Methods and early findings from a study comparing next-generation sequencing versus traditional cultures for penile implants concerning for low-grade infection

Introduction

Penile implant infections are a rare yet detrimental complication that cause loss of sexual function, physical and emotional morbidity, and increased healthcare costs (1). Inflatable penile prostheses (IPPs) have been used to treat erectile dysfunction since 1973, with in recent years, the annual number of IPP surgeries has risen to an estimated 25,000 implantations in the United States per year per industry sources. Infections occur in less than 3% of primary cases, but rates increase significantly in revision surgeries, with reported infection rates ranging from 3% to as high as 25% (1,2). In addition, a systematic review of post-implantation infection showed rates ranging from 0% to 24.6% across all series (3). Due to such findings, preventing infection following implantation of IPPs remains a primary concern (4). Although IPP infection is considered a catastrophic outcome for patients, there is limited published data on optimal prevention strategies, clinical classification, and conservative management of low-grade infections (3,4). Furthermore, even use of peri-operative antibiotic recommendations provided by the American Urologic Association results in higher risk of infection compared to nonstandard antibiotic regiments (5).

Several techniques are employed to minimize infection risk, including thorough history and physical exams to rule out active infections, broad-spectrum antimicrobial prophylaxis, alcohol-based skin preparation, infection-resistant coated implants, minimizing skin contact, and performing revision washout procedures (6). Despite these precautions, infections still occur. Furthermore, 30% to 50% of IPPs removed due to clinical infection are found to be culture-negative (7); thus, no causative organism is identified.

Traditional culture is the current standard for determining the best antibiotic therapy. Next-generation sequencing (NGS) of DNA provides a rapid and thorough analysis of biofilm composition, not only to identify microorganisms, but also determine relative abundance of specific microorganisms, which culture cannot. The relative abundance measure contributes a new way to evaluate infections by determining which isolate is the majority present (most abundant) at the time of infection. For example, the NGS technique using 16S ribosomal RNA molecular identification, has detected bacteria in blood cultures or in previously concealed anaerobic bacteria in prosthetic joint infections (8,9).

The main goals of this ongoing study are to characterize presentations of penile implants concerning for low-grade infection and to evaluate whether NGS, compared to microbial culture, can better guide the management, antibiotic selection and device survival rates. In the present study, we describe the overall study methodology and analyze device survival rates, classify clinical presentations of IPP infections, and determine infected implant microbial composition and antibiotic resistance among an early cohort of patients.

Methods

Study subjects included male patients aged 18 to 80 years who had received antimicrobial treatment for at least 7 days without surgical replacement for IPPs concerning for low-grade infection, occurring within 6 months of penile prosthesis implantation. For inclusion in this ongoing prospective study, patients must present with at least one of the following: device part stuck to thinning skin; any drainage from the wound site; red and swollen genitalia; exposed penile prosthesis parts; draining open tract; or draining hematoma. Participants were not included if they were non-compliant; had device removal surgery within 7 days of enrollment; had an active addiction; or had implant pain as their primary issue. Patients also were not included if they were unable to sign their own consent, if they were not healthy enough for general anesthesia, or if antibiotics were initiated prior to collection of samples. There were no restrictions based upon race or ethnic origin, and none of the subjects were vulnerable, toxic, or septic. Samples will be collected upon clinic presentation prior to initiating antibiotics. The study was conducted in accordance with the Declaration of Helsinki and its subsequent amendments. This study has been approved under the institutional review board (IRB) number Pro00055322 by Advarra.

A minimum of 40 subjects will be enrolled. Enrollees will be randomized using Captivate by ClinCapture to one of two analytic arms specific to the method used for identifying microbiome: standard-of-care traditional culture or NGS. This randomization is done to ensure that there is no bias in terms of participant selection for each analytic arm. All patients are started on empiric antibiotics as agreed to by the principal investigators (PIs) in the protocol after samples have been collected. For the traditional culture arm, the treating urologist will prescribe antibiotics as they have traditionally done. Patients start on the protocol empiric antibiotic (first choice trimethoprim-sulfamethoxazole followed by amoxicillin/clavulanate and levofloxacin if allergies present), then with known culture results, the local PI will adjust the antibiotic accordingly. In contrast, patients randomized to the NGS arm will not have their NGS data shown to the local treating PI after starting the same empiric protocol antibiotics. An infectious disease (ID) specialist will have access to the NGS results and will recommend antibiotic treatments; the local PI will treat patients randomized to the NGS arm based on antibiotic recommendations adjusted for patients’ contraindications and co-morbidities. This blinding of data was agreed upon by all PIs to keep physicians unbiased, and to ensure the most accurate analyses.

