Impact of Rapid Molecular Diagnostic Testing of Respiratory Viruses on Outcomes of Adults Hospitalized with Respiratory Illness: a Multicenter Quasi-experimental Study

European Society of Clinical Microbiology and Infectious Diseases (ESCMID) guidelines for Antimicrobial Stewardship in Emergency Departments (endorsed by European Association of Hospital Pharmacists)

SCOPE

This ESCMID guideline provides evidence-based recommendations to support a selection of appropriate antibiotic use practices for patients seen in the emergency department (ED) and guidance for their implementation. The topics addressed in this guideline are: 1) Do biomarkers or rapid pathogen tests improve antibiotic prescribing and/or clinical outcomes? 2) Does taking blood cultures in common infectious syndromes improve antibiotic prescribing and/or clinical outcomes? 3) Does watchful waiting without antibacterial therapy or with delayed antibiotic prescribing reduce antibiotic prescribing without worsening clinical outcomes in patients with specific infectious syndromes? 4) Do structured culture follow-up programs in patients discharged from the ED with cultures pending improve antibiotic prescribing?

METHODS

An expert panel was convened by ESCMID and the guideline chair. The panel selected in consensus the four most relevant AMS topics according to pre-defined relevance criteria. For each main question for the four topics, a systematic review was performed, including randomized controlled trials and observational studies. Both clinical outcomes as well as stewardship process outcomes related to antibiotic use were deemed relevant. The literature searches were conducted between May 2021 and March 2022. In April 2022, the panel members were formally asked to suggest additional studies that were not identified in the initial searches. Data were summarized in a meta-analysis if possible or otherwise summarized narratively. The certainty of the evidence was classified according to the Grading of Recommendations Assessment, Development and Evaluation (GRADE) criteria. The guideline panel reviewed the evidence per topic critically appraising the evidence and formulated recommendations through a consensus-based process. The strength of the recommendations was classified as strong or weak. To substantiate the implementation process, implementation trials or observational studies describing facilitators/barriers for implementation were identified from the same searches and were summarized narratively.

RECOMMENDATIONS

The recommendations on the use of biomarkers and rapid pathogen diagnostic tests focus on the initiation of antibiotics in patients admitted through the ED. Their effect on the discontinuation or de-escalation of antibiotics during hospital stay was not reported, neither was their effect on hospital infection prevention and control practices. The recommendations on watchful waiting (i.e., withholding antibiotics with some form of follow-up) focus on specific infectious syndromes for which the primary care literature was also included. The recommendations on blood cultures focus on the indication in three common infectious syndromes in the ED explicitly excluding patients with sepsis or septic shock. Most recommendations are based on very-low- and low-certainty of evidence, leading to weak recommendations or, when no evidence was available, to best practice statements. Implementation of these recommendations needs to be adapted to the specific settings and circumstances of the ED. The scarcity of high-quality studies in the area of antimicrobial stewardship in the ED highlights the need for future research in this field.

Clinical impact of rapid molecular diagnostic tests in patients presenting with viral respiratory symptoms: A systematic literature review

BACKGROUND

Molecular tests can detect lower concentrations of viral genetic material over a longer period of respiratory infection than antigen tests. Delays associated with central laboratory testing can result in hospital-acquired transmission, avoidable patient admission, and unnecessary use of antimicrobials, all which may lead to increased cost of patient management. The aim of this study was to summarize comparisons of clinical outcomes associated with rapid molecular diagnostic tests (RMDTs) versus other diagnostic tests for viral respiratory infections.

METHODS

A systematic literature review (SLR) conducted in April 2023 identified studies evaluating clinical outcomes of molecular and antigen diagnostic tests for patients suspected of having respiratory viral infections.

RESULTS

The SLR included 21 studies, of which seven and 14 compared RMDTs (conducted at points of care or at laboratories) to standard (non-rapid) molecular tests or antigen tests to detect SARS-CoV-2 and influenza, respectively. In studies testing for SARS-CoV-2, RMDTs led to reductions in time to test results versus standard molecular tests (range of the reported medians: 0.2-3.8 hours versus 4.3-35.9 hours), with similar length of emergency department stay (3.2-8 hours versus 3.7-28.8 hours). Similarly, in studies testing for influenza, RMDTs led to reductions in time to test results versus standard molecular tests (1-3.5 hours versus 18.2-29.2 hours), with similar length of emergency department stay (3.7-11 hours versus 3.8-11.9 hours). RMDTs were found to decrease exposure time of uninfected patients, rate of hospitalization, length of stay at the hospitals, and frequency of unnecessary antiviral and antibacterial therapy, while improving patient flow, compared to other tests.

