Accurate Detection of Streptococcus pyogenes at the Point of Care Using the cobas Liat Strep A Nucleic Acid Test

Molecular Point-of-Care Testing in the Emergency Department for Group A Streptococcus Pharyngitis: A Randomized Trial

OBJECTIVES

To compare clinical and health systems outcomes of rapid molecular testing versus throat culture recovery for the management of group A Streptococcus (GAS) pharyngitis in a pediatric emergency department (PED).

METHODS

We conducted a single-center randomized trial of children (3-17 years) presenting to a PED with suspected GAS pharyngitis. A single dual-headed throat swab was collected, and participants were randomized to 1 of 2 parallel treatment groups with 1:1 allocation: point-of-care (POC) nucleic acid amplification testing or standard throat culture. The primary outcomes were time to throat pain +/- fever resolution. Secondary outcomes included absenteeism, length of stay, return visits to care, and antibiotic prescriptions and utilization.

RESULTS

A total of 227 children were randomly assigned to culture (n = 115) or POC (n = 112) testing. Antibiotics were initiated earlier in the POC group by approximately 1 day (95% confidence interval, -0.40 to -1.58). No associated difference in time to throat pain or fever resolution was observed between groups. There was a decrease in the proportion of prescribed antibiotics in the POC group (0.35) compared with the culture group (0.79; P < 0.001). Otherwise, no significant differences in secondary outcomes were observed.

CONCLUSIONS

Establishing a POC nucleic acid amplification testing program for GAS in a PED facilitates earlier treatment and fewer antibiotic prescriptions. Although this did not translate to improved clinical and health systems outcomes in our study, it may serve as an important tool amid evolving pediatric febrile illnesses and growing antimicrobial resistance patterns.

Unlocking the molecular realm: advanced approaches for identifying clinically and environmentally relevant bacteria

Rapid, effective, and specific identification of clinical and environmental bacterial pathogens is of major importance for their control. Traditionally, bacteria have been identified by phenotypic methods based on morphological, biochemical, and metabolic properties. While these methods are very useful in clinical practice, they have limitations including a poor ability to differentiate within and between species and time-consuming workflows. Newly developed molecular methods can greatly improve the accuracy of taxonomic characterization, identifying specific strains of medical or environmental importance. However, due to high costs and the need for trained professionals, these methods are not yet routine in diagnostic laboratories. Thus, disseminating knowledge on advances in molecular identification techniques is pivotal to make these methodologies accessible. The objective of this work was to review and discuss current molecular techniques for bacteria identification aiming to track and monitor microbial agents in clinical and environmental samples.

Point-of-Care Testing for the Diagnosis of Fungal Infections

Invasive fungal infections are increasing worldwide due to factors such as climate change and immunomodulating therapies. Unfortunately, the detection of these infections is limited due to the low sensitivity and long periods required for laboratory testing. Point-of-care testing could lead to more rapid diagnosis of these often devasting infections. However, there are currently no true point-of-care tests on the market for the detection of fungi. In this article, the current state of fungal antigen and molecular testing is reviewed, with commentary on the potential for development and use in the point-of-care setting.

An automated, fully-integrated nucleic acid analyzer based on microfluidic liquid handling robot technique

On-site nucleic acid testing (NAT) plays an important role for disease monitoring and pathogen diagnosis. In this work, we developed an automated and fully-integrated nucleic acid analyzer by combining the automated liquid handling robot technique with the microfluidic droplet-based real-time PCR assay technique. The present analyzer could achieve multiple operations including sample introduction, nucleic acid extraction based on magnetic solid-phase extraction, reverse transcription and, sample droplet generation, PCR amplification, real-time and dual fluorescence detection of droplet array. A strategy of constructing an integrated compact and low-cost system was adopted to minimize the analyzer size to 50 × 45 × 45 cm (length × width × height), and reduce the instrument cost to ca. $900 with a single analysis cost less than $5. A simple chip was also designed to pre-load reagents and carry oil-covered PCR reaction droplets. We applied the analyzer to identify eight types of influenza pathogens in human throat swabs, and the results were consistent with the colloidal gold method.

Use of Host Response to Refine the Diagnosis of Group A Streptococcal Pharyngitis

BACKGROUND

Current diagnostic tests for pharyngitis do not distinguish between symptomatic group A Streptococcus (GAS) infection and asymptomatic colonization, resulting in over-diagnosis and unnecessary use of antibiotics. We assessed whether measures of host response could make this distinction.

