Multiplex PCR point of care testing versus routine, laboratory-based testing in the treatment of adults with respiratory tract infections: a quasi-randomised study assessing impact on length of stay and antimicrobial use

Respiratory tract infections (RTI) place a significant burden on health systems globally, particularly during the annual respiratory season epidemics [1]. Diagnostic tests for respiratory pathogens (RP) are usually laboratory–based with an inherent delay in time to result relating to specimen in transit to the laboratory and laboratory testing schedules, for example once a day, and/or not performed on weekends and holidays. For this reason or due to the nature of the test (culture, serology or batch molecular testing) results are rarely available to the clinician when the patient is first assessed. Consequently, though respiratory viruses are frequently isolated in community acquired pneumonia (CAP) [2] and are reported to be responsible for 12.8% of CAP cases admitted to UK hospitals [3], the decision to manage as a viral RTI or treat for bacterial infection including Mycoplasma pneumoniae or Chlamydia pneumoniae (‘atypical bacteria’) is based upon the clinical scenario and severity criteria such as the CURB-65 score. Thus a proportion of infections will be inappropriately managed with antibiotics or the result may arrive too late for influenza treatment to be effective [4]. The World Health Organization (WHO) states that antimicrobial resistance threatens the effective prevention and treatment of an ever-increasing range of infections [5]. The Centre for Evidence Based Medicine highlights the considerable number of new diagnostic technologies in development to underpin the rational prescribing of antibiotics [6], which extends to antivirals.

Point of care (POC) tests eliminate the need for specimen transportation to the testing laboratory and can be performed on demand by ward staff. By providing faster results, POC tests may influence early treatment decisions such as hospital admission and allow earlier discharge, targeted antimicrobial prescriptions and better antimicrobial stewardship. POC testing should also reduce cross-transmission and subsequent nosocomial outbreaks related to viral RTI cases that are undiagnosed and patients not placed in appropriate isolation. However, current POC tests for respiratory viruses are generally antigen detection tests, usually only detect influenza and respiratory syncytial virus (RSV) and their sensitivity can be suboptimal [7, 8]. The BioFire FilmArray® respiratory panel (BioFire Diagnostics, Salt Lake City, UT, a bioMerieux Company) detects 14 respiratory viruses: influenza virus types A and B (with influenza A subtyping), adenovirus, coronaviruses HKU1, NL63, 229E and OC43, human metapneumovirus, human rhinovirus/enterovirus, parainfluenza virus types 1–4 and RSV and 3 bacteria: Mycoplasma pneumoniae, Chlamydia pneumoniae and Bordetella pertussis. FilmArray® lends itself to POC testing as it is a small, desktop, fully-automated nested multiplex PCR in an enclosed disposable pouch requiring only 2 min of hands-on time with results available in about 1 hour [9]. Though more expensive than single or low multiplex laboratory or POC tests, clinical outcomes such as a reduced length of stay and reduction in inappropriate antimicrobial usage resulting from the rapid and extended panel may offset test costs. Thus understanding FilmArray®‘s clinical utility as a POC test early in a patient’s admission is important.

We undertook a study to assess the FilmArray® RP panel as a POC test compared to routine, laboratory-based detection methods in order to assess the impact on length of stay and antibiotic utilization. It is the first study, to our knowledge, in which ward-staff were performing the FilmArray® RP panel as a POC test.

The study ran from 5th January 2015 until 1st July 2015 as planned. No changes were made to the study protocol. During this time 606 patients met eligibility criteria (Fig. 1). Sixty-one (10.1%) of these patients were not included (33 in the intervention arm, 28 in the control arm) because 20 were discharged before enrolment, an interpreter was unavailable for three, 34 declined participation, one patient died before being approached, one patient consented but the test was not performed and information is missing for two patients. No patients withdrew from the study. Thus 545 (89.9%) patients were enrolled and included in the analysis, 211 in the control arm and 334 in the intervention arm. All statistical analyses were pre-specified; there were no post-hoc analyses.