CONCLUSIONS

Compared to other diagnostic tests, RMDTs improve clinical outcomes, test turnaround time, and stewardship by decreasing unnecessary use of antibiotics and antivirals. They also reduce hospital admission and length of stay, which may, in turn, reduce unnecessary exposure of patients to hospital-acquired infections and their associated costs.

Development of a Novel Multiplex PCR Method for the Rapid Detection of SARS-CoV-2, Influenza A Virus, and Influenza B Virus

Objective

A sensitive and specific multiplex fluorescence rapid detection method was established for simultaneous detection of SARS-CoV-2, influenza A virus, and influenza B virus in a self-made device within 30 min, with a minimum detection limit of 200 copies/mL.

Methods

Based on the genome sequences of SARS-CoV-2, influenza A virus (FluA), and influenza B virus (FluB) with reference to the Chinese Center for Disease Control and Prevention and related literature, specific primers were designed, and a multiplex fluorescent PCR system was established. The simultaneous and rapid detection of SARS-CoV-2, FluA, and FluB was achieved by optimizing the concentrations of Taq DNA polymerase as well as primers, probes, and Mg2+. The minimum detection limits of the nucleic acid rapid detection system for SARS-CoV-2, FluA, and FluB were evaluated.

Results

By optimizing the amplification system, the N enzyme with the best amplification performance was selected, and the optimal concentration of Mg2+ in the multiamplification system was 3 mmol/L; the final concentrations of SARS-CoV-2 NP probe and primer were 0.15 μmol/L and 0.2 μmol/L, respectively; the final concentrations of SARS-CoV-2 ORF probe and primer were both 0.15 μmol/L; the final concentrations of FluA probe and primer were 0.2 μmol/L and 0.3 μmol/L, respectively; the final concentrations of FluB probe and primer were 0.15 μmol/L and 0.25 μmol/L, respectively.

Conclusion

A multiplex real-time quantitative fluorescence RT-PCR system for three respiratory viruses of SARS-CoV-2, FluA, and FluB was established with a high amplification efficiency and sensitivity reaching 200 copies/mL for all samples. Combined with the automated microfluidic nucleic acid detection system, the system can achieve rapid detection in 30 minutes.

Correlation between Sputum Bacterial Culture Positive Rate and Drug Sensitivity Test Results and Disease Severity inInpatients and Its Clinical Significance: A SystematicReview and Meta-Analysis

Objective. To systematically evaluate the correlation between the positive rate of sputum bacterial culture and the results of drug sensitivity test and the severity of the disease and its clinical significance, so as to provide evidence-based medicine for clinical application. Methods. PubMed, Embase, ScienceDirect, Cochrane Library, China Knowledge Network Database (CNKI), China VIP Database, Wanfang Database, and China Biomedical Literature Database (CBM) online database were used. The retrieval time limit was from the establishment of the database to the present. Data for all included studies were extracted by two independent researchers, and the risk of bias for the quality of each included study was assessed by the Cochrane Handbook 5.1.0 criteria. RevMan5.4 statistical software was used to analyze the collected data by meta. Results. In the end, 6 RCT articles were included. Overall, 613 samples were included in 6 RCT studies. The correlation between the positive rate of sputum bacterial culture in inpatients and the severity of the disease was meta-analyzed. The heterogeneity test results showed that Chi2 = 177.20, df = 3, P < 0.00001, and I2 = 98%, indicating that there was obvious heterogeneity among the included research data. It was considered that there was a correlation between the positive rate of sputum bacterial culture and the severity of the disease. The correlation between the results of the drug sensitivity test of inpatients and the severity of the disease was evaluated. The results of the heterogeneity test showed that Chi2 = 0.00, df = 1, P = 1 > 0.05, and I2 = 0%, indicating that there was no heterogeneity among the included research data. In addition, the combined effect of WMD was analyzed by the fixed effect model. The combined effect dose WMD test was Z = 6.58 (P < 0.00001). It was considered that there was a correlation between the results of the drug sensitivity test and the severity of the disease. Conclusion. There is a correlation between positive sputum culture and drug sensitivity test results and the severity of the disease in hospitalized patients. In clinical practice, for hospitalized patients, the positive sputum bacterial culture rate and drug sensitivity test results can be used to guide the appropriate use of antibiotics. Due to the low input from the literature, more studies with higher methodological quality and longer follow-up are needed for further validation.