METHODS

We enrolled 18 children with pharyngitis having Centor scores of 4 or 5 and 21 controls without pharyngitis or other acute infections. Both groups had throat cultures, molecular tests for GAS and respiratory viruses and IgM serology for Epstein-Barr virus. Host response was evaluated with white blood cell count (WBC), C-reactive protein (CRP), procalcitonin (PCT), and sequencing of RNA from peripheral blood leukocytes.

RESULTS

Of 18 cases, 11 had GAS pharyngitis, 3 had adenovirus pharyngitis and 4 had other pharyngitis. Among asymptomatic controls, 5 were positive for GAS. WBC, CRP, and PCT were higher in subjects with pharyngitis compared to asymptomatic controls including those with GAS. Transcriptional profiles from children with symptomatic GAS were clearly distinct from those of children in all other groups. The levels of two genes, CD177 and TLR5 each individually accurately distinguished between symptomatic and asymptomatic GAS. Optimal diagnostic sensitivity and specificity were achieved by the combination of CRP and PCT, and by each of the two gene markers.

CONCLUSION

In this exploratory study, we showed that traditional measures of inflammation and markers of host gene expression distinguish between symptomatic and asymptomatic GAS. These results point to future rapid molecular approaches for improving the diagnosis of GAS pharyngitis, that may help reduce unnecessary antibiotic use.

Clinical Performance of the cobas Liat SARS-CoV-2 & Influenza A/B Assay in Nasal Samples

Background and Objective

Point-of-care type molecular diagnostic tests have been used for detecting SARS-CoV-2, although their clinical utility with nasal samples has yet to be established. This study evaluated the clinical performance of the cobas Liat SARS-CoV-2 & Influenza A/B (Liat) assay in nasal samples.

Methods

Nasal and nasopharyngeal samples were collected and were tested using the Liat, the cobas 6800 system and the cobas SARS-CoV-2 & Influenza A/B (cobas), and a method developed by National Institute of Infectious Diseases, Japan (NIID).

Results

A total of 814 nasal samples were collected. The Liat assay was positive for SARS-CoV-2 in 113 (13.9%). The total, positive, and negative concordance rate between the Liat and cobas/NIID assays were 99.3%/98.4%, 99.1%/100%, and 99.3%/98.2%, respectively. Five samples were positive only using the Liat assay. Their Ct values ranged from 31.9 to 37.2. The Ct values of the Liat assay were significantly lower (p < 0.001) but were correlated (p < 0.001) with those of other molecular assays. In the participants who tested positive for SARS-CoV-2 on the Liat assay using nasopharyngeal samples, 88.2% of their nasal samples also tested positive using the Liat assay.

Conclusion

The Liat assay showed high concordance with other molecular assays in nasal samples. Some discordance occurred in samples with Ct values > 30 on the Liat assay.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40291-022-00580-8.

Rapid antigen detection and molecular tests for group A streptococcal infections for acute sore throat: systematic reviews and economic evaluation

BACKGROUND

Sore throat is a common condition caused by an infection of the airway. Most cases are of a viral nature; however, a number of these infections may be caused by the group A Streptococcus bacterium. Most viral and bacterial sore throat infections resolve spontaneously within a few weeks. Point-of-care testing in primary care has been recognised as an emerging technology for aiding targeted antibiotic prescribing for sore throat in cases that do not spontaneously resolve.

OBJECTIVE

Systematically review the evidence for 21 point-of-care tests for detecting group A Streptococcus bacteria and develop a de novo economic model to compare the cost-effectiveness of point-of-care tests alongside clinical scoring tools with the cost-effectiveness of clinical scoring tools alone for patients managed in primary care and hospital settings.

DATA SOURCES

Multiple electronic databases were searched from inception to March 2019. The following databases were searched in November and December 2018 and searches were updated in March 2019: MEDLINE [via OvidSP (Health First, Rockledge, FL, USA)], MEDLINE In-Process & Other Non-Indexed Citations (via OvidSP), MEDLINE Epub Ahead of Print (via OvidSP), MEDLINE Daily Update (via OvidSP), EMBASE (via OvidSP), Cochrane Database of Systematic Reviews [via Wiley Online Library (John Wiley & Sons, Inc., Hoboken, NJ, USA)], Cochrane Central Register of Controlled Trials (CENTRAL) (via Wiley Online Library), Database of Abstracts of Reviews of Effects (DARE) (via Centre for Reviews and Dissemination), Health Technology Assessment database (via the Centre for Reviews and Dissemination), Science Citation Index and Conference Proceedings [via the Web of Science™ (Clarivate Analytics, Philadelphia, PA, USA)] and the PROSPERO International Prospective Register of Systematic Reviews (via the Centre for Reviews and Dissemination).

