Multiplex Polymerase Chain Reaction Panel Research Articles

Acute diarrhea in the hospitalized immunocompromised patient: what is new on diagnostic and treatment?

This article aims to provide an intuitive framework for diagnosing and managing healthcare-associated diarrhea (HCAD) in the immunocompromised (IC) host. Our understanding of diarrhea in hospitalized IC patients has significantly evolved. However, the challenge lies in distinguishing between these patients' numerous causes of diarrhea. The incorporation of gastrointestinal (GI) multiplex polymerase chain reaction (PCR) panels has led to a paradigm shift in our approach to diarrhea. However, using these panels judiciously is of utmost importance, as their misuse can lead to over-testing, overtreatment, and increased hospital costs. We propose a stepwise diagnostic algorithm that ensures diagnostic stewardship, optimal patient care, and resource utilization. Diarrhea is a common complication in hospitalized IC patients and is associated with significant morbidity and rare mortality. The advent of new diagnostics, such as GI multiplex PCR panels, holds promise in facilitating the detection of recognized pathogens and may allow for improved outcomes using pathogen-targeted therapy.

Implications of Measles Inclusion by Commercial Syndromic Polymerase Chain Reaction Panels - United States, May 2022-April 2023.

Syndromic polymerase chain reaction (PCR) panels are used to test for pathogens that can cause rash illnesses, including measles. Rash illnesses have infectious and noninfectious causes, and approximately 5% of persons experience a rash 7-10 days after receipt of a measles, mumps, and rubella (MMR) vaccine. MMR vaccine includes live attenuated measles virus, which is detectable by PCR tests. No evidence exists of person-to-person transmission of measles vaccine virus, and illness does not typically result among immunocompetent persons. During September 2022-January 2023, the Tennessee Department of Health received two reports of measles detected by syndromic PCR panels. Both reports involved children (aged 1 and 6 years) without known risk factors for measles, who were evaluated for rash that occurred 11-13 days after routine MMR vaccination. After public health responses in Tennessee determined that both PCR panels had detected measles vaccine virus, six state health departments collaborated to assess the frequency and characteristics of persons receiving a positive measles PCR panel test result in the United States. Information was retrospectively collected from a commercial laboratory testing for measles in syndromic multiplex PCR panels. During May 2022-April 2023, among 1,548 syndromic PCR panels, 17 (1.1%) returned positive test results for measles virus. Among 14 persons who received a positive test result and for whom vaccination and case investigation information were available, all had received MMR vaccine a median of 12 days before specimen collection, and none had known risk factors for acquiring measles. All positive PCR results were attributed to detection of measles vaccine virus. Increased awareness among health care providers about potential measles detection by PCR after vaccination is needed. Any detection of measles virus by syndromic PCR testing should be immediately reported to public health agencies, which can use measles vaccination history and assessment of risk factors to determine the appropriate public health response. If a person recently received MMR vaccine and has no risk factors for acquiring measles, additional public health response is likely unnecessary.

Diagnostic Accuracy of Cerebrospinal Fluid Multiplex Polymerase Chain Reaction Panel Testing in Patients With Suspected Central Nervous System Infections: A Multi-Center Study in the United Arab Emirates

Diagnostic Accuracy of Cerebrospinal Fluid Multiplex Polymerase Chain Reaction Panel Testing in Patients With Suspected Central Nervous System Infections: A Multi-Center Study in the United Arab Emirates

913. Incidentally Positive Measles Results with a Commercially Available Multiplex Polymerase Chain Reaction Panel for Exanthems — Tennessee, 2022–2023

Abstract Background In January 2023, the Tennessee Department of Health (TDH) received report of a positive measles result from a multiplex polymerase chain reaction (PCR) panel ordered to evaluate a fever and rash in a child. Immediate public health investigation concluded that the positive test was because of recent measles vaccination. Because multiplex PCR tests have not typically included measles, we assessed patient characteristics, provider responses, and measles virus strain when multiplex PCR identified measles to guide public health response in Tennessee. Methods We retrospectively identified Tennessee residents who tested positive for measles by 2 multiplex PCR panels, commercially available since 2022, that include 7–9 viruses and Streptococcus pyogenes. We queried the state immunization registry for measles vaccine records for those persons and asked ordering providers about their clinical assessment, test use, and response to the positive result. CDC performed the Measles Vaccine (MeVA) assay (real-time RT-PCR) on available clinical specimens. Results Of 296 multiplex PCR tests on Tennessee residents, 7 (2.4%) were positive for measles. Median age was 1 year (range: 1–6 years). All 7 received a measles vaccine within 8–15 days before the test. Among 7 providers, 6 did not suspect measles prior to testing. All ordered testing to evaluate a rash, with or without fever, and none were aware of patient exposure to persons with measles. After the positive result, 2 providers contacted TDH for guidance, 4 attributed the result to recent vaccination, and 1 reported not having received the test result. Three patients tested positive for additional viruses in the panel including enteroviruses (n = 2), human herpesvirus type 6 (n = 2), human herpesvirus type 7 (n = 1), and Epstein-Barr virus (n = 1). MeVA testing of 2 specimens identified measles vaccine strain in 1 specimen and an inconclusive result in the other. Conclusion Inclusion of measles in multiplex PCR panels can incidentally identify measles virus in recently vaccinated persons, requiring MeVA testing to confirm vaccine strain. In recently vaccinated persons, medical and public health professionals must carefully consider use and interpretation of measles results in multiplex PCR panels. Disclosures All Authors: No reported disclosures

Utility of a Viral Vesicular Panel Multiplex Polymerase Chain Reaction Assay for the Diagnosis of Monkeypox, Herpes Simplex, and Varicella Zoster Viruses.

