Randomized Clinical Trial Using Next Generation Microbial Sequencing to Direct Antibiotic Selection Before Kidney Stone Lithotripsy Using an Interprofessional Model
Phase: NA
Conditions: Kidney Stone, Renal Stone, Infection, Bacterial
Sponsor: The University of Texas Health Science Center at San Antonio

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COVER PAGE FOR PROTOCOL AND STATISTICAL ANALYSIS PLAN 
 
 
 
 
 
Official Study Title: Randomized clinical trial using next generation microbial 
sequencing to direct antibiotic selection before kidney stone lithotripsy using an 
interprofessional model 
 
NCT number: NCT04404855 
 
IRB Approval Date: 11-15-2021 
 
Unique Protocol ID: HSC20190678H 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
  
 
 
 

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Antibiotic Selection Using Next Generation Sequencing Versus Urine Culture  
For Stewardship Prior to Surgery using an Interprofessional Model 
 
 
Michael Liss, MD 
UT Health San Antonio 
7703 Floyd Curl Dr.  
San Antonio, TX 78229 
210-567-5676 
liss@uthscsa.edu  
 
 
 
 
 
 
 
 
 
 
IND Exempt 
 
PROTOCOL 4.0 
 
DATE: 11/11/2021 
 
 
 

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ABBREVIATIONS  
 
 
AE 
 
 
 
Adverse Event 
 
DSM  
 
 
Data Safety Monitoring 
DSMB  
 
 
Data Safety Monitoring Board 
DSMC 
 
 
Data Safety Monitoring Committee 
 
DSMP  
 
 
Data Safety and Monitoring Plan 
DSO  
 
 
Data and Safety Officer 
DQA  
 
 
Director of Quality Assurance 
GCP  
 
 
Good Clinical Practice 
ID 
 
 
 
Infectious Disease 
IIS 
 
 
 
Investigator Initiated Protocol 
IRB 
 
 
 
Institutional Review Board 
NGS  
 
 
Next Generation Sequencing 
OSP  
 
 
Office of Sponsored Programs (UT HEALTH) 
QAD  
 
 
Quality Assurance Division 
PI 
 
 
 
Principal Investigator 
SAE  
 
 
Serious Adverse Event 
SOC  
 
 
Standard of Care 
UPIRSO 
 
 
Unanticipated Problem Involving Risks to Subjects or Others  
UT Health  
 
 
University of Texas Health Science Center at San Antonio 
 
 
 
 

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Table of Contents 
 
 
 
  
 
 
 
  
 
 
 
 
 
 
 
 
 
 
 
 
 
Study Synopsis 
 
5 
Background & Significance  
 
6 
Statement of Study Objectives 
 
8 
Research Plan & Data Collection  
 
8 
Inclusion and Exclusion Criteria 
 
9 
Study Schedule  
 
10 
Screening & Recruitment 
 
10 
Study Procedures 
 
11 
Risks to Human Subjects 
 
12 
Method of Analysis/Statistics 
 
12 
Data Safety Monitoring Plan 
 
13 
References/Bibliography  
 
14 

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1.0 STUDY SYNOPSIS 
 
This is a randomized controlled clinical study evaluating the use of next-generation sequencing (NGS) to 
improve antibiotic prescribing before ureteroscopy or percutaneous nephrolithotomy. NGS will be performed on 
voided urine collected as routine care approximately 30 days prior to surgery. Results will be presented to ID 
pharmacist within 48-72 hours to help select the most appropriate antibiotics, and independently as part of 
routine care, surgeons will choose the antibiotic that they would use in each case, while the ID pharmacists 
would select their optimum choice. Pharmacists will account for site-specific antibiotic stewardship practices, 
allergies, medication adjustments, and C. difficile rates. Approximately 300 subjects will be randomly assigned 
in a 1:1 ratio to receive either NGS antibiotic recommendation or standard of care (SOC) prophylaxis 
prescribed treatment. All providers within the Department of Urology who perform urologic stone procedures 
(n=5) will also be approached in person with an information sheet.  Subjects assigned to standard of care will 
have urine cultures sent for analysis, and the physician will choose antibiotics based on results as per usual 
practice. Subjects assigned to the NGS group, in addition to routine urine culture results, will have NGS urine 
culture results sent to an ID pharmacist, and recommendations will be shared with the physician to determine 
the antibiotic selection. The physician will ultimately decide the appropriate antibiotics to prescribe. 
Approximately 7-14 days after surgery, the research staff will conduct a telephone call to ask about any post-
operative infections, complications, and any additional antibiotics that were prescribed.  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Patient selected to undergo 
transurethral procedure 
N=300 
Informed Consent 
Randomization 
Standard of Care Urine Culture and MicroGen DX NGS 
N=300 
ID Pharmacist  
Abx Recommendation 
N = 110 
Blinded NGS 
N = 110 
Transurethral 
procedure  
Transurethral 
procedure  
Follow-up: 7-14 days post sx; 
telephone call and/or chart 
review – infections, 
complications, abx 
Figure 1: Study Schema   

