UTI – Is Traditional Culture Testing Obsolete? - Edward Schaeffer

December 16, 2019

In urology, urinary tract infections are categorized into two main categories. Those with uncomplicated and those with complicated infections.  Patients who have uncomplicated infections are young women premenopausal, not pregnant, and they have limited comorbidities. The symptoms that we associate with an uncomplicated infection are predominantly lower urinary tract urgency, dysuria, blood in the urine and suprapubic pain. Complicated patients can be men or women. They're typically older. They may have urologic abnormalities in their urinary tract and they can be pregnant and the symptoms for a complicated infection can be more complex. In this 2019 LUGPA CME presentation, Dr. Edward Schaeffer touches on topics related to urinary tract infections including whether traditional culture testing is obsolete further detailing uncomplicated and complicated urinary tract infections.


Edward Schaeffer, MD, PhD, Chair, Department of Urology, Feinberg School of Medicine, Program Director, Genitourinary Oncology Program, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA.

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Ted Schaeffer: Thank you Neal and Dr. Henderson for inviting me. Okay, so Neal challenged me with this question, is traditional culture testing obsolete and I think that was an amazing introduction to several concepts that we'll circle back within a second. Now again, a brief overview. Individuals who have urinary tract infections, which is slightly different than individuals who have bacteria in their bladder, present with symptoms, and about 50% of women in their lifetime will present with symptoms. This accounts for a lot of offices, it's associated with a large expense. In urology, as you guys know, we break out urinary tract infections into two main bins. Those with uncomplicated and those with complicated infections and the patients who have uncomplicated infections, as everyone knows, are young women premenopausal, they're not pregnant and they have limited comorbidities. The symptoms that we associate with an uncomplicated infection are predominantly lower urinary tract urgency, dysuria, blood in the urine suprapubic pain.

Complicated patients can be men or women. They're typically older. They may have urologic abnormalities in their urinary tract and they can be pregnant and the symptoms for a complicated infection can be more complex. Pyelonephritis, a prostate infection. These kinds of things.

Now when is a culture indicated? So the Infectious Disease Society of America states that for an uncomplicated infection, uncomplicated cystitis, no culture is necessary and a treating physician or treating APP can move to empiric therapy. The empiric therapy recommended is nitrofurantoin, Bactrim® or fosfomycin and these are five-day, three-day and one-day dose medications. As a reminder, everybody in the audience knows fluoroquinolones are no longer recommended for an uncomplicated urinary tract infection and the optimal agent depends on clinical suspicion for the most likely uropathogenic and the local resistance data.

Now what does all the data tell us? So this is actually a publication that Jason Cohen, who is one of our urology residents, just published with my father, who of course is one of the experts on UTI. What they did was they looked in our enterprise data warehouse of over 7 million patients at Northwestern and they looked for individuals who are coded as having a urinary tract infection. So if you just took a hundred women from this study who presented with symptoms of an uncomplicated UTI, and you didn't even perform a UA on them, and you just gave them based on the Infectious Disease Society of America's recommendations, nitrofurantoin for three days. You could ask simple questions like, well how many of these individuals would have an infection and how many would return with bacteria which was resistant to the original agent given with symptoms?

This is the work that Jason did and it's pretty interesting what he's showed and so this does reflect what Dr. Wolfe was saying about, well how we set our thresholds for infection. But if you set your thresholds pretty low and you say well, of the hundred women who present to your clinic with symptoms of a urinary tract infection, how many could you actually culture out bacteria with? If you set your threshold pretty low, greater than 10 of the four CFUs, about half the women would have bacteria that you can culture out. If you used a more traditional cutoff of greater than 10 to the fifth, it'd be only about one third of those women. But if you had treated everybody as if they had a UTI, you didn't do a culture and you just looked, how many of these individuals would come back with bacteria resistant to the original pathogen? It would be very few. Actually one or three of the 100 women would come back with bacteria that was resistant to nitrofurantoin and that's because in Chicago it's a very sensitive bacteria for the uropathogens that are screened for in the culture. So that's without even doing a UA.

Can a UA help in these particular cases? It absolutely can. So if you have a patient who comes in with symptoms of an infection, you do a urine analysis, you can actually be even more certain whether or not, or convinced that they may or may not have a pathogen causing them to have symptoms. What you want to look for in a UA is actually not nitrates, but leukocyte esterase, which is very helpful in predicting whether or not the individual would have a negative or positive urine culture.

