This study, one of the first to analyze the potential impact of a M-PCR system on antimicrobial therapy in the ICU, suggests that it might help improving empiric antibiotic therapy in 63% (60/95) of the patients with suspected VAP or ventilated HAP. The M-PCR provided good overall performances for bacterial identification (sensitivity 80%, 95% CI 71-88% and specificity 99%, 95% CI 99-100%) and resistance gene detection.
Regarding microbiological performance, our results are very close to similar studies that used the same M-PCR system and reported a sensitivity between 73.1% and 88.8% and a specificity between 94.9% and 97.9% as compared to culture methods.19–21 As in our study, Papan et al. reported a better performance of the system for Gram-negative bacteria than for Gram-positive cocci on 79 respiratory samples from children and neonates.19 This might be due to the cell wall structure of Gram-positive bacteria, which have a thicker peptidoglycan than Gram-negative bacteria and thus may be more stable to the lysis process required for DNA extraction.
In our study, the sensitivity of the M-PCR for polymicrobial samples was lower than the overall sensitivity (73% vs 80%) but this difference was not statistically significant. This potential difference probably deserves to be studied in larger samples of patients. We did not encounter machine failure in our study but machine failure rates over 10% have been reported in the literature.20,22 In our study, the M-PCR had a sensitivity of 100% for the detection of carbapenemase genes but only of 63% for the detection of CTX-M genes. This result is difficult to compare with previous studies due to the low number of samples with resistance genes in all studies.19,23 The low CTX-M detection rate (63%) observed in our study may be due to the lack of detection of the CTX-M-9 group by the Unyvero HPN kit which only detects the CTX-M-1 group. Indeed, in a recent publication, the proportion of CTX-M-9 group among ESBL producing E. coli isolated in VAP was as high as 40%.24 This is a limitation of the test for the detection of ESBL, that may lead to inappropriate antibiotic prescription.
Obtaining antimicrobial susceptibility results usually takes 48–98h using conventional methods, thus the use of molecular diagnostic tools could be helpful to initiate the optimal empiric antibiotic. In this study, a multidisciplinary expert panel reviewed each case and estimated that the M-PCR results would have led to antibiotic changes in 63/95 (66%) patients (60 appropriate changes and 3 inappropriate). It is important to note that we considered a carbapenem as the only effective therapy in patients infected by an ESBL-producing Enterobacterales. This is in line with the results of the MERINO trial25 and with recent studies showing a superiority of carbapenems over piperacillin-tazobactam.26–28 However, de-escalation to piperacillin-tazobactam could be discussed for stabilized patients infected by bacteria with a MIC under 4 mg/L to piperacillin-tazobactam.29 Very few studies have assessed the potential impact of a M-PCR system for pneumonia on patient management.30 In a study on 49 patients with severe HAP, the authors observed that initial empirical treatment was modified in 67.3% of the patients based on the availability of the M-PCR.14 However, in this study, the authors considered all the pathogens found by the Unyvero system as causative bacteria for the pneumonia and did not report the sensitivity or specificity of the M-PCR as compared to conventional culture. In a case-control study using the BioFire FilmArray (BioMerieux);31 the authors described an early modification of the antibiotic therapy in 37/56 (66%) patients with severe pneumonia in the ICU.
We identified in our study 3 species of bacteria that are not included in the M-PCR but were involved in 8 pneumonia: Hafnia alvei (n=5), Citrobacter koseri (n=2) and Serratia rubidaea (n=1). The lack of a common marker for Enterobacteriales which could detect the presence of any of the species included in this family was considered as a limit by the expert panel. A recent review also underlined the need to include a larger range of targets to improve the sensitivity.32 It is thus important to note that these tools, because of their lack of exhaustivity, must be used in addition to conventional culture techniques but cannot replace them. M-PCR equipment and cartridge are more costly than conventional methods and cost-effectiveness studies are needed to decide which samples should be tested with a M-PCR.
The turn-around time of the Unyvero system is longer than the only other M-PCR system currently available for respiratory samples, the BioFire FilmArray (BioMerieux), that allows a diagnosis in 65 minutes instead of 4-5 hours. Moreover, owing to the development of new techniques, M-PCR might become outdated even before they are widely used. Indeed, clinical metagenomics, the comprehensive sequencing of microbial and host genetic material in clinical samples,33 has the potential to improve microbiological diagnostics.34 In a recent proof of concept study, Langelier et al. combined microbiological and host transcriptome data in tracheal aspirates of 26 patients with a lower respiratory tract infection in the ICU and identified the causative pathogens with an AUC of 0.91 (95% CI, 0.83– 0.97) however this kind of techniques is expensive and not routinely available.
The interpretation and integration of the results into clinical practice required microbiological and antimicrobial expertise, a good knowledge of the performances and limitations of the M-PCR system and an in-depth discussion between microbiologists and clinicians. Indeed, clinical microbiologists are at the interface between physicians and diagnostic tools and can bridge the gap between demand and supply of innovative systems that could help clinicians take the right decisions at the point of care. It is essential to know the spectrum of the panel to avoid missing treatment for HAP or VAP caused by bacteria that are not included in the panel. The results of this study have to be interpreted in light of the wider context of diagnostics in the ICU: accelerating the microbiology diagnosis is only a part of what is needed to improve empiric antimicrobial therapy.35 Indeed, the time from sampling to diagnosis is often shorter than the delay between the suspicion of infection and sampling or between microbiological results and change of therapy.36,37 Full exploitation of the advantages offered by M-PCR requires a re-organization of the clinical microbiology laboratory, an organized implementation of the technique tailored to the routine workflow and trained physicians to best integrate the results within clinical care.38
This study presents several limitations. We simulated the potential impact of the M-PCR results but clinical studies are obviously needed to evaluate the impact of a M-PCR system in real-life settings. The design of our study does not allow to easily separate what is directly related to the M-PCR results from the impact of a multidisciplinary review of each file. As with other innovative tools,39 clinical trials, preferably randomized and multicentric, should be conducted to evaluate clinical outcomes, including adverse outcomes, process improvement and ecological impact. Special attention should be paid to the integration and implementation of systems into clinical practice, and their adoption and utilisation by clinicians. While waiting for the results of clinical trials, implementation outcomes such as appropriateness or fidelity may be key intermediate outcomes to study the success of strategies aiming to bring M-PCR systems to the clinical practice.34 The question of whether or not M-PCR reduces antibiotic use, antibiotic resistance, direct costs, and indirect costs should be a priority area for future research. In our study, each episode of VAP or ventilated HAP was analyzed by a multidisciplinary expert panel of senior intensivists and clinical microbiologists. In routine practice, this may not always be the case and trials should aim to study the potential difficulties of the integration of M-PCR in the clinical practice such as the management of the results in case of lack of experienced clinical staff to interpret the results. Our results are limited regarding the detection of resistance because of a low number of patients with ESBL or carbapenemase-producing Enterobacteriaceae (CPE). Finally, we only included samples with Gram-negative bacilli or clustered Gram-positive cocci on Gram staining in three ICUs in the same hospital preventing the extrapolation of our results to other samples or other contexts. Indeed, the performance of the M-PCR could be different in another setting characterized by a higher proportion of Gram-positive bacteria and/or a different prevalence of Enterobacterales.