6 research outputs found
Comparison of rapid molecular testing methods for detecting respiratory viruses in emergency care: a prospective study
No full textBackground: Respiratory tract infections (RTIs) caused by contagious viruses are common among patients presenting to the emergency department (ED). Early detection of these viruses can help prevent nosocomial transmission.Aim: To investigate the efficacy of three rapid molecular methods, namely FilmArray® Pneumonia Panel plus (FAP plus), ID NOW™ Influenza A and B 2 (ID NOW2) point-of-care test, and an in-house real-time polymerase chain reaction (RT-PCR) test, to identify patients with viral RTIs requiring isolation in an emergency setting.Methods: We included a FilmArray® Pneumonia Panel plus in the initial workup of patients with suspected RTIs during a flu season. The RT-PCR and the influenza point-of-care test were performed as part of routine diagnostics, on demand from the treating physicians. We compared viral detections and compared time to positive test results for each method.Findings: The FAP plus significantly reduced the turnaround time and was able to identify 95% patients with potential contagious viral RTI. Routine diagnostics ordered by the treating physician had a turnaround time of a median 22 h and detected 87% of patients with potential contagious viral RTI. In patients that had all three tests, the ID NOW2 detected 62% of patients with influenza.Conclusions: The FAP plus was able to rapidly and reliably identify patients with potential contagious viral RTIs; its use was feasible in the ED setting. Failing to test patients with viral RTI and using tests with long turnaround time may lead to nosocomial transmission of viral infections and adverse patient outcomes
Rapid syndromic PCR testing in patients with respiratory tract infections reduces time to results and improves microbial yield
Get PDFLack of rapid and comprehensive microbiological diagnosis in patients with community acquired pneumonia (CAP) hampers appropriate antimicrobial therapy. This study evaluates the real-world performance of the BioFire FilmArray Pneumonia panel plus (FAP plus) and explores the feasibility of evaluation in a randomised controlled trial. Patients presenting to hospital with suspected CAP were recruited in a prospective feasibility study. An induced sputum or an endotracheal aspirate was obtained from all participants. The FAP plus turnaround time (TAT) and microbiological yield were compared with standard diagnostic methods (SDs). 96/104 (92%) enrolled patients had a respiratory tract infection (RTI); 72 CAP and 24 other RTIs. Median TAT was shorter for the FAP plus, compared with in-house PCR (2.6 vs 24.1 h, p < 0.001) and sputum cultures (2.6 vs 57.5 h, p < 0.001). The total microbiological yield by the FAP plus was higher compared to SDs (91% (162/179) vs 55% (99/179), p < 0.0001). Haemophilus influenzae, Streptococcus pneumoniae and influenza A virus were the most frequent pathogens. In conclusion, molecular panel testing in adults with CAP was associated with a significant reduction in time to actionable results and increased microbiological yield. The impact on antibiotic use and patient outcome should be assessed in randomised controlled trials
Syndromic molecular testing in adults hospitalized for suspected community-acquired pneumonia
Get PDFDen mikrobielle etiologien hos pasienter med samfunnservervet lungebetennelse (CAP) blir ofte ikke avklart på grunn av utilstrekkelige mikrobiologiske metoder og vanskeligheter med å skaffe prøver fra nedre luftveier. Rask påvisning av luftveismikrober kan potensielt redusere unødvendig bruk av empirisk antimikrobiell behandling og øke andelen pasienter som får mikrobiologistyrt behandling. Moderne syndrombaserte PCR-paneler muliggjør rask deteksjon av både virale- og bakterielle luftveismikrober. CAPNOR Feasibility studien undersøkte gjennomførbarheten av flere viktige ledd fra vår planlagte CAPNOR RCT (Paper I). Studien viste at det var mulig å skaffe nedre luftveisprøver fra CAP pasienter allerede i akuttmottaket. Ved bruk av et syndrombasert PCR-panel, fant vi betydelig flere luftveismikrober på kortere tid, sammenliknet med bruk av standard metoder, noe som indikerer at det er mulig å oppnå mikrobiologiske resultater allerede i akuttmottaket. Vår CAPNOR RCT fokuserer på andelen som mottar mikrobiologistyrt behandling og tiden det tar. Prøver fra nedre luftveier ble randomisert til testing med kun standardmetoder eller med tillegg av et syndrombasert PCR-panel (Paper II). COVID-19 pandemien traff Norge da vi skulle starte vår RCT, noe som resulterte i forsinket start av studien og behov for justeringer av protokollen. I denne unike situasjonen valgte vi å undersøke pandemiens potensielle implikasjoner på både antall sykehusinnleggelser og detekterte mikrober hos pasienter med mistenkt CAP, ved å sammenlikne pasienter inkludert før og etter utbruddet av COVID-19 (Paper III). Smitteverntiltak relatert til COVID-19 forverret utfordringene med prøvetakning fra nedre luftveier ytterligere. Dette bidro til en studie som viste at testing av halsprøver med et syndrombasert PCR-panel oppdaget de vanligste bakterielle luftveismikrober med høy positiv og negativ prosentvis overensstemmelse sammenlignet med testing av nedre luftveisprøver (Paper IV). Dette antyder at halsprøver analysert av et syndrombasert PCR-panel kan representere en alternativ metode for