Figure 1 details the flow of subjects throughout the study. The first step is to collect samples and start empirical treatment for infected IPPs. Then, participants are divided into two separate arms: standard-of-care microbial cultures and NGS. Specimens for culture were sent to the local hospital laboratory for routine evaluation. Specimens for NGS testing were stored in sterile containers and shipped overnight at ambient temperature to MicroGenDX for analysis (Lubbock, TX, USA). MicroGenDX is a College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA) certified high-complexity molecular diagnostic laboratory, and contaminant screening by technicians in comparison to extraction and polymerase chain reaction (PCR) controls was conducted for each sample. At MicroGenDX, total genomic DNA was extracted, and PCR amplifications and quantification for each micro-organism were conducted as previously described (10,11). Bioinformatic processing of sequences was the same as was described previously using Usearch7, UCHIME, and PEAR analysis tools (10,11). The relative abundances of species detected at greater than 2% are provided on resulting clinical reports and were used for subsequent analyses. In the standard-of-care arm, positive culture analysis will follow local standards of care, while negative cultures will continue empirical treatment for 2 weeks or be treated as clinically indicated. In the NGS arm, patients with a positive NGS will be given tailored antimicrobial therapy by the central ID; the clinician will follow antibiotic and dosage instructions from the ID. NGS patients with a negative result will continue empiric treatment for 2 weeks or be treated as clinically indicated. Throughout the study, investigators and patients will complete questionnaires to compare the patient outcomes between both arms. All patients will fill out safety and compliance questionnaires as well as a score card within 10 days of starting antibiotic therapy. All patients will be followed up for their status at 6 months after the baseline visit by filling out a scorecard as well. In all cases where the patient deteriorates, they will be taken to the operating room for removal or salvage/rescue where additional culture and NGS samples will be obtained to determine replacement/revision microbial composition and resistance data in the surgical setting, among clinically infected patients. Afterwards, a surgeon’s questionnaire is completed, followed by local standard of care.

Figure 1 Methodology comparing samples analyzed by standard culture versus NGS. ID, infectious disease; NGS, next generation sequencing; OR, operating room.

Relative abundances of identified bacterial species will be calculated as the proportion of sequence reads that were assigned to each species. The threshold for retaining species for statistical comparison will be a study-wide average species relative abundance of 0.5% percent. Bacterial species will be summarized by ranking the proportion of samples in which species occur and their average relative abundance. The ability of culture to detect the bacterial species will be assessed by categorizing NGS-detected species into rare (0.5–1%), common (2–10%), and dominant (>10%) for each sample and tabulating the percentage of samples in which the culture-detected species fall into each category. Binomial probability tests will assess how well culture detects dominant species. Significant differences in primary endpoints between the NGS arm and the standard-of-care arm will be assessed using analysis of variance or non-parametric analog analysis depending on variance structure and data normality.

Through analysis of microbial composition, device survival, patient questionnaires, and score cards, we will analyze outcomes of treatment guided by NGS versus traditional cultures. With the final total sample of patients’ data, certain antibiotics may be shown to be more effective for optimal patient outcomes and clinical presentations of infections may ultimately define a clinical standard.

Results

Nine patients are presented to date; more subjects are being added and followed. Table 1 offers a detailed overview of subject data. All 9 subjects gave consent to having outcomes evaluated for this study. Out of 9 subjects, 6 were seen in the clinic while 3 were seen in the hospital/emergency department; 8 out of 9 subjects reported white/Caucasian race. Only two subjects had prior implants; thus, the implants studied herein were replacements. Clinical symptoms presented most frequently at the pump site compared to the cylinders and reservoir (Figure 2). Drainage and swelling were both common, with all patients displaying at least 1 of these traits (Figure 3 and Table 2). Empiric antibiotics were recorded as follows: Augmentin was prescribed to 4 patients; Bactrim was prescribed to 3 patients, and 2 patients had differing antibiotic treatments.

Figure 2 Proportion of implant components exhibiting clinical symptoms.

Figure 3 Number of patients exhibiting most common symptoms. IPP, inflatable penile prosthesis.

Patients underwent device removal if there was worsening infection within 7 days of initiating empiric antibiotic treatment. Of the 9 patients, 4 continued beyond the initial 7 days of empiric antibiotic treatment. Among the remaining patients, all those who experienced penile shaft tenderness required PP removal before 7 days, while those without tenderness had device survival of at least 10 days. Currently, 11 active sites are participating, with additional patients and centers being enrolled in the study.

Discussion

Currently, in the field of IPP clinical and research work, prevention of clinical infection following implantation remains a primary concern (4). Despite IPP infection being considered a severe complication, scarce published data describe how to treat patients who present with low-grade clinical infections. Moreover, no clinical classification guidelines are available for classifying risks of clinical infections or for methods to mitigate this risk.

