Hidden pathogens uncovered: metagenomic analysis of urinary tract infections

Field-Deployable Colorimetric Array for On-Site Diagnosis of Urinary Tract Infection and Identification of Causative Pathogens

Urinary tract infection (UTI) is a common and prevalent disease caused by a spectrum of pathogens. Lack of access to rapid, portable, and high-quality diagnostics in resource-limited settings aggravates the improper treatment of UTIs, which is also a major driver of antibiotic misuse worldwide. Here, we describe a custom-made portable colorimetric array (PoCA) for reading out polymerase chain reaction (PCR) amplicons, the rationale of which is to transfer the previously developed dsDNA-based photosensitization colorimetric assay (solution) onto paper discs for detection. By integrating mini-LED irradiation and paper discs, the PoCA can read out 96 PCR tests in one pot, thus allowing diagnosis and identification of 12 prevailing UTI pathogens in less than 2 h, coupled with a portable thermal cycler for PCR. After analyzing 200 clinical urine samples, the pathogen profiling accuracy of the PoCA was demonstrated to be higher than the standard urine culture (confirmed with metagenomic next-generation sequencing). The PoCA platform could be used in primary care for rapid UTI diagnosis and pathogen identification.

Molecular Diagnostic Methods Versus Conventional Urine Culture for Diagnosis and Treatment of Urinary Tract Infection: A Systematic Review and Meta-analysis

Context

Objective

Evidence acquisition

Evidence synthesis

Conclusions

Patient summary

Comparison Analysis of Different DNA Extraction Methods on Suitability for Long-Read Metagenomic Nanopore Sequencing

Metagenomic next-generation sequencing (mNGS) is a novel useful strategy that is increasingly used for pathogens detection in clinic. Some emerging mNGS technologies with long-read ability are useful to decrease sequencing time and increase diagnosed accuracy, which is of great significance in rapid pathogen diagnosis. Reliable DNA extraction is considered critical for the success of sequencing; hence, there is thus an urgent need of gentle DNA extraction method to get unbiased and more integrate DNA from all kinds of pathogens. In this study, we systematically compared three DNA extraction methods (enzymatic cell lysis based on MetaPolyzyme, mechanical cell lysis based on bead beating, and the control method without pre-cell lysis, respectively) by assessing DNA yield, integrity, and the microbial diversity based on long-read nanopore sequencing of urine samples with microbial infections. Compared with the control method, the enzymatic-based method increased the average length of microbial reads by a median of 2.1-fold [Inter Quartile Range (IQR), 1.7-2.5; maximum, 4.8) in 18 of the 20 samples and the mapped reads proportion of specific species by a median of 11.8-fold (Inter Quartile Range (IQR), 6.9-32.2; maximum, 79.27]. Moreover, it provided fully (20 of 20) consistent diagnosed results to the clinical culture and more representative microbial profiles (P < 0.05), which all strongly proves the excellent performance of enzymatic-based method in long-read mNGS-based pathogen identification and potential diseases diagnosis of microbiome related.

A Proteomics Approach to Identify Possible Biomarkers of Early and Late Stages of E. coli-induced Urinary Tract Infections

As one of the most common bacterial infections globally, urinary tract infections (UTI)s affect the bladder and kidneys of many the bladders and kidneys of many. Along with gram-negative bacteria, Escherichia coli (E. coli) causes nearly 40% of nosocomial UTIs, 25% of recurrent infections, and between 80 to 90% of community-acquired infections. Proteomics, commonly used to study changes in protein expression of organisms, can be used to explore candidate biomarkers useful for the diagnosis of pathological conditions. Here, protein profiles of samples from patients diagnosed with E. coli-induced UTI were compared to identify distinctive proteins. Extracted proteins from bacteria from patients’ urine samples were separated into excisable spots using 2D-gel electrophoresis. The gels were then analyzed using Progenesis SameSpot software to select uniquely expressed protein spots, excised, and analyzed by LC/MS. The results were then compared against a database of known proteins. We identified two proteins, outer membrane protein A (OmpA) and RNA polymerase-binding transcription factor (DksA), involved in the survival of E. coli in the harsh environment of the host. We suggest their use as a part of a battery of possible biomarkers proteins for E. coli-induced UTI, and suggest that their overexpression is possibly associated with the stage of infection, early or late.

Using Functional Annotations to Study Pairwise Interactions in Urinary Tract Infection Communities

The behaviour of microbial communities depends on environmental factors and on the interactions of the community members. This is also the case for urinary tract infection (UTI) microbial communities. Here, we devise a computational approach that uses indices of complementarity and competition based on metabolic gene annotation to rapidly predict putative interactions between pair of organisms with the aim to explain pairwise growth effects. We apply our method to 66 genomes selected from online databases, which belong to 6 genera representing members of UTI communities. This resulted in a selection of metabolic pathways with high correlation for each pairwise combination between a complementarity index and the experimentally derived growth data. Our results indicated that Enteroccus spp. were most complemented in its metabolism by the other members of the UTI community. This suggests that the growth of Enteroccus spp. can potentially be enhanced by complementary metabolites produced by other community members. We tested a few putative predicted interactions by experimental supplementation of the relevant predicted metabolites. As predicted by our method, folic acid supplementation led to the increase in the population density of UTI Enterococcus isolates. Overall, we believe our method is a rapid initial in silico screening for the prediction of metabolic interactions in microbial communities.

Urinary Microbiome: Yin and Yang of the Urinary Tract

The application of next generation sequencing techniques has allowed the characterization of the urinary tract microbiome and has led to the rejection of the pre-established concept of sterility in the urinary bladder. Not only have microbial communities in the urinary tract been implicated in the maintenance of health but alterations in their composition have also been associated with different urinary pathologies, such as urinary tract infections (UTI). Therefore, the study of the urinary microbiome in healthy individuals, as well as its involvement in disease through the proliferation of opportunistic pathogens, could open a potential field of study, leading to new insights into prevention, diagnosis and treatment strategies for urinary pathologies. In this review we present an overview of the current state of knowledge about the urinary microbiome in health and disease, as well as its involvement in the development of new therapeutic strategies.

Actinotignum schaalii: Relation to Concomitants and Connection to Patients' Conditions in Polymicrobial Biofilms of Urinary Tract Catheters and Urines

Actinotignum schaalii is an emerging, opportunistic pathogen and its connection to non-infectious diseases and conditions, such as prostate or bladder cancer, or chronic inflammation has been proposed. Here, we analyzed 297 urine, ureteral and urinary catheter samples from 128 patients by Polymerase Chain Reaction followed by Denaturing Gradient Gel Electrophoresis and Sequencing (PCR-DGGE-S), and culture, and 29 of these samples also by 16S rRNA Illumina sequencing, to establish A. schaalii’s prevalence in urinary tract-related samples, its relation to other bacteria, and its potential association with patients’ conditions and samples’ characteristics. A. schaalii-positive samples were significantly more diverse than A. schaalii negative and between-group diversity was higher than intra-group. Propionimicrobium lymphophilum, Fusobacterium nucleatum, Veillonella sp., Morganella sp., and Aerococcus sp. were significantly more often present in A. schaalii-positive samples; thus, we suggest these species are A. schaalii’s concomitants, while Enterobacter and Staphylococcaceae were more often identified in A. schaalii-negative samples; therefore, we propose A. schaalii and these species are mutually exclusive. Additionally, a significantly higher A. schaalii prevalence in patients with ureter stricture associated hydronephrosis (p = 0.020) was noted. We suggest that A. schaalii could be an early polybacterial biofilm colonizer, together with concomitant species, known for pro-inflammatory features.