Diagnostic stewardship aiming at expectorated or induced sputum promotes microbial diagnosis in community-acquired pneumonia

Purpose

Studies on aetiology of community-acquired pneumonia (CAP) vary in terms of microbial sampling methods, anatomical locations, and laboratory analyses, since no gold standard exists. In this large, multicentre, retrospective, regional study from Norway, our primary objective was to report the results of a strategic diagnostic stewardship intervention, targeting diagnostic yield from lower respiratory tract sampling. The secondary objective was to report hospitalized CAP aetiology and the diagnostic yield of various anatomical sampling locations.

Methods

Medical records from cases diagnosed with hospitalized CAP were collected retrospectively from March throughout May for three consecutive years at six hospitals. Between year one and two, we launched a diagnostic stewardship intervention at the emergency room level for the university teaching hospital only. The intervention was multifaceted aiming at upscaling specimen collection and enhancing collection techniques. Year one at the interventional hospital and every year at the five other emergency hospitals were used for comparison.

Results

Of the 1280 included cases of hospitalized CAP, a microbiological diagnosis was established for 29.1% among 1128 blood cultures and 1444 respiratory tract specimens. Blood cultures were positive for a pathogenic respiratory tract microbe in 4.9% of samples, whereas upper and lower respiratory tract samples overall provided a probable microbiological diagnosis in 21.3% and 47.5%, respectively. Expectorated or induced sputum overall provided aetiology in 51.7% of the samples. At the interventional hospital, the number of expectorated or induced sputum samples were significantly increased, and diagnostic yield from expectorated or induced sputum was significantly enhanced from 41.2 to 62.0% after the intervention (p = 0.049). There was an over-representation of samples from the interventional hospital during the study period. Non-typeable Haemophilus influenza and Streptococcus pneumoniae accounted for 25.3% and 24.7% of microbiologically confirmed cases, respectively.

Conclusion

Expectorated or induced sputum outperformed other sampling methods in providing a reliable microbiological diagnosis for hospitalized CAP. A diagnostic stewardship intervention significantly improved diagnostic yield of lower respiratory tract sampling.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07199-4.

Timeliness of Microbiology Test Result Reporting and Association with Outcomes of Adults Hospitalised with Unspecified Pneumonia: A Data Linkage Study

BACKGROUND

Pneumonia is one of the leading causes of mortality and morbidity worldwide. Microbiology tests play a critical role in the diagnosis of pneumonia. Our study aimed to determine microbiology result reporting times and evaluate their association with outcomes of adult patients (≥18 years) hospitalised with pneumonia.

METHODS

This is a 3-year (2016-2018) retrospective cohort study in six hospitals in New South Wales, Australia. The study data were obtained by linking hospital and laboratory system databases. Result reporting times including time from admission to the first and the last microbiology test results were determined. The outcome measures were hospital length of stay (LOS) and in-hospital mortality. We fit median and logistic regression to evaluate the association of time-to-first microbiological result with hospital LOS and in-hospital mortality, respectively.

RESULTS

A total of 6,298 patients met the inclusion criteria. Of these, 85.3% (n = 5,375) ordered at least one microbiology test. The top 5 microbiology tests were blood culture, urine culture, respiratory polymerase chain reaction (PCR), urine antigen, and sputum culture. The median time-to-first microbiology result was 26 hrs while the median time-to-last test result was 144 hrs. The rate of in-hospital mortality was 5.9% (n = 371). After adjusting for confounders, every 5 hrs increase in the time-to-first microbiology test was associated with an increase of 3.9 hrs in the median hospital LOS [95% Confidence Interval (CI), 3.5 to 4.3; P ≤ 0.001]. There was no association between time-to-first microbiology result and in-hospital mortality (OR 1.01; 95% CI 1.00-1.02; P=0.122).

CONCLUSION

Time-to-first microbiology result reporting was significantly associated with hospital LOS but not with in-hospital mortality. Further research should be conducted to understand if improving result reporting times can reduce the length of hospital stay of patients.

OUP accepted manuscript

Background

Respiratory syncytial virus (RSV) causes a substantial burden in older adults. Viral load in RSV-infected adults is generally lower compared to young children, which could result in suboptimal sensitivity of RSV diagnostics. Although the Xpert® Xpress Flu/RSV assay has been used in routine clinical care, its sensitivity to diagnose RSV infection in older adults is largely unknown. We aimed to compare the performance of the Xpert® Xpress Flu/RSV assay with real-time reverse-transcription polymerase chain reaction (RT-PCR) in home-dwelling older adults (≥60 years of age).

Methods

Nasopharyngeal swabs were tested with Xpert® Xpress Flu/RSV and compared to RSV RT-PCR in older adults with acute respiratory tract infections with different levels of disease severity.