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2.0 BACKGROUND AND SIGNIFICANCE 
 
Antibiotic selection before surgery is usually left to the surgeon to make the best selection; however, there is 
considerable variation noted in antibiotic prophylaxis. The American Urological Association published a Best 
Practices white paper; however, a large proportion of surgeons continue to not abide by recommendations.1 
Efforts are needed to reduce variation from recommended antimicrobial prophylaxis for common 
urological procedures to reduce antibiotic adverse events and complications.2 
 
The benefit of antimicrobial prophylaxis has been shown in multiple studies; however, some countries do not 
use antibiotic prophylaxis and have comparable infection rates. Prophylactic antibiotics should be effective 
against an organism's characteristic of the operative site with excellent safety profiles in short duration. The 
most common antibiotics utilized in urologic endoscopic surgery are cephalosporins, fluoroquinolones, and 
aminoglycosides. These antibiotics are usually used in short duration, but recently a rise in antibiotic resistance 
has led to increased risk of infection. The escalation of one or multiple broad-spectrum could be related to 
health policy changes indicating that insurance companies would not pay for readmission for infectious 
complications after surgical procedures. Surgeons are then utilizing more antibiotics or antibiotics that should 
be reserved for significant infections and not necessarily prophylaxis. 
 
Ureteroscopy for urinary tract urolithiasis is a common procedure with an estimated 9,200 cases in the US per 
year.3 However, the incidence of systemic inflammatory response syndrome (SIRS) after flexible ureteroscopic 
(URS) lithotripsy is 7.1%, despite the use of recommended antibiotic prophylaxis.4 Obtaining a urine culture 
prior to surgery is standard of care, and physicians start   culture-specific antibiotic treatment on patients with a 
positive culture— and  preferably found to be negative on repeat culture— before their urologic stone 
procedure. One of the challenges when choosing a prophylactic agent is that preoperative urine cultures often 
show no growth for patients who later develop SIRS.5-7 Singh et al. found no significant association between 
pelvic urine cultures or stone cultures and the occurrence or SIRS.8 We hypothesize the stone or previously 
placed stent may allow bacteria to form biofilms or not detected by standard cultures.  
 
Next Generation Sequencing (NGS) technology could assist physicians in selecting antibiotic prophylaxis 
therapy before surgery in patients that have a normal urine culture. Urine culture is a technique that utilizes 
specialized agar to select the bacterial presence in a fluid. Issues with standard culture are that one must use a 
priori select particular groups of bacteria and assume they would grow on the plate, which requires the bacteria 
to be at a certain concentration. NGS testing can use the combination of PCR and 16sRNA to identify the 
bacterial presence and does not discriminate by growth patterns and are not limited by bacterial counts. NGS 
can also identify fungal species, which require a separate technique when using standard culture. Our proposal 
focuses on the identification of high-risk cases and antibiotic prophylaxis patterns and how NGS can assist with 
antibiotic prophylaxis decision making. Anticipating the use of NGS may have unintended consequences, we 
address issues with implementation and how to establish an interpersonal healthcare approach to abide by 
antibiotic stewardship programs.   
 
We performed NGS and PCR for common resistance genes in subjects prior to ureteroscopy. Of the urine 
being sent for culture, approximately 5-10mL was sent to Microgen Dx for the analysis. NGS results were 
blinded to the physician, and analysis was done after surgery. Surgery, as scheduled per the physician and 
prophylaxis antibiotics, were prescribed as the standard of care. After the surgery, we made 3 case studies 
that were reviewed by board-certified Urologists to determine if they would change their prophylactic antibiotic 
regimen and what antibiotic they would prescribe. Two infectious disease pharmacists also reviewed the case 
reports and provided the “ideal” antibiotic regimen to be prescribed.  
 
After IRB approval, we obtained samples from urine specimens already provided as a preoperative urine 
culture from twenty patients scheduled for urologic stone surgery. Two cultures returned positive with 
Enterococcus, and the NGS result was the same. One sample had two species (enterococcus and coagulase-
negative Staphylococcus), in which NGS was able to find both organisms and speciated the staphylococcus to 

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be Staphylococcus epidermidis. Of the 18 cultures with no 
growth, 56% (10/18) did show a dominant-bacteria on NGS.  
Eight urologists returned the three case scenarios, and in 
each of the 3 cases 100%, 88%, and 88% of the physicians 
would have prescribed a different prophylaxis antibiotic 
given these results. The ideal antibiotic of choice based on 
the ID Pharmacist is oral Bactrim for all cases, and only 
50%, 0%, and 0% selected this option, and 38%, 25%, and 
63% chose to escalate the antibiotic to vancomycin, Zosyn, 
or amikacin in conjunction with a second antibiotic. Overall 
on the exit survey urologists feel it is moderately important 
(n=2, 25%), important (n=4, 50%), or very important (n=2, 
25%) to test this technology in this context and 38% have 
concerns about using this technology for antibiotic 
prophylaxis. 
 