Conceptualizing the Vertebrate Sterolbiome

Vertebrates synthesize a diverse set of steroids and bile acids that undergo bacterial biotransformations. The endocrine literature has principally focused on the biochemistry and molecular biology of host synthesis and tissue-specific metabolism of steroids. Host-associated microbiota possess a coevolved set of steroid and bile acid modifying enzymes that match the majority of host peripheral biotransformations in addition to unique capabilities. The set of host-associated microbial genes encoding enzymes involved in steroid transformations is known as the sterolbiome. This review focuses on the current knowledge of the sterolbiome as well as its importance in medicine and agriculture.

Reincubation of culture-negative urines for an additional 20 hours does not identify additional UTI cases

Introduction

The question of whether a single day of incubation is sufficient for urine cultures has been a matter of debate.

Aim

The aim of this study was to investigate the potential benefit of prolonged incubation for initially culture-negative urines.

Methodology

Eight hundred and twelve urine specimens with no growth after incubation for 20 h were incubated for an additional 20 h to detect slower growing uropathogenic organisms.

Results

This study included a considerable number of urine cultures from immunocompromised and/or kidney-transplanted patients. For 99.9 % of the specimens, there was no difference in the interpretation of results.

Conclusion

Twenty hours of incubation did not have any negative effect on the detection of uropathogens.

A rare case of bacteremia caused by Propionibacterium (Propionimicrobium) lymphophilum

Propionibacterium (Propionimicrobium) lymphophilum is a Gram-positive anaerobic rod involved in few human diseases. We report a rare case of bacteremia due to this microorganism in an elderly patient. A 95-year-old woman without a remarkable medical history presented with dyspnea, chest pain and fever for seven days. Blood cultures resulted in isolation of P. lymphophilum. Resistance only to metronidazole was found. Treatment with amoxicillin-clavulanic acid was established, and the patient was discharged and improvement of her general condition was documented.

High prevalence of urogenital infection/inflammation in patients with azoospermia does not impede surgical sperm retrieval

Considering infection/inflammation to be an important risk factor in male infertility, the aim of this study was to make a comprehensive evaluation of the prevalence of urogenital tract infection/inflammation and its potential impact on sperm retrieval in azoospermic patients. In this prospective study, 71 patients with azoospermia were subjected to an extensive andrological workup including comprehensive microbiological diagnostics (2-glass test, semen, testicular swab and testicular tissue analysis) and testicular biopsy/testicular sperm extraction (TESE). Medical history suggested urogenital tract infection/inflammation in 7% of patients, 11% harboured STIs, 14% showed significant bacteriospermia, 15% had seminal inflammation, 17% fulfilled the MAGI definition, and 27% had relevant pathogens. At the testicular level, 1 patient had a swab positive for bacteria, no viruses were detected, tissue specimens never indicated pathogens, whereas histopathology revealed focal immune cell infiltrates in 23% of samples. Testicular sperm retrieval rate was 100% in obstructive and 46% in nonobstructive azoospermia. None of the infection/inflammation-related variables was associated with the success of sperm retrieval or inflammatory lesions in the testis. The high prevalence of urogenital infection/inflammation among azoospermic men underpins their role as significant aetiologic factors in male infertility. However, this observation does not refer to the chances of sperm retrieval at the time of surgery/TESE.

Relationship between alterations of urinary microbiota and cultured negative lower urinary tract symptoms in female type 2 diabetes patients

Background

Lower urinary tract symptoms (LUTS) is the most common complication of diabetes. However, the underlying pathogenesis of cultured negative LUTS (cn-LUTS) in diabetic patients has not been well understood. Numerous evidence indicates that urinary dysbiosis is related to urologic disorders. We aim to study alterations of the urinary microbiota of cn-LUTS in type 2 diabetes (T2D) patients.

Methods

Female T2D patients and controls were recruited and requested to finish the American Urological Association Symptom Index. Mid-stream urine was collected for culturing and extracting DNA. Microbial diversity and composition were analyzed by targeting to 16S rDNA. Linear discriminant analysis effect size (LEfSe) was carried out to identify significantly different bacteria.

Results

32 female T2D patients and 26 controls were enrolled. No significant differences in alpha diversity were observed between patients and controls. However, statistically decreased richness (ACE index and Chao 1 index, 85.52(13.75, 204.84) vs. 129.82(63.89, 280.30) and 83.86(11.00, 210.77) vs. 125.19(62.00, 251.77), P = 0.005; Observed Species, 76(10, 175) vs. 98(54, 234), P = 0.011) and decreased species diversity (Shannon index, 1.37(0.04, 3.48) vs. 2.09(0.98, 3.43), P = 0.033; Simpson index, 0.46 (0.06, 0.99) vs. 0.23(0.07, 0.64), P = 0.029) were shown in moderate-to-severe LUTS group and high Hemoglobin A1c group, respectively. A significant difference of beta diversity was found between T2D patients and controls and T2D patients with different severity of cn-LUTS as well as the different level of Hemoglobin A1c. LEfSe revealed that 10 genera (e.g., Escherichia-Shigella and Klebsiella) were increased and 7 genera were decreasing in T2D patients, 3 genera (e.g., Escherichia-Shigella and Campylobacter) were increased and 16 genera (e.g., Prevotella) were reduced in moderate-to-severe LUTS group, 2 genera (Escherichia-Shigella and Lactobacillus) were over-represented and 10 genera (e.g., Prevotella) were under-represented in high Hemoglobin A1c group. Finally, Hemoglobin A1c was found positively correlated with the total score of the American Urological Association Symptom Index (r = 0.509, P = 0.003).

Conclusions

Urinary dysbiosis may be related to cn-LUTS in female T2D patients. A better understanding of urinary microbiota in the development and progression of cn-LUTS in female T2D patients was necessary. The severity of cn-LUTS was correlated to hyperglycemia and chronic hyperglycemia might induce or promote cn-LUTS by influencing urinary microbiota.

Electronic supplementary material

The online version of this article (10.1186/s12894-019-0506-0) contains supplementary material, which is available to authorized users.