REVIEW METHODS

Eligible studies included those of people aged ≥ 5 years presenting with sore throat symptoms, studies comparing point-of-care testing with antibiotic-prescribing decisions, studies of test accuracy and studies of cost-effectiveness. Quality assessment of eligible studies was undertaken. Meta-analysis of sensitivity and specificity was carried out for tests with sufficient data. A decision tree model estimated costs and quality-adjusted life-years from an NHS and Personal Social Services perspective.

RESULTS

The searches identified 38 studies of clinical effectiveness and three studies of cost-effectiveness. Twenty-six full-text articles and abstracts reported on the test accuracy of point-of-care tests and/or clinical scores with biological culture as a reference standard. In the population of interest (patients with Centor/McIsaac scores of ≥ 3 points or FeverPAIN scores of ≥ 4 points), point estimates were 0.829 to 0.946 for sensitivity and 0.849 to 0.991 for specificity. There was considerable heterogeneity, even for studies using the same point-of-care test, suggesting that is unlikely that any single study will have accurately captured a test's true performance. There is some randomised controlled trial evidence to suggest that the use of rapid antigen detection tests may help to reduce antibiotic-prescribing rates. Sensitivity and specificity estimates for each test in each age group and care setting combination were obtained using meta-analyses where appropriate. Any apparent differences in test accuracy may not be attributable to the tests, and may have been caused by known differences in the studies, latent characteristics or chance. Fourteen of the 21 tests reviewed were included in the economic modelling, and these tests were not cost-effective within the current National Institute for Health and Care Excellence's cost-effectiveness thresholds. Uncertainties in the cost-effectiveness estimates included model parameter inputs and assumptions that increase the cost of testing, and the penalty for antibiotic overprescriptions.

LIMITATIONS

No information was identified for the elderly population or pharmacy setting. It was not possible to identify which test is the most accurate owing to the paucity of evidence.

CONCLUSIONS

The systematic review and the cost-effectiveness models identified uncertainties around the adoption of point-of-care tests in primary and secondary care settings. Although sensitivity and specificity estimates are promising, we have little information to establish the most accurate point-of-care test. Further research is needed to understand the test accuracy of point-of-care tests in the proposed NHS pathway and in comparable settings and patient groups.

STUDY REGISTRATION

The protocol of the review is registered as PROSPERO CRD42018118653.

FUNDING

This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 24, No. 31. See the NIHR Journals Library website for further project information.

Diagnostic accuracy of rapid nucleic acid tests for group A streptococcal pharyngitis: systematic review and meta-analysis

BACKGROUND

Acute pharyngitis is one of the most common conditions in outpatient settings and an important source of inappropriate antibiotic prescribing. Rapid antigen detection tests (RADTs) offer diagnosis of group A streptococcus at the point of care but have limited sensitivity. Rapid nucleic acid tests (RNATs) are now available; a systematic review of their accuracy is lacking.

OBJECTIVES

To evaluate the accuracy of RNATs in patients with pharyngitis; to explore test-level and study-level factors that could explain variability in accuracy; and to compare the accuracy of RNATs with that of RADTs.

DATA SOURCES

MEDLINE, Embase, Web of Science (1990-2020).

STUDY ELIGIBILITY CRITERIA

Cross-sectional studies and randomized trials.

PARTICIPANTS

Patients with pharyngitis.

INDEX TEST/S AND REFERENCE STANDARDS

RNAT commercial kits compared with throat culture.

METHODS

We assessed risk of bias and applicability using QUADAS-2. We performed meta-analysis of sensitivity and specificity using the bivariate random-effects model. Variability was explored by subgroup analyses and meta-regression.

RESULTS

We included 38 studies (46 test evaluations; 17 411 test results). RNATs were most often performed in a laboratory. The overall methodological quality of primary studies was uncertain because of incomplete reporting. RNATs had a summary sensitivity of 97.5% (95% CI 96.2%-98.3%) and a summary specificity of 95.1% (95% CI 93.6%-96.3%). There was low variability in estimates across studies. Variability in sensitivity and specificity was partially explained by test type (p < 0.05 for both). Sensitivity analyses limited to studies with low risk of bias showed robust accuracy estimates. RNATs were more sensitive than RADTs (13 studies; 96.8% versus 82.3%, p 0.004); there was no difference in specificity (p 0.92).

CONCLUSIONS

The high diagnostic accuracy of RNATs may allow their use as stand-alone tests to diagnose group A streptococcus pharyngitis. Based on direct comparisons, RNATs have greater sensitivity than RADTs and equal specificity. Further studies should evaluate RNATs in point-of-care settings.