Mpox (monkeypox) represents a diagnostic challenge due to varied clinical presentations and multiple mimics. A commercially available multiplex polymerase chain reaction panel accurately detects mpox virus as well as common mimics (herpes simplex virus, varicella zoster virus) in clinical specimens and could be used in routine clinical, surveillance, and outbreak settings.

Nasopharyngeal detection of atypical bacteria by multiplex polymerase chain reaction panel in acutely ill children was associated with an increased risk of pneumonia.

We aimed to assess whether detection of respiratory bacteria by multiplex polymerase chain reaction (PCR) testing associates with clinical outcomes in acutely ill children. This cross-sectional study enrolled children under the age of 18 with a suspected respiratory infection treated in a paediatric emergency department of Oulu University Hospital, Finland from January 2015 through December 2015. Nasopharyngeal samples were routinely analysed for 16 respiratory viruses and later, after storage, analysed with a multiplex PCR panel for seven respiratory bacteria. At least one bacterial pathogen was detected in 600 out of the 1195 children (50%). The mean age was 3.3 (SD 3.7) years and 54% were boys. Atypical bacteria were associated with a risk of pneumonia (adjusted odds ratio [aOR] 14.1, 95% CI 3.98-50.1). Co-detection of rhinovirus with Streptococcus pneumoniae was not associated with risk of pneumonia (aOR 2.39, 95% CI 0.78-7.30). Detection of Streptococcus pneumoniae, Haemophilus influenzae or both was not associated with the risk of hospital admission or prescription of antibiotics. Nasopharyngeal detection of atypical bacteria in acutely ill children was associated with a markedly increased risk of pneumonia. The clinical utility of wide testing for other respiratory bacteria needs further evaluation.

1996. Association between Multiplex Polymerase Chain Reaction Stool Diagnostic Testing and Pathogen Detection, Healthcare Resource Use, and Cost Among Adult Outpatients Treated in United States Hospitals for Acute Infectious Gastroenteritis

Abstract Background Multiplex polymerase chain reaction (PCR) gastroenteritis testing panels simultaneously detect multiple pathogens with rapid turnaround, allowing more accurate and timely diagnosis and treatment. This retrospective observational study assessed the association between stool test type (i.e., multiplex PCR panel with < 12 target pathogens [PCR< 12], multiplex PCR panel with ≥ 12 target pathogens [PCR12], traditional work-up [TW]) and healthcare resource use (HRU), cost, and diagnostic yield in adult outpatients treated in U.S. hospitals for acute infectious gastroenteritis (AIG). Methods Using large geographically diverse PINC AI Healthcare Database data from January 1, 2016–June 30, 2021, we analyzed adults (≥ 18-years) with an AIG diagnosis and stool test performed during an outpatient visit. Pathogen analysis was performed in those with microbiology data available. Results Among 36,787 patients, TW was most often performed (57.0%), followed by PCR12 (30.2%) and PCR< 12 (12.8%). Patients with PCR12 were more likely younger, Hispanic/Latino, and uninsured, and less likely socially vulnerable compared to TW (all p< 0.01, Table 1). PCR12 was more common in patients from large (500+ beds), teaching, urban hospitals in the Midwest, compared to patients with TW (all p< 0.01, Table 2). Patients with PCR12 were more likely to have a history of transplantation or HIV/AIDS (both p< 0.01). PCR12 was associated with a higher mean index visit cost (by $101) but lower mean 30-day follow-up cost (by $130) than TW (Table 3). Patients with PCR12 had lower 30-day AIG-related admission risk than TW (1.7% vs. 2.7% p< 0.01). Among 8,451 patients with microbiology data, PCR12 was associated with fewer stool tests per patient (mean:1.61 vs. 1.26), faster turnaround time (mean: 6.3 vs. 25.7 hours) and less likelihood of receiving in-hospital antibiotics (39.4% vs. 47.1%, all p< 0.01) than TW. A higher percentage of patients with PCR12 had a target pathogen detected (73.1%) compared to PCR< 12 (63.6%) or TW (45.4%, p< 0.01). Table 1.Patient characteristics of hospital-based infectious gastroenteritis outpatients during January 1, 2016 - June 30, 2021, stratified by type of stool testTable 2.Clinical and hospital characteristics of hospital-based infectious gastroenteritis outpatients during January 1, 2016 - June 30, 2021, stratified by type of stool testTable 3.Outcomes of hospital-based infectious gastroenteritis outpatients during January 1, 2016 - June 30, 2021, stratified by the type of stool test Conclusion PCR12 multiplex panels were associated with lower 30-day follow-up cost and risk of IG-related hospitalization. PCR12 was also associated with less secondary testing, reduced in-hospital antibiotic use, faster turnaround, and increased diagnostic yield compared to TW. Disclosures Rena Moon, MD, MPH, Premier Inc: Employee Tammy C. Bleak, PharmD, MSc, bioMerieux: Employee of bioMerieux Ning Rosenthal, MD, PhD, MPH, Premier Inc: Employee|Premier Inc: Stocks/Bonds Brianne Couturier, PhD, bioMerieux: Employee of bioMerieux Rachael Hemmert, MSPH, bioMerieux: Employee of bioMerieux Tristan T. Timbrook, PharmD, bioMerieux: Employee of bioMerieux Harold Brown, MBA, MHA, Premier Inc: Employee Ferric C. Fang, MD, bioMerieux: Advisor/Consultant.