rask mikrobiologisk testing i akuttmottaket. Oppsummert har våre studier demonstrert at det er mulig å oppnå omfattende mikrobiologiske resultater hos en stor andel CAP pasienter få timer etter innleggelse. Fremtidige studier av syndrombaserte PCR-paneler bør fokusere videre på kliniske endepunkter, kostnadseffektivitet og utvikling av implementeringsstrategier for innføring i klinisk praksis.The microbial etiology of patients with community-acquired pneumonia (CAP) is often not established due to insufficient methods for microbial detection and difficulties in obtaining lower respiratory tract (LRT) samples. Early microbial detections could potentially reduce unnecessary empirical antimicrobial treatment and improve the proportion of patients receiving pathogen-directed treatment. Recently introduced syndromic PCR-based panels enable rapid detection of both viral- and bacterial pathogens. The CAPNOR Feasibility study (Paper I) was initiated with a view to informing the design of a planned RCT and demonstrated that obtaining LRT samples from CAP patients in the emergency department (ED) was feasible. The microbial yield and time to results improved significantly by using a syndromic PCR-based panel compared to standard methods, indicating that it is possible to obtain microbiological results already in the ED. In the CAPNOR RCT, LRT samples were randomized to testing by either standard methods alone or with the addition of syndromic PCR-based testing, focusing on the time to, and provision of pathogen-directed treatment in CAP patients (Paper II). When we were about to initiate the CAPNOR RCT, Norway faced the COVID-19 pandemic, resulting in a delayed start, with mandatory adjustments needed in the protocol. Faced with this unprecedented situation, we evaluated the pandemic’s potential implications on both hospital admissions and microbial detections in patients with suspected CAP, i.e., before and after the outbreak of COVID-19 and the subsequent strict infection control measures (Paper III). Moreover, the COVID-19-related infection control measures further hampered the difficulties of LRT sampling. This fostered a study where we demonstrated that syndromic PCR-based testing of oropharyngeal (OP) swabs could detect the most common bacterial CAP pathogens with high positive and negative percent agreement compared with testing of LRT samples (Paper IV). These findings suggest that OP swabs analyzed by a syndromic panel could represent an alternative approach for rapid microbiological testing in the ED. In conclusion, our studies have demonstrated an ability to provide close to real-time microbiological results for CAP patients. Future studies should focus on the impact of rapid syndromic testing in terms of clinical outcomes, cost-effectiveness, and the development of implementation strategies to facilitate integration into clinical practice.Doktorgradsavhandlin
Impact of rapid molecular testing on diagnosis, treatment and management of community-acquired pneumonia in Norway: a pragmatic randomised controlled trial (CAPNOR)
Get PDFBackground: Community-acquired pneumonia (CAP) causes a large burden of disease. Due to difficulties in obtaining representative respiratory samples and insensitive standard microbiological methods, the microbiological aetiology of CAP is difficult to ascertain. With a few exceptions, standard-of-care diagnostics are too slow to influence initial decisions on antimicrobial therapy. The management of CAP is therefore largely based on empirical treatment guidelines. Empiric antimicrobial therapy is often initiated in the primary care setting, affecting diagnostic tests based on conventional bacterial culture in hospitalized patients. Implementing rapid molecular testing may improve both the proportion of positive tests and the time it takes to obtain test results. Both measures are important for initiation of pathogen-targeted antibiotics, involving rapid de-escalation or escalation of treatment, which may improve antimicrobial stewardship and potentially patient outcome. Methods: Patients presenting to the emergency department of Haukeland University Hospital (HUH) in Bergen, Norway, will be screened for inclusion into a pragmatic randomised controlled trial (RCT). Eligible patients with a suspicion of CAP will be included and randomised to receive either standard-of-care methods (standard microbiological testing) or standard-of-care methods in addition to testing by the rapid and comprehensive real-time multiplex PCR panel, the BioFire® FilmArray® Pneumonia Panel plus (FAP plus) (bioMérieux S.A., Marcy-l’Etoile, France). The results of the FAP plus will be communicated directly to the treating staff within ~2 h of sampling. Discussion: We will examine if rapid use of FAP plus panel in hospitalized patients with suspected CAP can improve both the time to and the proportion of patients receiving pathogen-directed treatment, thereby shortening the exposure to unnecessary antibiotics and the length of hospital admission, compared to the standard-of-care arm. The pragmatic design together with broad inclusion criteria and a straightforward intervention could make our results generalizable to other similar centres. Trial registration: ClinicalTrials.govNCT04660084. Registered on December 9, 2020</p
The changing spectrum of microbial aetiology of respiratory tract infections in hospitalized patients before and during the COVID-19 pandemic.