Diagnostic Methods, Clinical Guidelines, and Antibiotic Treatment for Group A Streptococcal Pharyngitis: A Narrative Review

The most common bacterial cause of pharyngitis is infection by Group A β-hemolytic streptococcus (GABHS), commonly known as strep throat. 5-15% of adults and 15-35% of children in the United States with pharyngitis have a GABHS infection. The symptoms of GABHS overlap with non-GABHS and viral causes of acute pharyngitis, complicating the problem of diagnosis. A careful physical examination and patient history is the starting point for diagnosing GABHS. After a physical examination and patient history is completed, five types of diagnostic methods can be used to ascertain the presence of a GABHS infection: clinical scoring systems, rapid antigen detection tests, throat culture, nucleic acid amplification tests, and machine learning and artificial intelligence. Clinical guidelines developed by professional associations can help medical professionals choose among available techniques to diagnose strep throat. However, guidelines for diagnosing GABHS created by the American and European professional associations vary significantly, and there is substantial evidence that most physicians do not follow any published guidelines. Treatment for GABHS using analgesics, antipyretics, and antibiotics seeks to provide symptom relief, shorten the duration of illness, prevent nonsuppurative and suppurative complications, and decrease the risk of contagion, while minimizing the unnecessary use of antibiotics. There is broad agreement that antibiotics with narrow spectrums of activity are appropriate for treating strep throat. But whether and when patients should be treated with antibiotics for GABHS remains a controversial question. There is no clearly superior management strategy for strep throat, as significant controversy exists regarding the best methods to diagnose GABHS and under what conditions antibiotics should be prescribed.

Antibody Modified Gold Electrode as an Impedimetric Biosensor for the Detection of Streptococcus pyogenes

Streptococcus pyogenes is a known cause of a wide spectrum of diseases, from mild and acute to severe invasive infections. This paper concerns the development of a novel impedimetric biosensor for the detection of the mentioned human pathogen. The proposed biosensor is a gold disk electrode modified with commercially available antibodies attached to the surface of the electrode by carbodiimide chemistry. The conducted tests confirmed the specificity of the antibodies used, which was also demonstrated by the results obtained during the detection of S. pyogenes using electrochemical impedance spectroscopy. The developed sensor successfully detected the presence of S. pyogenes in the sample and the detection limit was calculated as 9.3 cfu/mL. The results obtained show a wide linear range for verified concentrations of this pathogen in a sample from 4.2 × 10² to 4.2 × 10⁶ cfu/mL. Furthermore, the optimal experimentally determined time required to perform pathogen detection in the sample was estimated as 3 min, and the test did not lead to the degradation of the sample.

Multicenter Clinical Evaluation of the Revogene Strep A Molecular Assay for Detection of Streptococcus pyogenes from Throat Swab Specimens

Group A streptococcus (GAS) species cause bacterial pharyngitis in both adults and children. Early and accurate diagnosis of GAS is important for appropriate antibiotic therapy to prevent GAS sequalae. The Revogene Strep A molecular assay (Meridian Bioscience Canada Inc, Quebec City, QC, Canada) is an automated real-time PCR assay for GAS detection from throat swab specimens within approximately 70 min. This multicenter prospective study evaluated the performance of the Revogene Strep A molecular assay compared to that of bacterial culture.

Group A streptococcus (GAS) species cause bacterial pharyngitis in both adults and children. Early and accurate diagnosis of GAS is important for appropriate antibiotic therapy to prevent GAS sequalae. The Revogene Strep A molecular assay (Meridian Bioscience Canada Inc, Quebec City, QC, Canada) is an automated real-time PCR assay for GAS detection from throat swab specimens within approximately 70 min. This multicenter prospective study evaluated the performance of the Revogene Strep A molecular assay compared to that of bacterial culture. Dual throat swab specimens in either liquid Amies or Stuart medium were collected from eligible subjects (pediatric population and adults) enrolled across 7 sites (USA and Canada). Revogene Strep A and reference testing was performed within 7 days and 48 h of sample collection, respectively. Of the 604 evaluable specimens, GAS was detected in 154 (25.5%) samples by the reference method and in 175 (29%) samples by the Revogene Strep A assay. Revogene Strep A assay sensitivity and specificity were reported to be 98.1% (95% confidence interval [CI], 94.4 to 99.3) and 94.7% (95% CI, 92.2 to 96.4), respectively. The positive predictive value was 86.3% (95% CI, 80.4 to 90.6), negative predictive value was 99.3% (95% CI, 98.0 to 99.8) with a 1.0% invalid rate. Discrepant analysis with alternative PCR/bidirectional sequencing was performed for 24 false-positive (FP) and 3 false-negative (FN) specimens. Concordant results were reported for 17 (FP only) of 27 discordant specimens. The Revogene Strep A assay had high sensitivity and specificity for GAS detection and provides a faster alternative for GAS diagnosis.