364. Diagnosis of Amebic Liver Abscess by a Commercial Multiplex Stool Amplification Assay. A Potentially Useful Alternative in Limited-Resources Settings.

Abstract Background Amoebic liver abscess (ALA) is caused by the protozoan parasite Entamoeba histolytica. Clinical and radiological features of ALA often mimic those of pyogenic liver abscess (PLA). Currently, differential diagnosis between ALA and PLA relys on microscopic examination, anti-amoebic IgG serology, and culture of aspirate for pyogenic organisms. Therefore, there is a need for new, rapid and more accurate microbiological methods for diagnosing ALA. Unfortunately, with few exceptions, available reports involved the use of inhouse or laboratory-tailored polymerase chain reaction (PCR) assays. We herein report our recent experience with the successful use of a commercial multiplex, nested PCR assay designed for stool, in the diagnosis of two cases of ALA. Methods Two severely ill adult Latin American migrants presented with fever, malaise, non-bloody diarrhea, abdominal pain and leukocytosis. CT scans revealed single large hypodense, inflammatory, liver cystic lesions. Results Necrotic material obtained by needle aspiration under guidance and stool samples were processed by FilmArray Gastrointestinal Panel (BioFire Diagnostics, Salt Lake City), designed to detect 13 bacterial, 5 viral and 4 parasitic pathogens, both amplified only for E. hystolitica DNA. ELISA serology for amoeba was also positive. Bacterial cultures were sterile. Treatment with Metronidazole and paromomycin resulted in complete recovery. Conclusion Analysis of liver abscess content using a commercially available, multiplex, nested PCR assay designed for stool, may represent a convenient alternative to currently available diagnostic methods, providing rapid results and allowing for immediate choosing of specific therapy targeting single pathogens on more rational basis. Since there are several commercially available multiplex PCR panels containing primers for E. histolytica, their use for evaluation of liver abscess samples has some theoretical advantages for the diagnosis of ALA, such as simplicity, ample availability, rapid processing time and capacity to exclude simultaneously several potential pathogens. Nevertheless, further testing is necessary to validate their use in liver abscess diagnosis and define their false positivity and negativity rates. Disclosures All Authors: No reported disclosures.

560. Meningitis/encephalitis PCR panel result and antimicrobial use in children

Abstract Background The meningitis/encephalitis multiplex polymerase chain reaction panel (ME PCR) detects common pathogens associated with community acquired CNS infections. The impact of this test on antimicrobial use in children is not well characterized. Methods We performed a retrospective, observational study in children < 18 years of age who had ME PCR performed on CSF collected within 24 hours of admission to the hospital, presentation to the ED, or outpatient encounter from January 2018 to April 2022. Decision to order ME PCR was determined by the treating team. There are no restrictions on ordering ME PCR at our institution. The total calendar days of antimicrobial use from 24 hours prior to CSF collection to 7 days after CSF collection was evaluated. Our primary objective was to compare antimicrobial duration between subgroups based on ME PCR results: negative, virus positive, bacteria positive, and positive for both. Results Of 1282 ME PCR tests performed, 806 were done within the first 24 hours of the encounter. 190 (23.6%) patients never received antimicrobials for empiric treatment of meningitis/encephalitis and were excluded from subsequent analyses. Demographics and antimicrobial use are summarized for patients receiving at least one dose of an antimicrobial in Tables 1 and 2. CSF WBC was highest in bacteria positive CSF (p< 0.001) followed by viral positive (p=0.0066). A positive bacterial result was associated with a longer duration of ceftriaxone, vancomycin and penicillin G and a shorter duration of acyclovir compared to viral and negative results (Table 2). A positive viral result was associated with a shorter length of total antimicrobial treatment (LOT) than negative (p=0.041) and bacterial positive (p< 0.001). Conclusion Positive ME PCR results for bacteria may promote faster initiation of targeted therapy. Positive viral tests were associated with shorter LOT than both negative and bacteria positive ME PCR. Median LOT for negative testing was still 2 days suggesting rapid negative testing does not impact LOT. Prioritizing ME PCR for use in CSF samples with high pretest probability of a positive test may increase its effect on antimicrobial use. Disclosures Anne J. Blaschke, MD, PhD, BioFire Diagnostics/Biomerieux: Advisor/Consultant|BioFire Diagnostics/Biomerieux: Grant/Research Support|BioFire Diagnostics/Biomerieux: IP licensed to BioFire Diagnostics through the University of Utah and royalties received through the University of Utah related to the FilmArray|Merck: Advisor/Consultant.