NGS may be more effective and specific than those predicated upon SOC preoperative urine cultures mostly 
negative before surgery. For example, we identified several culture negative patients with dominant bacterial 
types that may influence a physician to prescribe a 1st generation cephalosporin compared to a gram-negative 
dominant group that may need a fluoroquinolone or 3rd generation cephalosporin.  Importantly, urologists do 
not typically send a urine specimen specifically for fungi (Candida sp.). The PCR/NGS test readily makes this 
information available and in one patient that was positive did 
have sepsis caused by Candida, which was later cultured 
from the patient's blood. Many studies have reported the low 
sensitivity of preoperative urine cultures for predicting 
infectious complications of urologic stone procedures.5-7, 9 
Eswara et al. (2013) compared sensitivities among preoperative and perioperative pelvic urine and stone 
cultures for pathogen detection, reporting that of the patients who develop urosepsis, 0% had positive 
midstream preoperative urine cultures, while 73% had positive stone cultures.10 However, they report a 64% 
concordance rate in urosepsis patients between stone cultures and readmission cultures, indicating that stone 
cultures did not always appropriately guide antibiotic selection in up to 36% of cases. Moreover, an antibiotic 
selection from stone culture rarely is provided in a timely fashion to alter postoperative antibiotics, and many of 
our patients go home the same day of the procedure. Our study, while small, found that NGS was able to 
detect pathogens and provide alternate antimicrobial prophylaxis, especially in those who did have an 
infection.  
 
Our findings are consistent with those of Long et al. (2016) and Grumaz et al. (2016), who reported that NGS is 
more sensitive than blood cultures for detecting pathogens in ICU patients.9, 10 Notably, their studies observe 
the clinical utility of NGS to guide therapy in a high-risk population of ICU patients. Many studies have reported 
the increased sensitivity of NGS when compared to cultures, but further research is needed to establish cases 
where the improved sensitivity delivers cost-effective, clinically applicable data.11, 12 The results of this study 
suggest that NGS may improve the standard of care in patients undergoing invasive urologic stone 
procedures. 
 
Infectious complications are the most common cause of death following urologic stone procedures and present 
a sizeable economic drain on the American healthcare system.3, 13 Other studies have found that up to 17% of 
urosepsis cases follow urologic interventions.14-18 Koras et al. (2014) observed signs of SIRS in up to 27% of 
patients who underwent PCNL, 7.6% of which were diagnosed with sepsis.14 Given the mortality rates and 
economic costs of urosepsis, SOC practices must be optimized to reduce the risk of infectious complications 
following urologic procedures.  
 
NGS identifies a targetable bacterium in up to 50% of negative urine cultures prior to urologic stone surgery. 
Many physicians chose to escalate IV antibiotics rather than utilized oral medications. Therefore, working with 
an infectious disease pharmacist may be helpful in guiding the selection and operating room availability of 
Figure 2: Preliminary results from NGS 
compared to standard urine culture prior to 
urologic surgery.   

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antibiotics based on NGS results to improve antibiotic stewardship. Larger long-term studies are needed to 
determine if this strategy will lead to reduced infection rates. 
 
3.0 SPECIFIC AIMS 
 
Specific Aim 1: To perform a randomized clinical trial investigating the use of NGS for antibiotic 
selection to lower post-operative infection rates over the standard of care. 
Hypothesis: utilization of NGS for the selection of preoperative antibiotics reduces postoperative infection rates 
by 75%. Our baseline rate of infection was 11-15% in our pilot study and nearly 5-10% in our investigation of 
those ureteroscopies (not PCNL, which has a higher rate) of infections at a university hospital. We expect with 
the correct antibiotics that the infection rate may drop from 11% to 1% or less. The control arm will be utilized 
to determine if NGS may have predicted infections or high-risk groups. Retrospective databases include 
anywhere from 2-15% of patients will present with a postoperative infection after transurethral surgery. Current 
prophylaxis strategies do not always follow guidelines, and with concerns over current non-reimbursement for 
infectious complications, surgeons may be using more antibiotics. 
 
