Abstract
Background:
Urinary tract infections (UTI) are common and costly, but standard urine culture (SUC) diagnostic tests have significant limitations. Emerging molecular techniques like multiplex polymerase chain reaction (PCR) offer rapid simultaneous detection of uropathogens and antimicrobial resistance (AMR) genes allowing timely targeted therapy.
Objectives:
To compare the performance of Urine-ID™ test, an expanded multiplex PCR panel designed to detect 26 uropathogens and 49 AMR markers against SUC for pathogen detection in individuals with suspected complicated UTI.
Design and methods:
A total of 56 urine specimens from individuals aged 50 and older, who exhibited UTI symptoms and failed previous therapy based on SUC results, were retrospectively analyzed using Urine-ID™ using the TaqMan® OpenArray plates on the QuantStudio 12K Flex Real-Time PCR System. Results of simultaneously collected PCR and SUC were compared at patient follow-ups.
Results:
Of the 56 suspected UTI cases, SUC failed to detect pathogens in 19.64% (N = 11/56) of the specimens while PCR yielded negative results in 7.14% (N = 4/56) of cases. SUC identified a specific organism in 50% (N = 28/56) while PCR detected at least one uropathogen in 92.86% (N = 52/56) of specimens. Data also revealed that a nonspecific result, “Mixed urogenital flora” (MUG), was the most frequent outcome (N = 18/45) obtained with SUC among positive samples. While SUC identified a single pathogen in 92.80% (N = 26/28) of positive specimens, PCR detected additional co-infecting uropathogens in 71.20% (N = 37/52) of positive samples. Of the 18 MUG and 11 negative samples using SUC, PCR identified treatable pathogens in 13 and 7 samples, respectively.
Conclusion:
These results highlight the effectiveness of expanded real-time PCR panels for quickly and accurately identifying uropathogens, surpassing traditional SUC sensitivity. Adopting these advanced molecular techniques, particularly in suspected complicated UTI cases, improves diagnosis efficiency, leading to faster pathogen identification and treatment, ultimately reducing patient morbidity.
Plain language summary
Urinary tract infections (UTIs) are diagnosed as the most common infection worldwide. The American Urological Association (AUA) defines a simple, uncomplicated UTI as an “infection in a healthy, non-pregnant, pre-menopausal female patient with an anatomically and functionally normal urinary tract.” A complicated UTI is defined as any infection outside of this uncomplicated definition, such as in patients with weakened immune systems, pregnant patients, males, and those with abnormalities or conditions affecting the kidneys or other structures of the urinary tract. Complicated UTIs present a higher risk for treatment failure and clinical complications. Standard urine culture (SUC), a methodology that has been in use for over 150 years, continues to be used for UTI testing despite its several limitations. SUC is unable to identify more than one infecting bacteria, fails to grow atypical bacteria on certain culture plates, requires time- and temperature-sensitive collections, and recent antibiotic use can affect results. Our findings suggest that patients who fall under the complicated UTI diagnosis should be considered for urine testing by Polymerase Chain Reaction (PCR) over SUC. Complicated UTIs are typically caused by a wide range of bacteria and involve multiple or drug-resistant pathogens. In our study, utilizing SUC for these infections failed to detect multiple or atypical pathogens, as well as the full spectrum of antibiotic resistance factors that PCR identified. PCR can enhance the accuracy of pathogen detection by identifying the DNA of an organism and its antibiotic resistance genes allowing PCR to detect multiple organisms in even a small amount of urine. Coupled with the fast identification of antibiotic resistance genes, PCR-based UTI testing can help providers treat this subset of patients with the most appropriate medication and ultimately resolve their symptoms quicker to avoid adverse outcomes.