Baseline characteristics were similar between the two study arms (Table 2). CURB-65 score was missing for 62.9% of patients for whom it was relevant and was omitted from the analysis. One hundred and sixty-five (30%) patients had a negative time to antibiotics changed to 0 h (median − 1.5 h [IQR −3.5 to −0.8]).

Overall, 124 (22.8%) of the 545 patients had a positive result (Table 3), 43 (20.4%) in the control arm and 81 (24.3%) in the intervention arm. The viruses and bacteria detected are shown in Table 3. Every virus on the panels was identified except parainfluenza virus type 1, type 2 and type 4. Only single pathogens were detected by routine testing but FilmArray® detected dual infections in five samples. FilmArray® also detected coronaviruses, not detected using standard tests. There were three and four invalid tests in the control and intervention arms respectively, the remaining tests were negative (78.2% control, 74.6% intervention).

M. pneumoniae was the only bacterium on the panels which was identified. Four patients in the control arm had an elevated Mycoplasma CFT (1:64, 1:64, 1:32, >1:16). Convalescent serology was not sent, rendering results uninterpretable. All of these results were available after ward discharge, three after hospital discharge, and did not influence management. The TAT was 8–13 days. Five patients in the intervention arm had M. pneumoniae detected by FilmArray®. Antibiotics were started for 2 of these cases and extended in 2 after discussion with the Microbiologist.

For all but one of the secondary outcomes, there was no evidence that the intervention had an effect (Table 4). Only the prescribing decision within 24 h following the diagnostic results under investigation showed evidence of a difference between study arms (Table 5, p < 0.001, Pearson’s Chi-squared test, p-value calculated by 10,000 Monte Carlo replicates).

Fifty-one patients had influenza A virus and/or influenza B virus detected by either the routine assay (21) or by the FilmArray® (30). Of these patients, 13 of 21 (62%) in the control arm and 24 of 30 (80%) in the intervention arm were given antivirals. The time to the first dose from the time of admission was known for all but one patient in each arm and was considerably reduced in the intervention arm: median of 60.4 h in the control arm (IQR 22.7–85.2) and 24 h in the intervention arm (IQR 11.6–33.0). Only one patient in each arm was given empiric antivirals but had a no viruses detected.

We found no evidence for an association between respiratory multiplex PCR (BioFire FilmArray®) POC testing and length of hospital stay when compared to our routine, laboratory-based respiratory PCR and serology testing. There was an association between POC testing and the antibiotic prescribing decision within 24 h after the result. POC testing also produced results considerably faster than laboratory-based assays. We did not investigate whether the POC results actually influenced decision making and the association with the prescribing decision may only reflect that the FilmArray® result was available before the antibiotics were prescribed and not that the prescriber considered the FilmArray® result in their decision making. Similar percentages of patients received antibiotics in both study arms. There were no significant differences for the remaining secondary outcomes between the two study arms.

The hypothesis was that POC testing would reduce the length of stay. However, though the POC test was 1 day faster than laboratory-based testing, the results were available later than anticipated. This was not due to testing performance of FilmArray®, which took only 65 min but related to a delay in the processing of the specimen by the clinical staff on the ward. Sixty-eight percent of POC tests were performed by study investigators reflecting the fact that the study protocol was not initiated by clinical staff as soon as the patient was admitted to the study ward in many cases. Instead testing was delayed until the study investigators visiting the study wards initiated the study protocol. This resulted in a significant delay in time to results. This is in contrast to a trial of MRSA POC screening by our AMU ward staff that had a TAT from admission of 3.7 h [20]. MRSA testing is mandatory and most patients were eligible for inclusion. The delay in the present study may be related to screening for more complex eligibility criteria than the MRSA study and an additional reliance on study investigators present on the ward to perform the test. If this is the case, the TAT would be faster if FilmArray® was embedded as a routine, diagnostic POC test. When ward staff did perform the test, they were from all grades and they performed it without incident. Others report a TAT of 2.3 h for FilmArray® POC testing, though the TAT was from the time of decision to test to the time of result and testing was conducted by trial staff [21]. Thus FilmArray® POC testing can be successfully implemented but this study failed to achieve the optimum TAT.