Specific Aim 2: Accuracy of NGS and PCR compared to standard urine culture prior to transurethral 
procedures. Hypothesis: NGS can identify 50% of negative urine cultures that could harbor uropathogenic 
bacteria. We anticipate a substantial number of patients have uropathogenic bacteria present yet are not 
detected by traditional approaches. We seek to expand our investigation on this topic in order to understand 
how best to interpret the results and present them to physicians. All participants will have both a standard of 
care urine culture and NGS testing/ID Pharmacy review for comparative analysis. Only subjects assigned to 
the NGS group (n=110) will have NGS urine culture results and ID Pharmacist recommendations shared with 
the physician to determine antibiotic selection.  Operating characteristics to include sensitivity, specificity, 
positive, and negative predictive value will then be performed and area under the receiver operative curve 
calculated. We will enroll a minimum of 250 patients and 5 urology provider-participants into this study. We 
anticipate that 20 of the patients will have positive urine cultures and 200 will have negative cultures. Of the 
200 negative cultures we anticipate that 100 (50%) will harbor uropathogenic bacteria which will be identified 
via NGS. 
 
Specific Aim 3: To investigate the influence of Next Generation Sequencing (NGS) on physician 
prophylactic prescribing habits in patients with a negative preoperative urine culture. Hypothesis: NGS 
will cause any antibiotic change in prophylaxis in 50% of cases. Based on preliminary data, we identified that 
over 80% of physicians would change their antibiotic for surgery if given this information. However, we 
anticipate surgeons will use an antibiotic escalation approach compared to a pharmacist’s selected optimum 
prophylaxis antibiotic approach. Therefore, the control arm will receive standard of care antibiotics compared to 
the intervention group. The intervention group will get three levels of information: (1) standard of care culture, 
(2) full NGS report, and (3) infectious disease pharmacist recommendations based on NGS. The physician will 
then utilize these tools to select the best antibiotic for the case. 
 
4.0 RESEARCH PLAN AND DATA COLLECTION 
 
The goal of this proposal is to evaluate if the use of NGS on preoperative antibiotic selection reduces 
postoperative infection rates over the standard of care. Patients scheduled to receive a transurethral 
procedure, such as a ureteroscopy or percutaneous nephrolithotomy (PCNL), will be approached for 
enrollment prior to their procedure. After informed consent has been obtained, approximately 5-10 mL of left-
over urine, collected for a standard of care urine culture, will be obtained for research and sent to MicroGen Dx 
for NGS. Patients will be randomized to receive either standard of care culture results (only), versus NGS 
results and Infectious Disease (ID) Pharmacist antibiotic recommendation. The physician will utilize these 
results to select the best antibiotic for the case but is not required to abide by the ID pharmacist's 
recommendation. The standard of care group will also have a urine sample sent to MicroGen Dx, but the 
results will not be provided to the physician. All subjects enrolled will received a standard of care culture as 
part of routine care. A chart review and/or telephone follow up will be completed approximately 7-14 days post 
urologic procedure to assess for complications, infections related to the procedure, and antibiotics prescribed.   

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The treating physicians will have control over antibiotic administration. Their determination, interaction, and 
ultimately patient outcome will be documented and evaluated. As a result, the treating physicians will be 
considered participants in this study. A waiver of documentation of informed consent for the treating physicians 
will be included. In addition, an information sheet will be provided to treating physicians specifically.  
 
Subjects will be recruited from approved Urology clinics at time of their preoperative appointment, 
approximately 30 days, but up to 90 days, prior to the planned transurethral procedure. Patients with ureteral 
stents will not be excluded; therefore, essentially any patient going to surgery for percutaneous 
nephrolithotomy, ureteroscopy or other transurethral procedure, within two to four weeks will be screened for 
eligibility and approached for enrollment. In the event the standard of care urine culture was performed more 
than 45 days before the urologic procedure; the treating physician will ask the patient to provide an additional 
urine sample as part of normal practice. Research staff will obtain a second sample (5-10 mL) of left-over 
urine, which will then be sent to MicroGen Dx for analysis. If this occurs, the second sample will be used for 
analysis.  
 
Next Generation Sequencing: Approximately 30-50 mL voided whole urine will be collected as per routine 
care. Approximately 5-10mL of left-over urine will be obtained for research, placed in special vacutainers 
supplied by MicroGen DX, a CAP accredited and CLIA licensed clinical diagnostic lab, and sent for analysis. 
MicroGen DX will perform rapid PCR for common resistance genes prior to transurethral procedure, such as 
ureteroscopy or percutaneous nephrolithotomy. NGS results will be available within 48-72 hours. Additionally, 
NGS analysis will be performed on available or leftover urinary stones for a proportion of the subjects. 
 
Target bacterial or fungi DNA on the quantitative PCR (qPCR) panel assay on the Roche LightCycler 480 II 
instrument and sequencing of 16S ribosomal RNA hypervariable regions V1-V2 using Ion Torrent (Ion Torrent 
PGM) will be run.  
 