539. Impact of a Rapid Diagnostic Assay for the Detection of Bacterial and Viral Agents on Antimicrobial use in Critically Ill Patients with Pneumonia

Abstract Background Conventional diagnostic methods for pneumonia have a long turnaround time, and a pathogen is isolated in only 33% of cases. As a result, empiric therapy with broad-spectrum antimicrobials often becomes definitive therapy. Rapid molecular diagnostics paired with antimicrobial stewardship intervention have the potential to improve outcomes for patients with lower respiratory tract infections (LRTIs). However, data to support this hypothesis are scarce. This study examined the influence of a rapid multiplex polymerase-chain-reaction (PCR) test on antimicrobial use in critically ill patients with LRTIs. Methods This single-center study consisted of pre-implementation (PrIP, December 1, 2018, to February 28, 2019) and post-implementation periods (PoIP, December 1, 2021, to February 28, 2022). Both groups included intensive-care unit (ICU) patients with respiratory cultures from bronchoalveolar lavage (BAL), mini-BAL, or tracheal aspirates. Interventions during the PoIP included concurrent testing of specimens with the BioFire® Pneumonia Panel and clinical decision support tools to streamline treatment recommendations from ICU pharmacists. The primary outcome was the difference in time to optimal therapy (TTOT). Secondary outcomes included time to effective therapy (TTET) and duration of therapy (DOT) for antipseudomonal and anti-MRSA agents. Results A total of 163 patients were included (n = 80, PrIP; n = 83, PoIP). The mean age was 57 + 16 years, and medical ICU patients accounted for 60% (n = 97) of cases. The median APACHE II score was the only significant baseline difference between the two arms (22 vs. 18, interquartile range [IQR] 16, 28 vs. 12, 25, p = 0.01). The median TTOT was 38 hours in the PrIP and 21 hours in the PoIP (p < 0.001). TTET was 5.7 hours in the PrIP and 4.9 hours in the PoIP (p = 0.106). The median DOT for antipseudomonal agents decreased by 52% (4.4 days in the PrIP and 2.1 days in the PoIP, p < 0.001), and anti-MRSA agent DOT was 53% shorter in the PoIP (1.9 days vs. 0.9 days, p < 0.001). Conclusion Implementation of a rapid multiplex PCR panel for lower respiratory-tract pathogens significantly reduced the time to optimal therapy in critically ill patients with pneumonia. Clinically meaningful reductions in anti-MRSA and anti-pseudomonal agent duration were also noted. Disclosures Blake W. Buchan, PhD, Accelerate: Advisor/Consultant|Accelerate: Honoraria|BioFire: Honoraria|ChromaCode: Advisor/Consultant|ChromaCode: Honoraria|Pattern: Advisor/Consultant|Pattern: Honoraria.

Analysis by metagenomic next-generation sequencing of the lung virome during mechanical ventilation

Background: The lung microbiome is composed of bacteria, viruses and fungi that interplay with each other and participate in mucosal defense protecting the lungs from colonization and infection by pathogenic microorganisms. In intensive care, a change in the composition of the lung microbiome, called dysbiosis, could be associated to the occurrence of ventilator-associated pneumonia. The objective of the study was to test a method to assess the lung virome. Methods: We applied a protocol including the same nucleic acid extraction methods as used for bacterial lung microbiome and a metagenomic next-generation sequencing (mNGS) to detect eukaryotic RNA, DNA viruses and bacteriophages. Results: Our method was able to detect all viruses identified with multiplex polymerase chain reaction (PCR), other eukaryotic viruses not included in the multiplex PCR panel, and bacteriophages. Notably persistent viruses, mainly Herpesviridae, associated with opportunistic infections and those showing immunodepression such as Anellovirus have been identified. Conclusions: A better description of the global composition and evolution of the lung microbiome, including viruses, could help to better understand ventilator-associated pneumonia occurrence and outcomes.

Clinical Performance of FilmArray Meningitis/Encephalitis Multiplex Polymerase Chain Reaction Panel in Central Nervous System Infections.

