Evaluation of the BioFire® FilmArray® Pneumonia plus Panel for Detecting Bacterial Etiological Agents of Lower Respiratory Tract Infections in an Oncologic Hospital. Comparison with Conventional Culture Method

Cancer-related pneumonia is a severe disease with a poor outcome. The course of the disease is usually severe and characterized by high mortality, reaching 35.0% (ICNARC 2017). Many risk factors associated with cancer predispose patients to develop pneumonia. The most common is the disruption of anatomical surfaces, swallowing function, obstruction caused by tumor progression, neutropenia, lymphopenia, and impaired cellular and humoral immunity (Rolston 2001; 2017). In addition, frequent hospitalizations, typical for oncologic patients, increase the exposure of patients to nosocomial pathogens (Wong and Ewans 2017). Diagnosis of pneumonia based on clinical symptoms, which may be poorly expressed in oncologic patients, may be difficult (Wong and Ewans 2017). Therefore, well-documented risk factors for mortality in pneumonia, such as an unidentified etiology (Azoulay et al. 2017), a delay in antibiotic administration in patients with severe disease (Nauclér et al. 2021), and the inappropriate antimicrobial empiric therapy (Fernandez-Cruz et al. 2020) are of particular importance among these patients. Pneumonia can be caused by many pathogens, making empiric antibiotic therapy difficult (Leoni et al. 2016; Conway 2018). The type of pathogen depends on the type and stage of the cancer and the type of immunological deficits (Rolston 2001). Typical bacteria, such as Gram-negative bacilli, are a frequent pathogen of these infections (Ren et al. 2021). Infections caused by Gram-positive bacteria (except Streptococcus pneumoniae and Staphylococcus aureus), Mycobacterium tuberculosis, atypical bacteria, viruses, and fungi are diagnosed less frequently (Rolston 2001; Parody et al. 2007; Han et al. 2015; Tabatabai et al. 2022). It is estimated that up to 60% of these infections remain undiagnosed in terms of the pathogen (Jain et al. 2015; Roquilly et al. 2019). In addition, pneumonia, regardless of the pathogen, can cause similar symptoms, but depending on the group of microorganisms causing them, requires different treatment (Watkins 2022). The conventional culture method is among the recommended diagnostic methods for pneumonia caused by typical bacteria (Kumar et al. 2017). However, this method has a number of limitations, caused by, for example, the difficulty in culturing the pathogens and the time to obtain results, leading to unsatisfactory treatment results (Torres et al. 2016). Therefore, introducing new tests with better parameters, such as the ability to detect a wide range of microorganisms and short turnaround times (TAT), is highly anticipated. Molecular tests for microbiological diagnosis of pneumonia may play such a role. In particular, the use of the multiplex PCR (polymerase chain reaction) method, which enables the simultaneous detection and identification of nucleic acids of many bacteria and antibiotic resistance genes in tested samples, can improve diagnosis and enable earlier treatment of these infections, as well as reduce the use of broad-spectrum antibiotics, which are used when the pathogen is unknown. Although many studies have assessed the usefulness of multiplex tests in diagnosing pneumonia, publications on the usefulness of the test in groups of oncologic patients with solid tumors are scarce.

The aim of this study was to compare the results of the conventional quantitative culture method (CM) in determining the bacterial etiology of pneumonia and detecting the underlying mechanisms of microbial resistance with the results of the Pneumonia plus Panel test (PNP; BioFire® Diagnostics, USA) among oncologic patients with solid tumors.

In the current work, we analyzed the results of studies of bacterial pathogens in samples of BAL among patients with solid tumors using the rapid PNP test and CM. Only 20.3% of samples were TP for bacterial etiology in CM compared to 34.2% TP in the PNP test. More than 60.0% of the analyzed samples were TN in both methods. The most prevalent pathogens in both methods were S. aureus followed by E. coli, P. aeruginosa, and H. influenzae. The CM method, compared to the PNP test for total bacterial pathogens, achieved a sensitivity and specificity, of 59.3% and 98.1%, indicating that the etiology for only slightly more than half of the cases of bacterial infections could be established using conventional methods. The semiquantitative value reported by the PNP test was higher than reported by culture. The PNP test vs. combined tests (PNP test and CM methods) demonstrated PPV and NPV values of 100.0% and 98.1%, and a sensitivity and specificity of 96.4% and 100.0%.

These results correlate with the results described in other works, in which the authors emphasize the low sensitivity of the CM method compared to the high sensitivity of the PNP test (Kamel et al. 2022; Jitmuang et al. 2022). Ginochio et al. (2021) showed that the sensitivity of the PNP test in detecting the etiology of hospital-acquired and ventilator-associated pneumonia is over 98.0%. The advantage of the PNP test over the CM method is the detection of the presence of microbial genetic material. Since the method is not limited by the pathogen activity, detecting the DNA of damaged or non-viable pathogens can be a disadvantage if it generates FP results. It is also an advantage if the material is collected during antibiotic therapy, which is common among hospitalized patients (Buchan et al. 2020). Some bacteria are more difficult to detect using routine cultures (Ginocchio et al. 2021). In our study, differences in non-growth bacteria were found in M. catarrhalis and S. pneumoniae, but also in S. aureus, P. aeruginosa, and E. coli. It may be related to the frequent use of empiric broad-spectrum antibiotics among oncologic patients with suspicion of pneumonia rather than to the difficulty in obtaining the growth of bacteria in culture. Interpreting these results is problematic: it must refer to the specific clinical situation and requires close cooperation between the microbiologist and the clinician. In case of no growth of bacteria in culture, some guidelines recommend discontinuing antibiotic treatment. However, clinical factors should alter the decision (Kalil et al. 2016).