Data Collection: Prior to and after surgery, patient medical history, demographics, pre and post-surgical 
antibiotic treatment plans, and speciation results from the urine culture will be collected by research staff. 
Results obtained from the NGS/PCR analysis report, such as resistance gene data, will be recorded. 
Recommendations from the ID pharmacist will also be recorded.  
 
Case Study Creation: ID pharmacist will be provided with the NGS report and relevant de-identified clinical 
data, such as weight and allergy history, to decide the appropriate antibiotic treatment course for the 
intervention group. The treating physician will be provided with both NGS report and ID pharmacist 
recommendations to utilize these results to select the best antibiotic for the case, but is not required to abide 
by the ID pharmacist's recommendation. Subjects assigned to the standard of care group will have urine 
cultures sent for analysis, and the treating physician will choose antibiotics based on results as per usual 
practice. The treating physician will not receive NGS report or ID pharmacist recommendations for standard of 
care group. 
 
5.0 INCLUSION AND EXCLUSION CRITERIA 
Patients: 
Eligibility Criteria 
5.1 Patients planning to undergo kidney or bladder stone removal surgery using endoscopy including 
ureteroscopy and percutaneous nephrolithotomy or any other transurethral procedure 
5.2 Be age 18 or older 
5.3 Be able to give informed consent 
 
Exclusion Criteria 
5.4 Unable or unwilling to provide informed consent 
5.5  Age <18 
5.6 Does not meet inclusion criteria 
 

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Physicians: 
Eligibility Criteria 
5.1 Treating Physician within the Urology Clinic 
5.2 Has a patient that is eligible to participate in this research study 
 
6.0 STUDY CALENDAR 
Study Visit 
Visit 1 
Visit 2 
Visit 3 
Visit 4 
Baseline 
 Urine 
collection 
Transurethral Procedure 
(day of surgery) 
Follow-up  
Timeline 
Day 1 
Up to 90 
days from V1 
W/in 45 days of urine 
collection 
Approx. 7-14 days 
post-surgery 
Informed Consent 
R 
 
 
Demographics 
R 
 
 
 
Medical History 
R 
R 
 
R 
SOC Urine culture 
--------SOC1, 2--------- 
 
Whole Urine collection  
----------R1, 2---------- 
 
 
Randomization  
----------R1, 2---------- 
 
 
NGS Analysis of Urine 
Culture 
----------R1, 2---------- 
 
 
Results of NGS to Physician 
----------R1, 2---------- 
 
 
Antibiotic Prophylaxis 
--------SOC1, 2--------- 
 
 
Additional Antibiotics as 
needed 
--------SOC1, 2--------- 
 
 
Provider-Participant 
Questionnaire/Survey  
----------R1, 2---------- 
 
 
Urologic Stone Procedure 
 
 
SOC 
 
Urologic stone collection 
 
 
R* 
 
Chart Review and/or 
telephone follow up 
R3 
R3 
R3 
R3 
Adverse Events  
R 
R 
R 
R 
1 Indicated procedures may be completed at time of baseline or visit 2, up to 90 days from enrollment  
2Indicated procedures may be repeated if SOC urine culture is not completed within 45 days of procedure 
3Patient assessments may be completed over the phone 
*Any extra or leftover stone(s) available will be collected and sent to MicroGen DX for analysis 
 
7.0 SCREENING AND RECRUITMENT 
 
Patients will be identified and recruited through Urology outpatient clinics located at the Medical Arts and 
Research Center (MARC), University Hospital System (UHS), and the South Texas Veterans Healthcare 
System Audie L. Murphy Hospital in the genitourinary (GU) clinic. Eligible patients will be approached at 
the time of their standard of care visit. The inclusion of subjects, or refusal to participate in this study, will 
not affect the health care they will receive.   
 
Once a subject is identified who may meet eligibility criteria, the provider and/or approved research staff 
will explain to each potential subject the research purpose, voluntary nature of participation, study 
procedures, risks and benefits of participation, alternatives available and the subjects' rights and 
responsibilities. The informed consent process will be carried out by personnel who are IRB trained and 
designated for that role. There is no waiting period required before enrolling. The participant may decline to 

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participate, decide to participate, or take the consent home to think about participating. Subjects will 
consent in a private room, and usual privacy policy practices followed. Study procedures and objectives will 
be described to them, and they will be given a copy of the informed consent document. Subjects will also 
be given contact information for someone they can call with any questions.  No study procedures will occur 
until the patient has signed the informed consent. 
 