IntroductionEarly identification of etiology is very important for initiating appropriate therapy promptly in patients with meningoencephalitis (ME). BioFire FilmArray® meningitis/encephalitis (FA-ME) panel is a fully automated multiplex polymerase chain reaction (PCR) that detects 14 pathogens simultaneously in an hour. There is a dearth of studies highlighting its usefulness in ME syndrome in Indian patients.Materials and methodsWe performed a retrospective analysis of patients, admitted to the Kerala Institute of Medical Sciences Hospital, Thiruvananthapuram, Kerala, South India, with meningitis/encephalitis syndrome who underwent the multiplex PCR test on cerebrospinal fluid (CSF) over a period of 2 years from 2016 to 2018. Patients presenting with clinical diagnosis of acute meningitis, encephalitis, or ME who underwent CSF FA-ME panel were studied. The performance of the FA-ME panel was compared to CSF bacterial culture.ResultsTwo-hundred and fifty-nine patients between December 2016 and December 2018 underwent the FA-ME test in CSF. FA-ME test detected pathogens in 61 (23.6%) out of 259 patients with ME syndrome. Among the pathogens detected by FA-ME panel, enterovirus was the commonest accounting for 29 cases (47.5%), followed by varicella in 11 patients (18%) and pneumococci in 9 (14.8%). CSF bacterial culture yield was low, positive only in 8 (3%) out of 259 cases, and matched with FA-ME panel in only one sample that grew Streptococcus pneumoniae. Bacterial culture yielded seven pathogens in those whose FA-ME panels were negative.ConclusionFA-ME panel improves diagnostic yield as compared to bacterial culture (26.3 vs 3%). FA-ME test helps in the early initiation of targeted antibiotic therapy and greater antibiotic de-escalation.How to cite this articleChandran S, Arjun R, Sasidharan A, Niyas VKM, Chandran S. Clinical Performance of FilmArray Meningitis/Encephalitis Multiplex Polymerase Chain Reaction Panel in Central Nervous System Infections. Indian J Crit Care Med 2022;26(1):67–70.

The influence of hospitalization and HIV severity on gastrointestinal PCR panel evaluation of HIV-related acute diarrhea in New York City: a retrospective, cross-sectional study.

Introduction:Diarrhea is common in persons living with HIV (PLWH)/AIDS. With the increasing utilization of multiplex gastrointestinal PCR panel (GI panel) testing, we aimed to characterize the roles of CD4 count and hospitalization in GI panel assessments of PLWH with acute diarrhea.Methods:We performed a cross-sectional study of adult PLWH with acute diarrhea who underwent GI panel testing at two urban academic centers. Demographic, HIV disease, GI panel result, and hospitalization data were collected, and patients were cohorted by CD4 count (CD4 < 200, CD4 200–499, CD4 > = 500). The primary outcome was enteric infection as detected by GI panel, and hospitalization.Results:Of 298 PLWH, 119 (39.9%) had a CD4 count below 200, 195 (65.4%) were hospitalized, and 137 (46.0%) had enteric infection. Bacterial infection correlated with higher CD4 count (41.9% (CD4 > = 500) vs 31.2% (CD4 200–499) vs 25.2% (CD4 < 200), p = 0.041). Hospitalization correlated with poorly controlled HIV and fewer enteric infections (34.4% vs 68.0%, p < 0.001). After adjusting for HIV disease severity, a negative GI panel remained independently associated with hospitalization (adjusted odds ratio (aOR) 5.32, 95% confidence interval (CI) 2.72–10.9), even in patients tested within 72 hours of hospitalization. Despite better HIV control, men who have sex with men (MSM) had more frequent infectious diarrhea, including from E. coli, giardiasis, and multiple pathogens. MSM status independently predicted enteric infection (aOR 1.93, 95% CI: 1.02–3.67).Conclusions:GI panel results vary by HIV disease severity and hospitalization in PLWH. Clinicians – especially in the inpatient setting – should carefully consider these factors when interpreting GI panel results. Further characterization of diarrheal etiology in PLWH with a negative GI panel is needed.Plain Language Summary PCR stool test results are affected by certain factors in HIV-related diarrhea Diarrhea is common in people living with HIV (PLWH) and has a variety of causes, including infections, medications, and HIV itself. Multiplex polymerase chain reaction (PCR) stool testing simultaneously evaluates for a variety of common viral, bacterial, and parasitic infections of the gastrointestinal tract, and is increasingly being used in patients with diarrhea. However, patients with HIV and diarrheal illness may have uncommon infections not typically present in those with normal immune function – and thus not routinely evaluated for in stool testing. It is not known what factors, if any, might affect the results of PCR testing in HIV-related diarrhea.In this study, we examined all PLWH who underwent stool PCR testing for diarrhea over a 4-year period. We separated the patients into groups based on HIV disease severity as measured by CD4 T-cell count, or the count of the immune cells affected by HIV. We examined whether there were differences among groups in infection rates as detected by PCR stool testing. Separately, we studied the role of hospitalization in stool PCR test results.Of 298 PLWH who underwent stool PCR testing for diarrhea, 119 had a CD4 count less than 200 (low CD4 count), 195 were hospitalized at time of testing, and 137 had a positive stool PCR test. Compared to those with a low CD4 count, subjects with less severe HIV disease were more likely to have a bacterial infection on stool PCR testing and less likely to be hospitalized. Hospitalized patients were more likely to have a negative PCR stool test, regardless of CD4 count. Many patients with a low CD4 count had diarrheal etiologies not evaluated by multiplex stool PCR. In PLWH who experience diarrhea, stool PCR testing results vary by CD4 count and hospitalization. Providers should be mindful of these factors when interpreting stool PCR test results.