Results

We studied 758 respiratory samples from 561 older adults from 2 consecutive RSV seasons. Thirty-five (4.6%) samples tested positive for RSV by at least 1 of the assays, of which 2 samples were negative by Xpert® Xpress Flu/RSV and 3 samples by real-time RT-PCR. The positive percentage agreement (PPA) was 90.9% (95% confidence interval [CI], 76.4%–96.8%) and negative percentage agreement was 99.7% (95% CI, 99.0%–99.9%). Viral loads were low (≤103 copies/mL or cycle threshold value ≥34) in all cases with discordant results for the 2 assays.

Conclusions

The PPA of Xpert® Xpress Flu/RSV compared to routine RT-PCR is high for RSV detection in home-dwelling older adults. The assay is fast and easy to use at the point of care.

Clinical Trials Registration

NCT03621930.

Evaluation of Panbio rapid antigen test for SARS-CoV-2 in symptomatic patients and their contacts: a multicenter study

BACKGROUND

Point-of-care rapid tests to identify SARS-CoV-2 can have clinical benefits.

METHODS

A cross-sectional study in adults visiting emergency services or screening sites of referral hospitals for COVID-19 to validate the diagnostic performance of a rapid antigen test for SARS-CoV-2 (Abbott's Panbio) compared with reverse transcription-polymerase chain reaction (RT-PCR) testing. Tests were performed by health personnel in a routine situation during a COVID-19 outbreak.

RESULTS

A total of 1060 participants (mean age 47, 46% with a self-reported comorbidity) were recruited from 8 hospitals in Mexico. Participants provided 1060 valid Panbio rapid test-RT-PCR test pairs with 45% testing positive in the RT-PCR. Overall sensitivity of the Panbio test was 54.2% (95% CI 51%-57%), and 69.1% (95% CI 66%-73%) for patients during the first week of symptoms. Sensitivity depended on viral load (cycle threshold (Ct) of RT-PCR) and days of symptoms. With a Ct ≤25, sensitivity was 82% (95% CI, 76%-87%). Specificity of the Panbio test was >97.8% in all groups.

CONCLUSIONS

The Panbio rapid antigen test for SARS-CoV-2 had good specificity but low sensitivity. A negative test requires confirmation with RT-PCR, especially for testing after the first week of symptoms.

Setting analytical performance specifications using HbA1c as a model measurand

Analytical performance specifications (APS) for measurands describe the minimum analytical quality requirements for their measurement. These APS are used to monitor and contain the systematic (trueness/bias) and random errors (precision/imprecision) of a laboratory measurement to ensure the results are "fit for purpose" in informing clinical decisions about managing a patient's health condition. In this review, we highlighted the wide variation in the setting of APS, using different levels of evidence, as recommended by the Milan Consensus, and approaches. The setting of a priori defined outcome-based APS for HbA1c remains challenging. Promising indirect alternatives seek to link the clinical utility of HbA1c and APS by defining statistical confidence for interpreting the laboratory values, or through simulation of clinical performance at varying levels of analytical performance. APS defined based on biological variation estimates in healthy individuals using the current formulae are unachievable by nearly all routine laboratory methods for HbA1c testing. On the other hand, the APS employed in external quality assurance programs have been progressively tightened, and greatly facilitate the improved quality of HbA1c testing. Laboratories should select the APS that fits their intended clinical use and should document the data and rationale underpinning those selections. Where possible common APS should be adopted across a region or country to facilitate the movement of patients and patient data across health care facilities.

Fast Antibiotic Susceptibility Testing via Raman Microspectrometry on Single Bacteria: An MRSA Case Study

Despite recent advances in molecular diagnostics, ultrafast determination of the antibiotic susceptibility phenotype of pathogenic microorganisms is still a major challenge of in vitro diagnostics (IVD) of infectious diseases. Raman microspectroscopy has been proposed as a means to achieve this goal. Previous studies have shown that susceptibility phenotyping could be done through Raman analysis of microbial cells, either in large clusters or down to the single-cell level in the case of Gram-negative rods. Gram-positive cocci such as Staphylococcus aureus pose several challenges due to their size and their different metabolic and chemical characteristics. Using a tailored automated single-cell Raman spectrometer and a previously proposed sample preparation protocol, we acquired and analyzed 9429 S. aureus single cells belonging to three cefoxitin-resistant strains and two susceptible strains during their incubation in the presence of various concentrations of cefoxitin. We observed an effect on S. aureus spectra that is weaker than what was detected on previous bacteria/drug combinations, with a higher cell-to-cell response variability and an important impact of incubation conditions on the phenotypic resistance of a given strain. Overall, the proposed protocol was able to correlate strains' phenotype with a specific modification of the spectra using majority votes. We, hence, confirm that our previous results on single-cell Raman antibiotic susceptibility testing can be extended to the S. aureus case and further clarify potential limitations and development requirements of this approach in the move toward industrial applications.

