Recovery of bacteria by continuous renal replacement therapy in septic shock and by ultrafiltration from an in vitro model of bacteremia*

Culture-Dependent and Sequencing Methods Revealed the Absence of a Bacterial Community Residing in the Urine of Healthy Cats

A growing number of studies suggest that the lower urinary tract of humans and dogs can harbor a urinary microbiota. Nevertheless, a certain concern has developed that the microbiota reported could be due to unaccounted contamination, especially in low-biomass samples. The aim of this study was to investigate the bacterial community which populates the urine of healthy cats using two approaches: a culture-dependent approach which consisted of the expanded quantitative urine culture (EQUC) techniques capable of identifying live bacteria not growing in standard urine cultures, and a culture-independent approach which consisted of 16S ribosomal RNA next generation sequencing (16S rRNA NGS) capable of identifying bacterial DNA and exploring microbial diversity with high resolution. To avoid confounding factors of possible bacterial contamination, the urine was sampled using ultrasound-guided cystocentesis, and several sample controls and negative controls were analyzed. The urine sampled from the 10 cats included in the study showed no bacterial growth in the EQUC procedure. Although several reads were successfully originated using 16S rRNA NGS, a comparable pattern was observed between urine samples and the negative control, and no taxa were statistically accepted as non-contaminant. Taken together, the results obtained allowed stating that no viable bacteria were present in the urine of healthy cats without lower urinary tract disease and urinary tract infections, and that the bacterial DNA detected was of contaminant origin.

Residual of Bacterial Dna in Hemodialyzers: The Proof of Subclinical Infection Sustaining Chronic Inflammation

Background and purpose

Inflammation and infection seem to be important causes of morbidity and mortality in Chronic Kidney Disease (CKD) patients. Subclinical infections have been proposed as an important cause of inflammatory syndrome but to date this hypothesis remains speculative. In this investigation, we developed a method for molecular detection of the presence of bacterial DNA in a population of chronic kidney disease patients in order to correlate molecular data with the degree and level of inflammation and to evaluate the usefulness of the method in the diagnosis of subclinical infection.

Design

The study was divided into two phases: the study of a population of 81 CKD patients for prevalence and level of inflammation and infection; and the molecular evaluation of a subgroup of 38 patients without evident clinical causes of inflammation for molecular evaluation of subclinical infection.

Results

Patients hemoculture negative turned out positive for the presence of bacterial DNA when molecular methods were used. We found a trend of correlation with the presence of bacterial DNA and the increase in hs-CRP, IL-6 and oxidative stress (AOPP) levels and a reduction in MFI DR+. Hemodialyzer membranes seem to have properties that are “sticky” to bacteria/bacterial DNA and work as concentrators. Moreover our data suggest that DNA can traverse hemodialysis membranes.

Conclusions

Molecular methods have turned out to be far more sensitive than standard methods in detecting subclinical infection. The presence of bacterial DNA seems to influence the variation of some parameters of inflammation and immunity. Apart from the limitations and pitfalls, a molecular method could be useful for the screening of subclinical infection and diagnosis of sepsis when the hemoculture is negative. The identification of the microorganism involved, however, must be done with species-specific primers. These results are preliminary and more investigations will have to be performed in order to confirm our results.

Microbiology and epidemiology of Halomonas species

Halomonas has been organized as a genus since 1980, and comprises halophilic and/or halotolerant Gram-negative aerobic bacteria, typically found in saline environments. The genus is enlarging: at present, 76 species are taxonomically recognized, with more to be added. Increasing industrial uses have been found, largely in bioremediation and the production of desirable compounds. Originally seen as environmental contaminants, pathogenicity was initially not recognized; however, disease in algae, animals and humans has now been described. As the biotechnological use of these species increases, and the ability to isolate and recognize them improves, one might expect further pathogenic encounters with humans to be described.