Introduction
Urinary tract infections (UTIs) are common infections responsible for around 7 million visits to healthcare providers annually in the United States.1,2 UTIs are caused by a wide range of pathogens, among which Escherichia coli (E. coli), Klebsiella pneumoniae (K. pneumoniae), Proteus mirabilis (P. mirabilis), Enterococcus faecalis (E. faecalis), and Staphylococcus saprophyticus (S. saprophyticus) are the most frequently found. 3 UTIs impose a substantial burden on public health due to their high prevalence, recurrent nature, and economic implications. 4 In 2019, the economic burden of UTI was estimated to cost at least $1.6 billion annually to the US healthcare system. 5 If not promptly diagnosed and treated, UTIs can lead to a range of complications 4 making accurate and rapid identification of uropathogens essential for effective patient management. While many UTI cases are defined as uncomplicated, patients with weakened immune systems, pregnant patients, males, and those with anatomic or functional urinary tract abnormalities, as examples, can present with complicated UTIs that may involve a variety of pathogenic bacteria. These infections pose a higher risk for treatment failure and clinical complications. 6 In addition, an increase in antimicrobial resistance (AMR) in UTIs is an important public health concern as it limits treatment options and leads to recurrent UTIs. 3
Traditionally, standard urine culture (SUC) has been the gold standard for diagnosing UTIs, relying on the growth of bacterial colonies and subsequent susceptibility testing to determine appropriate antibiotic therapy. 7 However, this method is labor intensive, time-consuming, often taking 48 h or greater for results, and may lead to empirical antibiotic treatment before pathogen identification, contributing to AMR and suboptimal patient outcomes. 7 In recent years, molecular techniques such as Polymerase Chain Reaction (PCR)-based Nucleic Acid Amplification Tests (NAATs) have emerged as promising alternatives to conventional culture-based methods for uropathogen identification. 7 Multiplex PCR testing using a panel targeting UTI-causing pathogens enables simultaneous, rapid, and specific detection of a wide range of uropathogens, including coinfections, potentially reducing the time to diagnosis.8–11 Multiplex PCR panels have further enhanced the ability to detect AMR genes, allowing for timely administration of targeted therapy. 11
There is currently a gap in the literature for studies that directly compare multiplex PCR to SUC when diagnosing UTIs, specifically in patients with complicated infections who have a significantly higher risk of clinical complications. Kapoor et al. 12 discussed in their study that SUC may be an inadequate or insufficient test for patients with a complicated UTI diagnosis. Their data found that urine culture poorly identified fastidious organisms and all causative organisms in a polymicrobial infection. This limitation reduces the clinical utility of SUC, as complicated UTIs are known to have a broader spectrum of pathogens as an etiology and increased AMR. 3
The aim of this study was to evaluate the performance of a laboratory-developed test (Urine-ID™, an expanded PCR panel) against SUC for pathogen detection in patients with suspected complicated UTI. Treatment recommendations based on antimicrobial results obtained using Urine-ID™ and culture-based Minimum Inhibitory Concentration (MIC) assays were also compared.
Materials and methods
Clinical samples
A retrospective analysis was performed for urine samples collected from a cohort of 56 patients over age 50 (35 female and 21 male) who exhibited persistent symptoms of a UTI, such as increased urgency or frequency from baseline, dysuria, painful urination with or without other secondary symptoms such as continued malodorous urine, hematuria, fatigue, fever, feeling of incomplete bladder emptying, lower pelvic discomfort, or low back pain. Samples were collected at a single US academic institution between July 2021 and November 2021. Before being included in the study, all these subjects had initially undergone treatment guided by SUC and antimicrobial susceptibility testing; however, they failed to respond to the primary therapeutic intervention. Individuals currently undergoing antibiotic therapy exclusive of initial UTI treatment, those catheterized or who had undergone genitourinary surgery within the past 30 days, as well as those with a prior diagnosis of interstitial cystitis, a history of pelvic radiation, known stone disease, urothelial carcinoma on Bacillus Calmette-Guerin therapy, and those with indwelling stents were ineligible to participate. Urine samples were collected in sterile containers using the clean catch method or catheterization. All samples were de-identified and simultaneously tested using SUC and Urine-ID™ within 24 h of collection. For each urine sample, one sterile swab was immersed in the urine for subsequent PCR testing using Urine-ID™ while the remaining urine sample was shipped to LabCorp (Columbia, SC, USA) and used for SUC and MIC testing (Figure S1).
