Ramers C, Billman G, Hartin M, Ho S, Sawyer MH. Impact of a Diagnostic Cerebrospinal Fluid Enterovirus Polymerase Chain Reaction Test on Patient Management. JAMA. 2000;283(20):2680-2685. doi:10.1001/jama.283.20.2680
Author Affiliations: School of Medicine, Division of Pediatric Infectious Diseases, University of California, San Diego (Mr Ramers, Ms Ho, and Dr Sawyer); Departments of Pathology and Microbiology, Children's Hospital and Health Center, San Diego, Calif (Dr Billman and Ms Hartin).
Context Enterovirus (EV) infection, the most common cause of aseptic meningitis,
can be rapidly diagnosed with an EV-specific reverse transcriptase polymerase
chain reaction (EV-PCR) test. However, no studies have examined EV-PCR in
a clinical context in which it is routinely used.
Objective To determine the impact of EV-PCR testing on diagnosis and clinical
management of suspected aseptic meningitis cases.
Design and Setting Retrospective review of electronic medical records from a 220-bed tertiary
care pediatric medical center in San Diego, Calif.
Patients A total of 276 pediatric patients for whom a diagnostic EV-PCR test
was performed during the calendar year 1998.
Main Outcome Measures Clinical parameters such as length of stay, medication use, and ancillary
Results One hundred thirty-seven patients (49.6%) had a positive cerebrospinal
fluid EV-PCR result. Enterovirus-positive patients with results available
before hospital discharge (n=95) had significantly fewer ancillary tests performed
(26% vs 72% with at least 1 test performed; P<.001),
received intravenous antibiotics for less time (median, 2.0 vs 3.5 days; P<.001), and had shorter hospital stays (median, 42
vs 71.5 hours; P<.001) than EV-negative patients
(n=92). A positive EV-PCR result was associated with more rapid hospital discharge
(median EV-PCR–to–discharge time, 5.2 hours) compared with a negative
result (median EV-PCR–to–discharge time, 27.4 hours; P<.001).
Conclusions Our results suggest that a positive EV-PCR result may affect clinical
decision making and can promote rapid discharge of patients, and that unnecessary
diagnostic and therapeutic interventions can be reduced by use of EV-PCR testing.
Aseptic meningitis is a common infection in the United States, with
an estimated 75,000 cases each year.1,2
Approximately 80% to 92% of aseptic meningitis cases for which an etiologic
agent is identified are caused by enteroviruses (EVs). Occurring mainly in
the summer and fall, EV meningitis leads to a large number of hospitalizations
of both children and adults.3,4
Although new antiviral agents are being developed specifically for EV meningitis,
treatment is currently symptomatic, and the course of illness is usually benign.2 However, EV meningitis raises concern because of the
difficulty in distinguishing it from bacterial meningitis based on clinical
features alone. To distinguish the 2, hospitalization, empiric prescription
of antimicrobial agents, and use of diagnostic testing are common. The ability
to rapidly differentiate EV meningitis from bacterial illness has the potential
for reduction of such health care services and cost savings. A definitive
diagnosis is also prognostically useful in patients with central nervous system
Previously, the diagnosis of EV meningitis required isolation of the
virus in cell culture. Although older studies have shown viral culture to
be effective in reducing antimicrobial prescription and length of hospital
stay,5,6 these trials reported
rapid turnaround times (2-5 days) that have not been achieved in more recent
Hospital stays are shorter now, in general, further eroding the usefulness
of viral cultures in patient management decisions. Viral culture is also limited
by its relatively low sensitivity (65%-75%),11
as well as the poor growth of some EV serotypes.12
Conversely, the technique of nucleic acid amplification using EV-specific
reverse transcriptase polymerase chain reaction (EV-PCR) can provide prompt
results and may significantly alter the medical care offered to infected patients.
Conventional EV-PCR methods can produce results within 24 hours,8
and more recently developed colorimetric assays can be performed in approximately
5 hours.13- 15
Many studies have described its successful use as a diagnostic tool.7,8,11,13,16,17
In comparisons with viral culture, EV-PCR is more accurate, with a sensitivity
and a specificity of virtually 100%.8,10,11,13,17,18
One study has shown that at least two thirds of all cerebrospinal fluid (CSF)
specimens from suspected aseptic meningitis patients who had negative results
by cell culture had positive results by EV-PCR.8
Studies have alluded to the role of EV-PCR testing in achieving cost
savings through earlier diagnosis.7,8,10,18- 20
Unfortunately, these studies are largely hypothetical, extrapolating from
a single outbreak, retrospectively performing PCR in bulk on frozen specimens,
or attempting to predict clinical management based on modeled scenarios or
decision trees. One study21 has demonstrated
a clinical benefit from a new EV-PCR.
