Microbiology Spectrum

Ziehl-Neelsen (ZN) smear microscopy remains central to tuberculosis (TB) diagnosis and treatment monitoring, yet its sensitivity is limited by incomplete recovery of Mycobacterium tuberculosis during pre-analytical processing. This study evaluated whether modifying centrifugation force and duration improves bacillary recovery and ZN smear performance. Laboratory experiments were conducted using M. tuberculosis H37Rv and pulmonary TB sputum samples. Following NALC-NaOH decontamination, samples we...

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...

ObjectiveUrine cultures are frequently requested at an early stage in primary care and outpatient settings, often without a comprehensive clinical assessment. This practice increases healthcare costs and laboratory workload and may lead to misleading results due to asymptomatic bacteriuria and specimen contamination. This study aimed to evaluate whether routinely reported microscopic urinary leukocyte findings can predict urine culture positivity under real-world clinical conditions. The distri...

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...

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...

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...

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...

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 ...

IntroductionSequence-based typing (SBT) has been the standard molecular typing method for understanding Legionella pneumophila genetic relationships. However, genome-scale typing approaches, namely core-genome (cg) or whole-genome (wg) multilocus sequence typing (MLST), provide higher discriminatory power. To advance these capabilities, the Legionella International Typing (LIT) workgroup was established to develop, evaluate, and disseminate a novel cgMLST schema with enhanced wgMLST resolution f...

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...

Shigella flexneri 2a is the most common cause of shigellosis, a major public health concern in developing countries. Rapid and reliable diagnostic tools are critical for timely outbreak detection and management. Leveraging Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology, we developed a CRISPR-Cas12a-based assay for the rapid and specific detection of S. flexneri 2a and validated its performance using stool specimens from patients. Two guide RNAs targeting the gtrII ...

BackgroundHousehold contact investigation for tuberculosis (TB) is limited by referral for clinic-based testing services. We evaluated the performance of in-home tongue swab (TS) testing among symptom-agnostic household contacts (HHC) to inform HCI screening strategies. MethodsWe conducted a prospective cohort study among HHC of TB patients in Eastern Cape, South Africa. In-home testing of sputum and TSs, with TSs pooled from up to three HHCs, was performed using Xpert Ultra on portable GeneExp...

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...

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...

ObjectivesTo quantify how urine sample type and polymicrobial context impact antimicrobial resistance (AMR) in urinary tract infections (UTIs), using routine diagnostics at scale. MethodsIn this retrospective, single-centre study, we analysed 188,687 urine cultures from the Institute of Medical Microbiology, University of Zurich, Switzerland (January 2015 to May 2023). We compared midstream urine (MU), indwelling catheter (IDC), and intermittent catheter (IMC) samples. Samples were classified a...

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...

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...

BackgroundThe never-ending emergence of superbugs casts a shadow over the victorious age of antibiotics. In fact, the triumph of antibiotics was previously viewed in retrospection as our final victory over bacteria. Bacteria like Klebsiella pneumoniae, Acinetobacter baumannii, and Escherichia coli are now raising an alarming number of infections across hospitals and communities around the globe. The objective was to evaluate the implications for antimicrobial stewardship based on identifying the...

Carbapenem-resistant (CR) bacteria have emerged and been spreading beyond healthcare-associated facilities into the environment. It is recognized that toilet bowl water in patient rooms of healthcare-associated facilities can be one of internal reservoirs of CR bacteria. In accordance with this idea, toilet bowl water samples were collected from patient rooms in a tertiary healthcare-associated facility in North Macedonia, and meropenem (MEM)-resistant bacterial isolates were obtained from the t...

BackgroundClostridium perfringens can cause life-threatening extraintestinal infections in immunocompromised patients, an area in which we have little information regarding strain factors that impact patient risks and outcomes. MethodsWe conducted genomic-epidemiologic analyses on C. perfringens isolates from 70 patients seen at Brigham and Womens Hospital over 2021-2024. Genomic analyses evaluated strain profiles within a broader context of 2,321 C. perfringens genomes from foodborne, veterina...