So Neal asked me, is traditional culture testing obsolete? I would propose for an uncomplicated urinary tract infection, it's not obsolete, it's just not necessary at all. So when is a culture indicated? Cultures are indicated for individuals who have UTIs that are more complex and these are UTIs associated with decreased efficacy of therapy where the urinary tract is structurally or functionally abnormal. The host may be compromised or the individual has a history of suspected bacteria with increased virulence. That would be, for example, a healthcare provider, or a dentist, or a vet.

Risk factors for a complicated UTI, male gender, pregnancy, elderly patients, those with diabetes, and again, those who are in or around hospitals. So as Dr. Wolfe nicely illustrated, the gold standard for determining a urinary tract infection is urine culture and again, this is the basic idea. You take urine, you put it in agar with some food for the bacteria to grow and you see what happens. These are the traditional cutoffs greater than 10 to the fifth colony-forming unit. But if you suspect an infection, you can ask your lab to actually produce and give you information on bacterial pathogens at much lower counts.

Now the goal of therapy is to eliminate bacterial growth in the urinary tract and the antimicrobial selection should be based on the most probable pathogen or known pathogen if culture data is available. So what are the limitations? Well this takes time, there's a lag for when you have a patient present to when you get your culture result. As Dr. Wolfe nicely illustrated, there can be limited detection of the types of pathogens that these laboratories generally regularly grow out and there's a lack of really thoroughness in terms of what bacteria you're looking for.

So how can we better direct antimicrobial agents in individuals with suspected UTIs? So if you have a patient who may be complex, who you think may have a complicated UTI, you can certainly, and you should certainly do a UA and again if the UA is negative, negative for leukocyte esterase, then it's quite possible that their symptoms are not coming from actual infection. There may be other things going on we can talk about later. If they have a prior negative culture, then there's actually a very good chance that they won't have future cultures that are positive for bacteria. If their culture was positive in the past, their sensitivities typically remain stable over time, although that was really neat how much variability there is from day to day in the urinary microbiome.

So what's a workflow for a typical patient in our clinic? Well, if a patient presents with symptoms if you do a UA and it's positive you need to treat empirically and you culture the urine. If an individual presents with symptoms, if the UA's negative and they have a prior history of negative cultures, which is not unusual in our practices, then in Jason's study there was an 87% chance that symptoms for this particular person are not attributable to an infection and you need to evaluate for other causes. CPPS, cancer are several good examples. If a UA's negative but a patient has a history of positive cultures, in those situations we recommend empirically treating with antibiotics and looking historically at their sensitivities.

So is culture testing obsolete for those with complicated urinary tract infections? No, but certain cultures can be improved and so how can they be improved? This is a perfect complement to Dr. Wolfe's talk. There are certainly bacteria in the urine and this dogma that there are culture-negative urines in individuals who have symptoms is something that's been shown for several years in your lab and my father's lab, et cetera. There are several methods that Dr. Wolfe really nicely illustrated that are techniques that you can use to identify bacteria in "sterile urine". This includes exactly what he talked about. You can do advanced PCR-based assays to detect bacteria and you can do enhanced quantitative urine cultures to detect bacteria.

Now what do these novel diagnostic testings do and how are they translated into the clinics? Because that's important. So they take again a PCR-based approach and they can look for pathogens and they can look for resistance genes almost simultaneously. The proposed benefits, faster identification of the pathogen, improved accuracy for susceptibility to antibiotics and theoretically improve patient outcomes if you can do faster patient-specific antimicrobial planning.

So what are the three tests that are commercially available now? The first is by a company called Pathnostics and much of the data that I'm going to quote for you is off their webpage. There's very limited publications with these. They have PCR-based assays. They claim they can detect 45 different pathogens, and they can look for different resistance genes in those bacteria, and they can phenotype and they can provide antibiotic data for this polymicrobial environment. You can collect the urine, it can stay out at room temperature for up to five days and they report a 24 to 48 hour turnaround time. They report very high sensitivity and specificity for detecting bacteria in the urine of these symptomatic individuals. I would argue that we could probably detect bacteria in the bladders of anybody, so we have to be careful about what these tests are telling us.