PCR testing of urine samples
Nucleic acid extraction was performed using the MagMAX™ Microbiome Ultra Nucleic Acid Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA) on the Microbiome Bead Plate and the King Fisher™ Flex (Thermo Fisher Scientific), according to the manufacturer’s instructions for use. After extraction, real-time PCR testing was performed using Urine-ID™: an expanded PCR panel targeting 26 pathogens and 49 AMR targets using the TaqMan® OpenArray plates (Thermo Fisher Scientific) on the QuantStudio™ 12K Flex Real-Time PCR System (Thermo Fisher Scientific). The PCR reactions were carried out in accordance with the manufacturer’s instructions for use. For pathogen detection, microbial loads in urine samples were determined by extrapolating values within an analytical measurement range, which was established by comparing cycle thresholds (Ct) to known positive control values. The results were reported in copies per microliter, enabling classification into pathogenic versus normal flora. This distinction was based on the highest and lowest numbers, respectively, of copies per microliter (for PCR) or colony-forming units (cfu; for culture). A PCR microbial load exceeding 1000 copies/µL in asymptomatic patients or 100 copies/µL in symptomatic patients was considered positive.
Standard urine culture
SUC was performed at LabCorp according to a routine standard culture protocol (test reference: 008847). Mixed urogenital flora (MUG) is a term used for pathogens identified below the threshold considered positive, set at >10,000 cfu.
MIC assay
MIC was performed at LabCorp according to a standardized protocol.
Sample size calculation
Convenience sampling was done to include all patients with initial treatment failure following SUC-guided treatment who subsequently received PCR-guided therapeutic intervention. No power analysis for sample size calculation was performed.
Statistical analysis
Performance comparison included calculations of positive and negative percent agreements (NPA). NPA was calculated as the ratio between the number of negative results by both the evaluation method and its comparator and the number of negative results by the comparator method, multiplied by 100. Positive percent agreement (PPA) was calculated as the ratio between the number of positive results by both the evaluation method and its comparator and the number of positive results by the comparator method, multiplied by 100. The two-sided 95% confidence intervals were calculated using the Clopper-Pearson method. The study findings are reported following the Standards for Reporting Diagnostic Accuracy (STARD) 2015 guidelines. 13
Results
A total of 56 de-identified urine specimens were collected from individuals experiencing UTI symptoms with previous treatment failure after SUC, and results obtained after testing using Urine-ID™ and SUC are presented in Table 1.
Types of organisms and AMR identified using Urine-ID™ and standard urine culture among all specimens.
AMR, antimicrobial resistance; MUG, mixed urogenital flora.
Of the 56 suspected UTI cases, SUC failed to detect any pathogen in 19.64% (n = 11/56) of the specimens while PCR yielded negative results in only 7.14% (n = 4/56) of the cases (Figure 1(a)). Interestingly, of the 45 samples for which SUC failed to identify a specific pathogen, culture results showed unspecified MUG for 17 samples which accounted for 30.36% of all tested samples (Figure 1(a)). While SUC identified only one pathogen in 92.80% (n = 26/28) of the positive samples, PCR identified additional pathogens commonly associated with UTIs and showed an important incidence of coinfections with 71.20% (n = 37/52) of positive samples testing positive for two or more pathogens on Urine-ID™ (Figure 1(b)).

(a) Positivity rates for at least one organism with Urine-ID™ and standard urine culture. (b) Distribution of mono- and coinfections from samples tested with Urine-ID™ and Standard Urine Culture (not including MUG results).
Overall, Urine-ID™ was able to identify a total of 17 different types of organisms frequently associated with UTI among the positive specimens, whereas SUC identified only 11 different types of organisms in the positive cohort (Table S1). A detailed analysis of the overall relative prevalence of the microorganisms detected using Urine-ID™ among all positive specimens showed that E. faecalis (51.90%) was the most prevalent pathogen followed by E. coli (42.3%), K. pneumoniae (15.4%), and Streptococcus agalactiae (11.5%; Figure 2 and Table S1).

Relative prevalence of organisms identified using Urine-ID™ and standard urine culture among all positive specimens.
Data also revealed that MUG was the most frequent result (40.0%) obtained using SUC while E. coli was detected in 37.8% of the total positive samples (Figure 2). The remaining organisms detected using SUC accounted for less than 15% of all infections and comprised pathogens that had <5% relative prevalence (Figure 2). Although bacterial UTI were the most prevalent, fungal infections were also detected among positive specimens (Figure 2). Interestingly, SUC was unable to specifically identify fungal pathogens and provided a nonspecific result designated as “Yeast” whereas Urine-ID™ was able to differentiate several species of Candida spp., including Candida (C.) albicans and C. glabarta in several samples (Table 1 and Figure 2). Next, the performance of Urine-ID™ was compared to SUC for three of the most prevalent UTI pathogens: E. coli, E. faecalis, and K. pneumoniae and PPA and NPA between the two methods were calculated (Table 2).