Group A Streptococcus Testing in Pediatrics: the Move to Point-of-Care Molecular Testing

Each year, there are an estimated 11 million visits to ambulatory care centers for pharyngitis in children between the ages of 3 and 18 years. While there are many causes of pediatric pharyngitis, group A streptococcal pharyngitis represents 15 to 30% of infections and is the only cause for which treatment is recommended. Unfortunately, clinical suspicion is insufficient for the accurate diagnosis of group A streptococcal pharyngitis, and laboratory testing for confirmation of Streptococcus pyogenes infection is required to prevent complications of infection. Traditionally, throat swabs are inoculated onto agar plates for isolation of the large-zone beta-hemolytic streptococcus. However, traditional culture methods present a potential delay in treatment due to turnaround times of 18 to 48 h. In order to improve turnaround times and enhance antimicrobial stewardship, multiple point-of-care assays have been developed. This review describes current point-of-care testing for group A streptococcal pharyngitis, including rapid antigen detection tests and more recent molecular methods. Additional attention is given to the diagnostic considerations when choosing a method for group A streptococcal point-of-care testing, implementation of molecular group A streptococcal testing, and the institutional cost of immunoassays compared to those of newer molecular methods.

Low Uptake of Rapid Diagnostic Tests for Respiratory Tract Infections in an Urban Safety Net Hospital

Background

Rapid diagnostic tests (RDTs) have been developed with the aim of providing accurate results in a timely manner. Despite this, studies report that provider uptake remains low.

Methods

We conducted a retrospective analysis of ambulatory, urgent care, and emergency department (ED) encounters at an urban safety net hospital with a primary diagnosis of an upper or lower respiratory tract infection (eg, bronchitis, pharyngitis, acute sinusitis) from January 1, 2016, to December 31, 2018. We collected RDT type and results, antibiotics prescribed, demographic and clinical patient information, and provider demographics.

Results

RDT use was low; a test was performed at 29.5% of the 33494 visits. The RDT most often ordered was the rapid Group A Streptococcus (GAS) test (n = 7352), predominantly for visits with a discharge diagnosis of pharyngitis (n = 5818). Though antibiotic prescription was more likely if the test was positive (relative risk [RR], 1.68; 95% confidence interval [CI], 1.58–1.8), 92.46% of streptococcal pharyngitis cases with a negative test were prescribed an antibiotic. The Comprehensive Respiratory Panel (CRP) was ordered in 2498 visits; influenza was the most commonly detected pathogen. Physicians in the ED were most likely to order a CRP. Antibiotic prescription was lower if the CRP was not ordered compared with a negative CRP result (RR, 0.77; 95% CI, 0.7–0.84). There was no difference in prescribing by CRP result (negative vs positive).

Conclusions

RDTs are used infrequently in the outpatient setting, and impact on prescribing was inconsistent. Further work is needed to determine barriers to RDT use and to address potential solutions.

Comparison of 3 Nucleic Acid Amplification Tests and a Rapid Antigen Test with Culture for the Detection of Group A Streptococci from Throat Swabs

Background

Recently, the US Food and Drug Administration cleared 3 nucleic acid amplification test (NAAT) assays for detection of Streptococcus pyogenes [group A Streptococcus (GAS)] in pharyngeal specimens. However, there are limited studies evaluating the performance of these NAAT assays.

Methods

We compared the results of 3 NAATs (cobas Liat, Luminex Aries, and Cepheid Xpert Xpress) and a rapid antigen assay (Quidel QuickVue in-line strep A) with the accepted gold standard method, bacterial culture.

Results

Sixty-eight throat swab specimens collected between August and October 2017 were tested. Compared to bacterial culture, the sensitivities, specificities, positive predictive value, and negative predictive value for detecting GAS were as follows: cobas Liat: 100%, 97.4%, 96.7%, and 100%; Cepheid Xpert: 100%, 97.4%, 96.7%, and 100%; Luminex Aries: 95.2%, 100%, 100%, and 95.5%. The Quidel QuickVue in-line strep A assay showed poor sensitivity, detecting only 5.2% of culture-positive specimens.

Conclusion

The 3 NAATs have high sensitivity when compared with bacterial culture for detection of GAS. With rapid turnaround time and ease of use, these tests can be considered as reliable point-of-care tests for the diagnosis of GAS, replacing the need for back-up culture.