Detection of bacteria via multiplex PCR in respiratory samples of critically ill COVID-19patients with suspected HAP/VAP in the ICU.

BackgroundCritically ill Coronavirus disease 2019 (COVID-19) patients have high rates of bacterial superinfection. Multiplex polymerase chain reaction panels may be able to provide useful information about the incidence and spectrum of bacteria causing superinfections.MethodsIn this retrospective observational study we included all COVID-19 positive patients admitted to our intensive care unit with suspected hospital-acquired pneumonia/ventilator-associated pneumonia (HAP/VAP) in whom the BioFire® Pneumonia Panel (PP) was performed from tracheal aspirate or bronchoalveolar lavage fluid for diagnostic purposes. The aim of our study was to analyze the spectrum of pathogens detected with the PP.ResultsIn this study 60 patients with a median age of 62.5 years were included. Suspected VAP was the most frequent (48/60, 80%) indication for performing the PP. Tracheal aspirate was the predominant sample type (50/60, 83.3%).The PP led to a negative, monomicrobial and polymicrobial result in 36.7%, 35% and 28.3% of the patients, respectively. The three most detected bacteria were Staphylococcus aureus (13/60, 21.7%), Klebsiella pneumoniae (12/60, 20%) and Haemophilus influenzae (9/60, 15%). Neither atypical bacteria nor resistance genes were detected.Microbiological culture of respiratory specimens was performed in 36 (60%) patients concomitantly. The PP and microbiological culture yielded a non-concordant, partial concordant and completely concordant result in 13.9% (5/36), 30.6% (11/36) and 55.6% (20/36) of the analyzed samples, respectively.ConclusionIn critically ill COVID-19 patients with suspected HAP/VAP results of the PP and microbiological culture methods were largely consistent. In our cohort, S. aureus and K. pneumoniae were the most frequently detected organisms. A higher diagnostic yield may be achieved if both methods are combined.

105. Impact of a Multiplex Polymerase Chain Reaction Panel on Duration of Empiric Antibiotic Therapy in Suspected Bacterial Meningitis

BackgroundMultiplex polymerase chain reaction (PCR) panels allow for rapid detection or exclusion of pathogens causing community-acquired meningitis and encephalitis (ME). However, the clinical impact of rapid multiplex PCR ME panel results on the duration of empiric antibiotic therapy is not well characterized.MethodsWe performed a retrospective pre-post study to evaluate the implementation of the FilmArray ME panel (BioFire Diagnostics, LLC) for diagnosis of bacterial meningitis at our institution. We included adults who presented with suspected bacterial meningitis, received empiric antibiotic therapy, and underwent cerebrospinal fluid microbiological testing in the emergency department. The primary outcome was duration of empiric antibiotic therapy. A bivariable analysis that compared baseline demographics, clinical characteristics, and study outcomes between the pre-ME panel and post-ME panel periods was performed using Mann-Whitney tests, chi-squared tests, or Fisher’s exact tests. Time-to-event analysis used the Kaplan-Meier method and log-rank statistics.ResultsIn the pre-ME panel period, the positive detection rate of bacterial pathogens was 2.2% (3/137) by cerebrospinal fluid culture and 4.3% (3/69) in the post-ME panel period. Table 1 shows baseline characteristics of patients. Compared to the pre-ME panel period, there were significant reductions in the post-ME panel period for the duration of empiric antibiotic therapy (median 34.7 h, IQR 8.5–61.7, vs. 12.3 h, IQR 3.3–40.0, P=0.01), time to targeted therapy (59.3 h, IQR 36.5–74.6, vs 7.02 h, IQR 0.9–12.4, P< 0.001), and hospital length of stay (4 d, IQR 2–7, vs. 3 d, IQR 1–5, P=0.03), as shown in Table 2. There was also significant reduction in time to discontinuation or de-escalation of empiric antibiotic therapy (P=0.049) as shown in Figure 1.Table 1. Baseline characteristics for patients with suspected bacterial meningitis Table 2. Antimicrobial use and hospitalization outcomes Compared to the pre-ME panel period, there were significant reductions in the post-ME panel period for the duration of empiric antibiotic therapy (P=0.01), time to targeted therapy (P<0.001), and hospital length of stay (P=0.03).Figure 1. Probability of Empiric Antibiotic Therapy Between Pre- and Post-ME Panel Periods Kaplan-Meier analysis of the time from initiation of empiric antibiotic therapy to discontinuation or de-escalation of empiric antibiotic therapy between the pre- and post-ME panel periods. P value from log-rank test=0.049 (n=206). There was a significant difference in the time to discontinuation or de-escalation of empiric antibiotic therapy between the groups (sex- and immunosuppressant use-adjusted hazard ratio, 1.46 [95% confidence interval, 1.08–1.97]; P=0.01).ConclusionThe implementation of the FilmArray ME panel for suspected bacterial meningitis appears to reduce the duration of empiric antibiotic therapy, time to targeted therapy, and hospital length of stay compared to traditional culture-based microbiological testing methods.Disclosures Justin J. Choi, MD, Allergan (Consultant, Grant/Research Support)Roche (Consultant, Grant/Research Support) Lars Westblade, PhD, Accelerate Diagnostics Inc (Grant/Research Support)BioFire Diagnostics (Grant/Research Support)Hardy Diagnostics (Grant/Research Support)Roche (Consultant, Advisor or Review Panel member)Shionogi Inc (Advisor or Review Panel member)Talis Biomedical (Advisor or Review Panel member) Marshall J. Glesby, MD, Enzychem (Consultant)Gilead (Grant/Research Support)ReAlta Life Sciences (Consultant)Regeneron (Consultant, Grant/Research Support)Sobi (Consultant)Springer (Other Financial or Material Support, Royalties)UpToDate (Other Financial or Material Support, Royalties)