Performance comparison of Urine-ID™ and Standard Urine Culture for detection of Escherichia coli, Enterococcus faecalis, and Klebsiella pneumoniae.
Note. Detection thresholds were set at 10,000 CFU for culture and 1000 copies/µL for PCR, reduced to 100 copies/µL for PCR in symptomatic patients.
CFU, colony-forming units; CI, confidence interval; NPA, negative percent agreement; PCR, polymerase chain reaction; PPA, positive percent agreement.
Using the Urine-ID™ method, E. coli was identified in 22/56 samples, for which SUC provided a similar result for only 16 of these infections (Table 2). Similarly, E. faecalis was detected in 27/56 samples using the Urine-ID™ method, while SUC detected this pathogen in only one sample (Table 2). A total of eight samples tested positive for K. pneumoniae on Urine-ID™ while negative using SUC (Table 2). SUC identified one sample positive for K. pneumoniae and one for E. coli that tested negative on Urine-ID™ (Table 2). While Urine-ID™ and SUC showed concordant results for at least one organism in only 33.9% (19/56; Table S2) of the samples, both methods did not agree on the pathogens identified in 66.1% (37/56) of the total samples (Table S3). Pathogen resistance to antimicrobials was also investigated using both methods. Among all positive samples, antimicrobial genes were detected in 40 positive samples (76.9%) using Urine-ID™, whereas 22 positive samples (78.6%) exhibited resistance to one or more antibiotics in culture (Figure S2). Of the eight positive specimens in which PCR and culture identified the same pathogens, similar AMR results (at least partially) were obtained from MIC and AMR for seven samples (Table S4). Importantly, of the 18 MUG and 11 negative samples using SUC, PCR identified positive pathogens in 17 of 18 MUG and 10 of 11 negative samples, as well as relevant AMR genes (Table 1). Regarding the difference in processing times, the average time to result from sample collection to organism identification was shorter using PCR (⩽48 h) as compared to 3–4 days for SUC.
All participants in this study, except for four, exhibited symptom improvement following therapy guided by treatment recommendations derived from PCR results. Of the individuals who did not show symptom improvement, three were female. Among these, two females, despite receiving negative PCR results, were later diagnosed with painful bladder syndrome/interstitial cystitis. The third female’s symptoms resolved after 34 days, with the cause remaining unidentified. The sole male who did not show symptom improvement, was diagnosed with urothelial carcinoma, stage Tis (carcinoma in situ), and was followed up for immunotherapy treatment.
Discussion
Our study demonstrated that Urine-IDTM, an expanded PCR panel, outperformed SUC in detecting pathogens among patients aged >50 years old with suspected UTIs and previous treatment failure. Importantly, Urine-IDTM demonstrated significant advantages in UTI diagnosis, including detecting polymicrobial infections and pathogens missed by SUC, differentiating fungal species, identifying many AMR genes, and delivering faster results than SUC (<48 h for Urine-IDTM vs 3–4 days for SUC), all contributing to enhanced patient outcomes.
In this study, SUC did not detect significant pathogens in 50% of the analyzed samples. Of these, half yielded negative results, and the remaining were classified as MUG, accounting for 30% of all negative samples. In contrast, PCR demonstrated a markedly lower rate of negative results, successfully identifying at least one pathogen in 92.90% of the 56 samples examined. These findings are consistent with prior studies, which demonstrated that PCR exhibits greater sensitivity in detecting pathogens in UTIs compared to SUC.14–16
In individuals aged 50 years and older, our findings showed an increased detection rate of coinfections by PCR, especially compared to the identification of MUG or a single pathogen in SUC. Indeed, the presence of multiple microorganisms in urine culture, often reported as MUG, is commonly interpreted as sample contamination, leaving the clinical relevance of MUG poorly defined. 17 Recent studies have suggested that MUG samples might harbor pathogens associated with UTIs, indicating that the MUG classification could affect patient management decisions. 18 Several studies have reported that up to 39% of UTIs, particularly in the elderly population, are polymicrobial infections, which are often misclassified as contamination or MUG by SUC.18–20 Additional studies have consistently shown that SUC often failed to accurately detect coinfections, which PCR has successfully identified.8,14–16 These findings highlight PCR’s superior sensitivity over culture methods in identifying pathogens, especially in cases of polymicrobial infections. Although evidence seems to indicate that PCR can provide superior detection capabilities, the interpretation of its clinical relevance in cases where multiple organisms are identified, particularly in the presence of mixed flora, can be challenging. Determining the exact causative agent of the UTI becomes complicated, especially in differentiating between commensal organisms, colonization, and true infection. By utilizing quantification to determine thresholds and cut-off values, we were able to distinguish colonization or contamination from active pathogen replication in PCR results.