This study is designed to compare NGS and standard-of-care culture for clinically infected IPPs as to which led to better microbe identification and patient outcomes. As more patients and centers are being added to this study, additional data will be collected and analyzed in hopes of determining and solidifying risk stratification for low-grade clinical penile implant infections. A recent paper by Liss et al. showed in a “prospective randomized controlled clinical trial of patients undergoing urologic stone interventions” that NGS “improves antibiotic selection to reduce healthcare-associated urinary infections” (12). The authors noted that treatment efficacy might be constrained by the recommended protocol. However, this is less of a concern when treating IPP patients using NGS-guided antimicrobial decision-making, as several PIs preferred to rely on NGS results rather than traditional cultures. For the field of prosthetic urology, this is the first prospective randomized multicenter study directly examining data that could improve patient care in IPPs. The primary endpoint we intend to show by with a prospective randomized study, is that NGS gives better treatment options than traditional culture leading to better outcomes. Yet, the design had to consider that knowing (on the part of the PI) which arm a patient was in, is bound to influence therapy choice. Thus, the PIs insisted that NGS results be blinded. Theoretically, if the PI had the NGS results and patients in the traditional culture arm start doing poorly, the PI use NGS results to change antimicrobial treatment (thereby unofficially crossing the patient over) going against the primary endpoint of the study.

One key element of these results is that patients in the NGS arm included those that survived the entire 6-month period. This supports the concept that NGS may lead to better therapeutic strategies that result in improved patient outcomes and device survival. This is consistent with the fact that benefits of NGS include thorough analysis of biofilm composition and determination of relative abundance of specific microorganisms. Another key element of these results is that penile shaft tenderness was more common among patients who failed early antibiotic treatment for penile implant infection. This is especially important since there are no existing clinical classification guidelines for identifying patients at high risk of needing implant removal or methods for mitigating risk. The ongoing recruitment of additional patients to this prospective, randomized controlled trial will help to identify additional useful presentations of penile implant infection in addition to comparing the utility and outcomes of NGS and culture.

A key limitation of this study is that we only reveal the results for the first 9 patients in the study, although recruitment is ongoing with a goal of at least 40 patients. With only 9 subjects, certain similarities do not allow discussion of diverse patient populations. Furthermore, all the IPP types were Coloplast and patients of the same race, which will change with more participants. The data were collected from high-volume centers and interpretations may not be applicable to low-volume centers. One final limitation of this study is the blinding of the primary investigators to the NGS and standard culture data. This blinding was voted on by all primary investigators involved to maintain a neutral bias in terms of patient outcomes. However, this blinding could still have negative effects on the data. One future experiment could remove this aspect in its methodology and compare the outcomes to observe differences. Despite these limitations, this is the first prospective, randomized study to mitigate infection in prosthetic urology.

Conclusions

These preliminary results suggest that NGS microbial detection may be a valuable tool for enhancing patient outcomes and device survival. Additionally, the data indicate that penile shaft tenderness is a common symptom among patients who did not respond to early antibiotic treatment for penile implant infection. As more patients are recruited into this trial, further key presentations of infection will be explored, and the effectiveness of NGS and culture will be analyzed within a larger and more diverse patient population.

Acknowledgments

Caroline Jennermann, MS, ELS provided medical editing services.

Footnote

Provenance and Peer Review: This article was commissioned by the editorial office, Translational Andrology and Urology for the series “Genitourinary Prosthetic Infection”. The article has undergone external peer review.

Peer Review File: Available at https://tau.amegroups.com/article/view/10.21037/tau-2025-57/prf

Funding: This work was supported by funds from MicroGenDX (to G.D.H.).

Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://tau.amegroups.com/article/view/10.21037/tau-2025-57/coif). The series “Genitourinary Prosthesis Infection” was commissioned by the editorial office without any funding or sponsorship. P.H.C. served as an unpaid guest editor of this series, and serves as an unpaid editorial board member of Translational Andrology and Urology from December 2023 to November 2025. A.C.L. and G.D.H. served as the unpaid guest editors of this series. G.D.H. reports this study was sponsored by MicroGenDX. G.D.H. reports prior speakers bureau for Coloplast and Boston Scientific, and participated on Signati Medical advisory board (no pay). N.D. and C.D.P. report consulting fees received from Micro GenDX. A.C.L. reports contractual, consulting fees, and payments (lectures and preceptor) from Coloplast Corporation and Boston Scientific. A.C.L. received support from and participated on Coloplast Corporation. R.N. received consulting fees from Boston Scientific Corporation and is an ongoing consultant for malpractice case regarding a death following penile implant. P.H.C. reports contractual and payments (lectures and preceptor) from Coloplast Corporation and Boston Scientific. The authors have no other conflicts of interest to declare.

Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. The study was conducted in accordance with the Declaration of Helsinki and its subsequent amendments. The study was approved by Advarra (IRB No. Pro00055322) and informed consent was obtained from all individual participants.

Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.

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