Gestion du risque infectieux périopératoire en urologie : que faire de l’ECBU polymicrobien ? Revue systématique de la littérature. Par le Comité d’infectiologie de l’Association française d’urologie (CIAFU)

25 avril 2019

Auteurs : M. Vallée, V. Cattoir, S. Malavaud, A. Sotto, G. Cariou, P. Arnaud, H. Bugel, P. Coloby, E. Chartier-Kastler, F. Bruyère
Référence : Prog Urol, 2019, 5, 29, 253-262



The management of perioperative infectious risk is a daily concern for urologists. Many risk factors are now clearly identified and many procedures have been proposed to reduce the risk of infection associated with each of them [1]. The latest French [2, 3, 4] and European guidelines [5] have recently reasserted the need for highest quality risk management by suggesting simple principles that, if they are sometimes recommended with low levels of evidence, allow urologists to improve risk reduction.

Endourological surgery has the particularity of taking place frequently in a "clean contaminated" environment [3] (Altemeier class II). The risk of infection occurence in the operative site, evaluated between 2 and 5%, justifies the prescription of perioperative antibiotic prophylaxis thus reducing the risk of surgical site infections by approximately 50% [3, 4, 5]. Nonetheless, this classification does not seem adapted to modern urology. Indeed, some class-II surgeries do not require antibiotic prophylaxis as the last recommendations recalls [4]. The interest of this same antibiotic prophylaxis, when a preoperative urine culture is positive before a surgery in contact with urine (class III of Altemeier), seems uncertain. It is currently recommended in this situation to "preventively treat colonisation for at least 48hours before an operation in contact with the urine if it is not possible to obtain urine sterility otherwise, particularly by delaying the procedure or by changing ureteral stent or urinary catheter" [2]. The treatment of these urinary colonisations before surgery has become somewhat of a conundrum in the last ten years due to the emergence of multidrug-resistant bacteria and, particularly, as regards urology, extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae.

Nevertheless, these last recommendations do not refer to a common clinical situation and thus are the source of a recurrent question in our community: how should the infectious risk of a patient presenting a polymicrobial urine culture before urological surgery be managed?

The aim of this article is to answer this question by conducting a systematic review of the literature in order to assess the risk of postoperative infection in patients with preoperative polymicrobial urine culture and to provide the urologist with practices to minimise the risk of infection in these clinical situations.

Material and method

This systematic review of the literature was performed according to the criteria of Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) [6].

Eligibility criteria

The criteria for the studies to be retained were: all studies concerning patients over 18 years of age undergoing urological surgery with mention in the study of the outcome of preoperative urine culture, the notion of antibiotic prophylaxis and/or pre/post and postoperative antibiotic therapy and evaluation of the postoperative infection rate. A cut-off date was not chosen for the selection of articles since studies fulfilling the criteria were very rare. The studies selected were then grouped according to the type of surgery (endo-urological surgery, open surgery, surgery with material implantation).

Search strategy

All national and international recommendations were reviewed. A review of the literature was performed in both the Cochrane, LILACS and Medline libraries on 02/02/2018 using the following MeSH keywords: adenomectomy, antibiotic prophylaxis, artificial urinary sphincter, cystectomy, endourological surgery, ileal conduit, infection, incontinence, penile prosthesis, photo selective vaporization of the prostate, polymicrobial urine culture, preoperative, prostatectomy, prolapse, nephrectomy, neurologic bladder, urine, surgical wound infection, tension free vaginal tape, transobturator tape, transurethral prostate resections, TURB, TURP, urine exam, urine sample, urinary tract infection, urologic surgery, urological procedure, ureteral stent, ureteroscopy, urinary microbiota. The following search algorithm was used: ((polymicrobial) and ((urine culture) or (urine exam) or (urine sample) or (urinary tract infection) or ((infection) and (urine))) and ((urologic surgery) or (endourological surgery) or (preoperative) or (urological procedure) or (antibiotic prophylaxis) or (TURB) or (TURP) or (prolapse) or (nephrectomy) or (incontinence) or (adenomectomy) or (photo selective vaporization of the prostate) or (ureteral stent) or (neurologic bladder) or (ileal conduit) or (urinary tract infection) or (antibioprophylaxis) or (ureteroscopy) or (transurethral prostate resections) or (artificial urinary sphincter) or (penile prosthesis) or (cystectomy) or (prostatectomy) or (tension free vaginal tape) or (transobturator tape) or (urinary microbiota)). the articles were selected according to their methodology, language (English/French), and relevance to this study. An Internet search also identified other references, including guidelines.