Several studies have demonstrated that while urine culture is effective in identifying E. coli infections, it may fail to detect various non-E. coli uropathogens, notably K. pneumoniae.21–23 This diagnostic limitation may be clinically significant as undetected K. pneumoniae infections can cause chronic urinary tract symptoms, sepsis, and even death if not promptly treated.21,22 Consistent with previous research, 15 our study found the highest degree of concordance in the detection of E. coli, with PCR identifying it in 22 out of 56 samples, closely paralleled by SUC, which detected E. coli in 17 out of the same 56 samples. Conversely, for K. pneumoniae, there was a notable discrepancy; eight samples tested positive using the Urine-IDTM assay, yet these were not detected as positive in the SUC analysis. Furthermore, our findings revealed that PCR was able to detect E. faecalis in 27/56 samples, while SUC detected this pathogen in only one sample. Others have reported similar findings where SUC failed to identify E. faecalis that was detected by PCR methods.23,24 These results hold significant clinical importance, given that E. faecalis may be an invasive uropathogen with the ability to cause chronic UTIs. 25 In addition, E. faecalis is known to harbor strains that exhibit resistance to multiple drugs, 26 reinforcing the need for precise detection of polymicrobial UTIs. This accurate identification is pivotal for enhancing patient treatment strategies and overall clinical management.
Ureaplasma spp. and Mycoplasma hominis are two fastidious bacteria that are associated with UTIs. They lack cell walls and require special inoculation on A7 agar, which directly tests for the presence of urease, allowing differentiation of Ureaplasma spp. from other mycoplasma. 27 Often, these pathogens are not evaluated in SUC despite their known pathogenesis in recurrent or chronic UTIs and growing antibiotic resistance worldwide. 28
Although less prevalent than bacterial infections, fungal UTIs caused by Candida spp. pose considerable therapeutic and diagnostic challenges for clinicians. 29 Indeed, detection of Candida spp. in urine samples may indicate a more invasive infection that necessitates antifungal therapy. 30 SUC was only able to categorize Candida spp. generically as “yeast” while our PCR method was able to differentiate between different Candida species, including C. albicans and C. glabrata in patient urine samples. Yet, it is essential to differentiate between Candida species to ensure appropriate treatment, as C. albicans may be typically treated with fluconazole, while other non-albicans species, such as C. glabrata and C. krusei, exhibit inherent resistance to this drug, 31 necessitating alternative therapeutic approaches. Therefore, accurate identification of the specific Candida species is essential to guide the most effective therapeutic strategy, addressing the drug resistance challenges and improving patient care.
Given the rising prevalence of multidrug-resistant uropathogens, accurate detection of AMR in pathogens causing UTIs has become increasingly critical. This is especially essential for patients experiencing recurrent or persistent infections while undergoing recent or current antibiotic therapy, as it may allow the administration of a more precise and effective antimicrobial treatment. Unlike SUC, where a patient’s ongoing antibiotic therapy can influence outcomes, PCR may be less susceptible to the impact of antibiotic treatment. Among the evaluated samples in this study, AMR genes were identified in 40 of the PCR-positive samples utilizing PCR, whereas only 22 samples demonstrated antibiotic resistance when assessed using SUC methods. Notably, when the same pathogens were identified by both PCR and SUC, the results pertaining to antibiotic resistance were concordant which is in line with previous findings. 14 These findings underscored the enhanced sensitivity of PCR in identifying AMR, which may be beneficial in guiding clinicians to select the most effective antimicrobial therapy for their patients, thereby contributing to public health improvements by combating AMR. One limitation of the multiplex PCR assay approach, in comparison to routine culture, is that while it can identify resistance genes, many providers have limited training in utilizing these genes to guide patient care. We engaged specialized pharmacists trained in gene identification and utilization to provide treatment guidance in order to overcome this limitation.