Optimization of Turnaround Time for Group A Streptococcus PCR

The use of some nucleic acid amplification tests (NAATs) for the diagnosis of group A Streptococcus (GAS) pharyngitis allows laboratories to adopt single-tiered testing without reflex culture. However, centralization may delay the delivery of actionable information to the bedside, particularly in the outpatient setting. We describe two novel workflows at our institution and their effect on in-lab turnaround time (TAT) at a tertiary care microbiology lab. Laboratory records were extracted, and relevant data were analyzed after the implementation of qualitative in vitro diagnostic testing for GAS with the Xpert Xpress Strep A assay, performed using the GeneXpert Infinity-48s. Workflow optimization steps studied included: (i) direct specimen submission to the microbiology laboratory via the pneumatic tube system and (ii) autoverification of GAS NAAT results in the laboratory information system. Between April 2018 and October 2018, 2,595 unique specimens were tested for GAS by PCR. Of these, 2,523 were included in the final analysis. Linear regression established that the total in-lab TAT was significantly reduced by direct specimen submission to the microbiology laboratory, autoverification, and processing during the night shift. We describe two workflow optimization methods that reduced the in-lab TAT for GAS NAAT. Although microbiology labs historically use manual processes, the advent of total laboratory automation and the adoption of on-demand NAATs will allow for more streamlined processing of microbiology specimens. It may be beneficial to consider instrument interfacing and specimen processing optimization during the early phases of implementation planning for NAATs in the microbiology laboratory.

Diagnosis and Management of Group a Streptococcal Pharyngitis in the United States, 2011-2015

Background

Clinical guidelines for the diagnosis of group A streptococcal (GAS) pharyngitis recommend the use of a rapid antigen detection test (RADT) and/or bacterial culture. This study evaluated the overall diagnosis and treatment of acute pharyngitis in the United States, including predictors of test type and antibiotic prescription.

Methods

A retrospective analysis of pharyngitis events from 2011 through 2015 was conducted using the MarketScan commercial/Medicare databases. A pharyngitis event was defined as occurring within 2 weeks from the index visit. Patient and provider characteristics were examined across 5 testing categories: RADT, RADT plus culture, other tests, nucleic acid amplification testing (NAAT), and no test. Multivariate models were used to identify significant predictors of NAAT use and antibiotic prescription.

Results

A total of 18.8 million acute pharyngitis events were identified in 11.6 million patients. Roughly two-thirds of events (68.2%) occurred once, and roughly a third of patients (29.1%) required additional follow-up, but hospitalization was rare (0.3%). Across all events, 43% were diagnosed by RADT, while 20% were diagnosed by RADT plus culture. The proportion of events diagnosed by NAAT increased 3.5-fold from 2011 to 2015 (0.06% vs 0.27%). Antibiotic use was frequent (49.3%), less often in combination with RADT plus culture (31.2%) or NAAT alone (34.5%) but significantly more often with RADT alone (53.4%) or no test (57.1%). Pediatricians were significantly less likely than other providers to prescribe antibiotics in their patients, regardless of patient age (p < 0.0001).

Conclusions

Antibiotic use for sore throat remains common, with many clinicians not following current guidelines for diagnosis of GAS pharyngitis. Diagnosis of GAS pharyngitis using RADT plus culture or NAAT alone was associated with lower use of antibiotics. Diagnostic testing can help lower the incidence of inappropriate antibiotic use, and inclusion of NAAT in the clinical guidelines for GAS pharyngitis warrants consideration.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-3835-4) contains supplementary material, which is available to authorized users.

Assessment of Test Performance and Potential for Environmental Contamination Associated with a Point-of-Care Molecular Assay for Group A Streptococcus in an End User Setting

Although U.S. Food and Drug Administration-approved and CLIA-waived point-of-care (POC) molecular systems are being implemented in routine clinical practice, instrument reliability, test performance in the hands of end users, and the potential for environmental contamination resulting from use of POC molecular systems have not been extensively evaluated. We performed a prospective evaluation of the Roche cobas Liat group A streptococcus (GAS) assay compared to routine real-time PCR. We evaluated test accuracy, instrument failure rate, and monitored for environmental contamination when testing was performed by minimally trained end users in an Express Care Clinic environment. The overall concordance of the Liat GAS assay with routine testing was 97.2% (455/468). The average Liat failure rate across three analyzers was 6.6% (33/501) (range, 3.7 to 11.6%), and no environmental contamination was detected during the course of the study. The cobas Liat platform and GAS assay demonstrated reliable performance in the end user setting and may serve as a rapid, POC option for routine diagnostic testing for certain infectious diseases, including GAS.