Recurrent episodes of feline lower urinary tract disease with different causes: possible clinical implications

CASE SERIES SUMMARY

While descriptions of cats with recurrent episodes of feline idiopathic cystitis (FIC) exist, little is published on cats with recurrent episodes of feline lower urinary tract disease (FLUTD) where the cat is diagnosed with different causes of FLUTD at separate episodes. In the present paper, six cats, originally part of larger studies of FLUTD among Norwegian cats, are described. In the project period (2003-2009), these cats had several episodes of FLUTD. At each episode, the cats had a complete physical examination, abdominal imaging, blood work, urinalysis and urine culture performed. Two of the cats initially presented with urolithiasis and subsequently with episodes of non-obstructed FIC. Four of the cats presented with non-obstructed FIC at one or more episodes, but were later diagnosed with urolithiasis or bacterial cystitis without prior catheterisation or other known predisposing factors.

RELEVANCE AND NOVEL INFORMATION

Cats with recurrent episodes of FLUTD may present with different causes at different times. The need to thoroughly work-up cats with recurrent episodes of FLUTD at each presentation is emphasised. FIC may be considered as a predisposing factor in cats developing urolithiasis or bacterial cystitis; alternatively, interrelated FLUTD disease mechanisms exists. Thus, applying multimodal environmental enrichment and modification (MEMO) to cats with signs of FLUTD independent of diagnosis should be considered.

Molecular Techniques Complement Culture-Based Assessment of Bacteria Composition in Mixed Biofilms of Urinary Tract Catheter-Related Samples

Urinary or ureteral catheter insertion remains one of the most common urological procedures, yet is considered a predisposing factor for urinary tract infection. Diverse bacterial consortia adhere to foreign body surfaces and create various difficult to treat biofilm structures. We analyzed 347 urinary catheter- and stent-related samples, treated with sonication, using both routine culture and broad-range 16S rDNA PCR followed by Denaturing Gradient Gel Electrophoresis and Sanger sequencing (PCR-DGGE-S). In 29 selected samples, 16S rRNA amplicon Illumina sequencing was performed. The results of all methods were compared. In 338 positive samples, from which 86.1% were polybacterial, 1,295 representatives of 153 unique OTUs were detected. Gram-positive microbes were found in 46.5 and 59.1% of catheter- and stent-related samples, respectively. PCR-DGGE-S was shown as a feasible method with higher overall specificity (95 vs. 85%, p < 0.01) though lower sensitivity (50 vs. 69%, p < 0.01) in comparison to standard culture. Molecular methods considerably widened a spectrum of microbes detected in biofilms, including the very prevalent emerging opportunistic pathogen Actinotignum schaalii. Using massive parallel sequencing as a reference method in selected specimens, culture combined with PCR-DGGE was shown to be an efficient and reliable tool for determining the composition of urinary catheter-related biofilms. This might be applicable particularly to immunocompromised patients, in whom catheter-colonizing bacteria may lead to severe infectious complications. For the first time, broad-range molecular detection sensitivity and specificity were evaluated in this setting. This study extends the knowledge of biofilm consortia composition by analyzing large urinary catheter and stent sample sets using both molecular and culture techniques, including the widest dataset of catheter-related samples characterized by 16S rRNA amplicon Illumina sequencing.

ProteoStorm: An Ultrafast Metaproteomics Database Search Framework

Shotgun metaproteomics has the potential to reveal the functional landscape of microbial communities but lacks appropriate methods for complex samples with unknown compositions. In the absence of prior taxonomic information, tandem mass spectra would be searched against large pan-microbial databases, which requires heavy computational workload and reduces sensitivity. We present ProteoStorm, an efficient database search framework for large-scale metaproteomics studies, which identifies high-confidence peptide-spectrum matches (PSMs) while achieving a two-to-three orders-of-magnitude speedup over popular tools. A reanalysis of a urinary tract infection (UTI) dataset of 110 individuals revealed a complex pattern of polymicrobial expression, including sub-types of UTIs, cases of bacterial vaginosis, and evidence of no underlying disease. Importantly, compared to the initial UTI study that restricted the search database to a manually curated list of 20 genera, ProteoStorm identified additional genera that were previously unreported, including a case of infection with the rare pathogen Propionimicrobium.

Presence of anaerobic bacteria in the urinary tract of catheterized ICU patients

The purpose of our study was to examine the extent of anaerobic bacteriuria in catheterized patients in the intensive care unit (ICU) and to search for risk factors for anaerobic bacteriuria. A urine culture was collected from each patient every 2 days during their ICU stay and incubated under aerobic and anaerobic conditions. Aerobic and anaerobic blood cultures were collected as well. Demographic, clinical, and laboratory data were collected from patient files. Ninety patients were included in this study, 32 women (35.6%) and 58 men (64.4%). A total of 663 cultures were obtained. Twenty-three patients (25.6%) had growth of anaerobic bacteria in a urinary culture at some point during ICU stay, with Bifidobacterium being the most common pathogen. Aerobic urinary cultures were positive in 38 patients (42.2%). A significant statistical correlation was found between the presence of aerobic and anaerobic bacteria in urine culture (p = 0.0004). Treatment with glycopeptides was found to be inversely associated with anaerobic bacteriuria (p = 0.0292), and treatment with imidazoles was associated with an increased risk of anaerobic bacteriuria (p = 0.0186). None of the patients developed bacteremia with the same anaerobic pathogen that was isolated from their urine. Anaerobic bacteriuria is a common phenomenon in catheterized patients in the ICU. Further studies are needed in order to define the clinical significance of these findings in such patients and in other patient groups as well as in healthy people.

Significant increase in cultivation of Gardnerella vaginalis, Alloscardovia omnicolens, Actinotignum schaalii, and Actinomyces spp. in urine samples with total laboratory automation

While total laboratory automation (TLA) is well established in laboratory medicine, only a few microbiological laboratories are using TLA systems. Especially in terms of speed and accuracy, working with TLA is expected to be superior to conventional microbiology. We compared in total 35,564 microbiological urine cultures with and without incubation and processing with BD Kiestra TLA for a 6-month period each retrospectively. Sixteen thousand three hundred thirty-eight urine samples were analyzed in the pre-TLA period and 19,226 with TLA. Sixty-two percent (n = 10,101/16338) of the cultures processed without TLA and 68% (n = 13,102/19226) of the cultures processed with TLA showed growth. There were significantly more samples with two or more species per sample and with low numbers of colony forming units (CFU) after incubation with TLA. Regarding the type of bacteria, there were comparable amounts of Enterobacteriaceae in the samples, slightly less non-fermenting Gram-negative bacteria, but significantly more Gram-positive cocci, and Gram-positive rods. Especially Alloscardivia omnicolens, Gardnerella vaginalis, Actinomyces spp., and Actinotignum schaalii were significantly more abundant in the samples incubated and processed with TLA. The time to report was significantly lower in the TLA processed samples by 1.5 h. We provide the first report in Europe of a large number of urine samples processed with TLA. TLA showed enhanced growth of non-classical and rarely cultured bacteria from urine samples. Our findings suggest that previously underestimated bacteria may be relevant pathogens for urinary tract infections. Further studies are needed to confirm our findings.