The simultaneous use of the CM method and the PNP test can increase the sensitivity of the diagnostics. Edin et al. (2020), combining the PNP test with CM, determined the etiology in 73.0% of the examined patients, which helped to make quick therapeutic decisions. With the PNP test, we also identified many more positive samples. Using the PNP test allowed us to determine the bacterial etiology in 11 (13.9%) out of the 79 samples tested.

The ability of the PNP test to identify genes responsible for important resistance mechanisms is helpful, especially in the case of the high prevalence of resistance detected by the PNP test in a given area. In the samples tested in the current study, the gene responsible for the production of CTX-M-type ESBLs cephalosporinases in E. coli was detected, which was confirmed by the phenotypic method. ESBLs hydrolyze expanded spectrum cephalosporins (ceftriaxone, cefepime). A positive result suggests that anti-Gram-negative therapy should usually be escalated to a carbapenem as ESBLs confer resistance to cephalosporins (Rodríguez-Baño et al. 2018). However, we did not detect other resistance mechanisms; it is worth emphasizing that the lack of resistance gene does not rule out antibiotic resistance in mechanisms other than those determined in PNP. In the present study, resistance to carbapenems, not resulting from the production of carbapenemases, was found in P. aeruginosa. Therefore, due to the large variety of bacterial resistance patterns, especially in hospitalized patients, and the different mechanisms of their occurrence, it is necessary to perform conventional culture and susceptibility tests in parallel with the PNP test. When choosing empiric therapy based on the results of the PNP test, local microbiological maps and the risk of multidrug-resistant microorganisms should also be taken into account (Murphy et al. 2020).

Viruses are the second most common group of pathogens in lower respiratory tract infections. With respiratory viral infections, mainly of community origin, caused by influenza, parainfluenza, adenoviruses, rhinoviruses/enteroviruses, and RSV, their detections by the PNP test were very useful in the choice of oncologic patient treatment, especially during the infectious season. Using the PNP test allowed the detection of bacterial and viral co-infection in 3.8% of the tested samples. Also, the ability to detect infections caused by atypical bacteria, including Legionella pneumophila, without other tests and collection of further samples is an advantage of the PNP test. Although our work aimed not to compare methods for detecting atypical bacteria, it is known that culture, which is the gold standard for detecting Legionella infections, is characterized by low sensitivity and takes a long time (Cristovam et al. 2017). The PNP test, characterized by greater sensitivity and a short time for obtaining results, may be an alternative to a standard diagnostic procedure in oncologic patients with impaired cellular immunity (Bai et al. 2023).

The PNP test does not detect infections caused by Candida spp., Aspergillus spp., and Pneumocystis jirovecii, which is a limitation in the use of the test in diagnosing pneumonia in oncologic patients. However, pulmonary candidiasis is a rare disease entity. It occurs mainly during neutropenia, in the case of using immunosuppressive drugs, and in severely ill patients with solid tumors treated with broad-spectrum antibiotics for a long time (Schmiedel and Zimmerli 2016). However, very often in cancer patients, the respiratory tract is colonized by fungi. Our research confirmed this. Growth of fungi was obtained in slightly less than 41.0% of the samples tested, but only in one sample at a significant level. In prolonged neutropenia, severe infections caused by Aspergillus and other molds may also develop. We found the growth of Aspergillus fumigatus in about 10.0% (7/69) of the tested samples. Therefore, among patients with an increased risk of developing an infection caused by Aspergillus, especially among patients with acute leukemia and recipients of hematopoietic stem cell transplantation (HSCTs), available mycological diagnostics should additionally be performed aimed at timely diagnosis of infections (Latgé and Chamilos 2019).

Non-infectious pneumonia caused by neoplastic changes, post-radiation complications, pulmonary edema, and drug-induced pneumonia may have a similar course to infectious pneumonia (Black 2016). Since the PNP test is characterized by a high NPV, reaching 90–100%, which is also confirmed by our research, a negative PNP test result may likely indicate a possible cause of pneumonia other than an infectious one. It should be noted, however, that a negative result in the PNP test does not confirm the existence of a non-infectious cause of pneumonia. However, it can be a good tool in the hands of a clinician and complement the diagnostic process and thus influence the direction of the treatment (Azoulay et al. 2020).

The PNP test allows for quick identification of pneumonia pathogens among oncologic patients. It can be used to assess bacterial etiology and to diagnose especially community-acquired viral infections. Due to the various levels of immunosuppression and different stages of cancer in oncologic patients, which are associated with the presence of a specific profile of microorganisms responsible for infections, the benefits of molecular diagnostics should be considered after validations in specific groups of patients with cancer. Similarly, in other works, the authors emphasize that rapid molecular tests should be an additional tool, which, at the present stage of clinical effectiveness, assessment should be supplemented with the standard microbiological tests (Alnimr 2023). Due to the difficulty in predicting etiology, diagnosis of opportunistic pneumonia requires extensive diagnostics, going beyond the microorganisms covered by the panel, appropriate for the type of immunodeficiency, clinical course, and additional tests performed. Therefore, until studies are conducted in groups of oncologic patients who may receive particular benefits from performing molecular tests, tests should be performed in parallel.

This study presents some limitations. The limitation is the lack of clinical characteristics of the patients. Due to the large diversity in the group of patients who were tested (outpatients and hospitalized patients), and the relatively small number of tests performed and the possible impact of local epidemiology, the results cannot be generalized.

In conclusion, the PNP test is a good tool for determining the etiology of bacterial pneumonia in oncologic patients with solid tumors. It provides important diagnostic information, which may support the care of an oncologic patient. However, further large-sample studies are needed to research in strictly defined groups of oncologic patients.