Enhancing urinary tract infection diagnosis for negative culture patients with metagenomic next-generation sequencing (mNGS)

Abstract

BackgroundMetagenomic next-generation sequencing (mNGS) is a promising technology that allows unbiased pathogen detection and is increasingly being used for clinical diagnoses. However, its application in urinary tract infection (UTI) is still scarce.MethodsThe medical records of 33 patients with suspected UTI who were admitted to the Second Hospital of Tianjin Medical University from March 2021 to July 2022 and received urine mNGS were retrospectively analyzed. The performance of mNGS and conventional urine culture in diagnosing infection and identifying causative organisms was compared, and the treatment effects were evaluated in terms of changes in urinalyses and urinary symptoms.ResultsIn the detection of bacteria and fungi, mNGS detected at least one pathogen in 29 (87.9%) cases, including 19 (57.6%) with positive mNGS but negative culture results and 10 (30.3%) with both mNGS and culture positive results. The remaining 4 (12.1%) patients were negative by both tests. Overall, mNGS performed better than culture (87.9% vs. 30.3%, P < 0.001). Within the 10 double-positive patients, mNGS matched culture results exactly in 5 cases, partially in 4 cases, and not at all in 1 case. In addition, mNGS detected a broader pathogen spectrum, detecting 26 species compared to only 5 species found in culture. The most abundant bacteria detected by mNGS was Escherichia coli, detected in 9 (27.2%) patients. All anaerobic bacteria, Mycobacterium Tuberculosis and all mixed pathogens were detected by mNGS. The final clinical diagnosis of UTI was made in 25 cases, and the sensitivity of mNGS was significantly higher than culture (100.0% vs 40.0%; P < 0.001) when using the diagnosis as a reference standard; the positive predictive value, negative predictive value and specificity were 86.2%, 100% and 50.0%, respectively. Importantly, targeted antibiotic therapy based on mNGS resulted in significant improvement in urinalyses and urinary symptoms in patients.ConclusionsmNGS is a technology that has shown clear advantages over culture, particularly in the context of mixed infections and UTIs that are difficult to diagnose and treat. It helps to improve the detection of pathogens, guide changes in treatment strategies, and is an effective complement to urine culture.

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, 89–92). 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.…”

“…Like other molecular-based studies, BIOTIA-ID showed increased detection of atypical pathogens including Candida, G. vaginalis, Aerococcus spp., anaerobic bacteria (Prevotella spp.) and fastidious bacteria, organisms not reported with culture-based diagnostics (30,(82)(83)(84)(85). Although the rise of molecular based diagnostics and clinical studies using these technologies have revealed that gram-positive, atypical, or fastidious pathogens account for a larger percentage of cUTI infections, more interventional, and clinical utilization studies are needed to understand the pathogenesis and epidemiology of these understudied microbes (19,62,(86)(87)(88).…”

A case of chronic wounds caused by Sporothrix schenckii infection was rapidly detected by metagenomic next generation sequencing

“…Comparing the performance of mNGS and conventional urine culture in the diagnosis of infection and identification of pathogenic microorganisms, it was found that the detection rate and sensitivity of mNGS were significantly higher than that of culture. In addition, mNGS detected a wider range of pathogens [ 13 ]. In a study on 641 patients with infectious diseases, by comparing the detection efficiency of mNGS and traditional culture method for different pathogens, the positive rate of mNGS was 69.89 %, significantly higher than that of traditional culture 22.31 % [ 14 ].…”

Molecular Diagnostics for Invasive Fungal Diseases: Current and Future Approaches

“…With regards to urine, in a single centre study of 33 patients from China, mNGS detected at least 1 pathogen in 29 (97.9%) cases, of which four instances of fungus (3 species-Talaromcyes marneffei, C. parapsilosis and C. albicans twice) were identified [216].…”