Remote Consent/Waiver of documentation of informed consent: Eligible subjects undergoing standard of 
care visits via telephone, video conference or telemedicine will be consented remotely in the absence of 
face-to-face contact. The purpose of remote consent is to allow the study investigator/designee and 
potential subject to engage in the informed consent process similar to what would be conducted face-to-
face under normal circumstances. Initially, subjects will be introduced to the study by urology provider and 
explain the consent process. Subjects will be informed that a consent form will be sent via e-mail, mail or 
fax. Following delivery of the consent form, approved research staff will call subject and conduct the 
consent interview via telephone when the subject can read the consent form during the discussion. 
Research staff will confirm subject's name and date of birth from subject before discussion to ensure the 
identity of the subject. If agreed to participate, subject will provide verbal consent.  No study procedures will 
occur until the subject and research staff have provided verbal consent.  
 
Each participant will be assigned a unique subject identifier (subject ID) that has no meaning external to 
the study database. The participant identifiers will be further masked and password protected, and stored 
only on a secure server behind a "firewall."  Only the PI of the IRB approved protocol (Dr. Michael Liss) and 
approved research staff will have access to these identifiers.  A research study file will be kept for each 
participant accrued.  This file will include the participant's consent, the assigned unique subject identifier, 
research records, and copies of relevant source documents.  All participant records will be securely stored 
in the Urology research offices.  A data entry system will be prepared in RedCap, Excel, or equivalent 
software interface for the study.  Both the subject identifier and sequence number for each patient will be 
entered into the database together with clinical outcome data collected across visits. 
 
For the providers, all providers within the Department of Urology who perform urologic stone procedures 
(n=5) will be sent an email, informing them about the research study. These providers will also be 
approached in person with an information sheet. Prior to study entry, approved study staff will explain to 
each potential provider-participant the research purpose, voluntary nature of participation, study 
procedures, risks and benefits of participation, and their rights and responsibilities as participants. The 
informed consent process will be carried out by personnel who are IRB trained and designated for that role. 
No study procedures will occur until the provider-participant has provided verbal informed consent, which 
will be documented with a research note by a member of the research team. 
 
No identifiable information will be collected about or from provider-participants. Surveys completed by 
provider participants will be stored within the specific subject’s (i.e. patient’s) research record.  
 
8.0 STUDY PROCEDURES 
 
After signing informed consent, participants will complete approximately 4 study visits. The study will enroll 
250 completers (and 5 Urology provider-participants). Data collected will include demographics, medical 
history, laboratory values pre, and post-operative procedure, medications, and treatment history. Data 
collected from the Urology provider-participants will include information from the provider-participant 
questionnaire.  The following procedures will be completed: 
 
8.1 Enrollment (research) 
After shared decision making with their physician, if patients have elected to undergo a urologic 
stone procedure that will require transurethral surgery and access to the urinary system, the study 
team will be alerted. After screening the chart to confirm inclusion and exclusion criteria are met, 
the approved study team will approach for enrollment and engage in informed consent process.  

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8.2 Urine Collection (standard of care) 
Approximately 30-50 mL of whole urine will be collected for a standard of care urine culture 
corresponding to the patients’ pre-operative visit. Approximately 5-10 mL of left-over urine will be 
obtained for research and sent to MicroGen Dx, a CAP-accredited and CLIA licensed clinical 
diagnostic lab, for analysis. Urine will be collected by research staff, placed in collection containers 
supplied by MicroGen Dx and labeled with unique subject ID. De-identified samples will be sent to 
MicroGen Dx in accordance with their guidelines. In the event, the urine culture was performed more 
than 45 days before the urologic procedure; the treating physician will ask the patient to provide an 
additional urine sample. Research staff will obtain an additional 5-10 mL of urine, which will then be 
sent to MicroGen Dx for analysis.  
8.2a Urinary Stone Analysis 
During the patients' surgical procedure, the treating physician will remove the stone (s) and send 
to a laboratory/pathologist for analysis as part of routine care. The removed stone specimens are 
diluted in a saline solution, and the laboratory will analyze for the stone's chemical composition. 
Any extra or leftover stone (s) available that will not be sent for routine analysis will be sent to 
MicroGen DX for analysis and bacteria detection. Urinary stone analysis completed by MicroGen 
DX will be done only for a proportion of the samples (n=20). Samples will be de-identified with 
the same study ID as the subject's research urine sample.  
 
8.3 Medical History/Demographics (research) 
Data collected will include demographics, medical history, to include but not limited to, medication 
and treatment history, laboratory and vitals results, diagnosis results, and procedure and surgical 
history.  
 
8.4 Randomization (research) 
A randomization list will be generated using a computer-based-random number generator 
www.randomizer.org. Randomization will be created 1:1, n=110 per group. Once created, individual 
envelopes will be created, and study staff will pull an envelope after the participant signs consent. 
The research staff will not be blinded to the randomization groups. The standard of care group will 
have urine culture results directed to treating physician. The intervention group will have NGS 
results sent to Infectious Disease pharmacist, Dr. Kelly Reveles to provide an antibiotic 
recommendation. The antibiotic recommendation, along with NGS results, will then be provided to 
treating physician. The physician will then utilize these tools to select the best antibiotic for the case 
but is not required to abide by the ID pharmacist's recommendation. The standard of care group will 
have a urine sample sent to MicroGen Dx, but the results will not be provided to the physician. 
 