No full textBackground: the COVID-19 pandemic was met with strict containment measures. We hypothesized that societal infection control measures would impact the number of hospital admissions for respiratory tract infections, as well as, the spectrum of pathogens detected in patients with suspected community acquired pneumonia (CAP).Methods: this study is based on aggregated surveillance data from electronic health records of patients admitted to the hospitals in Bergen Hospital Trust from January 2017 through June 2021, as well as, two prospective studies of patients with suspected CAP conducted prior to and during the COVID-19 pandemic (pre-COVID cohort versus COVID cohort, respectively). In the prospective cohorts, microbiological detections were ascertained by comprehensive PCR-testing in lower respiratory tract specimens. Mann-Whitney's U test was used to analyse continuous variables. Fisher's exact test was used for analysing categorical data. The number of admissions before and during the outbreak of SARS-CoV-2 was compared using two-sample t-tests on logarithmic transformed values.Results: admissions for respiratory tract infections declined after the outbreak of SARS-CoV-2 (p < 0.001). The pre-COVID and the COVID cohorts comprised 96 and 80 patients, respectively. The proportion of viruses detected in the COVID cohort was significantly lower compared with the pre-COVID cohort [21% vs 36%, difference of 14%, 95% CI 4% to 26%; p = 0.012], and the proportion of bacterial- and viral co-detections was less than half in the COVID cohort compared with the pre-COVID cohort (19% vs 45%, difference of 26%, 95% CI 13% to 41%; p < 0.001). The proportion of bacteria detected was similar (p = 0.162), however, a difference in the bacterial spectrum was observed in the two cohorts. Haemophilus influenzae was the most frequent bacterial detection in both cohorts, followed by Streptococcus pneumoniae in the pre-COVID and Staphylococcus aureus in the COVID cohort.Conclusion: during the first year of the COVID-19 pandemic, the number of admissions with pneumonia and the microbiological detections in patients with suspected CAP, differed from the preceding year. This suggests that infection control measures related to COVID-19 restrictions have an overall and specific impact on respiratory tract infections, beyond reducing the spread of SARS-CoV-2
The changing spectrum of microbial aetiology of respiratory tract infections in hospitalized patients before and during the COVID-19 pandemic
Get PDFBACKGROUND: The COVID-19 pandemic was met with strict containment measures. We hypothesized that societal infection control measures would impact the number of hospital admissions for respiratory tract infections, as well as, the spectrum of pathogens detected in patients with suspected community acquired pneumonia (CAP). METHODS: This study is based on aggregated surveillance data from electronic health records of patients admitted to the hospitals in Bergen Hospital Trust from January 2017 through June 2021, as well as, two prospective studies of patients with suspected CAP conducted prior to and during the COVID-19 pandemic (pre-COVID cohort versus COVID cohort, respectively). In the prospective cohorts, microbiological detections were ascertained by comprehensive PCR-testing in lower respiratory tract specimens. Mann–Whitney’s U test was used to analyse continuous variables. Fisher’s exact test was used for analysing categorical data. The number of admissions before and during the outbreak of SARS-CoV-2 was compared using two-sample t-tests on logarithmic transformed values. RESULTS: Admissions for respiratory tract infections declined after the outbreak of SARS-CoV-2 (p < 0.001). The pre-COVID and the COVID cohorts comprised 96 and 80 patients, respectively. The proportion of viruses detected in the COVID cohort was significantly lower compared with the pre-COVID cohort [21% vs 36%, difference of 14%, 95% CI 4% to 26%; p = 0.012], and the proportion of bacterial- and viral co-detections was less than half in the COVID cohort compared with the pre-COVID cohort (19% vs 45%, difference of 26%, 95% CI 13% to 41%; p < 0.001). The proportion of bacteria detected was similar (p = 0.162), however, a difference in the bacterial spectrum was observed in the two cohorts. Haemophilus influenzae was the most frequent bacterial detection in both cohorts, followed by Streptococcus pneumoniae in the pre-COVID and Staphylococcus aureus in the COVID cohort. CONCLUSION: During the first year of the COVID-19 pandemic, the number of admissions with pneumonia and the microbiological detections in patients with suspected CAP, differed from the preceding year. This suggests that infection control measures related to COVID-19 restrictions have an overall and specific impact on respiratory tract infections, beyond reducing the spread of SARS-CoV-2. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-022-07732-5
