Letter to the Editor: Diagnostic Criteria in Urological Diseases do not Always Match with Findings by Extended Culture Techniques and Metagenomic Sequencing of 16S rDNA

Application of metagenomic next-generation sequencing in the diagnosis of urinary tract infection in patients undergoing cutaneous ureterostomy

Objective

Urinary tract infection (UTI) is an inflammatory response of the urothelium to bacterial invasion and is a common complication in patients with cutaneous ureterostomy (CU). For such patients, accurate and efficient identification of pathogens remains a challenge. The aim of this study included exploring utility of metagenomic next-generation sequencing (mNGS) in assisting microbiological diagnosis of UTI among patients undergoing CU, identifying promising cytokine or microorganism biomarkers, revealing microbiome diversity change and compare virulence factors (VFs) and antibiotic resistance genes (ARGs) after infection.

Methods

We performed a case-control study of 50 consecutive CU patients from December 2020 to January 2021. According to the clinical diagnostic criteria, samples were divided into infected group and uninfected group and difference of urine culture, cytokines, microorganism, ARGs and VFs were compared between the two groups.

Results

Inflammatory responses were more serious in infected group, as evidenced by a significant increase in IFN-α (p=0.031), IL-1β (0.023) and IL-6 (p=0.018). Clinical culture shows that there is higher positive rate in infected group for most clinical pathogens like Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, Candida auris etc. and the top three pathogens with positive frequencies were E. coli, K. pneumoniae, and Enterococcus faecalis. Benchmarking clinical culture, the total sensitivity is 91.4% and specificity is 76.3% for mNGS. As for mNGS, there was no significant difference in microbiome α- diversity between infected and uninfected group. Three species biomarkers including Citrobacter freundii, Klebsiella oxytoca, and Enterobacter cloacae are enriched in infected group based on Lefse. E. cloacae were significantly correlated with IL-6 and IL-10. K. oxytoca were significantly correlated with IL-1β. Besides, the unweighted gene number and weighted gene abundance of VFs or ARGs are significantly higher in infected group. Notablely, ARGs belonging to fluoroquinolones, betalatmas, fosfomycin, phenicol, phenolic compound abundance is significantly higher in infected group which may have bad effect on clinical treatment for patients.

Conclusion

mNGS, along with urine culture, will provide comprehensive and efficient reference for the diagnosis of UTI in patients with CU and allow us to monitor microbial changes in urine of these patients. Moreover, cytokines (IL-6, IL-1β, and IFN-a) or microorganisms like C. freundii, K. oxytoca or E. cloacae are promising biomarkers for building effective UTI diagnostic model of patients with CU and seriously the VFs and ARGs abundance increase in infected group may play bad effect on clinical treatment.

Epidemiology, definition and treatment of complicated urinary tract infections

UTIs are amongst the most frequent bacterial infections. However, the clinical phenotypes of UTI are heterogeneous and range from rather benign, uncomplicated infections to complicated UTIs (cUTIs), pyelonephritis and severe urosepsis. Stratification of patients with UTIs is, therefore, important. Several classification systems exist for the description and classification of UTIs, with the common rationale that cUTIs have a higher risk of recurrence or chronification, progression or severe outcome than uncomplicated UTIs. The pathophysiology and treatment of cUTIs and pyelonephritis are driven more by host factors than by pathogen attributes. cUTIs and pyelonephritis are associated with high antimicrobial resistance rates among causative pathogens. However, antimicrobial resistance rates can differ substantially, depending on the population being studied and whether the data being analysed are from surveillance studies, registry data or interventional studies, in which specific inclusion and exclusion criteria are used for patient selection. For example, antibiotic resistance rates are higher in patients with urosepsis than in those with less severe infections. Thus, treatment outcomes differ substantially among studies, ranging from 50% to almost 100% clearance of infection, depending on the patient population analysed, the UTI entities included and the primary outcome of the study. Pyelonephritis and cUTIs have emerged as infection models for the study of novel antibiotics, including extensive investigation of novel substances active against Gram-negative bacteria.

