologies including polymerase chain reaction (PCR). The results from these techniques are potentially available within minutes to hours rather than hours to days, as with traditional culture methods. There are many potential benefits of rapid diagnostic technologies over traditional microbiological techniques. Faster pathogen identification time can allow for quicker optimisation of antimicrobial therapy, including shortening courses. Molecular technologies such as PCR are more sensitive than traditional culture techniques. This means small volumes of culture, low levels of pathogen burden or difficult-to-culture pathogens can more readily be detected. Furthermore, they are not reliant on the presence of viable organisms, so they can still be positive even after effective antimicrobial therapy has been commenced. There are also several potential drawbacks to their use. Rapid technologies are generally much more costly than traditional methods and are usually used in conjunction with them, rather than as a replacement. Many techniques cannot determine antimicrobial sensitivity or can only detect a limited range of genes associated with specific resistance patterns. Multiplex panels for PCR can only detect a limited, specific range of pathogens, which are usually targeted to the specimen or indication. Due to the high sensitivity of the test, it may also detect pathogens of uncertain clinical significance; for example when detecting fragments of genetic material from past infection, or low-level carriage in non-sterile sites. Perhaps the biggest barrier to implementation has been difficulty in determining their impact on clinical outcomes, which is often considered necessary to justify their cost. Several studies shave investigated their use for invasive infections in adult populations. More rapid detection of contaminants in blood cultures with multiplex PCR did not improve length of hospital stay or average antibiotic duration in a recent observational study.1 A pre–post observational study of the use of a rapid, direct blood culture pathogen identification using matrix-assisted desorption ionisation time of flight mass spectrometry (MALDI-TOF MS) found a significant reduction in time to effective and optimal antibiotic therapy.2 However, in a randomised controlled trial, it failed to improve clinical outcomes including 28 day survival or effective antimicrobial duration despite a significantly faster pathogen identification time than conventional methods (38.5 h, 95% confidence interval 26.7–50.3, vs. 50.3 h, 95% CI 47.1–72.9).3 A randomised trial of the Accelerate PhenoTest BC Kit, which provides rapid pathogen identification and antimicrobial susceptibility testing within 7 h of positive blood cultures used in patients with gram negative bacilli in blood, found it significantly improved the speed of optimising antibiotic therapy.4 Whilst much of the existing literature focusses on adults, there is recognised scope for improving microbiological diagnostics in children to aid in antimicrobial stewardship efforts and to improve therapy. An area of known antibiotic overprescribing in children is in acute respiratory tract infections, but it has proven challenging to impact outcomes in this setting. A previous clinical trial of multiplex PCR testing vs. usual care in 583 children <12 years with suspected respiratory tract infections found no difference in hospital admissions, length of stay or antibiotic usage.5 A more recent randomised trial of respiratory pathogen PCR (18 respiratory viruses and 3 bacteria) in 1243 children with respiratory symptoms found no difference in overall antibiotic prescriptions, use of diagnostic tests or imaging or healthcare associated costs.6 An RCT of on-site influenza and RSV PCR testing for inpatients in Canada found a significant reduction in the use of oseltamivir and chest radiographs in children, but not antibiotic prescriptions or hospital length of stay.7 PCR is also useful for infections where pathogen yield via traditional culture is known to be low, such as the case with Kingella kingae in septic arthritis. For example, a recent study from Geneva found that of 47 children with confirmed K. kingae septic arthritis, only 6 were positive on culture whereas 44 were positive with PCR assays.8 A new study by Nygaard et al.,9 looks at a novel method of deploying multiplex PCR diagnostics in the context of severe pneumonia in children with accompanying parapneumonic effusion. Such invasive infections are often treated empirically with a collection of broad-spectrum antibiotics, and ensuring rapid transition to definitive therapy is essential in ensuring the best clinical outcomes. In their cohort of 21 children, the multiplex PCR panel identified a pathogen in 20 (95%) cases. In comparison, culture of blood or pleural fluid was only positive in 7 out of 21 patients (33%), which may be in part due to all patients having received antibiotics before pleural fluid was drawn. The high rates of Group A Streptococcus (GAS) detected during this study (13 out of 21, 54.2% overall and 10 out of 12, 83.3% since 2023) could otherwise have gone unnoticed, given that before the study period starting in 2021 the most commonly identified organisms were Staphylococcus aureus and Streptococcus pneumonia. These findings are particularly relevant given the elevated levels of GAS empyema being observed in several locations, as pathogens, which were suppressed during the COVID-19 pandemic return into regular circulation.10 Although the precise reason for this significant resurgence is unknown, it is thought that it may be due to a combination of lower levels of population immunity in children following a prolonged period of reduced exposure, along with the co-circulation of several respiratory viruses (such as influenza), which would not normally occur in the usual seasonal patterns of GAS transmission.10 A study of children from Scotland in 2022 who presented with empyema found a large excess of cases due to GAS in the autumn compared to previous years. Of the 16 cases, 15 were tested for a respiratory virus using multiplex PCR, and 9 tested positive (hMPV in 4, RSV in 2 and Flu A, VZV and Rhinovirus in 1 each).11 These findings are replicated by Nygaard et al., who found that of the 21 cases in their series 14 tested positive for a respiratory virus, including once more high numbers with hMPV (hMPV in 6, rhinovirus, influenza and varicella in 3 each, RSV in 2 and adenovirus and parainfluenza in one each). More specifically a respiratory virus was identified in 11 of the 13 cases alongside GAS.9 A case series from England of invasive GAS infections in children (<15 years) during the 2022 surge found over 25% to have a respiratory virus coinfection within ±24 h.12 A similar surge was noted in the Netherlands of invasive GAS during 2022, and 7 of 42 cases in children <5 years had a preceding or coinciding Varicella zoster infection.13 Further research is needed to explore the role of respiratory viruses as a risk factor for invasive lower respiratory tract infections in children. The role of virus interaction with invasive bacterial infection is particularly noteworthy given potential risks of assuming a positive respiratory virus PCR panel excludes the possibility of a bacterial coinfection or superinfection. The findings from Nygaard et al. highlight the potential utility of multiplex PCR testing in improving the speed and accuracy of pathogen identification in invasive infections in children, such as those presenting with parapneumonic effusions. Further research is needed to determine the impact of rapid and molecular diagnostics on clinical outcomes and antimicrobial stewardship efforts, particularly given the increasing challenges of antimicrobial resistance. A priority will be ensuring these technologies are made increasingly available and affordable for use in both high and low-income settings, alongside evidence to support their use in different demographics. None to declare.