Turnaround times for molecular testing of pediatric viral cerebrospinal fluid samples in United Kingdom laboratories

BACKGROUND Rapid molecular testing has revolutionized the management of suspected viral meningitis and encephalitis by providing an etiological diagnosis in<90 min with potential to improve outcomes and shorten inpatient stays.However,use of molecular assays can vary widely.AIM To evaluate current practice for molecular testing of pediatric cerebrospinal fluid(CSF)samples across the United Kingdom using a structured questionnaire.METHODS A structured telephone questionnaire survey was conducted between July and August 2020.Data was collected on the availability of viral CSF nucleic acid amplification testing(NAAT),criteria used for testing and turnaround times including the impact of the coronavirus disease 2019 pandemic.RESULTS Of 196/212(92%)microbiology laboratories responded;63/196(32%)were excluded from final analysis as they had no on-site microbiology laboratory and outsourced their samples.Of 133 Laboratories included in the study,47/133(35%)had onsite facilities for viral CSF NAAT.Hospitals currently undertaking onsite NAAT(n=47)had much faster turnaround times with 39 centers(83%)providing results in≤24 h as compared to those referring samples to neighboring laboratories(5/86;6%).CONCLUSION Onsite/near-patient rapid NAAT(including polymerase chain reaction)is recommended wherever possible to optimize patient management in the acute setting.

Determination of the predictive factors for diagnostic positivity of nucleic acid amplification tests for diagnosing pulmonary tuberculosis

Background:Tuberculosis(TB)remains a major threat to human health,and TB diagnostic methods remain unsatisfactory.Nucleic acid amplification tests(NAATs)show higher sensitivity compared with culture for the diagnosis of pulmonary TB(PTB).However,NAATs are expensive and cannot be easily implemented outside major medical centers.To improve the sensitivity of NAATs for PTB diagnosis,we investigated the predictive factors that might optimize NAAT utilization.Methods:A total of 1263 patients with suspected PTB were enrolled for evaluation.The sensitivity,specificity,and accuracy of methods including smear-microbiology,culture of Mtb and NAAT for Mycobacterium tuberculosis(Mtb)detection in sputum and bronchoalveolar lavage fluid samples were compared.Odds ratios and 95%confidence intervals were used to assess variables that might be associated with positive NAAT results for sputum and bronchoalveolar lavage fluid from patients with suspected PTB.Results:NAAT showed higher sensitivity for Mtb detection(61.1%)when compared with smear(9.0%)and Mtb culture(47.8%).We found that an elevated erythrocyte sedimentation rate,the presence of cavities,and positive interferon-𝛾release assay(IGRA)results were indicative of positive Mtb detection by NAAT.Moreover,individuals who had all three of these characteristics showed an 86%diagnostic positivity for PTB from Mtb detection by NAAT.Conclusions:Our study suggests that an elevated erythrocyte sedimentation rate,a positive IGRA result,and the presence of pulmonary cavities are helpful factors for predicting positive Mtb detection by NAAT.Patients with the three positive clinical markers should undergo NAAT for Mtb detection because they are the most likely individuals to be bacteriologically confirmed as having TB.

An outlook on coronavirus disease 2019 detection methods

Diagnostic testing plays a fundamental role in the mitigation and containment of coronavirus disease 2019(COVID-19),as it enables immediate quarantine of those who are infected and contagious and is essential for the epidemiological characterization of the virus and estimating the number of infected cases worldwide.Confirmation of viral infections,such as COVID-19,can be achieved through two general approaches:nucleic acid amplification tests(NAATs)or molecular tests,and serological or antibody-based tests.The genetic material of the pathogen is detected in NAAT,and in serological tests,host antibodies produced in response to the pathogen are identified.Other methods of diagnosing COVID-19 include radiological imaging of the lungs and in vitro detection of viral antigens.This review covers different approaches available to diagnosing COVID-19 by outlining their advantages and shortcomings,as well as appropriate indications for more accurate testing.

Laboratory diagnosis of nonpolio enteroviruses:A review of the current literature

Infections by nonpolio enteroviruses(EVs)are highly prevalent,particularly among children and neonates,where they may cause substantial morbidity and mortality.Laboratory diagnosis of these viral infections is important in patient prognosis and guidance of clinical management.Although the laboratory diagnosis of non-polio EVs is mainly based on molecular techniques,classical virus-isolation techniques are still used in refer-ence laboratories.Other techniques,such as antigen detection and serology,are becoming obsolete and rarely used in diagnosis.An important part of diagnosis and surveillance of EV infections is viral typing by VP1 gene sequencing using conventional Sanger technique and more recently,full-genome next-generation sequencing.The latter allows the typing of all EVs,better investigation of EV outbreaks,detection of coinfec-tion,and identification of severity markers in the EV genome.