Journal of Clinical Microbiology

Over-the-counter (OTC) lateral flow tests for respiratory viruses have newly emerged since the beginning of the coronavirus disease 2019 (COVID-19) pandemic and are increasingly available to consumers. While all marketed tests have met standards for Emergency Use Authorization (EUA), De Novo classification or 510(k) clearance, limited data are available to inform consumers of their relative performance. We performed a head-to-head benchtop analytical assessment of OTC tests available for purchas...

ObjectiveThe rapid availability of phenotypic antimicrobial susceptibility results is crucial for the timely detection of multidrug-resistant Gram-negative organisms and for guiding optimized treatment strategies. Recently, novel methods have been introduced that enable direct antimicrobial susceptibility testing (AST) from positive blood cultures. However, their performance has not yet been systematically compared in head-to-head evaluations. This study aimed to assess the analytical performanc...

BackgroundClinical metagenomics (CMg) offers high-throughput respiratory pathogen detection with a wider range than targeted, probe-dependent diagnostics. Sequencing cost and the challenges of high host biomass in non-invasive samples are barriers to the use of CMg in high-throughput respiratory pathogen detection. MethodsWe optimised a long-read sequencing workflow to detect RNA viruses in nasopharyngeal swabs, employing pathogen enrichment and ONT sequencing. As a pre-requisite for agnostic p...

Influenza A, Influenza B, SARS-CoV-2, Respiratory Syncytial Virus and other respiratory pathogens are an ongoing public health concern. The ability to rapidly identify these viruses early in infection is essential for effective treatment and outbreak control. The AMDI Fast PCR Mini Respiratory Panel (MRP) incorporates sample preparation and real-time RT-PCR for detection of Flu A, Flu B, SARS-CoV-2 and RSV from anterior nasal swab (ANS) specimens in less than 10 minutes at the point of care. We ...

Clostridioides difficile (C. diff) is a leading cause of hospital-acquired infections with severity ranging from mild diarrhea to fulminant colitis and death. Current antigen tests lack adequate sensitivity and DNA-based nucleic acid amplification tests (DNA-NAATs) exhibit limited specificity for active infection, leading to either underdiagnosis or inappropriate treatment of colonized individuals. Unlike DNA, mRNA is expressed only by metabolically active bacteria and is rapidly hydrolyzed, pro...

BackgroundTalaromycosis, caused by the fungus Talaromyces marneffei, is a leading cause of HIV-associated death in Southeast Asia. Current culture-based diagnosis only identifies late-stage infection, limiting understanding of disease burden and disease spectrum. We evaluated the clinical performance of anti-Mp1p IgM and IgG enzyme immunoassays (EIA) for talaromycosis diagnosis. MethodsThis diagnostic study included 423 adults with advanced HIV disease and culture-confirmed talaromycosis as cas...

BackgroundMpox has spread to 35 countries in Africa, yet many face challenges achieving nationwide PCR-based testing due to cost and limited access in remote and rural areas. Point-of-care antigen-based rapid diagnostic tests (AgRDTs) may help improve diagnostic access. ObjectivesTo evaluate the diagnostic accuracy of five mpox AgRDTs manufactured by Beijing Hotgen Biotech (China), Contipharma (Belgium), Hangzhou Testsea Biotechnology (China), Guangdong Wesail Biotech (China), and NG Biotech (F...

BackgroundsFollowing an increase in mpox clade Ib cases in several African countries, the World Health Organization recognized mpox as a public health emergency of international concern, highlighting the need for reliable and accessible diagnostic tools. As several mpox clades are co-circulating in endemic countries, the analytical sensitivity of diagnostic assays should be evaluated for all of them in a comparative manner. MethodsThis study evaluated the analytical sensitivity of three rapid t...

The COVID-19 pandemic led to significantly disrupted tuberculosis case detection and management. Additionally, overlapping symptoms, radiological findings and risk factors make differentiating tuberculosis and COVID-19 disease difficult. We conducted a prospective multicentre diagnostic accuracy study to determine sensitivity, specificity and operational characteristics of the Truenat MTB Ultima/COVID-19 assay, using a combined sputum plus nasopharyngeal swab specimen, in a single multiplex mol...

BackgroundMycobacterium tuberculosis (Mtb) genomic epidemiology often relies on culturing patient sputum, a time and labor-intensive process. Hybrid capture approaches have been successfully used to enrich Mtb DNA from complex clinical samples, yet the accuracy of variant identification from captured samples has not been systematically evaluated. MethodsWe created artificial strain mixtures of two well-characterized Mtb isolates such that the minor strain comprised 0-50% of Mtb DNA and serially...