Study selection and data extraction

All articles were selected by two authors (M.V. and F.B.), were then also audited by the other authors. All the studies collected, whether retrospective or prospective, were analysed. Only data related to studies linking polymicrobial urine culture before urological surgery to postoperative risk of infection were retained to be analysed. The notion of antibiotic prophylaxis or preoperative antibiotic therapy had to be mentioned.

Studies whose abstract was not available were excluded from the outset, as were basic research studies. Other reasons for exclusions included: abstract solely available, studies published in another foreign language or unable to be retrieved, endpoint/patient group not relevant, link between polymicrobial urine culture and postoperative infection not analysed, missing data to link postoperative infection with preoperative polymicrobial urine culture. The selection of studies is summarized in Figure 1.

Figure 1
Figure 1. 

PRISMA flow diagram detailing the search strategy.

The first part of this systematic review consisted in accurately defining the polymicrobial urine culture and clarifying the situations in which this clinical situation is encountered in urological surgery by explaining the mechanism of its occurrence. Data collection was then done liberally by M.V., followed by verification by all other authors.


The latest recommendations provide some details and recall the need to detect any urinary colonisation before any surgery in contact with urine [2]. Moreover, the optimal timeframe proposed for performing a urine culture seems to be between 10 to 4 days before the operative date [7]: beyond 10 days, the detection of a microorganism is likely to change, especially for patients who have ureteral stents or urinary catheters (see dedicated section). Performing 4 days or less before the operative date does not allow time enough to implement a possible antibiotic therapy [2].

A polymicrobial urine culture is defined as a urine culture isolating at least three microorganisms, of which none is predominant (as this would be considered as a pathogen). In such a case, the microbiologist usually does not perform identification nor antibiogram for isolated microorganisms except at the request of the clinician. The therapeutic attitude towards a urine culture revealing co-infection by two microorganisms is clearly defined for cystitis in premenopausal women [8]. On the other hand, there are no data for other clinical situations, especially febrile urinary tract infections.

Finally, it is important to make the difference between two clinical situations whose infectious risk is quite different: the polymicrobial urine culture in a patient with urinary stents or urinary catheters and that in a patient with no indwelling material.

Polymicrobial urine culture in a patient without ureteral stents or urinary catheters

In women, the presence of lactobacilli and/or a polymorphic flora, when associated with numerous epithelial cells, on direct examination, is highly suggestive of peri-urethral flora contamination. Similarly, a culture of Lactobacillus spp. or a polymorphic culture at 103 or 104 CFU/ml with more than two bacterial species is usually the result of contamination [2, 9].

In men, this evaluation is evaluated, in a single retrospective cohort of 370 patients, at 1.26% in patients before photo selective vaporization of the prostate among those suffering lower urinary tract symptoms [10].

The absence of leukocyturia (<104/mL), in both men and women, has an excellent negative predictive value nearly 97% but a low positive predictive value (<50%) [2].

In total, the absence of any symptoms associated with a leukocyturia <104/mL on the same polymicrobial urine culture could make it possible to exclude almost certainly the possibility of urinary colonisation.

This attitude is obviously gauged according to the clinical situation and the type of patients concerned. Indeed, the prevalence of urinary colonisation, less than 1% in young women, can reach 50% in older women and over 70% for these living in institutions. Similarly, the prevalence in men ranges from 0.7 to 40% depending on the population [11] with, more specifically, colonisation found in nearly 10% of the men without urinary catheters eligible for trans-urethral resection of prostate [12]. This may also be seen in infected stones (see dedicated section) [13]. It will therefore be necessary to know how to repeat the urine culture if the risk of urinary colonisation remains too high.

The practical attitude proposed to respond to such a clinical situation is summarised in Figure 2.

Figure 2
Figure 2. 

Management of polymicrobial urine culture in a patient without ureteral stents, urinary catheters or infected stones.