POC testing was associated with a reduction in time to antivirals for those identified with influenza virus. Antivirals were given a day and a half quicker in the intervention arm and within a day of admission. Given that these drugs are of clinical benefit only if administered within 48 h of symptom onset [4], this is a key, clinical outcome. POC testing allowed changes to therapy for the appropriate treatment of mycoplasma infection; in the control arm, positive results were uninterpretable and were predominantly available after discharge. The ability of FilmArray® to detect coronaviruses allowed for a diagnosis to be made in 15 samples that would have been missed using routine methods. Routine testing only identified single pathogens as opposed to FilmArray® which identified dual infection in 5 patients, of importance for infection control and virus surveillance. Parainfluenza virus types 1, 2 and 4, Chlamydia pneumoniae and Bordetella pertussis were not detected during the course of this study which did not span the entire winter.

The positive impact on antivirals of the faster time to detection of influenza with FilmArray® was reported by an observational study of paediatric patients, 81% of who were given oseltamivir in a timely manner, which was not possible with the comparator test [22]. An observational study reported a faster time to a negative influenza result with FilmArray® compared to another RT-PCR (46.4 h versus 3.1 h) which shortened unnecessary oseltamivir use by 2 days with an estimated cost saving per patient of $34.16 US [23].

Seventy-five percent of the POC results were negative, providing no information about the aetiology of the infection or the predicted clinical course. Negative results would not be expected to expedite discharge or antibiotic cessation, the main outcomes under consideration here. A paediatric observational study found that patients with a positive respiratory virus PCR result had a 42% shorter duration of intravenous antibiotics [24]. A retrospective study noted a reduced length of stay in children with a positive FilmArray® result reported within 4 h, not seen with negative tests [25]. The reduced time to detection of influenza with laboratory-based FilmArray® was associated with significantly lower odds ratios for admission, length of stay, duration of antibiotics and chest X-rays when compared to positive routine tests in a retrospective study of adults [26]. A randomised trial noted that patients with positive FilmArray® POC results received shorter courses of antibiotics and had shorter hospital stays than those with negative POC results [21]. Our 20–24% positive yield may be because our study was seasonally limited and extended in to the summer months. Further, we did not record the types of RTI, which may have resulted in this lower than expected percentage. Another UK, adult study between September 2012 and February 2014 identified viruses in 30% of patients with lower RTI [27].

The POC result was too slow to influence initial antibiotic decision making as the median time to antibiotics from admission was 0 h. This rapid initiation of antibiotics was also found in a randomised trial of FilmArray® POC testing [21] and is consistent with guidelines that recommend antibiotic treatment for CAP within 4 h of presentation to hospital [3]. Therefore, we would expect almost all patients to be initially started on an antibiotic. However with the delay in POC testing we would not expect this parameter to be impacted, i.e. if testing had been done in an appropriate time frame (<4 h after patient evaluation) the subsequent initiation or discontinuation may have been significantly influenced. Some of this reflects a continuation on the study wards of antibiotics started in the ED. Even with a positive POC result, AMU doctors may be dissuaded on safety grounds from stopping or de-escalating antibiotics that were started on the basis of a clinical assessment that they did not witness in the ED. Our findings are consistent with a randomised trial of FilmArray® POC testing, which found that the mean duration of antibiotics did not differ between the FilmArray® and control arms. However that group identified that a greater proportion of patients in the intervention arm (with a POC result) than in the control arm received only a single dose of antibiotics or <48 h of antibiotics [21], something that we did not assess in the present study. Other trials of RP diagnostics in adults, including FilmArray®, have found that PCR detection of only a viral pathogen coupled with a low procalcitonin level led to antibiotic cessation in only 32% of cases [28] or a trend towards fewer days of antibiotic treatment off-set by only 4/18 patients having their antibiotics stopped [29]. The authors of the latter study advocate real-time stewardship with RP results, which was omitted from the intervention in the present study. Rapid pathogen identification with antimicrobial stewardship has been associated with a significant reduction of hospital costs for adult in-patients [17].