Gram-Positive Uropathogens, Polymicrobial Urinary Tract Infection, and the Emerging Microbiota of the Urinary Tract

Gram-positive bacteria are a common cause of urinary-tract infection (UTI), particularly among individuals who are elderly, pregnant, or who have other risk factors for UTI. Here we review the epidemiology, virulence mechanisms, and host response to the most frequently isolated Gram-positive uropathogens: Staphylococcus saprophyticus, Enterococcus faecalis, and Streptococcus agalactiae. We also review several emerging, rare, misclassified, and otherwise underreported Gram-positive pathogens of the urinary tract including Aerococcus, Corynebacterium, Actinobaculum, and Gardnerella. The literature strongly suggests that urologic diseases involving Gram-positive bacteria may be easily overlooked due to limited culture-based assays typically utilized for urine in hospital microbiology laboratories. Some UTIs are polymicrobial in nature, often involving one or more Gram-positive bacteria. We herein review the risk factors and recent evidence for mechanisms of bacterial synergy in experimental models of polymicrobial UTI. Recent experimental data has demonstrated that, despite being cleared quickly from the bladder, some Gram-positive bacteria can impact pathogenic outcomes of co-infecting organisms. When taken together, the available evidence argues that Gram-positive bacteria are important uropathogens in their own right, but that some can be easily overlooked because they are missed by routine diagnostic methods. Finally, a growing body of evidence demonstrates that a surprising variety of fastidious Gram-positive bacteria may either reside in or be regularly exposed to the urinary tract and further suggests that their presence is widespread among women, as well as men. Experimental studies in this area are needed; however, there is a growing appreciation that the composition of bacteria found in the bladder could be a potentially important determinant in urologic disease, including susceptibility to UTI.

Microbiomic Analysis of Intra-Abdominal Infections by Using Denaturing High-Performance Liquid Chromatography: A Prospective Observational Study

BACKGROUND

Intra-abdominal infections represent a subgroup of septic syndromes with high death rates and the need for prompt and appropriate antimicrobial therapy. Conventional culture-based microbial identification has notable shortcomings in the diagnostics of polymicrobial infections. Modern culture-independent molecular methods may represent a new diagnostic approach. The current study aimed to compare the results obtained from the denaturing high-performance liquid chromatography WAVE^® system as a culture-independent diagnostic tool with those obtained from standard culture-based microbiologic testing in the clinical setting of severe intra-abdominal sepsis.

PATIENTS AND METHODS

The study included 42 samples of pathologic intra-abdominal fluids, collected from 37 patients with intra-abdominal sepsis. Micro-organisms grown in culture and detected by the WAVE system were compared. Further, we recorded clinical data including baseline characteristics and the use of antibiotic agents.

RESULTS

In 38.1% of the analyzed samples, the classic, culture-based methods showed no bacterial growth on agar plates, in comparison with the microbiomic analysis in which the proportion of samples with negative signal was 31%. In about 40% of the patients, both methods detected one microbiologic agent, whereas in approximately one quarter of the samples, two or more agents were identified. The detection rate of certain bacteria such as Enterobacteriacae or Enterococcus faecium was significantly higher using the microbiomic analysis. Bacteria such as Haemophilus, Lactobacillus, Clostridium, Methylobacterium, Collinsella aerofaciens, and Solobacterium moorei were detected exclusively using microbiomic analysis.

CONCLUSION

The culture independent molecular WAVE system provided additional information, especially concerning unusual, fastidious bacteria in patients with intra-abdominal infections. Further, it has a higher detection rate for polymicrobial infection and delivers results much sooner than conventional microbiologic methods.

Propionimicrobium lymphophilum and Actinotignum schaalii bacteraemia: a case report

Propionimicrobium lymphophilum is an anaerobic Gram-positive bacillus that exists in human skin and urinary tract. The pathogenicity is, however, not well known. Only two cases of urinary tract infection have been described recently. In the case presented here, the bacterium was isolated, concomitant with Actinotignum schaalii, from blood culture of a patient with fever and difficulty of urination. The bacteria were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA sequencing. The case was successfully treated with ampicillin/sulbactam.

Changes in Urinary Microbiome Populations Correlate in Kidney Transplants With Interstitial Fibrosis and Tubular Atrophy Documented in Early Surveillance Biopsies

An unbalanced microbiome may lead to disease by creating aberrant immune responses. A recent association of cellular rejection with the development of interstitial fibrosis and tubular atrophy (IFTA) suggests the role of immune-mediated tissue injury. We hypothesized that developing IFTA correlates with altered urinary tract microbiomes (UMBs). UMBs at two serial time points, 1 and 6-8 months posttransplant, were assessed by 16S microbial ribosomal gene sequencing in 25 patients developing biopsy-proven IFTA compared to 23 transplant patients with normal biopsies and excellent function (TX) and 20 healthy nontransplant controls (HC). Streptococcus, the dominant genera in HC males, was lower in IFTA and TX males at 1 month compared to HCs. At 6-8 months, Streptococcus was further decreased in IFTA males, but normalized in TX. IFTA males and females had increases in number of genera per sample at 6-8 months. UMB composition varied substantially between individuals in all groups. Despite the wide variation in UMBs between individuals, IFTA was associated with a loss in dominant resident urinary microbes in males, and a parallel increase in nonresident, pathogenic bacteria in males and females. UMB changes may contribute to IFTA development by alteration of the host immune response.

ANTIBIOFILM EFFECTS of Citrus limonum and Zingiber officinale Oils on BIOFILM FORMATION of Klebsiella ornithinolytica, Klebsiella oxytoca and Klebsiella terrigena SPECIES

BACKGROUND

Microbial cells growing in biofilms, play a huge role in the spread of antimicrobial resistance. In this study, biofilm formation of Klebsiella strains belonging to 3 different Klebsiella species (K. ornithinolytica, K. oxytoca and K. terrigena), cooccurences' effect on biofilm formation amount and anti-biofilm effects of Citrus limon and Zingiber officinale essential oils on biofilm formations of highest biofilm forming K. ornithinolytica, K. oxytoca and K. terrigena strains were determined.

MATERIALS AND METHODS

Anti-biofilm effects of Citrus limon and Zingiber officinale essential oils on biofilm formations of highest biofilm forming K. ornithinolytica, K. oxytoca and K. terrigena strains were investigated.

RESULTS

57% of K. ornithinolytica strains and 50% of K. oxytoca strains were found as Strong Biofilm Forming (SBF), there wasn't any SBF strain in K. terrigena species. In addition to this, clinical materials of urine and sperm were found as the most frequent clinical materials for strong biofilm forming K. ornithinolytica and K. oxytoca isolations respectively (63%; 100%) Secondly, all K. ornithinolytica strains isolated from surgical intensive care unit and all K. oxytoca strains isolated from service units of urology were found as SBF. Apart from these, although the amount of biofilm, formed by co-occurence of K. ornithinolytica - K. oxytoca and K. oxytoca - K. terrigena were more than the amount ofbiofilm formed by themselves separately, biofilm formation amount of co-occurrence of K. ornitholytica - K. terrigena strains was lower than biofilm formation amount of K. ornithinolytica but higher than biofilm formation amount of K. terrigena.