BackgroundThe effectiveness of current drug-resistant tuberculosis (DR-TB) regimens is limited by the absence of rapid diagnostics that comprehensively predict resistance to included drugs. Next-generation sequencing (NGS), through culture-free targeted sequencing (tNGS) and culture-based whole-genome sequencing (cWGS) of the Mycobacterium tuberculosis complex (MTBC), offers a powerful framework for precision diagnosis, surveillance, and trial applications. We evaluated two novel assays enabling...

We evaluated the BOSCH Vivalytic MPXV assay using serial dilutions of monkeypox virus clade Ib, a new offshoot of clade I identified in 2023. The assay detected viral DNA down to [~]100 copies/mL demonstrating comparable analytical sensitivity to our in-house reference PCR and to other commercial platform-based mpox molecular assays.

BackgroundAccurate and comparable human papillomavirus (HPV) testing is essential for HPV vaccine research, HPV surveillance, and cervical cancer screening. In 2008, the WHO HPV Laboratory Network initiated global HPV proficiency testing traceable to International Standards (IS), which has been issued regularly since. Here, we summarize recent results and trends over time. MethodsThe HPV genotyping panel, used since 2008, consists of 43 blinded samples, including HPV 6, HPV 11, all oncogenic an...

Severe Acute Respiratory Infection (SARI) remains a major global health burden, yet conventional diagnostics frequently fail to identify the causative pathogens. This study aimed to comprehensively characterize the respiratory microbial landscape in adult SARI and to evaluate the clinical utility of an optimized long-read metagenomic next-generation sequencing (mNGS) workflow. A total of 101 respiratory specimens from hospitalized adults in northern Thailand (November 2023 to April 2024) were an...

BackgroundTransfusion-transmitted malaria remains a concern in non-endemic regions due to asymptomatic parasitemia in donors with prior residence in or travel to malaria-endemic areas. Nucleic acid testing (NAT)-based screening has been proposed to mitigate this risk, and supplemental assays are needed to confirm reactive donations. We developed a pan-Plasmodium reverse transcription quantitative PCR (RT-qPCR) assay with species identification capability as a supplemental tool for malaria donor ...

BackgroundNeutralising antibody titres are widely used as key immunogenicity endpoints in Ebola virus (EBOV) vaccine and monoclonal antibody clinical trials. However, direct comparison of results across studies remains challenging due to the use of heterogeneous neutralisation platforms, ranging from pseudotyped viruses to live EBOV assays. These limitations restrict assay standardisation, validation, scalability, and compliance with good clinical laboratory practice (GCLP), particularly in outb...

BackgroundNeonatal IgM antibodies reflect an in-utero immune response to Treponema pallidum and may offer added diagnostic value. This study evaluated the test performance of treponemal IgM levels measured by the research-use-only (RUO) DPP Syphilis TnT point-of-care (POC) assay for CS risk stratification. MethodsConducted from May 2023 to May 2025, this study tested neonatal serum samples from infants born to mothers with syphilis using the DPP Syphilis TnT RUO POC assay, which reports trepone...

BackgroundShigella causes severe diarrheal disease, and S. flexneri and S. sonnei are the targets for multivalent vaccine development. Culture-based agglutination has been the gold standard for serotyping, but it is limited by logistics, subjectivity, and the availability of antisera for emerging serotypes. Newer methods, including a qPCR-based approach and whole-genome sequencing offer alternatives, but their performance in Shigella endemic populations are not well documented. MethodsShigella ...

Mycobacterium tuberculosis (MTB) disease is a major global health threat with most tuberculosis (TB) cases occurring in low-and middle-income countries (LMIC) with limited healthcare infrastructure. Near-point-of-care testing which can be deployed at peripheral clinical settings is needed to start treatment earlier and thereby improve treatment outcomes. Here we report the development and preliminary characterization of an MTB detection assay that utilizes tongue swab or sputum specimens for The...

BACKGROUNDDiagnostic performance of tongue swab Mycobacterium tuberculosis PCR has been evaluated for facility-based triage of symptomatic tuberculosis (TB). It is unknown whether tongue swab performance differs for detection of asymptomatic TB in community-based screening. METHODSTongue swabs were collected from adult household contacts of TB patients (HHC Cohort), and symptomatic adults presenting to clinics with presumptive TB (Clinic Cohort), at eight South African sites. TB Cases were defi...