Polymicrobial urine culture in patients with ureteral stents or urinary catheters

Biofilm and colonisation of ureteral stents or urinary catheters

Colonisation of ureteral stents or urinary catheters is unavoidable. With respect to urinary catheters, the incidence of asymptomatic bacteriuria is estimated to be between 3 and 8% per day of catheterization [14]. This amounts to saying that after one month of urinary catheterisation, 100% of the patients will present a colonisation of urinary catheters. For ureteral stents, colonisation of the latter appears to be slower and variable depending on the patients' medical history, ranging from 4.2 to 74.4% in the first 90 days [15, 16, 17, 18]. Ureteral stents colonisation was observed in all patients with permanent ureteral stents which had been placed for a long time with iterative changes [15, 16, 17, 18]. In the case of colonised ureteral stents, the sensibility of urine culture, which counts only planktonic bacteria, remains low since it is only positive in 24 to 45% of cases [15, 16, 17, 18, 19, 20, 21]. Thus, in 55 to 75% of cases, a urinary colonisation would be neglected despite the fact that the ureteral stent is certainly colonised. This is explained by the life cycle of the biofilm [22, 23]. It is important to remember that the biofilm can also be built on other inert materials such as stones [13].

The presence of any preoperative endourological material is a factor favouring postoperative infection [24]. Nevertheless, it is nowadays demonstrated and admitted that there is no interest in preventive treatment, or in long-term antibiotic prophylaxis, to prevent the risk of colonisation of the ureteral stents or urinary catheters [2, 15, 17, 18, 19]. Moreover such a treatment could select multidrug-resistant bacteria (MDRB) [25, 26].

In addition, colonisation of ureteral stents or urinary catheters is usually polymicrobial and changes with time and type of patients. The colonisation of the material (detected by the culture of the ureteral stents) is variable according to the series: Gram-positive cocci (Enterococcus spp. , Staphylococcus aureus or coagulase-negative staphylococci) in 40 to 84% of cases, Pseudomonas aeruginosa in 14 to 23% of cases and Enterobacteriaceae in 23 to 31% of cases. In these same studies, a urine culture detects Enterobacteriaceae in 40 to 60% of cases, P. aeruginosa in 35 to 50% of cases, a Gram-positive coccus in 25 to 31% of cases and a Candida spp. in 0 to 10% of cases [15, 16, 17, 18, 19, 20]. The microorganisms isolated in urine culture are the same as those detected by ureteral stents culture in 30 to 45% of cases [15, 16, 17, 18, 19, 20].

Co-infection is thus common and it is in such situations that a polymicrobial urine culture is sometimes obtained. This appears to represent about 6 to 24% of patients with indwelling catheters or stents [21, 27, 28], but there is little data available.

Polymicrobial urine culture and endourological surgery

Obtaining a polymicrobial urine culture in this type of patient should not neglect the very high risk of urinary colonisation and should therefore be exceptionally considered as sterile. Indeed, one should keep in mind, although there are few studies, that the link between patients with ureteral stents or urinary catheters and infection after endo-urological surgery seems non-negligible, having been evaluated in the literature at 8% (TURP or laser vaporization of the prostate but without multivariate analysis) to 11% after ureteroscopy (risk factor in multivariate analysis for patients with preoperatively ureteral stent or percutaneous nephrostomy) [27, 29]. However, the many biases of these studies do not allow us to be sure about this risk. In addition, another retrospective cohort assessing the risk factors for severe infections after flexible ureteroscopy was not able to find any link between the presence of preoperative ureteral stents (number of days between ureteral stents placement and unspecified procedure) and postoperative infection [30].

A single, monocentric, retrospective cohort of 370 patients, evaluating the rate of complications after laser vaporization of the prostate, found a direct link between polymicrobial urine culture and postoperative urinary tract infection. In this study, a postoperative infection rate of 18.5% was found when a polymicrobial urine culture (at bacteriuria rates of 103 CFU/mL) existed despite intraoperative antibiotic prophylaxis. In addition, polymicrobial urine culture was a predicting factor in multivariate analysis of the occurrence of other complications [10].

The polymicrobial urine culture may be found sometimes in the absence of ureteral stents or urinary catheters but is often linked to the presence of stones on which biofilm also develops. Some authors mention rates of postoperative urinary tract infections at nearly 35% in the case of endoscopic surgery on a colonised stone [13].