CONCLUSION

The antibiofilm effects of Citrus limonum and Zingiber officinale essential oils could be used against biofilm Klebsiella aquired infections.

Draft Genome Sequence of Lactobacillus delbrueckii Strain #22 Isolated from a Patient with Short Bowel Syndrome and Previous d-Lactic Acidosis and Encephalopathy

d-Lactic acidosis with associated encephalopathy caused by overgrowth of intestinal lactic acid bacteria is a rarely diagnosed neurological complication of patients with short bowel syndrome. Here, we report the draft genome sequence of Lactobacillus delbrueckii strain #22 isolated from a patient with short bowel syndrome and previous d-lactic acidosis/encephalopathy.

Absence of bacterial DNA in culture-negative urine from cats with and without lower urinary tract disease

A diagnosis of bacterial cystitis commonly relies on a positive microbiological culture demonstrating the presence of a significant number of colony-forming units/ml urine, as urine within the upper urinary tract, bladder and proximal urethra generally is considered sterile. Recent studies from human and veterinary medicine indicate the presence of non-culturable bacteria in culture-negative urine samples. The aim of the present study was to determine the occurrence of bacterial DNA in culture-negative urine samples from cats with signs of feline lower urinary tract disease (FLUTD) and healthy control cats by 16S ribosomal DNA PCR and subsequent sequencing. The study sample included 38 culture-negative urine samples from cats with FLUTD and 43 culture-negative samples from control cats. Eight culture-positive urine samples from cats with FLUTD were included as external positive controls in addition to negative reaction controls. Of possible methodological limitations, degradation of DNA due to storage, the use of non-sedimented urine for DNA isolation and lack of internal positive reaction controls should be mentioned. The positive controls were recognised, but occurrence of bacterial DNA in culture-negative urine from cats with or without signs of lower urinary tract disease was not demonstrated. However, considering the possible methodological limitations, the presence of bacterial DNA in the urine of culture-negative FLUTD cats cannot be excluded based on the present results alone. Therefore, a prospective study reducing the possibility of degradation of DNA due to storage, in combination with modifications enhancing the chance of detecting even lower levels of bacterial DNA in culture-negative samples, seems warranted.

Similar Neutrophil-Driven Inflammatory and Antibacterial Responses in Elderly Patients with Symptomatic and Asymptomatic Bacteriuria

Differential diagnosis of asymptomatic bacteriuria (ASB) and urinary tract infection (UTI) is based on the presence of diverse symptoms, including fever (≥38.5°C), rigors, malaise, lethargy, flank pain, hematuria, suprapubic discomfort, dysuria, and urgent or frequent urination. There is consensus in the medical community that ASB warrants antibiotic treatment only for patients undergoing urological procedures that lead to mucosal bleeding, catheterized individuals whose ASB persists for more than 48 h after catheter removal, and pregnant women. Pyuria is associated with UTI and implicates host immune responses via release of antibacterial effectors and phagocytosis of pathogens by neutrophils. Such responses are not sufficiently described for ASB. Metaproteomic methods were used here to identify the pathogens and evaluate molecular evidence of distinct immune responses in cases of ASB compared to UTI in elderly patients who were hospitalized upon injury. Neutrophil-driven inflammatory responses to invading bacteria were not discernible in most patients diagnosed with ASB compared to those with UTI. In contrast, proteomic urine analysis for trauma patients with no evidence of bacteriuria, including those who suffered mucosal injuries via urethral catheterization, rarely showed evidence of neutrophil infiltration. The same enzymes contributing to the synthesis of leukotrienes LTB4 and LTC4, mediators of inflammation and pain, were found in the UTI and ASB cohorts. These data support the notion that the pathways mediating inflammation and pain in most elderly patients with ASB are not quantitatively different from those seen in most elderly patients with UTI and warrant larger clinical studies to assess whether a common antibiotic treatment strategy for elderly ASB and UTI patients is justified.

Two Cases of Urinary Tract Infection Caused by Propionimicrobium lymphophilum

The first case reports involving Propionimicrobium lymphophilum, a rarely encountered anaerobic Gram-positive non-spore-forming rod, are presented here as urinary tract infections. Initial detection of these bacteria required urine Gram stains. Comparison of the type strain to the two isolates by various methods is depicted and includes antimicrobial susceptibility data.

Human urine is not sterile - shift of paradigm

OBJECTIVE

Until recently the generally accepted paradigm implied that urine of healthy people is sterile. In the present study, urine of healthy subjects was investigated by extended bacteriological methods.

MATERIAL AND METHODS

Three midstream urine samples from 52 healthy subjects each (24 females, 28 males; 18-25 years of age) were investigated by an extended set of culture media for identification of facultative aerobic (FAB) and nonclostridial anaerobic bacteria (NCAB). Ward's method (Euclidean distance) was used for similarity analysis.

RESULTS

The bacterial count of FAB in urine was usually low (≤ 10(2) colony-forming units/ml) in both groups. In contrast, the bacterial count of NCAB was higher (≥ 10(3) colony-forming units/ml), at least in some species, with significant differences between genders. The average number of bacterial species found was 5.8 in female and 7.1 in male urine. Half of the females were assigned to a specific 'female' microbial spectrum, different from that of males. In the mixed-gender clusters, the males showed a greater similarity among themselves.

CONCLUSIONS

As also shown by other investigators, urine of healthy people is normally not sterile. The role of the routinely not cultivated bacteria in healthy and diseased subjects needs to be established. It may alter the diagnostics of infectious and inflammatory diseases of the urogenital tract.

Pathogens in Urine from a Female Patient with Overactive Bladder Syndrome Detected by Culture-independent High Throughput Sequencing: A Case Report

INTRODUCTION

Overactive bladder syndrome (OAB) is described as urgency, with or without urgency incontinence. A range of medical conditions shares the symptoms of OAB, however the diagnosis is contingent on the exclusion of urinary tract infection (UTI). Knowing that urine dipstick and routine culture of bacteria can miss UTI diagnosis caused by low-count bacteriuria or "difficult-to-culture" pathogens, we examined a case of OAB with a culture-independent approach.

CASE PRESENTATION

A 61-year-old Norwegian female with a long history of urinary symptoms and a diagnosis of OAB was selected as a suitable subject for a culture-independent 16S rDNA analysis on the patient´s urine. The patient's medical records showed no history of recurrent UTI, however, when the urine specimen was sent to routine culture at the time of study it showed a significant bacteriuria caused by a single bacterium, and the patient was prescribed antibiotics. The 16S rDNA analysis revealed not one, but many different bacteria, including a considerable amount of fastidious bacteria, indicating a polymicrobial state. One year later, the subject was still experiencing severe symptoms, and a follow-up analysis was performed. This time the urine-culture was negative, however, the 16S rDNA profile was quite similar to that of the first sample, again displaying a complex bacterial profile.