Role of continuous renal replacement therapy ultrafiltrate cultures in the microbial diagnosis of sepsis

In a cohort of 23 critically ill patients receiving continuous renal replacement therapy, we investigated the role of ultrafiltrate fluid cultures as an adjunct to blood cultures in identifying the microbial etiology of sepsis. We found they provided no additional benefit and may yield false positives due to contamination.

Screening for bacteremia in sepsis and renal failure using hemofilters for renal replacement therapy

BACKGROUND

In patients with sepsis and renal failure, extracorporeal blood flow during renal replacement therapy may lead to the deposition of bacteria on artificial membranous surfaces, which might be suitable for the detection of pathogens. We studied whether discarded dialysis hemofilters can be used for the detection of bacteremia in patients with sepsis and renal failure.

METHODS

Hemofilters of 16 ICU patients with sepsis were sampled. The hemofilters were incubated with soy broth and dehisced under sterile conditions. Samples were plated on blood agar and analyzed. Patient's characteristics were assessed.

RESULTS

Despite the use of antibiotics in 87.5 % (14/16), a true positive detection rate of 31.3 % (5/16) for bacteremia was found by using cultures from hemofilters. The overall true positive rate of blood cultures was significantly lower (10.7 %, 8/75, p = 0.048). Bacteria detected in hemofilters were similar to those found in blood cultures or by cultures from other sources of infection in 80 % (4/5).

CONCLUSIONS

Cultures from used hemofilters of patients with sepsis and renal failure provide the opportunity to identify pathogenic microorganisms as an add-on approach. Further studies should investigate whether this method is applicable in clinical practice to enhance the sensitivity of microbiological diagnostics.

Halomonas, a newly recognized human pathogen causing infections and contamination in a dialysis center: three new species

Our Renal Care Center (RCC) is a separate building, performing almost 2500 outpatient dialysis runs per month. In May 2007, 2 patients developed, days apart, bacteremia with an apparently identical nonfermentative Gram-negative rod. Because of difficulty identifying the organism, testing in the Biolog system identified them as a Halomonas species. Sequencing of approximately 1500 bases of the 16S rRNA gene in both organisms in 3 reference laboratories confirmed, searching against 3 databases, that the organisms were identical and were Halomonas species. There were 54 recognized species of this genus, associated with marine or saline sites. Initial attempts at environmental isolation as primary cultures, including a 4% salt agar plate, or initial incubation in 6.5% salt broth enrichment culture with subculture to agar, to exploit the halophilicity of Halomonas, were successful in demonstrating the colonies seen in the blood cultures, only from sites not contaminated with other organisms, because of competing growth. A more selective method was developed for use on samples suspected to be heavily contaminated with other organisms, using the strategy of increased salt concentration in a broth enrichment culture to further exploit Halomonas halotolerance, and thereby inhibit other organisms. A 16.5% salt concentration in brain-heart infusion broth, incubated at 35 degrees C for 48-72 hours, then subcultured to agar plates incubated in room air at 35 degrees C, proved optimal for selection and secondary isolation. With a combination of these techniques, 14/15 cultures of dialysates and 10/38 from the outflow pathways of the machines were Halomonas positive, compared to 0/31 cultures from the inflow side of the machines (including water supplies and storing, mixing, and preparation tanks). The exception was sites associated with or downstream of bicarbonate influx, 12/54 of which were positive. Two other local hospitals' dialysis centers, and our own inpatient dialysis facility, were cultured at sites that yielded Halomonas from our RCC, and Halomonas was not isolated. Further study by 16S rRNA gene sequencing and DNA-DNA hybridization revealed the cultures represented 3 novel species: 1 (H. stevensii sp. nov.) in the patients and environment and 2 (H. hamiltonii sp. nov., H. johnsoniae sp. nov.) in the environment, most closely related to H. magadiensis. Of 35 speciated isolates, 22 were H. stevensii, 10 H. johnsoniae, and 3 H. hamiltonii. We hypothesize that the RCC became contaminated with these halophilic organisms from bicarbonate used to prepare dialysis fluid, and they persist despite cleaning and flushing procedures because of biofilm in machines and bicarbonate fluid inflow sites. Our experience, together with the review of the literature presented here, indicates the genus Halomonas has pathogenic potential.