To examine the impact of EV-PCR on the diagnosis and clinical management
of patients with suspected EV meningitis, we analyzed, via retrospective chart
review, 276 inpatients for whom an EV-PCR was performed at the molecular diagnostics
laboratory at the Children's Hospital, San Diego, Calif (CHSD). The CHSD established
an in-house PCR laboratory in 1996 and as of January 1, 1999, had performed
more than 4200 PCR tests (1906 EV-PCR tests). Viral culture is offered at
an offsite location, but its usage has waned since introduction of PCR testing.
Rather than attempt to predict what decisions would have been made if PCR
results were available, this study directly evaluated the impact of EV-PCR
on clinical interventions.
All patients hospitalized at CHSD between January 1, 1998, and December
31, 1998, for whom an EV-PCR test was ordered were included. We identified
280 patients, 4 of whom were subsequently excluded due to prolonged hospitalizations.
Three of these excluded patients had the diagnosis of extreme prematurity,
and 1 had acute lymphocytic leukemia. Clinical data for the remaining 276
patients were accessed through the CHSD's electronic medical record system.
Information collected included date and time of admission, date and time EV-PCR
test was ordered, date and time EV-PCR results were reported, date and time
of discharge, whether ancillary tests were performed (computed tomographic
scan, magnetic resonance imaging, chest or abdominal x-ray, electroencephalogram),
CSF findings, attending physician, clinical diagnoses, administration and
duration of medications, and demographics.
A viral meningitis discharge diagnosis was defined by the following International Classification of Diseases, Ninth Revision (ICD-9) codes: meningitis due to EV (047.0 and 047.1), unspecified viral meningitis
(047.8 and 047.9), and unspecified meningitis (322.9). Cerebrospinal fluid
pleocytosis was defined, as in previously published studies, as a leukocyte
count in excess of the following normal limits: 0.035 × 109/L
for neonates younger than 1 month old, 0.025 × 109/L for
infants 1 to 2 months old, and 0.005 × 109/L for those older
than 2 months.19,22,23
Analysis of the medications administered was limited to anti-infective medications
and central nervous system agents. To analyze seasonal effects on clinical
practice, the calendar year was divided into an EV season that included June
1, 1998, through September 30, 1998, corresponding with the seasonal pattern
of viral meningitis.3,24,25
To determine whether different physicians used the PCR test similarly, the
managing physician was classified as either a hospitalist or an outside physician.
Diagnostic EV-PCR tests were performed by the CHSD's molecular diagnostics
laboratory 3 days per week (Monday, Wednesday, and Friday) in the months of
January through May and 6 days per week (Monday through Saturday) for the
remainder of the year. The PCR assay uses primers that amplify a segment of
the highly conserved 5′ end of the EV genome and was performed as previously
described.8 Preliminary results were reported
based on detection of the PCR-amplified product on ethidium bromide–stained
agarose gels and confirmed via liquid hybridization of the PCR product with
a radioactive phosphorus–labeled EV-specific probe followed by electrophoresis
and overnight autoradiography. Standard methods to prevent carryover contamination
were used, including positive-pressure PCR tips, dedicated workspace for different
stages of the PCR process, and use of uracil-N-glycosylase
and deoxyuridine triphosphate in the reaction mixture.
The data were organized in a database for the purposes of statistical
analysis. Additional calculated parameters were PCR-to-discharge time (date
and time of discharge minus date and time of PCR result), PCR turnaround time
(date and time PCR result was reported minus date and time PCR was ordered),
and length of stay (date and time of discharge minus date and time of admission).
Comparisons were performed using the Kruskal-Wallis test for comparisons of
3 groups and the Mann-Whitney test for comparisons of 2 groups. The Fisher
exact test was used for comparisons of electroencephalogram use because of
small sample sizes. All calculations were performed with statistical software
(version 9.0, SPSS Inc, Chicago, Ill).