CONCLUSION

The use of 16S rDNA pyrosequencing and sequence analysis to uncover "difficult-to-culture" bacteria should be considered when examining patients with chronic urinary symptoms. These methods may contribute to further elucidation of the etiology of overactive bladder syndrome and other urinary syndromes.

Detection of bloodstream infections and prediction of bronchopulmonary dysplasia in preterm neonates with an electronic nose

We show that smellprints of volatile organic components measured with an electronic nose (Cyranose 320; Smiths Detection Group Ltd, Watford, United Kingdom) differ between tracheal aspirates from preterm neonates with or without laboratory-confirmed bloodstream infections and with or without subsequent development of bronchopulmonary dysplasia. Tracheal aspirate smellprints could be useful noninvasive diagnostic markers for preterm neonates.

Distinct polymicrobial populations in a chronic foot ulcer with implications for diagnostics and anti-infective therapy

Background

Polymicrobial infections caused by combinations of different bacteria are being detected with an increasing frequency. The evidence of such complex infections is being revealed through the use of novel molecular and culture-independent methods. Considerable progress has been made in the last decade regarding the diagnostic application of such molecular techniques. In particular, 16S rDNA-based sequencing and even metagenomic analyses have been successfully used to study the microbial diversity in ecosystems and human microbiota. Here, we utilized denaturing high-performance liquid chromatography (DHPLC) as a diagnostic tool for identifying different bacterial species in complex clinical samples of a patient with a chronic foot ulcer.

Case presentation

A 45-year-old female suffered from a chronic 5x5cm large plantar ulcer located in the posterior calcaneal area with subcutaneous tissue infection and osteomyelitis. The chronic ulcer developed over a period of 8 years. Culture and DHPLC revealed a distinct and location-dependent polymicrobial infection of the ulcer. The analysis of a superficial biopsy revealed a mixture of Staphylococcus aureus, Proteus vulgaris, and Fusobacterium nucleatum, whereas the tissue-deep biopsy harbored a mixture of four different bacterial species, namely Gemella morbillorum, Porphyromonas asaccharolytica, Bacteroides fragilis, and Arcanobacterium haemolyticum.

Conclusions

This clinical case highlights the difficulties in assessing polymicrobial infections where a mixture of fastidious, rapid and slow growing bacteria as well as anaerobes exists as structured communities within the tissue architecture of chronic wound infections. The diagnosis of this multilayered polymicrobial infection led to a microbe-adapted antibiotic therapy, targeting the polymicrobial nature of this infection in addition to a standard local wound treatment. However, a complete wound closure could not be achieved due to the long-lasting extensive destruction of tissue.

Mechanisms of synergy in polymicrobial infections

Communities of microbes can live almost anywhere and contain many different species. Interactions between members of these communities often determine the state of the habitat in which they live. When these habitats include sites on the human body, these interactions can affect health and disease. Polymicrobial synergy can occur during infection, in which the combined effect of two or more microbes on disease is worse than seen with any of the individuals alone. Powerful genomic methods are increasingly used to study microbial communities, including metagenomics to reveal the members and genetic content of a community and metatranscriptomics to describe the activities of community members. Recent efforts focused toward a mechanistic understanding of these interactions have led to a better appreciation of the precise bases of polymicrobial synergy in communities containing bacteria, eukaryotic microbes, and/or viruses. These studies have benefited from advances in the development of in vivo models of polymicrobial infection and modern techniques to profile the spatial and chemical bases of intermicrobial communication. This review describes the breadth of mechanisms microbes use to interact in ways that impact pathogenesis and techniques to study polymicrobial communities.

Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant in situ populations

Urinary tract infections (UTIs) are one of the most commonly acquired bacterial infections in humans, and uropathogenic Escherichia coli strains are responsible for over 80% of all cases. The standard method for identification of uropathogens in clinical laboratories is cultivation, primarily using solid growth media under aerobic conditions, coupled with morphological and biochemical tests of typically a single isolate colony. However, these methods detect only culturable microorganisms, and characterization is phenotypic in nature. Here, we explored the genotypic identity of communities in acute uncomplicated UTIs from 50 individuals by using culture-independent amplicon pyrosequencing and whole-genome and metagenomic shotgun sequencing. Genus-level characterization of the UTI communities was achieved using the 16S rRNA gene (V8 region). Overall UTI community richness was very low in comparison to other human microbiomes. We strain-typed Escherichia-dominated UTIs using amplicon pyrosequencing of the fimbrial adhesin gene, fimH. There were nine highly abundant fimH types, and each UTI sample was dominated by a single type. Molecular analysis of the corresponding clinical isolates revealed that in the majority of cases the isolate was representative of the dominant taxon in the community at both the genus and the strain level. Shotgun sequencing was performed on a subset of eight E. coli urine UTI and isolate pairs. The majority of UTI microbial metagenomic sequences mapped to isolate genomes, confirming the results obtained using phylogenetic markers. We conclude that for the majority of acute uncomplicated E. coli-mediated UTIs, single cultured isolates are diagnostic of the infection.

In clinical practice, the diagnosis and treatment of acute uncomplicated urinary tract infection (UTI) are based on analysis of a single bacterial isolate cultured from urine, and it is assumed that this isolate represents the dominant UTI pathogen. However, these methods detect only culturable bacteria, and the existence of multiple pathogens as well as strain diversity within a single infection is not examined. Here, we explored bacteria present in acute uncomplicated UTIs using culture-independent sequence-based methods. Escherichia coli was the most common organism identified, and analysis of E. coli dominant UTI samples and their paired clinical isolates revealed that in the majority of infections the cultured isolate was representative of the dominant taxon at both the genus and the strain level. Our data demonstrate that in most cases single cultured isolates are diagnostic of UTI and are consistent with the notion of bottlenecks that limit strain diversity during UTI pathogenesis.

Proteomic analysis of uropathogenic Escherichia coli

Urinary tract infections (UTIs) are among the most common of bacterial infections in humans. Although a number of Gram-negative bacteria can cause UTIs, most cases are due to infection by uropathogenic E. coli (UPEC). Genomic studies have shown that UPEC encode a number of specialized activities that allow the bacteria to initiate and maintain infections in the environment of the urinary tract. Proteomic analyses have complemented the genomic data and have documented differential patterns of protein synthesis for bacteria growing ex vivo in human urine or recovered directly from the urinary tracts of infected mice. These studies provide valuable insights into the molecular basis of UPEC pathogenesis and have aided the identification of putative vaccine targets. Despite the substantial progress that has been achieved, many future challenges remain in the application of proteomics to provide a comprehensive view of bacterial pathogenesis in both acute and chronic UTIs.