Finally, the assessment of leukocyturia on urine sample seems to be an indirect manner to assess the importance of postoperative infectious risk. Indeed, a retrospective study, with 153 patients, of all types of ureteroscopy for urinary stones suggested that the risk of febrile UTI during ureteroscopy is directly correlated with the importance of pyuria in preoperative urine culture. In multivariate analysis, pyuria is a risk factor (OR=3.62 (1.26-8.11) P =0.017) of postoperative febrile urinary tract infection, which seems all the more serious since preoperative pyuria is highly prevalent [31].

Polymicrobial urine exam and open surgery

Performing open surgery on the urinary tract with presence of ureteral stents or urinary catheters is a less common clinical situation since the advent and development of endourological surgery. Nevertheless, this situation is sometimes encountered during carcinological or functional surgery such as adenomectomy. During this surgery, one study seems to find an important link between postoperative infection, presence of endourological ureteral stents or urinary catheters and polymicrobial urine culture even if the authors did not establish a direct link [32].

Polymicrobial urine exam and open surgery with implantation of artificial urinary sphincter, penile prosthesis or tension free vaginal tape

There are no referenced studies on the link between preoperative polymicrobial urine culture and postoperative infection requiring the removal of artificial urinary sphincter (AUS), penile prosthesis or tension free vaginal tape (TVT). On the other hand, a recent retrospective study has revealed results leading us to reconsider the relevance of a preoperative urine analysis and a fortiori that of treating a possible urinary colonisation before the AUS or penile prosthesis placement [33]. Indeed, there was no relationship between the microorganism isolated on preoperative urine culture and that isolated during infection of the material in 93% of cases (1 in 15 identical cases). This is reinforced by the fact that the few studies reporting infection on AUS mainly show infections with Gram-positive cocci (2 in 3 cases) and, in 1 in 3 cases Enterobacteriaceae or P. aeruginosa [34], indicating a cutaneous rather than urinary entry. The difficulties related to AUS implantation to obtain a reliable preoperative urine culture should also be recalled. Soaking, brought on by incontinence and the wearing of penis cases or protections, is probably responsible for the low value of leukocyturia and any microorganisms isolated. This seems consistent with the findings of the study by Kavoussy et al. The risk of having a positive preoperative urine culture before AUS is 4.5 times greater without increasing the risk of surgical site infections [33].

Regarding the tension-free vaginal tape (TVT) or tension-free vaginal tape-obturator (TVT-O), the risk of infection of the surgical site after TVT-O or TVT exposure seems low and evaluated at less than 1% in the literature with an almost non-existent risk of need for ablation of the tape [35, 36]. On the other hand, the risk of urinary infection is evaluated between 2.5 and 22% postoperatively [36]. No study referenced to date evaluates the polymicrobial urine culture before TVT.

Polymicrobial urine culture on Bricker ileal conduit

There is no scientific data available in this area. This case obviously sets a problem insofar as a urine culture in this type of patient is most of the time polymicrobial and bacterial colonisation obvious.


This review of the literature unfortunately suffers from the weakness of the scientific data (studies only at evidence level 3 and 4, meaning retrospective cohorts or case series) and so does not allow formal establishment of a strong scientific link between preoperative polymicrobial urine culture and postoperative infection.

First of all, it is important to remember that urine culture is currently the only reliable method for demonstrating the presence of urinary colonisation [5]. Indeed, the urinary dipstick must absolutely be banished since in 20 to 34% of cases, it neglects to demonstrate an authentic urinary colonisation [5, 37] which would lead to operate in a septic environment in the presence of an uncontrolled bacterial inoculum. The management of polymicrobial urine culture remains quite contested as it is based on little scientific data. However, this situation is frequently found in clinical practice and some attitudes could be generalised according to these results, such as in the case of patients with non-colonised ureteral stents, urinary catheters, or stones, as shown in Figure 2.

Regarding the same situation in patients with ureteral stents, urinary catheter or colonised stones the generalisation seems much less obvious. Indeed, the risk of misrecognising an authentic urinary colonisation during these clinical situations is much greater. Also, considering a polymicrobial urine culture as sterile seems inappropriate, especially before endourological surgery with epithelium breakages and tears such as transurethral resection or photo selective vaporization of the prostate. A retrospective study of Peyronnet et al. with 370 patients found a direct link between polymicrobial urine culture and postoperative infection: nearly one in five patients with polymicrobial urine culture had a postoperative septic complication while increasing the rate of other complications [10]. This is the only study that sought to highlight this link. It therefore seems difficult to neglect a polymicrobial urine culture in this population by calling it "contamination". Moreover, uteroscopy, where hyperpressure can increase risks of bacteremia, also seems a risky surgery in case of polymicrobial urine culture even if this link has never been shown in the literature. Finally, the risk also seems important in case of open surgery although there is little scientific data.