Of the 276 patients analyzed, 139 (50.4%) had CSF that was negative
by EV-PCR test and 137 (49.6%) had CSF that was positive by EV-PCR test. Among
the 137 patients with positive EV-PCR results, 100 (72.9%) were admitted within
our empirically defined EV season. One hundred fifty-five (56.2%) of the 276
patients had a discharge diagnosis of viral meningitis and these patients
had a median length of stay of 41 hours. Only 15 patients with a discharge
diagnosis of viral meningitis during this period did not have an EV-PCR test
performed on their CSF, indicating that this test was ordered for the vast
majority of viral meningitis patients at this institution. In the total sample
of 276 patients, males were more common than females, constituting 64.5%.
The median age of the patient sample was 5.5 months, with a range of 0 to
201 months. The PCR tests were ordered a median of 5 hours after admission
(range, 0-333.60 hours). Overall, positive PCR results were available more
rapidly (median, 25.8 hours) than negative results (median, 41.6 hours). During
the EV season and thereafter when the test was offered 6 days per week, the
median turnaround time was 33.9 hours compared with 45.8 hours earlier in
To conduct more meaningful comparisons, we further divided our 276 patients
on the basis of the time that the PCR result became available relative to
hospital discharge. Ninety-two patients had a negative EV-PCR result available
before discharge (EV-negative available), 95 patients had a positive EV-PCR
result available before discharge (EV-positive available), and 89 patients
were discharged before their PCR result was available (not available). The
demographic and clinical features of these patient groups are shown in Table 1.
Table 2 summarizes the results
of comparisons of service use between EV-negative and EV-positive patients
with test results available prior to discharge. The EV-positive available
patients showed a significant reduction in length of stay, number of ancillary
tests, and antibiotic use relative to EV-negative available patients. Of particular
importance, EV-positive available patients had a significantly shorter median
PCR result to discharge time (5.2 hours) compared with EV-negative available
patients (27.4 hours), indicating that EV-positive available patients were
discharged shortly after their PCR results were reported. With respect to
ancillary testing, differences between patient groups were statistically significant
both for individual tests (Table 2)
and in the percentage of each group receiving any test (26% EV-positive vs
72% EV-negative had at least 1 test performed; P<.001),
as well as the total number of tests performed (EV-positive group had 37 tests
vs EV-negative group with 162 tests; P<.001).
Most patients in this study (224/276 [81%]) received intravenous antibiotics
during the course of their hospital stay, and EV-positive available patients
showed a 1.5-day reduction in the usage of intravenous antibiotics compared
with EV-negative available patients. We also noted that EV-positive available
patients had shorter stays in our step-down intermediate care unit compared
with EV-negative available patients. No differences in intensive care unit
or neonatal intensive care unit stays were seen. Importantly, of the total
group of 137 patients with a positive EV-PCR result, only 2 (1.5%) were rehospitalized
within 14 days of initial discharge. Of the 139 total patients with a negative
EV-PCR result, 11 (8%) were rehospitalized, indicating that EV-PCR identifies
patients in whom an uncomplicated recovery can be expected.
Overall, 155 (56.2%) of 276 patients in this study had a discharge diagnosis
of viral meningitis. Of these, 90 (58.1%) were EV-positive available, 19 (12.3%)
were EV-negative available, and 46 (29.7%) were discharged before the PCR
result was available. Comparisons between EV-negative available and EV-positive
available patients with a viral meningitis diagnosis are summarized in Table 3. Differences between groups in
length of stay, PCR-to-discharge time, number of ancillary tests, and intravenous
antibiotic use remained statistically significant when the subset of patients
with viral meningitis diagnoses were evaluated.
In addition to the patients with a positive EV-PCR result with a discharge
diagnosis of viral meningitis, 10 other patients also had a positive EV-PCR
result. These 10 patients included 8 patients with diagnoses of unspecified
viral infection (ICD-9 codes 057.9, 079.6, 079.99,
and 790.8) and 2 with diagnoses of temperature disturbance in the newborn
(ICD-9 code 778.4) and convulsions in the newborn
(ICD-9 code 779.0). Twenty-eight (20.1%) of the 139
patients with a negative PCR left the hospital with diagnoses of viral meningitis.
Nine of these 28 patients' EV-PCR results were not available at the time of
discharge, and 19 were discharged with a viral meningitis diagnosis despite
the availability of negative EV-PCR results.
Overall, 250 (90.6%) of 276 patients had CSF cell count data available.