What else do we have? So Vikor™ is a second commercially available test. Again, it uses the same basic principle, PCR-based assays. They report that they can detect multiple bacteria and up to 30 different resistance genes. They have a nice additional platform which they call antibiotic assist, which incorporates regional sensitivities and susceptibility patterns, costs and so forth into their kind of clinical output. Again, they have a very fast turnaround time. The last test is MicroGen DX. This is actually a two-stage test. So the initial part of the testing is again PCR-based. They look for bacteria in the urine. It's a more limited panel of bacteria but if you ask, they can actually do a much more detailed next-gen sequencing approach to look for even more bacteria. As you can imagine from the last talk, you can actually identify bacteria in almost everybody with this test.

The work is just beginning to be done in these particular platforms as to whether or not they actually can help with the clinical outcomes of the patients. This is a recently published paper looking at a head to head comparison of the previous assay, the MicroGenDX assay compared to traditional urine-based culture testing. So this is the beginning of very nice work in this area. So what do these tests do? They all have molecular pathogen detection. You can look for resistance genes. They have very fast turnaround times and of course, the hope is with these tests we can actually change the symptoms and improve the quality of life of our patients.

So in conclusion, standard urine culture testing is not necessary for uncomplicated urinary tract infections. Empiric treatment per the Infectious Disease Society of America guidelines is an appropriate first step. For those patients with complicated UTIs, they should have formal urine culture testing. Empiric antibiotics need to be started anyway in these individuals so you need to reference your local antibiograms for this. The new molecular-based urine testings offer methodologies that identify pathogens and resistance genes with the potentially accelerated timeline. They can detect pathogens in up to 67% of no growth standard cultures and so really the key question remains will this impact our patients and the duration and extent of their symptoms. And with that, I'll conclude and we can maybe take some questions. Thank you. Thank you.

Sandip Prasad: Can you pull up the discussing UTI slides quickly? I just have a quick question. How many members of the audience are utilizing these next-generation type tests now in the office? So a good number. Sorry, can you go to the next UTI discussing slides? I just want to show... You can go to the next slide, please. So this is a report from one of my patients and you can hit, just go ahead and advance once. So this is the report for a patient who had symptoms but no UTI. You can just advance and we'll highlight the next...Go ahead and just advance once, please. Yeah. So this is a MicroGen test for those of you that haven't used it. So this is a patient that was symptomatic. This is what I received from my next-generation DNA sequencing, which identified a number of organisms, the last of which was E. coli.

You can advance once. The next gives us the proportion of the DNA that's found in each of those. You can advance, please. And it gives you a percentile of each of the representation and on the right are the recommended antimicrobials for this type of patient. So I worry sometimes with these tests that we get so much information that I don't really know what to do with this patient when they come back in except to tell them we have a lot of things that we potentially can treat. I certainly would welcome anyone's advice on that.

Alan Wolfe: Yeah, that's the problem, right? So we now know the bladder is not sterile and in fact the urethra isn't either and we can detect bacteria. Some of them we know there are the favorite bacteria to dislike, but there's a whole bunch of organisms we don't want anything about. Some of them are likely pathogens and some of them are beneficial. We just don't know. So if you get a report like this... By the way, that list looks really familiar. These are organisms that we see on a regular basis. You'll note that E. coli was only 3% of the sequence rates. So if this person has symptoms, are they having symptoms because of the E. coli or because Actinomyces neuii? I don't know. So what we don't want to do is to have clinicians over-treat, try to sterilize the bladder, right? You want to get rid of the symptoms.

But you also don't want to solve a problem that's short term. Okay, the UTI goes away. But how many women, for example, suffer from lower urinary tract symptoms at the age of 50 or 60 because their microbiome was disrupted because when they were 20 they had an uncomplicated UTI? So I would challenge everybody to try to figure out how to identify the organisms that you need to know about. The bad ones, the good ones, and have them on a panel that you could within 15 minutes or a half an hour or even a couple hours, get a result. Then you can figure out, based upon the output of that panel, what the results of that panel is to work out the treatment algorithms that clinicians would use. Now that's a little futuristic, but I don't think it's that far off.

Neal Shore: So just for time, Ted, any final closing comments for us on the panel?

Ted Schaeffer: Yeah, I think those are great comments and it's not just the bad bacteria and the good bacteria, it's likely the ratio of the two of them together in the individual host. Because the other thing that factors is the host response to the bacteria. Everybody has bacteria all over their body, and it's not just the presence of it or the absence of it, it's the host response to the bacteria that's causing the symptoms. And so there's a lot of work to be done is the bottom line. This is just the tip of a gigantic iceberg.

Neal Shore: Yep. Fantastic. Thank you so much.

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