Evaluation of the accuracy of diagnostic coding for influenza compared to laboratory results: the availability of test results before hospital discharge facilitates improved coding accuracy

Background

Assessing the accuracy of diagnostic coding is essential to ensure the validity and reliability of administrative coded data. The aim of the study was to evaluate the accuracy of assigned International Classification of Diseases version 10-Australian Modification (ICD-10-AM) codes for influenza by comparing with patients’ results of their polymerase chain reaction (PCR)-based laboratory tests.

Method

A retrospective study was conducted across seven public hospitals in New South Wales, Australia. A total of 16,439 patients who were admitted and tested by either cartridge-based rapid PCR or batched multiplex PCR between January 2016 and December 2017 met the inclusion criteria. We calculated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of ICD-10-AM coding using laboratory results as a gold standard. Separate analyses were conducted to determine whether the availability of test results at the time of hospital discharge influenced diagnostic coding accuracy.

Results

Laboratory results revealed 2759 positive influenza cases, while ICD-10-AM coding identified 2527 patients. Overall, 13.7% (n = 378) of test positive patients were not assigned an ICD-10-AM code for influenza. A further 5.8% (n = 146) patients with negative test results were incorrectly assigned an ICD-10-AM code for influenza. The sensitivity, specificity, PPV and NPV of ICD-10-AM coding were 93.1%; 98.9%; 94.5% and 98.6% respectively when test results were received before discharge and 32.7%; 99.2%; 87.8% and 89.8% respectively when test results were not available at discharge. The sensitivity of ICD-10-AM coding varied significantly across hospitals. The use of rapid PCR or hospitalisation during the influenza season were associated with greater coding accuracy.

Conclusion

Although ICD-10-AM coding for influenza demonstrated high accuracy when laboratory results were received before discharge, its sensitivity was substantially lower for patients whose test results were not available at discharge. The timely availability of laboratory test results during the episode of care could contribute to improved coding accuracy.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12911-021-01531-9.

Potentially redundant repeat liver function test ordering practices in australian hospitals: A 5-year multicentre retrospective observational study

BACKGROUND

Repeat Liver Function Tests (LFTs) are often necessary for monitoring purposes, but retesting within a short time interval may suggest potentially redundant repeat test (PRRT) ordering practices. We aimed to determine the proportion of potentially redundant repeat LFT ordering and identify associated factors in hospitals.

METHODS

A 5-year (2014-2018) retrospective cohort study in six hospitals in New South Wales, Australia. A total of 131 885 patient admissions with repeat LFTs in the general ward (n = 102 852) and intensive care unit (ICU) (n = 29 033) met the inclusion criteria. Existing guidelines do not support retesting LFT for at least 48-72 hours. We used 24 hours as a conservative minimum retesting interval to examine PRRT ordering. We fit binary logistic regression to identify factors associated with PRRT ordering in two conditions with the highest repeat LFTs.

RESULTS

There were a total of 298 567 repeat LFTs (medians of 2 repeats/admission and retesting interval of 25.6 hours) in the general ward and 205 929 (medians of 4 repeats/admission and retesting interval of 24.1 hours) in the ICU. The proportions of PRRT ordering were 35.2% (105 227/298 567) and 47.7% (98 307/205 929) in the general ward and ICU, respectively. The proportions of patients who received at least one PRRT were 52.3% (53 766/102 852) and 83.9% (24 365/29 033) in the general ward and ICU, respectively. Age, gender and the number of comorbidities and procedures were associated with the likelihood of ordering PRRT depending on the settings.

CONCLUSION

Repeat LFT testing is common in Australian hospitals, often within 24 hours, despite guidelines not supporting too-early repeat testing. Further research should be conducted to understand whether better adherence to existing guidelines is required, or if there is any case for guidelines to be updated based on certain patient subpopulations.

Differences in antibiotic and antiviral use in people with confirmed influenza: a retrospective comparison of rapid influenza PCR and multiplex respiratory virus PCR tests

Background

Influenza is a highly contagious respiratory virus with clinical impacts on patient morbidity, mortality and hospital bed management. The effect of rapid nucleic acid testing (RPCR) in comparison to standard multiplex PCR (MPCR) diagnosis in treatment decisions is unclear. This study aimed to determine whether RPCR influenza testing in comparison to standard MPCR testing was associated with differences in antibiotic and antiviral (oseltamivir) utilisation and hospital length of stay in emergency department and inpatient hospital settings.

