Selective media and real-time PCR improves diagnosis of melioidosis in community-acquired pneumonia in a low-incidence setting in Kuala Lumpur, Malaysia

Rhinovirus/enterovirus was the most common respiratory virus detected in adults with severe acute respiratory infections pre-COVID-19 in Kuala Lumpur, Malaysia

Background

Severe acute respiratory infections (SARI) pose a great global burden. The contribution of respiratory viruses to adult SARI is relatively understudied in Asia. We aimed to determine viral aetiology of adult SARI patients in Kuala Lumpur, Malaysia.

Methods

The prevalence of 20 common (mainly viral) respiratory pathogens, and MERS-CoV, SARS-CoV and 5 bacterial select agents was investigated from May 2017 to October 2019 in 489 SARI adult patients in Kuala Lumpur, Malaysia, using molecular assays (Luminex NxTAG-RPP kit and qPCR assays). Viral metagenomics analysis was performed on 105 negative samples.

Results

Viral respiratory pathogens were detected by PCR in 279 cases (57.1%), including 10 (2.0%) additional detections by metagenomics analysis. The most detected viruses were rhinovirus/enterovirus (RV/EV) (49.1%) and influenza virus (7.4%). Three melioidosis cases were detected but no SARS-CoV, MERS-CoV or other bacterial select agents. Bacterial/viral co-detections and viral co-detections were found in 44 (9.0%) and 27 (5.5%) cases respectively, mostly involving RV/EV. Independent predictors of critical disease were male gender, chronic lung disease, lack of runny nose and positive blood culture with a significant bacterial pathogen. Asthma and sore throat were associated with increased risk of RV/EV detection, while among RV/EV cases, males and those with neurological disease were at increased risk of critical disease.

Conclusions

Prior to the COVID-19 pandemic, the high prevalence of respiratory viruses in adults with SARI was mainly attributed to RV/EV. Continued surveillance of respiratory virus trends contributes to effective diagnostic, prevention, and treatment strategies.

Diagnosis of melioidosis: the role of molecular techniques

Melioidosis is an emerging infectious disease with an estimated global burden of 4.64 million disability-adjusted life years per year. A major determinant related to poor disease outcomes is delay to diagnosis due to the fact that identification of the causative agent Burkholderia pseudomallei may be challenging. Over the last 25 years, advances in molecular diagnostic techniques have resulted in the potential for rapid and accurate organism detection and identification direct from clinical samples. While these methods are not yet routine in clinical practice, laboratory diagnosis of infectious diseases is transitioning to culture-independent techniques. This review article aims to evaluate molecular methods for melioidosis diagnosis direct from clinical samples and discuss current and future utility and limitations.

Systematic review and meta-analysis of diagnostic tests for diagnosis of melioidosis

OBJECTIVES

Melioidosis is an emerging tropical disease caused by B. pseudomallei that can rapidly prove fatal and require prompt and appropriate antibiotic treatment. Diagnosis currently relies on culture; however, this delays appropriate antibiotics and contributes to mortality as results can take up to one week or more. Several non-culture based diagnostic tests are available; however, their role remains a point of contention. This review was performed to characterise the accuracy of various diagnostic tests.

METHODS

Medline/Pubmed, CINAHL, Informit, Scopus, The Cochrane Library, Web of Science and Embase databases were searched from inception to April 2020. Clinical trials investigating diagnostic tests capable of providing results in ≤48 hours using samples from suspected human cases; with bacterial culture as the reference test, and reporting sensitivity and specificity were eligible for inclusion. Data was pooled using bivariate analysis for diagnostic tests reported in ≥4 studies.

RESULTS

22 publications comprising 10963 individual tests were included. Meta-analysis was able to be performed for immunofluorescence assay (sensitivity 63.8% [95% CI, 45.6-78.7%]; specificity 99.4% [95% CI, 97.2-99.9%]), polymerase chain reaction (sensitivity 77.1 [95% CI, 20.8%-97.8%]; specificity 99.8 [95% CI, 91.6%-100.0%]) and lateral flow immunoassay (sensitivity 58.2% [95% CI, 34.1%-78.9%]; specificity 95.0% [95% CI, 93.3%-96.3%]). Measures of sensitivity were overall similar although specificity of immunofluorescence assay was statistically superior to lateral flow immunoassay. There was a trend for reduced sensitivity of direct detection methods applied to blood samples compared to other sample types, although statistically insignificant. Serological methods were unable to be meta-analysed due to an insufficient number of studies, but their sensitivities were generally higher than direct detection methods (median 84% [IQR 71.5-88%] vs 51% [IQR 39-79%]), however they lacked specificity compared to direct detection (median 82% [IQR 70-86%] vs 98% [IQR 95-100%]).

CONCLUSIONS

Overall, no method showed sensitivity and specificity which would allow it to substitute culture. Serological tests may play a role in ruling out infection in endemic regions given their higher sensitivity, with direct detection methods being used for diagnostic confirmation. Further research into cost-effectiveness and implementation studies are required before diagnostic tests can be introduced clinically in the detection of melioidosis.