Traditionally, uncomplicated UTIs have been treated empirically, often without awaiting culture results. However, studies have suggested that the emergence of resistant uropathogens is affecting the efficacy of this first-line empirical therapy approach. 32 In this context, the fast turnaround time of obtaining diagnostic results for UTI is critical to initiate timely treatment and minimize the risk of antibiotic resistance. In this study, PCR yielded results in less than 48 h compared to 3–4 days for SUC. Importantly, this study included patients with recurrent UTI symptoms, all of whom had previously been diagnosed and treated using SUC methods. Nearly all patients experienced resolution of symptoms, as documented in their follow-up appointments. Notably, within 30 days of treatment, no patients required hospital admission for suspected or confirmed UTI. The rapid turnaround time for results and precise pathogen detection offered by PCR not only led to appropriate therapeutic management, which differed from the initial prescriptions based solely on SUC, but also underscored, along with other studies, the ability of PCR to significantly enhance patient care.11,33 By enabling faster and more accurate therapeutic interventions, PCR can facilitate more effective antibiotic stewardship, ultimately improving clinical outcomes in the treatment of UTIs. A notable limitation of this study is its small sample size, as reflected in the wide confidence intervals obtained in Table 2. Due to the retrospective nature of the study, we were restricted to samples that met the inclusion criteria. Therefore, no power analysis was performed to determine the adequacy of the sample size. Future prospective studies with larger sample sizes and adequate power are needed to narrow the confidence intervals and enhance the statistical confidence in our findings. In addition, specimen collection was confined to a single community-based urology practice at one institution, limiting the generalizability of the results. While we address the clinical value in a specific subgroup of patients aged 50 and above who fail primary therapy with urine culture, are at risk for disease progression, and have persistent symptoms, our findings may not apply to all patients presenting with symptoms of UTI. The substantial benefits of using PCR over SUC for complicated UTI diagnosis, as demonstrated in this study, align with findings from other multi-institutional studies previously cited and contribute to the expanding body of literature. However, it is important to recognize that molecular techniques, unlike urine culture, do not exclusively detect viable or actively replicating organisms. Consequently, interpreting positive PCR findings in the absence of clinical UTI signs and symptoms is challenging and may lead to unnecessary antimicrobial therapy. PCR is not intended for UTI screening or use in patients with asymptomatic or uncomplicated UTI. To avoid overtreatment and reduce the rate of false positive results, PCR methods may benefit from quantification, rather than treatment based solely on qualitative results. This study shows that in clinically symptomatic patients who fail initial therapy using SUC, PCR-based NAATs were beneficial for pathogen identification and subsequent successful therapeutic intervention. Due to the high risk of emergency room visits and hospitalizations with delayed diagnosis and treatment, especially in at-risk populations, utilization of NAATs as a primary diagnostic should be given consideration. In addition to faster and more accurate detection of pathogens, treatment guidance was provided by specialized pharmacists trained in the management of infectious diseases and therapeutic application of antibiotic microbial resistance genes.
Supplemental Material
sj-docx-1-tau-10.1177_17562872251342421 – Supplemental material for Expanded PCR panel for uropathogen identification and treatment recommendations in urinary tract infections
Supplemental material, sj-docx-1-tau-10.1177_17562872251342421 for Expanded PCR panel for uropathogen identification and treatment recommendations in urinary tract infections by Lindsey Leech, Christopher Bigley, Marshall Chew, Ashley Crawford, JeanAnn Vawter and Manish P. Patel in Therapeutic Advances in Urology
Supplemental Material
sj-docx-2-tau-10.1177_17562872251342421 – Supplemental material for Expanded PCR panel for uropathogen identification and treatment recommendations in urinary tract infections
Supplemental material, sj-docx-2-tau-10.1177_17562872251342421 for Expanded PCR panel for uropathogen identification and treatment recommendations in urinary tract infections by Lindsey Leech, Christopher Bigley, Marshall Chew, Ashley Crawford, JeanAnn Vawter and Manish P. Patel in Therapeutic Advances in Urology
Footnotes
References
Supplementary Material
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