Advantage of precision metagenomics for urinary tract infection diagnostics

Abstract

BackgroundUrinary tract infections (UTIs) remain a diagnostic challenge and often promote antibiotic overuse. Despite urine culture being the gold standard for UTI diagnosis, some uropathogens may lead to false-negative or inconclusive results. Although PCR testing is fast and highly sensitive, its diagnostic yield is limited to targeted microorganisms. Metagenomic next-generation sequencing (mNGS) is a hypothesis-free approach with potential of deciphering the urobiome. However, clinically relevant information is often buried in the enormous amount of sequencing data.MethodsPrecision metagenomics (PM) is a hybridization capture-based method with potential of enhanced discovery power and better diagnostic yield without diluting clinically relevant information. We collected 47 urine samples of clinically suspected UTI and in parallel tested each sample by microbial culture, PCR, and PM; then, we comparatively analyzed the results. Next, we phenotypically classified the cumulative microbial population using the Explify® data analysis platform for potential pathogenicity.ResultsResults revealed 100% positive predictive agreement (PPA) with culture results, which identified only 13 different microorganisms, compared to 19 and 62 organisms identified by PCR and PM, respectively. All identified organisms were classified into phenotypic groups (0–3) with increasing pathogenic potential and clinical relevance. This PM can simultaneously quantify and phenotypically classify the organisms readily through bioinformatic platforms like Explify®, essentially providing dissected and quantitative results for timely and accurate empiric UTI treatment.ConclusionPM offers potential for building effective diagnostic models beyond usual care testing in complex UTI diseases. Future studies should assess the impact of PM-guided UTI management on clinical outcomes.

Analytical Validation of a Highly Accurate and Reliable Next-Generation Sequencing-Based Urine Assay

“…Polymicrobial infections with more than two pathogens are usually considered contamination under the current SOC and reporting of these results as infection is a topic of debate (18). In accordance with other UTI studies employing molecular approaches, about 40 % of clinical specimens tested in this validation showed more than one pathogen detected (83,85,(89)(90)(91)(92). Most clinical algorithms designed for uropathogen detection provide optimal growth conditions for a limited number of microbes and are based on a threshold of 10 5 CFU/mL.…”

Atuação do enfermeiro empreendedor e seus desafios de negócio

“…Algumas razões para isso são a descrição recente da bactéria, o diagnóstico equivocado do real agente infectante por similitude fenotípica a outras bactérias ou imprecisão de métodos bioquímicos (MAHLEN e CLARRIDGE, 2009), a baixa incidência da bactéria tanto como componente da microbiota quanto como agente infeccioso oportunista ( (2018) apontam que o processo de automação laboratorial no cultivo de bactérias demonstrou um significante aumento na taxa de detecção de Alloscardovia omnicolens -dez vezes superior à incidência registrada antes das mudanças de rotina laboratorial -sugerindo que essa espécie pode ser subestimada como patógeno causador de infecções do trato urinário. A disponibilização recente de métodos de diagnóstico baseados em identificação por PCR e análise metagenômica pode auxiliar na real determinação da prevalência de colonização e infecções por essa bactéria (MOUSTAFA et al, 2018;WOJNO et al, 2020;ALMAS et al, 2023). Análises por inteligência artificial da mudança da composição de microbiomas também poderão fornecer informações importantes tanto para a identificação de Alloscardovia omnicolens quanto para o tratamento e dedução de doenças de base em que a predominância da bactéria seja um marcador biológico (KARTAL et al, 2022).…”

Advancing Clinical Microbiology: Applications and Future of Next-Generation Sequencing

“…There is currently no prospective controlled clinical trial data assessing the effectiveness of NGSbased tests for unbiased pathogen detection directly from clinical specimens. The majority of existing literature consists of case reports or retrospective studies that compare the results of diagnostic NGS tests to those of standard care testing [18]. Theoretically, agnostic mNGS could provide a substantial advantage over traditional testing methods in certain patient populations, such as immunocompromised individuals who may be infected with rare or obscure pathogens, or in samples from patients who have previously received antimicrobial treatment, where culture-based tests might yield falsenegative results.…”