Methods

A retrospective cohort study of positive influenza RPCR and MPCR patients was performed utilising data from the 2017 influenza season. Medical records of correlating patient presentations were reviewed for data collection. An analysis of RPCR versus MPCR patient outcomes was performed examining test turnaround time, antibiotic initiation, oseltamivir initiation and hospital length of stay for both emergency department and inpatient hospital stay. Subgroup analysis was performed to assess oseltamivir use in high risk populations for influenza complications. Statistical significance was assessed using Mann-Whitney test for numerical data and Chi-squared test for categorical data. Odds ratio with 95% confidence intervals were calculated where appropriate.

Results

Overall, 122 RPCR and 362 MPCR positive influenza patients were included in this study. Commencement of antibiotics was less frequent in the RPCR than MPCR cohorts (51% vs 67%; p < 0.01, OR 0.52; 95% CI 0.34–0.79). People at high risk of complications from influenza who were tested with the RPCR were more likely to be treated with oseltamivir compared to those tested with the MPCR (76% vs 63%; p = 0.03, OR 1.81; 95% CI 1.07–3.08). Hospital length of stay was not impacted when either test was used in the emergency department and inpatient settings.

Conclusions

These findings suggest utilisation of RPCR testing in influenza management can improve antibiotic stewardship through reduction in antibiotic use and improvement in oseltamivir initiation in those at higher risk of complications. Further research is required to determine other factors that may have influenced hospital length of stay and a cost-benefit analysis should be undertaken to determine the financial impact of the RPCR test.

Molecular Testing for Acute Respiratory Tract Infections: Clinical and Diagnostic Recommendations From the IDSA's Diagnostics Committee

The clinical signs and symptoms of acute respiratory tract infections (RTIs) are not pathogen specific. Highly sensitive and specific nucleic acid amplification tests have become the diagnostic reference standard for viruses, and translation of bacterial assays from basic research to routine clinical practice represents an exciting advance in respiratory medicine. Most recently, molecular diagnostics have played an essential role in the global health response to the novel coronavirus pandemic. How best to use newer molecular tests for RTI in combination with clinical judgment and traditional methods can be bewildering given the plethora of available assays and rapidly evolving technologies. Here, we summarize the current state of the art with respect to the diagnosis of viral and bacterial RTIs, provide a practical framework for diagnostic decision making using selected patient-centered vignettes, and make recommendations for future studies to advance the field.

Impact of on-site compared to off-site testing for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) on duration of isolation and resource utilization

Rapid detection and isolation of coronavirus disease 2019 (COVID-19) patients is the only means of reducing hospital transmission. We describe the impact of implementation of on-site severe acute respiratory coronavirus virus 2 (SARS-CoV-2) reverse-transcription polymerase chain reaction (RT-PCR) testing on reducing turnaround time, isolation duration, pathology test ordering, and antibiotic use in patients who do not have COVID-19.

Cepheid Xpert® Flu/RSV and Seegene Allplex™ RP1 show high diagnostic agreement for the detection of influenza A/B and respiratory syncytial viruses in clinical practice

Background

Molecular assays based on reverse transcription‐polymerase chain reaction (RT‐PCR) provide reliable results for the detection of respiratory pathogens, although diagnostic agreement varies. This study determined the agreement between the RT‐PCR assays (Xpert^® Flu/RSV vs Allplex^™ RP1) in detecting influenza A, influenza B, and respiratory syncytial viruses (RSVs) in clinical practice.

Methods

We retrospectively identified 914 patient encounters where testing with both Xpert^® Flu/RSV and Allplex^™ RP1 was undertaken between October 2015 and September 2019 in seven hospitals across New South Wales, Australia. The diagnostic agreement of the two assays was evaluated using positive percent agreement, negative percent agreement, and prevalence and bias‐adjusted kappa.

Results

The positive percent agreement was 95.1% for influenza A, 87.5% for influenza B, and 77.8% for RSV. The negative percent agreement was 99.4% for influenza A, 99.9% for influenza B, and 100% for RSV. The prevalence and bias‐adjusted kappa was 0.98 for influenza A, 0.99 for influenza B, and 0.97 for RSV. In a sensitivity analysis, the positive percent agreement values were significantly higher during the non‐influenza season than the influenza season for influenza B and RSV.