Occurrence and disease burden of respiratory syncytial virus and other respiratory pathogens in adults aged ≥65 years in community: A prospective cohort study in Japan.

BackgroundThe frequency and clinical profile of respiratory syncytial virus (RSV)–acute respiratory disease (ARD) in older adults in Japan has not been well‐characterized.MethodsThis was a multicenter prospective observational cohort study to evaluate the occurrence rate of ARD in 1000 older adult participants (≥65 years) for 52 weeks during the 2019 to 2020 season. A multiplex polymerase chain reaction panel was used for pathogen detection in nasopharyngeal swab from participants diagnosed with ARD. Symptoms and impact of ARD was assessed using the Respiratory Infection Intensity and Impact Questionnaire (RiiQ™). The study was registered at UMIN (https://www.umin.ac.jp/ctr/): UMIN000037891.ResultsRSV–ARD was detected in 24/1000 (2.4%) participants and RSV‐lower respiratory tract disease in 8/1000 (0.8%) participants. The median duration of RSV–ARD was 18 days. All 24 participants had utilized the medical services of outpatient visits and only 1 (4.2%) participant was hospitalized for RSV–ARD. The most common viruses other than RSV that caused ARD (detected in >10 participants) were human rhinovirus/enterovirus, parainfluenza 3, coronavirus OC43, human metapneumovirus, and influenza A/H1. The most frequent symptoms of RSV–ARD were cough, sore throat, nasal congestion, and expectoration.ConclusionsRSV was reported as a major pathogen for respiratory infections in older adults in Japan.

Impact of a Multiplex Polymerase Chain Reaction Panel on Duration of Empiric Antibiotic Therapy in Suspected Bacterial Meningitis.

BackgroundMultiplex polymerase chain reaction (PCR) panels allow for rapid detection or exclusion of pathogens causing meningitis and encephalitis (ME). The clinical impact of rapid multiplex PCR ME panel results on the duration of empiric antibiotic therapy is not well characterized.MethodsWe performed a retrospective prepost study at our institution that evaluated the clinical impact of a multiplex PCR ME panel among adults with suspected bacterial meningitis who received empiric antibiotic therapy and underwent lumbar puncture in the emergency department. The primary outcome was the duration of empiric antibiotic therapy.ResultsThe positive pathogen detection rates were similar between pre- and post-multiplex PCR ME panel periods (17.5%, 24 of 137 vs 20.3%, 14 of 69, respectively). The median duration of empiric antibiotic therapy was significantly reduced in the post-multiplex PCR ME panel period compared with the pre-multiplex PCR ME panel period (34.7 vs 12.3 hours, P = .01). At any point in time, 46% more patients in the post-multiplex PCR ME panel period had empiric antibiotic therapy discontinued or de-escalated compared with the pre-multiplex PCR ME panel period (sex- and immunosuppressant use-adjusted hazard ratio 1.46, P = .01). The median hospital length of stay was shorter in the post-multiplex PCR ME panel period (3 vs 4 days, P = .03).ConclusionsThe implementation of the multiplex PCR ME panel for bacterial meningitis reduced the duration of empiric antibiotic therapy and possibly hospital length of stay compared with traditional microbiological testing methods.

Clinical Significance of Positive Results of the BioFire Cerebrospinal Fluid FilmArray Meningitis/Encephalitis Panel at a Tertiary Medical Center in the United States.