This study has other limitations, nearly all due to limited resources. We employed a pragmatic quasi-randomised design, allocating patients to the intervention arm on even days making the study vulnerable to bias due to differences in patients allocated to the study arms. Though we found no evidence for such differences, and the outcome analysis adjusted for several pre-specified potential confounders, a fully randomised design would have provided a stronger level of evidence. There were more patients in the intervention arm suggesting that the patient recruitment processes in the two arms were not equivalent and this may reflect enthusiasm for the FilmArray®. This may also reflect increased disease severity in the intervention arm and a need to identify the cause of the disease, thereby resulting in a biased use of the FilmArray® in this cohort. CURB-65 scores were not assessed and therefore an accurate comparison of the severity of the pneumonia in the two arms of the study could not be determined. Further, we did not collect data on the type of RTI; a randomised trial of FilmArray® POC testing recorded a shorter duration of antibiotics for patients with asthma and COPD who were in the intervention arm versus the control and a shorter length of stay for COPD patients in the FilmArray® arm [21]. The ED does not routinely use EPMA and so we do not know exactly how many patients received antibiotics there. A negative time to antibiotics, due to administrative errors, was changed to 0 h in 30% of patients however the median was small (−1.5 h) and this phenomenon occurred in both study arms. As in other similar studies on this subject [21] we did not include routine bacteriology results in the analysis however the hypothesis had greater dependence upon the predominantly viral panel results under investigation and bacteriology results would not be expected to differ between the study arms and thus influence results. Finally, the number of eligible patients admitted to the study wards was less than predicted by the data used to plan the study and hence the number of cases recruited fell short of the statistical calculation that required 1131 patients in each arm to detect a fall of 0.6 days. It is not clear why this was the case but may be related to patients by-passing the study wards during the busy winter months of January to March and due to the inclusion of some summer months in the study.

We have selected for patients who required admission and possibly antibiotics by placing the FilmArray® systems on hospital wards. A panel which includes common bacterial causes of lower RTI would probably have identified more pathogens in this setting. A recent study in the UK identified bacteria in lower respiratory tract specimens from 81% of patients with pneumonia [27]. Though we did not record the type of RTI in this study, as in-patients, most patients probably had a lower RTI. A study in the ED might have tested a greater number of patients with a viral illness. There, POC results could provide reassurance that discharge is reasonable. With a rapid result and the broader RP panel afforded by FilmArray®, it is plausible that safety-netting antibiotic prescriptions would have reduced. Due to the mandated maximum 4-h wait for patients in English EDs [30] and a perceived lack of understanding of these results vocalised by our ED staff (because with laboratory-based testing the patient has left ED when results are available), we moved the study one step in to the hospital. This highlights an important knowledge gap. An ED-based study of POC testing incorporating decision making support is therefore advisable.

We found no association between respiratory multiplex PCR (BioFire FilmArray®) POC testing and length of hospital stay when compared to our routine, laboratory-based respiratory PCR and serology testing. This result was most likely influenced by the delay in the rapid POC testing. POC testing produced results considerably faster than the routine tests but the results were not rapid as designed to be. This was not the fault of the POC test, but highlights the fact that new technology itself is not enough: the correct systems must be in place in order to reap their benefits. Patients who had the POC test received time-critical antivirals for influenza significantly faster and appropriate therapy for mycoplasma infection, not seen in the control arm. Ward staff of all grades performed the POC test without incident meaning that this test has potential across a range of healthcare. Further studies are required that focus on implementing respiratory multiplex PCR POC testing with rapid results, in order to fully assess the impact on length of stay and antibiotic use.