Interesting data on the other hand during open surgery with material placement argue in favour of the absence of screening for colonisation and a fortiori the failure to take into account a possible polymicrobial urine culture. Nevertheless, it is only a single study and the serious consequences of a possible infection after implantation of AUS and penile prosthesis will probably outweigh the precautionary principle within our community.

The change of the urinary catheter before the collection of a urine sample, carried out in the context of a future urological surgery, could make it possible to reduce the proportion of polymicrobial urine culture but to date there are no recommendations to this effect. In fact, the latest recommendations recall that "in a future urological surgery where the indwelling catheter is colonised, it is recommended to change the catheter after 24hours of curative antibiotic therapy and to operate after at least 48 hours" [2]. This would be the situation, if any colonisation, to change the urinary catheter twice within 10 days, which seems hardly feasible in clinical practice.

In total, all the scientific data collected make it possible to propose the decision tree in Figure 3.

Figure 3
Figure 3. 

Management of polymicrobial urine culture in patient with ureteral stents, urinary catheters or colonised stones.

In this decision algorithm, during an intervention with a high risk of postoperative infections risk, we propose the principle of a probabilistic antibiotic therapy in case of polymicrobial urine culture without possible identification. In this case, coverage antibiotics should be used, with the following characteristics: good urinary diffusion, low impact on the microbiota, wide coverage of enterobacteriaceae, good tolerance and ease of use. Fosfomycin-tromethamine appears to be a good compromise in this indication. Assuming there is no organ infection during colonisation and the need for tissue penetration is not essential, this molecule may be of interest in this treatment. Indeed, its spectrum of activity covers most of the bacteria responsible for colonisation/urinary tract infection outside Gram-positive cocci (nevertheless, efficacy on methicillin-susceptible staphylococci, with the exception of Staphylococcus saprophyticus ) [38]. Following the recommendations [2], treatment could be started 48hours before the surgical procedure with a single dose renewed the morning of the intervention. Indeed, the large urinary diffusion of this molecule offers effective concentrations for at least 36 to 48hours [39, 40, 41]. This attitude is not consensual but a prescription of probabilistic antibiotic treatment, in case of preoperative polymicrobial urine culture (especially before ureteroscopy or transurethral resection or photo selective vaporization of the prostate), could be an acceptable compromise. Indeed, a prescription of a perioperative antibiotic prophylaxis seems insufficient in these situations.


This literature review concerning polymicrobial urine culture shows the insufficiency of current knowledge to define a simple and optimal management of this situation in the context of a urological surgical procedure.

Nevertheless, the management of it in the context of patients without ureteral stents or urinary catheters seems to be generalisable. This is not the case, however, in patients with ureteral stents, urinary catheters or colonised stones and so a cautious attitude towards a polymicrobial urine culture must be adopted to avoid being simplistically and hastily considered "contaminated". On the contrary, the assessment infection risk should be even more rigorous and the prescription of a probabilistic antibiotic therapy could be an acceptable alternative, especially during a photo selective vaporization of the prostate or the infectious risk when the preoperative urine culture is polymicrobial or the risk of postoperative infection approaches 20%.

Finally, future prospects and studies, in particular on the urinary microbiota, will probably make it possible to advance our understanding of the colonisation of the urothelium and the way it should be managed in a surgical urological procedure.

Financial disclosure

Maxime Vallée is currently a research fellow and has received the financial support of the European Association of Urology (European Urological Scholarship Programme) and the French Association of Urology (AFU).

Author's contribution

M. Vallée: protocol/project development.

M. Vallée and F. Bruyère: data collection or management.

M. Vallée and F. Bruyère: data analysis.

M. Vallée, V. Cattoir, S. Malavaud, A. Sotto, G. Cariou, P. Arnaud, H. Bugel, P. Coloby, E. Chartier-Kastler and F. Bruyère: Manuscript writing/editing.

Disclosure of interest

The authors declare that they have no competing interest.


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