Diagnosis and antibiotic treatment of group a streptococcal pharyngitis in children in a primary care setting: impact of point-of-care polymerase chain reaction

BACKGROUND

To compare the sensitivity and specificity of the recommended 2-step rapid antigen detection test (RADT) with confirmatory culture vs the point-of-care (POC) polymerase chain reaction (PCR) Roche cobas® Liat® Strep A test for detection of group A Streptococcus (GAS) in pediatric patients with pharyngitis, and to investigate the impact of these tests on antibiotic use in a large pediatric clinic.

METHODS

This prospective, open-label study was conducted at a single site during fall/winter 2016-2017. A total of 275 patients aged 3 to 18 years with symptoms of pharyngitis had a throat-swab specimen analyzed using RADT, POC PCR, and culture. The sensitivity, specificity, and percentage agreement (95% CI) between assays and a laboratory-based nucleic acid amplification test were calculated. DNA sequencing was used to adjudicate discrepancies. The RADT or POC PCR result was provided to clinicians on alternating weeks to compare the impact on antibiotic use.

RESULTS

A total of 255 samples were evaluated; 110 (43.1%) were GAS positive. Sensitivities (95% CI) for POC PCR, RADT, and culture were 95.5% (89.7-98.5%), 85.5% (77.5-1.5%), and 71.8% (62.4-80.0%), respectively. Specificities (95% CI) for POC PCR, RADT, and culture were 99.3% (96.2-99.98%), 93.7% (88.5-97.1%), and 100% (97.5-100%), respectively. Compared with RADT, POC PCR resulted in significantly greater appropriate antibiotic use (97.1% vs 87.5%; P = .0065).

CONCLUSION

Under real-world conditions, RADT results were less specific and culture results were less sensitive than found in established literature and led to increased rates of inappropriate antibiotic use. POC PCR had high sensitivity and specificity and rapid turnaround times, and led to more appropriate antibiotic use.

TRIAL REGISTRATION

ID number ISRCTN84562679 . Registered October 162,018, retrospectively registered.

Multicenter Clinical Evaluation of the Automated Aries Group A Strep PCR Assay from Throat Swabs

Group A Streptococcus (GAS) is one of the leading causes of bacterial pharyngitis. Early GAS diagnosis is critical for appropriate antibiotic administration that reduces the risk of GAS sequelae and limits spread of the infection. The Aries Group A Strep (GAS) assay (Luminex, Austin, TX) is a fully automated PCR assay for direct detection of GAS in throat swab specimens in less than 2 h with minimum hands-on time. This multicenter prospective study evaluated the clinical performance of the Aries GAS assay compared to that of Streptococcus pyogenes culture. Subjects with symptoms consistent with pharyngitis were enrolled across four sites in the United States, and a throat swab in liquid Amies medium was obtained. Aries and reference testing was performed within 72 and 48 h after sample collection, respectively. Of 623 throat swab specimens from patients with pharyngitis (93.6% <18 years old, 54.3% female), the reference method yielded valid results for 618 specimens. Reference and Aries assay testing showed GAS-positive results for 160 (25.9%) and 166 (26.9%) specimens, respectively. Compared to the reference method, Aries assay sensitivity was 97.5% (95% confidence interval [CI], 93.7% to 99.0%), specificity was 97.8% (95% CI, 96.0 to 98.8%), positive predictive value was 94.0% (95% CI, 89.3% to 96.7%), and negative predictive value was 99.1% (95% CI, 97.7% to 99.7%). There were 10 false-positive and four false-negative detections with the Aries assay. Discrepant analysis with bidirectional sequencing yielded concordant results with the Aries assay for nine of 14 discordant samples. The Aries assay had high sensitivity and specificity for qualitative detection of group A Streptococcus from patients with pharyngitis.

A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiology

The critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician/advanced practice provider and the microbiologists who provide enormous value to the healthcare team. This document, developed by experts in laboratory and adult and pediatric clinical medicine, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. This document presents a system-based approach rather than specimen-based approach, and includes bloodstream and cardiovascular system infections, central nervous system infections, ocular infections, soft tissue infections of the head and neck, upper and lower respiratory infections, infections of the gastrointestinal tract, intra-abdominal infections, bone and joint infections, urinary tract infections, genital infections, and other skin and soft tissue infections; or into etiologic agent groups, including arthropod-borne infections, viral syndromes, and blood and tissue parasite infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. In addition, the pediatric needs of specimen management are also emphasized. There is intentional redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a guidance for physicians in choosing tests that will aid them to quickly and accurately diagnose infectious diseases in their patients.