Conclusions

The Xpert^® Flu/RSV and Allplex^™ RP1 demonstrated a high diagnostic agreement for all three viruses assessed. The seasonal variation in the positive percent agreement of the two assays for influenza B and RSV may have been due to lower numbers assessed, variability in the virology of infections outside the peak season, or changes in the physiology of the infected host in different seasons.

Point of care testing of Influenza A/B and RSV in an adult respiratory assessment unit is associated with improvement in isolation practices and reduction in hospital length of stay

Introduction. Every winter seasonal influenza and other viral respiratory infections increase pressure on the health services and are associated with nosocomial infection and morbidity.Aim. To compare provision of point-of-care (POC) testing with laboratory-based testing for influenza and RSV detection on an adult respiratory assessment unit to assess the impact on isolation practices and length of stay (LOS).Methodology. Prospective interrupted 'on-off' study in adults admitted to the respiratory unit between December 2018 and April 2019 with a suspected respiratory tract infection. Nasopharyngeal samples were tested using either the GeneXpert rapid POC test for influenza and RSV (on-period), or were sent to the laboratory for multiplex PCR testing against a panel of 12 respiratory viruses (off-period). Outcome measures were time to patient isolation for infection control, LOS and turnaround time from admission to test results.Results. Of 1145 patients evaluated, 755 were tested with POC and 390 with laboratory multiplex; a respiratory virus was identified in 164 (21.7 %) and 138 (35.4 %) patients respectively. A positive POC test was associated with a shorter time to isolation (mean difference 16.9 h, P<0.001), shorter LOS (mean difference 15.5 h, P=0.05,) and shorter turnaround time (mean difference 28.3 h, P<0.001), compared to laboratory testing.Conclusion. Use of GeneXpert POC testing for Flu/RSV is associated with rapid reporting of results with significant improvements in isolation practices and reductions in LOS.

Opportunities Revealed for Antimicrobial Stewardship and Clinical Practice with Implementation of a Rapid Respiratory Multiplex Assay

Few studies assess the utility of rapid multiplex molecular respiratory panels in adult patients. Previous multiplex PCR assays took hours to days from order time to result. We analyze the clinical impact of switching to a molecular assay with a 3-h test-turnaround-time (TAT). We performed a retrospective review of adult patients who presented to our emergency departments with respiratory symptoms and had a respiratory viral panel (xTAG RVP; RVP) or respiratory pathogen panel (ePlex RP; RPP) within 48 h of presentation. The average TATs for the RVP and RPP were 27.9 and 3.0 h, respectively (P < 0.0001). In RVP-positive and RPP-positive patients, 68.9 and 44.5% of those with normal chest imaging received antibiotics (P = 0.013), while 95.4 and 89.6% of those with abnormal imaging received antibiotics, respectively (P = 0.187). There was no difference in antibiotic duration in RVP-positive and RPP-positive patients with abnormal chest imaging (6.2 and 6.0 days, respectively; P = 0.923) and normal chest imaging (4.5 and 4.3 days, respectively; P = 0.922). Fewer patients were admitted in the RPP-positive compared to the RVP-positive group (76.9 and 88.6%, respectively; P = 0.013), while the proportion of admissions were similar among RPP-negative and RVP-negative patients (85.3 and 87.1%, P = 0.726). Switching to a multiplex respiratory panel with a clinically actionable TAT is associated with reduced hospital admissions and, in admitted adults without focal radiographic findings, reduced antibiotic initiation. Opportunities to further mitigate inappropriate antibiotic use may be realized by combining rapid multiplex PCR with provider education, clinical decision-care algorithms, and active antibiotic stewardship.

Cost-Effective Respiratory Virus Testing

The timely and accurate diagnosis of respiratory virus infections has the potential to optimize downstream (posttesting) use of limited health care resources, including antibiotics, antivirals, ancillary testing, and inpatient and emergency department beds. Cost-effective algorithms for respiratory virus testing must take into consideration numerous factors, including which patients should be tested, what testing should be performed (for example, antigen testing versus reverse transcription-PCR testing or influenza A/B testing versus testing with a comprehensive respiratory virus panel), and the turnaround time necessary to achieve the desired posttesting outcomes. Despite the clinical impact of respiratory virus infections, the cost-effectiveness of respiratory virus testing is incompletely understood. In this article, we review the literature pertaining to the cost-effectiveness of respiratory virus testing in pediatric and adult patient populations, in emergency department, outpatient, and inpatient clinical settings. Furthermore, we consider the cost-effectiveness of a variety of testing methods, including rapid antigen tests, direct fluorescent antibody assays, and nucleic acid amplification tests.