To examine the correlation between CSF pleocytosis and EV disease, patients
were divided into groupings of neonates and nonneonates based on the fact
that neonates younger than 1 month with evidence of EV in their CSF may not
In the subset of 187 nonneonates, 145 (77.5%) had pleocytosis and 42 (22.5%)
did not. Of these 42 older patients without pleocytosis, 38 (90.5%) had a
negative EV-PCR result.
The age and pleocytosis breakdown of all 122 patients with a positive
EV-PCR result for whom CSF data were available is shown in Figure 1. Only 4 patients older than 1 month had a positive EV-PCR
result without pleocytosis, indicating that in nonneonates who lack pleocytosis
it is rare to detect EV in the CSF. Neonates showed no apparent correlation
between pleocytosis and EV-PCR result, supporting the observation that EV
infection can occur in the absence of pleocytosis. We performed an analysis
of services use in the subset of patients who were neonates or who had CSF
pleocytosis. Table 4 compares
patients with EV-positive available and EV-negative available results. As
with the viral meningitis diagnosis subset, the differences in hospital stay,
PCR-to-discharge time, number of ancillary tests, and intravenous antibiotic
use between EV-positive and EV-negative groups remained statistically significant.
In an attempt to define those patients who did not benefit from EV-PCR,
we analyzed the 89 patients who were discharged before their EV-PCR results
became available. Since EV-PCR results did not play a role in the management
of these patients, many of the PCR tests may have been unwarranted. These
89 patients were significantly older (median age, 1.9 years) than EV-negative
available and EV-positive available patients (median age, 3 months; P=.01; Table 1).
Additionally, the median PCR result turnaround time for patients without available
results was significantly longer (47.55 hours) than that for patients who
received a result before discharge (31.57 hours; P<.001).
While 73 (82.0%) of the 89 patients without EV-PCR results available had turnaround
times of greater than 36 hours, only 68 (36.4%) of the 187 EV-negative and
EV-positive available patients waited for results for more than 36 hours.
Overall, 46 (51.7%) of the 89 patients without available PCR results
left the hospital with a viral meningitis diagnosis, despite their PCR results
not being available at time of discharge. This occurred more frequently during
the EV season (31/49 [63.3%]) than in the off-season (15/40 [37.5%]; P=.008). Findings for CSF were available for 79 patients
who were discharged from the hospital without available results. Of these
79, only 48 (61%) had pleocytosis. Of the patients without available EV-PCR
results with pleocytosis, 38 (79.2%) left the hospital with a viral meningitis
diagnosis, while none of the 31 patients without available results and without
pleocytosis were diagnosed as having viral meningitis.
In our comparisons, we were unable to find disparities in patient management
between hospitalists and outside physicians related to EV-PCR results. In
addition, aside from an increase in the percentage of patients without available
results that left the hospital with a viral meningitis diagnosis during the
EV season, we detected no significant differences in patient management related
to EV-PCR results between the EV season and the off-season.
The management of patients suspected of having viral meningitis is associated
with significant health care interventions that would be largely unnecessary
if a rapid, definitive diagnosis were available. Several recent studies have
alluded to the potential of EV-PCR to streamline the diagnosis and treatment
of viral meningitis patients, and thus abrogate much of this avoidable use.7,8,10,18,20,21
The findings of this study suggest that the impact of EV-PCR on the
management of patients suspected of viral meningitis may be significant. Patients
with a positive CSF EV-PCR result showed significantly lower use of most of
the clinical services we measured and a reduction in length of hospital stay
of nearly 30 hours. A positive EV-PCR result may help establish a definitive
diagnosis and promote immediate discharge of patients. Although negative PCR
results took longer to report than positive results in this study, this does
not account for the differences observed. The EV-positive patients were discharged
a median of 5.2 hours after their result was returned, compared with a median
of 27.4 hours for EV-negative patients. A negative EV-PCR result is associated
with delayed hospital discharge and further diagnostic evaluation.
However, due to the retrospective nature of the study, it cannot be
concluded that positive EV-PCR results were the sole cause of the significant
reductions we observed. Other factors undoubtedly played a role in the management
of each patient. Rather, it should be emphasized that the utility of EV-PCR
appears to lie in helping the clinician to identify the subset of patients
that do not need further medical intervention and that EV-PCR allows this
to be done more quickly than clinical judgment alone. Most patients with negative
EV-PCR results had conditions other than viral meningitis that may have led
to longer hospital stays and more diagnostic testing even without a PCR result.