8.5 The patient is scheduled for surgery (standard of care) 
 
8.6 Presentation of data to the primary surgeon (research) 
Antibiotics are standard of care prior to urologic stone surgery, yet generic recommendations allow for 
variable prescribing practices. In order to provide precise, individualized prophylaxis antibiotics, we 
will provide the primary surgery and prescriber the following information without mandating a specific 
antibiotic: 
1. Standard of care urine culture. 
2. Next-generation sequencing report – contains bacteria presence and resistance gene profiles.  
3. Infectious disease pharmacist first and second choice antibiotics based on NGS report.   
4. When NGS report and ID pharmacist recommendations are provided, enrolled provider-
participants will be asked to complete a survey (research only) regarding their antibiotic selection 
with rationale.  
 
8.7 Follow-up phone call contact (research) 

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The study staff will conduct a chart review and/or telephone follow up approximately 7-14 days post 
urologic procedure to assess for complications, infections related to the procedure, and antibiotics 
prescribed. In the event an infection or complication related to the procedure is identified by study 
staff before patient’s clinical follow up visit, study staff will alert medical team and provider if patient 
has not done so.  
 
8.8 Clinic follow up (standard of care) 
The chart will be reviewed for infections missed on phone calls. 
 
9.0 RISKS TO HUMAN SUBJECTS 
 
Each patient will be consented prior to treatment and appropriate IRB and HIPAA guidelines will be 
followed. The selection of antibiotics can vary with treating physician if the urine test is negative. In some 
cases during the study, the treating physician will receive additional information and choose an antibiotic 
based on the data rather than their personal preference. Alternatively, the treating physician may choose 
to select their personal preference despite the additional information provided, as the treating physician 
will select the best antibiotics for the subject. The American Urological Association best practice statement 
will be included to the ID Pharmacist and treating physician to ensure that guidelines are met.   
 
No adverse events are anticipated as this is a minimal risk study. Participation in this study is completely 
voluntary and will not affect their healthcare in any way. The alternative to this study is to not participate. 
Separately, any risks associated with the standard of care transurethral procedure will be discussed and 
outlined with the treating physician and medical team.    
 
Each provider will consent before initiation of research procedures. Providers will be informed that the data 
collected from them will not be used for purposes outside of the research and that their decision to 
participate or not participate will not positively or negatively affect their standing as UTHSA employees and 
their participation is voluntary. No identifiable information will be collected from providers. Providers are to 
follow best practices when prescribing and select what they believe is best for the subject.  
 
 
 
10.0 METHOD OF ANALYSIS/STATISTICS 
 
Next Generation Sequencing: Standard of care whole urine will be collected (approximately 30-50 mL) utilizing 
special vacutainers supplied by MicroGen Dx. Approximately 5-10mL of urine taken for culture will be sent to 
MicroGen Dx, a CAP-accredited and CLIA licensed clinical diagnostic lab, for analysis. MicroGen Dx will 
perform rapid PCR for common resistance genes prior to ureteroscopy or percutaneous nephrolithotomy. The 
plan will be to run target bacterial or fungi DNA on the quantitative PCR (qPCR) panel assay on the Roche 
LightCycler 480 II instrument and sequencing of 16S ribosomal RNA hypervariable regions V1-V2 using Ion 
Torrent (Ion Torrent PGM).  
 
Microbiome: Sequencing reads were demultiplexed using QIIME2 software and denoised using dada2 
software, using a phred score threshold of 28. Alpha diversity will be measured using the Shannon index, and 
a Wilcoxon test was used to determine whether the Shannon index differed between patients with stents and 
those without stents at the time of urine collection. Principle coordinates analysis (PCoA) of Bray-Curtis 
dissimilarity will be performed to visualize differences in species composition between patients with and without 
stents, and Linear discriminant analysis Effect Size (LEfSe) analysis was conducted to identify differentially 
abundant taxa between stent and non-stent groups. 
 
Sample size: This will be a randomized trial of Microgen Dx versus standard of care. The primary endpoint is 
infection within 14 days of surgery. The primary objective of the study is to evaluate whether Microgen Dx 
reduces an infection rate compared to the standard of care. The null hypothesis is that infection rates within 14 
days of surgery are the same between the randomization arms. The alternative hypothesis is that infection 

19-678H, Liss, Form BB, 11-15-21, AMD.docx 
 
 
 
 
 
14 
 
rates within 14 days of surgery are not equal between the randomization arms. The infection rates are 
assumed to be 11% in the control arm and 1% in the experimental arm based on our preliminary data. A 
sample size of 85 per group will give 80% power to detect a 10% difference in infection rate when the two-
sided Z-test with alpha=0.05 is used.  Demographics and potential confounding factors will be summarized by 
randomization arm. A logistic regression model will be used to measure the association between the primary 
outcome and treatment arm with adjustment for the observed covariates. 
 