Clinical Utility of Advanced Microbiology Testing Tools

Advanced microbiology technologies are rapidly changing our ability to diagnose infections, improve patient care, and enhance clinical workflow. These tools are increasing the breadth, depth, and speed of diagnostic data generated per patient, and testing is being moved closer to the patient through rapid diagnostic technologies, including point-of-care (POC) technologies.

Advanced microbiology technologies are rapidly changing our ability to diagnose infections, improve patient care, and enhance clinical workflow. These tools are increasing the breadth, depth, and speed of diagnostic data generated per patient, and testing is being moved closer to the patient through rapid diagnostic technologies, including point-of-care (POC) technologies. While select stakeholders have an appreciation of the value/importance of improvements in the microbial diagnostic field, there remains a disconnect between clinicians and some payers and hospital administrators in terms of understanding the potential clinical utility of these novel technologies. Therefore, a key challenge for the clinical microbiology community is to clearly articulate the value proposition of these technologies to encourage payers to cover and hospitals to adopt advanced microbiology tests. Specific guidance on how to define and demonstrate clinical utility would be valuable. Addressing this challenge will require alignment on this topic, not just by microbiologists but also by primary care and emergency room (ER) physicians, infectious disease specialists, pharmacists, hospital administrators, and government entities with an interest in public health. In this article, we discuss how to best conduct clinical studies to demonstrate and communicate clinical utility to payers and to set reasonable expectations for what diagnostic manufacturers should be required to demonstrate to support reimbursement from commercial payers and utilization by hospital systems.

Timing of respiratory virus molecular testing in emergency departments and its association with patient care outcomes: a retrospective observational study across six Australian hospitals

OBJECTIVE

A rapid molecular diagnostic test (RMDT) offers a fast and accurate detection of respiratory viruses, but its impact on the timeliness of care in the emergency department (ED) may depend on the timing of the test. The aim of the study was to determine if the timing of respiratory virus testing using a RMDT in the ED had an association with patient care outcomes.

DESIGN

Retrospective observational study.

SETTING

Linked ED and laboratory data from six EDs in New South Wales, Australia.

PARTICIPANTS

Adult patients presenting to EDs during the 2017 influenza season and tested for respiratory viruses using a RMDT. The timing of respiratory virus testing was defined as the time from a patient's ED arrival to time of sample receipt at the hospital laboratory.

OUTCOME MEASURES

ED length of stay (LOS), >4 hour ED LOS and having a pending RMDT result at ED disposition.

RESULTS

A total of 2168 patients were included. The median timing of respiratory virus testing was 224 min (IQR, 133-349). Every 30 min increase in the timing of respiratory virus testing was associated with a 24.0 min increase in the median ED LOS (95% CI, 21.8-26.1; p<0.001), a 51% increase in the likelihood of staying >4 hours in ED (OR, 1.51; 95% CI, 1.41 to 1.63; p<0.001) and a 4% increase in the likelihood of having a pending RMDT result at ED disposition (OR, 1.04; 95% CI, 1.02 to 1.05; p<0.001) after adjustment for confounders.

CONCLUSION

The timing of respiratory virus molecular testing in EDs was significantly associated with a range of outcome indicators. Results suggest the potential to maximise the benefits of RMDT by introducing an early diagnostic protocol such as triage-initiated testing.

Impact of Rapid Molecular Detection of Respiratory Viruses on Clinical Outcomes and Patient Management

To determine if rapid molecular testing for respiratory viruses in patients with respiratory illnesses can provide advantages to patients and hospitals, rigorous investigations on the impacts of using these assays are required. Well-conducted studies are needed to inform decisions about implementation of new rapid assays to replace standard molecular testing or to initiate testing in laboratories that are currently not doing molecular tests for respiratory viruses due to the complex nature of standard panels. In this issue of the Journal of Clinical Microbiology, N. Wabe et al. (J Clin Microbiol 57:e01727-18, 2019, https://doi.org/10.1128/JCM.01727-18) report the results of their evaluation of the impact of using a rapid molecular test for influenza A/influenza B and RSV on outcomes for adults hospitalized with respiratory illness. The median time from admission to test result of the rapid test was 7.5 h compared to 40.3 h for the standard PCR assay. Compared to the use of the standard molecular assay, use of a rapid test significantly shortened time in the hospital and reduced the number of other microbiology tests performed. The authors concluded that rapid PCR testing of adults hospitalized with respiratory illnesses could provide benefits to both the patients and the hospital. Patients were able to leave the hospital earlier and a greater proportion of them had received their test results before discharge, which would allow appropriate treatment to be provided more quickly.