Percutaneous nephrolithotomy of patients with staghorn stone and incidental purulent fluid suggestive of infection

BACKGROUND AND PURPOSE

Patients undergoing percutaneous nephrolithotomy (PCNL) sometimes have purulent fluid in the puncture site in spite of having no signs or symptoms of infection preoperatively. We report the safety and effectiveness of PCNL in 45 patients with staghorn renal stones and incidental purulent fluid in the pelvicaliceal system.

PATIENTS AND METHODS

Of 1264 patients who underwent PCNL at our medical center from February 2002 to May 2006, 45 patients had purulent fluid in the initial puncture. These patients were asymptomatic, and the preoperative work-up did not suggest infection. In 29 patients (group 1), stone removal was accomplished during the first session, while for 16 patients (group 2), a nephrostomy tube remained in place and stone removal occurred 3 to 5 days later when results of urine and nephrostomy fluid cultures were negative. We studied preoperative findings, stone-free rate, intraoperative and postoperative complications, and final outcome of these patients.

RESULTS

The stone-free rate was almost similar in the two groups (86.2% v 81.25%, P = 0.9). In groups 1 and 2, three (10.3%) and two (12.5%) patients experienced low-grade fever for 12 to 24 hours (P = 0.179). In group 1, urine cultures revealed Escherichia coli in three patients and Pseudomonas aeruginosa in two patients, while 24 (82.7%) patients had negative fluid cultures. In group 2, results of urine cultures showed E coli in two patients and Klebsiella pneumoniae in one patient; results of urine cultures of 13 (81.2%) patients were negative (P = 0.78). Mean operative time was 70 minutes in both groups. No intraoperative or postoperative complications other than fever were seen in both groups.

CONCLUSION

In patients who undergo PCNL, purulent fluid may be found incidentally in the puncture site. PCNL may be performed with full antibiotic coverage at the same session.

Inflammation and Subclinical Infection in Chronic Kidney Disease: A Molecular Approach

Inflammation and infection seem to be important causes of morbidity and mortality in chronic kidney disease (CKD) patients; subclinical infections have been proposed as an important cause of inflammatory syndrome, but to date this hypothesis remains speculative. We developed a method for the molecular detection of the presence of bacterial DNA in a population of CKD patients in order to correlate the molecular data with the degree and level of inflammation and to evaluate its usefulness in the diagnosis of subclinical infection. The study was divided into two phases: (1) a population of 81 CKD patients was screened for the prevalence and level of inflammation and the presence of possible infection, and (2) a subgroup of 38 patients, without evident clinical causes of inflammation, underwent complete molecular evaluation for subclinical infection using bacterial DNA primers for sequencing. Additionally, complete analysis was carried out in the blood and dialysate compartments of the hemodialyzers used. The general population showed a certain degree of subclinical inflammation and no difference was found between patients with and without evident causes of inflammation. Hemoculture-negative patients were positive for the presence of bacterial DNA when molecular methods were used. We found a correlation trend between the presence of bacterial DNA and the increase in hs-CRP, IL-6 and oxidative stress (advanced oxidation protein product) levels and a reduction in the mean fluorescence intensity for HLA-DR. Hemodialyzer membranes seem to have properties that stick to bacteria/bacterial DNA and work as concentrators. In fact, patients with negative bacterial DNA in the circulating blood displayed positivity in the blood compartment of the dialyzer. The dialysate was negative for bacterial DNA but the dialysate compartment of the hemodialyzers used was positive in a high percentage. Moreover our data suggest that bacterial DNA can traverse hemodialysis membranes. Molecular methods have been found to be far more sensitive than standard methods in detecting subclinical infection. The presence of bacterial DNA seems to influence the variation in some parameters of inflammation and immunity. Apart from the limitations and pitfalls, the molecular method could be useful to screen for subclinical infection and diagnose subclinical sepsis when the hemoculture is negative. However, the identification of the microorganism implicated must be done with species-specific primers.