The differences in use observed between EV-positive and EV-negative patients
remained significant when we evaluated the subsets of patients with a viral
meningitis diagnosis or those with pleocytosis, supporting our conclusion
that EV-PCR affects the management of patients with suspected viral meningitis.
Once positive EV-PCR results were returned, patients were discharged
from the hospital quickly. This potential for immediate discharge coupled
with the relatively short length of stay of viral meningitis patients in general,
necessitates an EV-PCR system that provides results quickly. In our experience,
offering EV-PCR 6 days per week represents the optimal balance of rapid turnaround
and use of laboratory resources. Our data suggest that EV-PCR must be ordered
early in the evaluation process to have a maximum impact on patient management.
In many patients who had computed tomographic scans or magnetic resonance
imaging performed, the decision to undergo these expensive imaging studies
was made before PCR results were even returned. If included earlier in the
diagnostic workup, the value of a positive EV-PCR result may increase, especially
in reducing unnecessary diagnostic tests.
Based on our analysis of patients' critical care usage, EV-PCR results
may also be valuable in decreasing use of intermediate care units by contributing
to a more rapid transfer to routine care once a definitive diagnosis is established.
Positive EV-PCR results were associated with a median reduction in time spent
in an intermediate care unit of 1 day per patient. In the neonatal intensive
care unit and pediatric intensive care unit, however, EV-PCR results appear
to have no impact on patient management, most likely due to the overshadowing
severity of illness.
This study suggests that EV-PCR results can be clinically valuable and
affect patient management in certain situations. Yet, 89 patients in this
study were discharged before their results became available, suggesting no
role for EV-PCR in their management. In characterizing these patients, we
found that they were significantly older (median age, 1.9 years vs 3 months).
It is probable that physicians are more comfortable discharging older patients
with presumed viral meningitis based on clinical diagnosis alone. The EV-PCR
may be more valuable in younger children, for whom clinical differences between
viral and bacterial disease are less pronounced.
Another distinguishing feature of these 89 patients discharged without
available results was the longer median turnaround from the time the EV-PCR
was ordered to the time of reported results (47.55 vs 31.57 hours; P<.001). This finding further supports the necessity for rapid turnaround
of PCR results and suggests a direct relationship between the turnaround time
and the potential for the results to affect patient management.
Some PCR tests ordered in this study appear to have been unwarranted.
Many of the 89 patients without available results did not have clinical criteria
suggestive of EV central nervous system disease and nearly half (49%) left
the hospital without a diagnosis of viral meningitis. Our data support the
findings of previous studies that viral infection of the central nervous system
can be present in the absence of pleocytosis, but this phenomenon is primarily
seen in neonates; in our study, 11 (45.8%) of 24 EV-positive neonates did
not have pleocytosis. Sixteen of the patients without available results were
not neonates and lacked pleocytosis, yet a PCR was still ordered. The EV-PCR
results for all 16 of these patients were negative when completed. Furthermore,
an additional 23 nonneonates from the EV-negative available group lacked pleocytosis,
again suggestive of unwarranted EV-PCR. It is not known whether the CSF cell
count data were available when the EV-PCR was ordered for these patients but
it is possible that the managing physician ordered the PCR prematurely, at
the time of lumbar puncture. The EV-PCR should not be ordered until CSF data
In addition to the 89 patients without available results, 19 patients
left the hospital with a diagnosis of viral meningitis despite having negative
EV-PCR results. It is unclear how many of these patients had false-negative
EV-PCR results, how many were infected with viruses other than EV, and how
many were misdiagnosed. It is likely that most of these patients represent
the 8% to 20% of aseptic meningitis cases not caused by EVs.2,24
Although EV-PCR has been proven to be extremely sensitive, the possibility
remains that false-negative results can occur.
Among the limitations of this study is that we did not attempt to perform
a detailed economic analysis. However, conclusions about cost savings can
be inferred from the units of service approach used in this study. In addition,
because of the retrospective design, we cannot clearly separate the impact
of the PCR result from the clinical presentation on patient management. Furthermore,
this study may not be generalizable to all institutions since it took place
over the course of a single year in a single hospital. Although CHSD serves
a patient population representative of the general population of San Diego
County, even this large population is not representative of some areas of
the United States.
In our institution, EV-PCR has largely replaced viral culture for the
diagnosis of viral meningitis. The rapid results are valued by clinicians
and this study suggests that EV-PCR may decrease use of services as well.
Further studies of the impact of PCR testing on patient management are warranted.