Evaluation of urinalyses from untreated adult cats with lower urinary tract disease and healthy control cats: predictive abilities and clinical relevance

This case-controlled study evaluated urinalyses from 111 primary cases diagnosed with feline lower urinary tract disease (FLUTD) and 101 healthy control cats. Urine samples were analysed by standardised procedures, and differences between the two groups were compared by multivariable logistic regression analysis, while controlling for age, body weight, gender and reproductive status. Further, the ability of using urine sediment findings to predict bacteriuria was evaluated. In addition, urinalyses from cats with bacterial cystitis, idiopathic cystitis, urolithiasis and urethral plugs were compared. The main findings were that increasing body weight was significantly associated with increased odds of FLUTD, while the influence of age and reproductive status was of less importance. Increasing amounts of red blood cells and epithelial cells were significantly associated with increased odds of FLUTD. The predictive ability of using bacterial sediment findings to predict bacterial growth was dependent on subjective grading of the amount of bacteria in the sediment and was, at best, only moderate. The few significant differences found between the different FLUTD diagnoses were of limited diagnostic value.

Diagnostics, therapy and outcome prediction in abdominal sepsis: current standards and future perspectives

PURPOSE

In the perioperative phase, sepsis and sepsis-associated death are the most important problems for both the surgeon and the intensivist. Critically ill patients profit from an early identification and implementation of an interdisciplinary therapy. The purpose of this review on septic peritonitis is to give an update on the diagnosis and its evidence-based treatment.

RESULTS

Rapid diagnosis of sepsis is essential for patient´s survival. A bundle of studies was performed on early recognition and on new diagnostic tools for abdominal sepsis. Although surgical intervention is considered as an essential therapeutic step in sepsis therapy the time-point of source control is still controversially discussed in the literature. Furthermore, the Surviving Sepsis Campaign (SSC) guidelines were updated in 2012 to facilitate evidence-based medicine for septic patients.

CONCLUSION

Despite many efforts, the mortality of surgical septic patients remains unacceptably high. Permanent clinical education and further surgical trials are necessary to improve the outcome of critically ill patients.

Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples

Whole-genome sequencing (WGS) is becoming available as a routine tool for clinical microbiology. If applied directly on clinical samples, this could further reduce diagnostic times and thereby improve control and treatment. A major bottleneck is the availability of fast and reliable bioinformatic tools. This study was conducted to evaluate the applicability of WGS directly on clinical samples and to develop easy-to-use bioinformatic tools for the analysis of sequencing data. Thirty-five random urine samples from patients with suspected urinary tract infections were examined using conventional microbiology, WGS of isolated bacteria, and direct sequencing on pellets from the urine samples. A rapid method for analyzing the sequence data was developed. Bacteria were cultivated from 19 samples but in pure cultures from only 17 samples. WGS improved the identification of the cultivated bacteria, and almost complete agreement was observed between phenotypic and predicted antimicrobial susceptibilities. Complete agreement was observed between species identification, multilocus sequence typing, and phylogenetic relationships for Escherichia coli and Enterococcus faecalis isolates when the results of WGS of cultured isolates and urine samples were directly compared. Sequencing directly from the urine enabled bacterial identification in polymicrobial samples. Additional putative pathogenic strains were observed in some culture-negative samples. WGS directly on clinical samples can provide clinically relevant information and drastically reduce diagnostic times. This may prove very useful, but the need for data analysis is still a hurdle to clinical implementation. To overcome this problem, a publicly available bioinformatic tool was developed in this study.

Microbiota of the seminal fluid from healthy and infertile men

OBJECTIVE

To explore potential causes of male infertility by determining the composition and structure of commensal bacterial communities in seminal fluids.

DESIGN

Microscopy of Gram-stained semen samples and classification of 16S rRNA gene sequences to determine the species composition of semen bacterial communities.

SETTING

Clinical andrology laboratory and academic research laboratories.

PATIENT(S)

Nineteen sperm donors and 58 infertility patients.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Classification of 16S rRNA gene sequences, clustering of seminal microbial communities, and multiple statistical tests.

RESULT(S)

High numbers of diverse kinds of bacteria were present in most samples of both sperm donors and infertility patients. The bacterial communities varied widely among subjects, but they could be clustered into six groups based on similarities in composition and the rank abundances of taxa. Overall, there were no significant differences between sperm donors and infertility patients. However, multiple statistical tests showed a significant negative association between sperm quality and the presence of Anaerococcus. The results also indicated that many of the bacterial taxa identified in semen also occur in the vaginal communities of some women, especially those with bacterial vaginosis, which suggests that heterosexual sex partners may share bacteria.

CONCLUSION(S)

Diverse kinds of bacteria were present in the human semen, but there were no significant differences between sperm donors and infertility patients. The presence of Anaerococcus might be a biomarker for low sperm quality.

The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults

The urinary microbiome of healthy individuals and the way it alters with ageing have not been characterized and may influence disease processes. Conventional microbiological methods have limited scope to capture the full spectrum of urinary bacterial species. We studied the urinary microbiota from a population of healthy individuals, ranging from 26 to 90 years of age, by amplification of the 16S rRNA gene, with resulting amplicons analyzed by 454 pyrosequencing. Mid-stream urine (MSU) was collected by the “clean-catch” method. Quantitative PCR of 16S rRNA genes in urine samples, allowed relative enumeration of the bacterial loads. Analysis of the samples indicates that females had a more heterogeneous mix of bacterial genera compared to the male samples and generally had representative members of the phyla Actinobacteria and Bacteroidetes. Analysis of the data leads us to conclude that a “core” urinary microbiome could potentially exist, when samples are grouped by age with fluctuation in abundance between age groups. The study also revealed age-specific genera Jonquetella, Parvimonas, Proteiniphilum, and Saccharofermentans. In conclusion, conventional microbiological methods are inadequate to fully identify around two-thirds of the bacteria identified in this study. Whilst this proof-of-principle study has limitations due to the sample size, the discoveries evident in this sample data are strongly suggestive that a larger study on the urinary microbiome should be encouraged and that the identification of specific genera at particular ages may be relevant to pathogenesis of clinical conditions.

Application of denaturing high-performance liquid chromatography for monitoring sulfate-reducing bacteria in oil fields

Sulfate-reducing bacteria (SRB) participate in microbially induced corrosion (MIC) of equipment and H2S-driven reservoir souring in oil field sites. Successful management of industrial processes requires methods that allow robust monitoring of microbial communities. This study investigated the applicability of denaturing high-performance liquid chromatography (DHPLC) targeting the dissimilatory sulfite reductase ß-subunit (dsrB) gene for monitoring SRB communities in oil field samples from the North Sea, the United States, and Brazil. Fifteen of the 28 screened samples gave a positive result in real-time PCR assays, containing 9 × 10(1) to 6 × 10(5) dsrB gene copies ml(-1). DHPLC and denaturing gradient gel electrophoresis (DGGE) community profiles of the PCR-positive samples shared an overall similarity; both methods revealed the same samples to have the lowest and highest diversity. The SRB communities were diverse, and different dsrB compositions were detected at different geographical locations. The identified dsrB gene sequences belonged to several phylogenetic groups, such as Desulfovibrio, Desulfococcus, Desulfomicrobium, Desulfobulbus, Desulfotignum, Desulfonatronovibrio, and Desulfonauticus. DHPLC showed an advantage over DGGE in that the community profiles were very reproducible from run to run, and the resolved gene fragments could be collected using an automated fraction collector and sequenced without a further purification step. DGGE, on the other hand, included casting of gradient gels, and several rounds of rerunning, excising, and reamplification of bands were needed for successful sequencing. In summary, DHPLC proved to be a suitable tool for routine monitoring of the diversity of SRB communities in oil field samples.