Comparison of Alere i Strep A Rapid Molecular Assay With Rapid Antigen Testing and Culture in a Pediatric Outpatient Setting

OBJECTIVES

Group A Streptococcus (GAS) is the most common bacterial cause of pediatric acute pharyngitis, and its quick identification is important for subsequent treatment. We sought to determine whether molecular GAS-based testing can successfully replace GAS antigen testing and subsequent culture in a pediatric urgent care center.

METHODS

We tested 160 patient oropharyngeal samples by a rapid antigen GAS test, the Alere i Strep A test, and throat culture in a pediatric urgent care setting and calculated basic statistical metrics.

RESULTS

The sensitivity and specificity of the molecular test were 98% and 100%, respectively, compared with culture. There was a 9% false-positive rate with the rapid antigen-based testing.

CONCLUSIONS

The Alere test is sufficiently sensitive and specific for definitive GAS testing in a pediatric urgent care setting. This implementation has enabled us to provide definitive patient results at the time of each patient encounter.

The spectrum of intraoral bacteria seen in patients with cleft palates in an African setting

Dehiscence or palatal fistula formation following palatoplasty is a complication that has grave consequences for the patient that include tissue loss, emotional distress to the parents and patient, and further medical costs. Palatal dehiscence or fistula formation is multifactorial following surgery—tension of wound closure, poor patient adherence to postoperative orders and wound infection are the most common causes for this. Oral colonization with pathogenic organisms could play a role in wound healing complications. Identification of intraoral bacteria among patients with cleft palates has thus far not been performed. To identify the spectrum of intraoral bacteria in cleft palate patients in an African setting; a retrospective, chart review was performed at Inkosi Albert Luthuli Central Hospital—a quaternary hospital in Durban, South Africa. All patients with unrepaired cleft palates who underwent palatoplasty in 2015 were included. Fifty‐two patients were included. Preoperative throat/palatal swabs were taken prior to palatoplasty. The various bacteria cultured from the aforementioned swabs were cataloged. Various bacteria were cultured. In total, 23 patients (44.2%) had positive swab cultures. Eighteen cultures (34.6%) had gram‐positive growth only, four cultures (7.7%) had gram‐negative growth only, while one patient (1.9%) cultured both a gram‐positive and a gram‐negative organism. Streptococcus viridans was the most commonly cultured organism (19.2%) while beta‐hemolytic streptococci were cultured from only 4 swabs (7.7%). Our study cataloged the commonly occurring bacteria found in unrepaired cleft palate patients in Africa. Further research into the clinical significance of each bacteria is advised.

Comparison of the Alere i Strep A Test and the BD Veritor System in the Detection of Group A Streptococcus and the Hypothetical Impact of Results on Antibiotic Utilization

Rapid detection of group A Streptococcus (GAS) is an integral component of treatment decisions in the clinic, especially in the pediatric population. We prospectively collected 216 specimens from symptomatic, predominantly pediatric patients and evaluated the performance of the Alere i Strep A test (Alere i; Alere Inc., Scarborough, ME) and the BD Veritor system (BD Veritor; Becton, Dickinson and Company, Sparks, MD), with culture results being used as a comparator. Real-time PCR (RT-PCR) was performed as an arbiter in discordant cases. Comprehensive chart review was also done to determine the hypothetical impact of the results on antibiotic use. Alere i had a sensitivity and a specificity of 100% and 91.3%, respectively, and BD Veritor had a sensitivity and a specificity of 76.2% and 93.6%, respectively, when the results were compared to those of GAS culture. Further analysis of discordant results using RT-PCR revealed that while BD Veritor missed 13 confirmed positive cases, Alere i detected 100% (n = 13) of the same cases. Analysis of assay agreement showed that Alere i and BD Veritor had only moderate agreement (agreement = 0.888 [95% confidence interval {CI}, 0.838 to 0.927]; kappa index = 0.689 [95% CI, 0.91 to 0.974]). We also found both the underutilization and the overutilization of antibiotics based on the results of molecular testing. Overall, Alere i showed superior performance over BD Veritor in the detection of GAS pharyngitis and could potentially assist in better antibiotic utilization.

Right-Sizing Technology in the Era of Consumer-Driven Health Care

Technology for modern clinical and public health microbiology laboratories has evolved at an impressive rate over the last two decades. Contemporary diagnostics can rapidly provide powerful data that can impact patient lives and support infectious disease outbreak investigations. At the same time, dramatic changes to health care delivery are putting new pressures on a system that is now focusing on patient-centric, value-driven, convenient care. For laboratories, balancing all these demands in a cost-contained environment remains a challenge. This article explores the current and future directions of diagnostics in our dynamic health care environment.