The FilmArray Meningitis/Encephalitis (ME) panel is the first US Food and Drug Administration-cleared multiplex polymerase chain reaction panel for the detection of central nervous system infections. While the assay's performance characteristics have been described, the real-world significance of positive results has not been fully characterized. To evaluate the clinical significance of positive ME panel results in a tertiary care medical center in New York, New York. Four physicians independently performed retrospective clinical assessments of all positive ME panel results at Columbia University Irving Medical Center, including the Children's Hospital of New York, during an 18-month period. Each reviewer determined the likelihood of central nervous system infection for all cases and whether cases fit Brighton diagnostic criteria for meningitis, encephalitis, or meningoencephalitis. Among 119 cases, there was 75% positive agreement (95% CI, 54%-89%) between ME panel results and clinical consensus, which varied among panel targets. The ME panel showed good agreement with expert clinical consensus for patients presenting with acute meningitis/encephalitis. Factors contributing to clinically insignificant ME positive results included low pretest probability, traumatic lumbar puncture, specimen contamination, and detection of incidental viral targets such as human herpesvirus 6. Notably, the ME panel detected more than twice the number of cases of bacterial meningitis detected by culture alone, particularly among patients receiving empiric antimicrobial therapy before lumbar puncture. Appropriate test use and contextual interpretation of results are critical to leveraging the advantages of the platform while avoiding potential pitfalls.

Evidence of False Positivity forVibrioSpecies Tested by Gastrointestinal Multiplex PCR Panels, Minnesota, 2016–2018

Syndromic gastrointestinal multiplex polymerase chain reaction (PCR) panels (GMPPs) are used by an increasing number of clinical laboratories to identify enteric pathogens. Vibrio species are included on GMPPs, but because of the low prevalence of vibriosis, performance characteristics for these panels have been difficult to measure. All Vibrio spp. cases identified by GMPPs in Minnesota during 2016-2018 (n = 100) were assessed to identify differences between culture-confirmed cases and those that were PCR-positive only. Overall, 47% of cases had Vibrio species recovered by culture. Two GMPPs were used in Minnesota, Verigene EPT and FilmArray GIP, and the recovery rate of Vibrio spp. was significantly different between these platforms (Verigene EPT 63%, compared with FilmArray GIP 28%). No distinct seasonality was identified among GMPP-positive, culture-negative cases, whereas culture-confirmed case incidence peaked during July and August. Among cases with no other pathogen detected by the GMPP, confirmed cases reported a lower rate of bloody diarrhea (odds ratio [OR], 0.7; P = .004) and were less likely to have a symptom duration >14 days (OR, 0.3; P = .04). Confirmed cases were also more likely to include reports of consuming food items typically associated with Vibrio spp. infection or to have another likely source of infection (eg, international travel or contact with an untreated body of fresh or salt water or marine life; OR, 9.6; P = .001). The combined findings indicate that cases identified by GMPP that did not have culture confirmation were less likely to include symptoms or exposures consistent with vibriosis. These findings emphasize the need for improvements to testing platform specificity and the importance of combining clinical and exposure information when diagnosing an infection. This study underscores the importance of maintaining the ability to culture Vibrio species to aid in accurate diagnoses.

Incidence and Prognostic Factors of Respiratory Viral Infections in Severe Acute Exacerbation of Chronic Obstructive Pulmonary Disease.

PurposeSevere acute exacerbations of chronic obstructive pulmonary disease (AECOPD) that require hospitalization and emergency department visits are associated with considerable morbidity and mortality. Respiratory viral infection is an important cause of severe AECOPD. We evaluated the incidence and prognostic factors of viral infection in severe AECOPD.Patients and MethodsWe performed a retrospective study of 262 cases of severe AECOPD in 192 patients who required hospitalization and emergency department visits at a tertiary teaching hospital in Daegu, Korea. A multiplex polymerase chain reaction panel using a nasopharyngeal swab sample was performed to detect viral infection.ResultsViral infection was detected in 108 events (41.2%) from 96 patients. The most common virus was rhinovirus/enterovirus (27.5%), followed by influenza virus (22.5%), respiratory syncytial virus (13.3%), parainfluenza virus (12.5%), coronavirus (12.5%), metapneumovirus (7.5%), and adenovirus (4.2%). Virus-positive exacerbations, compared to virus-negative exacerbations, had a higher frequency of symptoms of rhinopharyngitis, higher neutrophil count and C-reactive protein (CRP) level, and lower eosinophil count. Multivariate analysis demonstrated that elevated CRP levels (odds ratio [OR], 2.76; 95% confidence interval [CI], 1.24–6.15), symptoms of rhinopharyngitis (OR, 1.98; 95% CI, 1.03–3.78), low eosinophil count (OR, 1.74; 95% CI, 1.03–2.92), and inhaled corticosteroid (ICS) use (OR, 1.70; 95% CI 1.04–2.80) were associated with viral infection in severe AECOPD.ConclusionThe incidence of viral infection in severe AECOPD was 41.2%, and the most commonly detected virus was rhinovirus/enterovirus. Increased CRP level, symptoms of rhinopharyngitis, low eosinophil count, and use of ICS were associated with viral infection in severe AECOPD.