Transcriptional responses of uropathogenic Escherichia coli to increased environmental osmolality caused by salt or urea

Uropathogenic Escherichia coli (UPEC) is the most common causative agent of urinary tract infections in humans. The majority of urinary infections develop via ascending route through the urethra, where bacterial cells come in contact with human urine prior to reaching the bladder or kidneys. Since urine contains significant amounts of inorganic ions and urea, it imposes osmotic and denaturing stresses on bacterial cells. In this study, we determined the transcriptional adaptive responses of UPEC strain CFT073 to the presence of 0.3 M NaCl or 0.6 M urea in the growth medium. The cell responses to these two osmolytes were drastically different. Although most of the genes of the osmotically inducible regulon were overexpressed in medium with salt, urea failed to stimulate osmotic stress response. At the same time, UPEC colonization genes encoding type 1 and F1C fimbriae and capsule biosynthesis were transcriptionally induced in the presence of urea but did not respond to increased salt concentration. We speculate that urea can potentially be sensed by uropathogenic bacteria to initiate infection program. In addition, several molecular chaperone genes were overexpressed in the presence of urea, whereas adding NaCl to the medium led to an upregulation of a number of anaerobic metabolism pathways.

Day of surgery urine cultures identify urogynecologic patients at increased risk for postoperative urinary tract infection

PURPOSE

Despite preoperative screening and treatment for urinary tract infections, a postoperative urinary tract infection develops in approximately 1 in 5 urogynecologic patients. In this study we assess the proportion of urogynecologic patients with a positive day of surgery urine culture, the clinical consequences of a positive day of surgery culture and differences in postoperative urinary tract infection risks based on day of surgery culture.

MATERIALS AND METHODS

After institutional review board approval, patients undergoing urogynecologic surgery at Loyola University Medical Center were recruited for the study. Catheterized urine samples were collected in the operating room before intravenous antibiotic administration. Clinical cultures were considered positive if 1,000 colonies per ml or more bacteria were found on routine culture. For analysis we matched each woman with a positive culture with 2 women with negative culture by age within 10 years and within surgical groups (ie prolapse and/or incontinence). Data were analyzed using SPSS® version 19.

RESULTS

Nearly a tenth (9.5%) of participants had positive day of surgery cultures. The clinical and demographic characteristics were similar in women with negative vs positive day of surgery cultures. However, women with positive day of surgery cultures were more likely to experience a postoperative urinary tract infection despite standard perioperative antibiotic administration (29.6% vs 5.6%, p = 0.005, odds ratio 7.2). Regardless of day of surgery culture status no participant experienced postoperative systemic urinary complications.

CONCLUSIONS

Nearly a tenth of urogynecologic patients had positive day of surgery cultures. Patients with a positive day of surgery culture had an increased risk (29.6%) of postoperative urinary tract infection within 6 weeks of surgery. These findings highlight an opportunity to identify and treat patients with positive day of surgery cultures and reduce the incidence of postoperative urinary tract infections.

Analysis of the distribution of bacteria within urinary catheter biofilms using four different molecular techniques

BACKGROUND

Most nosocomial urinary tract infections are associated with the long-term use of urinary catheters. Such urinary catheter-associated infections are caused by bacteria that reside in biofilms. We determined the distribution of fastidious/nonculturable bacteria in biofilm of urinary catheters and evaluated the availability of concurrent applying various molecular techniques.

METHODS

The biofilms were isolated from urinary catheters that had been installed in patients for 3 or 4 weeks and examined by the following 4 different 16S ribosomal RNA (rRNA) analysis techniques: capillary electrophoresis, terminal restriction fragment length polymorphism (T-RFLP), denaturing gradient gel electrophoresis (DGGE), and pyrosequencing.

RESULTS

A total of 329 isolates was identified by capillary electrophoresis. The most common genera were Edwardsiella, Enterobacter, Escherichia, and Pseudomonas. A total of 32 bacterial strains was identified by T-RFLP. Escherichia, Pseudomonas, Enterobacter, Moraxella, Proteus, Serratia, and Yersinia were the most represented genera. Similarly, Escherichia, Pseudomonas, and Enterobacter were the most prevalent according to DGGE. Burkholderia, Corynebacterium, Achromobacter, Alcaligenes, Citrobacter, Stenotrophomonas, and Streptococcus were also detected. Escherichia and Pseudomonas were abundantly detected by pyrosequencing. Enterobacter, Bacteroides, Klebsiella, Corynebacterium were also seen.

CONCLUSION

These 4 techniques detected different kinds of bacteria, suggesting that the simultaneous application of multiple techniques is necessary to accurately detect fastidious/nonculturable bacteria. Because bacterial growth within urinary catheter biofilms may be associated with urinary tract infections, further comprehensive studies are required.

Rapid discrimination of Gram-positive and Gram-negative bacteria in liquid samples by using NaOH-sodium dodecyl sulfate solution and flow cytometry

Background

For precise diagnosis of urinary tract infections (UTI), and selection of the appropriate prescriptions for their treatment, we explored a simple and rapid method of discriminating gram-positive and gram-negative bacteria in liquid samples.

Methodology/Principal Findings

We employed the NaOH-sodium dodecyl sulfate (SDS) solution conventionally used for plasmid extraction from Escherichia coli and the automated urine particle analyzer UF-1000i (Sysmex Corporation) for our novel method. The NaOH-SDS solution was used to determine differences in the cell wall structures between gram-positive and gram-negative bacteria, since the tolerance to such chemicals reflects the thickness and structural differences of bacterial cell walls. The UF-1000i instrument was used as a quantitative bacterial counter. We found that gram-negative bacteria, including E. coli, in liquid culture could easily be lysed by direct addition of equal volumes of NaOH-SDS solution. In contrast, Enterococcus faecalis, which is a gram-positive bacterium, could not be completely lysed by the solution. We then optimized the reaction time of the NaOH-SDS treatment at room temperature by using 3 gram-positive and 4 gram-negative bacterial strains and determined that the optimum reaction time was 5 min. Finally, in order to evaluate the generalizability of this method, we treated 8 gram-positive strains and 8 gram-negative strains, or 4 gram-positive and 4 gram-negative strains incubated in voluntary urine from healthy volunteers in the same way and demonstrated that all the gram-positive bacteria were discriminated quantitatively from gram negative bacteria using this method.

Conclusions/Significance

Using our new method, we could easily discriminate gram-positive and gram-negative bacteria in liquid culture media within 10 min. This simple and rapid method may be useful for determining the treatment course of patients with UTIs, especially for those without a prior history of UTIs. The method may be easily applied in order to obtain additional information for clinical prescriptions from bacteriuria.