Usefulness of next-generation DNA sequencing for the diagnosis of urinary tract infection

Acute urinary tract infection (UTI) is a highly common clinical condition. Although bacterial culture is the gold standard diagnostic test, false negative results may be possible, leading to the pathogen being unidentified. In recent years, bacterial DNA sequencing analysis has garnered much attention, but clinical studies are rare in Japan. In this study, we assessed the usefulness of next-generation DNA sequencing (NGS) analysis for acute UTI patients. We thus performed an observational, retrospective case series study. Urine and blood samples were collected from ten acute UTI patients, of whom four had also been diagnosed with urosepsis. Seven variable regions of bacterial 16S rRNA genes were amplified by PCR and then sequenced by IonPGM. The identified bacterial species were compared with those identified using the culture tests and the clinical parameters were analyzed. As a result, the NGS method effectively identified predominant culture-positive bacteria in urine samples. The urine NGS also detected several culture-negative species, which have been reported to be potentially pathogenic. Out of four urosepsis cases, three were pathogen-positive in blood NGS results, while two were pathogen-negative in blood culture. In one sepsis case, although blood culture was negative for Escherichia coli, this species was detected by blood NGS. For non-sepsis cases, however, blood NGS, as well as blood culture, was less effective in detecting bacterial signals. In conclusion, NGS is potentially useful for identifying pathogenic bacteria in urine from acute UTI patients but is less applicable in patients who do not meet clinical criteria for sepsis.

Metagenomics in diagnosis and improved targeted treatment of UTI

INTRODUCTION

The genomic revolution has transformed our understanding of urinary tract infection. There has been a paradigm shift from the dogmatic statement that urine is sterile in healthy people, as we are becoming forever more familiar with the knowledge that bacterial communities exist within the urinary tracts of healthy people. Metagenomics can investigate the broad populations of microbial communities, analysing all the DNA present within a sample, providing comprehensive data regarding the state of the microenvironment of a patient's urinary tract. This permits medical practitioners to more accurately target organisms that may be responsible for disease-a form of 'precision medicine'.

METHODS AND RESULTS

This paper is derived from an extensive review and analysis of the available literature on the topic of metagenomic sequencing in urological science, using the PubMed search engine. The search yielded a total of 406 results, and manual selection of appropriate papers was subsequently performed. Only one randomised clinical trial comparing metagenomic sequencing to standard culture and sensitivity in the arena of urinary tract infection was found.

CONCLUSION

Out of this process, this paper explores the limitations of traditional methods of culture and sensitivity and delves into the recent studies involving new high-throughput genomic technologies in urological basic and clinical research, demonstrating the advances made in the urinary microbiome in its entire spectrum of pathogens and the first attempts of clinical implementation in several areas of urology. Finally, this paper discusses the challenges that must be overcome for such technology to become widely used in clinical practice.

Presence of anaerobic bacteria in the urinary tract of catheterized ICU patients

The purpose of our study was to examine the extent of anaerobic bacteriuria in catheterized patients in the intensive care unit (ICU) and to search for risk factors for anaerobic bacteriuria. A urine culture was collected from each patient every 2 days during their ICU stay and incubated under aerobic and anaerobic conditions. Aerobic and anaerobic blood cultures were collected as well. Demographic, clinical, and laboratory data were collected from patient files. Ninety patients were included in this study, 32 women (35.6%) and 58 men (64.4%). A total of 663 cultures were obtained. Twenty-three patients (25.6%) had growth of anaerobic bacteria in a urinary culture at some point during ICU stay, with Bifidobacterium being the most common pathogen. Aerobic urinary cultures were positive in 38 patients (42.2%). A significant statistical correlation was found between the presence of aerobic and anaerobic bacteria in urine culture (p = 0.0004). Treatment with glycopeptides was found to be inversely associated with anaerobic bacteriuria (p = 0.0292), and treatment with imidazoles was associated with an increased risk of anaerobic bacteriuria (p = 0.0186). None of the patients developed bacteremia with the same anaerobic pathogen that was isolated from their urine. Anaerobic bacteriuria is a common phenomenon in catheterized patients in the ICU. Further studies are needed in order to define the clinical significance of these findings in such patients and in other patient groups as well as in healthy people.