Usefulness of a Molecular Strategy for the Detection of Bacterial DNA in Patients with Severe Sepsis Undergoing Continuous Renal Replacement Therapy

INTRODUCTION

Sepsis is a major cause of morbidity and mortality in critically ill patients. Sepsis is associated with cell necrosis and apoptosis. Circulating plasma levels of DNA have been found in conditions associated with cell death, including sepsis, pregnancy, stroke, myocardial infarction and trauma. Plasma DNA can also derive from bacteria. We have recently implemented a method to detect bacterial DNA and, in the present study, we validated this technique comparing it to standard blood culture in terms of diagnostic efficacy.

METHODS

We examined a cohort of 9 critically ill patients with a diagnosis of severe sepsis and acute renal failure requiring continuous renal replacement therapy (CRRT). We analyzed bacterial DNA in blood, hemofilters, and ultrafiltrate (UF) by polymerase chain reaction amplification of 16S rRNA gene sequence analysis. Standard blood cultures were performed for all patients.

RESULTS

The blood cultures from 2 of the 9 (22%) patients were positive. However, bacterial DNA was identified in the blood of 6 patients (67%), including the 2 septic patients with positive blood cultures. In 9 (100%) patients bacterial DNA was found on the filter blood side, whereas in 7 (78%) subjects it was found in the dialysate compartment of the hemofilters. Bacterial DNA was never detected in the UF.

CONCLUSIONS

Using the 16S rRNA gene, the detection of bacterial DNA in blood and adsorbed within the filter could be a useful screening tool in clinically septic, blood culture-negative patients undergoing CRRT. However, the identification of the etiologic agent is not feasible with this technique because specific primers for the defined bacteria must be used to further identify the suspected pathogenic organisms.

Incidental detection of purulent fluid in kidney at percutaneous nephrolithotomy for branched renal calculi

BACKGROUND AND PURPOSE

Some patients undergoing percutaneous nephrolithotomy (PCNL) have purulent fluid in the pelvicaliceal system at the time of puncture, although preoperative features are not suggestive of infection. We report the management and outcome of 19 such patients.

PATIENTS AND METHODS

Among the 639 patients who underwent PCNL at our center from July 2000 to October 2003, 19 had purulent fluid in the kidney at initial puncture. The preoperative findings, operative details, hospital course, and final outcome in these patients were analyzed. Twelve patients had stone removal at the first sitting (option 1), while seven had a nephrostomy tube placed initially with stone removal deferred for 3 to 7 days (option 2).

RESULTS

With option 1, stones were cleared with one to three tracts in 45 to 120 minutes. Seven patients recovered smoothly, three had transient fever, while one had grade I and another had grade II sepsis. The purulent fluid grew E. coli in two cases and Proteus or Serratia in one case each and was sterile in eight. With option 2, stones were cleared using one to three tracts in 60 to 100 minutes. The fluid grew E. coli or Klebsiella in one case each and was sterile in five. Three patients had a smooth recovery, two had transient fever, one had grade I sepsis, and another had grade II sepsis. Risk factors for sepsis, irrespective of the option, were a recent history of febrile urinary-tract infection, borderline elevation of total leukocyte count, thick or foul pus as opposed to mere turbidity, the use of a single tube or tract or delayed creation of second tracts, and operating time >90 minutes.

CONCLUSIONS

Despite normal preoperative urine and blood values, one may find purulence on puncture during PCNL, which is not always infected. If any one or more of the above risk factors is present, it is safer to drain the kidney initially, making sure that all blocked calices are drained, inserting multiple tubes if necessary.