Statistical analysis: Our primary outcome is infection after surgery as a dichotomous outcome. We will utilize a 
chi-squared analysis to determine the difference between intervention and control groups. We will assess 
demographics between groups using chi-squared for dichotomous variables and Student's t-test for continuous 
variables. Additionally, we will investigate the utilization of antibiotic in a mixed-model regarding a number of 
antibiotics and antibiotic class utilization. 
 
11.0 DATA REPORTING / REGULATORY REQUIREMENTS 
 
Data and Safety Monitoring Oversight 
 
 
 
A Data and Safety Monitoring Plan (DSMP) is required for all individual protocols conducted at UT 
Health San Antonio. All protocols conducted at UT Health San Antonio are covered under the 
auspices of the UT Health San Antonio Institutional Data Safety Monitoring Plan.   
 
The UT Health San Antonio Institutional DSMP global policies provide individual trials with:  
 
• 
institutional policies and procedures for institutional data safety and monitoring,  
• 
    an institutional guide to follow, 
• 
monitoring of protocol accrual by the UT Health San Antonio Protocol Review Committee, 
• 
    review of study forms and orders by the Forms Committee, 
• 
    tools for monitoring safety events, 
• 
monitoring of UPIRSO’s by the Director of Quality Assurance and DSMC, 
• 
    determining the level of risk (Priority of Audit Level Score – PALS) , 
• 
    oversight by the Data Safety Monitoring Committee (DSMC),  and 
• 
verification of protocol adherence via annual audit for all Investigator Initiated Studies 
by the UT Health San Antonio Quality Assurance Division. 
  
Monitoring Safety  
Due to the low risk associated with participation in this protocol, The Principal Investigator will 
conduct independent quarterly (every 3 months) review and report any findings to the Data Safety 
Monitoring Board (DSMB) and the UT Health IRB.  It is not anticipated that any safety issues will 
arise from this study because it is an observational study. 
 
             Reporting Requirements 
As per our UT health San Antonio Data Safety Monitoring Board, any protocol modifications, 
problematic safety reports, unanticipated problems, and suspension or early termination of a trial 
must be reported to all members of the research team and study site research offices (UTHSCSA).  
Suspension and early termination of a trial must also be reported immediately to the Director of 
Quality Assurance (DQA) who will promptly notify the sponsor and the UT Health IRB. 
 
Assuring Compliance with Protocol and Data Accuracy 
As with all studies conducted at UT Health San Antonio, the PI has ultimate responsibility for ensuring 
protocol compliance, data accuracy/integrity, and responding to recommendations that emanate from 
monitoring activities. Source verification of data will be performed every six months. Protocol 
compliance, data accuracy and reporting of events is further ensured by an annual audit conducted 
by the Data Safety Officer, whose audit report is shared with the PI, the research team, and will be 
reviewed by the data safety monitoring committee (DSMC).  

19-678H, Liss, Form BB, 11-15-21, AMD.docx 
 
 
 
 
 
15 
 
 
 
Safety Definitions: 
 
For this study, the following safety definitions will be applicable: 
 
Unanticipated Problems Involving Risks to Subjects or Others Definition: Unanticipated problem involving risk 
to subjects or others includes any incident, experience, or outcome that meets all of the following criteria: 
 
A. unexpected (in terms of nature, severity, or frequency) given (a) the research procedures that are 
described in the protocol-related documents, such as the IRB-approved research protocol and informed 
consent document; and (b) the characteristics of the subject population being studied (note: the 
unfounded classification of a serious adverse event as “anticipated” constitutes serious non-
compliance); 
B. definitely related or probably related to participation in the research; and 
C. suggests that the research places subjects or others at a greater risk of harm (including physical, 
psychological, economic, or social harm) than was previously known or recognized 
 
 
All UPRISO’s will be reported following UT HEALTH institutional guidelines. 
 
 
UT HEALTH UPRISO REPORTING REQUIREMENTS 
Type Event 
Report to 
Timeframe 
UPIRSO - life-threatening 
UT Health IRB and QA 
Director 
within 48 hours of the PI determining a 
UPIRSO exists 
UPIRSO - non-life threatening 
UT Health IRB and QA 
Director 
within 7 days of the PI determining a 
UPIRSO exists 

19-678H, Liss, Form BB, 11-15-21, AMD.docx 
 
 
 
 
 
16 
 
 
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